Citrus Sinensis ID: 017842

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-----
Protein Sequence
MSSSTASVLKPLSSMADSTSLLSPPSIFARNPYFSIHPRPRPIKLHLSDSSLSSKGFSFKLKKTTHFSSFTTFVAQTSDWADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEGNLSDWGEPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEcccccccccccccEEEEEEEccEEEEEcccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEcccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHcccccccEEEEEEccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccHHHHHcccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccHHccccHHHHccccccEEEEEccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEEccccHHHHHccccccccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEEccccccHHHHHHccccccccccEEEEccccccEEEEEEEEEccHHHHHHHHHHHccccccccEEEEEccccccHHHHcccccccccEEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHHccccccccccccEEcccccHHccc
Coil and Loop (DISEMBL)
mssstasvlkplssmadstsllsppsifarnpyfsihprprpiklhlsdsslsskgfsfklkktthfssFTTFvaqtsdwadqeedkdntTITLEQEqeengeeepnwenqgadetegnlsdwgepegedTVVEAGErqeesgeegvfeeeefveppedaklfvgnlpydvdsEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNretdrsrgfgfvTMSTVEEAEKAVEMFHRYdidgrlltvnkaaprgtqperaprvfepgfriyvgnlpwevdNARLEQVFSEHGKVVNARVVYdretgrsrgfgfvTMSSETELNDAIAaldgqnldgrAIRVNVAEdrqrrssf
Flexible Loop (DISEMBL)
mssstasvlkplssmadstsllsPPSIFARNPYFSIHPRPRPIKLHLSDSSLSSKGFSFKLKKTTHFSSFTTfvaqtsdwadqeedKDNTTITLEQeqeengeeepnwenqgadetegnlsdwgepEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTvnkaaprgtqperaprvfepgfRIYVGNLPWEVDNARLEQVFsehgkvvnarvvydretgrsrgFGFVTMSSETELNDAIAaldgqnldgrairvnvaedrqrrssf
Low Complexity Region (SEG)
MSSSTASVLKPLSSMADSTSLLSPPSIFARNPYFSIHPRPRPIklhlsdsslsskgfsfklkktthfssfttfVAQTSDWADQEEDKDNTTITLeqeqeengeeepnwenqGADETEGNLSDWGEPEGEDTVVEAGERQeesgeegvfeeeefveppeDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF
Disordered region (IsUnstruct)
********************************YFS**********************SFKLKKTTHFSSFTTFVAQ************************************************************************************KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK************RVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL*******************
Disordered Region (DISOPRED)
*****************************************************************************************************************************************************************LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLT***********************IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN***********
Disordered Region (DISEMBL)
*******************SLLSPPSIFARNPYFSIHPRPRPIKLHLSDSSLSSKGFSFKLKKTTHFSSFTTFVAQTSDWADQEEDKDNTTITL************************NLSDWGEPE****************************PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA*********
Disordered Region (DISPRO)
****************DSTSLLSPPSIFARNPYFSIHPRPRPIKLHLSDSS****************SSFTTFVAQTSDWADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEGNLSDWGEPEGEDTVVEAGERQ*****E************EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ***APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED*******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSSTASVLKPLSSMADSTSLLSPPSIFARNPYFSIHPRPRPIKLHLSDSSLSSKGFSFKLKKTTHFSSFTTFVAQTSDWADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEGNLSDWGEPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	365	2.2.26 [Sep-21-2011]
Q04836	329	31 kDa ribonucleoprotein,	yes	no	0.884	0.981	0.554	4e-92
P19682	276	28 kDa ribonucleoprotein,	N/A	no	0.745	0.985	0.504	8e-83
P28644	233	28 kDa ribonucleoprotein,	N/A	no	0.613	0.961	0.649	2e-81
P19683	315	31 kDa ribonucleoprotein,	N/A	no	0.841	0.974	0.530	4e-81
P49314	292	31 kDa ribonucleoprotein,	N/A	no	0.515	0.643	0.465	3e-47
Q08937	291	29 kDa ribonucleoprotein	N/A	no	0.534	0.670	0.46	4e-47
Q08935	273	29 kDa ribonucleoprotein	N/A	no	0.526	0.703	0.478	9e-47
Q9ZUU4	289	Ribonucleoprotein At2g372	no	no	0.523	0.660	0.450	5e-45
P49313	279	30 kDa ribonucleoprotein,	N/A	no	0.495	0.648	0.472	3e-43
P19684	324	33 kDa ribonucleoprotein,	N/A	no	0.490	0.552	0.364	1e-30

>sp|Q04836|ROC3_ARATH 31 kDa ribonucleoprotein, chloroplastic OS=Arabidopsis thaliana GN=RBP31 PE=1 SV=1

 Score =  338 bits (866), Expect = 4e-92,   Method: Compositional matrix adjust.
 Identities = 204/368 (55%), Positives = 244/368 (66%), Gaps = 45/368 (12%)

Query: 2   SSSTASVLKPLSSMADSTS--LLSPPSIFARNPYFSIHPRPRPIKLHLSDSSLSSKGFSF 59
           SS   S LKPL+ MADS+S  + S PSI +      I      +     +  LS    S 
Sbjct: 3   SSIVTSSLKPLA-MADSSSSTIFSHPSISSTISSSRIRSSSVSLLTGRINLPLSFSRVSL 61

Query: 60  KLKKTTHF--SSFTTFVAQTSDWADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETE 117
            LK  TH   S F +FVAQTSDWA   E+    ++ +E       E E + E+Q  D +E
Sbjct: 62  SLKTKTHLKKSPFVSFVAQTSDWA---EEGGEGSVAVE-------ETENSLESQ--DVSE 109

Query: 118 GNLSDWGEPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLA 177
           G+ S+    EG+  V E  E + +  E  V E  EF EP E+AKLFVGNL YDV+S+ LA
Sbjct: 110 GDESEGDASEGD--VSEGDESEGDVSEGAVSERAEFPEPSEEAKLFVGNLAYDVNSQALA 167

Query: 178 MLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV 237
           MLFE+AGTVEIAEV                          IYNRETD+SRGFGFVTMS+V
Sbjct: 168 MLFEQAGTVEIAEV--------------------------IYNRETDQSRGFGFVTMSSV 201

Query: 238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLE 297
           +EAE AVE F+RYD++GRLLTVNKAAPRG++PERAPRV+EP FR+YVGNLPW+VDN RLE
Sbjct: 202 DEAETAVEKFNRYDLNGRLLTVNKAAPRGSRPERAPRVYEPAFRVYVGNLPWDVDNGRLE 261

Query: 298 QVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE 357
           Q+FSEHGKVV ARVVYDRETGRSRGFGFVTMS   ELN+AI+ALDGQNL+GRAIRVNVAE
Sbjct: 262 QLFSEHGKVVEARVVYDRETGRSRGFGFVTMSDVDELNEAISALDGQNLEGRAIRVNVAE 321

Query: 358 DRQRRSSF 365
           +R  R  +
Sbjct: 322 ERPPRRGY 329

Probably involved in the 3'-end processing of chloroplast mRNA's.
Arabidopsis thaliana (taxid: 3702)

>sp|P19682|ROC3_NICSY 28 kDa ribonucleoprotein, chloroplastic OS=Nicotiana sylvestris PE=1 SV=1

 Score =  307 bits (786), Expect = 8e-83,   Method: Compositional matrix adjust.
 Identities = 179/355 (50%), Positives = 224/355 (63%), Gaps = 83/355 (23%)

Query: 15  MADSTSLLSPPSIFARNPYFSIHP----RPRPIKLHLSDSSLSSKGFSFKLKKTTHFSSF 70
           MA +  L+S P  F      S +P    + +PI L  S  +L S       K+TT F +F
Sbjct: 1   MATNGCLISLPPFFTTTKSISSYPFLSTQLKPISLSSSLPTLLSLN-----KRTTQFPTF 55

Query: 71  TTFVAQTSDWADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEGNLSDWGEPEGED 130
            + +++           DNT +  +QEQ   G + P++                      
Sbjct: 56  VSVLSE----------DDNTLVLDDQEQ---GGDFPSF---------------------- 80

Query: 131 TVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAE 190
            V EAGE             EE+ EP EDAKLFVGNLPYD+DSE LA LF++AG VEIAE
Sbjct: 81  -VGEAGE------------TEEYQEPSEDAKLFVGNLPYDIDSEGLAQLFQQAGVVEIAE 127

Query: 191 VKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRY 250
           V                          IYNRETDRSRGFGFVTMSTVEEA+KAVE++ +Y
Sbjct: 128 V--------------------------IYNRETDRSRGFGFVTMSTVEEADKAVELYSQY 161

Query: 251 DIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNAR 310
           D++GRLLTVNKAAPRG++PERAPR F+P +RIYVGN+PW++D+ARLEQVFSEHGKVV+AR
Sbjct: 162 DLNGRLLTVNKAAPRGSRPERAPRTFQPTYRIYVGNIPWDIDDARLEQVFSEHGKVVSAR 221

Query: 311 VVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
           VV+DRE+GRSRGFGFVTMSSE E+++AIA LDGQ LDGR IRVN AE+R RR+++
Sbjct: 222 VVFDRESGRSRGFGFVTMSSEAEMSEAIANLDGQTLDGRTIRVNAAEERPRRNTY 276

Probably involved in the 3'-end processing of chloroplast mRNA's.

Nicotiana sylvestris (taxid: 4096)

>sp|P28644|ROC1_SPIOL 28 kDa ribonucleoprotein, chloroplastic OS=Spinacia oleracea PE=1 SV=1

 Score =  303 bits (775), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 167/257 (64%), Positives = 189/257 (73%), Gaps = 33/257 (12%)

Query: 108 WENQGADETEGNLSDWGEPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNL 167
           WE +G+  T   L    +PEG    V  G   + S E GV   + F EPPE+AKLFVGNL
Sbjct: 8   WEQEGS--TNAVLEGESDPEG---AVSWGSETQVSDEGGVEGGQGFSEPPEEAKLFVGNL 62

Query: 168 PYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSR 227
           PYDVDSEKLA +F+ AG VEIAEV                          IYNRETDRSR
Sbjct: 63  PYDVDSEKLAGIFDAAGVVEIAEV--------------------------IYNRETDRSR 96

Query: 228 GFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRV-FEPGFRIYVGN 286
           GFGFVTMSTVEEAEKAVE+ + YD+DGR LTVNKAAPRG+ PERAPR  FEP  R+YVGN
Sbjct: 97  GFGFVTMSTVEEAEKAVELLNGYDMDGRQLTVNKAAPRGS-PERAPRGDFEPSCRVYVGN 155

Query: 287 LPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL 346
           LPW+VD +RLEQ+FSEHGKVV+ARVV DRETGRSRGFGFVTMSSE+E+NDAIAALDGQ L
Sbjct: 156 LPWDVDTSRLEQLFSEHGKVVSARVVSDRETGRSRGFGFVTMSSESEVNDAIAALDGQTL 215

Query: 347 DGRAIRVNVAEDRQRRS 363
           DGRA+RVNVAE+R RR+
Sbjct: 216 DGRAVRVNVAEERPRRA 232

Probably involved in the 3'-end processing of chloroplast mRNA's.

Spinacia oleracea (taxid: 3562)

>sp|P19683|ROC4_NICSY 31 kDa ribonucleoprotein, chloroplastic OS=Nicotiana sylvestris PE=1 SV=1

 Score =  301 bits (772), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 198/373 (53%), Positives = 240/373 (64%), Gaps = 66/373 (17%)

Query: 1   MSSSTASVLKPLSSMADSTSLLSPPSIFARN--------PYFSIHPRPRPIKLHLSDSSL 52
           MS +T  ++KP SSMA ++ L+S P +FA          PY S   +P  + LHLS    
Sbjct: 1   MSCATKPIIKP-SSMATNSCLISLPPLFATTTKSKSFAYPYLSNTLKPIKL-LHLS---- 54

Query: 53  SSKGFSFKLKKTTHFSSFTTFVAQTSDWADQEEDKDNTTITLEQEQEENGEEEPNWENQG 112
                       T+     +   +TS  A QEE+    T+ L+ + +E+G+   N+E  G
Sbjct: 55  -----------CTYSPCILSPKKKTSVSALQEEEN---TLILDGQGQESGDLF-NFEPSG 99

Query: 113 ADETEGNLSDWGEPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVD 172
            +  E           E  V   G+  E    E   EEEEF EPPEDAKLFVGNLPYDVD
Sbjct: 100 EETEE-----------EGFVEAVGDAGESDEVEADEEEEEFQEPPEDAKLFVGNLPYDVD 148

Query: 173 SEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFV 232
           SE LA LFE+AG VEIAEV                          IYNR+TD+SRGFGFV
Sbjct: 149 SEGLARLFEQAGVVEIAEV--------------------------IYNRDTDQSRGFGFV 182

Query: 233 TMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVD 292
           TMSTVEEAEKAVEM++RYD++GRLLTVNKAA RG +PER PR FE  +RIYVGN+PW +D
Sbjct: 183 TMSTVEEAEKAVEMYNRYDVNGRLLTVNKAARRGERPERPPRTFEQSYRIYVGNIPWGID 242

Query: 293 NARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR 352
           +ARLEQ+FSEHGKVV+ARVVYDRETGRSRGFGFVTM+SE E++DAIA LDGQ+LDGR IR
Sbjct: 243 DARLEQLFSEHGKVVSARVVYDRETGRSRGFGFVTMASEAEMSDAIANLDGQSLDGRTIR 302

Query: 353 VNVAEDRQRRSSF 365
           VNVAEDR RR++F
Sbjct: 303 VNVAEDRSRRNTF 315

Could be involved in splicing and/or processing of chloroplast RNA's.

Nicotiana sylvestris (taxid: 4096)

>sp|P49314|ROC2_NICPL 31 kDa ribonucleoprotein, chloroplastic OS=Nicotiana plumbaginifolia PE=2 SV=1

 Score =  189 bits (479), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 113/243 (46%), Positives = 141/243 (58%), Gaps = 55/243 (22%)

Query: 149 EEEEFVEPP---EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMW 205
           ++ E  E P   ED KLFVGNLP+ VDS  LA LFE+AG VEI EV              
Sbjct: 74  DDVEVAEQPRFSEDLKLFVGNLPFSVDSAALAGLFERAGNVEIVEV-------------- 119

Query: 206 VCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA-AP 264
                       IY++ + RSRGFGFVTMST EE E A + F+ Y+IDGR + VN   AP
Sbjct: 120 ------------IYDKLSGRSRGFGFVTMSTKEEVEAAEQQFNGYEIDGRAIRVNAGPAP 167

Query: 265 -----------RGTQPE--------------RAPRVFEPGFRIYVGNLPWEVDNARLEQV 299
                      RG                  R  R  +   R+YVGNL W VD+  L+++
Sbjct: 168 AKRENSSFGGGRGGNSSYGGGRDGNSSFGGARGGRSVDSSNRVYVGNLSWGVDDLALKEL 227

Query: 300 FSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR 359
           FSE G VV+A+VVYDR++GRSRGFGFVT SS  E+NDAI +L+G +LDGR+IRV+ AE+R
Sbjct: 228 FSEQGNVVDAKVVYDRDSGRSRGFGFVTYSSAKEVNDAIDSLNGIDLDGRSIRVSAAEER 287

Query: 360 QRR 362
            RR
Sbjct: 288 PRR 290

Nicotiana plumbaginifolia (taxid: 4092)

>sp|Q08937|ROC2_NICSY 29 kDa ribonucleoprotein B, chloroplastic OS=Nicotiana sylvestris PE=2 SV=1

 Score =  189 bits (479), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 115/250 (46%), Positives = 145/250 (58%), Gaps = 55/250 (22%)

Query: 142 SGEEGVFEEEEFVEPP---EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFG 198
           SG + + ++ E  E P   ED KLFVGNLP+ VDS  LA LFE+AG VE+ EV       
Sbjct: 66  SGFDQLEDDVEVAEQPRFSEDLKLFVGNLPFSVDSAALAGLFERAGNVEMVEV------- 118

Query: 199 NQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLT 258
                              IY++ T RSRGFGFVTMST EE E A + F+ Y+IDGR + 
Sbjct: 119 -------------------IYDKLTGRSRGFGFVTMSTKEEVEAAEQQFNGYEIDGRAIR 159

Query: 259 VNKA-AP-----------RGTQPE--------------RAPRVFEPGFRIYVGNLPWEVD 292
           VN   AP           RG                  R  R  +   R+YVGNL W VD
Sbjct: 160 VNAGPAPAKRENSSFGGGRGGNSSYGGGRDGNSSFGGARGGRSVDSSNRVYVGNLSWGVD 219

Query: 293 NARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR 352
           +  L+++FSE G VV+A+VVYDR++GRSRGFGFVT SS  E+NDAI +L+G +LDGR+IR
Sbjct: 220 DLALKELFSEQGNVVDAKVVYDRDSGRSRGFGFVTYSSSKEVNDAIDSLNGVDLDGRSIR 279

Query: 353 VNVAEDRQRR 362
           V+ AE+R RR
Sbjct: 280 VSAAEERPRR 289

Could be involved in splicing and/or processing of chloroplast RNA's.

Nicotiana sylvestris (taxid: 4096)

>sp|Q08935|ROC1_NICSY 29 kDa ribonucleoprotein A, chloroplastic OS=Nicotiana sylvestris PE=2 SV=1

 Score =  187 bits (476), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 113/236 (47%), Positives = 139/236 (58%), Gaps = 44/236 (18%)

Query: 141 ESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQ 200
           E G++GV EE  F     D K+FVGNLP+  DS  LA LFE+AG VE+ EV         
Sbjct: 71  EDGDDGVEEERNF---SPDLKIFVGNLPFSADSAALAELFERAGNVEMVEV--------- 118

Query: 201 GFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
                            IY++ T RSRGFGFVTMS+ EE E A + F+ Y++DGR L VN
Sbjct: 119 -----------------IYDKLTGRSRGFGFVTMSSKEEVEAACQQFNGYELDGRALRVN 161

Query: 261 KAAPRGTQPERAPRVFEPGF-----------RIYVGNLPWEVDNARLEQVFSEHGKVVNA 309
              P    PE+       G            R+YVGNL W VD   LE +FSE GKVV+A
Sbjct: 162 SGPP----PEKRENSSFRGGSRGGGSFDSSNRVYVGNLAWGVDQDALETLFSEQGKVVDA 217

Query: 310 RVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
           +VVYDR++GRSRGFGFVT SS  E+N+AI +LDG +L+GRAIRV+ AE R  R  F
Sbjct: 218 KVVYDRDSGRSRGFGFVTYSSAEEVNNAIESLDGVDLNGRAIRVSPAEARPPRRQF 273

Could be involved in splicing and/or processing of chloroplast RNA's.

Nicotiana sylvestris (taxid: 4096)

>sp|Q9ZUU4|ROC1_ARATH Ribonucleoprotein At2g37220, chloroplastic OS=Arabidopsis thaliana GN=At2g37220 PE=1 SV=1

 Score =  182 bits (461), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 110/244 (45%), Positives = 138/244 (56%), Gaps = 53/244 (21%)

Query: 149 EEEEF--VEPPE------DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQ 200
           EE+ F  V PP+      D KLFVGNLP++VDS +LA LFE AG VE+ EV         
Sbjct: 72  EEDGFADVAPPKEQSFSADLKLFVGNLPFNVDSAQLAQLFESAGNVEMVEV--------- 122

Query: 201 GFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
                            IY++ T RSRGFGFVTMS+V E E A + F+ Y++DGR L VN
Sbjct: 123 -----------------IYDKITGRSRGFGFVTMSSVSEVEAAAQQFNGYELDGRPLRVN 165

Query: 261 KAAPRGTQPE---RAPRVFEPGF----------------RIYVGNLPWEVDNARLEQVFS 301
              P   + +   R PR                      R+YVGNL W VD+  LE +FS
Sbjct: 166 AGPPPPKREDGFSRGPRSSFGSSGSGYGGGGGSGAGSGNRVYVGNLSWGVDDMALESLFS 225

Query: 302 EHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR 361
           E GKVV ARV+YDR++GRS+GFGFVT  S  E+ +AI +LDG +LDGR IRV+ AE R  
Sbjct: 226 EQGKVVEARVIYDRDSGRSKGFGFVTYDSSQEVQNAIKSLDGADLDGRQIRVSEAEARPP 285

Query: 362 RSSF 365
           R  +
Sbjct: 286 RRQY 289

Could be involved in splicing and/or processing of chloroplast RNA's.

Arabidopsis thaliana (taxid: 3702)

>sp|P49313|ROC1_NICPL 30 kDa ribonucleoprotein, chloroplastic OS=Nicotiana plumbaginifolia PE=2 SV=1

 Score =  176 bits (445), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 104/220 (47%), Positives = 130/220 (59%), Gaps = 39/220 (17%)

Query: 159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVI 218
           D K+FVGNL +  DS  LA LFE+AG VE+ EV                          I
Sbjct: 86  DLKIFVGNLLFSADSAALAELFERAGNVEMVEV--------------------------I 119

Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR---- 274
           Y++ T RSRGFGFVTMS+ EE E A + F+ Y++DGR L VN   P   +   + R    
Sbjct: 120 YDKLTGRSRGFGFVTMSSKEEVEAACQQFNGYELDGRALRVNSGPPPEKRENSSFRENSS 179

Query: 275 ---------VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGF 325
                     F+   R+YVGNL W VD   LE +FSE GKVV+A+VVYDR++GRSRGFGF
Sbjct: 180 FRGGSRGGGSFDSSNRVYVGNLAWGVDQDALETLFSEQGKVVDAKVVYDRDSGRSRGFGF 239

Query: 326 VTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
           VT SS  E+N+AI +LDG +L+GRAIRV+ AE R  R  F
Sbjct: 240 VTYSSAEEVNNAIESLDGVDLNGRAIRVSPAEARPPRRQF 279

Could be involved in splicing and/or processing of chloroplast RNA's.

Nicotiana plumbaginifolia (taxid: 4092)

>sp|P19684|ROC5_NICSY 33 kDa ribonucleoprotein, chloroplastic OS=Nicotiana sylvestris PE=1 SV=1

 Score =  134 bits (337), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 78/214 (36%), Positives = 117/214 (54%), Gaps = 35/214 (16%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
            +L+VGNLP+ + S +L+ +F +AGTV   E+                          +Y
Sbjct: 114 GRLYVGNLPFSMTSSQLSEIFAEAGTVANVEI--------------------------VY 147

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN-KAAPRGTQPERAP---RV 275
           +R TDRSRGF FVTM +VEEA++A+ +F    + GR + VN    PRG + E      R 
Sbjct: 148 DRVTDRSRGFAFVTMGSVEEAKEAIRLFDGSQVGGRTVKVNFPEVPRGGEREVMSAKIRS 207

Query: 276 FEPGF-----RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSS 330
              GF     ++YV NL W + +  L   F++    ++A+V+YDR +GRSRGFGF+T SS
Sbjct: 208 TYQGFVDSPHKLYVANLSWALTSQGLRDAFADQPGFMSAKVIYDRSSGRSRGFGFITFSS 267

Query: 331 ETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
              +N A+  ++   L+GR +R+NVA  +   SS
Sbjct: 268 AEAMNSALDTMNEVELEGRPLRLNVAGQKAPVSS 301

Could be involved in splicing and/or processing of chloroplast RNA's.

Nicotiana sylvestris (taxid: 4096)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	365
224119514	327	predicted protein [Populus trichocarpa]	0.887	0.990	0.613	1e-105
225456840	327	PREDICTED: 31 kDa ribonucleoprotein, chl	0.890	0.993	0.607	1e-104
255540443	319	ribonucleoprotein, chloroplast, putative	0.863	0.987	0.635	1e-104
297733663	306	unnamed protein product [Vitis vinifera]	0.832	0.993	0.588	2e-98
147838354	1122	hypothetical protein VITISV_039575 [Viti	0.717	0.233	0.643	2e-97
224133740	295	predicted protein [Populus trichocarpa]	0.789	0.976	0.595	1e-95
449440612	330	PREDICTED: 31 kDa ribonucleoprotein, chl	0.879	0.972	0.589	1e-93
356508744	305	PREDICTED: 31 kDa ribonucleoprotein, chl	0.739	0.885	0.577	4e-93
19032260	300	RNA-binding protein precursor [Persea am	0.808	0.983	0.594	1e-91
225452270	312	PREDICTED: 31 kDa ribonucleoprotein, chl	0.843	0.987	0.560	7e-91

>gi|224119514|ref|XP_002318093.1| predicted protein [Populus trichocarpa] gi|222858766|gb|EEE96313.1| predicted protein [Populus trichocarpa]

 Score =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 224/365 (61%), Positives = 256/365 (70%), Gaps = 41/365 (11%)

Query: 1   MSSSTASVLKPLSSMADSTSLLSPPSIFARNPYFSIHP-RPRPIKLHLSDS-SLSSKGFS 58
           MS+++A   KPL  +   T L S PS FA  P     P   RP KL LS S SLS     
Sbjct: 1   MSAASAFTFKPL--LMAETCLCSLPSTFASKPPLKSLPISQRPSKLQLSYSHSLSP---- 54

Query: 59  FKLKKTTHFSSFTTFVAQTSDWADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEG 118
           F LK  TH S    FV QTSDWA Q E+ DNTTITL + ++E   E  NW N+ +++ EG
Sbjct: 55  FSLKPKTHLSLTIPFVTQTSDWAQQGEE-DNTTITLTESEQEEQGES-NWVNEESNDFEG 112

Query: 119 NLSDWGEPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAM 178
            + +W E EGED       R E    +    EE FVEPPE+AK+FVGNLPYDVDSEKLAM
Sbjct: 113 KVPEW-EAEGEDAAATEAIRGEGESGD----EEGFVEPPEEAKIFVGNLPYDVDSEKLAM 167

Query: 179 LFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE 238
           LFE+AGTVEIAEV                          IYNRETD SRGFGFVTMSTVE
Sbjct: 168 LFEQAGTVEIAEV--------------------------IYNRETDTSRGFGFVTMSTVE 201

Query: 239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQ 298
           E+EKAVEM HRYD+DGR LTVNKAAPRG++PER PRV EPG+RIYVGNLPW+VD+ RLEQ
Sbjct: 202 ESEKAVEMLHRYDLDGRFLTVNKAAPRGSRPERPPRVSEPGYRIYVGNLPWDVDSGRLEQ 261

Query: 299 VFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED 358
           +FSEHGKVV+ARVV+DRET RSRGFGFVTMS+E+ELNDAIAALDGQNLDGR IRVNVAE+
Sbjct: 262 IFSEHGKVVSARVVFDRETNRSRGFGFVTMSTESELNDAIAALDGQNLDGRPIRVNVAEE 321

Query: 359 RQRRS 363
           R RR+
Sbjct: 322 RPRRT 326

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225456840|ref|XP_002278832.1| PREDICTED: 31 kDa ribonucleoprotein, chloroplastic [Vitis vinifera]

 Score =  384 bits (987), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 223/367 (60%), Positives = 255/367 (69%), Gaps = 42/367 (11%)

Query: 1   MSSSTASVLKPLSSMADSTSLLSPPSIFARNPYFSIHPRP--RPIKLHLSDSSLSSKGFS 58
           MSS+T  +LKP S    + S +S P+IF+     S  P P  +PIKL LS S  S    S
Sbjct: 1   MSSATHHLLKPFS--IPNGSPISLPTIFSTKTPHSYLPIPPHKPIKLLLSCSQSSLFSPS 58

Query: 59  FKLKKTTHFSSFTTFVAQTSDWADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEG 118
             LK  T  SS  TFVAQTSDWA QEED    T+ +E+EQEE       WEN+  +  + 
Sbjct: 59  LFLKSKTLSSSVVTFVAQTSDWAQQEEDN---TVIIEEEQEEKV----TWENEEVEGPDA 111

Query: 119 NLSDWGEPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAM 178
             SDW E EGE  V EA        +     E+ + EPPE+AK+FVGNLPYDVDSE+LA 
Sbjct: 112 QASDW-ESEGEGAVTEAISDDGVVDDG----EDSYSEPPEEAKVFVGNLPYDVDSERLAR 166

Query: 179 LFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE 238
           LFE+AG VEIAEV                          IYNRETDRSRGFGFV+MSTVE
Sbjct: 167 LFEQAGVVEIAEV--------------------------IYNRETDRSRGFGFVSMSTVE 200

Query: 239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQ 298
           EAEKAV+MFHRY++DGRLLTVNKAAPRG+QPER PRVFEP FR+YVGNLPW+VD+ARLEQ
Sbjct: 201 EAEKAVDMFHRYELDGRLLTVNKAAPRGSQPERPPRVFEPAFRMYVGNLPWDVDSARLEQ 260

Query: 299 VFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED 358
           VFSEHGKVV ARVV+DRETGRSRGFGFVTMSS+TEL DAIAA DGQ LDGR IRVNVAE+
Sbjct: 261 VFSEHGKVVEARVVFDRETGRSRGFGFVTMSSQTELEDAIAATDGQTLDGRTIRVNVAEE 320

Query: 359 RQRRSSF 365
           R RRS+F
Sbjct: 321 RPRRSAF 327

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255540443|ref|XP_002511286.1| ribonucleoprotein, chloroplast, putative [Ricinus communis] gi|223550401|gb|EEF51888.1| ribonucleoprotein, chloroplast, putative [Ricinus communis]

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 228/359 (63%), Positives = 262/359 (72%), Gaps = 44/359 (12%)

Query: 7   SVLKPLSSMADSTSLLSPPSIF-ARNPYFSIH-PRPRPIKLHLSDSSLSSKGFSFKLKKT 64
           +  KPLS MADS  LLS PSIF ++ PY S+  P   PIKLH++ S  S       LK  
Sbjct: 2   TTFKPLS-MADSC-LLSLPSIFTSKPPYLSLSVPSRPPIKLHITQSYSS-------LKSK 52

Query: 65  THFSSFTTFVAQTSDWADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEGNLSDWG 124
           THFSS    VAQTSDWA QEE+  + T+TL + ++E   E      +   ETE  +SDW 
Sbjct: 53  THFSSLVPLVAQTSDWAQQEEN--DATVTLAESEQEQEWEG----QESETETEARVSDW- 105

Query: 125 EPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAG 184
           + EGE   V+    +EE   EG   EE F EPPEDAK+FVGNLPYDVDS+KLAMLFE+AG
Sbjct: 106 DSEGESAAVDGQGEEEEEVFEGSEPEEAFEEPPEDAKIFVGNLPYDVDSQKLAMLFEQAG 165

Query: 185 TVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAV 244
           TVEIAEV                          IYNRETD SRGFGFV+MSTVEEAEKAV
Sbjct: 166 TVEIAEV--------------------------IYNRETDTSRGFGFVSMSTVEEAEKAV 199

Query: 245 EMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHG 304
           EMFHR+D+DGRLLTVNKAAPRG++PER PRVFEPG+RIYVGNLPW+VDNARLEQ+FSEHG
Sbjct: 200 EMFHRHDLDGRLLTVNKAAPRGSRPERPPRVFEPGYRIYVGNLPWDVDNARLEQIFSEHG 259

Query: 305 KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRS 363
           KVV+ARVVYDR+TGRSRGFGFVTMS+ETELNDAIAALDG++LDGRAIRVNVAE R RR+
Sbjct: 260 KVVDARVVYDRDTGRSRGFGFVTMSTETELNDAIAALDGRSLDGRAIRVNVAEQRPRRN 318

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297733663|emb|CBI14910.3| unnamed protein product [Vitis vinifera]

 Score =  365 bits (937), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 216/367 (58%), Positives = 247/367 (67%), Gaps = 63/367 (17%)

Query: 1   MSSSTASVLKPLSSMADSTSLLSPPSIFARNPYFSIHPRP--RPIKLHLSDSSLSSKGFS 58
           MSS+T  +LKP S    + S +S P+IF+     S  P P  +PIKL LS S  S    S
Sbjct: 1   MSSATHHLLKPFS--IPNGSPISLPTIFSTKTPHSYLPIPPHKPIKLLLSCSQSSLFSPS 58

Query: 59  FKLKKTTHFSSFTTFVAQTSDWADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEG 118
             LK  T  SS  TFVAQTSDWA QEED    T+ +E+EQEE       WEN+ A   +G
Sbjct: 59  LFLKSKTLSSSVVTFVAQTSDWAQQEEDN---TVIIEEEQEEKV----TWENEEAISDDG 111

Query: 119 NLSDWGEPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAM 178
            + D                           E+ + EPPE+AK+FVGNLPYDVDSE+LA 
Sbjct: 112 VVDD--------------------------GEDSYSEPPEEAKVFVGNLPYDVDSERLAR 145

Query: 179 LFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE 238
           LFE+AG VEIAE                          VIYNRETDRSRGFGFV+MSTVE
Sbjct: 146 LFEQAGVVEIAE--------------------------VIYNRETDRSRGFGFVSMSTVE 179

Query: 239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQ 298
           EAEKAV+MFHRY++DGRLLTVNKAAPRG+QPER PRVFEP FR+YVGNLPW+VD+ARLEQ
Sbjct: 180 EAEKAVDMFHRYELDGRLLTVNKAAPRGSQPERPPRVFEPAFRMYVGNLPWDVDSARLEQ 239

Query: 299 VFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED 358
           VFSEHGKVV ARVV+DRETGRSRGFGFVTMSS+TEL DAIAA DGQ LDGR IRVNVAE+
Sbjct: 240 VFSEHGKVVEARVVFDRETGRSRGFGFVTMSSQTELEDAIAATDGQTLDGRTIRVNVAEE 299

Query: 359 RQRRSSF 365
           R RRS+F
Sbjct: 300 RPRRSAF 306

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147838354|emb|CAN61133.1| hypothetical protein VITISV_039575 [Vitis vinifera]

 Score =  361 bits (927), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 193/300 (64%), Positives = 222/300 (74%), Gaps = 38/300 (12%)

Query: 66   HFSSFTTFVAQTSDWADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEGNLSDWGE 125
             +++  TFVAQTSDWA QEED    T+ +E+EQEE    +  WEN+  +  +   SDW E
Sbjct: 861  QYNAEVTFVAQTSDWAQQEEDN---TVIIEEEQEE----KVTWENEEVEGPDAQASDW-E 912

Query: 126  PEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGT 185
             EGE  V EA        +     E+ + EPPE+AK+FVGNLPYDVDSE+LA LFE+AG 
Sbjct: 913  SEGEGAVTEAISDDGVVDDG----EDSYSEPPEEAKVFVGNLPYDVDSERLARLFEQAGV 968

Query: 186  VEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVE 245
            VEIAEV                          IYNRETDRSRGFGFV+MSTVEEAEKAV+
Sbjct: 969  VEIAEV--------------------------IYNRETDRSRGFGFVSMSTVEEAEKAVD 1002

Query: 246  MFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGK 305
            MFHRY++DGRLLTVNKAAPRG+QPER PRVFEP FR+YVGNLPW+VD+ARLEQVFSEHGK
Sbjct: 1003 MFHRYELDGRLLTVNKAAPRGSQPERPPRVFEPAFRMYVGNLPWDVDSARLEQVFSEHGK 1062

Query: 306  VVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
            VV ARVV+DRETGRSRGFGFVTMSS+TEL DAIAA DGQ LDGR IRVNVAE+R RRS+F
Sbjct: 1063 VVEARVVFDRETGRSRGFGFVTMSSQTELEDAIAATDGQTLDGRTIRVNVAEERPRRSAF 1122

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133740|ref|XP_002321649.1| predicted protein [Populus trichocarpa] gi|222868645|gb|EEF05776.1| predicted protein [Populus trichocarpa]

 Score =  356 bits (913), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 209/351 (59%), Positives = 240/351 (68%), Gaps = 63/351 (17%)

Query: 19  TSLLSPPSIFARNPYFSIHPRP---RPIKLHLSDS-SLSSKGFSFKLKKTTHFSSFTTFV 74
           T + S PSIF   P   + P P   RPIKL LS S SLS+      +K  TH S    FV
Sbjct: 4   TCICSFPSIFTSKP--PLKPLPISHRPIKLQLSYSHSLST----LSVKPKTHLSLTIPFV 57

Query: 75  AQTSDWADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEGNLSDWGEPEGEDTVVE 134
           AQTSDWA QEE+ +NTTITL +                       +SDW E EGED    
Sbjct: 58  AQTSDWAQQEEE-NNTTITLTE-----------------------VSDW-EAEGEDAA-- 90

Query: 135 AGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFH 194
           A E +   GE    +EE FVEPPE+AK++VGNLPYDV SEKLAMLF++AGTVEI+EV   
Sbjct: 91  ASETEAVRGEGERGDEEGFVEPPEEAKIYVGNLPYDVTSEKLAMLFDQAGTVEISEV--- 147

Query: 195 FLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDG 254
                                  IYN ETD SRGFGFVTMSTVEE++KA+EMF+RY++DG
Sbjct: 148 -----------------------IYNTETDTSRGFGFVTMSTVEESDKAIEMFNRYNLDG 184

Query: 255 RLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYD 314
           RLLTVNKAAPRG++PER PRV EP +RIYVGNLPW VD+ RLE+VFSEHGKVV+A+VV D
Sbjct: 185 RLLTVNKAAPRGSRPERPPRVSEPSYRIYVGNLPWGVDSGRLEEVFSEHGKVVSAQVVSD 244

Query: 315 RETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
            ETGRSRGFGFVTMSSE+ELNDAIAALDGQ LDGRAIRVNVA +R RRSSF
Sbjct: 245 WETGRSRGFGFVTMSSESELNDAIAALDGQELDGRAIRVNVAAERPRRSSF 295

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449440612|ref|XP_004138078.1| PREDICTED: 31 kDa ribonucleoprotein, chloroplastic-like [Cucumis sativus]

 Score =  349 bits (896), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 217/368 (58%), Positives = 253/368 (68%), Gaps = 47/368 (12%)

Query: 2   SSSTASVLKPLSSMADSTSLLSPPSIFARNPYFSIHPRP-RPIKLHLSDSSLSSKGFSFK 60
           SSS  S+ KPLS     +  LS PS+F   P  +    P + I  HLS SS  S G    
Sbjct: 3   SSSATSLFKPLSK--PDSCFLSLPSLFTGRPPHTFLSFPSKFIPFHLSSSSSYSSG-FSP 59

Query: 61  LKKTTHFSSFTTFVAQTSDWADQEEDKDNTTITLEQEQEENGEEE--PNWENQGADETEG 118
            KK  H  S    VAQTSDWA ++   D  TI  + + +ENG EE  P+WEN+   ETE 
Sbjct: 60  SKKKPHLPS----VAQTSDWAQED---DTITIDPKLDNDENGGEEGGPHWENEELSETES 112

Query: 119 NLSDW---GEPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEK 175
            +SDW   GE  G +  V   E ++E GE+G +E     EP EDAKLFVGNLPYD+DSEK
Sbjct: 113 RISDWEGEGEDGGSEAEVGGDEEEDEEGEQGPYE-----EPNEDAKLFVGNLPYDIDSEK 167

Query: 176 LAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS 235
           LAMLFEKAGTVEIAE                          VIYNRETDRSRGFGFVTMS
Sbjct: 168 LAMLFEKAGTVEIAE--------------------------VIYNRETDRSRGFGFVTMS 201

Query: 236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNAR 295
           TVEEAEKAV+ F+RYD+ GRLLTVNKAAPRG++ ER PR F+P FRIYVGNLPW+VDN R
Sbjct: 202 TVEEAEKAVDTFNRYDLSGRLLTVNKAAPRGSRQEREPRPFQPTFRIYVGNLPWDVDNGR 261

Query: 296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV 355
           LEQ+FSEHGKVV+ARV+YDR++GRSRGFGFVTM+ ET +NDAIAALDGQ+LDGRAIRVNV
Sbjct: 262 LEQLFSEHGKVVDARVLYDRDSGRSRGFGFVTMADETGMNDAIAALDGQSLDGRAIRVNV 321

Query: 356 AEDRQRRS 363
           AE+R RR+
Sbjct: 322 AEERPRRN 329

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356508744|ref|XP_003523114.1| PREDICTED: 31 kDa ribonucleoprotein, chloroplastic-like [Glycine max]

 Score =  347 bits (891), Expect = 4e-93,   Method: Compositional matrix adjust.
 Identities = 201/348 (57%), Positives = 219/348 (62%), Gaps = 78/348 (22%)

Query: 20  SLLSPPSIFARNPYFSIHPRPRPIKLHLSDSSLSSKGFSFKLKKTTHFSSFTTFVAQTSD 79
           SL SPPS              +P+ L  S     +   S  L    H S   T VAQTSD
Sbjct: 34  SLFSPPS--------------KPLTLQFS---CINSSVSLSLAARAHRSPLVTRVAQTSD 76

Query: 80  WADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEGNLSDWGEPEGEDTVVEAGERQ 139
           WA QEED    T T + E+            QG  ET+  LS W EP GED    AGE  
Sbjct: 77  WAQQEEDD---TATFQDEE------------QGLSETQAGLSSW-EPNGED----AGE-- 114

Query: 140 EESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGN 199
                      E F EPPE+AKLFVGNLPYDVDS+KLAMLFE+AGTVEIAEV        
Sbjct: 115 -----------ESFAEPPEEAKLFVGNLPYDVDSQKLAMLFEQAGTVEIAEV-------- 155

Query: 200 QGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
                             IYNRETD+SRGFGFVTMSTVEEAE AVE F RYD DGRLLTV
Sbjct: 156 ------------------IYNRETDQSRGFGFVTMSTVEEAENAVEKFSRYDFDGRLLTV 197

Query: 260 NKAAPRGTQPERAP--RVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRET 317
           NKA+PRGT+PER P    FEP   IYVGNLPW+VDN RLEQ+FSEHG VVNARVVYDRET
Sbjct: 198 NKASPRGTRPERPPPRHSFEPSLSIYVGNLPWDVDNTRLEQIFSEHGNVVNARVVYDRET 257

Query: 318 GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
            RSRGFGFVTMS ETE+ DA+AALDGQ+LDGR IRV+VAEDR RR SF
Sbjct: 258 RRSRGFGFVTMSDETEMKDAVAALDGQSLDGRPIRVSVAEDRPRRGSF 305

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|19032260|emb|CAD18921.1| RNA-binding protein precursor [Persea americana]

 Score =  342 bits (878), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 205/345 (59%), Positives = 233/345 (67%), Gaps = 50/345 (14%)

Query: 23  SPPSIFARNPYFSIHPRP-RPIKL-HLSDSSLSSKGFSFKLKKTTHFSSFTTFVAQTSDW 80
           S P +F+  P     P P +PIKL HLS SS S    SFK   +    S TT VAQTSDW
Sbjct: 4   SSPILFSSKPPCPFLPIPSKPIKLIHLSTSSSSWV--SFKKSPSPSSRSLTTLVAQTSDW 61

Query: 81  ADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEGNLSDWGEPEGEDTVVEAGERQE 140
           A QEED +    TL   + E   E       GA++        GE  G D  VE GE   
Sbjct: 62  AQQEEDSNVAEATLSDWEGEGEGEGEEQTESGAED--------GEESGGDGFVEGGE--- 110

Query: 141 ESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQ 200
                    E+ +  PPE+AKLFVGNLPYDVD + LA LF++AGTVE+AEV         
Sbjct: 111 ---------EDSYPLPPEEAKLFVGNLPYDVDHQALAELFDQAGTVEVAEV--------- 152

Query: 201 GFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
                            IYNRETD+SRGFGFVTMSTVEEAEKAVEMF+RYDI+GRLLTVN
Sbjct: 153 -----------------IYNRETDQSRGFGFVTMSTVEEAEKAVEMFNRYDINGRLLTVN 195

Query: 261 KAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRS 320
           KAAPRG + +R PR FEP FR+YVGNLPW+VD+ARLEQVFSEHGKVV ARVVYDRETGRS
Sbjct: 196 KAAPRGARVDRPPRAFEPAFRMYVGNLPWQVDDARLEQVFSEHGKVVEARVVYDRETGRS 255

Query: 321 RGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
           RGFGFVTMS++TEL+DAIAALDGQ+LDGRAIRVNVAEDR RR+SF
Sbjct: 256 RGFGFVTMSTQTELDDAIAALDGQSLDGRAIRVNVAEDRPRRASF 300

Source: Persea americana

Species: Persea americana

Genus: Persea

Family: Lauraceae

Order: Laurales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225452270|ref|XP_002270233.1| PREDICTED: 31 kDa ribonucleoprotein, chloroplastic-like [Vitis vinifera]

 Score =  340 bits (871), Expect = 7e-91,   Method: Compositional matrix adjust.
 Identities = 207/369 (56%), Positives = 251/369 (68%), Gaps = 61/369 (16%)

Query: 1   MSSSTASVLKPLSSMADSTSLLSPPSIFA-RNPYFSIHPRPRPIKL-HLSDSSLSSKGFS 58
           M+SS A +LKP S MA+S     P ++F  + P+  +   P+P++L HLS S  SS    
Sbjct: 1   MASSNA-LLKPFS-MAESCLTSVPTTLFTTKTPHPLLSLPPKPVRLFHLSCSCSSSW--- 55

Query: 59  FKLKKTTHFSSFTTFVAQTSDWADQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEG 118
             LK  T  ++   FVAQTSDWA QEE+++   +T              W+++G +E E 
Sbjct: 56  VSLKTKTSPTTLVPFVAQTSDWAQQEEEEEKGGLT--------------WDSEGGEEIEA 101

Query: 119 NLSD--WGEPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKL 176
           + S+  W                 E GEE    E+ + EPPE+AKLFVGNLPYD+DSEKL
Sbjct: 102 SGSEEAWEG------------EVGEDGEESEGSEDTYSEPPEEAKLFVGNLPYDIDSEKL 149

Query: 177 AMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST 236
           A LF++AG VEIAEV                          IYNRETD+SRGFGF+TMST
Sbjct: 150 AQLFDEAGVVEIAEV--------------------------IYNRETDQSRGFGFITMST 183

Query: 237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARL 296
           VEEAEKAVEMF+RYD++GR LTVNKAAPRG++PER P+ FEP FRIYVGNLPW+VD+ARL
Sbjct: 184 VEEAEKAVEMFNRYDLNGRFLTVNKAAPRGSRPERPPQAFEPSFRIYVGNLPWQVDDARL 243

Query: 297 EQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA 356
           EQVFSEHGKVV+ARVVYDR+T RSRGFGFVTMSSETELNDAIAALDGQ+LDGRAIRVNVA
Sbjct: 244 EQVFSEHGKVVDARVVYDRDTQRSRGFGFVTMSSETELNDAIAALDGQSLDGRAIRVNVA 303

Query: 357 EDRQRRSSF 365
           E+R RR S+
Sbjct: 304 EERPRRGSY 312

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	365
TAIR|locus:2157702	289	CP31B "chloroplast RNA-binding	0.413	0.522	0.748	2.9e-72
TAIR|locus:2122009	329	RBP31 "AT4G24770" [Arabidopsis	0.668	0.741	0.558	5.4e-67
TAIR|locus:2049721	289	AT2G37220 [Arabidopsis thalian	0.238	0.301	0.597	1.2e-37
TAIR|locus:2079874	329	CP33 "chloroplast RNA-binding	0.402	0.446	0.403	3.5e-36
TAIR|locus:2202740	258	AT1G60000 [Arabidopsis thalian	0.397	0.562	0.462	9.2e-36
TAIR|locus:2083810	253	PSRP2 "plastid-specific	0.397	0.573	0.414	8.4e-28
SGD|S000003391	414	NSR1 "Nucleolar protein that b	0.391	0.345	0.34	2.4e-23
TAIR|locus:2062379	308	AT2G35410 [Arabidopsis thalian	0.380	0.451	0.319	7.5e-22
UNIPROTKB|G4MY43	486	MGG_01268 "Nuclear localizatio	0.413	0.310	0.35	2.1e-21
TAIR|locus:2200975	294	AT1G01080 [Arabidopsis thalian	0.410	0.510	0.337	7.2e-20

TAIR|locus:2157702 CP31B "chloroplast RNA-binding protein 31B" [Arabidopsis thaliana (taxid:3702)]

 Score = 599 (215.9 bits), Expect = 2.9e-72, Sum P(2) = 2.9e-72
 Identities = 113/151 (74%), Positives = 137/151 (90%)

Query:   212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
             V + +VIYNR+TD+SRGFGFVTMSTVEEAEKAVE F+ ++++GR LTVN+AAPRG++PER
Sbjct:   139 VEISEVIYNRDTDQSRGFGFVTMSTVEEAEKAVEKFNSFEVNGRRLTVNRAAPRGSRPER 198

Query:   272 APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
              PRV++  FRIYVGNLPW+VD+ RLE++FSEHGKVV+ARVV DRETGRSRGFGFV MS+E
Sbjct:   199 QPRVYDAAFRIYVGNLPWDVDSGRLERLFSEHGKVVDARVVSDRETGRSRGFGFVQMSNE 258

Query:   332 TELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
              E+N AIAALDGQNL+GRAI+VNVAE+R RR
Sbjct:   259 NEVNVAIAALDGQNLEGRAIKVNVAEERTRR 289

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0045087 "innate immune response" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009451 "RNA modification" evidence=IMP

GO:0000023 "maltose metabolic process" evidence=RCA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

GO:0009409 "response to cold" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0009814 "defense response, incompatible interaction" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0019684 "photosynthesis, light reaction" evidence=RCA

GO:0042742 "defense response to bacterium" evidence=RCA

TAIR|locus:2122009 RBP31 "AT4G24770" [Arabidopsis thaliana (taxid:3702)]

 Score = 647 (232.8 bits), Expect = 5.4e-67, Sum P(2) = 5.4e-67
 Identities = 139/249 (55%), Positives = 167/249 (67%)

Query:   121 SDWGEPEGEDTV-VEAGERQXXXXXXXXXXXXXXXXXXXDAKL---FVGNLPYDVDSEKL 176
             SDW E  GE +V VE  E                     D        G++     SE+ 
Sbjct:    82 SDWAEEGGEGSVAVEETENSLESQDVSEGDESEGDASEGDVSEGDESEGDVSEGAVSER- 140

Query:   177 AMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST 236
             A   E +   ++      +   +Q   M       V + +VIYNRETD+SRGFGFVTMS+
Sbjct:   141 AEFPEPSEEAKLFVGNLAYDVNSQALAMLFEQAGTVEIAEVIYNRETDQSRGFGFVTMSS 200

Query:   237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARL 296
             V+EAE AVE F+RYD++GRLLTVNKAAPRG++PERAPRV+EP FR+YVGNLPW+VDN RL
Sbjct:   201 VDEAETAVEKFNRYDLNGRLLTVNKAAPRGSRPERAPRVYEPAFRVYVGNLPWDVDNGRL 260

Query:   297 EQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA 356
             EQ+FSEHGKVV ARVVYDRETGRSRGFGFVTMS   ELN+AI+ALDGQNL+GRAIRVNVA
Sbjct:   261 EQLFSEHGKVVEARVVYDRETGRSRGFGFVTMSDVDELNEAISALDGQNLEGRAIRVNVA 320

Query:   357 EDRQRRSSF 365
             E+R  R  +
Sbjct:   321 EERPPRRGY 329

GO:0003723 "RNA binding" evidence=ISS;IDA;TAS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0045087 "innate immune response" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0009451 "RNA modification" evidence=IMP

GO:0009073 "aromatic amino acid family biosynthetic process" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0016226 "iron-sulfur cluster assembly" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0045036 "protein targeting to chloroplast" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

GO:0009631 "cold acclimation" evidence=IMP

GO:0016553 "base conversion or substitution editing" evidence=IMP

GO:0043489 "RNA stabilization" evidence=IMP

GO:0006396 "RNA processing" evidence=TAS

TAIR|locus:2049721 AT2G37220 [Arabidopsis thaliana (taxid:3702)]

 Score = 267 (99.0 bits), Expect = 1.2e-37, Sum P(2) = 1.2e-37
 Identities = 52/87 (59%), Positives = 65/87 (74%)

Query:   279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
             G R+YVGNL W VD+  LE +FSE GKVV ARV+YDR++GRS+GFGFVT  S  E+ +AI
Sbjct:   203 GNRVYVGNLSWGVDDMALESLFSEQGKVVEARVIYDRDSGRSKGFGFVTYDSSQEVQNAI 262

Query:   339 AALDGQNLDGRAIRVNVAEDRQRRSSF 365
              +LDG +LDGR IRV+ AE R  R  +
Sbjct:   263 KSLDGADLDGRQIRVSEAEARPPRRQY 289

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009409 "response to cold" evidence=IEP;RCA

GO:0010319 "stromule" evidence=IDA

GO:0045087 "innate immune response" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0009737 "response to abscisic acid stimulus" evidence=IEP

GO:0009534 "chloroplast thylakoid" evidence=IDA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0009814 "defense response, incompatible interaction" evidence=RCA

GO:0019684 "photosynthesis, light reaction" evidence=RCA

GO:0042742 "defense response to bacterium" evidence=RCA

TAIR|locus:2079874 CP33 "chloroplast RNA-binding protein 33" [Arabidopsis thaliana (taxid:3702)]

 Score = 320 (117.7 bits), Expect = 3.5e-36, Sum P(2) = 3.5e-36
 Identities = 63/156 (40%), Positives = 103/156 (66%)

Query:   215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN-KAAPRGTQPE--R 271
             +Q++Y++ TDRSRGFGFVTM ++EEA++A++MF+   I GR + VN    PRG + E  R
Sbjct:   145 VQIVYDKVTDRSRGFGFVTMGSIEEAKEAMQMFNSSQIGGRTVKVNFPEVPRGGENEVMR 204

Query:   272 AP-----RVF-EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGF 325
                    R + +   ++Y GNL W + +  L+  F +   V+ A+V+Y+R TGRSRGFGF
Sbjct:   205 TKIRDNNRSYVDSPHKVYAGNLGWNLTSQGLKDAFGDQPGVLGAKVIYERNTGRSRGFGF 264

Query:   326 VTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR 361
             ++  S   +  A+A ++G  ++GRA+R+N+A +R++
Sbjct:   265 ISFESAENVQSALATMNGVEVEGRALRLNLASEREK 300

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0009579 "thylakoid" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009793 "embryo development ending in seed dormancy" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0016226 "iron-sulfur cluster assembly" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0048481 "ovule development" evidence=RCA

TAIR|locus:2202740 AT1G60000 [Arabidopsis thaliana (taxid:3702)]

 Score = 320 (117.7 bits), Expect = 9.2e-36, Sum P(2) = 9.2e-36
 Identities = 68/147 (46%), Positives = 95/147 (64%)

Query:   214 LLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAP 273
             L++V+YNR+T +SRGF FVTMS VE+    ++     +  GR L VN A     +P + P
Sbjct:   113 LVEVLYNRDTGQSRGFAFVTMSNVEDCNIIIDNLDGTEYLGRALKVNFADK--PKPNKEP 170

Query:   274 RVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETE 333
                E   +++VGNL W V +  L   F E G VV ARVV+D +TGRSRG+GFV  SS+ E
Sbjct:   171 LYPETEHKLFVGNLSWTVTSESLAGAFRECGDVVGARVVFDGDTGRSRGYGFVCYSSKAE 230

Query:   334 LNDAIAALDGQNLDGRAIRVNVAEDRQ 360
             +  A+ +LDG  L+GRAIRVN+A+ ++
Sbjct:   231 METALESLDGFELEGRAIRVNLAQGKK 257

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0019344 "cysteine biosynthetic process" evidence=RCA

TAIR|locus:2083810 PSRP2 "plastid-specific ribosomal protein 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 259 (96.2 bits), Expect = 8.4e-28, Sum P(2) = 8.4e-28
 Identities = 63/152 (41%), Positives = 89/152 (58%)

Query:   212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN-KAAPRGTQPE 270
             V  +QV+Y++ + RSR FGF TM +VE+A   VE  +   ++GR + VN    P  + P+
Sbjct:   102 VEKVQVMYDKYSGRSRRFGFATMKSVEDANAVVEKLNGNTVEGREIKVNITEKPIASSPD 161

Query:   271 RAPRVFEPG------FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFG 324
              +    E        +++YVGNL   V    LE +FSE GKVV+A+V     T +S GFG
Sbjct:   162 LSVLQSEDSAFVDSPYKVYVGNLAKTVTKEMLENLFSEKGKVVSAKVSRVPGTSKSTGFG 221

Query:   325 FVTMSSETELNDAIAALDGQNLDGRAIRVNVA 356
             FVT SSE ++  AI AL+   L+G+ IRVN A
Sbjct:   222 FVTFSSEEDVEAAIVALNNSLLEGQKIRVNKA 253

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009773 "photosynthetic electron transport in photosystem I" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0045036 "protein targeting to chloroplast" evidence=RCA

SGD|S000003391 NSR1 "Nucleolar protein that binds nuclear localization sequences" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 235 (87.8 bits), Expect = 2.4e-23, Sum P(2) = 2.4e-23
 Identities = 51/150 (34%), Positives = 87/150 (58%)

Query:   216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLT--VNKAAPRGTQPERAP 273
             +VIY R TDRSRG+G+V       AEKA++     +IDGR +   ++ + P G   +RA 
Sbjct:   198 RVIYERGTDRSRGYGYVDFENKSYAEKAIQEMQGKEIDGRPINCDMSTSKPAGNN-DRAK 256

Query:   274 RV----FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMS 329
             +      EP   +++GNL +  D   + ++F++HG+VV+ R+    ET + +GFG+V  S
Sbjct:   257 KFGDTPSEPSDTLFLGNLSFNADRDAIFELFAKHGEVVSVRIPTHPETEQPKGFGYVQFS 316

Query:   330 SETELNDAIAALDGQNLDGRAIRVNVAEDR 359
             +  +   A+ AL G+ +D R +R++ +  R
Sbjct:   317 NMEDAKKALDALQGEYIDNRPVRLDFSSPR 346

GO:0003723 "RNA binding" evidence=IEA;IDA

GO:0003677 "DNA binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0006364 "rRNA processing" evidence=IEA;TAS

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0005730 "nucleolus" evidence=IEA;IDA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006950 "response to stress" evidence=IEA

GO:0000028 "ribosomal small subunit assembly" evidence=TAS

TAIR|locus:2062379 AT2G35410 [Arabidopsis thaliana (taxid:3702)]

 Score = 215 (80.7 bits), Expect = 7.5e-22, Sum P(2) = 7.5e-22
 Identities = 47/147 (31%), Positives = 86/147 (58%)

Query:   212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN------KAAPR 265
             V+ +++I  ++  ++RGF FVTM++ EEA+ A++ F  + + GR+++V+      K  P+
Sbjct:   121 VNNVEIIRQKD-GKNRGFAFVTMASGEEAQAAIDKFDTFQVSGRIISVSFARRFKKPTPK 179

Query:   266 GTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHG-KVVNARVVYDRETGRSRGFG 324
                   +P   +   ++YV NL W+  +  L ++F+      V+ARVV+    GRS G+G
Sbjct:   180 SPNDLPSPAPGDTRHKLYVSNLAWKARSTHLRELFTAADFNPVSARVVFADPEGRSSGYG 239

Query:   325 FVTMSSETELNDAIAALDGQNLDGRAI 351
             FV+ ++  E  +AI  L+G+ + GR I
Sbjct:   240 FVSFATREEAENAITKLNGKEIMGRPI 266

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0006364 "rRNA processing" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0015979 "photosynthesis" evidence=RCA

GO:0015995 "chlorophyll biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0042793 "transcription from plastid promoter" evidence=RCA

UNIPROTKB|G4MY43 MGG_01268 "Nuclear localization sequence binding protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 218 (81.8 bits), Expect = 2.1e-21, Sum P(2) = 2.1e-21
 Identities = 56/160 (35%), Positives = 90/160 (56%)

Query:   212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPE- 270
             V+  +VI +RE+ RS+GFG+V  +T EEAEKA        IDGR + V+ +  + T    
Sbjct:   265 VTSARVITDRESGRSKGFGYVDFATPEEAEKAHGEKQGAFIDGREIKVDFSTGKATNSND 324

Query:   271 ----RAPR----VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRG 322
                 RA +    V      ++VGNLP++ D   +   FSE  +V + R+  ++E+GR +G
Sbjct:   325 AAGARAKKYGDTVSPESDTLFVGNLPFDADEDSVGAFFSEVAEVKSLRLPTEQESGRRKG 384

Query:   323 FGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
             FG+VT +S  +   A   L+GQ+++GR  R++ +  R  R
Sbjct:   385 FGYVTFNSVEDAKSAFEQLNGQSINGRNCRLDYSTPRPPR 424

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2200975 AT1G01080 [Arabidopsis thaliana (taxid:3702)]

 Score = 210 (79.0 bits), Expect = 7.2e-20, Sum P(2) = 7.2e-20
 Identities = 55/163 (33%), Positives = 89/163 (54%)

Query:   212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR--GTQ- 268
             +S+  V  N +T  SRG G+VTM ++  A+ A+      ++ GR + V  +     GT+ 
Sbjct:   135 ISVEVVSRNPQTGESRGSGYVTMGSINSAKIAIASLDGTEVGGREMRVRYSVDMNPGTRR 194

Query:   269 -PE---RAPR---VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSR 321
              PE     P+   ++E   ++YVGNLPW      L   FS+ G +V+ RV++DR+TGR+R
Sbjct:   195 NPEVLNSTPKKILMYESQHKVYVGNLPWFTQPDGLRNHFSKFGTIVSTRVLHDRKTGRNR 254

Query:   322 GFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
              F F++ +S  E  DA  + +G   +GR  R+ V E  ++  S
Sbjct:   255 VFAFLSFTSGEE-RDAALSFNGTQYEGR--RIIVREGIEKSES 294

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0006655 "phosphatidylglycerol biosynthetic process" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q04836	ROC3_ARATH	No assigned EC number	0.5543	0.8849	0.9817	yes	no
P19683	ROC4_NICSY	No assigned EC number	0.5308	0.8410	0.9746	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	365
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	5e-33
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	5e-27
smart00360	73	smart00360, RRM, RNA recognition motif	1e-24
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	7e-24
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-23
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-23
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-23
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-20
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-20
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-19
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-19
smart00360	73	smart00360, RRM, RNA recognition motif	7e-19
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-18
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	5e-18
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-17
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-17
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	7e-17
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-16
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-16
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	3e-16
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	4e-16
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-16
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-15
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-15
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	3e-15
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	4e-15
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	8e-15
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	9e-15
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	9e-15
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-14
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-14
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-14
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	4e-14
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	5e-14
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	5e-14
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-14
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-14
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	9e-14
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	9e-14
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-13
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-13
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-13
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-13
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-13
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-13
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-13
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	3e-13
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	3e-13
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-13
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	4e-13
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	4e-13
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	6e-13
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	7e-13
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	8e-13
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-12
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-12
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-12
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	3e-12
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	3e-12
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	4e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-12
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	4e-12
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	4e-12
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	5e-12
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	5e-12
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	6e-12
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	7e-12
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	8e-12
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	9e-12
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-11
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-11
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	1e-11
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-11
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-11
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-11
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	3e-11
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	3e-11
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	3e-11
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-11
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	5e-11
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	5e-11
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	6e-11
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	6e-11
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	7e-11
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	8e-11
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	9e-11
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-10
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	1e-10
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	2e-10
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-10
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	3e-10
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	5e-10
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	5e-10
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	5e-10
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	5e-10
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	6e-10
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	7e-10
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	8e-10
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	9e-10
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	9e-10
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-09
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	1e-09
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-09
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-09
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-09
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	4e-09
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	5e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	5e-09
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	5e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-09
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	5e-09
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	6e-09
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	6e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	7e-09
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	9e-09
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	9e-09
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-08
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	1e-08
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-08
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-08
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	1e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-08
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	1e-08
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-08
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-08
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	2e-08
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-08
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-08
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	3e-08
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-08
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	3e-08
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	3e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-08
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-08
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	4e-08
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	4e-08
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	4e-08
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	5e-08
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	5e-08
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	5e-08
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	5e-08
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	5e-08
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	7e-08
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	9e-08
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	9e-08
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	1e-07
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-07
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	1e-07
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-07
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-07
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	1e-07
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	1e-07
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-07
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	2e-07
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	2e-07
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-07
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	2e-07
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	2e-07
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-07
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	2e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-07
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	3e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	3e-07
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	3e-07
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	3e-07
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	3e-07
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	3e-07
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-07
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	4e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	5e-07
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	5e-07
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	6e-07
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	6e-07
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	6e-07
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	7e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	8e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	8e-07
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	9e-07
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	9e-07
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	1e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-06
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	1e-06
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	1e-06
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	1e-06
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	1e-06
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-06
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	1e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-06
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	1e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-06
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	1e-06
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	1e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-06
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-06
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-06
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	2e-06
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	2e-06
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-06
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	2e-06
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-06
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	2e-06
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-06
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	2e-06
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	2e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-06
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-06
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	3e-06
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-06
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	3e-06
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	3e-06
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	3e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	3e-06
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	3e-06
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-06
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	3e-06
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	4e-06
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-06
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	4e-06
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	4e-06
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	4e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-06
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	5e-06
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	5e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	6e-06
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	6e-06
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	6e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	6e-06
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	7e-06
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	7e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	7e-06
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	7e-06
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	9e-06
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	1e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-05
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	1e-05
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-05
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-05
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	1e-05
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-05
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-05
cd12644	90	cd12644, RRM_CFIm59, RNA recognition motif of pre-	2e-05
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	2e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-05
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	3e-05
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	3e-05
cd12410	93	cd12410, RRM2_RRT5, RNA recognition motif 2 in yea	3e-05
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	3e-05
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	3e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	4e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-05
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	4e-05
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	4e-05
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	4e-05
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	4e-05
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	5e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	5e-05
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	5e-05
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	5e-05
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	5e-05
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	5e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	6e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	7e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	7e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	7e-05
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	7e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	8e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	8e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	8e-05
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	8e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	8e-05
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	9e-05
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-04
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	1e-04
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	1e-04
cd12755	86	cd12755, RRM2_RBM5, RNA recognition motif 2 in ver	1e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	1e-04
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	1e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-04
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	1e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	1e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-04
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	2e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	2e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-04
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	2e-04
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	2e-04
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	2e-04
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	2e-04
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	2e-04
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	3e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-04
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	3e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	3e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	3e-04
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	3e-04
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	3e-04
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	3e-04
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	4e-04
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	4e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	4e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	4e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	4e-04
cd12562	86	cd12562, RRM2_RBM5_like, RNA recognition motif 2 i	4e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	4e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	4e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	5e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	5e-04
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	5e-04
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	5e-04
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	5e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	6e-04
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	6e-04
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	6e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	7e-04
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	7e-04
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	7e-04
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	8e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	8e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	8e-04
cd12664	70	cd12664, RRM1_RAVER2, RNA recognition motif 1 in v	8e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	8e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	8e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.001
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	0.001
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.001
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	0.001
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	0.001
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	0.001
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	0.001
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	0.001
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	0.001
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.001
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.001
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.001
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	0.001
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	0.001
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	0.002
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.002
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.002
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	0.002
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	0.002
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	0.002
cd12605	69	cd12605, RRM_RALYL, RNA recognition motif in verte	0.002
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	0.002
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	0.002
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	0.002
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	0.002
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.003
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.003
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.003
cd12426	79	cd12426, RRM4_PTBPH3, RNA recognition motif 4 in p	0.003
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	0.003
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	0.003
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	0.004
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.004
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	0.004
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.004
cd12600	72	cd12600, RRM2_SRSF4_like, RNA recognition motif 2	0.004
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.004
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	0.004
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	0.004

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score =  117 bits (296), Expect = 5e-33
 Identities = 39/77 (50%), Positives = 51/77 (66%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            +YVGNLP+ V    L+ +F + G+V +ARV+ DRETGRSRGFGFV M +  E N AI  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 341 LDGQNLDGRAIRVNVAE 357
           L+G +  GR + VN A 
Sbjct: 61  LNGTDFGGRTLTVNEAR 77

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score =  101 bits (255), Expect = 5e-27
 Identities = 44/104 (42%), Positives = 51/104 (49%), Gaps = 26/104 (25%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            L+VGNLPY+V  E L  LF + G V  A V                          I +
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARV--------------------------ITD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP 264
           RET RSRGFGFV M T EEA  A+E  +  D  GR LTVN+A P
Sbjct: 35  RETGRSRGFGFVEMETAEEANAAIEKLNGTDFGGRTLTVNEARP 78

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 95.0 bits (237), Expect = 1e-24
 Identities = 33/73 (45%), Positives = 50/73 (68%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            ++VGNLP +     L ++FS+ GKV + R+V D+ETG+S+GF FV   SE +   A+ A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 341 LDGQNLDGRAIRV 353
           L+G+ LDGR ++V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 95.5 bits (237), Expect = 7e-24
 Identities = 40/79 (50%), Positives = 54/79 (68%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L W  D+A L   F+  G VV+A+V+ DRETGRSRGFGFV  + E     AI+ 
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 341 LDGQNLDGRAIRVNVAEDR 359
           +DG+ L+GR IRVN A DR
Sbjct: 96  MDGKELNGRHIRVNPANDR 114

Length = 144

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 92.7 bits (231), Expect = 1e-23
 Identities = 32/78 (41%), Positives = 46/78 (58%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G +++V  L        LE +FS+ G+V    ++ D ETG SRGFGFVT  S  + + AI
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 339 AALDGQNLDGRAIRVNVA 356
             L+G+ L+GR I+V  A
Sbjct: 61  RDLNGKELEGRVIKVEKA 78

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 92.5 bits (230), Expect = 1e-23
 Identities = 39/76 (51%), Positives = 51/76 (67%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            ++VGNL W VD+  L+  F + G VV ARV+ DRETGRSRGFG+V   S  +   AI A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 341 LDGQNLDGRAIRVNVA 356
           +DG+ LDGR I V+ +
Sbjct: 61  MDGKELDGRPINVDFS 76

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score =  101 bits (252), Expect = 2e-23
 Identities = 70/227 (30%), Positives = 102/227 (44%), Gaps = 42/227 (18%)

Query: 150 EEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAV 209
           E E     +   L+V NL   V+ +KL  LF K G +  A V                  
Sbjct: 169 EREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVM----------------- 211

Query: 210 FYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDID----GRLLTVNKAAPR 265
                        + RSRGF FV     E+A KAVE  +   I     G+ L V +A  R
Sbjct: 212 ----------KDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKR 261

Query: 266 GTQPERAPRVFEP----------GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR 315
             +     R FE           G  +YV NL   V + +L ++FSE G++ +A+V+ D 
Sbjct: 262 AEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD- 320

Query: 316 ETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
           E G SRGFGFV  S+  E N A+  + G+ L G+ + V +A+ +++R
Sbjct: 321 EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQR 367

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 83.8 bits (208), Expect = 2e-20
 Identities = 30/71 (42%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGNLP +     L+ +FS+ G + + R+V D ETGRS+GF FV    E +   A+ AL
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 342 DGQNLDGRAIR 352
           +G+ L GR +R
Sbjct: 60  NGKELGGRELR 70

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 83.1 bits (206), Expect = 4e-20
 Identities = 30/75 (40%), Positives = 48/75 (64%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGN+P++    +L ++FSE G VV+ R+V DR+TG+ +G+GF           AI  L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 342 DGQNLDGRAIRVNVA 356
           +G   +GRA+RV+ A
Sbjct: 61  NGYEFNGRALRVDFA 75

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 80.7 bits (199), Expect = 3e-19
 Identities = 35/78 (44%), Positives = 55/78 (70%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L ++ +   LEQVFS++G++    VV DRET RSRGFGFVT  +  +  DA+ A
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 341 LDGQNLDGRAIRVNVAED 358
           ++G+++DGR IRV+ A  
Sbjct: 62  MNGKSVDGRQIRVDQAGK 79

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 80.0 bits (198), Expect = 4e-19
 Identities = 28/73 (38%), Positives = 48/73 (65%), Gaps = 1/73 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGNLP +     L ++FS+ G++ + R+V D+  G+S+GF FV   S  +   A+ AL
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 342 DGQNLDGRAIRVN 354
           +G+ LDGR ++V+
Sbjct: 60  NGKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 79.6 bits (197), Expect = 7e-19
 Identities = 35/99 (35%), Positives = 49/99 (49%), Gaps = 26/99 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            LFVGNLP D   E+L  LF K G VE   V+                        ++ +
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVE--SVR------------------------LVRD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
           +ET +S+GF FV   + E+AEKA+E  +  ++DGR L V
Sbjct: 35  KETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 77.9 bits (192), Expect = 3e-18
 Identities = 31/73 (42%), Positives = 47/73 (64%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I+VG+L  EV +A L   FS      +ARV++D ++GRSRG+GFV+  S+ +  +AI  +
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 342 DGQNLDGRAIRVN 354
           +G+ L  R IR N
Sbjct: 62  NGKWLGSRPIRCN 74

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 77.4 bits (191), Expect = 5e-18
 Identities = 32/73 (43%), Positives = 50/73 (68%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I+VG+L  E+D   L   F+  G++ +ARVV D +TG+S+G+GFV+   + +  +AI ++
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 342 DGQNLDGRAIRVN 354
           +GQ L GRAIR N
Sbjct: 62  NGQWLGGRAIRTN 74

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 75.1 bits (185), Expect = 3e-17
 Identities = 33/75 (44%), Positives = 49/75 (65%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G+ I+V NLP + D + L Q+FS  G V N +V+ D  T + +G+GFVTM++  E   AI
Sbjct: 1   GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

Query: 339 AALDGQNLDGRAIRV 353
           A+L+G  L GR ++V
Sbjct: 61  ASLNGYRLGGRVLQV 75

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 74.2 bits (183), Expect = 7e-17
 Identities = 33/102 (32%), Positives = 48/102 (47%), Gaps = 26/102 (25%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLFV  L      ++L  LF K G VE  EV                         ++ +
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVE--EV------------------------LLMKD 36

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
            ET  SRGFGFVT  +VE+A+ A+   +  +++GR++ V KA
Sbjct: 37  PETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKVEKA 78

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 74.2 bits (183), Expect = 7e-17
 Identities = 26/78 (33%), Positives = 43/78 (55%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++V NLP++  + +LE+ FSE G +    VV D+ + + RGFG+VT + E +   A+   
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 342 DGQNLDGRAIRVNVAEDR 359
                 GR I V  A+ +
Sbjct: 62  KKTKFGGRKIHVEFAKKK 79

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 73.1 bits (180), Expect = 2e-16
 Identities = 32/79 (40%), Positives = 48/79 (60%), Gaps = 2/79 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            ++VGNL W  +   LE+ F E G+VV+ R+  D + GRS+GFG V  ++E     A+  
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKAL-E 58

Query: 341 LDGQNLDGRAIRVNVAEDR 359
             G+ L GR IRV++A +R
Sbjct: 59  KSGEELLGREIRVDLATER 77

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 78.8 bits (193), Expect = 2e-16
 Identities = 41/137 (29%), Positives = 61/137 (44%), Gaps = 4/137 (2%)

Query: 229 FGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR----GTQPERAPRVFEPGFRIYV 284
                     E ++  E       DG      +           P+   +  E    ++V
Sbjct: 61  PPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFV 120

Query: 285 GNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQ 344
           GNLP++V    L ++F + G V   R+V DRETG+SRGF FV   SE     AI  L+G+
Sbjct: 121 GNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGK 180

Query: 345 NLDGRAIRVNVAEDRQR 361
            L+GR +RV  A+   +
Sbjct: 181 ELEGRPLRVQKAQPASQ 197

Length = 306

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 72.3 bits (178), Expect = 3e-16
 Identities = 29/76 (38%), Positives = 45/76 (59%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG LP+   +  L + FS+ G++  A V+ DR+TG+SRG+GFVT   +     A   
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 341 LDGQNLDGRAIRVNVA 356
            +   +DGR   VN+A
Sbjct: 62  PN-PIIDGRKANVNLA 76

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 71.9 bits (177), Expect = 4e-16
 Identities = 27/57 (47%), Positives = 41/57 (71%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
           +++VGNLPW V +  L++ FS+ GKV +  V +D+ETG S+G+GFV+ SS   L +A
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENA 57

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 76.9 bits (188), Expect = 7e-16
 Identities = 59/230 (25%), Positives = 90/230 (39%), Gaps = 42/230 (18%)

Query: 136 GERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHF 195
            E +EE        +       E+  LFVGNLPYDV  E L  LF+K G V+   +    
Sbjct: 92  KEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLV--- 148

Query: 196 LFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGR 255
                                   +RET +SRGF FV   + E AEKA+E  +  +++GR
Sbjct: 149 -----------------------RDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGR 185

Query: 256 LLTVNKAAPRGTQPERAPRVFEPGFR----------------IYVGNLPWEVDNARLEQV 299
            L V KA P            +  F                 +YVGNLP +     L  +
Sbjct: 186 PLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADL 245

Query: 300 FSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGR 349
           F   G +V A +   ++    +   FV   +  +  ++ +  + + + GR
Sbjct: 246 FKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKKKILGR 295

Length = 306

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 70.7 bits (174), Expect = 1e-15
 Identities = 34/102 (33%), Positives = 45/102 (44%), Gaps = 27/102 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG LPY    + L   F + G +E A V                          I +
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVV--------------------------ITD 35

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           R+T +SRG+GFVT    E AE+A +  +   IDGR   VN A
Sbjct: 36  RQTGKSRGYGFVTFKDKESAERACKDPNPI-IDGRKANVNLA 76

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 70.2 bits (172), Expect = 2e-15
 Identities = 32/75 (42%), Positives = 50/75 (66%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGN+P+E    +L+ +FSE G VV+ R+VYDRETG+ +G+GF     +     A+  L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 342 DGQNLDGRAIRVNVA 356
           +G  L+GR +RV+ A
Sbjct: 61  NGYELNGRQLRVDNA 75

This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. . Length = 75

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 69.7 bits (171), Expect = 3e-15
 Identities = 29/72 (40%), Positives = 41/72 (56%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++V  L      A L+Q+FS++GKVV A++V +  +  +R FGFVTM+S  E    I  L
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 342 DGQNLDGRAIRV 353
               L GR I V
Sbjct: 62  HRTELHGRVISV 73

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 69.3 bits (170), Expect = 4e-15
 Identities = 38/102 (37%), Positives = 51/102 (50%), Gaps = 26/102 (25%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            LFVGNL + VD E L   FEK GTV  A                          +VI +
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGA--------------------------RVITD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           RET RSRGFG+V   + E+A+KA+E     ++DGR + V+ +
Sbjct: 35  RETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 68.5 bits (168), Expect = 8e-15
 Identities = 26/75 (34%), Positives = 47/75 (62%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV NLP+ + N  L ++FS++GKVV   +V D+ET +S+G  F+      + +  + AL
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 342 DGQNLDGRAIRVNVA 356
           + + L GR ++ ++A
Sbjct: 64  NNKELFGRTLKCSIA 78

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 68.4 bits (168), Expect = 9e-15
 Identities = 29/58 (50%), Positives = 39/58 (67%)

Query: 296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV 353
           L +VFS +G +   +VVYD++TGRSRGFGFV   S  +  +A   L+G  +DGR IRV
Sbjct: 16  LREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRV 73

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 68.2 bits (167), Expect = 9e-15
 Identities = 26/73 (35%), Positives = 47/73 (64%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGNL ++ D   + + F E+G++ + R+  D ++GR +GFG+V  SS+     A+ AL
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 342 DGQNLDGRAIRVN 354
            G +L GR +R++
Sbjct: 61  GGTDLLGRPVRLD 73

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 67.6 bits (166), Expect = 1e-14
 Identities = 28/70 (40%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +++G L W+     L + FS++G+VV+  ++ D  TGRSRGFGFVT +  + ++  +AA 
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA- 59

Query: 342 DGQNLDGRAI 351
               LDGR I
Sbjct: 60  KPHVLDGREI 69

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 67.6 bits (166), Expect = 1e-14
 Identities = 29/71 (40%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV NLP  V    L + FS +GKV   R+V +++  R RGF FV  +S  +   A+  L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 342 DGQNLDGRAIR 352
           +G  LDGR +R
Sbjct: 59  NGLVLDGRTLR 69

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 66.8 bits (164), Expect = 2e-14
 Identities = 32/97 (32%), Positives = 40/97 (41%), Gaps = 27/97 (27%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           LFVGNLP D   E L  LF K G +E   +                              
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD--------------------------- 33

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLT 258
           ET RS+GF FV     E+AEKA+E  +  ++ GR L 
Sbjct: 34  ETGRSKGFAFVEFEDEEDAEKALEALNGKELGGRELR 70

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 67.0 bits (164), Expect = 2e-14
 Identities = 30/72 (41%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I+V NL ++V   +L++VF   GKVV A +  D+E G+SRG G V      E   AI+  
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59

Query: 342 DGQNLDGRAIRV 353
           +GQ L  R +RV
Sbjct: 60  NGQMLFDRPMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 66.9 bits (164), Expect = 4e-14
 Identities = 31/79 (39%), Positives = 49/79 (62%), Gaps = 1/79 (1%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G  +YV NL   +D+ RL + FS  G + +A+V+ D E GRS+GFGFV  SS  E   A+
Sbjct: 1   GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAV 59

Query: 339 AALDGQNLDGRAIRVNVAE 357
             ++G+ + G+ + V +A+
Sbjct: 60  TEMNGRIIGGKPLYVALAQ 78

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 66.2 bits (162), Expect = 5e-14
 Identities = 33/99 (33%), Positives = 45/99 (45%), Gaps = 27/99 (27%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           LFVGNLP D   E L  LF K G +E   V+                         I   
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIE--SVR-------------------------IVRD 33

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
           +  +S+GF FV   + E+AEKA+E  +  ++DGR L V+
Sbjct: 34  KDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 66.1 bits (162), Expect = 5e-14
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVV-NARVVYDRETGRSRGFGFVTMSSETELNDAI 338
             I+VG+L  +V +  L++ F      V  A+VV D  TGRS+G+GFV    E E + A+
Sbjct: 2   HSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRAL 61

Query: 339 AALDGQNLDGRAIRVNVA 356
             ++G     R +RV+ A
Sbjct: 62  TEMNGVYCSSRPMRVSPA 79

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 72.5 bits (178), Expect = 6e-14
 Identities = 54/206 (26%), Positives = 91/206 (44%), Gaps = 37/206 (17%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +FV NL   VD++ L   F K              FGN    +  C V            
Sbjct: 91  IFVKNLDKSVDNKALFDTFSK--------------FGN----ILSCKVA---------TD 123

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGF- 280
           E  +SRG+GFV     E A+ A++  +   ++ + + V +   +  + E AP      F 
Sbjct: 124 ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKK-HEREAAP---LKKFT 179

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            +YV NL   V+  +L ++F++ G++ +A V+ D  +GRSRGF FV      +   A+  
Sbjct: 180 NLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEE 238

Query: 341 LDGQNLDGRA----IRVNVAEDRQRR 362
           ++G+ +        + V  A+ R  R
Sbjct: 239 MNGKKIGLAKEGKKLYVGRAQKRAER 264

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 72.1 bits (177), Expect = 7e-14
 Identities = 56/204 (27%), Positives = 89/204 (43%), Gaps = 35/204 (17%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
           A L+VG+L  DV   KL  LF+  G V                            ++V  
Sbjct: 1   ASLYVGDLDPDVTEAKLYDLFKPFGPV--------------------------LSVRVCR 34

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPG 279
           +  T RS G+G+V      +AE+A+E  +   + G+ + +  +       +R P +   G
Sbjct: 35  DSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWS-------QRDPSLRRSG 87

Query: 280 F-RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
              I+V NL   VDN  L   FS+ G +++ +V  D E G+SRG+GFV    E     AI
Sbjct: 88  VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAI 146

Query: 339 AALDGQNLDGRAIRVNVAEDRQRR 362
             ++G  L+ + + V     +  R
Sbjct: 147 QKVNGMLLNDKEVYVGRFIKKHER 170

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 71.9 bits (176), Expect = 9e-14
 Identities = 64/240 (26%), Positives = 98/240 (40%), Gaps = 47/240 (19%)

Query: 129 EDTVVEAGERQEESGEEGVFEEEEFVEPPEDAK-LFVGNLPYDVDSEKLAMLFEKAGTVE 187
            D      +R+  SG      +E   E   D + +FV  L        L   F K G V 
Sbjct: 63  GDRSYRRDDRR--SGRN---TKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKV- 116

Query: 188 IAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMF 247
             +V                        Q I +R + RS+G  +V    VE   KA+ + 
Sbjct: 117 -RDV------------------------QCIKDRNSRRSKGVAYVEFYDVESVIKALAL- 150

Query: 248 HRYDIDGRLLTVNKAAPRGTQPE--RAPR------VFEPGF-RIYVGNLPWEVDNARLEQ 298
                 G++L       + +Q E  RA +         P F ++YVGNL + +    L Q
Sbjct: 151 -----TGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQ 205

Query: 299 VFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED 358
           +F   G + + ++  D ETGRS+GFGF+      E  +A+  ++G  L GR I+V  A+D
Sbjct: 206 IFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD 265

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 65.7 bits (161), Expect = 9e-14
 Identities = 24/72 (33%), Positives = 49/72 (68%), Gaps = 1/72 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV NL  ++D+ +L+++F ++GK+ +A+V+ D + G+S+GFGFV   +      A+  L
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 342 DGQNLDGRAIRV 353
           +G+ ++G+ + V
Sbjct: 63  NGKEVNGKKLYV 74

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 64.9 bits (159), Expect = 1e-13
 Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 8/73 (10%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VGNLP    +  L  +F ++G V    VV        + +GFV M  E +  DAI A
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKA 52

Query: 341 LDGQNLDGRAIRV 353
           L+G    G+ I V
Sbjct: 53  LNGYEFMGKRINV 65

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 64.9 bits (158), Expect = 1e-13
 Identities = 31/78 (39%), Positives = 47/78 (60%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++V NL + V    L   FS+   + +A VV D ETG SRG+GFVT +   +  +A+A L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 342 DGQNLDGRAIRVNVAEDR 359
             + L GR +R+++AE R
Sbjct: 62  KNKKLHGRILRLDIAERR 79

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 65.1 bits (158), Expect = 2e-13
 Identities = 30/77 (38%), Positives = 49/77 (63%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           F ++VG+L  E+    ++  F+  G++ +ARVV D  TG+S+G+GFV+  ++ +  +AI 
Sbjct: 2   FHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61

Query: 340 ALDGQNLDGRAIRVNVA 356
            + GQ L GR IR N A
Sbjct: 62  QMGGQWLGGRQIRTNWA 78

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 64.5 bits (158), Expect = 2e-13
 Identities = 28/72 (38%), Positives = 45/72 (62%), Gaps = 1/72 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGNLP++++   L + F + G V   R+V DR+TG  +GFG+V   ++  +  A+  L
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KL 60

Query: 342 DGQNLDGRAIRV 353
           +G  L GR IRV
Sbjct: 61  NGIKLKGRKIRV 72

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 64.6 bits (158), Expect = 2e-13
 Identities = 24/73 (32%), Positives = 45/73 (61%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +++ +LP E  +  L Q+F+  G V++A+V  D+ TG+S+ FGFV+  +      AI A+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 342 DGQNLDGRAIRVN 354
           +G  + G+ ++V 
Sbjct: 61  NGFQVGGKRLKVQ 73

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 70.4 bits (172), Expect = 2e-13
 Identities = 38/129 (29%), Positives = 65/129 (50%), Gaps = 8/129 (6%)

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRV 275
           +++ ++ T +S G+GFV     E+AEKAV   +   +  + + V+ A P     +     
Sbjct: 34  KLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSDSIK----- 88

Query: 276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELN 335
              G  +YV  LP  +    LE +FS  G+++ +R++ D  TG S+G GF+      E +
Sbjct: 89  ---GANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEAD 145

Query: 336 DAIAALDGQ 344
            AI  L+G 
Sbjct: 146 RAIKTLNGT 154

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 64.6 bits (158), Expect = 2e-13
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R+ V NLP++   A L+++FS  G V    +      G+ +GF FV  +S+ +   AI  
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKG 59

Query: 341 LDGQNLDGRAIRVNVA 356
           ++G+ + GR + V+ A
Sbjct: 60  VNGKKIKGRPVAVDWA 75

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 63.8 bits (156), Expect = 3e-13
 Identities = 24/77 (31%), Positives = 44/77 (57%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
            RIYV ++  ++    ++ VF   GK+ +  +  D ETG+ +G+GF+   +     DAIA
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 340 ALDGQNLDGRAIRVNVA 356
           +++  +L G+ +RV  A
Sbjct: 61  SMNLFDLGGQQLRVGKA 77

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 63.8 bits (156), Expect = 3e-13
 Identities = 34/98 (34%), Positives = 48/98 (48%), Gaps = 27/98 (27%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +FV NLP+ V  + L  LF + G V  A+VK      N G                    
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKT----DNDG-------------------- 36

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
              RS+GFG V   + E+A++A+EMF+ YD++GR L V
Sbjct: 37  ---RSKGFGTVLFESPEDAQRAIEMFNGYDLEGRELEV 71

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 63.8 bits (156), Expect = 4e-13
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVGNL + +    L  +F   G++   ++  D ETGRS+G+GF+  +   +   A+  L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 342 DGQNLDGRAIRVN 354
           +G  L GR I+V 
Sbjct: 61  NGFELAGRPIKVG 73

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 64.0 bits (155), Expect = 4e-13
 Identities = 31/77 (40%), Positives = 49/77 (63%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           F ++VG+L  E+    ++  F+  GK+ +ARVV D  TG+S+G+GFV+  ++ +  +AI 
Sbjct: 2   FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61

Query: 340 ALDGQNLDGRAIRVNVA 356
            + GQ L GR IR N A
Sbjct: 62  HMGGQWLGGRQIRTNWA 78

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 63.5 bits (155), Expect = 4e-13
 Identities = 32/76 (42%), Positives = 48/76 (63%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG LP +V     ++ FS+ GKVV+A+++ D +TGRSRGFGFVT  SE+ +    +A
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 341 LDGQNLDGRAIRVNVA 356
                L G+ + V  A
Sbjct: 61  -GMLELGGKQVEVKRA 75

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 63.4 bits (155), Expect = 6e-13
 Identities = 27/74 (36%), Positives = 47/74 (63%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           FRI+VG+L  EV +  L + FS++     A+VV D+ TG+S+G+GFV+ S   +   A+ 
Sbjct: 7   FRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMK 66

Query: 340 ALDGQNLDGRAIRV 353
            ++G+ +  R I++
Sbjct: 67  EMNGKYVGNRPIKL 80

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 63.1 bits (154), Expect = 7e-13
 Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 2/77 (2%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           F  +VGNLP+      L+ +F +   V + R+V D+ET + +GF +V       L +A+ 
Sbjct: 2   FTAFVGNLPFNTVQGDLDAIF-KDLSVKSVRLVRDKETDKFKGFCYVEFEDVESLKEAL- 59

Query: 340 ALDGQNLDGRAIRVNVA 356
             DG   D R++RV++A
Sbjct: 60  EYDGALFDDRSLRVDIA 76

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 63.2 bits (153), Expect = 8e-13
 Identities = 33/85 (38%), Positives = 51/85 (60%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G+ I+V NL  E D + L Q+F   G V N +V+ D  T + +GFGFVTM++  E   AI
Sbjct: 1   GWCIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAI 60

Query: 339 AALDGQNLDGRAIRVNVAEDRQRRS 363
           A+L+G  L  R ++V+    +Q ++
Sbjct: 61  ASLNGYRLGDRVLQVSFKTSKQHKA 85

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 67.7 bits (165), Expect = 1e-12
 Identities = 28/84 (33%), Positives = 48/84 (57%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G+ I+V NL  + D   L Q+F   G V N +++ D  T + +G+GFV+M++  E   AI
Sbjct: 269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAI 328

Query: 339 AALDGQNLDGRAIRVNVAEDRQRR 362
            +L+G  L  R ++V+   ++  R
Sbjct: 329 LSLNGYTLGNRVLQVSFKTNKAYR 352

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 24/78 (30%), Positives = 45/78 (57%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++V  L ++   ++L + F E+G +   R+V D++TG+ RG+ F+    E ++  A    
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 342 DGQNLDGRAIRVNVAEDR 359
           DG+ +DGR + V+V   R
Sbjct: 64  DGKKIDGRRVLVDVERGR 81

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 62.3 bits (151), Expect = 1e-12
 Identities = 27/74 (36%), Positives = 45/74 (60%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV  LP  +    LEQ+FS++G+++ +R++ D+ TG SRG GF+      E  +AI  L
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 342 DGQNLDGRAIRVNV 355
           +GQ  +G +  + V
Sbjct: 63  NGQKPEGASEPITV 76

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 61.1 bits (149), Expect = 3e-12
 Identities = 29/72 (40%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I+V NLP+ V    L+ +F E G V+ A V  D + GRS+GFG V   S  +   AI   
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59

Query: 342 DGQNLDGRAIRV 353
           +G +L+GR + V
Sbjct: 60  NGYDLEGRELEV 71

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 28/72 (38%), Positives = 46/72 (63%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           IY+G LP+E+    +  VFS++G++V+  +V D++TG+S+GF F+    +     A+  L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 342 DGQNLDGRAIRV 353
           +G  L GR IRV
Sbjct: 72  NGIKLLGRTIRV 83

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 61.1 bits (149), Expect = 4e-12
 Identities = 29/104 (27%), Positives = 47/104 (45%), Gaps = 26/104 (25%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           LFV NLPYD   E+L   F      E+  +K       + F              V+ ++
Sbjct: 2   LFVRNLPYDTTDEQLEEFFS-----EVGPIK-------RCF--------------VVKDK 35

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
            + + RGFG+VT +  E+A++A+E   +    GR + V  A  +
Sbjct: 36  GSKKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVEFAKKK 79

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 60.6 bits (148), Expect = 4e-12
 Identities = 28/94 (29%), Positives = 36/94 (38%), Gaps = 28/94 (29%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L+V NLP  V  E L   F   G VE                             V   R
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVE----------------------------GVRLVR 32

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGR 255
             DR RGF FV  ++ E+AE A++  +   +DGR
Sbjct: 33  NKDRPRGFAFVEFASPEDAEAALKKLNGLVLDGR 66

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 61.0 bits (148), Expect = 4e-12
 Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 4/71 (5%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG L WE     L + FS++G+VV+  ++ D+ T RSRGFGFV       +   +A 
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 341 ----LDGQNLD 347
               LDG+ +D
Sbjct: 61  GPHTLDGRTID 71

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 60.8 bits (148), Expect = 4e-12
 Identities = 25/67 (37%), Positives = 37/67 (55%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV  LP  +    LE +FS +G+++ +R++ D  TG SRG GF+      E   AI AL
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 342 DGQNLDG 348
           +G    G
Sbjct: 63  NGTIPPG 69

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 60.7 bits (148), Expect = 5e-12
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
            R+ V NL ++V    LE++F   G+V   ++ YDR +GRS G   V      +   AI 
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIK 59

Query: 340 ALDGQNLDGRAIRVNV 355
             +G  LDG+ ++V +
Sbjct: 60  QFNGVLLDGQPMQVEL 75

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 60.7 bits (147), Expect = 5e-12
 Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 2/82 (2%)

Query: 281 RIYVGNLPWEV-DNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           ++ + NLPW +    +L+++F  +GKV  A +   R  G+  GF FVTM        A+ 
Sbjct: 2   KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIALE 60

Query: 340 ALDGQNLDGRAIRVNVAEDRQR 361
             +G  +DGR + V+ A  + R
Sbjct: 61  NTNGLEIDGRPVAVDWAVQKNR 82

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 60.4 bits (147), Expect = 6e-12
 Identities = 23/73 (31%), Positives = 39/73 (53%)

Query: 284 VGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDG 343
           V  LP ++    L  +F   G + + ++V DR TG+S G+GFV    E +   AI  L+G
Sbjct: 5   VNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNG 64

Query: 344 QNLDGRAIRVNVA 356
             +  + ++V+ A
Sbjct: 65  FEIRNKRLKVSYA 77

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 60.1 bits (146), Expect = 7e-12
 Identities = 26/76 (34%), Positives = 47/76 (61%), Gaps = 2/76 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++V N+P+   +  L Q+F + G +++  ++++ E G S+GFGFVT ++  + + A   
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFN-ERG-SKGFGFVTFANSADADRAREK 59

Query: 341 LDGQNLDGRAIRVNVA 356
           L G  ++GR I VN A
Sbjct: 60  LHGTVVEGRKIEVNNA 75

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 60.1 bits (146), Expect = 8e-12
 Identities = 29/79 (36%), Positives = 42/79 (53%), Gaps = 1/79 (1%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
             +I+VG LP  V    L + FS+ G V    V+YD E  R RGFGF+T  SE +  D +
Sbjct: 2   TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESE-DSVDQV 60

Query: 339 AALDGQNLDGRAIRVNVAE 357
                 +++G+ + V  AE
Sbjct: 61  VNEHFHDINGKKVEVKRAE 79

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 59.9 bits (146), Expect = 9e-12
 Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           RI V NLP  V   RL + F   G+V + +V+  R+ G+SR FGFV   SE +   A+  
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQAVKY 60

Query: 341 LDGQNLDGRAIRVNVA 356
            +   +D   I V +A
Sbjct: 61  FNKTFIDTSKISVELA 76

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 59.9 bits (145), Expect = 1e-11
 Identities = 33/103 (32%), Positives = 50/103 (48%), Gaps = 26/103 (25%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
            KLF+G L +D + + L  +F K G   I+EV                         V+ 
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQ--ISEV------------------------VVVK 34

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           +RET RSRGFGFVT    ++A+ A+   +   +DGR + V++A
Sbjct: 35  DRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRVDQA 77

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 60.1 bits (145), Expect = 1e-11
 Identities = 31/84 (36%), Positives = 50/84 (59%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G+ I+V NL  + D + L Q+F   G V N +V+ D  T + +GFGFVTM++  E   AI
Sbjct: 3   GWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

Query: 339 AALDGQNLDGRAIRVNVAEDRQRR 362
           A+L+G  L  R ++V+   ++  +
Sbjct: 63  ASLNGYRLGDRVLQVSFKTNKTHK 86

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 59.3 bits (144), Expect = 1e-11
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            +Y+GNL W++    + + F    ++ + R+  D+ETG  +GFG V  + E  L+ A+  
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL-K 58

Query: 341 LDGQNLDGRAIRVN 354
           LDG  L GR IR+ 
Sbjct: 59  LDGTVLCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 58.4 bits (142), Expect = 2e-11
 Identities = 31/99 (31%), Positives = 41/99 (41%), Gaps = 34/99 (34%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLFVGNLP    SE+L  LFEK GTV                                  
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVT--------------------------------- 27

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
            E D  + +GFV M   E+AE A++  + Y+  G+ + V
Sbjct: 28  -ECDVVKNYGFVHMEEEEDAEDAIKALNGYEFMGKRINV 65

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 59.1 bits (143), Expect = 2e-11
 Identities = 23/74 (31%), Positives = 39/74 (52%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV NLP ++    L ++F  +G +V   ++ D+ TG  RG  FV      E   AI++L
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 342 DGQNLDGRAIRVNV 355
           +G    G  + ++V
Sbjct: 63  NGTIPPGSTMPLSV 76

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 28/70 (40%), Positives = 41/70 (58%)

Query: 284 VGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDG 343
           V NL +      L +VF ++G+V +  +  DR T  SRGF FV    + +  DA+ A+DG
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 344 QNLDGRAIRV 353
           + LDGR +RV
Sbjct: 63  KELDGRELRV 72

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 58.9 bits (142), Expect = 3e-11
 Identities = 31/84 (36%), Positives = 50/84 (59%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G+ I+V NL  + D + L Q+F   G V N +V+ D  T + +GFGFVTM++  E   AI
Sbjct: 3   GWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

Query: 339 AALDGQNLDGRAIRVNVAEDRQRR 362
           A+L+G  L  R ++V+   ++  +
Sbjct: 63  ASLNGYRLGDRVLQVSFKTNKTHK 86

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 58.7 bits (143), Expect = 3e-11
 Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVV--NARVVYDRETGRSRGFGFVTMSS---ETELND 336
           + +  L        + Q  S    V   + R++ D+ TG SRGF FV   S    T+  D
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64

Query: 337 AIAALDGQNLDGRAIRVNVA 356
           A+  LD   +DGR +RV+ A
Sbjct: 65  ALNNLDPFVIDGRVVRVSYA 84

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 58.5 bits (141), Expect = 3e-11
 Identities = 29/84 (34%), Positives = 48/84 (57%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G+ I++ NL  + D   L Q+F   G V N +V+ D  T + +GFGFVTM++  E   AI
Sbjct: 1   GWCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAI 60

Query: 339 AALDGQNLDGRAIRVNVAEDRQRR 362
           A+L+G  L  + ++V+    +  +
Sbjct: 61  ASLNGYRLGDKILQVSFKTSKSHK 84

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 58.0 bits (141), Expect = 3e-11
 Identities = 32/76 (42%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVG L  EVD   L   F   G + + ++  D ET + RGF FV      E  DA AA+
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFE---EPEDAAAAI 57

Query: 342 DGQN---LDGRAIRVN 354
           D  N   L GR IRVN
Sbjct: 58  DNMNESELFGRTIRVN 73

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 57.8 bits (139), Expect = 5e-11
 Identities = 26/67 (38%), Positives = 41/67 (61%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV  LP  +    LEQ+FS++G+++ +R++ D+ TG SRG GF+      E  +AI  L
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 342 DGQNLDG 348
           +GQ   G
Sbjct: 65  NGQKPSG 71

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 57.7 bits (140), Expect = 5e-11
 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 8/77 (10%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVT-MSSETELNDAIA 339
           R++V NLP+      L ++F   G++    +  D+ET RS+GF FV+ M  E     A+ 
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPE----HAVK 56

Query: 340 A---LDGQNLDGRAIRV 353
           A   LDG    GR + V
Sbjct: 57  AYSELDGSIFQGRLLHV 73

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 62.7 bits (152), Expect = 6e-11
 Identities = 36/145 (24%), Positives = 76/145 (52%), Gaps = 10/145 (6%)

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRV 275
           +++ + +T  S G+ FV   +  ++++A++  +   +  + L V+ A P G   +     
Sbjct: 138 RIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGESIKDT--- 194

Query: 276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELN 335
                 +YV NLP  + + +L+ +F ++G++V   ++ D+ TG  RG  FV  +   E  
Sbjct: 195 -----NLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQ 249

Query: 336 DAIAALDGQNLDG--RAIRVNVAED 358
           +AI+AL+    +G  + + V +AE+
Sbjct: 250 EAISALNNVIPEGGSQPLTVRLAEE 274

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 57.7 bits (140), Expect = 6e-11
 Identities = 31/79 (39%), Positives = 48/79 (60%), Gaps = 3/79 (3%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEH-GKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           F ++VG+L  +VD+ +L + FS+       A+VV D + G SRG+GFV  S E+E   A+
Sbjct: 2   FSLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDESEQKRAL 60

Query: 339 AALDG-QNLDGRAIRVNVA 356
             + G   L G+ IRV++A
Sbjct: 61  TEMQGASGLGGKPIRVSLA 79

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 57.3 bits (139), Expect = 7e-11
 Identities = 26/73 (35%), Positives = 44/73 (60%), Gaps = 6/73 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++VGNLP ++     +++FS++G+V  + V  ++E    +GFGF+ + + T    A A 
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEV--SEVFLNKE----KGFGFIRLDTRTNAEKAKAE 56

Query: 341 LDGQNLDGRAIRV 353
           LDG    GR +RV
Sbjct: 57  LDGIMRKGRQLRV 69

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 57.3 bits (138), Expect = 8e-11
 Identities = 27/74 (36%), Positives = 44/74 (59%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV  LP  +    +EQ+FS++G+++ +R++ D+ TG SRG GF+      E  +AI  L
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 342 DGQNLDGRAIRVNV 355
           +GQ   G A  + V
Sbjct: 64  NGQKPLGAAEPITV 77

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 57.3 bits (139), Expect = 9e-11
 Identities = 29/79 (36%), Positives = 45/79 (56%), Gaps = 1/79 (1%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNA-RVVYDRETGRSRGFGFVTMSSETELNDA 337
           G  +++GNL  EVD   L   FS  G ++   +++ D +TG S+GF F++  S    + A
Sbjct: 1   GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA 60

Query: 338 IAALDGQNLDGRAIRVNVA 356
           I A++GQ L  R I V+ A
Sbjct: 61  IEAMNGQYLCNRPITVSYA 79

This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 83

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 56.8 bits (138), Expect = 1e-10
 Identities = 29/73 (39%), Positives = 42/73 (57%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVGNL  +V    L ++F + G VVN  +  DR T   +G+GFV   SE + + AI  +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 342 DGQNLDGRAIRVN 354
           +   L G+ IRVN
Sbjct: 61  NMIKLYGKPIRVN 73

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 57.1 bits (137), Expect = 1e-10
 Identities = 26/67 (38%), Positives = 41/67 (61%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV  LP  +    LEQ+FS++G+++ +R++ D+ TG SRG GF+      E  +AI  L
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 342 DGQNLDG 348
           +GQ   G
Sbjct: 68  NGQKPPG 74

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 56.4 bits (136), Expect = 2e-10
 Identities = 27/78 (34%), Positives = 44/78 (56%), Gaps = 1/78 (1%)

Query: 280 FRIYVGNLPWEVDNARLEQVF-SEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           + I+VG+L  EV+ + L  +F S      +A+++ D  TG SRG+GFV  S E +   A+
Sbjct: 2   YSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRAL 61

Query: 339 AALDGQNLDGRAIRVNVA 356
             + G    GR +R++ A
Sbjct: 62  IEMQGVYCGGRPMRISTA 79

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 19/71 (26%), Positives = 43/71 (60%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +++G+L   +D A +   F+E G+V + +++ +++TG+S G+GFV  ++      A+ +L
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 342 DGQNLDGRAIR 352
           +G+ +     R
Sbjct: 62  NGKPIPNTQQR 72

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 55.7 bits (134), Expect = 3e-10
 Identities = 27/59 (45%), Positives = 36/59 (61%)

Query: 296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN 354
           L +VFS +G +    VVYD+ TGRSRGF FV      +  +A+   +G  LDGR IRV+
Sbjct: 16  LREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRVD 74

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 54.7 bits (132), Expect = 5e-10
 Identities = 28/98 (28%), Positives = 44/98 (44%), Gaps = 26/98 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L+V  L     +  L  LF K G V  A                          +++ N 
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGA--------------------------KIVTNA 35

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
            +  +R FGFVTM++VEEA K ++  HR ++ GR+++V
Sbjct: 36  RSPGARCFGFVTMASVEEAAKCIQHLHRTELHGRVISV 73

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 55.2 bits (134), Expect = 5e-10
 Identities = 22/64 (34%), Positives = 36/64 (56%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG LP       +  +F E+G +    ++ D++TG+S+G  FV  SS  E   AI A
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 341 LDGQ 344
           L G+
Sbjct: 61  LHGK 64

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 54.9 bits (133), Expect = 5e-10
 Identities = 23/72 (31%), Positives = 39/72 (54%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VG L   V+   L+++FS +G V +  +  DRE    RG+ +V   S  +   AI  +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 342 DGQNLDGRAIRV 353
           DG  +DG+ + V
Sbjct: 61  DGGQIDGQEVTV 72

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 54.9 bits (133), Expect = 5e-10
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I++ NL   +DN  L   FS  G +++ +V  D E G S+G+GFV   +E     AI  +
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 342 DGQNLDGRAIRVN 354
           +G  L+ + + V 
Sbjct: 64  NGMLLNDKKVFVG 76

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 54.5 bits (132), Expect = 6e-10
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++V  L  +V    L + FS+ GKV + R++ DR + RS+G  +V    E  +  A+  L
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GL 60

Query: 342 DGQNLDGRAIRV 353
            GQ L G+ I V
Sbjct: 61  TGQRLLGQPIMV 72

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 54.6 bits (132), Expect = 7e-10
 Identities = 20/47 (42%), Positives = 31/47 (65%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVT 327
           +++VG L  +V    L + FS++G V +  +V D+ETG+ RGF FVT
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVT 47

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 54.2 bits (131), Expect = 8e-10
 Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 11/79 (13%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVN---ARVVYDRETGRSRGFGFVTMSSETELNDA 337
           ++YVGNL        LE  F ++G + +   AR           GF FV      +  DA
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR--------NPPGFAFVEFEDPRDAEDA 52

Query: 338 IAALDGQNLDGRAIRVNVA 356
           + ALDG+ + G  +RV ++
Sbjct: 53  VRALDGRRICGNRVRVELS 71

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 54.2 bits (131), Expect = 9e-10
 Identities = 28/100 (28%), Positives = 45/100 (45%), Gaps = 26/100 (26%)

Query: 163 FVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRE 222
           FVGN+PYD   E+L  +F + G V    V F                       ++ +R+
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPV----VSFR----------------------LVTDRD 35

Query: 223 TDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           T + +G+GF     +E A  A+   + Y+ +GR L V+ A
Sbjct: 36  TGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRALRVDFA 75

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 54.3 bits (131), Expect = 9e-10
 Identities = 22/77 (28%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++V  LP+ V    LE++F +HG V + R+V +R +G+ +G  +V   +E+  + A+  
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVLK 62

Query: 341 LDGQNLDGRAIRVNVAE 357
           +DG  +  + I V ++ 
Sbjct: 63  MDGTEIKEKTISVAISN 79

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 28/79 (35%), Positives = 47/79 (59%), Gaps = 1/79 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L +E  +  L+  FS+ G++ +  V+ D  T RSRGFGFVT +S +E++ A+ A
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 341 LDGQNLDGRAIRVNVAEDR 359
                +DGR +    A  R
Sbjct: 61  RP-HKVDGREVEPKRAVPR 78

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 53.9 bits (130), Expect = 1e-09
 Identities = 24/73 (32%), Positives = 41/73 (56%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++V NLP+      LE++FS+ G++    V  D+++G+S+GF +V      +   A   
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 341 LDGQNLDGRAIRV 353
           LDG+   GR I +
Sbjct: 64  LDGKVFQGRLIHI 76

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 53.7 bits (129), Expect = 1e-09
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 4/74 (5%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA- 340
           +++G L WE  +  L + F + G+V +  V+ D  TGRSRGFGF+T      +N+ +   
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 341 --LDGQNLD-GRAI 351
             LDG+ +D  RAI
Sbjct: 61  HILDGKIIDPKRAI 74

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 6/77 (7%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           RI+VG +P +     L   FS  G V + +++ DR  G S+G+GFVT  ++ +    +A 
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAM 62

Query: 341 ----LDGQNLD-GRAIR 352
                 G+ L+ G AIR
Sbjct: 63  GNLNFRGKKLNIGPAIR 79

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 5/80 (6%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +++ NLP++     L+++FS+ G+V  AR+V D+ TG S+G  FV   ++      + A 
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 342 DGQN-----LDGRAIRVNVA 356
           D        LDGR + V +A
Sbjct: 63  DNAEDSGLSLDGRRLIVTLA 82

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 53.7 bits (130), Expect = 2e-09
 Identities = 29/74 (39%), Positives = 40/74 (54%), Gaps = 6/74 (8%)

Query: 283 YVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD 342
           YVG+L  +V  A L ++FS  G V++ RV  D  T RS G+ +V   +     DA  ALD
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQN---PADAERALD 59

Query: 343 GQNLD---GRAIRV 353
             N D   G+ IR+
Sbjct: 60  TLNFDVIKGKPIRI 73

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 29/101 (28%), Positives = 44/101 (43%), Gaps = 27/101 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           ++V NL  D+D EKL  LF K G +  A                            +   
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSA---------------------------KVMKD 36

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           +  +S+GFGFV     E A+KAVE  +  +++G+ L V +A
Sbjct: 37  DEGKSKGFGFVNFENHEAAQKAVEELNGKEVNGKKLYVGRA 77

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 52.9 bits (127), Expect = 3e-09
 Identities = 26/73 (35%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG L  +  ++ L + F+ +GK+    V+ D  T RSRGFGF+T SS  E ++A+ A
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63

Query: 341 LDGQNLDGRAIRV 353
               ++DG  I +
Sbjct: 64  Q-PHSIDGNQIEL 75

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 52.7 bits (126), Expect = 4e-09
 Identities = 23/74 (31%), Positives = 41/74 (55%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+  LP  +    +E +FS  G+++N+RV+ D+ TG SRG  F+     +E  +AI + 
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 342 DGQNLDGRAIRVNV 355
           +G    G +  + V
Sbjct: 63  NGHKPPGSSEPITV 76

This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 52.3 bits (126), Expect = 5e-09
 Identities = 28/104 (26%), Positives = 46/104 (44%), Gaps = 28/104 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           LFVGNL +  + + L   F++ G  E+ +V+                           + 
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECG--EVVDVRIA------------------------QDD 35

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
           +  RS+GFG V  +T E A+KA+E     ++ GR + V+ A  R
Sbjct: 36  D-GRSKGFGHVEFATEEGAQKALEK-SGEELLGREIRVDLATER 77

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 52.2 bits (126), Expect = 5e-09
 Identities = 21/40 (52%), Positives = 31/40 (77%)

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGR 255
           QV+Y+++T RSRGFGFV   +VE+A++A E  +  +IDGR
Sbjct: 30  QVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGR 69

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 52.2 bits (126), Expect = 5e-09
 Identities = 29/88 (32%), Positives = 41/88 (46%), Gaps = 26/88 (29%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLFVG LP     E +  LFE+ G +E  EV                         +I +
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIE--EV------------------------TIIRD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFH 248
           ++T +S+G  FV  S+ EEA+KA+E  H
Sbjct: 35  KDTGQSKGCAFVKFSSREEAQKAIEALH 62

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 52.2 bits (126), Expect = 5e-09
 Identities = 24/67 (35%), Positives = 34/67 (50%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            I V NL  + D   L ++F   G +    +  D+ETG+SRGF FVT  +  +   AI  
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 341 LDGQNLD 347
           L+G   D
Sbjct: 61  LNGFGYD 67

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 52.4 bits (126), Expect = 5e-09
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 4/74 (5%)

Query: 284 VGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDG 343
           V  LPW+     L+  FS  G+++  +V  D +TG+S+GFGFV  +      D +  L  
Sbjct: 4   VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYE---DQVKVLSQ 60

Query: 344 Q-NLDGRAIRVNVA 356
           +  +DGR   V + 
Sbjct: 61  RHMIDGRWCDVKIP 74

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 52.1 bits (125), Expect = 6e-09
 Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVGN+P     A L  +F   G ++  R   DR      GF FV + +  +   AI  L
Sbjct: 3   VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDR------GFAFVKLDTHEQAAMAIVQL 56

Query: 342 DGQNLDGRAIRVNVAEDR 359
            G  + GR +R    +DR
Sbjct: 57  QGFPVHGRPLRCGWGKDR 74

This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 52.2 bits (125), Expect = 6e-09
 Identities = 24/65 (36%), Positives = 39/65 (60%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G  +++ +LP E  +A L Q+F   G V++A+V  DR T +S+ FGFV+  +      AI
Sbjct: 4   GCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAI 63

Query: 339 AALDG 343
            A++G
Sbjct: 64  QAMNG 68

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 51.8 bits (125), Expect = 7e-09
 Identities = 28/106 (26%), Positives = 42/106 (39%), Gaps = 31/106 (29%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +F+ NLP+D   E+L  LF + G V+                       Y     ++ ++
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVK-----------------------YAR---IVKDK 36

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEM-----FHRYDIDGRLLTVNKA 262
            T  S+G  FV   T E A+K +E           +DGR L V  A
Sbjct: 37  LTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLDGRRLIVTLA 82

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 51.3 bits (123), Expect = 9e-09
 Identities = 22/51 (43%), Positives = 34/51 (66%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
           +I+VG L        +++ FS+ GKV +A +++D++T R RGFGFVT  SE
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESE 51

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 51.4 bits (123), Expect = 9e-09
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VG L W+     L++ FS+ G+VV+  +  D  TGRSRGFGFV +  +    + +   
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFV-LFKDAASVEKVLDQ 59

Query: 342 DGQNLDGRAI 351
               LDGR I
Sbjct: 60  KEHKLDGRVI 69

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 51.0 bits (122), Expect = 1e-08
 Identities = 29/104 (27%), Positives = 46/104 (44%), Gaps = 26/104 (25%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           LFV NL + V  E L   F      ++A +K                        V+ + 
Sbjct: 2   LFVRNLAFSVTQEDLTDFFS-----DVAPIKHAV---------------------VVTDP 35

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
           ET  SRG+GFVT + +E+A++A+       + GR+L ++ A  R
Sbjct: 36  ETGESRGYGFVTFAMLEDAQEALAKLKNKKLHGRILRLDIAERR 79

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 33/99 (33%), Positives = 42/99 (42%), Gaps = 26/99 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +LFV NLP+    E+L  LFE  G  EI+EV                         +  +
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFG--EISEV------------------------HLPLD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
           +ET RS+GF FV+    E A KA          GRLL V
Sbjct: 35  KETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGRLLHV 73

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 51.2 bits (123), Expect = 1e-08
 Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 3/73 (4%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           RIYVGNLP ++    +E +F ++G +    +   R   R   F FV      +  DA+  
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRR---RGPPFAFVEFEDPRDAEDAVRG 57

Query: 341 LDGQNLDGRAIRV 353
            DG + DG  +RV
Sbjct: 58  RDGYDFDGYRLRV 70

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 26/72 (36%), Positives = 40/72 (55%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + VGNLP E  + +  ++ S  G V    +VY   TG S+G+GFV  +S+     A   L
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 342 DGQNLDGRAIRV 353
           DG+ + GR ++V
Sbjct: 62  DGKQIGGRKLQV 73

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 56.2 bits (135), Expect = 1e-08
 Identities = 33/137 (24%), Positives = 66/137 (48%), Gaps = 9/137 (6%)

Query: 223 TDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN------KAAPRGTQPERAPRVF 276
           T + +GF FV     E A+ A+E  +   + GR + V       +A P     +   + F
Sbjct: 145 TGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKF 204

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
               RIYV ++  ++    ++ VF   G++V  ++         +G+GF+  ++    ++
Sbjct: 205 ---NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSE 261

Query: 337 AIAALDGQNLDGRAIRV 353
           AIA+++  +L G+ +RV
Sbjct: 262 AIASMNLFDLGGQYLRV 278

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 51.2 bits (122), Expect = 1e-08
 Identities = 24/59 (40%), Positives = 38/59 (64%)

Query: 296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN 354
           L +VFS++G + +  +VYD+++ RSRGF FV   +  +  +A    +G  LDGR IRV+
Sbjct: 26  LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 84

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVGNLP  +    L++ FS  G +   RV  D+      G+ FV   +      AI A+
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIVAV 56

Query: 342 DGQNLDGRAIRV 353
           +G +++G+ ++ 
Sbjct: 57  NGTSINGQTVKC 68

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+ NLP  +D   LE +   +G+V++ R++ D   G+SRG GF  M S  +  D I+  
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRD-SKGQSRGVGFARMESREKCEDIISKF 61

Query: 342 DGQNLDG 348
           +G+ L G
Sbjct: 62  NGKYLKG 68

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 23/94 (24%), Positives = 41/94 (43%), Gaps = 26/94 (27%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           LFVGNL +D D + +   F + G +                          S +++  + 
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEI--------------------------SSVRLPTDP 34

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGR 255
           ++ R +GFG+V  S+ E A+ A++     D+ GR
Sbjct: 35  DSGRPKGFGYVEFSSQEAAQAALDALGGTDLLGR 68

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 27/103 (26%), Positives = 44/103 (42%), Gaps = 30/103 (29%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +L V N+P+      L  +F + G +   E+                          I+N
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEI--------------------------IFN 35

Query: 221 RETDR-SRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
              +R S+GFGFVT +   +A++A E  H   ++GR + VN A
Sbjct: 36  ---ERGSKGFGFVTFANSADADRAREKLHGTVVEGRKIEVNNA 75

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 22/79 (27%), Positives = 44/79 (55%), Gaps = 3/79 (3%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR---ETGRSRGFGFVTMSSETELNDA 337
           R+++GNL   +    L ++FS++GK+     ++ +     G+ RG+ FVT  ++ E   A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 338 IAALDGQNLDGRAIRVNVA 356
           + +L+G+   G+ + V  A
Sbjct: 61  LKSLNGKTALGKKLVVRWA 79

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 21/72 (29%), Positives = 44/72 (61%), Gaps = 2/72 (2%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++V NL + V    L ++FS+ G++ + R+V + + G+S+G+ +V   +E  + +A+  L
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEAL-KL 59

Query: 342 DGQNLDGRAIRV 353
           D + + GR + V
Sbjct: 60  DRELIKGRPMFV 71

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 50.4 bits (120), Expect = 2e-08
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG L W+     L+  F++ G+V +  +  D  TGRSRGFGF+ +  +    + +  
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFI-LFKDASSVEKVLE 59

Query: 341 LDGQNLDGRAI 351
                LDGR I
Sbjct: 60  QKEHRLDGRLI 70

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++ V N+P+E     L ++FS  G+V + R+    + G  RGF FV   ++ E  +A+ A
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFD-GSHRGFAFVEFVTKQEAQNAMEA 60

Query: 341 LDGQNLDGR 349
           L   +L GR
Sbjct: 61  LKSTHLYGR 69

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 50.2 bits (121), Expect = 2e-08
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMS-SETELNDAIA 339
           R++VG L   V  + LE+ FS  G V +  ++  ++ G  RGF ++ +  SE +L    +
Sbjct: 1   RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKS 60

Query: 340 ALDGQNLDGRAIRVNVA 356
            L+G    G  +++  A
Sbjct: 61  TLNGTKWKGSVLKIEEA 77

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 49.7 bits (119), Expect = 3e-08
 Identities = 27/101 (26%), Positives = 39/101 (38%), Gaps = 33/101 (32%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +FV NL Y V  +KL  +F+ AG V  A++K                             
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIK----------------------------- 31

Query: 222 ETDR---SRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
             D+   SRG G V      EA +A+ MF+   +  R + V
Sbjct: 32  -EDKEGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRPMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 49.6 bits (119), Expect = 3e-08
 Identities = 26/99 (26%), Positives = 48/99 (48%), Gaps = 26/99 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L+VGNL +++  + L  +FE  G +E                           +Q+  + 
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIE--------------------------FVQLQRDP 34

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
           ET RS+G+GF+  +  E+A+KA+E  + +++ GR + V 
Sbjct: 35  ETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKVG 73

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 49.7 bits (119), Expect = 3e-08
 Identities = 24/99 (24%), Positives = 36/99 (36%), Gaps = 28/99 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            L V  LP+    + L   F   G + + +VK                           +
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVK--------------------------KD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
            +T +S+GFGFV  +  E+  K +   H   IDGR   V
Sbjct: 35  PKTGQSKGFGFVRFADYEDQVKVLSQRHM--IDGRWCDV 71

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 49.8 bits (119), Expect = 3e-08
 Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            +YVGNLP ++    +E +F ++G +V+  +   +   R  G+ F+      +  DAI  
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRG 57

Query: 341 LDGQNLDGRAIRVNV 355
            DG + DG+ +RV +
Sbjct: 58  RDGYDFDGQRLRVEL 72

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 4/76 (5%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSR---GFGFVTMSSETELNDAI 338
           IYV NL +++D   L  +FS+ G+V + R+   ++  + R   GF FVT    +   +A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 339 AALDGQNLDGRAIRVN 354
             L+G  L GR I V+
Sbjct: 63  -QLNGTELGGRKISVS 77

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 49.4 bits (118), Expect = 4e-08
 Identities = 29/101 (28%), Positives = 48/101 (47%), Gaps = 26/101 (25%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +FVGN+PY+   E+L  +F + G V    V F                      +++Y+R
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPV----VSF----------------------RLVYDR 34

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           ET + +G+GF      E A  A+   + Y+++GR L V+ A
Sbjct: 35  ETGKPKGYGFCEYKDQETALSAMRNLNGYELNGRQLRVDNA 75

This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. . Length = 75

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 26/102 (25%), Positives = 39/102 (38%), Gaps = 27/102 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +L V NLP+      L  LF   G V   EV                          I  
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVW--EVT-------------------------IPR 33

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           +   + +GF FV  ++  +AEKA++  +   I GR + V+ A
Sbjct: 34  KPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRPVAVDWA 75

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 49.7 bits (119), Expect = 4e-08
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+GNL  +V+ + L Q+F EH   V++ +V      +  G+ FV    ++  + AI  L
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLV------KKGGYAFVDCPDQSWADKAIEKL 54

Query: 342 DGQNLDGRAIRV 353
           +G+ L G+ I V
Sbjct: 55  NGKILQGKVIEV 66

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 29/101 (28%), Positives = 44/101 (43%), Gaps = 28/101 (27%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +FVG +P D+  ++L  LFEKAG +    +   F  G                       
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFS-GL---------------------- 40

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDID-GRLLTVNK 261
               +RG+ FVT +  E A++AV+  H Y+I  G+ L V  
Sbjct: 41  ----NRGYAFVTYTNKEAAQRAVKQLHNYEIRPGKRLGVCI 77

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 49.9 bits (120), Expect = 4e-08
 Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 2/81 (2%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VG L  +     L +VFS +G +   R+V D  TG S+G+ FV    E +   A    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 342 DGQNLDGRAIRVNVAEDRQRR 362
               +DG  I V+   +R+R 
Sbjct: 66  HKLVIDGSEIFVDF--ERERT 84

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 49.3 bits (118), Expect = 5e-08
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV 355
           L + FS  G++    +  DRETG S+GF ++   S   +  A+  LDG +L G  + V+ 
Sbjct: 20  LTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKAL-ELDGSDLGGGNLVVDE 78

Query: 356 A 356
           A
Sbjct: 79  A 79

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 49.2 bits (117), Expect = 5e-08
 Identities = 28/74 (37%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++V NL ++V   +L++VFS  G VV A ++ D++ G+SRG G VT     E   AI+  
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKD-GKSRGIGTVTFEQPIEAVQAISMF 61

Query: 342 DGQNLDGRAIRVNV 355
           +GQ L  R + V +
Sbjct: 62  NGQLLFDRPMHVKM 75

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 49.3 bits (117), Expect = 5e-08
 Identities = 24/73 (32%), Positives = 41/73 (56%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++V  L      A L+ +F ++GKV++A+VV +  +  ++ +G VTMSS  E+   I+ L
Sbjct: 2   LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61

Query: 342 DGQNLDGRAIRVN 354
               L G+ I V 
Sbjct: 62  HRTELHGQQISVE 74

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 49.5 bits (119), Expect = 5e-08
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 4/74 (5%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVY--DRETGRSRGFGFVTMSSETELNDAIA 339
           +YVGNL +     ++ ++FS  G +   R++   DR T    GF FV   +  +  +A+ 
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDI--KRIIMGLDRFTKTPCGFCFVEYYTREDAENAVK 58

Query: 340 ALDGQNLDGRAIRV 353
            L+G  LD R IRV
Sbjct: 59  YLNGTKLDDRIIRV 72

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 49.2 bits (118), Expect = 5e-08
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGNL   V    L ++F + G +   ++  D   G+ + F FVT   E  +  AI  L
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 342 DGQNLDGRAIRV 353
           +G  L GR +R+
Sbjct: 63  NGIRLFGRELRI 74

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 49.0 bits (116), Expect = 7e-08
 Identities = 28/75 (37%), Positives = 40/75 (53%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G  ++V  L        L+ +FS++GKVV A+VV +  +  +R +GFVTMS+  E    I
Sbjct: 1   GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCI 60

Query: 339 AALDGQNLDGRAIRV 353
             L    L GR I V
Sbjct: 61  NHLHRTELHGRMISV 75

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 48.6 bits (116), Expect = 9e-08
 Identities = 22/73 (30%), Positives = 39/73 (53%)

Query: 284 VGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDG 343
           V  LP  +    +  +FS  G++ + +++ D+ TG+S G+GFV      +   AI  L+G
Sbjct: 6   VNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNG 65

Query: 344 QNLDGRAIRVNVA 356
             L  + I+V+ A
Sbjct: 66  LRLQNKTIKVSYA 78

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 48.8 bits (116), Expect = 9e-08
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L W+     L +  S  G+V++  +  D  TGRSRGFGFV +  +    D +  
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFV-LFKDAASVDKVLE 59

Query: 341 LDGQNLDGRAI 351
           L    LDG+ I
Sbjct: 60  LKEHKLDGKLI 70

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 32/98 (32%), Positives = 43/98 (43%), Gaps = 26/98 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +FV NLP D D   L  LF   G V    VK                        VI + 
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAV--TNVK------------------------VIRDL 37

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
            T++ +G+GFVTM+  EEA  A+   + Y + GR+L V
Sbjct: 38  TTNKCKGYGFVTMTNYEEAYSAIASLNGYRLGGRVLQV 75

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 32/103 (31%), Positives = 41/103 (39%), Gaps = 27/103 (26%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
             L+V NL   +D E+L   F   GT+  A+V                            
Sbjct: 2   VNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD------------------------- 36

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
             E  RS+GFGFV  S+ EEA KAV   +   I G+ L V  A
Sbjct: 37  --EKGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALA 77

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 48.5 bits (116), Expect = 1e-07
 Identities = 32/104 (30%), Positives = 47/104 (45%), Gaps = 27/104 (25%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG LP +V    L   F + GTV   EV                         V+Y+
Sbjct: 4   KIFVGGLPPNVTETDLRKYFSQFGTVT--EV------------------------VVMYD 37

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP 264
            E  R RGFGF+T  + +  ++ V   H +DI+G+ + V +A P
Sbjct: 38  HEKKRPRGFGFITFESEDSVDQVVNE-HFHDINGKKVEVKRAEP 80

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 32/106 (30%), Positives = 46/106 (43%), Gaps = 29/106 (27%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLF+G L Y+   + L   F + G  EI +                          V+ +
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWG--EITDC------------------------VVMKD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHR-YDIDGRLLTVNKAAPR 265
             T RSRGFGFVT ++  E + A  M  R + +DGR +   +A PR
Sbjct: 35  PNTKRSRGFGFVTFASASEVDAA--MNARPHKVDGREVEPKRAVPR 78

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 48.6 bits (116), Expect = 1e-07
 Identities = 28/75 (37%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +++G L W+     L + FS+ G++    V+ D  T RSRGFGFVT S    + D + A 
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASV-DKVLAQ 59

Query: 342 DGQNLDGRAIRVNVA 356
               LDG+ I   VA
Sbjct: 60  GPHELDGKKIDPKVA 74

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 48.1 bits (114), Expect = 1e-07
 Identities = 26/70 (37%), Positives = 40/70 (57%), Gaps = 1/70 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +++G L W+     L+  FS+ G+VV+  +  D  TGRSRGFGFV +  E+E  D +   
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFV-LFKESESVDKVMDQ 59

Query: 342 DGQNLDGRAI 351
               L+G+ I
Sbjct: 60  KEHKLNGKVI 69

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 7/77 (9%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
            ++ V NL + V +  ++++F+E G +  A V YDR +GRS G   V         DA+ 
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDR-SGRSLGTADVVFERRA---DALK 56

Query: 340 AL---DGQNLDGRAIRV 353
           A+   +G  LDGR +++
Sbjct: 57  AMKQYNGVPLDGRPMKI 73

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 49.3 bits (117), Expect = 2e-07
 Identities = 32/110 (29%), Positives = 45/110 (40%), Gaps = 26/110 (23%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
            KLF+G L +  D   L   F   G  ++ + K                        VI 
Sbjct: 35  TKLFIGGLSWGTDDASLRDAFAHFG--DVVDAK------------------------VIV 68

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP 269
           +RET RSRGFGFV  +    A  A+      +++GR + VN A  R + P
Sbjct: 69  DRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSAP 118

Length = 144

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 21/101 (20%), Positives = 43/101 (42%), Gaps = 24/101 (23%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +++V NL + +D + L  +F K G VE                        + + +    
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVE-----------------------SIRIPKKQDE 38

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK 261
           ++   + GF FVT      AE A+++ +  ++ GR ++V+ 
Sbjct: 39  KQGRLNNGFAFVTFKDASSAENALQL-NGTELGGRKISVSL 78

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 48.2 bits (114), Expect = 2e-07
 Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L +E     L   + + GK+ +  V+ D  + RSRGFGFVT S   E++ A+AA
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63

Query: 341 LDGQNLDGRAI 351
                +DGR +
Sbjct: 64  RP-HTIDGRVV 73

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 20/73 (27%), Positives = 38/73 (52%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I++G LP  +   +++++    GK+    +V D  TG S+G+ F      +  + AIA 
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 341 LDGQNLDGRAIRV 353
           L+G  L  + + V
Sbjct: 62  LNGMQLGDKKLTV 74

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 22/74 (29%), Positives = 38/74 (51%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R+YVG++ +E+    + Q FS  G + +  + +D  T + +GF FV          A+  
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 341 LDGQNLDGRAIRVN 354
           ++G  L GR I+V 
Sbjct: 62  MNGVMLGGRNIKVG 75

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 47.7 bits (113), Expect = 2e-07
 Identities = 23/75 (30%), Positives = 42/75 (56%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G  +++ +LP E  +  L Q F   G V++A+V  D++T  S+ FGFV+  +      AI
Sbjct: 4   GCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAI 63

Query: 339 AALDGQNLDGRAIRV 353
            A++G  +  + ++V
Sbjct: 64  QAMNGFQIGTKRLKV 78

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 47.7 bits (113), Expect = 2e-07
 Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L W+     L + F + G+V    V+ D  T RSRGFGFVT   +  + D + A
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV-DKVLA 60

Query: 341 LDGQNLDGRAIRVNVA 356
                LD + I   VA
Sbjct: 61  QSRHELDSKTIDPKVA 76

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 25/70 (35%), Positives = 35/70 (50%)

Query: 287 LPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL 346
           LP  + +     +F   G V N ++V D+ TG S GFGFV   S  +   AI  L+G  L
Sbjct: 8   LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQL 67

Query: 347 DGRAIRVNVA 356
             + I+V  A
Sbjct: 68  QNKRIKVAYA 77

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 47.8 bits (113), Expect = 2e-07
 Identities = 27/79 (34%), Positives = 45/79 (56%), Gaps = 1/79 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L +E  +  L + F + G + +  V+ D +T RSRGFGFVT S   E++ A++A
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63

Query: 341 LDGQNLDGRAIRVNVAEDR 359
                +DGR +    A  R
Sbjct: 64  RP-HKVDGRVVEPKRAVSR 81

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 51.7 bits (124), Expect = 3e-07
 Identities = 36/126 (28%), Positives = 48/126 (38%), Gaps = 27/126 (21%)

Query: 137 ERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFL 196
           ER+ E   +    ++E     +   L+V NL   V  EKL  LF + G +  A+V     
Sbjct: 263 EREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-- 320

Query: 197 FGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRL 256
                                    E   SRGFGFV  S  EEA +AV   H   + G+ 
Sbjct: 321 -------------------------EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKP 355

Query: 257 LTVNKA 262
           L V  A
Sbjct: 356 LYVALA 361

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 47.5 bits (114), Expect = 3e-07
 Identities = 22/105 (20%), Positives = 40/105 (38%), Gaps = 29/105 (27%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L +  L      E +        +V I +V+                        +I ++
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASVPIKDVR------------------------LIRDK 40

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVE----MFHRYDIDGRLLTVNKA 262
            T  SRGF FV   ++E+A + ++    +     IDGR++ V+ A
Sbjct: 41  LTGTSRGFAFVEFPSLEDATQWMDALNNLDPFV-IDGRVVRVSYA 84

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 31/102 (30%), Positives = 43/102 (42%), Gaps = 23/102 (22%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +L++GNL   +    L  LF K G ++    KF FLF   G                   
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIK----KFDFLFHKSG------------------- 37

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
               + RG+ FVT  T EEAEKA++  +     G+ L V  A
Sbjct: 38  PLKGQPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVVRWA 79

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 47.3 bits (112), Expect = 3e-07
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGNL   V    L ++F + G +    +  D+E G+ + FGFV       +  AIA L
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIALL 62

Query: 342 DGQNLDGRAIRVN 354
           +G  L GR I+V+
Sbjct: 63  NGIRLYGRPIKVH 75

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 48.0 bits (114), Expect = 3e-07
 Identities = 21/61 (34%), Positives = 31/61 (50%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
            F ++V NLP++     L   FS+ G V  A  V D+ TGR++G GFV    +   N  +
Sbjct: 1   DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

Query: 339 A 339
            
Sbjct: 61  K 61

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR---ETGRSRGFGFVTMSSETELNDAI 338
           +YVGNL  +V    L Q F   G + + ++++ R   E  R+R  GFV   +  +   A+
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 339 AALDGQNLDGRAIRV 353
             LDG+++ G  +++
Sbjct: 64  DELDGKDVMGYELKL 78

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 47.4 bits (112), Expect = 3e-07
 Identities = 28/79 (35%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L +E  +  L   F + G + +  V+ D  T RSRGFGFVT SS  E++ A+ A
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

Query: 341 LDGQNLDGRAIRVNVAEDR 359
                +DGR +    A  R
Sbjct: 64  RP-HKVDGRVVEPKRAVSR 81

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 46.9 bits (112), Expect = 4e-07
 Identities = 28/98 (28%), Positives = 36/98 (36%), Gaps = 26/98 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L VGNLP +   E+   L    G VE       FL                     +Y+ 
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERC-----FL---------------------VYSE 35

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
            T  S+G+GFV  ++   A KA        I GR L V
Sbjct: 36  STGESKGYGFVEYASKASALKAKNQLDGKQIGGRKLQV 73

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 47.0 bits (112), Expect = 4e-07
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVT-MSSETELNDAIA 339
           R+++ NL +      LE++FS++G +    +  D+ T + +GF FVT M  E  +  A A
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVK-AFA 62

Query: 340 ALDGQNLDGRAIRV 353
            LDG    GR + +
Sbjct: 63  ELDGTVFQGRLLHL 76

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 46.4 bits (111), Expect = 5e-07
 Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 26/84 (30%)

Query: 163 FVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRE 222
           FVGNLP+D++ E+L   FE  G VE                    AV      +++ +R+
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVE--------------------AV------RIVRDRK 36

Query: 223 TDRSRGFGFVTMSTVEEAEKAVEM 246
           T   +GFG+V   T +    A+++
Sbjct: 37  TGIGKGFGYVLFKTKDSVALALKL 60

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 46.1 bits (110), Expect = 5e-07
 Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I+VGN+ +      L++ F   G +    ++ D+ TG+ +GF ++    ++ + +A+  L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LL 60

Query: 342 DGQNLDGRAIRV 353
           +     GR I+V
Sbjct: 61  NESEFRGRQIKV 72

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 46.3 bits (110), Expect = 6e-07
 Identities = 24/101 (23%), Positives = 46/101 (45%), Gaps = 27/101 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG L  +   + +   F + G VE A                           ++++
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDA--------------------------MLMFD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK 261
           ++T+R RGFGFVT  + +  +K  E+ H ++I+ +++   K
Sbjct: 35  KQTNRHRGFGFVTFESEDVVDKVCEI-HFHEINNKMVECKK 74

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 50.8 bits (121), Expect = 6e-07
 Identities = 60/212 (28%), Positives = 89/212 (41%), Gaps = 54/212 (25%)

Query: 125 EPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAG 184
           E  G   V E G+R+      G       V+P    ++FVG +P D+  ++L  LFEKAG
Sbjct: 28  ERTGYTLVQENGQRKYGGPPPGW----SGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAG 83

Query: 185 TVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAV 244
              I E++    F  Q                         +RG+ FVT    EEA++AV
Sbjct: 84  --PIYELRLMMDFSGQ-------------------------NRGYAFVTFCGKEEAKEAV 116

Query: 245 EMFHRYDI-DGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEH 303
           ++ + Y+I  GRLL V  +                  R++VG +P    N + E++  E 
Sbjct: 117 KLLNNYEIRPGRLLGVCISVDNC--------------RLFVGGIP---KNKKREEILEEF 159

Query: 304 GKVVNARV---VYDR--ETGRSRGFGFVTMSS 330
            KV    V   VY    +  ++RGF FV   S
Sbjct: 160 SKVTEGVVDVIVYHSAADKKKNRGFAFVEYES 191

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 46.4 bits (111), Expect = 6e-07
 Identities = 22/75 (29%), Positives = 39/75 (52%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            ++VGN+P  V +  + ++  + GKV++ + V D  TG+ + FGF           A+  
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61

Query: 341 LDGQNLDGRAIRVNV 355
           L+G  L G+ + V V
Sbjct: 62  LNGLELGGKKLLVKV 76

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 46.5 bits (111), Expect = 7e-07
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 282 IYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++V  LP    D + L ++FS+ GK    ++      G+ RGF FV  ++  +  +A  A
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEEAQQA 63

Query: 341 LDGQNLDGRAIRV 353
           L+G +L G  IRV
Sbjct: 64  LNGHSLQGSPIRV 76

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 45.8 bits (109), Expect = 8e-07
 Identities = 28/99 (28%), Positives = 44/99 (44%), Gaps = 27/99 (27%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLFVGNLP+ V S++L   F + G                           V    V ++
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFG--------------------------KVKSCNVPFD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
           +ET  S+G+GFV+ S+ +  E A     ++ ++G  L V
Sbjct: 35  KETGLSKGYGFVSFSSRDGLENA-LQKQKHILEGNKLQV 72

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 45.8 bits (109), Expect = 8e-07
 Identities = 19/60 (31%), Positives = 29/60 (48%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV  LP    +  L+ VFS++G VV   +   + TG  +GF F+   +  E   A   L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 45.7 bits (109), Expect = 9e-07
 Identities = 25/84 (29%), Positives = 33/84 (39%), Gaps = 26/84 (30%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLFVG L  DV  E L   F + G VE  E                          ++ +
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVE--------------------------IVTD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAV 244
           +ET + RGF FVT    +  +K V
Sbjct: 35  KETGKKRGFAFVTFDDYDPVDKIV 58

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 45.5 bits (108), Expect = 9e-07
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 4/73 (5%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           RIYVGNLP ++    +E +F ++G + +     D +  R   F FV      +  DA+  
Sbjct: 1   RIYVGNLPPDIRTKDIEDLFYKYGAIRDI----DLKNRRGPPFAFVEFEDPRDAEDAVYG 56

Query: 341 LDGQNLDGRAIRV 353
            DG + DG  +RV
Sbjct: 57  RDGYDYDGYRLRV 69

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 26/96 (27%), Positives = 43/96 (44%), Gaps = 27/96 (28%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
           P  D ++FVG+L  +V  E LA  F K  + + A                          
Sbjct: 3   PENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKA-------------------------- 36

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAV-EMFHRY 250
           +V+ ++ T +S+G+GFV+ S   +  KA+ EM  +Y
Sbjct: 37  KVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEMNGKY 72

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 29/98 (29%), Positives = 40/98 (40%), Gaps = 26/98 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L V NL Y    + L  +FEK G  E+ +V                   Y+       +R
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYG--EVGDV-------------------YIPR-----DR 34

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
            T  SRGF FV      +AE A++     ++DGR L V
Sbjct: 35  YTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRELRV 72

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 17/50 (34%), Positives = 28/50 (56%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
           +Y+G+LP       L + FS+ G V   R+   ++TG+S+G+ FV   S 
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESP 51

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 5/79 (6%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHG-KVVNARVVYDR-ETGRSRGFGFVTMSSETELNDA 337
           +  Y+GNLP++V    +++ F   G  V + R+  +  + GR RGFG+        L  A
Sbjct: 2   YTAYLGNLPYDVTEEDIKEFF--RGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQA 59

Query: 338 IAALDGQNLDGRAIRVNVA 356
           + +L+ ++L  R IRV++A
Sbjct: 60  L-SLNDESLKNRRIRVDIA 77

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 46.2 bits (109), Expect = 1e-06
 Identities = 24/81 (29%), Positives = 45/81 (55%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G  +++ +LP E  +  L Q+F   G VV+A+V  D++T  S+ FGFV+  +      AI
Sbjct: 7   GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 66

Query: 339 AALDGQNLDGRAIRVNVAEDR 359
            A++G  +  + ++V +   +
Sbjct: 67  QAMNGFQIGMKRLKVQLKRSK 87

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 18/76 (23%)

Query: 281 RIYVGNLPWEVDNARLEQVFSE---------HGKVVNARVVYDRE------TGRSRGFGF 325
           R+ + NLP  VD  +L+++F +           K+   +++ D +       G+S+G+GF
Sbjct: 2   RLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGF 61

Query: 326 VTMSSETELNDAIAAL 341
           V     T    A+ AL
Sbjct: 62  VEF---TNHEHALKAL 74

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R+ V NLP  +   +L ++F   G + + ++ Y ++ G+ R FGFV   +E E   A+  
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKALKH 60

Query: 341 LDGQNLDGRAIRV 353
            +   +D   I V
Sbjct: 61  FNNSFIDTSKITV 73

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 8/73 (10%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VGNLP E     +  +F ++GKV+   ++        + +GFV M  +T  ++AI  
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRN 53

Query: 341 LDGQNLDGRAIRV 353
           L    L G AI V
Sbjct: 54  LHHYKLHGVAINV 66

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 44.8 bits (107), Expect = 1e-06
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 5/59 (8%)

Query: 298 QVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA 356
           ++FS  G V   +++         GF FV  S+E     A+  L+G    GR +RV+ +
Sbjct: 3   KLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 45.5 bits (107), Expect = 1e-06
 Identities = 24/75 (32%), Positives = 40/75 (53%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP  +    L  +FS  G+V +A+++ D+  G S G+GFV   +  +   AI  L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 342 DGQNLDGRAIRVNVA 356
           +G  L  + I+V+ A
Sbjct: 64  NGLRLQSKTIKVSYA 78

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 14/72 (19%)

Query: 281 RIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           R++VGNL  + V    LE++FS++GK++   +         +G+GFV   +E    DA A
Sbjct: 2   RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEE---DARA 50

Query: 340 ALDGQNLDGRAI 351
           A+ G+N  GR I
Sbjct: 51  AVAGEN--GREI 60

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 45.5 bits (107), Expect = 1e-06
 Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L W+     L   FS+ G++    V+ D  T RSRGFGFVT +    + D + A
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASV-DKVLA 59

Query: 341 LDGQNLDGRAIRVNVA 356
                LD + I   VA
Sbjct: 60  QPHHELDSKTIDPKVA 75

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 45.0 bits (106), Expect = 1e-06
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 9/77 (11%)

Query: 281 RIYVGNL-PWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           R+++GNL    V  + +E +FS++GK+V   V         +GF FV   +E     A+A
Sbjct: 3   RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVA 54

Query: 340 ALDGQNLDGRAIRVNVA 356
             DG+ + G+ + +N+A
Sbjct: 55  GEDGRMIAGQVLDINLA 71

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 8/73 (10%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VGN+     +  L  +F E G+VV    V        + + FV M  E E   AI A
Sbjct: 2   KIFVGNVSATCTSDELRGLFEEFGRVVECDKV--------KDYAFVHMEREEEALAAIEA 53

Query: 341 LDGQNLDGRAIRV 353
           L+G+ + GR I V
Sbjct: 54  LNGKEVKGRRINV 66

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 25/94 (26%), Positives = 34/94 (36%), Gaps = 27/94 (28%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           LF+G L +D   E L   F K G V    +                            + 
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIM--------------------------KDP 34

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGR 255
            T RSRGFGFVT +     +K +     + +DGR
Sbjct: 35  ITGRSRGFGFVTFADPSSVDKVLAA-KPHVLDGR 67

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 26/84 (30%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L++G+L   +D   +   F + G  E+  VK                        +I N+
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECG--EVTSVK------------------------IIRNK 35

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVE 245
           +T +S G+GFV  +T E AE+A++
Sbjct: 36  QTGKSAGYGFVEFATHEAAEQALQ 59

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 44.8 bits (107), Expect = 2e-06
 Identities = 28/99 (28%), Positives = 41/99 (41%), Gaps = 32/99 (32%)

Query: 164 VGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY---N 220
           V NL  D D + L  LF   G +                               +Y   +
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPI-----------------------------SRVYLAKD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
           +ET +SRGF FVT  T E+AE+A+E  + +  D  +L+V
Sbjct: 35  KETGQSRGFAFVTFHTREDAERAIEKLNGFGYDNLILSV 73

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 44.7 bits (105), Expect = 2e-06
 Identities = 19/44 (43%), Positives = 30/44 (68%)

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
           +V+ N  +  +R +GFVTMST EEA K +   HR ++ GR+++V
Sbjct: 32  KVVTNARSPGARCYGFVTMSTSEEATKCINHLHRTELHGRMISV 75

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 2/78 (2%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGNLP ++    L++ F E G V+  R+      GR   FGFV       +   +A  
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 342 DGQNLDGRAIRVNVAEDR 359
                     R+NV E +
Sbjct: 66  PIYFRGDH--RLNVEEKK 81

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 23/78 (29%), Positives = 40/78 (51%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G+ I+V  +  E     +   F+E G++ N  +  DR TG  +G+  +   ++ E   AI
Sbjct: 6   GWIIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAI 65

Query: 339 AALDGQNLDGRAIRVNVA 356
             L+G+ L G+ I V+ A
Sbjct: 66  EGLNGKELLGQTISVDWA 83

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 31/100 (31%), Positives = 44/100 (44%), Gaps = 28/100 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLF-EKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
           ++F+ N+PYD+  + L  LF EK G V                        YV L +   
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVT-----------------------YVELFK--- 34

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
             E  +SRG G V     E  +KA+E  +RY++ GR L V
Sbjct: 35  -DEEGKSRGCGVVEFKDKESVQKALETMNRYELKGRKLVV 73

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 21/64 (32%), Positives = 36/64 (56%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG++P  +    +  +F EHG V+   ++ D+ TG  +G  FV  S+  E + AI A
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 341 LDGQ 344
           L  Q
Sbjct: 61  LHNQ 64

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I+V NL ++V   +L++VFS  G V  A +  D++ G+SRG G VT     E   AI+  
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKD-GKSRGMGTVTFEQPIEAVQAISMF 61

Query: 342 DGQNLDGRAIRVNV 355
           +GQ L  R + V +
Sbjct: 62  NGQFLFDRPMHVKM 75

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVV--YDRETGR---SRGFGFVTMSSETELND 336
           ++V NL ++     L++ F + G V +  +    D +      S G+GFV   S+     
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 337 AIAALDGQNLDGRAI 351
           A+  L G  LDG A+
Sbjct: 63  ALKRLQGTVLDGHAL 77

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 21/53 (39%), Positives = 34/53 (64%)

Query: 307 VNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR 359
           + AR+V DR+TG S+GFGFV  SSE +   A  A++   +DG  + ++ A+ +
Sbjct: 25  IAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEIDGNKVTLDFAKPK 77

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 22/51 (43%), Positives = 32/51 (62%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
           +I+VG L        ++Q F + GKV +A +++D+ T R RGFGFVT  SE
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 8/76 (10%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV NLP      +L ++FSE+G+V   RV       + + + FV      +   A+  +
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVE--RVK------KIKDYAFVHFEERDDAVKAMEEM 55

Query: 342 DGQNLDGRAIRVNVAE 357
           +G+ L+G  I V++A+
Sbjct: 56  NGKELEGSPIEVSLAK 71

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 1/80 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV N+        L ++F ++G +V+  +  D  T R RGF +V      +  DA+  L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 342 DGQNLDGRAIRVNVAE-DRQ 360
           D     GR I +  A+ DR+
Sbjct: 63  DRTRFLGREIEIQFAQGDRK 82

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 44.9 bits (106), Expect = 3e-06
 Identities = 28/108 (25%), Positives = 42/108 (38%), Gaps = 28/108 (25%)

Query: 161 KLFVGNLPYDV-DSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
           KL + NLP+ +    KL  +F + G V  A                            I 
Sbjct: 2   KLIIRNLPWSIKKPVKLKKIFGRYGKVREAT---------------------------IP 34

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT 267
            +   +  GF FVTM   + AE A+E  +  +IDGR + V+ A  +  
Sbjct: 35  RKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDWAVQKNR 82

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 31/100 (31%), Positives = 40/100 (40%), Gaps = 32/100 (32%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
            +LFVGNLP D+  E+   LF K G  E++EV     F N+                   
Sbjct: 2   CRLFVGNLPNDITEEEFKELFSKYG--EVSEV-----FLNKE------------------ 36

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
                  +GFGF+ + T   AEKA          GR L V
Sbjct: 37  -------KGFGFIRLDTRTNAEKAKAELDGIMRKGRQLRV 69

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 44.3 bits (105), Expect = 3e-06
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           F ++VGNLP++     L   F   G   + R++ D++TG+S+G  FV   +   +  A+ 
Sbjct: 1   FILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL- 59

Query: 340 ALDGQNLDGRAIRV 353
            L    L GR I V
Sbjct: 60  KLHHTLLKGRKINV 73

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 44.7 bits (105), Expect = 3e-06
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+ NLP  +D   LE +    G+V++ R++ D  +G SRG GF  M S  +    I+  
Sbjct: 3   LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVISHF 61

Query: 342 DGQ 344
           +G+
Sbjct: 62  NGK 64

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 11/75 (14%)

Query: 282 IYVGNLPWEVDNARLE-------QVFSEHG--KVVNARVVYDRETGRSRGFGFVTMSSET 332
           + V  LP  V   +LE       ++FS+ G  K+V   +  D ETG+++G+ FV  ++  
Sbjct: 4   VVVDGLP-VVGEEKLEKLKKVLRKIFSKFGVGKIVGIYMPVD-ETGKTKGYAFVEFATPE 61

Query: 333 ELNDAIAALDGQNLD 347
           E  +A+ AL+G  LD
Sbjct: 62  EAKEAVKALNGYKLD 76

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 16/63 (25%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL--DGRAIRV 353
           L + F+  G++ +  VV D++T  S+G  +V  +  +    A+  ++G+ L  D + ++V
Sbjct: 19  LREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDTKPLKV 78

Query: 354 NVA 356
            +A
Sbjct: 79  LIA 81

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 44.7 bits (105), Expect = 3e-06
 Identities = 22/75 (29%), Positives = 40/75 (53%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP  +     + +F   G++ + ++V D+ TG+S G+GFV      + + AI  L
Sbjct: 6   LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65

Query: 342 DGQNLDGRAIRVNVA 356
           +G  L  + I+V+ A
Sbjct: 66  NGLKLQTKTIKVSYA 80

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 44.0 bits (104), Expect = 3e-06
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 3/76 (3%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGNL +E     L   F   G++   R++   ++G+ +GF FV      E+  A  AL
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFE---EIEFATNAL 57

Query: 342 DGQNLDGRAIRVNVAE 357
            G++L+GRA+RV   E
Sbjct: 58  KGKHLNGRALRVEYGE 73

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 44.5 bits (105), Expect = 3e-06
 Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 1/80 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG L  +V    L + FS+ G V  A V+ D++TG+ RGFGFV   +    + A A 
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA-AV 59

Query: 341 LDGQNLDGRAIRVNVAEDRQ 360
           +    ++G  + V  A  ++
Sbjct: 60  VKFHPINGHRVEVKKAVPKE 79

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 43.7 bits (103), Expect = 4e-06
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 8/73 (10%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VGN+  +     L  +F  +G V++  V+        R F FV +  E   + AI  
Sbjct: 2   KIFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIEE 53

Query: 341 LDGQNLDGRAIRV 353
           L+G+ L GR + V
Sbjct: 54  LNGRELHGRKLVV 66

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 44.0 bits (104), Expect = 4e-06
 Identities = 23/76 (30%), Positives = 41/76 (53%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           IY+G+LP       L++ FS+ G V N RV   ++TG S+ +GF+   +      A  ++
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 342 DGQNLDGRAIRVNVAE 357
           +   L G+ ++V+V  
Sbjct: 62  NNYLLMGKVLQVHVLP 77

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 48.0 bits (114), Expect = 4e-06
 Identities = 48/221 (21%), Positives = 80/221 (36%), Gaps = 50/221 (22%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEK---AGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
           +L+VG +P +   E +   F     A     AE   H                      V
Sbjct: 177 RLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVS-------------------SV 217

Query: 218 IYNRETDRSRGFGFVTMSTVEEAEKAV----EMFHRYDIDGRLLT----VNKAAPRGTQP 269
             N+E +    F F+   TVEEA  A+     ++    +  R       V +  P  +Q 
Sbjct: 218 NINKEKN----FAFLEFRTVEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQK 273

Query: 270 ERAPRVFEPGF--------------RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR 315
              P                     RIY+GNLP  +   +++++    G +    ++ D 
Sbjct: 274 N--PDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDI 331

Query: 316 ETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA 356
            TG S+G+ F      +  + AIAAL+G++     + V  A
Sbjct: 332 ATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA 372

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 43.9 bits (103), Expect = 4e-06
 Identities = 21/51 (41%), Positives = 32/51 (62%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
           +I+VG L        ++Q F + GKV +A +++D+ T R RGFGFVT  +E
Sbjct: 5   KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENE 55

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 43.7 bits (103), Expect = 4e-06
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++VGNLP ++    + ++F ++GK     +  D+      GFGF+ + + T    A A 
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDK------GFGFIRLETRTLAEIAKAE 56

Query: 341 LDGQNLDGRAIRV 353
           LD   L G+ +RV
Sbjct: 57  LDNMPLRGKQLRV 69

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 25/99 (25%), Positives = 41/99 (41%), Gaps = 26/99 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L+VG L  +VD + L   F   G  +I ++                        Q+  + 
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFG--DIKDI------------------------QIPLDY 34

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
           ET + RGF FV     E+A  A++  +  ++ GR + VN
Sbjct: 35  ETQKHRGFAFVEFEEPEDAAAAIDNMNESELFGRTIRVN 73

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 44.0 bits (104), Expect = 5e-06
 Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 10/79 (12%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           RI+VG + ++ +   L + FS++G V   ++V DR  G S+G+GFVT  ++         
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQE-------- 54

Query: 341 LDGQNLDGRAIRVNVAEDR 359
            D Q +   A R+   + +
Sbjct: 55  -DAQKILQEANRLCFRDKK 72

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEH-GKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           R+ V NLP  +  A L++ FS+H G++ + +++   E G+SR   F+   +E E   A  
Sbjct: 2   RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLR-TEDGKSRRIAFIGYKTEEEAQKAKD 60

Query: 340 ALDGQNLDGRAIRVNVA 356
             +   ++   I V  A
Sbjct: 61  YFNNTYINTSKISVEFA 77

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 27/102 (26%), Positives = 42/102 (41%), Gaps = 27/102 (26%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
            +L V NL YDV  E L  LF + G V+  ++                           Y
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKIN--------------------------Y 34

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK 261
           +R + RS G   V     E+AE+A++ F+   +DG+ + V  
Sbjct: 35  DR-SGRSEGTADVVFEKREDAERAIKQFNGVLLDGQPMQVEL 75

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 43.5 bits (103), Expect = 6e-06
 Identities = 27/101 (26%), Positives = 42/101 (41%), Gaps = 26/101 (25%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L V  LP D+  E+L  LFE  G   I   K                        ++ +R
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIG--PIESCK------------------------IVRDR 36

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
            T +S G+GFV      +A+KA+   + ++I  + L V+ A
Sbjct: 37  ITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLKVSYA 77

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 43.4 bits (102), Expect = 6e-06
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++VGNLP ++     +++F ++G       V+     R RGFGF+ + S T    A A 
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYG---EPSEVF---INRDRGFGFIRLESRTLAEIAKAE 56

Query: 341 LDGQNLDGRAIRV 353
           LDG  L  R +R+
Sbjct: 57  LDGTILKNRPLRI 69

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 43.7 bits (103), Expect = 6e-06
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 5/71 (7%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARV--VYDRETGRSRGFGFVTMSSETELNDAI 338
           +I V NLP+E     +  +FS +G++ + RV   +D+     RGF FV  S+  E  +A+
Sbjct: 2   KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSA---RGFAFVEFSTAKEALNAM 58

Query: 339 AALDGQNLDGR 349
            AL   +L GR
Sbjct: 59  NALKDTHLLGR 69

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 43.2 bits (102), Expect = 7e-06
 Identities = 20/47 (42%), Positives = 31/47 (65%), Gaps = 3/47 (6%)

Query: 217 VIYNRETDRSRGFGFVTMSTVEEAEKAVE-MFHRYDIDGRLLTVNKA 262
           V+ +  T RSRGFGF+T S+ +EA++A+E   H   IDG  + + +A
Sbjct: 34  VMVDPNTKRSRGFGFITFSSADEADEAMEAQPHS--IDGNQIELKRA 78

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 43.8 bits (104), Expect = 7e-06
 Identities = 26/104 (25%), Positives = 37/104 (35%), Gaps = 28/104 (26%)

Query: 162 LFVGNLPYD-VDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           LFV  LP    D   L  LF + G        F             C +      Q    
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKP-----TF-------------CQLAIAPNGQ---- 42

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP 264
                 RGF FV  +T E+AE+A +  + + + G  + V+   P
Sbjct: 43  -----PRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRVSFGNP 81

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 43.5 bits (103), Expect = 7e-06
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           + I+VG L  +V    L + FS HGK++   ++       +  F F+    E     A+ 
Sbjct: 4   YSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAVE 61

Query: 340 ALDGQNLDGRAIRV 353
           + +   L  + + V
Sbjct: 62  SENHSMLKNKTMHV 75

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 43.5 bits (102), Expect = 7e-06
 Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+ NLP  +D   LE +    G+V++ R++ D  +G SRG GF  M S  +    I   
Sbjct: 3   LYISNLPLSMDEQELESMLKPFGQVISTRILRD-ASGTSRGVGFARMESTEKCEAIITHF 61

Query: 342 DGQ 344
           +G+
Sbjct: 62  NGK 64

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 43.2 bits (101), Expect = 9e-06
 Identities = 23/75 (30%), Positives = 40/75 (53%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP  +    L+ +F   G++ + ++V D+ TG+S G+GFV      +   AI  L
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 342 DGQNLDGRAIRVNVA 356
           +G  L  + I+V+ A
Sbjct: 67  NGLRLQTKTIKVSYA 81

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 42.8 bits (100), Expect = 1e-05
 Identities = 32/105 (30%), Positives = 48/105 (45%), Gaps = 27/105 (25%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLF+G L ++   + L   FEK GT+                          +   V+ +
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTL--------------------------TDCVVMRD 37

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
            +T RSRGFGFVT S VEE + A+     + +DGR++   +A  R
Sbjct: 38  PQTKRSRGFGFVTYSCVEEVDAAM-SARPHKVDGRVVEPKRAVSR 81

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 42.6 bits (100), Expect = 1e-05
 Identities = 35/106 (33%), Positives = 46/106 (43%), Gaps = 29/106 (27%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLFVG L  DV    L   F + G VE AEV                          I +
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEV--------------------------IAD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEM-FHRYDIDGRLLTVNKAAPR 265
           ++T + RGFGFV     + A+KA  + FH   I+G  + V KA P+
Sbjct: 35  KQTGKKRGFGFVYFQNHDSADKAAVVKFHP--INGHRVEVKKAVPK 78

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG L  E    ++ + F + G +V   +  D++T + RGF F+T  SE E    I  
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSE-EPVKKILE 59

Query: 341 LDGQNLDGRAIRVNVA 356
                + G+ + V  A
Sbjct: 60  TQFHVIGGKKVEVKKA 75

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 18/58 (31%), Positives = 32/58 (55%)

Query: 296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV 353
           LE +FS  GK+ +  V+ D++TG S  + F+   ++ +  +A   +D   +D R I V
Sbjct: 20  LEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRIHV 77

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 3/75 (4%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVGNL   V    L ++FS+ G + + +++  RE G    + FV          A+  +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLI--REHGND-PYAFVEYYDHRSAAAALQTM 57

Query: 342 DGQNLDGRAIRVNVA 356
           +G+ + G+ I+VN A
Sbjct: 58  NGRLILGQEIKVNWA 72

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 5/80 (6%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR-----SRGFGFVTMSSETELND 336
           ++V NL +   N  L   F      V ARV    +  R     S GFGFV   ++ +   
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 337 AIAALDGQNLDGRAIRVNVA 356
           A+ A+DG  LDG  + V  +
Sbjct: 63  ALKAMDGFVLDGHTLVVKFS 82

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 27/86 (31%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           ++FVG +P D   E+L   F + G+V+  +VK                        +I +
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVK--DVK------------------------IITD 37

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEM 246
           R    S+G+GFVT  T E+AEK + M
Sbjct: 38  R-AGVSKGYGFVTFETQEDAEKILAM 62

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 29/98 (29%), Positives = 41/98 (41%), Gaps = 27/98 (27%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           LFVGNLPYD  +E L   F+ AG    A      L                       ++
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAG----APPSVRLL----------------------TDK 36

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
           +T +S+G  FV   T E   KA+++ H   + GR + V
Sbjct: 37  KTGKSKGCAFVEFDTAEAMTKALKLHHTL-LKGRKINV 73

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|241088 cd12644, RRM_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 28/86 (32%), Positives = 44/86 (51%), Gaps = 3/86 (3%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHG--KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           +YVGN  W   + +L QV    G   VV  +   +R  G+S+G+  V ++SE  ++  + 
Sbjct: 4   VYVGNFSWWTTDQQLIQVIRSVGVKDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 63

Query: 340 ALDGQNLDGRAIRVNVAEDRQRRSSF 365
            L G+ L+G  + V  A  RQ  S F
Sbjct: 64  LLPGKVLNGEKVDVRPA-TRQNLSQF 88

This subgroup corresponds to the RRM of CFIm59. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. The two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59). CFIm59 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm59 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping. . Length = 90

>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVGNL  +V  A + Q+FS+ G   + +++ D  T  +  + FV          ++AA+
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59

Query: 342 DGQNLDGRAIRVNVA 356
           +G+ + G+ ++VN A
Sbjct: 60  NGRKIMGKEVKVNWA 74

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 41.6 bits (98), Expect = 3e-05
 Identities = 25/99 (25%), Positives = 46/99 (46%), Gaps = 26/99 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +FVG+L  ++D+E L   F   G  EI++ +                        V+ + 
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFG--EISDAR------------------------VVKDM 35

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
           +T +S+G+GFV+    E+AE A++  +   + GR +  N
Sbjct: 36  QTGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAIRTN 74

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 24/99 (24%), Positives = 42/99 (42%), Gaps = 26/99 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           LF+ +LP +   + L  LF   G V  A+V                   +V       ++
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKV-------------------FV-------DK 34

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
            T +S+ FGFV+    E A+ A++  + + + G+ L V 
Sbjct: 35  NTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 32/105 (30%), Positives = 48/105 (45%), Gaps = 27/105 (25%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLF+G L ++   E L   FE+ GT+                          +   V+ +
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTL--------------------------TDCVVMRD 37

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
             T RSRGFGFVT S+VEE + A+     + +DGR++   +A  R
Sbjct: 38  PNTKRSRGFGFVTYSSVEEVDAAMNA-RPHKVDGRVVEPKRAVSR 81

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG +  + +   L   F E+GK+    ++ DR++G+ RGFGFVT      + D I  
Sbjct: 2   KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPV-DKIVL 60

Query: 341 LDGQNLDGRAIRVNVAEDRQ 360
                ++G    V  A  RQ
Sbjct: 61  QKYHTINGHNAEVRKALSRQ 80

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240856 cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 14/83 (16%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYD-RETGRSRGFGF---------VTMSS 330
            +Y G LP +V +  L + F ++    N + ++  R     R             VT+ +
Sbjct: 4   TVYCGKLPKKVTDEDLREFFKDY----NPQEIWIFRTRKSKRNPLQLHRHFTAALVTLDT 59

Query: 331 ETELNDAIAALDGQNLDGRAIRV 353
           E  L++ I +L  + L+G+ I +
Sbjct: 60  EETLDEIIESLKSKKLNGKKISL 82

This subfamily corresponds to the RRM2 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 93

>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV 355
           LE+ FS  GKV + R++ DR + RS+G  +V     + +  AI  L GQ + G  I V  
Sbjct: 18  LEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI-GLTGQRVLGVPIIVQA 76

Query: 356 AEDRQRRSS 364
           ++  + R++
Sbjct: 77  SQAEKNRAA 85

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+ NLP  +D   LE +    G V++ R++ D   G SRG GF  M S  +    I   
Sbjct: 4   LYISNLPVSMDEQELENMLKPFGHVISTRILRD-ANGVSRGVGFARMESTEKCEVVIQHF 62

Query: 342 DGQNL 346
           +G+ L
Sbjct: 63  NGKYL 67

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 41.0 bits (97), Expect = 4e-05
 Identities = 29/102 (28%), Positives = 47/102 (46%), Gaps = 27/102 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           ++ V NLP  V  ++L   FE  G  E+ +VK                        V+  
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKG--EVTDVK------------------------VMRT 35

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           R+  +SR FGFV   + E+A++AV+ F++  ID   ++V  A
Sbjct: 36  RD-GKSRRFGFVGFKSEEDAQQAVKYFNKTFIDTSKISVELA 76

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 40.6 bits (96), Expect = 4e-05
 Identities = 16/39 (41%), Positives = 21/39 (53%)

Query: 224 DRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
            +  GF FV  ST E AEKAV+  +     GR L V+ +
Sbjct: 18  KKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 20/51 (39%), Positives = 34/51 (66%)

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG 266
           +++ +R+T  S+GFGFV  S+ E+A+ A E     +IDG  +T++ A P+G
Sbjct: 28  RIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEIDGNKVTLDFAKPKG 78

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 14/36 (38%), Positives = 21/36 (58%)

Query: 229 FGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP 264
           F FVT  + EE +KA+E+   +   GR+L+   A P
Sbjct: 44  FAFVTFRSEEERQKALEILDGFKWKGRVLSARLAKP 79

This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. . Length = 79

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 24/58 (41%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           + V NL   V N  LEQ FS+ G+V  A V+ D + GRS G G V  S +     AI 
Sbjct: 2   LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVD-DRGRSTGEGIVEFSRKPGAQAAIK 58

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 41.3 bits (96), Expect = 4e-05
 Identities = 22/75 (29%), Positives = 38/75 (50%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP  +       +F   G++ + ++V D+ TG+S G+GFV      +   AI  L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 342 DGQNLDGRAIRVNVA 356
           +G  L  + I+V+ A
Sbjct: 65  NGLRLQTKTIKVSYA 79

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 40.8 bits (96), Expect = 5e-05
 Identities = 28/103 (27%), Positives = 42/103 (40%), Gaps = 29/103 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG LP DV  E+    F + G V  A                          Q++ +
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDA--------------------------QLMQD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEM-FHRYDIDGRLLTVNKA 262
            +T RSRGFGFVT  +    E+         ++ G+ + V +A
Sbjct: 35  HDTGRSRGFGFVTFDSESAVERVFSAGML--ELGGKQVEVKRA 75

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 41.0 bits (97), Expect = 5e-05
 Identities = 25/97 (25%), Positives = 37/97 (38%), Gaps = 33/97 (34%)

Query: 164 VGNLPYDVDSEKLAML-------FEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQ 216
           V  LP  V  EKL  L       F K G  +I  V  +      G               
Sbjct: 6   VDGLP-VVGEEKLEKLKKVLRKIFSKFGVGKI--VGIYMPVDETG--------------- 47

Query: 217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDID 253
                   +++G+ FV  +T EEA++AV+  + Y +D
Sbjct: 48  --------KTKGYAFVEFATPEEAKEAVKALNGYKLD 76

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 41.0 bits (96), Expect = 5e-05
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVGNL   V    L+Q+F   G V N +++ D+   +   +GFV      +   A+  L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNN-KGVNYGFVEYHQSHDAEIALQTL 59

Query: 342 DGQNLDGRAIRVNVA 356
           +G+ ++   IRVN A
Sbjct: 60  NGRQIENNEIRVNWA 74

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 1/80 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG +  + +   L   F ++GK+    V+ DR++G+ RGF FVT      + D I  
Sbjct: 2   KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTV-DKIVV 60

Query: 341 LDGQNLDGRAIRVNVAEDRQ 360
                ++G    V  A  +Q
Sbjct: 61  QKYHTINGHNCEVKKALSKQ 80

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 31/102 (30%), Positives = 49/102 (48%), Gaps = 30/102 (29%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLF-GNQGFHMWVCAVFYVSLLQVI 218
            ++F+G LP D+  ++L  L EK G  +I E++    F GN                   
Sbjct: 2   CEIFIGKLPRDLFEDELIPLCEKIG--KIYEMRMMMDFNGN------------------- 40

Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI-DGRLLTV 259
                  +RG+ FVT S  +EA+ A++  + Y+I +GRLL V
Sbjct: 41  -------NRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGV 75

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 40.8 bits (95), Expect = 5e-05
 Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+V NLP+++   +L++ FS+ G V+ A +    E G+S+G G V   S      A   
Sbjct: 1   QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEI--KMENGKSKGCGTVRFDSPESAEKACRL 58

Query: 341 LDGQNLDGRAIRVNV 355
           ++G  ++GR I V +
Sbjct: 59  MNGIKINGREIDVRL 73

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 18/67 (26%), Positives = 36/67 (53%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+  LP    +  LE++    GK+++ + + D++T + +G+GFV   S      AI  L
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 342 DGQNLDG 348
           +G+ +  
Sbjct: 63  NGRGVQA 69

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 40.3 bits (95), Expect = 7e-05
 Identities = 24/94 (25%), Positives = 40/94 (42%), Gaps = 28/94 (29%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +FV NL Y V  ++L  LF K G  EI +V+   +   +G                    
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCG--EITDVR--LVKNYKG-------------------- 37

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGR 255
              +S+G+ +V     E  ++A+++  R  I GR
Sbjct: 38  ---KSKGYAYVEFENEESVQEALKL-DRELIKGR 67

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 40.5 bits (95), Expect = 7e-05
 Identities = 22/105 (20%), Positives = 40/105 (38%), Gaps = 26/105 (24%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L +  LP  +  E+   LF   G V+                            +++ ++
Sbjct: 3   LIINYLPQTLTDEEFRSLFLAVGPVKNC--------------------------KIVRDK 36

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG 266
            T  S GFGFV   + E+A++A+   +   +  + + V  A P G
Sbjct: 37  RTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYARPGG 81

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 41.0 bits (95), Expect = 7e-05
 Identities = 17/68 (25%), Positives = 35/68 (51%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+  LP    +  L ++   +GK+V+ + + D+ T + +G+GFV   S      A++AL
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69

Query: 342 DGQNLDGR 349
               +  +
Sbjct: 70  KASGVQAQ 77

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 40.2 bits (95), Expect = 7e-05
 Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++V N P   D + +  +F ++G++++ R    R   ++R F +V  +S      A+A L
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLR-FNKTRRFCYVQFTSPESAAAAVALL 61

Query: 342 DGQNLDGRAIRV 353
           +G+  +G  + V
Sbjct: 62  NGKLGEGYKLVV 73

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 40.4 bits (95), Expect = 8e-05
 Identities = 24/101 (23%), Positives = 44/101 (43%), Gaps = 26/101 (25%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           ++V NLP+ + +  L  +F K G V    VK                      + ++ ++
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKV----VK----------------------VTIVKDK 37

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           ET +S+G  F+     E+A K V+  +  ++ GR L  + A
Sbjct: 38  ETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTLKCSIA 78

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 43.8 bits (103), Expect = 8e-05
 Identities = 22/80 (27%), Positives = 42/80 (52%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           E    + V  LP  +    +  +F+  G++ + ++V D+ TG+S G+GFV      +   
Sbjct: 1   ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60

Query: 337 AIAALDGQNLDGRAIRVNVA 356
           A+ +L+G  L  + I+V+ A
Sbjct: 61  AVNSLNGLRLQNKTIKVSYA 80

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 26/98 (26%), Positives = 41/98 (41%), Gaps = 29/98 (29%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L+V NLP+ + SE+L  LF K G   I +++     GN                     +
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYG--AIRQIR----IGNT--------------------K 38

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
           ET   RG  FV    + +A+ A +    +++  R L V
Sbjct: 39  ET---RGTAFVVYEDIYDAKNACDHLSGFNVANRYLVV 73

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 40.2 bits (94), Expect = 8e-05
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVGN+ +      LE  F   G V    ++ D+ +G  +GF ++  S +  +  A+ AL
Sbjct: 2   VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTAL-AL 60

Query: 342 DGQNLDGRAIRVN 354
           D     GR I+V 
Sbjct: 61  DESLFRGRQIKVM 73

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 40.0 bits (94), Expect = 8e-05
 Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 8/76 (10%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R+Y+G LP+      +E+ F  +G++        RE     GFGFV      + +DA+  
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRI--------REINLKNGFGFVEFEDPRDADDAVYE 52

Query: 341 LDGQNLDGRAIRVNVA 356
           L+G+ L G  + V  A
Sbjct: 53  LNGKELCGERVIVEHA 68

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 40.3 bits (94), Expect = 9e-05
 Identities = 27/100 (27%), Positives = 47/100 (47%), Gaps = 28/100 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           ++FVG +P D+  ++L  LFE+AG  +I E +    F  +                    
Sbjct: 3   EVFVGKIPRDMYEDELVPLFERAG--KIYEFRLMMEFSGE-------------------- 40

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI-DGRLLTV 259
                +RG+ FV  +T EEA+ A+ + + Y+I  G+ + V
Sbjct: 41  -----NRGYAFVMYTTKEEAQLAIRILNNYEIRPGKFIGV 75

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 43.1 bits (101), Expect = 1e-04
 Identities = 23/78 (29%), Positives = 40/78 (51%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G  + V  LP ++ +  L  +F   G +   R++ D +TG S G+ FV   SE +   AI
Sbjct: 107 GTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAI 166

Query: 339 AALDGQNLDGRAIRVNVA 356
             L+G  +  + ++V+ A
Sbjct: 167 KNLNGITVRNKRLKVSYA 184

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G  I++G LP ++    L  +  + GK+   R++ D   G +RG+ FVT S++ E  +AI
Sbjct: 1   GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDF-NGNNRGYAFVTFSNKQEAKNAI 59

Query: 339 AALDGQNL-DGRAIRV 353
             L+   + +GR + V
Sbjct: 60  KQLNNYEIRNGRLLGV 75

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 28/99 (28%), Positives = 42/99 (42%), Gaps = 28/99 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           ++FV NLP+D+  +KL   F + G V  AE+K                            
Sbjct: 1   QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKM--------------------------- 33

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
            E  +S+G G V   + E AEKA  + +   I+GR + V
Sbjct: 34  -ENGKSKGCGTVRFDSPESAEKACRLMNGIKINGREIDV 71

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate RNA-binding protein 5 (RBM5)

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 19/56 (33%), Positives = 33/56 (58%), Gaps = 4/56 (7%)

Query: 306 VVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQN----LDGRAIRVNVAE 357
           V N R++ D++T ++RGF FV +SS  E +  +  L   +    +DG+ I V+ A+
Sbjct: 31  VNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQSLHPPLKIDGKTIGVDFAK 86

This subgroup corresponds to the RRM2 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. . Length = 86

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 3/80 (3%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG +P  ++   L  +F + GK+    V+ D+ TG  +G  F+T  +      A +A
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66

Query: 341 LDGQ-NLDG--RAIRVNVAE 357
           L  Q  L G  R I+V  A+
Sbjct: 67  LHEQKTLPGMNRPIQVKPAD 86

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGK--VVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           +YVGNL W   +  LE   +E G   V + +    +  G+S+GF +V  +SE        
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 340 ALDGQNLDGRAIRV 353
            L+G+  +G+   V
Sbjct: 61  KLEGREFNGKKCVV 74

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG L  +     +E+VFS +G+V +  ++ D E  +SRG  FV  SS+     AI A
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKA 59

Query: 341 LDG 343
           L+G
Sbjct: 60  LNG 62

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELN---DAI 338
           ++VG +   +D   +   F+++G V   +++ DR TG S+G+GFV+   + ++    ++ 
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVESQ 66

Query: 339 AALDGQNLD-GRAIR 352
               G+ L  G AIR
Sbjct: 67  INFHGKKLKLGPAIR 81

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 39.8 bits (92), Expect = 1e-04
 Identities = 17/68 (25%), Positives = 35/68 (51%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+  LP    +  L ++   +GK+V+ + + D+ T + +G+GFV   S      A+A+L
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

Query: 342 DGQNLDGR 349
               +  +
Sbjct: 67  KANGVQAQ 74

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 23/99 (23%), Positives = 39/99 (39%), Gaps = 26/99 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +FVG+L  +V    L   F    +   A V            MW              + 
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARV------------MW--------------DM 35

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
           ++ RSRG+GFV+  + ++AE A+   +   +  R +  N
Sbjct: 36  KSGRSRGYGFVSFRSQQDAENAINEMNGKWLGSRPIRCN 74

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 18/49 (36%), Positives = 32/49 (65%)

Query: 212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
           V+ ++VI +  T++ +GFGFVTM+  EEA  A+   + Y +  ++L V+
Sbjct: 28  VTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVS 76

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 16/46 (34%), Positives = 32/46 (69%)

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
           + V+Y++ T RSRGF FV    ++++++A+E  +  ++DGR + V+
Sbjct: 29  VNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRVD 74

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 28/103 (27%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGN-QGFHMWVCAVFYVSLLQVIY 219
           K+F+G LP  +  +++  L E               FG  + F+             ++ 
Sbjct: 2   KIFIGGLPNYLSEDQVKELLES--------------FGKLKAFN-------------LVK 34

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           +  T  S+G+ F         ++A+   +   +  + LTV +A
Sbjct: 35  DSATGLSKGYAFCEYLDPSVTDQAIAGLNGMQLGDKKLTVQRA 77

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 29/99 (29%), Positives = 43/99 (43%), Gaps = 27/99 (27%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +L V NLP  +  +KL  LFE  GT+   ++K+                           
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKY--------------------------- 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
            +  + R FGFV   T EEA+KA++ F+   ID   +TV
Sbjct: 35  TKDGKFRKFGFVGYKTEEEAQKALKHFNNSFIDTSKITV 73

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 23/101 (22%), Positives = 33/101 (32%), Gaps = 26/101 (25%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L+V N+      + L  LF K G +    +   F                          
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFY------------------------- 37

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
            T R RGF +V    V +AE A+    R    GR + +  A
Sbjct: 38  -TRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIEIQFA 77

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 28/102 (27%), Positives = 46/102 (45%), Gaps = 27/102 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG L  +   E +   FE+ G VE A                           ++++
Sbjct: 5   KIFVGGLSANTVVEDVKQYFEQFGKVEDA--------------------------MLMFD 38

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           + T+R RGFGFVT    +  EK  E+ H ++I+ +++   KA
Sbjct: 39  KTTNRHRGFGFVTFENEDVVEKVCEI-HFHEINNKMVECKKA 79

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++VGNLP ++     +++F+++G+     +       + +GFGF+ + S      A A 
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAE 56

Query: 341 LDGQNLDGRAIRV 353
           LD   + GR +RV
Sbjct: 57  LDDTPMRGRQLRV 69

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 5/82 (6%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++YVGNL        LE+ FS +G +    +  +       GF FV      +  DA+  
Sbjct: 1   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 55

Query: 341 LDGQNLDGRAIRVNVAEDRQRR 362
           LDG+ + G  +RV ++    RR
Sbjct: 56  LDGKVICGSRVRVELSTGMPRR 77

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 16/47 (34%), Positives = 28/47 (59%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVT 327
           +I+VG +  + +   L   F ++GK+    ++ DR +G+ RGF FVT
Sbjct: 2   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT 48

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV 355
           LE  FS  GKV + R++ DR + RS+G  +V       +  AI  L GQ L G  I V  
Sbjct: 18  LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQA 76

Query: 356 AEDRQRRSS 364
           ++  + R +
Sbjct: 77  SQAEKNRLA 85

This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In contrast to RBM39, RBM23 contains only two RRMs. . Length = 85

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 39.3 bits (91), Expect = 3e-04
 Identities = 18/49 (36%), Positives = 32/49 (65%)

Query: 212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
           V+ ++VI +  T++ +GFGFVTM+  +EA  A+   + Y +  R+L V+
Sbjct: 30  VTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVS 78

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 42.4 bits (99), Expect = 3e-04
 Identities = 22/74 (29%), Positives = 39/74 (52%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R+YVG++ +E+    + + F   G + +  + +D  TG+ +GF FV          A+  
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168

Query: 341 LDGQNLDGRAIRVN 354
           ++GQ L GR I+V 
Sbjct: 169 MNGQMLGGRNIKVG 182

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 23/96 (23%), Positives = 38/96 (39%), Gaps = 32/96 (33%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           ++VGNLP+ +  E+L   F   G +E  EV+                VF           
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIE--EVR----------------VF----------- 33

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLL 257
              + +G+ FV   T E A  A+   +   I+G+ +
Sbjct: 34  ---KDKGYAFVRFDTHEAAATAIVAVNGTSINGQTV 66

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 26/102 (25%), Positives = 41/102 (40%), Gaps = 26/102 (25%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +L V NLP  +   +L   F K G  EI +VK                        ++  
Sbjct: 2   RLIVKNLPASLTEAELKEHFSKHGG-EITDVK------------------------LLRT 36

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
            +  +SR   F+   T EEA+KA + F+   I+   ++V  A
Sbjct: 37  EDG-KSRRIAFIGYKTEEEAQKAKDYFNNTYINTSKISVEFA 77

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 26/92 (28%), Positives = 47/92 (51%), Gaps = 26/92 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           ++FVG +P D+  ++L  LFEKAG +                  W         L+++ +
Sbjct: 3   EIFVGKIPRDLFEDELVPLFEKAGPI------------------WD--------LRLMMD 36

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI 252
             T  +RG+ FVT  T E A++AV++++ ++I
Sbjct: 37  PLTGLNRGYAFVTFCTKEAAQEAVKLYNNHEI 68

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 9/76 (11%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGF-GFVTMSSETELNDAIAA 340
           I+VG +   +    L++ FS  G+V   R+  DR+      F  F    S      A++A
Sbjct: 3   IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAES------ALSA 56

Query: 341 L--DGQNLDGRAIRVN 354
           L   G  L G  +RV+
Sbjct: 57  LNLSGTLLGGHPLRVS 72

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+V NLP++     L+  F+E G V+ A +    E G+S+G G V   S      A   
Sbjct: 1   QIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVRFESPEVAERACRM 58

Query: 341 LDGQNLDGRAIRVNV 355
           ++G  L+GR I V +
Sbjct: 59  MNGYKLNGREIDVRI 73

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++V NLP+ +    L++VF +    V+ R+   ++ G S+G  ++   +E E   A+   
Sbjct: 6   LFVKNLPYNITVDELKEVFED---AVDIRLPSGKD-GSSKGIAYIEFKTEAEAEKALEEK 61

Query: 342 DGQNLDGRAIRVN 354
            G  +DGR+I V+
Sbjct: 62  QGAEVDGRSIVVD 74

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 4/73 (5%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            +Y G  P     + ++++F   G V    ++    +   +   F+T  +      AI  
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIET 56

Query: 341 LDGQNLDGRAIRV 353
           L+G ++DG  I+V
Sbjct: 57  LNGASVDGNCIKV 69

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 21/102 (20%), Positives = 43/102 (42%), Gaps = 26/102 (25%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +++V ++  D+  + +  +FE               FG          +   SL     +
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEA--------------FGK---------IKSCSLAP---D 35

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
            ET + +G+GF+     + A+ A+   + +D+ G+ L V KA
Sbjct: 36  PETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQQLRVGKA 77

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 38.9 bits (90), Expect = 4e-04
 Identities = 18/49 (36%), Positives = 32/49 (65%)

Query: 212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
           V+ ++VI +  T++ +GFGFVTM+  +EA  A+   + Y +  R+L V+
Sbjct: 30  VNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVS 78

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 16/49 (32%), Positives = 34/49 (69%)

Query: 212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
           ++ + ++Y++++ RSRGF FV    V++A++A E  +  ++DGR + V+
Sbjct: 36  IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 84

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 37.9 bits (88), Expect = 4e-04
 Identities = 25/99 (25%), Positives = 37/99 (37%), Gaps = 34/99 (34%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLFVGNLP +   +++  LFE+ G V                                  
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVL--------------------------------- 28

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
            E D  + +GFV M     A++A+   H Y + G  + V
Sbjct: 29  -ECDIIKNYGFVHMDDKTAADEAIRNLHHYKLHGVAINV 66

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 37.9 bits (88), Expect = 4e-04
 Identities = 27/99 (27%), Positives = 37/99 (37%), Gaps = 34/99 (34%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVGN+  D   E+L  LFE  G V                    CAV           
Sbjct: 2   KIFVGNVDEDTSQEELRALFEAYGAV------------------LSCAVM---------- 33

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
                 R F FV +     A++A+E  +  ++ GR L V
Sbjct: 34  ------RQFAFVHLRGEAAADRAIEELNGRELHGRKLVV 66

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 4/54 (7%)

Query: 308 NARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQN----LDGRAIRVNVAE 357
           N R++ D++T ++RGF FV +SS  E +  +  L   +    +DG+ I V+ A+
Sbjct: 33  NIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQALHPPLKIDGKTIGVDFAK 86

This subgroup corresponds to the RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 86

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR-ETGRSRGFGFVTMSSETELNDAIA 339
           +I V N+P+E     L ++FS  G++   R+      TG  RGFGFV   ++ +   A  
Sbjct: 2   KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61

Query: 340 AL-DGQNLDGR 349
           AL    +L GR
Sbjct: 62  ALCHSTHLYGR 72

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 38.3 bits (89), Expect = 4e-04
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGNL  +V    + ++F + G V+  ++  D++ G+ + F FV    E  +  A+  L
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKD-GKPKQFAFVNFKHEVSVPYAMNLL 62

Query: 342 DGQNLDGRAIRV 353
           +G  L GR + +
Sbjct: 63  NGIKLYGRPLNI 74

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 37.9 bits (89), Expect = 5e-04
 Identities = 15/40 (37%), Positives = 25/40 (62%)

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
           +RE +  RG+ +V   + E+AEKA++      IDG+ +TV
Sbjct: 33  DREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTV 72

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 28/102 (27%), Positives = 43/102 (42%), Gaps = 26/102 (25%)

Query: 158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
           E  +LFV NLPY    + L  LF K G  E++EV                         V
Sbjct: 1   ETGRLFVRNLPYSCKEDDLEKLFSKFG--ELSEV------------------------HV 34

Query: 218 IYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
             ++++ +S+GF +V     E+A KA +        GRL+ +
Sbjct: 35  AIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVFQGRLIHI 76

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVG +P+      +   FS  G++    ++   +TGR RG  F+T  +E E      AL
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTE-EAAKRALAL 59

Query: 342 DGQNLDGRAIRV 353
           DG+++ GR ++V
Sbjct: 60  DGEDMGGRFLKV 71

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 5/74 (6%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           FR+ V  LP       L+    + G V  A V  D+E     G G V  +S+ ++  A+ 
Sbjct: 1   FRVVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQE-----GEGVVEFTSQEDMERALR 55

Query: 340 ALDGQNLDGRAIRV 353
            LDG    GR +RV
Sbjct: 56  KLDGTEFRGRRVRV 69

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++YVGNL    +   LE+ F  +G + +  V  +       GF FV      +  DA+  
Sbjct: 6   KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRE 60

Query: 341 LDGQNLDGRAIRVNVAEDRQR 361
           LDG+ L G  +RV ++   +R
Sbjct: 61  LDGRTLCGCRVRVELSNGEKR 81

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 81

>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 38.2 bits (88), Expect = 6e-04
 Identities = 18/49 (36%), Positives = 32/49 (65%)

Query: 212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
           V+ ++VI +  T++ +GFGFVTM+  +EA  A+   + Y +  R+L V+
Sbjct: 28  VTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVS 76

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 37.9 bits (88), Expect = 6e-04
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 8/61 (13%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++ GN  ++   + +E++F ++G+V       DR   +S GF FV M  E +  DAI  L
Sbjct: 3   VFCGNFEYDARQSEIERLFGKYGRV-------DRVDMKS-GFAFVYMEDERDAEDAIRGL 54

Query: 342 D 342
           D
Sbjct: 55  D 55

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 37.6 bits (87), Expect = 6e-04
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 8/76 (10%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R+Y+G L + V    +++ F  +GK++        E     G+GFV      + +DA+  
Sbjct: 1   RVYIGRLSYHVREKDIQRFFGGYGKLL--------EIDLKNGYGFVEFEDSRDADDAVYE 52

Query: 341 LDGQNLDGRAIRVNVA 356
           L+G++L G  + V  A
Sbjct: 53  LNGKDLCGERVIVEHA 68

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 37.5 bits (87), Expect = 7e-04
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           RIYVGNLP +V    LE +F ++G++   R +  +       F FV      +  DA+  
Sbjct: 1   RIYVGNLPSDVREKDLEDLFYKYGRI---RDIELKNRRGLVPFAFVRFEDPRDAEDAVFG 57

Query: 341 LDGQNLDGRAIRV 353
            +G +     +RV
Sbjct: 58  RNGYDFGQCRLRV 70

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding protein Raly

 Score = 37.7 bits (87), Expect = 7e-04
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 9/77 (11%)

Query: 281 RIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           R+++GNL    V  + +E +FS++G+VV   V         +G+ FV  S+E     A+ 
Sbjct: 3   RVFIGNLNTAVVKKSDVETIFSKYGRVVGCSV--------HKGYAFVQYSNERHARGAVI 54

Query: 340 ALDGQNLDGRAIRVNVA 356
             +G+ L G+ + +N+A
Sbjct: 55  GENGRVLAGQTLDINMA 71

This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch. . Length = 76

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 37.5 bits (88), Expect = 7e-04
 Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 3/73 (4%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNA-RVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           + +  LP+      +   FS      +   +VYD + GR  G  +V  +S  +   A+  
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDD-GRPTGEAYVEFASPEDARRAL-R 59

Query: 341 LDGQNLDGRAIRV 353
                + GR I V
Sbjct: 60  KHNNKMGGRYIEV 72

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.4 bits (87), Expect = 8e-04
 Identities = 28/102 (27%), Positives = 37/102 (36%), Gaps = 26/102 (25%)

Query: 158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
           E  +LF+ NL Y    E L  LF K G   ++EV                          
Sbjct: 1   ESGRLFIRNLAYTCTEEDLEKLFSKYGP--LSEVHLPI---------------------- 36

Query: 218 IYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
             ++ T + +GF FVT    E A KA          GRLL +
Sbjct: 37  --DKLTKKPKGFAFVTYMIPEHAVKAFAELDGTVFQGRLLHL 76

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 41.1 bits (96), Expect = 8e-04
 Identities = 27/97 (27%), Positives = 48/97 (49%), Gaps = 9/97 (9%)

Query: 266 GTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGF 325
           G QP R       G  ++VG +P ++    L  +F + G +   R++ D   G++RG+ F
Sbjct: 52  GVQPGR-------GCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFS-GQNRGYAF 103

Query: 326 VTMSSETELNDAIAALDGQNL-DGRAIRVNVAEDRQR 361
           VT   + E  +A+  L+   +  GR + V ++ D  R
Sbjct: 104 VTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVDNCR 140

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 37.6 bits (88), Expect = 8e-04
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 281 RI-YVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           RI YV NLP+++ +  L  +F ++G +   R+   +ET   RG  FV      +  +A  
Sbjct: 3   RILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACD 59

Query: 340 ALDGQNLDGRAIRV 353
            L G N+  R + V
Sbjct: 60  HLSGFNVANRYLVV 73

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|241108 cd12664, RRM1_RAVER2, RNA recognition motif 1 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 37.2 bits (86), Expect = 8e-04
 Identities = 12/36 (33%), Positives = 22/36 (61%)

Query: 224 DRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
           DR++   FVT+   E+A+ A+  FH+  + G+ + V
Sbjct: 31  DRNKRTAFVTLLNGEQAQDAIRTFHQTSVRGKDINV 66

This subgroup corresponds to the RRM1 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 70

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 37.5 bits (88), Expect = 8e-04
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 282 IYVGNLPWEVDNARLEQ----VFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
           +Y+ NL  ++    L++    +FS+ G V++   +   +T + RG  FV         +A
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLD---IVASKTLKMRGQAFVVFKDVESATNA 58

Query: 338 IAALDGQNLDGRAIRVNVA 356
           + AL G     + +R+  A
Sbjct: 59  LRALQGFPFYDKPMRIQYA 77

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 37.6 bits (87), Expect = 8e-04
 Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++V N+  +  +  L + F  +G +V+  V  D  T R RGF +V      +  DA+  L
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 342 DGQNLDGRAIRVNVAE-DRQ 360
           D + + GR I +  A+ DR+
Sbjct: 63  DRKWICGRQIEIQFAQGDRK 82

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 40.3 bits (94), Expect = 0.001
 Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 26/98 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +FV NL  D D   L  LF   G V+   VK                        +I + 
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQ--NVK------------------------IIRDL 305

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
            T++ +G+GFV+M+  +EA  A+   + Y +  R+L V
Sbjct: 306 TTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQV 343

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 29/102 (28%), Positives = 39/102 (38%), Gaps = 27/102 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG L +D   + L   F K G V    +K                           +
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKM--------------------------D 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
             T RSRGFGF+        EK +E    + +DGRL+   KA
Sbjct: 35  PNTGRSRGFGFILFKDASSVEKVLEQ-KEHRLDGRLIDPKKA 75

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 25/100 (25%), Positives = 41/100 (41%), Gaps = 26/100 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L+VGNL +    E++  LF + G ++        + G                     +R
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIK------RIIMG--------------------LDR 34

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK 261
            T    GF FV   T E+AE AV+  +   +D R++ V+ 
Sbjct: 35  FTKTPCGFCFVEYYTREDAENAVKYLNGTKLDDRIIRVDW 74

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 28/105 (26%), Positives = 45/105 (42%), Gaps = 27/105 (25%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLF+G L ++   E L   +E+ G +                          +   V+ +
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKL--------------------------TDCVVMRD 37

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
             + RSRGFGFVT S + E + A+     + IDGR++   +A  R
Sbjct: 38  PASKRSRGFGFVTFSCMNEVDAAMAA-RPHTIDGRVVEPKRAVAR 81

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 24/86 (27%), Positives = 34/86 (39%), Gaps = 26/86 (30%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           ++V  LP +   E L  +F K GTV                        YVSL +    +
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVV-----------------------YVSLPRY---K 35

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMF 247
            T   +GF F+   T EEA+KA +  
Sbjct: 36  HTGDIKGFAFIEFETPEEAQKACKHL 61

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 36.5 bits (84), Expect = 0.001
 Identities = 26/101 (25%), Positives = 46/101 (45%), Gaps = 27/101 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG L  +   E +   FE+ G V+ A                           ++++
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDA--------------------------MLMFD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK 261
           + T+R RGFGFVT  + +  EK  E+ H ++I+ +++   K
Sbjct: 35  KTTNRHRGFGFVTFESEDIVEKVCEI-HFHEINNKMVECKK 74

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           F++ + NLP  +   +L++   +         +  +   R   F FVT  SE E   A+ 
Sbjct: 6   FKVEIKNLPKYIGFKQLKKFLKKQL--FKPHKI--KLLKRQ-DFAFVTFRSEEERQKALE 60

Query: 340 ALDGQNLDGRAIRVNVA 356
            LDG    GR +   +A
Sbjct: 61  ILDGFKWKGRVLSARLA 77

This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. . Length = 79

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 7/82 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VGNLP +VD + L++ F ++G VV  R+      G+   FGFV       +      
Sbjct: 5   QLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSEPVQK---I 58

Query: 341 LDGQNLDGRA-IRVNVAEDRQR 361
           L  + +  R  +R+NV E + R
Sbjct: 59  LSNRPIMFRGDVRLNVEEKKTR 80

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 15/30 (50%), Positives = 21/30 (70%)

Query: 157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTV 186
           P+  +LFVGNLP+DVD  +L   F++ G V
Sbjct: 1   PDSHQLFVGNLPHDVDKSELKEFFQQYGNV 30

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 26/92 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           ++FVG +P D+  ++L  LFEKAG +                  W         L+++ +
Sbjct: 3   EVFVGKIPRDLYEDELVPLFEKAGPI------------------WD--------LRLMMD 36

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI 252
             + ++RG+ F+T    E A++AV++   Y+I
Sbjct: 37  PLSGQNRGYAFITFCGKEAAQEAVKLCDNYEI 68

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 16/64 (25%), Positives = 35/64 (54%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G  ++VG +P ++    L  +F + G + + R++ D  +G++RG+ F+T   +    +A+
Sbjct: 1   GTEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV 60

Query: 339 AALD 342
              D
Sbjct: 61  KLCD 64

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G  ++VG +P +V    L  VF   G++   R++ D + G++RG+ FV  + + E   A+
Sbjct: 1   GCEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFD-GKNRGYAFVMYTQKHEAKRAV 59

Query: 339 AALD 342
             L+
Sbjct: 60  RELN 63

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 36.7 bits (84), Expect = 0.001
 Identities = 16/68 (23%), Positives = 34/68 (50%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+  L     +  L ++   +GK+V+ + + D+ T + +G+GFV   S +    A+ AL
Sbjct: 4   LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63

Query: 342 DGQNLDGR 349
               +  +
Sbjct: 64  KASGVQAQ 71

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 18/83 (21%)

Query: 282 IYVGNLPWEVDNARLEQV--------FSEHGK----VVNARVVYDRETGRSRGFGFVTMS 329
           +YV  LP      RL           F ++GK    V+N    Y+   G S    +VT S
Sbjct: 8   VYVVGLP-----PRLADEEVLKKPEYFGQYGKIKKIVINRNTSYNGSQGPSAS-AYVTYS 61

Query: 330 SETELNDAIAALDGQNLDGRAIR 352
            + +    I A+DG  LDGR ++
Sbjct: 62  RKEDALRCIQAVDGFYLDGRLLK 84

This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T. Length = 98

>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 24/103 (23%), Positives = 39/103 (37%), Gaps = 34/103 (33%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L+V NLP     E+L  LF + G VE   VK                             
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVE--RVK----------------------------- 32

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP 264
              + + + FV     ++A KA+E  +  +++G  + V+ A P
Sbjct: 33  ---KIKDYAFVHFEERDDAVKAMEEMNGKELEGSPIEVSLAKP 72

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 18/60 (30%), Positives = 34/60 (56%)

Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G  I+VG +P ++    L  +F + G + + R++ D  TG +RG+ FVT  ++    +A+
Sbjct: 1   GTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV 60

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +++G+L  +V    L+ +F E+G++ +  ++        RG  +V M +  + + A+  L
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRALQKL 58

Query: 342 DGQNLDGRAIRV 353
               L G+ I+V
Sbjct: 59  RNVKLAGKKIKV 70

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 7/83 (8%)

Query: 278 PGFRIYVGNLPWEVDNARLEQV----FSEHGKVVNARVVYDRETGRSRGFGFVTMSSETE 333
           P   ++V +LP    +  LE      FS++G +V  +V+ D    R R + FV  +++ +
Sbjct: 1   PSACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDW---RQRPYAFVQFTNDDD 57

Query: 334 LNDAIAALDGQNLDGRAIRVNVA 356
             +A+A   G  LDGR IR   A
Sbjct: 58  AKNALAKGQGTILDGRHIRCERA 80

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 8/67 (11%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR--SRGFGFVTMSSETELNDAI 338
           +++VG +P       L ++F ++G V    V+ DR      S+G  FVT  +        
Sbjct: 3   KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRK------ 56

Query: 339 AALDGQN 345
           AAL+ QN
Sbjct: 57  AALEAQN 63

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 22/99 (22%), Positives = 40/99 (40%), Gaps = 22/99 (22%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +L+V NL   V  E L  +F +                ++  +M     F + L+     
Sbjct: 3   RLYVKNLSKRVTEEDLVYIFGR-----------FVDSSSEEKNM-----FDIRLMT---- 42

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
               R +G  FVT  + E A KA+ + + Y + G+ + +
Sbjct: 43  --EGRMKGQAFVTFPSEEIATKALNLVNGYVLKGKPMVI 79

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate RNA-binding Raly-like protein (RALYL)

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 9/75 (12%)

Query: 281 RIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           R+++GNL    V  A +E +F+++GK+V   V         +G+ FV   SE     A+A
Sbjct: 3   RVFIGNLNTAIVKKADIEAIFAKYGKIVGCSV--------HKGYAFVQYISERHARAAVA 54

Query: 340 ALDGQNLDGRAIRVN 354
             + + + G+ + +N
Sbjct: 55  GENARIIAGQPLDIN 69

This subgroup corresponds to the RRM of RALYL, also termed heterogeneous nuclear ribonucleoprotein C-like 3, or hnRNP core protein C-like 3, a putative RNA-binding protein that shows high sequence homology with Raly, an RNA-binding protein playing a critical role in embryonic development. The biological role of RALYL remains unclear. Like Raly, RALYL contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. . Length = 69

>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding protein PIN4, fission yeast RNA-binding post-transcriptional regulators cip1, cip2 and similar proteins

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 25/101 (24%), Positives = 37/101 (36%), Gaps = 26/101 (25%)

Query: 159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVI 218
              + + N+P+ +  E+L  + E  G        +HF  G          VF        
Sbjct: 1   PTAIVIKNIPFSLRKEQLLDIIEDLGIPLPYAFNYHFDNG----------VF-------- 42

Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
                   RG  F    + EEA+  VE  + Y+I GR L V
Sbjct: 43  --------RGLAFANFRSPEEAQTVVEALNGYEISGRRLRV 75

This subfamily corresponds to the RRM in PIN4, also termed psi inducibility protein 4 or modifier of damage tolerance Mdt1, a novel phosphothreonine (pThr)-containing protein that specifically interacts with the pThr-binding site of the Rad53 FHA1 domain. It is encoded by gene MDT1 (YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is involved in normal G2/M cell cycle progression in the absence of DNA damage and functions as a novel target of checkpoint-dependent cell cycle arrest pathways. It contains an N-terminal RRM, a nuclear localization signal, a coiled coil, and a total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein 1) and cip2 (Csx1-interacting protein 2) are novel cytoplasmic RRM-containing proteins that counteract Csx1 function during oxidative stress. They are not essential for viability in fission yeast Schizosaccharomyces pombe. Both cip1 and cip2 contain one RRM. Like PIN4, Cip2 also possesses an R3H motif that may function in sequence-specific binding to single-stranded nucleic acids. . Length = 79

>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 11/80 (13%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+GN+   +   +L   FS++G++    V Y RE    +   FV   + T +++AI A+
Sbjct: 6   VYIGNIDDSLTEEKLRNDFSQYGEI--ESVNYLRE----KNCAFV---NFTNISNAIKAI 56

Query: 342 DG--QNLDGRAIRVNVAEDR 359
           DG   +   +  +++  +DR
Sbjct: 57  DGVKSHPLFKKFKISYGKDR 76

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGNL +E     L +VF + G +   R+V D +T   +GF +V    E  +  A+  L
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL-LL 60

Query: 342 DGQN---LDGRAIRV 353
           + +    +  R +RV
Sbjct: 61  NEKKFPPMLPRELRV 75

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVGN+ +      LE  FS  G +    ++ D+ +G  +G+ ++  ++   +  A+ AL
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAV-AL 60

Query: 342 DGQNLDGRAIRV 353
           D  +  GR I+V
Sbjct: 61  DESSFRGRVIKV 72

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 24/104 (23%), Positives = 39/104 (37%), Gaps = 38/104 (36%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           LFV  L YD    KL   FE+ G ++                           ++++ ++
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIK--------------------------RIRLVRDK 37

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYD------IDGRLLTV 259
           +T + RG+ F+      E E   +M   Y       IDGR + V
Sbjct: 38  KTGKPRGYAFI------EFEHERDMKAAYKYADGKKIDGRRVLV 75

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 28/100 (28%), Positives = 44/100 (44%), Gaps = 28/100 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           ++FVG +P DV  ++L  +FE  G   I E++    F                       
Sbjct: 3   EVFVGKIPRDVYEDELVPVFESVG--RIYEMRLMMDFDG--------------------- 39

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI-DGRLLTV 259
               ++RG+ FV  +   EA++AV   + Y+I  GRLL V
Sbjct: 40  ----KNRGYAFVMYTQKHEAKRAVRELNNYEIRPGRLLGV 75

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 39.6 bits (92), Expect = 0.003
 Identities = 29/86 (33%), Positives = 42/86 (48%), Gaps = 1/86 (1%)

Query: 78  SDWADQEEDKDNTTITLEQEQEENGEEEPNWENQG-ADETEGNLSDWGEPEGEDTVVEAG 136
           +   D+ E +  T     + ++E GE+E N ENQG A + E  +   G  +G D+  E  
Sbjct: 809 AGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEEEE 868

Query: 137 ERQEESGEEGVFEEEEFVEPPEDAKL 162
           E +EE  EE   EEEE  E   +  L
Sbjct: 869 EEEEEEEEEEEEEEEEEEEEENEEPL 894

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3)

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I+V NLP +V    +    +EHG +VN +V      G+ +    V  ++E +  +A+A  
Sbjct: 10  IHVSNLPSDVTEEDVINHLAEHGVIVNVKVF--ESNGKKQ--ALVEFATEEQATEALACK 65

Query: 342 DGQNLDGRAIRV 353
              +L+G  IR+
Sbjct: 66  HASSLNGSTIRL 77

This subfamily corresponds to the RRM4 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 23/94 (24%), Positives = 38/94 (40%), Gaps = 31/94 (32%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L V NL Y    + L  +FEKA ++ I +        N G                    
Sbjct: 4   LVVNNLSYSASEDSLQEVFEKATSIRIPQ--------NNG-------------------- 35

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGR 255
              R +G+ FV   + E+A++A+   +  +I+GR
Sbjct: 36  ---RPKGYAFVEFESAEDAKEALNSCNNTEIEGR 66

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 4/79 (5%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEH-GKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           R+++ N+P+++    ++ +  E  G+V    +  D E G+SRG G V    E  +  A+ 
Sbjct: 1   RVFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAE-GKSRGCGVVEFKDEEFVKKALE 59

Query: 340 ALDGQNLDGRAIRVNVAED 358
            ++  +L+GR +  N+ ED
Sbjct: 60  VMNKYDLNGRPL--NIKED 76

This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 23/103 (22%), Positives = 44/103 (42%), Gaps = 25/103 (24%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
           A LF+GNL  +VD + L   F   G +                         +   +++ 
Sbjct: 2   ANLFIGNLDPEVDEKLLYDTFSAFGVI-------------------------LQTPKIMR 36

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           + +T  S+GF F++  + E ++ A+E  +   +  R +TV+ A
Sbjct: 37  DPDTGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPITVSYA 79

This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 83

>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 35.2 bits (82), Expect = 0.004
 Identities = 21/98 (21%), Positives = 41/98 (41%), Gaps = 26/98 (26%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +++G+LP+     +L   F + GTV                          + L++  ++
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTV--------------------------TRLRLSRSK 35

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
           +T +S+G+ FV   + E A+   E  + Y +  RLL  
Sbjct: 36  KTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKC 73

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 35.6 bits (82), Expect = 0.004
 Identities = 19/68 (27%), Positives = 30/68 (44%)

Query: 284 VGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDG 343
           V NLP        E++   +G +    +VY   TG S+G+GFV    +   + A   L G
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63

Query: 344 QNLDGRAI 351
           + L    +
Sbjct: 64  KQLGESTL 71

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 8/81 (9%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R+Y+G L ++     +E+ F  +GK++        E     G+GFV      + +DA+  
Sbjct: 1   RVYIGRLSYQARERDVERFFKGYGKIL--------EVDLKNGYGFVEFDDLRDADDAVYE 52

Query: 341 LDGQNLDGRAIRVNVAEDRQR 361
           L+G++L G  + V  A   +R
Sbjct: 53  LNGKDLCGERVIVEHARGPRR 73

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 5/74 (6%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           +R+ V NL   V    L+    + G+V      Y     +    G V  ++ +++  AI 
Sbjct: 1   YRLIVENLSSRVSWQDLKDFMRKAGEVT-----YADAHKQRPNEGVVEFATYSDMKRAIE 55

Query: 340 ALDGQNLDGRAIRV 353
            LDG  L+GR I++
Sbjct: 56  KLDGTELNGRKIKL 69

This subfamily corresponds to the RRM2 of three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and is essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 19/90 (21%), Positives = 34/90 (37%), Gaps = 18/90 (20%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNAR---VVYDRETGRSRGF--------------G 324
           ++VGNLP       L+++F + G + + R   V    +    +                 
Sbjct: 3   VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNA 62

Query: 325 FVTMSSETELNDAIAALDGQNLDGRAIRVN 354
           +V    E E  +    L+G   +G  IRV+
Sbjct: 63  YVVFKEE-ESAEKALKLNGTEFEGHHIRVD 91

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 35.3 bits (81), Expect = 0.004
 Identities = 20/71 (28%), Positives = 33/71 (46%)

Query: 284 VGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDG 343
           + NLP      + E++    G +    +VY   TG S+G+GFV    +     A + L G
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 344 QNLDGRAIRVN 354
           + L  R + V+
Sbjct: 64  KQLGSRTLYVH 74

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 17/46 (36%), Positives = 27/46 (58%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFV 326
           +++VGNLP ++D + L++ F   G VV  R+      G+   FGFV
Sbjct: 7   QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFV 52

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	365
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.98
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.97
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.96
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.95
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.95
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.95
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.94
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.93
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.93
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.93
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.92
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.92
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.91
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.9
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.89
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.88
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.86
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.84
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.83
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.8
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.8
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.77
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.77
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.75
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.74
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.74
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.73
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.7
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.7
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.68
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.65
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.64
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.64
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.62
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.61
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.6
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.59
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.59
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.57
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.54
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.54
KOG0122	270	consensus Translation initiation factor 3, subunit	99.53
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.53
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.53
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.53
PLN03120	260	nucleic acid binding protein; Provisional	99.51
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.5
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.49
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.47
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.47
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.47
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.46
PLN03213	759	repressor of silencing 3; Provisional	99.46
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.45
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.44
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.44
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.44
PLN03121	243	nucleic acid binding protein; Provisional	99.43
smart00362	72	RRM_2 RNA recognition motif.	99.42
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.42
PLN03120	260	nucleic acid binding protein; Provisional	99.41
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.4
smart00360	71	RRM RNA recognition motif.	99.4
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.4
KOG0122	270	consensus Translation initiation factor 3, subunit	99.39
PLN03213	759	repressor of silencing 3; Provisional	99.38
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.38
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.37
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.37
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.37
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.36
KOG4210	285	consensus Nuclear localization sequence binding pr	99.36
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.35
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.35
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.34
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.32
smart00362	72	RRM_2 RNA recognition motif.	99.3
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.29
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.29
PLN03121	243	nucleic acid binding protein; Provisional	99.28
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.28
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.28
smart00361	70	RRM_1 RNA recognition motif.	99.25
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.24
smart00360	71	RRM RNA recognition motif.	99.24
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.23
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.22
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.21
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.2
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.2
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.18
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.16
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.13
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.12
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.1
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.05
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.04
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.03
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.98
smart00361	70	RRM_1 RNA recognition motif.	98.97
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.91
KOG0226	290	consensus RNA-binding proteins [General function p	98.9
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.9
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.89
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.88
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.87
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.87
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.85
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.84
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.83
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.82
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.82
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.72
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.71
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.68
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.65
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.63
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.55
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.54
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.52
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.51
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.47
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.47
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.43
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.42
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.38
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.36
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.34
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.32
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.28
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.28
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.27
KOG0151	877	consensus Predicted splicing regulator, contains R	98.26
KOG0226	290	consensus RNA-binding proteins [General function p	98.25
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.21
KOG0151	877	consensus Predicted splicing regulator, contains R	98.2
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.16
KOG3152	278	consensus TBP-binding protein, activator of basal	98.16
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.02
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.96
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.88
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.76
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.63
KOG3152	278	consensus TBP-binding protein, activator of basal	97.6
KOG2314	698	consensus Translation initiation factor 3, subunit	97.57
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.51
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.49
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.39
KOG4210	285	consensus Nuclear localization sequence binding pr	97.36
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.33
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.24
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.23
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.17
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.14
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.94
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.88
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.88
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.86
KOG2314	698	consensus Translation initiation factor 3, subunit	96.78
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.77
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.55
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.47
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.43
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.12
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.01
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.98
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.98
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	95.97
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.8
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	95.74
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.7
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.64
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	95.58
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.45
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.03
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.4
KOG1996	378	consensus mRNA splicing factor [RNA processing and	93.79
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.43
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.25
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	93.11
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	92.64
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	92.24
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	92.04
KOG2068	327	consensus MOT2 transcription factor [Transcription	91.61
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	91.38
KOG2135	526	consensus Proteins containing the RNA recognition	91.35
KOG2318	650	consensus Uncharacterized conserved protein [Funct	91.25
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	91.07
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.01
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	90.9
PF10446	458	DUF2457: Protein of unknown function (DUF2457); In	90.42
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	90.39
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	90.08
KOG2068	327	consensus MOT2 transcription factor [Transcription	90.05
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	89.99
KOG2591	684	consensus c-Mpl binding protein, contains La domai	89.83
KOG2135	526	consensus Proteins containing the RNA recognition	88.74
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	88.4
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	87.86
KOG2891	445	consensus Surface glycoprotein [General function p	86.39
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	84.91
PF04147	840	Nop14: Nop14-like family ; InterPro: IPR007276 Emg	84.8
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	84.66
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	84.35
PF12220	94	U1snRNP70_N: U1 small nuclear ribonucleoprotein of	83.74
PF04931	784	DNA_pol_phi: DNA polymerase phi; InterPro: IPR0070	81.95
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	81.7
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	81.11

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=3.3e-32  Score=260.88  Aligned_cols=172  Identities=26%  Similarity=0.514  Sum_probs=157.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+++|..||.|..|+                          |+.+..+++++|||||+|.+
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~--------------------------i~~d~~tg~srGyaFVeF~~  158 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCR--------------------------IMRDYKTGYSFGYAFVDFGS  158 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEecCCCCccCcEEEEEEcc
Confidence            3578999999999999999999999999999887                          78888899999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE  316 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~  316 (365)
                      .++|.+|+..|||..+.++.|+|.++.+....        ...++|||+|||+.+++++|+++|+.||.|+.|+|++++.
T Consensus       159 ~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~~~~--------~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~  230 (346)
T TIGR01659       159 EADSQRAIKNLNGITVRNKRLKVSYARPGGES--------IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKL  230 (346)
T ss_pred             HHHHHHHHHHcCCCccCCceeeeecccccccc--------cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCC
Confidence            99999999999999999999999988654322        1234899999999999999999999999999999999999


Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eeEEEEEccccccC
Q 017842          317 TGRSRGFGFVTMSSETELNDAIAALDGQNLDG--RAIRVNVAEDRQRR  362 (365)
Q Consensus       317 ~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g--r~l~V~~a~~~~~~  362 (365)
                      +++++|||||+|.+.++|.+||..||+..+.|  ++|+|.+|+.+.+.
T Consensus       231 tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~~  278 (346)
T TIGR01659       231 TGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKA  278 (346)
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCccccc
Confidence            99999999999999999999999999998866  79999999876553

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.98  E-value=3.7e-31  Score=266.47  Aligned_cols=178  Identities=19%  Similarity=0.384  Sum_probs=157.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||||||+++++++|+.+|..||.|..++                          ++.++.+++++|||||+|.+.
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~--------------------------I~~D~~TgkskGfAFVeF~s~  159 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSIN--------------------------MSWDPATGKHKGFAFVEYEVP  159 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEE--------------------------EeecCCCCCcCCeEEEEeCcH
Confidence            357999999999999999999999999999987                          778888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCC---CCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEee
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPE---RAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYD  314 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~---~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d  314 (365)
                      ++|.+|+..|||..|+||.|+|.+.........   .........++|||+|||+.+++++|+++|+.||.|..|+|.++
T Consensus       160 e~A~~Ai~~lnG~~i~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D  239 (612)
T TIGR01645       160 EAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARA  239 (612)
T ss_pred             HHHHHHHHhcCCeEEecceeeecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEec
Confidence            999999999999999999999986543321110   00111223469999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccccc
Q 017842          315 RETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR  361 (365)
Q Consensus       315 ~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~  361 (365)
                      +.+++++|||||+|.+.++|.+|+..|||..|+|+.|+|.++..++.
T Consensus       240 ~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP~  286 (612)
T TIGR01645       240 PTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPD  286 (612)
T ss_pred             CCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCcc
Confidence            99999999999999999999999999999999999999999987554

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=4.8e-30  Score=248.53  Aligned_cols=179  Identities=27%  Similarity=0.474  Sum_probs=154.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...+|||+|||.++++++|+.+|..||.|..+.                          ++.+..++.++|||||+|.+.
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~--------------------------~~~~~~~~~~~g~~fv~f~~~  141 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSR--------------------------ILSDNVTGLSKGVGFIRFDKR  141 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEE--------------------------EEecCCCCCcCcEEEEEECCH
Confidence            356899999999999999999999999998877                          666777889999999999999


Q ss_pred             HHHHHHHHHHccCcccC--eeEEEeecCCCCCCCC----------------C----------------------------
Q 017842          238 EEAEKAVEMFHRYDIDG--RLLTVNKAAPRGTQPE----------------R----------------------------  271 (365)
Q Consensus       238 e~a~~Al~~lng~~~~g--r~l~V~~a~~~~~~~~----------------~----------------------------  271 (365)
                      ++|..|+..|||..+.|  ++|.|.++..+.....                .                            
T Consensus       142 ~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (352)
T TIGR01661       142 DEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGD  221 (352)
T ss_pred             HHHHHHHHHhCCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcch
Confidence            99999999999999877  6788877654331000                0                            


Q ss_pred             ----------------------------------------CCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEE
Q 017842          272 ----------------------------------------APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARV  311 (365)
Q Consensus       272 ----------------------------------------~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i  311 (365)
                                                              .+.....+.+|||+|||+.+++++|+++|+.||.|..|+|
T Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i  301 (352)
T TIGR01661       222 FTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKI  301 (352)
T ss_pred             hhhhhhhhhhhcccccccccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEE
Confidence                                                    0000112336999999999999999999999999999999


Q ss_pred             EeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccccC
Q 017842          312 VYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR  362 (365)
Q Consensus       312 ~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~~  362 (365)
                      ++|+.+|.++|||||+|.+.++|.+||..|||..|.||.|+|.|+.++.++
T Consensus       302 ~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~~~  352 (352)
T TIGR01661       302 IRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAYR  352 (352)
T ss_pred             eEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCCCC
Confidence            999999999999999999999999999999999999999999999988753

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=1.9e-29  Score=244.35  Aligned_cols=168  Identities=30%  Similarity=0.559  Sum_probs=154.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      ..+|||+|||+++++++|+++|+.||+|..++                          +++++.+|+++|||||+|.+.+
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~--------------------------i~~d~~~g~s~g~afV~f~~~~   56 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCK--------------------------LVRDKVTGQSLGYGFVNYVRPE   56 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEE--------------------------EEEcCCCCccceEEEEEECcHH
Confidence            57999999999999999999999999999988                          8888889999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETG  318 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~  318 (365)
                      +|.+|+..|||..+.|+.|+|.++.+....        ...++|||+|||..+++++|+.+|+.||.|..++++++..++
T Consensus        57 ~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~~--------~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~  128 (352)
T TIGR01661        57 DAEKAVNSLNGLRLQNKTIKVSYARPSSDS--------IKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTG  128 (352)
T ss_pred             HHHHHHhhcccEEECCeeEEEEeecccccc--------cccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCC
Confidence            999999999999999999999988754322        123489999999999999999999999999999999998889


Q ss_pred             CcceEEEEEecCHHHHHHHHHHhCCCccCC--eeEEEEEccccc
Q 017842          319 RSRGFGFVTMSSETELNDAIAALDGQNLDG--RAIRVNVAEDRQ  360 (365)
Q Consensus       319 ~~kG~afV~F~s~~~a~~Al~~l~~~~l~g--r~l~V~~a~~~~  360 (365)
                      .++|||||+|.+.++|..|+..|||..+.|  ++|+|.|+..+.
T Consensus       129 ~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       129 LSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             CcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCC
Confidence            999999999999999999999999999877  689999987554

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=2.4e-29  Score=223.05  Aligned_cols=197  Identities=29%  Similarity=0.480  Sum_probs=170.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeecc-------C-------CCcccceee----------------
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLF-------G-------NQGFHMWVC----------------  207 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~-------~-------~~~~~~~~~----------------  207 (365)
                      ..||||||||..++|++-|..||.+.|.|..++|.+.-+-       +       ++++|.++.                
T Consensus         5 ~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~~v~wa~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~   84 (321)
T KOG0148|consen    5 EPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDELKVNWATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFA   84 (321)
T ss_pred             CCceEEeeccChhhHHHHHHHHHHhccccccceeehhhhccccccCcccCCCCccccceeEEehhcchhcchHHHHHHhc
Confidence            4689999999999999999999999999999887655331       1       234443322                


Q ss_pred             eeeeeeeeeEEecCCCCCccceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCC--------CcCCCC
Q 017842          208 AVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAP--------RVFEPG  279 (365)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~--------~~~~~~  279 (365)
                      .-+.++..+|++|..|++++|||||.|-++++|+.||..+||.-|++|.||-+|+..+.......+        +..+.+
T Consensus        85 pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~N  164 (321)
T KOG0148|consen   85 PFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDN  164 (321)
T ss_pred             cccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccCCCCccHHHHhccCCCCC
Confidence            234578899999999999999999999999999999999999999999999999988764443322        234567


Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      |+|||||++..++++.|++.|+.||.|..|||.++      +||+||.|.++++|..||-.+||..+.|..+++.|.+..
T Consensus       165 tsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~  238 (321)
T KOG0148|consen  165 TSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEG  238 (321)
T ss_pred             ceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccC
Confidence            89999999999999999999999999999999988      899999999999999999999999999999999998754


Q ss_pred             c
Q 017842          360 Q  360 (365)
Q Consensus       360 ~  360 (365)
                      .
T Consensus       239 ~  239 (321)
T KOG0148|consen  239 D  239 (321)
T ss_pred             C
Confidence            3

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.96  E-value=1.3e-28  Score=246.65  Aligned_cols=176  Identities=30%  Similarity=0.536  Sum_probs=155.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+++|+.||.|..|+                          ++.+..+++++|||||+|.+
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~--------------------------i~~d~~~~~skg~afVeF~~  140 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQ--------------------------CIKDRNSRRSKGVAYVEFYD  140 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE--------------------------EeecCCCCCcceEEEEEECC
Confidence            3578999999999999999999999999998887                          77888899999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCC----CCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEE
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER----APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVV  312 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~----~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~  312 (365)
                      .++|.+|+. |+|..+.|+.|.|..+.........    .....+..++|||+|||+.+++++|+++|+.||.|..|.|+
T Consensus       141 ~e~A~~Al~-l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~  219 (457)
T TIGR01622       141 VESVIKALA-LTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLH  219 (457)
T ss_pred             HHHHHHHHH-hCCCEECCeeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEE
Confidence            999999997 5999999999999876433221111    11112335799999999999999999999999999999999


Q ss_pred             eeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          313 YDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       313 ~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      ++..+|.++|||||+|.+.++|.+|+..|||..|.|++|+|.||...
T Consensus       220 ~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~  266 (457)
T TIGR01622       220 RDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDS  266 (457)
T ss_pred             EcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCC
Confidence            99999999999999999999999999999999999999999998743

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.95  E-value=4.4e-27  Score=241.48  Aligned_cols=167  Identities=30%  Similarity=0.452  Sum_probs=150.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      +|||||||.++|+++|+++|+.||.|..|+                          ++++..+++++|||||+|.+.++|
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~--------------------------v~~d~~t~~s~G~afV~F~~~~~A   55 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVR--------------------------VCRDSVTRRSLGYGYVNFQNPADA   55 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEecCCCCCcceEEEEEECCHHHH
Confidence            799999999999999999999999998887                          888888999999999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCc
Q 017842          241 EKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRS  320 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~  320 (365)
                      .+|+..+|+..|.|+.|+|.++......      ......+|||+|||..+++++|+++|+.||.|..|+|.++. +|++
T Consensus        56 ~~Al~~ln~~~i~gk~i~i~~s~~~~~~------~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~s  128 (562)
T TIGR01628        56 ERALETMNFKRLGGKPIRIMWSQRDPSL------RRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKS  128 (562)
T ss_pred             HHHHHHhCCCEECCeeEEeecccccccc------cccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCc
Confidence            9999999999999999999987532211      11123479999999999999999999999999999999884 6889


Q ss_pred             ceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccc
Q 017842          321 RGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       321 kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      +|||||+|.+.++|.+|+..|||..+.|+.|.|.....+.
T Consensus       129 kg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~  168 (562)
T TIGR01628       129 RGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKH  168 (562)
T ss_pred             ccEEEEEECCHHHHHHHHHHhcccEecCceEEEecccccc
Confidence            9999999999999999999999999999999998766544

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=2.7e-27  Score=227.18  Aligned_cols=176  Identities=31%  Similarity=0.585  Sum_probs=157.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      ..||||++||+.++.++|.++|+.+|+|..+.                          ++++..++..+|||||.|+-.+
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~--------------------------vVt~~gs~~~RGfgfVtFam~E   58 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAV--------------------------VVTNKGSSEKRGFGFVTFAMEE   58 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeE--------------------------EecCCCcccccCccceeeehHh
Confidence            36999999999999999999999999999887                          8889999999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCCCCCCC----------------CC--CcCCCCceEEEeCCCCcCcHHHHHHHH
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER----------------AP--RVFEPGFRIYVGNLPWEVDNARLEQVF  300 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~----------------~~--~~~~~~~~lfV~nLp~~~tee~L~~~F  300 (365)
                      ++++|+..+++..|+||.|+|+.+.++......                ..  ....+..+|.|+||||.+.+.+|+.+|
T Consensus        59 D~qrA~~e~~~~kf~Gr~l~v~~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vF  138 (678)
T KOG0127|consen   59 DVQRALAETEQSKFEGRILNVDPAKKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVF  138 (678)
T ss_pred             HHHHHHHHhhcCcccceecccccccccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHH
Confidence            999999999999999999999988876543210                00  112336699999999999999999999


Q ss_pred             hccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccccc
Q 017842          301 SEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR  361 (365)
Q Consensus       301 ~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~  361 (365)
                      +.||.|..|.|++...++.+ |||||+|.+..+|..||..+|+..|+||+|-|.||-++..
T Consensus       139 s~~G~V~Ei~IP~k~dgklc-GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~  198 (678)
T KOG0127|consen  139 SNFGKVVEIVIPRKKDGKLC-GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDT  198 (678)
T ss_pred             hhcceEEEEEcccCCCCCcc-ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccccc
Confidence            99999999999988776666 9999999999999999999999999999999999987754

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.95  E-value=1.3e-26  Score=235.33  Aligned_cols=183  Identities=21%  Similarity=0.352  Sum_probs=143.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||||||+++|+++|+.+|..++........                    ..+..+.....+..+|||||+|.
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~--------------------~~~~~v~~~~~~~~kg~afVeF~  231 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKA--------------------EDGKHVSSVNINKEKNFAFLEFR  231 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCC--------------------CCCCceEEEEECCCCCEEEEEeC
Confidence            3457899999999999999999999886321110000                    00001122224467899999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCC---------------------CCCCcCCCCceEEEeCCCCcCcHH
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPE---------------------RAPRVFEPGFRIYVGNLPWEVDNA  294 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~---------------------~~~~~~~~~~~lfV~nLp~~~tee  294 (365)
                      +.++|..||. |+|..|.|+.|+|.........+.                     ..........+|||+|||+.++++
T Consensus       232 ~~e~A~~Al~-l~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~  310 (509)
T TIGR01642       232 TVEEATFAMA-LDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGED  310 (509)
T ss_pred             CHHHHhhhhc-CCCeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHH
Confidence            9999999995 799999999999975543321100                     000122345799999999999999


Q ss_pred             HHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          295 RLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       295 ~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      +|+++|+.||.|..+.|+++..+|.++|||||+|.+..+|..|+..|||..|+|++|.|.+|...
T Consensus       311 ~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       311 QIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             HHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence            99999999999999999999999999999999999999999999999999999999999998644

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=5.6e-27  Score=220.55  Aligned_cols=178  Identities=30%  Similarity=0.498  Sum_probs=151.6

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceE
Q 017842          151 EEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFG  230 (365)
Q Consensus       151 ~~~~~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~a  230 (365)
                      .+...++..+.||||.||.++.+++|.-+|++.|+|-.++                          +..++.+|.++|||
T Consensus        75 weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elR--------------------------LMmD~~sG~nRGYA  128 (506)
T KOG0117|consen   75 WEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELR--------------------------LMMDPFSGDNRGYA  128 (506)
T ss_pred             ccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEE--------------------------EeecccCCCCcceE
Confidence            4555567788999999999999999999999999999988                          77788899999999


Q ss_pred             EEEeCCHHHHHHHHHHHccCcc-cCeeEEEeecCCCCC-----------------------------------CCCCCCC
Q 017842          231 FVTMSTVEEAEKAVEMFHRYDI-DGRLLTVNKAAPRGT-----------------------------------QPERAPR  274 (365)
Q Consensus       231 fV~f~~~e~a~~Al~~lng~~~-~gr~l~V~~a~~~~~-----------------------------------~~~~~~~  274 (365)
                      ||.|.+++.|+.|++.||+++| .|++|.|+.+.....                                   .....++
T Consensus       129 FVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNR  208 (506)
T KOG0117|consen  129 FVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNR  208 (506)
T ss_pred             EEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCcccccccc
Confidence            9999999999999999999988 799999875532210                                   0000000


Q ss_pred             ----------------------------------------------cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEE
Q 017842          275 ----------------------------------------------VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVN  308 (365)
Q Consensus       275 ----------------------------------------------~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~  308 (365)
                                                                    ....-..|||+||+..+|++.|+++|+.||.|+.
T Consensus       209 GFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veR  288 (506)
T KOG0117|consen  209 GFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVER  288 (506)
T ss_pred             ceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEE
Confidence                                                          0011248999999999999999999999999999


Q ss_pred             EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccccC
Q 017842          309 ARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR  362 (365)
Q Consensus       309 v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~~  362 (365)
                      |..++|        ||||.|.++++|.+||+.+||+.|.|..|.|.+|++..+.
T Consensus       289 Vkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~  334 (506)
T KOG0117|consen  289 VKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKK  334 (506)
T ss_pred             eecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhh
Confidence            999876        9999999999999999999999999999999999987654

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.95  E-value=5.7e-27  Score=197.07  Aligned_cols=172  Identities=34%  Similarity=0.566  Sum_probs=155.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      .+.|||||||+..++++-|.++|-+.|+|..++                          +..++.+...+||||++|.++
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~--------------------------iPkDrv~~~~qGygF~Ef~~e   61 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLH--------------------------IPKDRVTQKHQGYGFAEFRTE   61 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeee--------------------------cchhhhcccccceeEEEEech
Confidence            467999999999999999999999999998887                          778888889999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEE-EEEeeCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNA-RVVYDRE  316 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v-~i~~d~~  316 (365)
                      ++|.-|++.||...+.||+|+|+.+....       .....+..|||+||.+.+++..|+..|+.||.+... .|.++..
T Consensus        62 edadYAikiln~VkLYgrpIrv~kas~~~-------~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~  134 (203)
T KOG0131|consen   62 EDADYAIKILNMVKLYGRPIRVNKASAHQ-------KNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPD  134 (203)
T ss_pred             hhhHHHHHHHHHHHhcCceeEEEeccccc-------ccccccccccccccCcchhHHHHHHHHHhccccccCCccccccc
Confidence            99999999999999999999999887221       122233589999999999999999999999987764 7899999


Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccccC
Q 017842          317 TGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR  362 (365)
Q Consensus       317 ~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~~  362 (365)
                      ||.++|||||.|.+.+.+.+|+..|||+.++.|+|+|.|+..+..+
T Consensus       135 tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  135 TGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTK  180 (203)
T ss_pred             CCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCC
Confidence            9999999999999999999999999999999999999999876543

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.94  E-value=2.6e-26  Score=235.78  Aligned_cols=175  Identities=37%  Similarity=0.599  Sum_probs=154.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||.++++++|+++|..||.|..+.                          +..+ .+++++|||||.|.+.
T Consensus       177 ~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~--------------------------i~~~-~~g~~~G~afV~F~~~  229 (562)
T TIGR01628       177 KFTNLYVKNLDPSVNEDKLRELFAKFGEITSAA--------------------------VMKD-GSGRSRGFAFVNFEKH  229 (562)
T ss_pred             CCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEE--------------------------EEEC-CCCCcccEEEEEECCH
Confidence            457899999999999999999999999998876                          4444 4688999999999999


Q ss_pred             HHHHHHHHHHccCccc----CeeEEEeecCCCCCCCCC----------CCCcCCCCceEEEeCCCCcCcHHHHHHHHhcc
Q 017842          238 EEAEKAVEMFHRYDID----GRLLTVNKAAPRGTQPER----------APRVFEPGFRIYVGNLPWEVDNARLEQVFSEH  303 (365)
Q Consensus       238 e~a~~Al~~lng~~~~----gr~l~V~~a~~~~~~~~~----------~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~  303 (365)
                      ++|.+|+..|+|..+.    |+.|.|.++..+..+...          .......+++|||+||++.+++++|+++|+.|
T Consensus       230 e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~  309 (562)
T TIGR01628       230 EDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSEC  309 (562)
T ss_pred             HHHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhc
Confidence            9999999999999999    999999988766543100          01113345689999999999999999999999


Q ss_pred             CCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccc
Q 017842          304 GKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       304 G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      |.|..|+|.++ .+|+++|||||.|.+.++|.+|+..|||..++|++|.|.+|..+.
T Consensus       310 G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~  365 (562)
T TIGR01628       310 GEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKE  365 (562)
T ss_pred             CCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcH
Confidence            99999999999 679999999999999999999999999999999999999998764

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.94  E-value=1.7e-25  Score=225.25  Aligned_cols=168  Identities=31%  Similarity=0.538  Sum_probs=126.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+.+|++||.|..++|.                          .+ .+++++|||||+|.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~--------------------------~D-~sG~sRGfaFV~F~  107 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLM--------------------------MD-FSGQNRGYAFVTFC  107 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEE--------------------------EC-CCCCccceEEEEeC
Confidence            3346899999999999999999999999999998843                          33 34445555555555


Q ss_pred             CHHHHHHHHHHHccCcc---------------------------------------------------------------
Q 017842          236 TVEEAEKAVEMFHRYDI---------------------------------------------------------------  252 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~---------------------------------------------------------------  252 (365)
                      +.++|.+||..||+..|                                                               
T Consensus       108 ~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFV  187 (578)
T TIGR01648       108 GKEEAKEAVKLLNNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFV  187 (578)
T ss_pred             CHHHHHHHHHHcCCCeecCCccccccccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEE
Confidence            55555555555444444                                                               


Q ss_pred             ----------------------cCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhcc--CCeEE
Q 017842          253 ----------------------DGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEH--GKVVN  308 (365)
Q Consensus       253 ----------------------~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~--G~V~~  308 (365)
                                            .|+.|.|+++.+.....   ........+|||+|||+.+++++|+++|+.|  |.|+.
T Consensus       188 eF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d---~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~r  264 (578)
T TIGR01648       188 EYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVD---EDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVER  264 (578)
T ss_pred             EcCCHHHHHHHHHHhhccceEecCceEEEEeeccccccc---ccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEE
Confidence                                  44444444443322111   1111234589999999999999999999999  99999


Q ss_pred             EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccccc
Q 017842          309 ARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR  361 (365)
Q Consensus       309 v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~  361 (365)
                      |+++        +|||||+|.+.++|.+|+..|||..|.|+.|+|.||+++.+
T Consensus       265 V~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       265 VKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             EEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCc
Confidence            9876        56999999999999999999999999999999999987644

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.94  E-value=3.6e-25  Score=224.68  Aligned_cols=175  Identities=17%  Similarity=0.274  Sum_probs=147.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||||||+.+++++|+++|..||.|..+.                          ++.+..+|.++|||||+|.+.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~--------------------------~~~~~~~g~~~g~afv~f~~~  347 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFN--------------------------LIKDIATGLSKGYAFCEYKDP  347 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE--------------------------EEecCCCCCcCeEEEEEECCH
Confidence            467999999999999999999999999998877                          777888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCC--------------------CCcCCCCceEEEeCCCCcC------
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERA--------------------PRVFEPGFRIYVGNLPWEV------  291 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~--------------------~~~~~~~~~lfV~nLp~~~------  291 (365)
                      ++|..|+..|||..|.|+.|.|.++..........                    .....+..+|+|.||....      
T Consensus       348 ~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~  427 (509)
T TIGR01642       348 SVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDE  427 (509)
T ss_pred             HHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcc
Confidence            99999999999999999999999885433211000                    0012345689999996431      


Q ss_pred             ----cHHHHHHHHhccCCeEEEEEEeeC---CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          292 ----DNARLEQVFSEHGKVVNARVVYDR---ETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       292 ----tee~L~~~F~~~G~V~~v~i~~d~---~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                          ..++|+++|..||.|..|.|+++.   .++.++|+|||+|.+.++|.+|+..|||..|.||.|.|.|...
T Consensus       428 ~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       428 EYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             hHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence                246899999999999999998753   3456789999999999999999999999999999999999763

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.94  E-value=4.2e-25  Score=222.32  Aligned_cols=166  Identities=20%  Similarity=0.218  Sum_probs=138.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +.++|||+|||+++++++|+++|+.||.|..+.                          ++      +++|||||+|.+.
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~--------------------------i~------~~k~~afVef~~~   48 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVM--------------------------ML------PGKRQALVEFEDE   48 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEE--------------------------EE------CCCCEEEEEeCch
Confidence            368999999999999999999999999999887                          33      2468999999999


Q ss_pred             HHHHHHHHHH--ccCcccCeeEEEeecCCCCCCCCCC----CCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEE
Q 017842          238 EEAEKAVEMF--HRYDIDGRLLTVNKAAPRGTQPERA----PRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARV  311 (365)
Q Consensus       238 e~a~~Al~~l--ng~~~~gr~l~V~~a~~~~~~~~~~----~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i  311 (365)
                      ++|.+|+..+  ++..+.|+.|+|.++..+.......    ........+|||+||++.+|+++|+++|+.||.|..|.|
T Consensus        49 e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i  128 (481)
T TIGR01649        49 ESAKACVNFATSVPIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVT  128 (481)
T ss_pred             HHHHHHHHHhhcCCceEcCeEEEEEecCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEE
Confidence            9999999864  7889999999999987653221110    011112347999999999999999999999999999999


Q ss_pred             EeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eeEEEEEcccc
Q 017842          312 VYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDG--RAIRVNVAEDR  359 (365)
Q Consensus       312 ~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g--r~l~V~~a~~~  359 (365)
                      .++.    .+|+|||+|.+.++|.+|+..|||..|.|  +.|+|.|++..
T Consensus       129 ~~~~----~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       129 FTKN----NVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             EecC----CceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCC
Confidence            8763    25799999999999999999999999964  58999998853

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.93  E-value=9e-26  Score=199.20  Aligned_cols=169  Identities=30%  Similarity=0.566  Sum_probs=156.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .+.|.|.-||.++|+++|+.+|...|+|++|+                          +++|+-+|++-|||||-|.+++
T Consensus        41 kTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScK--------------------------LvRDKitGqSLGYGFVNYv~p~   94 (360)
T KOG0145|consen   41 KTNLIVNYLPQNMTQDELRSLFGSIGEIESCK--------------------------LVRDKITGQSLGYGFVNYVRPK   94 (360)
T ss_pred             cceeeeeecccccCHHHHHHHhhcccceeeee--------------------------eeeccccccccccceeeecChH
Confidence            45799999999999999999999999999998                          8999999999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETG  318 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~  318 (365)
                      +|++|+..|||..+..+.|+|.++.|....-+.        ..|||.+||..+|..+|..+|+.||.|..-||+.|..+|
T Consensus        95 DAe~AintlNGLrLQ~KTIKVSyARPSs~~Ik~--------aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg  166 (360)
T KOG0145|consen   95 DAEKAINTLNGLRLQNKTIKVSYARPSSDSIKD--------ANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTG  166 (360)
T ss_pred             HHHHHHhhhcceeeccceEEEEeccCChhhhcc--------cceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccc
Confidence            999999999999999999999999877554333        279999999999999999999999999999999999999


Q ss_pred             CcceEEEEEecCHHHHHHHHHHhCCCccCCe--eEEEEEcccccc
Q 017842          319 RSRGFGFVTMSSETELNDAIAALDGQNLDGR--AIRVNVAEDRQR  361 (365)
Q Consensus       319 ~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr--~l~V~~a~~~~~  361 (365)
                      .+||.|||+|..+.+|..||+.|||.+--|.  +|.|.||.....
T Consensus       167 ~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq  211 (360)
T KOG0145|consen  167 LSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQ  211 (360)
T ss_pred             eecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCccc
Confidence            9999999999999999999999999987664  999999987654

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.93  E-value=8.9e-26  Score=211.59  Aligned_cols=169  Identities=28%  Similarity=0.475  Sum_probs=148.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +.-++|||-||..+++++|+.+|++||.|..|.                          +++|+.++.++|||||.|.+.
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~ein--------------------------l~kDk~t~~s~gcCFv~~~tr   86 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEIN--------------------------LIKDKSTGQSKGCCFVKYYTR   86 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEE--------------------------eecccccCcccceEEEEeccH
Confidence            355899999999999999999999999999987                          899999999999999999999


Q ss_pred             HHHHHHHHHHccCc-cc--CeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEee
Q 017842          238 EEAEKAVEMFHRYD-ID--GRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYD  314 (365)
Q Consensus       238 e~a~~Al~~lng~~-~~--gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d  314 (365)
                      ++|.+|+..|++.. |.  .++|.|.++.....+.       ....+||||-|+..+++.+++++|++||.|+.|+|.||
T Consensus        87 k~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er~-------~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd  159 (510)
T KOG0144|consen   87 KEADEAINALHNQKTLPGMHHPVQVKYADGERERI-------VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRD  159 (510)
T ss_pred             HHHHHHHHHhhcccccCCCCcceeecccchhhhcc-------ccchhhhhhhccccccHHHHHHHHHhhCccchhhheec
Confidence            99999999998744 44  4677787776543332       12238999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEecCHHHHHHHHHHhCCC-ccCC--eeEEEEEccccc
Q 017842          315 RETGRSRGFGFVTMSSETELNDAIAALDGQ-NLDG--RAIRVNVAEDRQ  360 (365)
Q Consensus       315 ~~~~~~kG~afV~F~s~~~a~~Al~~l~~~-~l~g--r~l~V~~a~~~~  360 (365)
                      . .+.+||+|||+|.+++.|..||+.|||. .+.|  .+|.|.||+.+.
T Consensus       160 ~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqk  207 (510)
T KOG0144|consen  160 P-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQK  207 (510)
T ss_pred             c-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCC
Confidence            5 5899999999999999999999999997 6666  599999999655

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.93  E-value=1.6e-24  Score=218.08  Aligned_cols=170  Identities=22%  Similarity=0.354  Sum_probs=142.1

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          157 PEDAKLFVGNLPY-DVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       157 ~~~~tvfVgnLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ++..+|||+|||+ .+++++|+++|+.||.|..++                          ++.+     .+|||||+|.
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vk--------------------------i~~~-----~~g~afV~f~  321 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVK--------------------------FMKN-----KKETALIEMA  321 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEeC-----CCCEEEEEEC
Confidence            3568999999998 699999999999999999887                          4433     3699999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCC-----------------------C------CCcCCCCceEEEeC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER-----------------------A------PRVFEPGFRIYVGN  286 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~-----------------------~------~~~~~~~~~lfV~n  286 (365)
                      +.++|..|+..|||..|.|+.|+|.++........+                       .      .....++.+|||+|
T Consensus       322 ~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~N  401 (481)
T TIGR01649       322 DPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSN  401 (481)
T ss_pred             CHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEec
Confidence            999999999999999999999999887543211000                       0      00124567999999


Q ss_pred             CCCcCcHHHHHHHHhccCC--eEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCee------EEEEEccc
Q 017842          287 LPWEVDNARLEQVFSEHGK--VVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRA------IRVNVAED  358 (365)
Q Consensus       287 Lp~~~tee~L~~~F~~~G~--V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~------l~V~~a~~  358 (365)
                      ||+.+++++|+++|+.||.  |..|++.... ++ .+|+|||+|.+.++|.+||..|||..|.|+.      |+|+|+++
T Consensus       402 Lp~~~tee~L~~lF~~~G~~~i~~ik~~~~~-~~-~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~  479 (481)
T TIGR01649       402 IPLSVSEEDLKELFAENGVHKVKKFKFFPKD-NE-RSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTS  479 (481)
T ss_pred             CCCCCCHHHHHHHHHhcCCccceEEEEecCC-CC-cceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccC
Confidence            9999999999999999998  8888886543 23 5899999999999999999999999999985      99999986


Q ss_pred             c
Q 017842          359 R  359 (365)
Q Consensus       359 ~  359 (365)
                      +
T Consensus       480 ~  480 (481)
T TIGR01649       480 R  480 (481)
T ss_pred             C
Confidence            5

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.92  E-value=2.4e-24  Score=190.21  Aligned_cols=178  Identities=31%  Similarity=0.489  Sum_probs=153.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ..+..|||.+||..+|.++|..+|++||.|-.-+                          |+.+..+|.++|-|||.|..
T Consensus       125 Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSR--------------------------iL~dqvtg~srGVgFiRFDK  178 (360)
T KOG0145|consen  125 IKDANLYVSGLPKTMTQKELEQIFSPFGRIITSR--------------------------ILVDQVTGLSRGVGFIRFDK  178 (360)
T ss_pred             hcccceEEecCCccchHHHHHHHHHHhhhhhhhh--------------------------hhhhcccceecceeEEEecc
Confidence            3466899999999999999999999999885544                          88888899999999999999


Q ss_pred             HHHHHHHHHHHccCcccC--eeEEEeecCCCCCCCCC----------------------------------------C--
Q 017842          237 VEEAEKAVEMFHRYDIDG--RLLTVNKAAPRGTQPER----------------------------------------A--  272 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~g--r~l~V~~a~~~~~~~~~----------------------------------------~--  272 (365)
                      .+.|..||+.|||..--|  .+|.|..+..+......                                        .  
T Consensus       179 r~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~  258 (360)
T KOG0145|consen  179 RIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPM  258 (360)
T ss_pred             hhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCc
Confidence            999999999999988765  68899877655321100                                        0  


Q ss_pred             -------------CCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHH
Q 017842          273 -------------PRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA  339 (365)
Q Consensus       273 -------------~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~  339 (365)
                                   +.....+.+|||.||..+.++.-||++|..||.|..|+|+||..++++||||||.+.+-++|..||.
T Consensus       259 ~~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~  338 (360)
T KOG0145|consen  259 TIDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIA  338 (360)
T ss_pred             cccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHH
Confidence                         0011224699999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhCCCccCCeeEEEEEccccc
Q 017842          340 ALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       340 ~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      .|||..+++|.|.|+|-.+++
T Consensus       339 sLNGy~lg~rvLQVsFKtnk~  359 (360)
T KOG0145|consen  339 SLNGYRLGDRVLQVSFKTNKA  359 (360)
T ss_pred             HhcCccccceEEEEEEecCCC
Confidence            999999999999999976654

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.92  E-value=3.5e-24  Score=205.85  Aligned_cols=175  Identities=31%  Similarity=0.534  Sum_probs=148.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      ...|.|+||||.+...+|+.+|+.||.|..|.                          |.+....+ ..|||||.|....
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~--------------------------IP~k~dgk-lcGFaFV~fk~~~  169 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIV--------------------------IPRKKDGK-LCGFAFVQFKEKK  169 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEE--------------------------cccCCCCC-ccceEEEEEeeHH
Confidence            56899999999999999999999999998887                          44444444 4499999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCCCCCCC-------------------------------------------C---
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER-------------------------------------------A---  272 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~-------------------------------------------~---  272 (365)
                      +|.+|++.+||..|.||+|.|+|+.++......                                           .   
T Consensus       170 dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~s  249 (678)
T KOG0127|consen  170 DAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNS  249 (678)
T ss_pred             HHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccc
Confidence            999999999999999999999999776422100                                           0   


Q ss_pred             ------------------------------------CCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCC
Q 017842          273 ------------------------------------PRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE  316 (365)
Q Consensus       273 ------------------------------------~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~  316 (365)
                                                          ......+.+|||+||||++|++.|.++|+.||.|.++.|+.++.
T Consensus       250 e~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~  329 (678)
T KOG0127|consen  250 EAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKD  329 (678)
T ss_pred             hhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccC
Confidence                                                00001135999999999999999999999999999999999999


Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHh-----CC-CccCCeeEEEEEccccc
Q 017842          317 TGRSRGFGFVTMSSETELNDAIAAL-----DG-QNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       317 ~~~~kG~afV~F~s~~~a~~Al~~l-----~~-~~l~gr~l~V~~a~~~~  360 (365)
                      |++++|.|||.|.+...|..||.+.     .| ..|.||.|.|..|-.|.
T Consensus       330 T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~Rk  379 (678)
T KOG0127|consen  330 TGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRK  379 (678)
T ss_pred             CCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchH
Confidence            9999999999999999999999966     23 57899999999987653

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.91  E-value=7.5e-24  Score=209.55  Aligned_cols=175  Identities=30%  Similarity=0.465  Sum_probs=148.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecC-CCCCccceEEEEeCCHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR-ETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~g~afV~f~~~e~  239 (365)
                      +|||.||+++++.+.|..+|...|.|..+.|..                        ..++ ..-.+.|||||+|.++++
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~k------------------------kkd~~~k~lSmGfgFVEF~~~e~  572 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISK------------------------KKDPANKYLSMGFGFVEFAKPES  572 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEec------------------------cccccccccccceeEEEecCHHH
Confidence            399999999999999999999999999987542                        1111 133577999999999999


Q ss_pred             HHHHHHHHccCcccCeeEEEeecCCCCCCCC-CCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCC
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKAAPRGTQPE-RAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETG  318 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~-~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~  318 (365)
                      |+.|+..|+|+.++||.|.|..+..+..... +.......++.|.|+||||..+..+++.+|..||.|..|||+.....+
T Consensus       573 A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~  652 (725)
T KOG0110|consen  573 AQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKG  652 (725)
T ss_pred             HHHHHHHhcCceecCceEEEEeccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcch
Confidence            9999999999999999999998873322221 111222336799999999999999999999999999999999875567


Q ss_pred             CcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          319 RSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       319 ~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      .++|||||.|.+.++|..|+.+|.++.|.||+|.+.||++-
T Consensus       653 a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d  693 (725)
T KOG0110|consen  653 AHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSD  693 (725)
T ss_pred             hhccceeeeccCcHHHHHHHHhhcccceechhhheehhccc
Confidence            78999999999999999999999999999999999999853

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.90  E-value=2e-22  Score=201.96  Aligned_cols=171  Identities=26%  Similarity=0.363  Sum_probs=142.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||+|||+++++++|+.+|+.||.|..+.                          +..+..+|.++|||||+|.+.+
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~--------------------------~~~d~~~g~~~g~afV~f~~~e  239 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQ--------------------------LHRDPETGRSKGFGFIQFHDAE  239 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEEcCCCCccceEEEEEECCHH
Confidence            68999999999999999999999999998887                          7778888899999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCCCCC----------------------------------C--------------
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP----------------------------------E--------------  270 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~----------------------------------~--------------  270 (365)
                      +|.+|+..|||..|.|+.|.|.++.......                                  .              
T Consensus       240 ~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  319 (457)
T TIGR01622       240 EAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKI  319 (457)
T ss_pred             HHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchh
Confidence            9999999999999999999999853210000                                  0              


Q ss_pred             --------------------------------CC--CCcCCCCceEEEeCCCCcCc----------HHHHHHHHhccCCe
Q 017842          271 --------------------------------RA--PRVFEPGFRIYVGNLPWEVD----------NARLEQVFSEHGKV  306 (365)
Q Consensus       271 --------------------------------~~--~~~~~~~~~lfV~nLp~~~t----------ee~L~~~F~~~G~V  306 (365)
                                                      ..  .....+..+|+|.||....+          .++|++.|++||.|
T Consensus       320 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v  399 (457)
T TIGR01622       320 ALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGV  399 (457)
T ss_pred             hhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCe
Confidence                                            00  00113456899999954433          37899999999999


Q ss_pred             EEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          307 VNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       307 ~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      +.|.|..    +.+.|++||+|.+.++|..|++.|||..|+||.|.|.|....
T Consensus       400 ~~v~v~~----~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       400 VHIYVDT----KNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVND  448 (457)
T ss_pred             eEEEEeC----CCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHH
Confidence            9999863    345899999999999999999999999999999999997643

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.89  E-value=3.6e-23  Score=185.51  Aligned_cols=151  Identities=28%  Similarity=0.569  Sum_probs=139.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      +|||||||-.+++.+|+.+|++||+|..+.                          |+        +.||||...++.++
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECD--------------------------Iv--------KNYgFVHiEdktaa   49 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECD--------------------------IV--------KNYGFVHIEDKTAA   49 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeee--------------------------ee--------cccceEEeeccccc
Confidence            699999999999999999999999999887                          33        56999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCc
Q 017842          241 EKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRS  320 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~  320 (365)
                      ..||..|+|..|+|..|.|..++.+.          ...++|+|+||.+.++..+|+..|++||.|..|.|+        
T Consensus        50 edairNLhgYtLhg~nInVeaSksKs----------k~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv--------  111 (346)
T KOG0109|consen   50 EDAIRNLHGYTLHGVNINVEASKSKS----------KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV--------  111 (346)
T ss_pred             HHHHhhcccceecceEEEEEeccccC----------CCccccccCCCCccccCHHHhhhhcccCCceeeeee--------
Confidence            99999999999999999999887662          223489999999999999999999999999999999        


Q ss_pred             ceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccccCC
Q 017842          321 RGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRS  363 (365)
Q Consensus       321 kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~~~  363 (365)
                      ++|+||.|.-.++|..|++.|+|..+.|++++|+++.+|-+..
T Consensus       112 kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrta  154 (346)
T KOG0109|consen  112 KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTA  154 (346)
T ss_pred             cceeEEEEeeccchHHHHhcccccccccceeeeeeeccccccC
Confidence            4599999999999999999999999999999999999887653

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.88  E-value=9.8e-23  Score=187.51  Aligned_cols=175  Identities=19%  Similarity=0.392  Sum_probs=151.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      -++||||.+.+...++.|+..|..||+|.++.                          .-.+..|++.+|||||+|.-++
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSIn--------------------------MSWDp~T~kHKgFAFVEYEvPE  166 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSIN--------------------------MSWDPATGKHKGFAFVEYEVPE  166 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceee--------------------------cccccccccccceEEEEEeCcH
Confidence            45799999999999999999999999999988                          4456679999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCC---CcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAP---RVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR  315 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~---~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~  315 (365)
                      .|.-|++.+||..++||.|+|.+...-...+....   .....-++|||..+..++.+++|+.+|+.||.|.+|.+.+++
T Consensus       167 aAqLAlEqMNg~mlGGRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~p  246 (544)
T KOG0124|consen  167 AAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAP  246 (544)
T ss_pred             HHHHHHHHhccccccCccccccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccC
Confidence            99999999999999999999986543322111000   011223599999999999999999999999999999999999


Q ss_pred             CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          316 ETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       316 ~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      .++.+||||||+|.+.++...|+..||-..|+|..|||-.|--.
T Consensus       247 t~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTP  290 (544)
T KOG0124|consen  247 TGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTP  290 (544)
T ss_pred             CCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccCC
Confidence            99999999999999999999999999999999999999877643

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.86  E-value=7e-21  Score=183.78  Aligned_cols=153  Identities=29%  Similarity=0.478  Sum_probs=141.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      .||||   +++|+..|.++|+.+|++.+++                          ++++. +  +-|||||.|.++.+|
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~r--------------------------vc~d~-t--slgy~yvnf~~~~da   50 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIR--------------------------VCRDA-T--SLGYAYVNFQQPADA   50 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEE--------------------------EeecC-C--ccceEEEecCCHHHH
Confidence            68999   9999999999999999999988                          88888 6  999999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCc
Q 017842          241 EKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRS  320 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~  320 (365)
                      .+|+..+|...+.|++|++.|+.....             .|||.||+..++...|..+|+.||+|.+|++..+...  +
T Consensus        51 ~~A~~~~n~~~~~~~~~rim~s~rd~~-------------~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g--~  115 (369)
T KOG0123|consen   51 ERALDTMNFDVLKGKPIRIMWSQRDPS-------------LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG--S  115 (369)
T ss_pred             HHHHHHcCCcccCCcEEEeehhccCCc-------------eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC--c
Confidence            999999999999999999998764332             3999999999999999999999999999999999653  8


Q ss_pred             ceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccccc
Q 017842          321 RGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR  361 (365)
Q Consensus       321 kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~  361 (365)
                      +|| ||+|.+...|.+|+..|||..+.|++|.|.....+.-
T Consensus       116 kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen  116 KGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             eee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            999 9999999999999999999999999999988776543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.84  E-value=6.6e-21  Score=178.19  Aligned_cols=174  Identities=32%  Similarity=0.558  Sum_probs=156.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...+||||+|+|+++++.|+..|.+||.|..+.                          +.+++.+++++||+||+|.++
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~--------------------------vm~d~~t~rsrgFgfv~f~~~   58 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCV--------------------------VMRDPSTGRSRGFGFVTFATP   58 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEE--------------------------EeccCCCCCcccccceecCCC
Confidence            567999999999999999999999999999887                          888899999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRET  317 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~  317 (365)
                      +.+..++.. .-..|.|+.|.+..+.++.........  .....|||++||..+++++|+.+|..||.|..+.+..|..+
T Consensus        59 ~~v~~vl~~-~~h~~dgr~ve~k~av~r~~~~~~~~~--~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~  135 (311)
T KOG4205|consen   59 EGVDAVLNA-RTHKLDGRSVEPKRAVSREDQTKVGRH--LRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTT  135 (311)
T ss_pred             cchheeecc-cccccCCccccceeccCcccccccccc--cceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccc
Confidence            999888876 677899999999999888765433211  13458999999999999999999999999999999999999


Q ss_pred             CCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccccc
Q 017842          318 GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR  361 (365)
Q Consensus       318 ~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~  361 (365)
                      .+++||+||.|.+.+++.+++. ..-+.|+|+.+.|..|.++.-
T Consensus       136 ~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~  178 (311)
T KOG4205|consen  136 SRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEV  178 (311)
T ss_pred             cccccceeeEeccccccceecc-cceeeecCceeeEeeccchhh
Confidence            9999999999999999999998 688999999999999988753

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.83  E-value=5.8e-21  Score=184.66  Aligned_cols=180  Identities=27%  Similarity=0.475  Sum_probs=153.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      +....+|||+--|+...+..+|..||+.+|+|..|+                          ++.+..+++++|-|||+|
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVr--------------------------iI~Dr~s~rskgi~Yvef  228 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVR--------------------------IIGDRNSRRSKGIAYVEF  228 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeE--------------------------eeccccchhhcceeEEEE
Confidence            344578999999999999999999999999999988                          899999999999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCC-CC----C-CCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEE
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP-ER----A-PRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVN  308 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~-~~----~-~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~  308 (365)
                      .+.+.+-.||. |.|..+.|.+|.|.......... ..    . .....|..+||||||.+++++++|+.+|+.||.|..
T Consensus       229 ~D~~sVp~aia-LsGqrllg~pv~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~  307 (549)
T KOG0147|consen  229 CDEQSVPLAIA-LSGQRLLGVPVIVQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIEN  307 (549)
T ss_pred             ecccchhhHhh-hcCCcccCceeEecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCccccee
Confidence            99999998986 59999999999996542211110 00    0 111223334999999999999999999999999999


Q ss_pred             EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccccc
Q 017842          309 ARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR  361 (365)
Q Consensus       309 v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~  361 (365)
                      |.+.+|..+|.++|||||+|.+..+|.+|+.+|||..|.||.|+|.....+..
T Consensus       308 v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~  360 (549)
T KOG0147|consen  308 VQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVD  360 (549)
T ss_pred             eeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecc
Confidence            99999999999999999999999999999999999999999999987766543

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.80  E-value=7.4e-19  Score=169.77  Aligned_cols=168  Identities=24%  Similarity=0.435  Sum_probs=148.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHHH
Q 017842          162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAE  241 (365)
Q Consensus       162 vfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~  241 (365)
                      |||.||+.+++...|+++|+.||.|.+|+                          +.++. .| ++|| ||.|.++++|+
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~k--------------------------v~~~~-~g-~kg~-FV~f~~e~~a~  129 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCK--------------------------VATDE-NG-SKGY-FVQFESEESAK  129 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEE--------------------------EEEcC-CC-ceee-EEEeCCHHHHH
Confidence            99999999999999999999999999998                          44443 33 8999 99999999999


Q ss_pred             HHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcc
Q 017842          242 KAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSR  321 (365)
Q Consensus       242 ~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~k  321 (365)
                      +|+.++||..+.|+.|.|.....+..+..........-+.++|.|++...++..|..+|..+|.|..+.++.+.. ++++
T Consensus       130 ~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~-g~~~  208 (369)
T KOG0123|consen  130 KAIEKLNGMLLNGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSI-GKSK  208 (369)
T ss_pred             HHHHHhcCcccCCCeeEEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCC-CCCC
Confidence            999999999999999999988777665443332333345799999999999999999999999999999998854 6699


Q ss_pred             eEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          322 GFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       322 G~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      |||||.|.+.++|..|+..|++..+.|..+.|..+..+
T Consensus       209 ~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk  246 (369)
T KOG0123|consen  209 GFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKK  246 (369)
T ss_pred             CccceeecChhHHHHHHHhccCCcCCccceeecccccc
Confidence            99999999999999999999999999999999887763

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.80  E-value=7.8e-18  Score=170.33  Aligned_cols=81  Identities=17%  Similarity=0.433  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|+.||.|..++                          +.++..+++++|||||+|.+.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svr--------------------------l~~D~~tgksKGfGFVeFe~~  256 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQ--------------------------LARAPTGRGHKGYGFIEYNNL  256 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEE--------------------------EEecCCCCCcCCeEEEEECCH
Confidence            457999999999999999999999999999988                          778888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      ++|.+|+..|||..|+|+.|+|.++.+
T Consensus       257 e~A~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       257 QSQSEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             HHHHHHHHHhCCCeeCCeEEEEEecCC
Confidence            999999999999999999999987653

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.77  E-value=9.1e-18  Score=141.84  Aligned_cols=154  Identities=29%  Similarity=0.414  Sum_probs=130.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||||||.++.+++|.++|-+||.|..|.++.                             .....+||||+|.+.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~-----------------------------r~g~ppfafVeFEd~   55 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKN-----------------------------RPGPPPFAFVEFEDP   55 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEecc-----------------------------CCCCCCeeEEEecCc
Confidence            468999999999999999999999999998887431                             224578999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCC------------------CCCCcCCCCceEEEeCCCCcCcHHHHHHH
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPE------------------RAPRVFEPGFRIYVGNLPWEVDNARLEQV  299 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~------------------~~~~~~~~~~~lfV~nLp~~~tee~L~~~  299 (365)
                      .+|..||.--+|..++|.+|+|.++........                  +.+....+.++|.|.+||....+++|+.+
T Consensus        56 RDAeDAiygRdGYdydg~rLRVEfprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDH  135 (241)
T KOG0105|consen   56 RDAEDAIYGRDGYDYDGCRLRVEFPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDH  135 (241)
T ss_pred             cchhhhhhcccccccCcceEEEEeccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHH
Confidence            999999999899999999999998865432111                  11112234468999999999999999999


Q ss_pred             HhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 017842          300 FSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD  347 (365)
Q Consensus       300 F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~  347 (365)
                      ..+.|.|....+.+|       |++.|.|-..++..-|+..|+...+.
T Consensus       136 mReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  136 MREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             HHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            999999999999887       47999999999999999999988763

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.77  E-value=1.7e-18  Score=153.82  Aligned_cols=183  Identities=28%  Similarity=0.481  Sum_probs=151.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ..++++||||-|...-.+++++.+|..||.|.++.                          ++ .-..|.++|+|||.|.
T Consensus        16 g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~t--------------------------vl-rg~dg~sKGCAFVKf~   68 (371)
T KOG0146|consen   16 GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECT--------------------------VL-RGPDGNSKGCAFVKFS   68 (371)
T ss_pred             CccchhhhhhhhcccccHHHHHHHhcccCCcceeE--------------------------Ee-cCCCCCCCCceEEEec
Confidence            33678999999999999999999999999999986                          33 3347789999999999


Q ss_pred             CHHHHHHHHHHHccCcc-cC--eeEEEeecCCCCCC--------------------------------------------
Q 017842          236 TVEEAEKAVEMFHRYDI-DG--RLLTVNKAAPRGTQ--------------------------------------------  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~-~g--r~l~V~~a~~~~~~--------------------------------------------  268 (365)
                      +.-+|..||..|+|..- -|  -.|.|.++.....+                                            
T Consensus        69 s~~eAqaAI~aLHgSqTmpGASSSLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~  148 (371)
T KOG0146|consen   69 SHAEAQAAINALHGSQTMPGASSSLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVA  148 (371)
T ss_pred             cchHHHHHHHHhcccccCCCCccceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhc
Confidence            99999999999998543 33  45666555322100                                            


Q ss_pred             --------------------------------------------------------------------------------
Q 017842          269 --------------------------------------------------------------------------------  268 (365)
Q Consensus       269 --------------------------------------------------------------------------------  268 (365)
                                                                                                      
T Consensus       149 ~~~L~p~~~~~~~~mQ~~aA~~angl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng  228 (371)
T KOG0146|consen  149 GPYLSPMAAFAAAQMQQMAALNANGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANG  228 (371)
T ss_pred             ccccChhhhhHHHHHHHHHHHhhcccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcC
Confidence                                                                                            


Q ss_pred             ----CCC------------------------------------------CCCcCCCCceEEEeCCCCcCcHHHHHHHHhc
Q 017842          269 ----PER------------------------------------------APRVFEPGFRIYVGNLPWEVDNARLEQVFSE  302 (365)
Q Consensus       269 ----~~~------------------------------------------~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~  302 (365)
                          +..                                          -.+..+.+|.|||..||-+..+.+|-++|-.
T Consensus       229 ~~pypaQsp~va~~lq~a~~g~~~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~P  308 (371)
T KOG0146|consen  229 LHPYPAQSPTVADPLQQAYAGVQQYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLP  308 (371)
T ss_pred             CccCCCCCccccchhhhhhhhHHHHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhcc
Confidence                000                                          0001245789999999999999999999999


Q ss_pred             cCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccccCCCC
Q 017842          303 HGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF  365 (365)
Q Consensus       303 ~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~~~~~  365 (365)
                      ||.|++.++..|+.|+.+|.||||.|.+..++..||..|||..|+-++|+|++-++|.-.++|
T Consensus       309 FGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkdanRPY  371 (371)
T KOG0146|consen  309 FGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDANRPY  371 (371)
T ss_pred             ccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCccccCCCC
Confidence            999999999999999999999999999999999999999999999999999998877655543

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.75  E-value=7.7e-18  Score=158.52  Aligned_cols=82  Identities=28%  Similarity=0.537  Sum_probs=77.9

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      ..|||++||.+.-+.+|-..|..||.|...++..|+.+|.++.|+||.|.+..+|..||..|||..+++++|.|+...++
T Consensus       425 anlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~  504 (510)
T KOG0144|consen  425 ANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDR  504 (510)
T ss_pred             cceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeecc
Confidence            38999999999999999999999999999999999999999999999999999999999999999999999999987766


Q ss_pred             cc
Q 017842          360 QR  361 (365)
Q Consensus       360 ~~  361 (365)
                      -.
T Consensus       505 ~n  506 (510)
T KOG0144|consen  505 NN  506 (510)
T ss_pred             CC
Confidence            54

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.74  E-value=1.7e-17  Score=140.23  Aligned_cols=85  Identities=47%  Similarity=0.852  Sum_probs=80.6

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ...++|||+|||+.+++++|+++|..||.|..|+|+.++.+++++|||||+|.+.++|..||..||+..|.|++|+|.++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            34569999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 017842          357 EDRQR  361 (365)
Q Consensus       357 ~~~~~  361 (365)
                      ..++.
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            87764

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.74  E-value=1.3e-16  Score=146.62  Aligned_cols=185  Identities=19%  Similarity=0.350  Sum_probs=143.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .+..+..|||.|||.++|-+++..+|++||-|..--     -.+             ...+++.++ ..|..+|-|.+.|
T Consensus       130 ~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~-----~t~-------------epk~KlYrd-~~G~lKGDaLc~y  190 (382)
T KOG1548|consen  130 EPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDP-----QTG-------------EPKVKLYRD-NQGKLKGDALCCY  190 (382)
T ss_pred             ccccCceEEecCCCCcccHHHHHHHHHhcceEeccC-----CCC-------------CeeEEEEec-CCCCccCceEEEe
Confidence            355577799999999999999999999999764310     000             111224444 4599999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCC-----------------------------C-CCCCcCCCCceEEE
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP-----------------------------E-RAPRVFEPGFRIYV  284 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~-----------------------------~-~~~~~~~~~~~lfV  284 (365)
                      --.+++.-|+..|++..|.|+.|+|..|.......                             . ..++.....++|.+
T Consensus       191 ~K~ESVeLA~~ilDe~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~  270 (382)
T KOG1548|consen  191 IKRESVELAIKILDEDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVIL  270 (382)
T ss_pred             ecccHHHHHHHHhCcccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEe
Confidence            99999999999999999999999998775321100                             0 01223344569999


Q ss_pred             eCCC----CcCc-------HHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          285 GNLP----WEVD-------NARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       285 ~nLp----~~~t-------ee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      +||-    +..+       .++|.+-|++||.|..|.|. +   +.+.|.+-|.|.+...|..|++.|+|+.|.||+|..
T Consensus       271 kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~-d---~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A  346 (382)
T KOG1548|consen  271 KNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVY-D---RHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTA  346 (382)
T ss_pred             eecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEe-c---cCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEE
Confidence            9993    2222       46788889999999999775 3   467999999999999999999999999999999999


Q ss_pred             EEccccccC
Q 017842          354 NVAEDRQRR  362 (365)
Q Consensus       354 ~~a~~~~~~  362 (365)
                      +....+.+.
T Consensus       347 ~i~DG~t~~  355 (382)
T KOG1548|consen  347 SIWDGKTKF  355 (382)
T ss_pred             EEeCCccee
Confidence            988776653

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.73  E-value=1.3e-16  Score=139.64  Aligned_cols=166  Identities=20%  Similarity=0.378  Sum_probs=140.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----HHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEE
Q 017842          158 EDAKLFVGNLPYDVDSEKLAM----LFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVT  233 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~----~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~  233 (365)
                      +..||||.||+-.+..++|+.    +|++||.|..|.                             -..+.+.+|.|||+
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~-----------------------------a~kt~KmRGQA~Vv   58 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDIS-----------------------------AFKTPKMRGQAFVV   58 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEE-----------------------------ecCCCCccCceEEE
Confidence            345999999999999988877    999999987664                             12467889999999


Q ss_pred             eCCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCC----------------------------C-------------
Q 017842          234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER----------------------------A-------------  272 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~----------------------------~-------------  272 (365)
                      |.+.+.|-.|+..|+|..|.|+.++|.++......-.+                            .             
T Consensus        59 Fk~~~~As~A~r~l~gfpFygK~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~  138 (221)
T KOG4206|consen   59 FKETEAASAALRALQGFPFYGKPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPF  138 (221)
T ss_pred             ecChhHHHHHHHHhcCCcccCchhheecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCc
Confidence            99999999999999999999999999988765421110                            0             


Q ss_pred             -CCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-Cee
Q 017842          273 -PRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD-GRA  350 (365)
Q Consensus       273 -~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~-gr~  350 (365)
                       .....+...||+.|||..++.+.|..+|..|.....||++...     .|.|||+|.+...|..|...|.|..+. ...
T Consensus       139 ~~~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~  213 (221)
T KOG4206|consen  139 LAQMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNT  213 (221)
T ss_pred             cccCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCce
Confidence             1124566799999999999999999999999999999998654     789999999999999999999998885 788


Q ss_pred             EEEEEcc
Q 017842          351 IRVNVAE  357 (365)
Q Consensus       351 l~V~~a~  357 (365)
                      +.|.+++
T Consensus       214 m~i~~a~  220 (221)
T KOG4206|consen  214 MQITFAK  220 (221)
T ss_pred             EEecccC
Confidence            8888875

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.70  E-value=5.3e-17  Score=146.58  Aligned_cols=82  Identities=28%  Similarity=0.455  Sum_probs=77.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +-+||||+.|++++++..|+..|+.||+|..|+                          ++.+..||.++|||||+|.++
T Consensus       100 Py~TLFv~RLnydT~EskLrreF~~YG~Ikrir--------------------------lV~d~vTgkskGYAFIeye~e  153 (335)
T KOG0113|consen  100 PYKTLFVARLNYDTSESKLRREFEKYGPIKRIR--------------------------LVRDKVTGKSKGYAFIEYEHE  153 (335)
T ss_pred             ccceeeeeeccccccHHHHHHHHHhcCcceeEE--------------------------EeeecccCCccceEEEEeccH
Confidence            688999999999999999999999999999988                          899999999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      .++..|.+..+|..|+|+.|.|++-.-+
T Consensus       154 rdm~~AYK~adG~~Idgrri~VDvERgR  181 (335)
T KOG0113|consen  154 RDMKAAYKDADGIKIDGRRILVDVERGR  181 (335)
T ss_pred             HHHHHHHHhccCceecCcEEEEEecccc
Confidence            9999999999999999999999876543

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.70  E-value=9.6e-17  Score=155.63  Aligned_cols=167  Identities=29%  Similarity=0.486  Sum_probs=133.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      +.||||||-+++++..|+..|+.||.|+.|.                          +..+..+|+++|||||+|.+.+.
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~--------------------------l~~d~~tG~skgfGfi~f~~~~~  332 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQ--------------------------LTKDSETGRSKGFGFITFVNKED  332 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeee--------------------------eccccccccccCcceEEEecHHH
Confidence            3499999999999999999999999999887                          67777899999999999999999


Q ss_pred             HHHHHHHHccCcccCeeEEEeecCCCCCCCCC------------------------------------------------
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER------------------------------------------------  271 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~------------------------------------------------  271 (365)
                      |.+|+..|||..+-|+.|+|.....+......                                                
T Consensus       333 ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~  412 (549)
T KOG0147|consen  333 ARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLL  412 (549)
T ss_pred             HHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhc
Confidence            99999999999999999999654322110000                                                


Q ss_pred             ----------------C-------CCcCCCCceEEEeCC--CCcCc--------HHHHHHHHhccCCeEEEEEEeeCCCC
Q 017842          272 ----------------A-------PRVFEPGFRIYVGNL--PWEVD--------NARLEQVFSEHGKVVNARVVYDRETG  318 (365)
Q Consensus       272 ----------------~-------~~~~~~~~~lfV~nL--p~~~t--------ee~L~~~F~~~G~V~~v~i~~d~~~~  318 (365)
                                      .       +....+.-++.+.|+  |...|        .+++.+-|.+||.|..|.+....   
T Consensus       413 ~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns---  489 (549)
T KOG0147|consen  413 AKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNS---  489 (549)
T ss_pred             cccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCC---
Confidence                            0       000022335556666  22222        37788999999999999886442   


Q ss_pred             CcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          319 RSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       319 ~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                        -|+.||.|.+.+.|..|+.+|||.+|.||-|.+.|-.
T Consensus       490 --~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  490 --AGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLP  526 (549)
T ss_pred             --CceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEee
Confidence              4899999999999999999999999999999998854

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.68  E-value=1.1e-15  Score=146.50  Aligned_cols=168  Identities=20%  Similarity=0.302  Sum_probs=135.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...-|-+++|||.+|+++|.+||+.|+ |++                            +++.+.+|+..|-|||+|.+.
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~----------------------------~~~~r~~Gr~sGeA~Ve~~se   59 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IEN----------------------------LEIPRRNGRPSGEAYVEFTSE   59 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeE----------------------------EEEeccCCCcCcceEEEeech
Confidence            456789999999999999999999986 444                            444556899999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCC---CCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEE-EEEEe
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER---APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVN-ARVVY  313 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~---~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~-v~i~~  313 (365)
                      +++++|+++ +...+..|.|.|-.+......-..   .+....+-..|.+++|||.||+++|.++|+..-.|.. +.++.
T Consensus        60 edv~~Alkk-dR~~mg~RYIEVf~~~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~  138 (510)
T KOG4211|consen   60 EDVEKALKK-DRESMGHRYIEVFTAGGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPM  138 (510)
T ss_pred             HHHHHHHHh-hHHHhCCceEEEEccCCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeec
Confidence            999999998 999999999999877554432111   1111133458999999999999999999998865555 33455


Q ss_pred             eCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          314 DRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       314 d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      + ..+++.|=|||+|.+.+.|++||. -|...|+-|-|.|-.+.
T Consensus       139 d-~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  139 D-QRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRSS  180 (510)
T ss_pred             c-CCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehhH
Confidence            5 457799999999999999999999 58888988988886543

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.65  E-value=5.9e-15  Score=139.27  Aligned_cols=171  Identities=33%  Similarity=0.560  Sum_probs=141.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHH-ccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFE-KAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~-~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ..|.|||.|||+++.+.+|+++|. +.|.|+.|.                          ++.+ ..++++|+|.|+|++
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yve--------------------------Ll~D-~~GK~rGcavVEFk~   95 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVE--------------------------LLFD-ESGKARGCAVVEFKD   95 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeee--------------------------eecc-cCCCcCCceEEEeeC
Confidence            466799999999999999999995 689999987                          4444 488999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCC--------------------------------------------CCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ--------------------------------------------PERA  272 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~--------------------------------------------~~~~  272 (365)
                      +|.+++|++.||.+.+.||.|.|.........                                            ..+.
T Consensus        96 ~E~~qKa~E~lnk~~~~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~  175 (608)
T KOG4212|consen   96 PENVQKALEKLNKYEVNGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRL  175 (608)
T ss_pred             HHHHHHHHHHhhhccccCceEEEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCccccccc
Confidence            99999999999999999999999644321000                                            0000


Q ss_pred             CC---------------------------------cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCC
Q 017842          273 PR---------------------------------VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR  319 (365)
Q Consensus       273 ~~---------------------------------~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~  319 (365)
                      .+                                 ..+-..++||.||.+.+....|++.|.-.|.|..|-+-.|+. |.
T Consensus       176 sr~~~t~t~~~~~~~~~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKe-G~  254 (608)
T KOG4212|consen  176 SRRNNTNTMSNDYNNSSNYNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKE-GN  254 (608)
T ss_pred             ccccCccccccccccchhhhcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccc-cc
Confidence            00                                 012235899999999999999999999999999999988865 68


Q ss_pred             cceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          320 SRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       320 ~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ++|||.|+|.+.-.|-.||..|++.-+..++..++..
T Consensus       255 s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~Rl~  291 (608)
T KOG4212|consen  255 SRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVRLD  291 (608)
T ss_pred             cCCeeEEEecchHHHHHHHHhhccCCCccccceeecc
Confidence            9999999999999999999999988888888777763

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.64  E-value=1.8e-15  Score=127.87  Aligned_cols=84  Identities=38%  Similarity=0.589  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|.+||.|..+.                          ++.+..+++++|||||+|.+.
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~--------------------------i~~d~~tg~~kGfaFV~F~~~   86 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAK--------------------------VIVDRETGRSRGFGFVNFNDE   86 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEE--------------------------EEecCCCCCcceEEEEEECCH
Confidence            467899999999999999999999999999988                          788888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|++|+..||+..|+|+.|+|.++..+..
T Consensus        87 e~A~~Al~~lng~~i~Gr~l~V~~a~~~~~  116 (144)
T PLN03134         87 GAATAAISEMDGKELNGRHIRVNPANDRPS  116 (144)
T ss_pred             HHHHHHHHHcCCCEECCEEEEEEeCCcCCC
Confidence            999999999999999999999999876544

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.64  E-value=2.3e-15  Score=149.73  Aligned_cols=171  Identities=25%  Similarity=0.342  Sum_probs=136.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...+.++|+|||..+..++|...|..||.|..+.+                            +    ...--|+|+|.+
T Consensus       383 rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvll----------------------------p----~~G~~aiv~fl~  430 (725)
T KOG0110|consen  383 RSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLL----------------------------P----PGGTGAIVEFLN  430 (725)
T ss_pred             hhcceeeeccCccccccHHHHHHhhcccccceeec----------------------------C----cccceeeeeecC
Confidence            35678999999999999999999999999987532                            1    122348999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCC-------------CC-------C-------CC---------------C
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ-------------PE-------R-------AP---------------R  274 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~-------------~~-------~-------~~---------------~  274 (365)
                      ...|.+|+..|....+...++++.++....-.             ..       +       ..               .
T Consensus       431 p~eAr~Afrklaysr~k~~plyle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~  510 (725)
T KOG0110|consen  431 PLEARKAFRKLAYSRFKSAPLYLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAE  510 (725)
T ss_pred             ccchHHHHHHhchhhhccCccccccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhh
Confidence            99999999999999999888888655311100             00       0       00               0


Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCC---CCcceEEEEEecCHHHHHHHHHHhCCCccCCeeE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRET---GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAI  351 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~---~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l  351 (365)
                      .....++|||.||+|..|.+.|..+|...|.|..+.|...+..   -.+.|||||+|.+.++|..|++.|+|+.++|+.|
T Consensus       511 ~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l  590 (725)
T KOG0110|consen  511 DEETETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKL  590 (725)
T ss_pred             ccccchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceE
Confidence            0112235999999999999999999999999999998765432   1245999999999999999999999999999999


Q ss_pred             EEEEcccc
Q 017842          352 RVNVAEDR  359 (365)
Q Consensus       352 ~V~~a~~~  359 (365)
                      .|+++..+
T Consensus       591 ~lk~S~~k  598 (725)
T KOG0110|consen  591 ELKISENK  598 (725)
T ss_pred             EEEeccCc
Confidence            99999833

>PF00076 RRM_1: RNA recognition motif

Probab=99.62  E-value=3.4e-15  Score=109.71  Aligned_cols=70  Identities=39%  Similarity=0.797  Sum_probs=67.7

Q ss_pred             EEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEE
Q 017842          282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR  352 (365)
Q Consensus       282 lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~  352 (365)
                      |||+|||..+++++|+++|+.||.|..+.+..+ .++..+|||||+|.+.++|.+|+..|+|..++|++||
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999998 6789999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.61  E-value=8.9e-15  Score=134.60  Aligned_cols=162  Identities=33%  Similarity=0.565  Sum_probs=126.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||||||+++++++|.++|..||.|..+.                          +..++.++.++|||||.|.+.+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~--------------------------~~~d~~~~~~~g~~~v~f~~~~  168 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVR--------------------------LVRDRETGKSRGFAFVEFESEE  168 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEE--------------------------eeeccccCccCceEEEEecCHH
Confidence            68999999999999999999999999998777                          6777789999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCC----CCCCCC------------CCCCcCCCCceEEEeCCCCcCcHHHHHHHHhc
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAP----RGTQPE------------RAPRVFEPGFRIYVGNLPWEVDNARLEQVFSE  302 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~----~~~~~~------------~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~  302 (365)
                      +|..|+..++|..|.|+.|.|.++..    +.....            ...........++++|++..++...+...|..
T Consensus       169 ~~~~a~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  248 (306)
T COG0724         169 SAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKS  248 (306)
T ss_pred             HHHHHHHHcCCCeECCceeEeeccccccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccc
Confidence            99999999999999999999999542    222210            01122344568999999999999999999999


Q ss_pred             cCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 017842          303 HGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL  346 (365)
Q Consensus       303 ~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l  346 (365)
                      +|.+..+.+..........++.++.+.....+..++........
T Consensus       249 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  292 (306)
T COG0724         249 RGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKKKI  292 (306)
T ss_pred             cccceeeeccCCCCCcccccccccchhHHHhhhhhhccccceee
Confidence            99997777766655444555555555555555555554333333

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.60  E-value=2e-15  Score=133.38  Aligned_cols=154  Identities=29%  Similarity=0.508  Sum_probs=130.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      ..||||+||+.+.+.+|..||..||.+..+.+                                  -.|||||+|.+..+
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~m----------------------------------k~gf~fv~fed~rd   47 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADM----------------------------------KNGFGFVEFEDPRD   47 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhcccccccee----------------------------------ecccceeccCchhh
Confidence            36999999999999999999999999988763                                  36899999999999


Q ss_pred             HHHHHHHHccCcccCeeEEEeecCCCCCCC------CC------CCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeE
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKAAPRGTQP------ER------APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVV  307 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a~~~~~~~------~~------~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~  307 (365)
                      |..|+..|||..|.|-.+.|.++.......      .+      ........++++|.|+...+.+++|..+|..+|.+.
T Consensus        48 a~Dav~~l~~~~l~~e~~vve~~r~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~  127 (216)
T KOG0106|consen   48 ADDAVHDLDGKELCGERLVVEHARGKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVT  127 (216)
T ss_pred             hhcccchhcCceecceeeeeecccccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCc
Confidence            999999999999999888888887532111      00      111234457899999999999999999999999996


Q ss_pred             EEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          308 NARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       308 ~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      +..+        ..+++||+|....+|.+|+..|+|..+.|++|.+.+
T Consensus       128 ~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  128 YVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             hhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            6655        266899999999999999999999999999999944

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.59  E-value=4e-14  Score=123.22  Aligned_cols=161  Identities=20%  Similarity=0.259  Sum_probs=121.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ..-|||||.+||.++...+|+.+|..|---+...+++                         +.+.....+.+||++|.+
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~-------------------------Tsk~~~~~~pvaFatF~s   86 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKY-------------------------TSKGDQVCKPVAFATFTS   86 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeee-------------------------ccCCCccccceEEEEecc
Confidence            3578999999999999999999999875555554432                         122222345899999999


Q ss_pred             HHHHHHHHHHHccCccc---CeeEEEeecCCCCCCCCCCCC---------------------------------------
Q 017842          237 VEEAEKAVEMFHRYDID---GRLLTVNKAAPRGTQPERAPR---------------------------------------  274 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~---gr~l~V~~a~~~~~~~~~~~~---------------------------------------  274 (365)
                      ...|..|+.+|||+.|+   +..|++..++.......+...                                       
T Consensus        87 ~q~A~aamnaLNGvrFDpE~~stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~  166 (284)
T KOG1457|consen   87 HQFALAAMNALNGVRFDPETGSTLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEP  166 (284)
T ss_pred             hHHHHHHHHHhcCeeeccccCceeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCc
Confidence            99999999999999994   678888776543221100000                                       


Q ss_pred             ---------------------------------------cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeC
Q 017842          275 ---------------------------------------VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR  315 (365)
Q Consensus       275 ---------------------------------------~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~  315 (365)
                                                             ....+.+|||-||..++++++|+.+|+.|-....++|... 
T Consensus       167 ~~a~al~~~~~t~~~~l~a~~~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~-  245 (284)
T KOG1457|consen  167 GNADALKENDTTKSEALSAPDSKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR-  245 (284)
T ss_pred             cccccCCCccccchhhhhhhhhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC-
Confidence                                                   0011348999999999999999999999988777777522 


Q ss_pred             CCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 017842          316 ETGRSRGFGFVTMSSETELNDAIAALDGQNL  346 (365)
Q Consensus       316 ~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l  346 (365)
                       +|  .-.||+.|.+.+.|..||..|.|..|
T Consensus       246 -~g--~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  246 -GG--MPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             -CC--cceEeecHHHHHHHHHHHHHhhccee
Confidence             23  34799999999999999999988766

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.59  E-value=8.4e-15  Score=140.84  Aligned_cols=85  Identities=27%  Similarity=0.467  Sum_probs=80.1

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      .....++|||+|||+++|+++|+++|+.||.|+.|+|++|..+++++|||||+|.+.++|.+||..||+..+.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            34456799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Ecccc
Q 017842          355 VAEDR  359 (365)
Q Consensus       355 ~a~~~  359 (365)
                      |+++.
T Consensus       183 ~a~p~  187 (346)
T TIGR01659       183 YARPG  187 (346)
T ss_pred             ccccc
Confidence            98754

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.57  E-value=6.7e-15  Score=117.48  Aligned_cols=78  Identities=29%  Similarity=0.503  Sum_probs=75.2

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .++|||+||.+.+++++|+++|+.+|.|..|.+-.|+.+..+.|||||+|.+.++|+.|++.++|..|..|.|+|.|.
T Consensus        36 S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   36 SCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             cceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            359999999999999999999999999999999999999999999999999999999999999999999999999874

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.54  E-value=1.5e-14  Score=127.11  Aligned_cols=78  Identities=36%  Similarity=0.648  Sum_probs=73.0

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      ++||||||+|.+..+.|+++|+.||+|+...|+.|+.+|++||||||+|.+.++|.+|++ --+-.|+||+..+.+|.-
T Consensus        13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~-dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACK-DPNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhc-CCCCcccccccccchhhh
Confidence            489999999999999999999999999999999999999999999999999999999999 356689999999988763

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.54  E-value=4.5e-14  Score=104.24  Aligned_cols=70  Identities=39%  Similarity=0.761  Sum_probs=65.3

Q ss_pred             EEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEE
Q 017842          282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR  352 (365)
Q Consensus       282 lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~  352 (365)
                      |||+|||+.+++++|+++|+.||.|..+++.+++. +.++|+|||+|.+.++|.+|+..++|..++||+|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999977 89999999999999999999999999999999985

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.53  E-value=3.2e-14  Score=125.55  Aligned_cols=83  Identities=31%  Similarity=0.488  Sum_probs=79.5

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|.|.||+.++++.+|+++|..||.|..|.|.+|+.||.+||||||.|.+.++|.+||..|||.-++.-.|+|.|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            34589999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 017842          358 DRQ  360 (365)
Q Consensus       358 ~~~  360 (365)
                      ++.
T Consensus       268 P~~  270 (270)
T KOG0122|consen  268 PSN  270 (270)
T ss_pred             CCC
Confidence            863

>PF00076 RRM_1: RNA recognition motif

Probab=99.53  E-value=4.7e-14  Score=103.56  Aligned_cols=70  Identities=40%  Similarity=0.697  Sum_probs=64.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHHH
Q 017842          162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAE  241 (365)
Q Consensus       162 vfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~  241 (365)
                      |||+|||.++++++|+.+|++||.|..+.                          +..+ ..++.+|+|||+|.+.++|.
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~--------------------------~~~~-~~~~~~~~a~V~F~~~~~a~   53 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIK--------------------------VMRN-SSGKSKGYAFVEFESEEDAE   53 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEE--------------------------EEEE-TTSSEEEEEEEEESSHHHHH
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccc--------------------------cccc-ccccccceEEEEEcCHHHHH
Confidence            79999999999999999999999998877                          4444 67889999999999999999


Q ss_pred             HHHHHHccCcccCeeEE
Q 017842          242 KAVEMFHRYDIDGRLLT  258 (365)
Q Consensus       242 ~Al~~lng~~~~gr~l~  258 (365)
                      +|+..|+|..++|+.|+
T Consensus        54 ~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen   54 KALEELNGKKINGRKIR   70 (70)
T ss_dssp             HHHHHHTTEEETTEEEE
T ss_pred             HHHHHcCCCEECccCcC
Confidence            99999999999999986

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.53  E-value=1.3e-14  Score=124.79  Aligned_cols=82  Identities=37%  Similarity=0.580  Sum_probs=78.6

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ....++|.|-||-+.++.++|+.+|++||.|-.|.|++|+.|+.++|||||.|....+|+.|+.+|+|.+|+|+.|+|++
T Consensus        10 v~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~   89 (256)
T KOG4207|consen   10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQM   89 (256)
T ss_pred             cccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehh
Confidence            34456999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q 017842          356 AE  357 (365)
Q Consensus       356 a~  357 (365)
                      |+
T Consensus        90 ar   91 (256)
T KOG4207|consen   90 AR   91 (256)
T ss_pred             hh
Confidence            87

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.53  E-value=7.3e-14  Score=141.41  Aligned_cols=118  Identities=23%  Similarity=0.365  Sum_probs=97.4

Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR  315 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~  315 (365)
                      -.++|.+|+..++|+.+........+..+.....   .......++|||+|||+++++++|+++|+.||.|..|+|++| 
T Consensus        18 ~~~~a~~a~~~~~gy~~~~~~g~r~~g~Pp~~~~---~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-   93 (578)
T TIGR01648        18 PDEAALKALLERTGYTLVQENGQRKYGGPPPGWS---GVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-   93 (578)
T ss_pred             ccHHHHHHHHHhhCccccccCCcccCCCCCCccc---CCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-
Confidence            3577888998889988877766666654443321   111234579999999999999999999999999999999999 


Q ss_pred             CCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CeeEEEEEcc
Q 017842          316 ETGRSRGFGFVTMSSETELNDAIAALDGQNLD-GRAIRVNVAE  357 (365)
Q Consensus       316 ~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~-gr~l~V~~a~  357 (365)
                      .+|+++|||||+|.+.++|.+||..||+..+. |+.|.|.++.
T Consensus        94 ~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~  136 (578)
T TIGR01648        94 FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV  136 (578)
T ss_pred             CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc
Confidence            78999999999999999999999999999885 7887776654

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.51  E-value=8.9e-14  Score=126.14  Aligned_cols=77  Identities=18%  Similarity=0.309  Sum_probs=71.5

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|+|+++..   .+|||||+|.+.++|..||. |+|..|.||.|+|.++.+
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            35999999999999999999999999999999998853   47999999999999999997 999999999999999975


Q ss_pred             c
Q 017842          359 R  359 (365)
Q Consensus       359 ~  359 (365)
                      -
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            4

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.50  E-value=4.3e-14  Score=124.26  Aligned_cols=80  Identities=38%  Similarity=0.540  Sum_probs=74.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      .-++||||+|+|.+..+.|+++|++||.|..+.                          |+.|+.+++++|||||+|.+.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eav--------------------------vitd~~t~rskGyGfVTf~d~   64 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAV--------------------------VITDKNTGRSKGYGFVTFRDA   64 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEE--------------------------EEeccCCccccceeeEEeecH
Confidence            356899999999999999999999999999987                          999999999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      ++|.+||+. .+-.|+||...|+++.-
T Consensus        65 ~aa~rAc~d-p~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   65 EAATRACKD-PNPIIDGRKANCNLASL   90 (247)
T ss_pred             HHHHHHhcC-CCCcccccccccchhhh
Confidence            999999997 66779999999988765

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.49  E-value=3.5e-15  Score=125.97  Aligned_cols=83  Identities=31%  Similarity=0.620  Sum_probs=78.7

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      .-|||||||+.+|+.+|-.+|+.||.|+.|.++||+.||+++||||+.|.+..+..-|+.+|||..|.||.|+|......
T Consensus        36 A~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~Y  115 (219)
T KOG0126|consen   36 AYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSNY  115 (219)
T ss_pred             eEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecccc
Confidence            37999999999999999999999999999999999999999999999999999999999999999999999999887765


Q ss_pred             ccC
Q 017842          360 QRR  362 (365)
Q Consensus       360 ~~~  362 (365)
                      ..+
T Consensus       116 k~p  118 (219)
T KOG0126|consen  116 KKP  118 (219)
T ss_pred             cCC
Confidence            554

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.47  E-value=1.5e-13  Score=125.77  Aligned_cols=81  Identities=35%  Similarity=0.644  Sum_probs=74.7

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|+|.||||...+-||+.+|.+||.|.+|.|+.+.  +-+||||||+|.+.++|.+|-..|||..+.||+|.|..|.
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            34599999999999999999999999999999999773  5579999999999999999999999999999999999987


Q ss_pred             ccc
Q 017842          358 DRQ  360 (365)
Q Consensus       358 ~~~  360 (365)
                      .|-
T Consensus       173 arV  175 (376)
T KOG0125|consen  173 ARV  175 (376)
T ss_pred             hhh
Confidence            653

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.47  E-value=1.3e-13  Score=123.21  Aligned_cols=102  Identities=36%  Similarity=0.638  Sum_probs=88.1

Q ss_pred             eEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHH
Q 017842          256 LLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELN  335 (365)
Q Consensus       256 ~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~  335 (365)
                      .|.|.++..+..+....   ...+.-+||+.|...++-+.|++.|.+||.|..++|+||..|+++||||||.|.++.+|+
T Consensus        42 e~~v~wa~~p~nQsk~t---~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAE  118 (321)
T KOG0148|consen   42 ELKVNWATAPGNQSKPT---SNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAE  118 (321)
T ss_pred             hhccccccCcccCCCCc---cccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHH
Confidence            56677766553222221   122557999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhCCCccCCeeEEEEEccccc
Q 017842          336 DAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       336 ~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      .||..|||..|++|.||-.||..|+
T Consensus       119 nAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen  119 NAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             HHHHHhCCeeeccceeeccccccCc
Confidence            9999999999999999999998765

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.47  E-value=1.7e-13  Score=115.35  Aligned_cols=78  Identities=33%  Similarity=0.586  Sum_probs=73.7

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+||+..+++.+|..+|..||.+..|.|.+.     +.|||||+|.+..+|..|+..|+|..|+|..|+|.++..
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            469999999999999999999999999999999875     489999999999999999999999999999999999988


Q ss_pred             ccc
Q 017842          359 RQR  361 (365)
Q Consensus       359 ~~~  361 (365)
                      +++
T Consensus        85 ~~r   87 (195)
T KOG0107|consen   85 RPR   87 (195)
T ss_pred             Ccc
Confidence            776

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.46  E-value=2.8e-13  Score=122.64  Aligned_cols=85  Identities=29%  Similarity=0.593  Sum_probs=80.3

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      +|-+||||+-|++++++..|+..|+.||.|+.|+|++|..||+++|||||+|...-+...|.+..+|.+|+|+.|.|.|-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            45569999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             ccccc
Q 017842          357 EDRQR  361 (365)
Q Consensus       357 ~~~~~  361 (365)
                      ..+..
T Consensus       179 RgRTv  183 (335)
T KOG0113|consen  179 RGRTV  183 (335)
T ss_pred             ccccc
Confidence            76654

>PLN03213 repressor of silencing 3; Provisional

Probab=99.46  E-value=2.1e-13  Score=130.64  Aligned_cols=78  Identities=27%  Similarity=0.463  Sum_probs=71.8

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCH--HHHHHHHHHhCCCccCCeeEEEEE
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE--TELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~--~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      .+.+||||||++.+++++|+.+|..||.|..|.|+|  .+|  ||||||+|.+.  .++.+||..|||..+.||.|+|.-
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            346999999999999999999999999999999994  456  99999999987  789999999999999999999999


Q ss_pred             cccc
Q 017842          356 AEDR  359 (365)
Q Consensus       356 a~~~  359 (365)
                      |++.
T Consensus        85 AKP~   88 (759)
T PLN03213         85 AKEH   88 (759)
T ss_pred             ccHH
Confidence            8764

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.45  E-value=3.3e-12  Score=123.71  Aligned_cols=160  Identities=19%  Similarity=0.343  Sum_probs=119.0

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCcc---ce
Q 017842          153 FVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSR---GF  229 (365)
Q Consensus       153 ~~~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---g~  229 (365)
                      ...+.-.++||||+||++++++.|...|..||.+.. .  |.-.                    .. .......+   ||
T Consensus       253 ~~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~V-d--WP~k--------------------~~-~~~~~ppkGs~~Y  308 (520)
T KOG0129|consen  253 YRSPRYSRKVFVGGLPWDITEAQINASFGQFGSVKV-D--WPGK--------------------AN-SRGRAPPKGSYGY  308 (520)
T ss_pred             CCccccccceeecCCCccccHHHHHhhcccccceEe-e--cCCC--------------------cc-ccccCCCCCcccE
Confidence            334456788999999999999999999999998742 1  1100                    00 00111233   59


Q ss_pred             EEEEeCCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCC---------------CCCCCcCCCCceEEEeCCCCcCcHH
Q 017842          230 GFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP---------------ERAPRVFEPGFRIYVGNLPWEVDNA  294 (365)
Q Consensus       230 afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~---------------~~~~~~~~~~~~lfV~nLp~~~tee  294 (365)
                      +|+.|.++.++...+..+.   .....+.++...+.-...               .......++..|||||+||..++.+
T Consensus       309 vflvFe~E~sV~~Ll~aC~---~~~~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~  385 (520)
T KOG0129|consen  309 VFLVFEDERSVQSLLSACS---EGEGNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAE  385 (520)
T ss_pred             EEEEecchHHHHHHHHHHh---hcccceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHH
Confidence            9999999999987766543   244444443333322111               1133456788899999999999999


Q ss_pred             HHHHHHh-ccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHH
Q 017842          295 RLEQVFS-EHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA  339 (365)
Q Consensus       295 ~L~~~F~-~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~  339 (365)
                      +|..+|. -||.|.++-|-.|++=+.++|-|-|+|.+.++-.+||.
T Consensus       386 eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  386 ELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             HHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHh
Confidence            9999998 79999999999998889999999999999999999998

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.44  E-value=3.4e-13  Score=132.56  Aligned_cols=175  Identities=17%  Similarity=0.266  Sum_probs=140.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ....+||||||...++..++++...||.+....                          ++.+..+|.++||||.+|-+.
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~--------------------------lv~d~~~g~skg~af~ey~dp  341 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFR--------------------------LVKDSATGNSKGFAFCEYCDP  341 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhhe--------------------------eecccccccccceeeeeeeCC
Confidence            456899999999999999999999999998876                          778888899999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCC----------------CCcCCCCceEEEeCCC--Cc--------C
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERA----------------PRVFEPGFRIYVGNLP--WE--------V  291 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~----------------~~~~~~~~~lfV~nLp--~~--------~  291 (365)
                      .....|+..|||..+.+..|.|..+..........                .....+...|++.|+=  -.        .
T Consensus       342 svtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~Eyee  421 (500)
T KOG0120|consen  342 SVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEE  421 (500)
T ss_pred             cchhhhhcccchhhhcCceeEeehhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHH
Confidence            99999999999999999999998776544322111                1122334456666651  11        1


Q ss_pred             cHHHHHHHHhccCCeEEEEEEeeCCC---CCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          292 DNARLEQVFSEHGKVVNARVVYDRET---GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       292 tee~L~~~F~~~G~V~~v~i~~d~~~---~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      --++++.-|.+||.|..|.|+++...   .-+.|-.||+|.+.+++++|+..|+|.+|.||.|...|...
T Consensus       422 IlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  422 ILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             HHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            12567777889999999999988222   34567789999999999999999999999999999998753

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.44  E-value=4.3e-13  Score=98.95  Aligned_cols=70  Identities=39%  Similarity=0.702  Sum_probs=62.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHHH
Q 017842          162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAE  241 (365)
Q Consensus       162 vfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~  241 (365)
                      |||+|||+++++++|.++|..||.|..++                          +..++. +..+|+|||+|.+.++|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~--------------------------~~~~~~-~~~~~~a~v~f~~~~~a~   53 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVR--------------------------LIKNKD-GQSRGFAFVEFSSEEDAK   53 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEE--------------------------EEESTT-SSEEEEEEEEESSHHHHH
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEE--------------------------EEeeec-cccCCEEEEEeCCHHHHH
Confidence            79999999999999999999999998877                          666666 889999999999999999


Q ss_pred             HHHHHHccCcccCeeEE
Q 017842          242 KAVEMFHRYDIDGRLLT  258 (365)
Q Consensus       242 ~Al~~lng~~~~gr~l~  258 (365)
                      +|+..++|..|+|++|+
T Consensus        54 ~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen   54 RALELLNGKEIDGRKLR   70 (70)
T ss_dssp             HHHHHHTTEEETTEEEE
T ss_pred             HHHHHCCCcEECCEEcC
Confidence            99999999999999985

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.44  E-value=1.6e-13  Score=116.10  Aligned_cols=81  Identities=38%  Similarity=0.561  Sum_probs=77.6

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      .+|||+||+..++++.||++|-..|.|..++|++|+.++..+|||||+|.+.++|.-|++.||...|.||+|+|..+...
T Consensus        10 ~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas~~   89 (203)
T KOG0131|consen   10 ATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKASAH   89 (203)
T ss_pred             ceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecccc
Confidence            49999999999999999999999999999999999999999999999999999999999999999999999999999844


Q ss_pred             c
Q 017842          360 Q  360 (365)
Q Consensus       360 ~  360 (365)
                      +
T Consensus        90 ~   90 (203)
T KOG0131|consen   90 Q   90 (203)
T ss_pred             c
Confidence            3

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.43  E-value=9.3e-13  Score=117.72  Aligned_cols=77  Identities=17%  Similarity=0.265  Sum_probs=71.2

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      .+++|||+||++.+|+++|+++|+.||.|..|+|+++.   ..+|||||+|.+..+|..|+. |+|..|.|++|.|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            45799999999999999999999999999999999884   456899999999999999997 99999999999999876


Q ss_pred             c
Q 017842          358 D  358 (365)
Q Consensus       358 ~  358 (365)
                      .
T Consensus        80 ~   80 (243)
T PLN03121         80 Q   80 (243)
T ss_pred             c
Confidence            4

>smart00362 RRM_2 RNA recognition motif

Probab=99.42  E-value=1e-12  Score=95.76  Aligned_cols=72  Identities=40%  Similarity=0.774  Sum_probs=67.8

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      +|+|+|||..++.++|+++|..||.|..+++.++.  +.++|+|||+|.+..+|..|+..|+|..+.|++|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999999876  7789999999999999999999999999999999874

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.42  E-value=6.6e-12  Score=118.10  Aligned_cols=165  Identities=25%  Similarity=0.396  Sum_probs=135.5

Q ss_pred             CCeEEEcCCCCC-CCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          159 DAKLFVGNLPYD-VDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       159 ~~tvfVgnLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...|.|.||... +|.+.|..+|+-||.|.+|.                          |.+++     +-.|.|.|.+.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVk--------------------------il~nk-----kd~ALIQmsd~  345 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVK--------------------------ILYNK-----KDNALIQMSDG  345 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEE--------------------------eeecC-----Ccceeeeecch
Confidence            578999999865 59999999999999999887                          55554     35699999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCC--------------------------C-CCcCCCCceEEEeCCCCc
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER--------------------------A-PRVFEPGFRIYVGNLPWE  290 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~--------------------------~-~~~~~~~~~lfV~nLp~~  290 (365)
                      ..|.-|+..|+|..+.|+.|+|.++++..-...+                          + ....+++.+|...|+|..
T Consensus       346 ~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~s  425 (492)
T KOG1190|consen  346 QQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPS  425 (492)
T ss_pred             hHHHHHHHHhhcceecCceEEEeeccCccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcc
Confidence            9999999999999999999999988766432111                          0 012356679999999999


Q ss_pred             CcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe-eEEEEEccc
Q 017842          291 VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGR-AIRVNVAED  358 (365)
Q Consensus       291 ~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr-~l~V~~a~~  358 (365)
                      +++++|+.+|...|.........    ++.+-+|++++.+.+.|..|+-.++++.+++. .|||+|++.
T Consensus       426 vsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  426 VSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             cchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            99999999999998765554432    23356999999999999999999999999765 999999875

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.41  E-value=1.3e-12  Score=118.69  Aligned_cols=78  Identities=19%  Similarity=0.248  Sum_probs=69.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||||||+.+++++|+++|+.||.|..++                          ++.+..   .+|||||+|.+.+
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~--------------------------I~~d~~---~~GfAFVtF~d~e   54 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVE--------------------------MQSENE---RSQIAYVTFKDPQ   54 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EeecCC---CCCEEEEEeCcHH
Confidence            57999999999999999999999999999988                          444432   4799999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      +|..|+. |||..|.|+.|+|.++....
T Consensus        55 aAe~All-LnG~~l~gr~V~Vt~a~~~~   81 (260)
T PLN03120         55 GAETALL-LSGATIVDQSVTITPAEDYQ   81 (260)
T ss_pred             HHHHHHH-hcCCeeCCceEEEEeccCCC
Confidence            9999995 79999999999999886543

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.40  E-value=1.6e-13  Score=119.24  Aligned_cols=82  Identities=33%  Similarity=0.550  Sum_probs=78.9

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++||||+|-..+++.-|...|-.||+|..|.|+.|.+++++||||||+|.-.++|..||..||+..|.||.|+|.||++
T Consensus        10 KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP   89 (298)
T KOG0111|consen   10 KRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKP   89 (298)
T ss_pred             ceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCC
Confidence            34999999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             cc
Q 017842          359 RQ  360 (365)
Q Consensus       359 ~~  360 (365)
                      ..
T Consensus        90 ~k   91 (298)
T KOG0111|consen   90 EK   91 (298)
T ss_pred             cc
Confidence            54

>smart00360 RRM RNA recognition motif

Probab=99.40  E-value=1.5e-12  Score=94.57  Aligned_cols=71  Identities=45%  Similarity=0.847  Sum_probs=67.4

Q ss_pred             EeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          284 VGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       284 V~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      |+|||..+++++|+.+|+.||.|..+.+..++.++.++|+|||+|.+.++|..|+..|++..+.|++|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57999999999999999999999999999988789999999999999999999999999999999999874

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.40  E-value=5.9e-13  Score=130.12  Aligned_cols=82  Identities=41%  Similarity=0.795  Sum_probs=79.8

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      +.|||||+|+.+++++|..+|+..|.|..++++.|+.+|+++||||++|.+.+.|..|++.|||..+.||+|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999877


Q ss_pred             cc
Q 017842          360 QR  361 (365)
Q Consensus       360 ~~  361 (365)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            65

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.39  E-value=1.5e-12  Score=115.00  Aligned_cols=82  Identities=29%  Similarity=0.493  Sum_probs=78.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +..+|-|.|||.++++.+|..+|..||.|..+.                          +.+++.||.++|||||.|.+.
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvy--------------------------lardK~TG~~kGFAFVtF~sR  241 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVY--------------------------LARDKETGLSKGFAFVTFESR  241 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeE--------------------------EEEccccCcccceEEEEEecH
Confidence            577899999999999999999999999999988                          899999999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      ++|.+||..|||+-++.-.|+|.++.|+
T Consensus       242 ddA~rAI~~LnG~gyd~LILrvEwskP~  269 (270)
T KOG0122|consen  242 DDAARAIADLNGYGYDNLILRVEWSKPS  269 (270)
T ss_pred             HHHHHHHHHccCcccceEEEEEEecCCC
Confidence            9999999999999999999999999875

>PLN03213 repressor of silencing 3; Provisional

Probab=99.38  E-value=1.5e-12  Score=124.93  Aligned_cols=78  Identities=26%  Similarity=0.430  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...+||||||++++++++|..+|..||.|..+.                          |+  +.+|  +|||||+|...
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVE--------------------------Ip--RETG--RGFAFVEMssd   58 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVE--------------------------FV--RTKG--RSFAYIDFSPS   58 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE--------------------------Ee--cccC--CceEEEEecCC
Confidence            356899999999999999999999999999988                          44  4566  99999999987


Q ss_pred             --HHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          238 --EEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       238 --e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                        .++.+||..|||..+.||.|+|..+.+.
T Consensus        59 ddaEeeKAISaLNGAEWKGR~LKVNKAKP~   88 (759)
T PLN03213         59 STNSLTKLFSTYNGCVWKGGRLRLEKAKEH   88 (759)
T ss_pred             cHHHHHHHHHHhcCCeecCceeEEeeccHH
Confidence              6899999999999999999999988654

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.38  E-value=1.8e-11  Score=115.97  Aligned_cols=72  Identities=35%  Similarity=0.576  Sum_probs=67.0

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      |+|||+|||+++|++.|+.-|..||.|.++.|.   +.|+++|  .|.|.+.++|++|+..|+|..+.||.|.|+|.
T Consensus       537 ~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  537 CQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            589999999999999999999999999999994   4577777  89999999999999999999999999999984

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.37  E-value=1.9e-11  Score=113.43  Aligned_cols=173  Identities=20%  Similarity=0.368  Sum_probs=135.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...+|||..+-.+.++.+|+..|+.||+|..|.                          +.+....+..+|||||+|.+.
T Consensus       209 ~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~--------------------------LAr~pt~~~HkGyGfiEy~n~  262 (544)
T KOG0124|consen  209 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQ--------------------------LARAPTGRGHKGYGFIEYNNL  262 (544)
T ss_pred             hhheEEeeecCCCccHHHHHHHHHhhcceeeEE--------------------------eeccCCCCCccceeeEEeccc
Confidence            467899999999999999999999999999887                          677777888999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCC-------------------------------------------------
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ-------------------------------------------------  268 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~-------------------------------------------------  268 (365)
                      .+...|+..+|-..++|..|+|-.+..+...                                                 
T Consensus       263 qs~~eAiasMNlFDLGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA  342 (544)
T KOG0124|consen  263 QSQSEAIASMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPA  342 (544)
T ss_pred             cchHHHhhhcchhhcccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCcc
Confidence            9999999999999999999999655322100                                                 


Q ss_pred             ---------------------------CCCC--CC---------------------------------------------
Q 017842          269 ---------------------------PERA--PR---------------------------------------------  274 (365)
Q Consensus       269 ---------------------------~~~~--~~---------------------------------------------  274 (365)
                                                 +.+.  +.                                             
T Consensus       343 ~~aa~p~~~l~qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~Q  422 (544)
T KOG0124|consen  343 PRAAQPLGTLPQAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQ  422 (544)
T ss_pred             ccccCCCCCccccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhh
Confidence                                       0000  00                                             


Q ss_pred             -------------------cCCCCceEEEeCC--CCcCcH---HHHHHHHhccCCeEEEEEEeeCCCCCc----ceEEEE
Q 017842          275 -------------------VFEPGFRIYVGNL--PWEVDN---ARLEQVFSEHGKVVNARVVYDRETGRS----RGFGFV  326 (365)
Q Consensus       275 -------------------~~~~~~~lfV~nL--p~~~te---e~L~~~F~~~G~V~~v~i~~d~~~~~~----kG~afV  326 (365)
                                         .....+.+.++|+  |.++++   .+|.+-|.+||.|..|.|...+.++.-    ----||
T Consensus       423 E~msI~G~sARhlvMqkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiVKIFV  502 (544)
T KOG0124|consen  423 EHMSISGSSARHLVMQKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIVKIFV  502 (544)
T ss_pred             hCccccCccHHHHHHHHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhheeee
Confidence                               0011236778898  555553   679999999999999988766543311    123699


Q ss_pred             EecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          327 TMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       327 ~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      +|.....+.+|..+|+|+.|+||++.....
T Consensus       503 efS~~~e~~rak~ALdGRfFgGr~VvAE~Y  532 (544)
T KOG0124|consen  503 EFSIASETHRAKQALDGRFFGGRKVVAEVY  532 (544)
T ss_pred             eechhhHHHHHHHhhccceecCceeehhhh
Confidence            999999999999999999999999976543

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.37  E-value=5.4e-12  Score=119.93  Aligned_cols=124  Identities=25%  Similarity=0.383  Sum_probs=95.5

Q ss_pred             EEEeCCHHHHHHHHHHHccCcccCeeEEEeecCCCCCC--CCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEE
Q 017842          231 FVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ--PERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVN  308 (365)
Q Consensus       231 fV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~--~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~  308 (365)
                      +-...+.++|.++|..-.|     ..|.|.....+-..  +...-.....++.||||.||.++.+++|.-+|++.|.|..
T Consensus        38 ~~~~~~~eaal~al~E~tg-----y~l~ve~gqrk~ggPpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~e  112 (506)
T KOG0117|consen   38 VAGVQSEEAALKALLERTG-----YTLVVENGQRKYGGPPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYE  112 (506)
T ss_pred             ccccccHHHHHHHHHHhcC-----ceEEEeccccccCCCCCcccCCCCCCCceEEecCCCccccchhhHHHHHhccceee
Confidence            3344457777777765343     44555433222111  1111122356789999999999999999999999999999


Q ss_pred             EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc-CCeeEEEEEcccc
Q 017842          309 ARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL-DGRAIRVNVAEDR  359 (365)
Q Consensus       309 v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l-~gr~l~V~~a~~~  359 (365)
                      +|+.+|+.+|.+||||||.|.+.+.|++|++.||+..| .|+.|.|..+..+
T Consensus       113 lRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan  164 (506)
T KOG0117|consen  113 LRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVAN  164 (506)
T ss_pred             EEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeec
Confidence            99999999999999999999999999999999999988 6899888776544

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.37  E-value=1.3e-12  Score=104.56  Aligned_cols=81  Identities=25%  Similarity=0.411  Sum_probs=74.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      .+.|||||||++-++++.|.++|++||.|..|.                          .-.++.+...=|||||+|-+.
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irrii--------------------------MGLdr~kktpCGFCFVeyy~~   88 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRII--------------------------MGLDRFKKTPCGFCFVEYYSR   88 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeE--------------------------eccccCCcCccceEEEEEecc
Confidence            578999999999999999999999999998876                          456677778889999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      ++|..|+..++|+.++.++|+|++-.-
T Consensus        89 ~dA~~AlryisgtrLddr~ir~D~D~G  115 (153)
T KOG0121|consen   89 DDAEDALRYISGTRLDDRPIRIDWDAG  115 (153)
T ss_pred             hhHHHHHHHhccCcccccceeeecccc
Confidence            999999999999999999999998653

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.36  E-value=4.7e-12  Score=97.62  Aligned_cols=82  Identities=32%  Similarity=0.560  Sum_probs=72.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .+...+.|||.|||+++|.+++.++|.+||.|..|+|-                             .+...+|.|||+|
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG-----------------------------~~k~TrGTAFVVY   64 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIG-----------------------------NTKETRGTAFVVY   64 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEec-----------------------------CccCcCceEEEEe
Confidence            34457899999999999999999999999999988742                             2446689999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      .+..+|++|+..|+|..+.++.|.|-+..+.
T Consensus        65 edi~dAk~A~dhlsg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   65 EDIFDAKKACDHLSGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             hHhhhHHHHHHHhcccccCCceEEEEecCHH
Confidence            9999999999999999999999999877654

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=99.36  E-value=1.6e-12  Score=121.55  Aligned_cols=178  Identities=21%  Similarity=0.306  Sum_probs=143.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...+.|+|++.+++.......++..+|......                          .........++|++++.|...
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~--------------------------~S~~~~~~~sk~~~s~~f~~k  140 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDAR--------------------------SSSLEDSLSSKGGLSVHFAGK  140 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccch--------------------------hhhhccccccccceeeccccH
Confidence            467999999999999999999999998765544                          444456778999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCC---CCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEee
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER---APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYD  314 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~---~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d  314 (365)
                      +.+..|+.+.-...+.++.+..............   ......+.+-.+|+||++.+++++|+.+|..+|.|..++++.+
T Consensus       141 s~~~~~l~~s~~~~~~~~~~~~dl~~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~  220 (285)
T KOG4210|consen  141 SQFFAALEESGSKVLDGNKGEKDLNTRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTD  220 (285)
T ss_pred             HHHHHHHHhhhccccccccccCcccccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCC
Confidence            9999999884445667777766555544421111   1122233334459999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccccC
Q 017842          315 RETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR  362 (365)
Q Consensus       315 ~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~~  362 (365)
                      ..++.++|||||.|.....+..++.. ....+.|+++++.+..+++..
T Consensus       221 ~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  267 (285)
T KOG4210|consen  221 EESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPKS  267 (285)
T ss_pred             CCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCccc
Confidence            99999999999999999999999986 888999999999999888654

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.35  E-value=8.6e-12  Score=91.33  Aligned_cols=74  Identities=42%  Similarity=0.803  Sum_probs=69.2

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      +|+|+|||..+++++|+++|..+|.|..+.+..+..+ .++|+|||+|.+.++|..|+..+++..+.|++|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999987654 7799999999999999999999999999999999875

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.35  E-value=4.9e-12  Score=116.27  Aligned_cols=79  Identities=44%  Similarity=0.807  Sum_probs=76.6

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      .++|||+|||+.+++++|+.+|..||.|..+++..++.+++++|||||.|.+..+|..|+..++|..|.|++|+|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            5799999999999999999999999999999999999899999999999999999999999999999999999999965

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.34  E-value=6.4e-12  Score=96.90  Aligned_cols=77  Identities=26%  Similarity=0.438  Sum_probs=71.2

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      +.-|||+|||+.+|.++..++|.+||.|..|||-..+.|   +|-|||.|.+..+|.+|+..|+|..+.+|.|.|-|..+
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            347999999999999999999999999999999866554   89999999999999999999999999999999998754

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.32  E-value=7.7e-12  Score=114.74  Aligned_cols=81  Identities=37%  Similarity=0.618  Sum_probs=73.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|+|.|||+...+.+|+..|.+||+|..|+                          |+.+  ...+||||||+|.+.
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVE--------------------------IIfN--ERGSKGFGFVTmen~  146 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVE--------------------------IIFN--ERGSKGFGFVTMENP  146 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEE--------------------------EEec--cCCCCccceEEecCh
Confidence            356899999999999999999999999999998                          4444  335899999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ++|++|-..|+|+.|.||+|.|+.+..+-
T Consensus       147 ~dadRARa~LHgt~VEGRkIEVn~ATarV  175 (376)
T KOG0125|consen  147 ADADRARAELHGTVVEGRKIEVNNATARV  175 (376)
T ss_pred             hhHHHHHHHhhcceeeceEEEEeccchhh
Confidence            99999999999999999999999988763

>smart00362 RRM_2 RNA recognition motif

Probab=99.30  E-value=1.9e-11  Score=88.95  Aligned_cols=72  Identities=43%  Similarity=0.699  Sum_probs=64.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      +|||+|||..++..+|+.+|..||.|..+.                          +..+.  +.++|+|||+|.+.+.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~--------------------------~~~~~--~~~~~~~~v~f~~~~~a   52 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVK--------------------------IPKDT--GKSKGFAFVEFESEEDA   52 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEE--------------------------EecCC--CCCCceEEEEeCCHHHH
Confidence            589999999999999999999999998876                          33333  67889999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEe
Q 017842          241 EKAVEMFHRYDIDGRLLTVN  260 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~  260 (365)
                      .+|+..++|..+.|+.|+|.
T Consensus        53 ~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362       53 EKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             HHHHHHhCCcEECCEEEeeC
Confidence            99999999999999999873

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.29  E-value=5.8e-11  Score=111.82  Aligned_cols=165  Identities=21%  Similarity=0.303  Sum_probs=127.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccce-EEEEeCC
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGF-GFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~-afV~f~~  236 (365)
                      .--.++|+|+-+-++-+-|+.+|++||.|..|.                            +-  + ++.|| |.|.|.+
T Consensus       149 ~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIi----------------------------TF--~-Knn~FQALvQy~d  197 (492)
T KOG1190|consen  149 PVLRTIIENMFYPVSLDVLHQVFSKFGFVLKII----------------------------TF--T-KNNGFQALVQYTD  197 (492)
T ss_pred             eeEEEEeccceeeeEHHHHHHHHhhcceeEEEE----------------------------EE--e-cccchhhhhhccc
Confidence            344689999999999999999999999987642                            11  1 23344 8999999


Q ss_pred             HHHHHHHHHHHccCcccC--eeEEEeecCCCC----------CC--------C------------------------C--
Q 017842          237 VEEAEKAVEMFHRYDIDG--RLLTVNKAAPRG----------TQ--------P------------------------E--  270 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~g--r~l~V~~a~~~~----------~~--------~------------------------~--  270 (365)
                      ...|..|...|+|..|-.  ..|++++++...          ..        .                        .  
T Consensus       198 ~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~ai  277 (492)
T KOG1190|consen  198 AVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAI  277 (492)
T ss_pred             hhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccC
Confidence            999999999999988833  556665543211          00        0                        0  


Q ss_pred             ---------CCCCcCCC--CceEEEeCC-CCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHH
Q 017842          271 ---------RAPRVFEP--GFRIYVGNL-PWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI  338 (365)
Q Consensus       271 ---------~~~~~~~~--~~~lfV~nL-p~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al  338 (365)
                               .......+  .+.|-|.|| +..+|.+-|..+|.-||+|..|.|.+++.     --|+|+|.+...|.-|+
T Consensus       278 p~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~  352 (492)
T KOG1190|consen  278 PSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAM  352 (492)
T ss_pred             CccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHH
Confidence                     00001111  357888888 56799999999999999999999998753     46999999999999999


Q ss_pred             HHhCCCccCCeeEEEEEccc
Q 017842          339 AALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       339 ~~l~~~~l~gr~l~V~~a~~  358 (365)
                      ..|+|..|.|++|||.+++-
T Consensus       353 ~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  353 EHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             HHhhcceecCceEEEeeccC
Confidence            99999999999999999873

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.29  E-value=9.8e-12  Score=100.33  Aligned_cols=89  Identities=26%  Similarity=0.432  Sum_probs=82.4

Q ss_pred             CCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeE
Q 017842          272 APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAI  351 (365)
Q Consensus       272 ~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l  351 (365)
                      .|+....+..|||.|+....|+++|...|..||.|.++.+-.|+.||..+|||+|+|.+...|++|+..|||..|-|.+|
T Consensus        65 gPqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v  144 (170)
T KOG0130|consen   65 GPQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNV  144 (170)
T ss_pred             CCccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCce
Confidence            34455567799999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEccccc
Q 017842          352 RVNVAEDRQ  360 (365)
Q Consensus       352 ~V~~a~~~~  360 (365)
                      .|.||--+.
T Consensus       145 ~VDw~Fv~g  153 (170)
T KOG0130|consen  145 SVDWCFVKG  153 (170)
T ss_pred             eEEEEEecC
Confidence            999997544

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.28  E-value=1.7e-11  Score=109.73  Aligned_cols=78  Identities=18%  Similarity=0.181  Sum_probs=68.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+||++.+|+++|++||+.||+|..++                          ++.+   +..+|+|||+|.++
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~--------------------------I~~D---~et~gfAfVtF~d~   54 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVE--------------------------IIRS---GEYACTAYVTFKDA   54 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EecC---CCcceEEEEEECCH
Confidence            467999999999999999999999999999988                          5555   35568999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      ++|..|+. |+|..|.|+.|.|..+...
T Consensus        55 ~aaetAll-LnGa~l~d~~I~It~~~~y   81 (243)
T PLN03121         55 YALETAVL-LSGATIVDQRVCITRWGQY   81 (243)
T ss_pred             HHHHHHHh-cCCCeeCCceEEEEeCccc
Confidence            99999995 5999999999999876543

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.28  E-value=5.3e-13  Score=112.88  Aligned_cols=84  Identities=23%  Similarity=0.479  Sum_probs=77.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...-|||||||++.|+.+|.-.|++||.|..|.                          ++++..||.++||||+.|.+.
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdin--------------------------LiRDk~TGKSKGFaFLcYEDQ   87 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDIN--------------------------LIRDKKTGKSKGFAFLCYEDQ   87 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEE--------------------------EEecCCCCcccceEEEEecCc
Confidence            456799999999999999999999999998887                          899999999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      .+-.-|+..|||..|.||.|+|+++.....
T Consensus        88 RSTILAVDN~NGiki~gRtirVDHv~~Yk~  117 (219)
T KOG0126|consen   88 RSTILAVDNLNGIKILGRTIRVDHVSNYKK  117 (219)
T ss_pred             cceEEEEeccCCceecceeEEeeecccccC
Confidence            999999999999999999999998876544

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.28  E-value=8.8e-12  Score=122.68  Aligned_cols=182  Identities=23%  Similarity=0.424  Sum_probs=142.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..+.++|+++|+.++++.+..+|..-=.  ..-+...+    .+.              -+.....+..++|||++|.+.
T Consensus       174 q~~r~~v~~~~~~~~e~~~~~f~~~~~~--~~gl~~~~----~g~--------------~~~s~~~n~~~nfa~ie~~s~  233 (500)
T KOG0120|consen  174 QARRLYVGNIPFTSNEESMMSFFNSRMH--ASGLNQAP----DGP--------------SFVSVQLNLEKNFAFIEFRSI  233 (500)
T ss_pred             hhhhhcccccCCccCcHhhhhhhhhhhh--hcccccCC----CCC--------------ceeeeeecccccceeEEecCC
Confidence            3567999999999999999999965200  00000000    000              111223456788999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCC---------------CCCCcCCCCceEEEeCCCCcCcHHHHHHHHhc
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPE---------------RAPRVFEPGFRIYVGNLPWEVDNARLEQVFSE  302 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~---------------~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~  302 (365)
                      +.|..|... ++..+.|+.+++.........+.               ..+........+||+|||..+++.+++++...
T Consensus       234 ~~at~~~~~-~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~  312 (500)
T KOG0120|consen  234 SEATEAMAL-DGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDS  312 (500)
T ss_pred             Cchhhhhcc-cchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHh
Confidence            999988776 99999999999965554433221               12233455679999999999999999999999


Q ss_pred             cCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccc
Q 017842          303 HGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       303 ~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      ||.+...+++.+..+|.++||||.+|.+......|+..|||..+++.+|.|+.|-...
T Consensus       313 fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~  370 (500)
T KOG0120|consen  313 FGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGA  370 (500)
T ss_pred             cccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccc
Confidence            9999999999999999999999999999999999999999999999999999886543

>smart00361 RRM_1 RNA recognition motif

Probab=99.25  E-value=2.7e-11  Score=89.55  Aligned_cols=62  Identities=26%  Similarity=0.478  Sum_probs=56.1

Q ss_pred             HHHHHHHHh----ccCCeEEEE-EEeeCCC--CCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          293 NARLEQVFS----EHGKVVNAR-VVYDRET--GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       293 ee~L~~~F~----~~G~V~~v~-i~~d~~~--~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      +++|+++|+    .||.|..|. |+.++.+  +.++|||||+|.+.++|.+|+..|||..+.||.|+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            567888888    999999996 7777766  8999999999999999999999999999999999863

>PF13893 RRM_5: RNA recognition motif

Probab=99.24  E-value=3.6e-11  Score=84.75  Aligned_cols=56  Identities=34%  Similarity=0.680  Sum_probs=51.2

Q ss_pred             HHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       296 L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      |+++|++||.|..+.+.+..     +|+|||+|.+.++|..|+..|||..++|++|+|.||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999997553     689999999999999999999999999999999996

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>smart00360 RRM RNA recognition motif

Probab=99.24  E-value=4.7e-11  Score=86.50  Aligned_cols=71  Identities=44%  Similarity=0.741  Sum_probs=64.2

Q ss_pred             EcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHHHHH
Q 017842          164 VGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKA  243 (365)
Q Consensus       164 VgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~~A  243 (365)
                      |+|||..++.++|+.+|..||.|..+.                          +..+..++.++|+|||.|.+.++|..|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~--------------------------i~~~~~~~~~~~~a~v~f~~~~~a~~a   54 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVR--------------------------LVRDKDTGKSKGFAFVEFESEEDAEKA   54 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEE--------------------------EEeCCCCCCCCceEEEEeCCHHHHHHH
Confidence            689999999999999999999998877                          555555788899999999999999999


Q ss_pred             HHHHccCcccCeeEEEe
Q 017842          244 VEMFHRYDIDGRLLTVN  260 (365)
Q Consensus       244 l~~lng~~~~gr~l~V~  260 (365)
                      +..+++..++|+.|+|.
T Consensus        55 ~~~~~~~~~~~~~~~v~   71 (71)
T smart00360       55 LEALNGKELDGRPLKVK   71 (71)
T ss_pred             HHHcCCCeeCCcEEEeC
Confidence            99999999999999873

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.23  E-value=1.4e-11  Score=106.33  Aligned_cols=79  Identities=35%  Similarity=0.476  Sum_probs=74.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      -.+|-|-||.+-++.++|..+|++||.|-.|.                          |..+..|..++|||||.|....
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVy--------------------------IPrdr~Tr~sRgFaFVrf~~k~   66 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVY--------------------------IPRDRYTRQSRGFAFVRFHDKR   66 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCccccee--------------------------cccccccccccceeEEEeeecc
Confidence            45799999999999999999999999999988                          8889999999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      +|+.|+..|+|.+++|+.|+|..|.
T Consensus        67 daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   67 DAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             hHHHHHHhhcceeeccceeeehhhh
Confidence            9999999999999999999998764

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.22  E-value=2.6e-11  Score=102.22  Aligned_cols=79  Identities=29%  Similarity=0.413  Sum_probs=69.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      -.++||||||+.++++.+|...|..||++..+-|                          ..     ...|||||+|.++
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWv--------------------------Ar-----nPPGfAFVEFed~   57 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWV--------------------------AR-----NPPGFAFVEFEDP   57 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEE--------------------------ee-----cCCCceEEeccCc
Confidence            3679999999999999999999999999877642                          21     5689999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      .+|..|+..|+|..|.|..|+|..+.-...
T Consensus        58 RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen   58 RDAEDAVRYLDGKDICGSRIRVELSTGRPR   87 (195)
T ss_pred             ccHHHHHhhcCCccccCceEEEEeecCCcc
Confidence            999999999999999999999998765543

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.21  E-value=4.3e-11  Score=111.75  Aligned_cols=170  Identities=20%  Similarity=0.308  Sum_probs=127.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHcc----CCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKA----GTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~----G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .-.|-.++||++++..++..||..-    |-.+.+                           +...+..|+..|-|||.|
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egv---------------------------LFV~rpdgrpTGdAFvlf  213 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGV---------------------------LFVTRPDGRPTGDAFVLF  213 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccce---------------------------EEEECCCCCcccceEEEe
Confidence            4468899999999999999999631    112222                           222334788999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCC-----------------CC------CCCCCCcCCCCceEEEeCCCCcC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG-----------------TQ------PERAPRVFEPGFRIYVGNLPWEV  291 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~-----------------~~------~~~~~~~~~~~~~lfV~nLp~~~  291 (365)
                      ..+++|..|+.+ |...++.|.|.+.++....                 ..      +.+.-....+..+|.+++||+..
T Consensus       214 a~ee~aq~aL~k-hrq~iGqRYIElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~A  292 (508)
T KOG1365|consen  214 ACEEDAQFALRK-HRQNIGQRYIELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEA  292 (508)
T ss_pred             cCHHHHHHHHHH-HHHHHhHHHHHHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhh
Confidence            999999999998 8888888888764332110                 00      00000111224589999999999


Q ss_pred             cHHHHHHHHhccC-CeEE--EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          292 DNARLEQVFSEHG-KVVN--ARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       292 tee~L~~~F~~~G-~V~~--v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +.++|..+|..|. .|..  |.++.+. .|++.|-|||+|.+.+.|..|....+++.+.+|.|.|--|.
T Consensus       293 tvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S  360 (508)
T KOG1365|consen  293 TVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCS  360 (508)
T ss_pred             hHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeecc
Confidence            9999999999885 4555  7777774 58999999999999999999999888888889999886553

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.20  E-value=3.7e-11  Score=117.60  Aligned_cols=81  Identities=37%  Similarity=0.688  Sum_probs=77.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      +.|||||+|+++++++|..+|+..|.|..++                          +++|+.+|+.+||||++|.+.+.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~--------------------------~v~D~~tG~~~G~~f~~~~~~~~   72 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFR--------------------------LVYDRETGKPKGFGFCEFTDEET   72 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceee--------------------------ecccccCCCcCceeeEecCchhh
Confidence            8999999999999999999999999998887                          89999999999999999999999


Q ss_pred             HHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      +..|+..|||..+.||.|+|.++....
T Consensus        73 ~~~a~~~lNg~~~~gr~l~v~~~~~~~   99 (435)
T KOG0108|consen   73 AERAIRNLNGAEFNGRKLRVNYASNRK   99 (435)
T ss_pred             HHHHHHhcCCcccCCceEEeecccccc
Confidence            999999999999999999999886543

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.20  E-value=1.7e-10  Score=84.35  Aligned_cols=74  Identities=45%  Similarity=0.722  Sum_probs=65.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      +|+|+|||+.+++++|+++|..+|.|..+.                          +..+... ..+|+|||.|.+.++|
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~--------------------------~~~~~~~-~~~~~~~v~f~s~~~a   53 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVR--------------------------IVRDKDT-KSKGFAFVEFEDEEDA   53 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEE--------------------------EeeCCCC-CcceEEEEEECCHHHH
Confidence            589999999999999999999999998876                          3333333 6789999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEee
Q 017842          241 EKAVEMFHRYDIDGRLLTVNK  261 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~  261 (365)
                      ..|+..+++..++|+.+.|.+
T Consensus        54 ~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590          54 EKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             HHHHHHhCCCeECCeEEEEeC
Confidence            999999999999999999863

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.18  E-value=6.5e-11  Score=95.64  Aligned_cols=84  Identities=20%  Similarity=0.358  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ....|||.++-..++++++.+.|..||+|.++.                          +..++.+|..+|||.|+|.+.
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNih--------------------------LNLDRRtGy~KGYaLvEYet~  124 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIH--------------------------LNLDRRTGYVKGYALVEYETL  124 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhccccccee--------------------------eccccccccccceeeeehHhH
Confidence            466899999999999999999999999999988                          777888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      +.|++|+..+||..+.|..|.|+|+-.+.+
T Consensus       125 keAq~A~~~~Ng~~ll~q~v~VDw~Fv~gp  154 (170)
T KOG0130|consen  125 KEAQAAIDALNGAELLGQNVSVDWCFVKGP  154 (170)
T ss_pred             HHHHHHHHhccchhhhCCceeEEEEEecCC
Confidence            999999999999999999999999866554

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=99.16  E-value=6.4e-12  Score=109.32  Aligned_cols=144  Identities=26%  Similarity=0.362  Sum_probs=122.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ..++||||+|+...++++-|.++|-+.|+|..+.|+                           +...+..+ ||||.|.+
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip---------------------------~~~d~~~k-Fa~v~f~~   58 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIP---------------------------SGQDQEQK-FAYVFFPN   58 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCC---------------------------CCccCCCc-eeeeeccc
Confidence            457899999999999999999999999999776532                           22233445 99999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeC----CCCcCcHHHHHHHHhccCCeEEEEEE
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGN----LPWEVDNARLEQVFSEHGKVVNARVV  312 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~n----Lp~~~tee~L~~~F~~~G~V~~v~i~  312 (365)
                      +-.+.-|+.++||..+.++.|.|                     +++.||    |...++.+.+.+.|+..|.+..+|+.
T Consensus        59 E~sv~~a~~L~ng~~l~~~e~q~---------------------~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~  117 (267)
T KOG4454|consen   59 ENSVQLAGQLENGDDLEEDEEQR---------------------TLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIP  117 (267)
T ss_pred             ccchhhhhhhcccchhccchhhc---------------------ccccCCCcchhhhhcchhhheeeecccCCCCCcccc
Confidence            99999999999999999999887                     455666    77789999999999999999999999


Q ss_pred             eeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCee
Q 017842          313 YDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRA  350 (365)
Q Consensus       313 ~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~  350 (365)
                      ++.. |+++.++|+.+--..+.-.++..+.+..+.-++
T Consensus       118 ~~~d-~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~  154 (267)
T KOG4454|consen  118 TDND-GRNRNFGFVTYQRLCAVPFALDLYQGLELFQKK  154 (267)
T ss_pred             cccc-CCccCccchhhhhhhcCcHHhhhhcccCcCCCC
Confidence            9875 888999999999888888999988877554333

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.13  E-value=8.2e-11  Score=106.48  Aligned_cols=75  Identities=33%  Similarity=0.669  Sum_probs=71.1

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      .|||||||..+++.+|+.+|+.||.|..|.|+++        ||||...+...+..||++|||..|.|..|.|.-+++|.
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            7999999999999999999999999999999954        99999999999999999999999999999999999986


Q ss_pred             cCC
Q 017842          361 RRS  363 (365)
Q Consensus       361 ~~~  363 (365)
                      +.+
T Consensus        76 k~s   78 (346)
T KOG0109|consen   76 KAS   78 (346)
T ss_pred             CCc
Confidence            654

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.12  E-value=4.4e-11  Score=104.13  Aligned_cols=84  Identities=29%  Similarity=0.510  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..||||||+|--.+++.-|...|-.||.|..|.                          +..+-.+.+.+|||||+|...
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIq--------------------------iPlDyesqkHRgFgFVefe~a   62 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQ--------------------------IPLDYESQKHRGFGFVEFEEA   62 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcc--------------------------cccchhcccccceeEEEeecc
Confidence            468999999999999999999999999999887                          667778999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|..|+..+|+..+.||.|+|+++.|...
T Consensus        63 EDAaaAiDNMnesEL~GrtirVN~AkP~ki   92 (298)
T KOG0111|consen   63 EDAAAAIDNMNESELFGRTIRVNLAKPEKI   92 (298)
T ss_pred             chhHHHhhcCchhhhcceeEEEeecCCccc
Confidence            999999999999999999999999988754

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=99.10  E-value=5.8e-12  Score=128.00  Aligned_cols=148  Identities=24%  Similarity=0.371  Sum_probs=127.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      ..++||.||++.+.+.+|...|..+|.|..++                          +......++.+|+||++|..++
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vq--------------------------i~~h~n~~~~rG~~Y~~F~~~~  720 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQ--------------------------IVIHKNEKRFRGKAYVEFLKPE  720 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHH--------------------------HHHHhhccccccceeeEeecCC
Confidence            34799999999999999999999999888876                          3344567889999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETG  318 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~  318 (365)
                      .+.+|+....+..++                         +..|||+|+|+..|.+.|+.+|..+|.+..++++..+ .|
T Consensus       721 ~~~aaV~f~d~~~~g-------------------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~g  774 (881)
T KOG0128|consen  721 HAGAAVAFRDSCFFG-------------------------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AG  774 (881)
T ss_pred             chhhhhhhhhhhhhh-------------------------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-cc
Confidence            999999985555444                         1279999999999999999999999999999988764 58


Q ss_pred             CcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          319 RSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       319 ~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      +++|.|+|.|.+..++.+++...++..+.-+.+.|+.+.+
T Consensus       775 kpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  775 KPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             ccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            9999999999999999999998888888877777777543

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.05  E-value=3.7e-10  Score=96.01  Aligned_cols=78  Identities=29%  Similarity=0.515  Sum_probs=70.3

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||..+.+.+|..+|-+||.|..|.+...   ..+..||||+|.+..+|..||..-+|..++|.+|+|.|+..
T Consensus         6 ~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    6 SRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             cceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            459999999999999999999999999999988532   34577999999999999999999999999999999999874


Q ss_pred             c
Q 017842          359 R  359 (365)
Q Consensus       359 ~  359 (365)
                      -
T Consensus        83 g   83 (241)
T KOG0105|consen   83 G   83 (241)
T ss_pred             C
Confidence            3

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.04  E-value=3.3e-10  Score=105.01  Aligned_cols=87  Identities=28%  Similarity=0.451  Sum_probs=80.6

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ..+|-+.|||.-|.+-+|.++|.-+|+.||.|.+|.|++|+.||.+--||||+|.+..++.+|.-.|++.-|.+|+|+|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            34556799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Ecccccc
Q 017842          355 VAEDRQR  361 (365)
Q Consensus       355 ~a~~~~~  361 (365)
                      |+.+-.+
T Consensus       315 FSQSVsk  321 (479)
T KOG0415|consen  315 FSQSVSK  321 (479)
T ss_pred             hhhhhhh
Confidence            9875443

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.03  E-value=8.8e-10  Score=96.96  Aligned_cols=77  Identities=26%  Similarity=0.518  Sum_probs=72.0

Q ss_pred             eEEEeCCCCcCcHHHHHH----HHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          281 RIYVGNLPWEVDNARLEQ----VFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~----~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ||||.||+..+..++|++    +|+.||.|..|...   .+.+.+|-|||.|.+.+.|-.|+++|+|..+.|+.++|+||
T Consensus        11 TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA   87 (221)
T KOG4206|consen   11 TLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYA   87 (221)
T ss_pred             eEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecc
Confidence            999999999999999888    99999999999887   35677999999999999999999999999999999999999


Q ss_pred             cccc
Q 017842          357 EDRQ  360 (365)
Q Consensus       357 ~~~~  360 (365)
                      +.+.
T Consensus        88 ~s~s   91 (221)
T KOG4206|consen   88 KSDS   91 (221)
T ss_pred             cCcc
Confidence            9765

>PF13893 RRM_5: RNA recognition motif

Probab=98.98  E-value=2.2e-09  Score=75.52  Aligned_cols=56  Identities=39%  Similarity=0.643  Sum_probs=47.8

Q ss_pred             HHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHHHHHHHHHccCcccCe
Q 017842          176 LAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGR  255 (365)
Q Consensus       176 L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~~Al~~lng~~~~gr  255 (365)
                      |+++|++||.|..+.+                          ..+.     +++|||+|.+.++|.+|+..|||..+.|+
T Consensus         1 L~~~f~~fG~V~~i~~--------------------------~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~   49 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKI--------------------------FKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGR   49 (56)
T ss_dssp             HHHHHTTTS-EEEEEE--------------------------ETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTE
T ss_pred             ChHHhCCcccEEEEEE--------------------------EeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            6889999999988763                          2111     69999999999999999999999999999


Q ss_pred             eEEEeec
Q 017842          256 LLTVNKA  262 (365)
Q Consensus       256 ~l~V~~a  262 (365)
                      .|+|.++
T Consensus        50 ~l~V~~a   56 (56)
T PF13893_consen   50 PLKVSYA   56 (56)
T ss_dssp             EEEEEEE
T ss_pred             EEEEEEC
Confidence            9999874

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>smart00361 RRM_1 RNA recognition motif

Probab=98.97  E-value=2.9e-09  Score=78.62  Aligned_cols=62  Identities=21%  Similarity=0.313  Sum_probs=53.3

Q ss_pred             HHHHHHHHH----ccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCC--CCccceEEEEeCCHHHHHHHHHH
Q 017842          173 SEKLAMLFE----KAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRET--DRSRGFGFVTMSTVEEAEKAVEM  246 (365)
Q Consensus       173 ~~~L~~~F~----~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~g~afV~f~~~e~a~~Al~~  246 (365)
                      +++|+++|+    .||.|..+..                         ++.+..+  ++++|||||.|.+.++|.+|+..
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~-------------------------v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~   56 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINK-------------------------IYIDNVGYENHKRGNVYITFERSEDAARAIVD   56 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEE-------------------------EEeCCCCCCCCCcEEEEEEECCHHHHHHHHHH
Confidence            467888888    9999988741                         4445545  88999999999999999999999


Q ss_pred             HccCcccCeeEEE
Q 017842          247 FHRYDIDGRLLTV  259 (365)
Q Consensus       247 lng~~~~gr~l~V  259 (365)
                      |||..+.|+.|++
T Consensus        57 l~g~~~~gr~l~~   69 (70)
T smart00361       57 LNGRYFDGRTVKA   69 (70)
T ss_pred             hCCCEECCEEEEe
Confidence            9999999999986

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.91  E-value=1.1e-09  Score=112.22  Aligned_cols=163  Identities=20%  Similarity=0.279  Sum_probs=134.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....+|||+|||+..+++.+|+..|..+|.|..|.|..                           +..+...-||||.|-
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKt---------------------------P~~~~esa~~f~~~~  421 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKT---------------------------PHIKTESAYAFVSLL  421 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhcccccccccc---------------------------CCCCcccchhhhhhh
Confidence            44678999999999999999999999999999987542                           235566789999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR  315 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~  315 (365)
                      +...+-.|+..+.+..|....+++.+-.+          ...+.+.++|++|+.++....|.+.|..||.|..|.+-   
T Consensus       422 n~dmtp~ak~e~s~~~I~~g~~r~glG~~----------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~---  488 (975)
T KOG0112|consen  422 NTDMTPSAKFEESGPLIGNGTHRIGLGQP----------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR---  488 (975)
T ss_pred             ccccCcccchhhcCCccccCccccccccc----------ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecc---
Confidence            99999999988888777665555544332          12234589999999999999999999999999997664   


Q ss_pred             CCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eeEEEEEcccccc
Q 017842          316 ETGRSRGFGFVTMSSETELNDAIAALDGQNLDG--RAIRVNVAEDRQR  361 (365)
Q Consensus       316 ~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g--r~l~V~~a~~~~~  361 (365)
                         ++.-||||+|.+...+..|+..|-|..|+|  ++|+|.||..-.+
T Consensus       489 ---hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~~  533 (975)
T KOG0112|consen  489 ---HGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPGA  533 (975)
T ss_pred             ---cCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCCC
Confidence               335699999999999999999999999976  6899999886543

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.90  E-value=1.2e-09  Score=97.26  Aligned_cols=172  Identities=22%  Similarity=0.365  Sum_probs=126.2

Q ss_pred             CCCCeEEEcCCCCCCCHHH-H--HHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEE
Q 017842          157 PEDAKLFVGNLPYDVDSEK-L--AMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVT  233 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~-L--~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~  233 (365)
                      +.-...|++|+-.++..+- |  ...|+-|-......                          ++.+ ..+.-+++||+.
T Consensus        94 P~vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk--------------------------~v~~-~p~~~~~~~~~~  146 (290)
T KOG0226|consen   94 PAVFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTK--------------------------LVRD-RPQPIRPEAFES  146 (290)
T ss_pred             cccccccccccccccCCCCCCcchhhhccchhhhhhh--------------------------hhhc-CCCccCcccccC
Confidence            3455677888877776554 2  45555544332221                          2222 355668999999


Q ss_pred             eCCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEe
Q 017842          234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVY  313 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~  313 (365)
                      |....+..++-..-++..+.-+.++......-...  ........-.+||.|.|-.+++.+-|-+.|.+|-.....++++
T Consensus       147 ~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedP--sl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviR  224 (290)
T KOG0226|consen  147 FKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDP--SLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIR  224 (290)
T ss_pred             cchhhhhhhhccccccccccCcceeeccccccCCc--ccccCccccceeecccccccccHHHHHHHHHhccchhhccccc
Confidence            98888777776655666666666555433222111  1122334456999999999999999999999999999999999


Q ss_pred             eCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          314 DRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       314 d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      |+.||+++|||||.|.+..++..|++.|+|+.++.|.|.++-+.
T Consensus       225 dkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~  268 (290)
T KOG0226|consen  225 DKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSE  268 (290)
T ss_pred             cccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhh
Confidence            99999999999999999999999999999999999988876543

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.90  E-value=2.9e-08  Score=92.81  Aligned_cols=167  Identities=16%  Similarity=0.203  Sum_probs=129.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .+...-.|.|++|-..+++.+|.+.++.||+|..+..                                ...+..|.|+|
T Consensus        27 k~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~--------------------------------~P~~r~alvef   74 (494)
T KOG1456|consen   27 KPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTC--------------------------------MPHKRQALVEF   74 (494)
T ss_pred             CCCCCceEEEeccccccchhHHHHHHhcCCceEEEEe--------------------------------ccccceeeeee
Confidence            4556778999999999999999999999999977652                                23456799999


Q ss_pred             CCHHHHHHHHHHH--ccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceE--EEeCCCCcCcHHHHHHHHhccCCeEEEE
Q 017842          235 STVEEAEKAVEMF--HRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRI--YVGNLPWEVDNARLEQVFSEHGKVVNAR  310 (365)
Q Consensus       235 ~~~e~a~~Al~~l--ng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~l--fV~nLp~~~tee~L~~~F~~~G~V~~v~  310 (365)
                      .+.+.|+.++...  +...+.|+.--++++.......... ....++..|  -|-|--+.+|-+-|..++..+|.|..|.
T Consensus        75 edi~~akn~Vnfaa~n~i~i~gq~Al~NyStsq~i~R~g~-es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIv  153 (494)
T KOG1456|consen   75 EDIEGAKNCVNFAADNQIYIAGQQALFNYSTSQCIERPGD-ESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIV  153 (494)
T ss_pred             ccccchhhheehhccCcccccCchhhcccchhhhhccCCC-CCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEE
Confidence            9999999988654  3455688888888875544332221 112222233  3556668899999999999999999998


Q ss_pred             EEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc--CCeeEEEEEcccc
Q 017842          311 VVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL--DGRAIRVNVAEDR  359 (365)
Q Consensus       311 i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l--~gr~l~V~~a~~~  359 (365)
                      |.+.  +   .--|.|+|.+.+.|.+|..+|||-.|  +.+.|.|.||++-
T Consensus       154 Ifkk--n---gVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~  199 (494)
T KOG1456|consen  154 IFKK--N---GVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPT  199 (494)
T ss_pred             EEec--c---ceeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcc
Confidence            8755  2   22599999999999999999999977  4579999999864

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.89  E-value=7.1e-09  Score=89.95  Aligned_cols=80  Identities=23%  Similarity=0.358  Sum_probs=74.2

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhcc-CCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEH-GKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~-G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ...++|+.+|+.+.+.++..+|..+ |.|..+|+-|++.||.++|||||+|.+.+.|.-|-..||+.-|.|+-|.|.|-.
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmp  128 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMP  128 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeC
Confidence            3489999999999999999999998 678888888999999999999999999999999999999999999999998865


Q ss_pred             c
Q 017842          358 D  358 (365)
Q Consensus       358 ~  358 (365)
                      +
T Consensus       129 p  129 (214)
T KOG4208|consen  129 P  129 (214)
T ss_pred             c
Confidence            4

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.88  E-value=1e-09  Score=101.76  Aligned_cols=86  Identities=27%  Similarity=0.377  Sum_probs=79.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      ..++...|||-.|.+-++.++|.-+|+.||+|.+|.                          ++++..+|-+..||||+|
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sce--------------------------VIRD~ktgdsLqyaFiEF  288 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCE--------------------------VIRDRKTGDSLQYAFIEF  288 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeee--------------------------EEecccccchhheeeeee
Confidence            345678999999999999999999999999999998                          999999999999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      .+.+++.+|.-+|++..|+++.|.|+.+.+-.
T Consensus       289 en~escE~AyFKMdNvLIDDrRIHVDFSQSVs  320 (479)
T KOG0415|consen  289 ENKESCEQAYFKMDNVLIDDRRIHVDFSQSVS  320 (479)
T ss_pred             cchhhHHHHHhhhcceeeccceEEeehhhhhh
Confidence            99999999999999999999999998775443

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.87  E-value=5.2e-09  Score=105.72  Aligned_cols=110  Identities=25%  Similarity=0.397  Sum_probs=90.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..+|||||+|+..+++.+|.++|+.||.|.+|.+.                                .++|+|||.+.+.
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li--------------------------------~~R~cAfI~M~~R  467 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI--------------------------------PPRGCAFIKMVRR  467 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeec--------------------------------cCCceeEEEEeeh
Confidence            57899999999999999999999999999998632                                5799999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhc
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSE  302 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~  302 (365)
                      .+|.+|+.+|+.+.+.++.|+|.|+..+..+..-..-+..   .+=|.-|||.--..+|..++..
T Consensus       468 qdA~kalqkl~n~kv~~k~Iki~Wa~g~G~kse~k~~wD~---~lGVt~IP~~kLt~dl~~~~eg  529 (894)
T KOG0132|consen  468 QDAEKALQKLSNVKVADKTIKIAWAVGKGPKSEYKDYWDV---ELGVTYIPWEKLTDDLEAWCEG  529 (894)
T ss_pred             hHHHHHHHHHhcccccceeeEEeeeccCCcchhhhhhhhc---ccCeeEeehHhcCHHHHHhhhh
Confidence            9999999999999999999999999988876522211111   3456667887555558877764

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.87  E-value=1.6e-07  Score=88.05  Aligned_cols=170  Identities=18%  Similarity=0.224  Sum_probs=130.7

Q ss_pred             CCCeEEEcCCCCC-CCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          158 EDAKLFVGNLPYD-VDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      +...++|-+|... ++-+.|.++|-.||.|..|++.                          +     .-.|.|.|++.+
T Consensus       286 ~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFm--------------------------k-----Tk~gtamVemgd  334 (494)
T KOG1456|consen  286 PGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFM--------------------------K-----TKPGTAMVEMGD  334 (494)
T ss_pred             CCcEEEEEeccccccchhhhhhhhhhcCceeeEEEe--------------------------e-----cccceeEEEcCc
Confidence            4668999999876 4778899999999999988743                          1     225789999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCC---------------------C--------CCCCCcCCCCceEEEeCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ---------------------P--------ERAPRVFEPGFRIYVGNL  287 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~---------------------~--------~~~~~~~~~~~~lfV~nL  287 (365)
                      ..++++|+..||+..+.|..|.|..++.....                     .        ....+...|.++|..-|.
T Consensus       335 ~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNa  414 (494)
T KOG1456|consen  335 AYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNA  414 (494)
T ss_pred             HHHHHHHHHHhccCccccceEEEeeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecC
Confidence            99999999999999999999999766533211                     0        112334567789999999


Q ss_pred             CCcCcHHHHHHHHhccC-CeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe----eEEEEEccccc
Q 017842          288 PWEVDNARLEQVFSEHG-KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGR----AIRVNVAEDRQ  360 (365)
Q Consensus       288 p~~~tee~L~~~F~~~G-~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr----~l~V~~a~~~~  360 (365)
                      |..+||+.|..+|...+ ....|+|..-+ +-+ .-.|.++|.+..+|..||..||...+.+.    +..+.||-+-+
T Consensus       415 P~~vtEe~l~~i~nek~v~~~svkvFp~k-ser-SssGllEfe~~s~Aveal~~~NH~pi~~p~gs~PfilKlcfsts  490 (494)
T KOG1456|consen  415 PLGVTEEQLIGICNEKDVPPTSVKVFPLK-SER-SSSGLLEFENKSDAVEALMKLNHYPIEGPNGSFPFILKLCFSTS  490 (494)
T ss_pred             CCccCHHHHHHHhhhcCCCcceEEeeccc-ccc-cccceeeeehHHHHHHHHHHhccccccCCCCCCCeeeeeeeccc
Confidence            99999999999998875 45667776554 222 23578999999999999999999988553    45555554433

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.85  E-value=9.8e-09  Score=100.42  Aligned_cols=87  Identities=36%  Similarity=0.505  Sum_probs=78.6

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEE
Q 017842          153 FVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFV  232 (365)
Q Consensus       153 ~~~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV  232 (365)
                      .....-.+.+||.+|...+...+|+++|++||+|.-+.                          ++++..+...++||||
T Consensus       399 kgrs~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAK--------------------------VVTNaRsPGaRCYGfV  452 (940)
T KOG4661|consen  399 KGRSTLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAK--------------------------VVTNARSPGARCYGFV  452 (940)
T ss_pred             ccccccccceeeeccccchhhhHHHHHHHHhcceecee--------------------------eeecCCCCCcceeEEE
Confidence            33455678999999999999999999999999998777                          8888888889999999


Q ss_pred             EeCCHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          233 TMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       233 ~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      ++.+.+.|.+||..|+.+.++|+.|.|..++..
T Consensus       453 TMSts~eAtkCI~hLHrTELHGrmISVEkaKNE  485 (940)
T KOG4661|consen  453 TMSTSAEATKCIEHLHRTELHGRMISVEKAKNE  485 (940)
T ss_pred             EecchHHHHHHHHHhhhhhhcceeeeeeecccC
Confidence            999999999999999999999999999887654

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.84  E-value=7.2e-09  Score=104.73  Aligned_cols=80  Identities=21%  Similarity=0.434  Sum_probs=73.4

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..+|||||+|+..+++.+|..+|+.||.|.+|.+..      ++|+|||.+...++|.+|+.+|++..+.++.|+|.||.
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            356999999999999999999999999999998864      38999999999999999999999999999999999998


Q ss_pred             ccccCC
Q 017842          358 DRQRRS  363 (365)
Q Consensus       358 ~~~~~~  363 (365)
                      .+.-++
T Consensus       494 g~G~ks  499 (894)
T KOG0132|consen  494 GKGPKS  499 (894)
T ss_pred             cCCcch
Confidence            776443

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.83  E-value=1.5e-08  Score=87.94  Aligned_cols=85  Identities=25%  Similarity=0.392  Sum_probs=74.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHcc-CCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEE
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKA-GTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVT  233 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~-G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~  233 (365)
                      .......++|+.+|....+..+..+|.++ |.+..++                          +-+++.||.++|||||+
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~r--------------------------lsRnkrTGNSKgYAFVE   98 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFR--------------------------LSRNKRTGNSKGYAFVE   98 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEE--------------------------eecccccCCcCceEEEE
Confidence            33456689999999999999999999988 6776655                          66888999999999999


Q ss_pred             eCCHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      |.+++.|.-|.+.||++.|.|+.|.|....+.
T Consensus        99 FEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   99 FESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             eccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            99999999999999999999999999876554

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.82  E-value=3.1e-09  Score=99.97  Aligned_cols=82  Identities=34%  Similarity=0.669  Sum_probs=76.2

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||++|+|.++++.|+.+|..||.|..|.+.+|+.+++++||+||+|.+..++.++|. ..-+.|.||.|.+..|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            34589999999999999999999999999999999999999999999999999999999988 57788999999999888


Q ss_pred             ccc
Q 017842          358 DRQ  360 (365)
Q Consensus       358 ~~~  360 (365)
                      ++.
T Consensus        84 ~r~   86 (311)
T KOG4205|consen   84 SRE   86 (311)
T ss_pred             Ccc
Confidence            765

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.82  E-value=6.3e-09  Score=93.31  Aligned_cols=88  Identities=28%  Similarity=0.512  Sum_probs=80.8

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEE
Q 017842          154 VEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVT  233 (365)
Q Consensus       154 ~~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~  233 (365)
                      .+-++.+.|||-+||......+|...|-.||.|.+.+                          +..|+.|+.+++||||.
T Consensus       280 reGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaK--------------------------VFvDRATNQSKCFGFVS  333 (371)
T KOG0146|consen  280 REGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAK--------------------------VFVDRATNQSKCFGFVS  333 (371)
T ss_pred             hcCCCcceEEEEeCchhhccHHHHHHhccccceeeee--------------------------eeehhccccccceeeEe
Confidence            3456789999999999999999999999999998887                          88899999999999999


Q ss_pred             eCCHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      |.++.+++.||..+||..|+=+.|+|....++..
T Consensus       334 fDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkda  367 (371)
T KOG0146|consen  334 FDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDA  367 (371)
T ss_pred             cCCchhHHHHHHHhcchhhhhhhhhhhhcCcccc
Confidence            9999999999999999999999999988776653

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.72  E-value=4e-08  Score=91.28  Aligned_cols=73  Identities=19%  Similarity=0.360  Sum_probs=66.5

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHh-CCCccCCeeEEEEEccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL-DGQNLDGRAIRVNVAED  358 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l-~~~~l~gr~l~V~~a~~  358 (365)
                      .+|||+||-..+++.+|+.+|-.||.|.++++...      +|.|||+|.+..+|..|...+ +...++|++|.|.|..+
T Consensus       229 ~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  229 KTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             eEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            49999999889999999999999999999999855      679999999999999998855 55578999999999988

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.71  E-value=1.4e-07  Score=73.62  Aligned_cols=81  Identities=20%  Similarity=0.272  Sum_probs=72.3

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhcc--CCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC----CeeEEE
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEH--GKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD----GRAIRV  353 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~--G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~----gr~l~V  353 (365)
                      +||.|+|+|...|.++|.+++...  |....+.++.|..++.+.|||||-|.+.+.|.+....++|+.+.    .+...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            599999999999999999999764  78889999999999999999999999999999999999999884    567788


Q ss_pred             EEccccc
Q 017842          354 NVAEDRQ  360 (365)
Q Consensus       354 ~~a~~~~  360 (365)
                      .||+-+.
T Consensus        82 ~yAriQG   88 (97)
T PF04059_consen   82 SYARIQG   88 (97)
T ss_pred             ehhHhhC
Confidence            8887543

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.68  E-value=1.1e-07  Score=89.21  Aligned_cols=166  Identities=19%  Similarity=0.293  Sum_probs=120.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +...|-.++|||..+..++..+|.-.....-.+                          ++.....|+..|.|.|.|.+.
T Consensus        59 ~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~--------------------------aKOG~~qgrRnge~lvrf~d~  112 (508)
T KOG1365|consen   59 DNVVVRARGLPWQSSDQDIARFFKGLNIANGGR--------------------------ALCLNAQGRRNGEALVRFVDP  112 (508)
T ss_pred             cceEEEecCCCCCcccCCHHHHHhhhhccccce--------------------------eeeehhhhccccceEEEecCc
Confidence            345678899999999999999997542221111                          444556778899999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCC-----CCCCCCcC---CCCceEEEeCCCCcCcHHHHHHHHhcc----CC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ-----PERAPRVF---EPGFRIYVGNLPWEVDNARLEQVFSEH----GK  305 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~-----~~~~~~~~---~~~~~lfV~nLp~~~tee~L~~~F~~~----G~  305 (365)
                      +.-.-|++. +...+.+|.|.|-.+....--     ........   ..--.|..++|||++++.++..+|...    |.
T Consensus       113 e~RdlalkR-hkhh~g~ryievYka~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g  191 (508)
T KOG1365|consen  113 EGRDLALKR-HKHHMGTRYIEVYKATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGG  191 (508)
T ss_pred             hhhhhhhHh-hhhhccCCceeeeccCchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCC
Confidence            999999998 888899999999776543210     00001111   112367889999999999999999643    35


Q ss_pred             eEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEE
Q 017842          306 VVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR  352 (365)
Q Consensus       306 V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~  352 (365)
                      ++.|-+++. ..|+..|=|||.|....+|..||.. |...|+-|.|.
T Consensus       192 ~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIE  236 (508)
T KOG1365|consen  192 TEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIE  236 (508)
T ss_pred             ccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHH
Confidence            666666654 3589999999999999999999983 65566555443

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.65  E-value=5.2e-07  Score=87.55  Aligned_cols=167  Identities=20%  Similarity=0.310  Sum_probs=123.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ....|-+++||+.||+++|.+||+-.-.+....                          .......++..|-|||.|.+.
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi--------------------------~l~~d~rgR~tGEAfVqF~sq  155 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGI--------------------------LLPMDQRGRPTGEAFVQFESQ  155 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccce--------------------------eeeccCCCCcccceEEEecCH
Confidence            466899999999999999999998754433311                          233345678999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC-------------------C----CC-------------------------
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG-------------------T----QP-------------------------  269 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~-------------------~----~~-------------------------  269 (365)
                      +.|++|+.. +...|+.|-|.|..+....                   .    +.                         
T Consensus       156 e~ae~Al~r-hre~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~  234 (510)
T KOG4211|consen  156 ESAEIALGR-HRENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYY  234 (510)
T ss_pred             HHHHHHHHH-HHHhhccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCcc
Confidence            999999998 8888999999885442100                   0    00                         


Q ss_pred             -----------------------CCC----CC---------c-CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEE
Q 017842          270 -----------------------ERA----PR---------V-FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVV  312 (365)
Q Consensus       270 -----------------------~~~----~~---------~-~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~  312 (365)
                                             ...    +.         . ...+..+..++||+..++.++..+|+.. ....|.|-
T Consensus       235 g~~~~~~~~d~~~~gs~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl-~p~~v~i~  313 (510)
T KOG4211|consen  235 GFSRYPSLQDYGNFGSYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPL-NPYRVHIE  313 (510)
T ss_pred             ccccCccccccccccccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCC-CceeEEEE
Confidence                                   000    00         0 0112478889999999999999999876 33466665


Q ss_pred             eeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          313 YDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       313 ~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      .. .+|+..|=|+|+|.+.++|..|+. -++..+..|-|.+-
T Consensus       314 ig-~dGr~TGEAdveF~t~edav~Ams-kd~anm~hrYVElF  353 (510)
T KOG4211|consen  314 IG-PDGRATGEADVEFATGEDAVGAMG-KDGANMGHRYVELF  353 (510)
T ss_pred             eC-CCCccCCcceeecccchhhHhhhc-cCCcccCcceeeec
Confidence            55 468889999999999999999998 47778877766654

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.63  E-value=1.6e-07  Score=82.48  Aligned_cols=83  Identities=19%  Similarity=0.358  Sum_probs=71.4

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCCcc---CCeeEEEEE
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE-TGRSRGFGFVTMSSETELNDAIAALDGQNL---DGRAIRVNV  355 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~-~~~~kG~afV~F~s~~~a~~Al~~l~~~~l---~gr~l~V~~  355 (365)
                      +||||.+||.++...+|..+|..|-.-+.+.+..... .+.++-+|||.|.+.+.|..|+..|||..|   .+..|+|.+
T Consensus        35 RTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiEl  114 (284)
T KOG1457|consen   35 RTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIEL  114 (284)
T ss_pred             ceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEeee
Confidence            5999999999999999999999997777776654432 345568999999999999999999999998   488999999


Q ss_pred             ccccccC
Q 017842          356 AEDRQRR  362 (365)
Q Consensus       356 a~~~~~~  362 (365)
                      |++.+|.
T Consensus       115 AKSNtK~  121 (284)
T KOG1457|consen  115 AKSNTKR  121 (284)
T ss_pred             hhcCccc
Confidence            9987764

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.55  E-value=2.8e-07  Score=83.65  Aligned_cols=80  Identities=31%  Similarity=0.587  Sum_probs=73.9

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      ++|+|.|||+.++.++|+++|..||.+..+-+.+++ .|++.|.|-|.|...++|.+|++.|+|..++|+.+.+....+.
T Consensus        84 ~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~  162 (243)
T KOG0533|consen   84 TKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSP  162 (243)
T ss_pred             ceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCc
Confidence            589999999999999999999999999999999885 5889999999999999999999999999999999999876644


Q ss_pred             c
Q 017842          360 Q  360 (365)
Q Consensus       360 ~  360 (365)
                      .
T Consensus       163 ~  163 (243)
T KOG0533|consen  163 S  163 (243)
T ss_pred             c
Confidence            3

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.54  E-value=1.1e-07  Score=86.24  Aligned_cols=78  Identities=29%  Similarity=0.503  Sum_probs=74.2

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      ..+||+|+.+.+|.+.+..+|+.||.|..|.|+.|+..+.++|||||.|.+...+..|+. |+|..|.|+.|.|.+..-
T Consensus       102 ~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r~  179 (231)
T KOG4209|consen  102 PSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKRT  179 (231)
T ss_pred             ceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeeee
Confidence            389999999999999999999999999999999999999999999999999999999999 999999999999988653

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.52  E-value=2.6e-07  Score=90.67  Aligned_cols=82  Identities=35%  Similarity=0.551  Sum_probs=75.6

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      +..|+|.+|...+...+|+.+|++||.|+...|+.+..+.-.+.||||++.+..+|.+||..||...|.||-|.|..+++
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            45899999999999999999999999999999998876666688999999999999999999999999999999999886


Q ss_pred             cc
Q 017842          359 RQ  360 (365)
Q Consensus       359 ~~  360 (365)
                      -+
T Consensus       485 Ep  486 (940)
T KOG4661|consen  485 EP  486 (940)
T ss_pred             Cc
Confidence            54

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.51  E-value=4.1e-07  Score=84.68  Aligned_cols=78  Identities=28%  Similarity=0.434  Sum_probs=67.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +..-.|||||||...+++.+|+++|-+||.|..+++.                                ..++.|||.|.
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~--------------------------------~~~~CAFv~ft  272 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRIL--------------------------------PRKGCAFVTFT  272 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEee--------------------------------cccccceeeeh
Confidence            3456799999999999999999999999999998742                                33669999999


Q ss_pred             CHHHHHHHHHH-HccCcccCeeEEEeecCCC
Q 017842          236 TVEEAEKAVEM-FHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       236 ~~e~a~~Al~~-lng~~~~gr~l~V~~a~~~  265 (365)
                      +.++|+.|... +|...|+|+.|.|.|..+.
T Consensus       273 TR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~~  303 (377)
T KOG0153|consen  273 TREAAEKAAEKSFNKLVINGFRLKIKWGRPK  303 (377)
T ss_pred             hhHHHHHHHHhhcceeeecceEEEEEeCCCc
Confidence            99999988755 5678889999999999883

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.47  E-value=1.7e-07  Score=85.02  Aligned_cols=84  Identities=23%  Similarity=0.404  Sum_probs=75.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .....+.|||||+.+.+|.+++..+|+.||.|..+.                          +.++...+.++|||||+|
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~t--------------------------i~~d~~~~~~k~~~yvef  150 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVT--------------------------VPKDKFRGHPKGFAYVEF  150 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCcccee--------------------------eeccccCCCcceeEEEec
Confidence            344678999999999999999999999999998877                          788888889999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      .+.+.+..|+. |+|..|.|+.|.|.+....
T Consensus       151 ~~~~~~~~ay~-l~gs~i~~~~i~vt~~r~~  180 (231)
T KOG4209|consen  151 SSYELVEEAYK-LDGSEIPGPAIEVTLKRTN  180 (231)
T ss_pred             ccHhhhHHHhh-cCCcccccccceeeeeeee
Confidence            99999999999 6999999999999876654

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.47  E-value=3.5e-07  Score=89.38  Aligned_cols=79  Identities=29%  Similarity=0.535  Sum_probs=68.1

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      ..+|||+|||++++..+|+++|..||.|+..+|....-.++...||||+|.+..++..||.+ +-..++||+|.|.--+.
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            34699999999999999999999999999999987654455559999999999999999994 67788999999975443

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.43  E-value=7.1e-07  Score=87.25  Aligned_cols=81  Identities=26%  Similarity=0.486  Sum_probs=67.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...+|||+|||.+++...|+++|..||.|....|..                        ..  ..+...+||||+|.+.
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~v------------------------r~--~~~~~~~fgFV~f~~~  340 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQV------------------------RS--PGGKNPCFGFVEFENA  340 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEE------------------------ec--cCCCcCceEEEEEeec
Confidence            345699999999999999999999999999888642                        22  2234449999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      +++..||.+ +-..++||.|.|..-.+.
T Consensus       341 ~~~~~~i~A-sp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  341 AAVQNAIEA-SPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             chhhhhhhc-CccccCCeeEEEEecccc
Confidence            999999998 788999999999765543

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.42  E-value=8.4e-07  Score=82.59  Aligned_cols=79  Identities=24%  Similarity=0.442  Sum_probs=71.0

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeE--------EEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCee
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVV--------NARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRA  350 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~--------~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~  350 (365)
                      ++.|||.|||..+|-+++.++|++||.|.        .|.+.++.. |..+|=|++.|.-.+++.-|++.|++..|.|++
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            34699999999999999999999999654        367777754 999999999999999999999999999999999


Q ss_pred             EEEEEccc
Q 017842          351 IRVNVAED  358 (365)
Q Consensus       351 l~V~~a~~  358 (365)
                      |+|+.|+=
T Consensus       213 ~rVerAkf  220 (382)
T KOG1548|consen  213 LRVERAKF  220 (382)
T ss_pred             EEEehhhh
Confidence            99999873

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.38  E-value=3.4e-07  Score=81.43  Aligned_cols=71  Identities=34%  Similarity=0.689  Sum_probs=67.0

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      .+|||+||+.+.+.+|..+|..||.+..|.+.        .||+||.|.+..+|..|+.-||+..|.|-++.|.|+...
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            79999999999999999999999999999886        679999999999999999999999999988999999854

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.36  E-value=1.8e-06  Score=78.38  Aligned_cols=82  Identities=29%  Similarity=0.477  Sum_probs=71.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      ..+|+|.|||+.++..+|+++|..||.+..+.                          +-++ ..|++.|.|-|.|...+
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~--------------------------vhy~-~~G~s~Gta~v~~~r~~  135 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVA--------------------------VHYD-RAGRSLGTADVSFNRRD  135 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEe--------------------------eccC-CCCCCCccceeeecchH
Confidence            46899999999999999999999999777765                          3333 47889999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      +|..|++.++|+.++|+.+.+....+...
T Consensus       136 DA~~avk~~~gv~ldG~~mk~~~i~~~~~  164 (243)
T KOG0533|consen  136 DAERAVKKYNGVALDGRPMKIEIISSPSQ  164 (243)
T ss_pred             hHHHHHHHhcCcccCCceeeeEEecCccc
Confidence            99999999999999999999987765543

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.34  E-value=6.3e-07  Score=88.21  Aligned_cols=71  Identities=27%  Similarity=0.405  Sum_probs=64.5

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR  352 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~  352 (365)
                      -+..+|+|-|||..++.++|+++|+.||+|..|+.-+.     .+|.+||+|.+..+|.+|++.|++..|.|+.|.
T Consensus        73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   73 MNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            34459999999999999999999999999999876544     489999999999999999999999999999887

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.32  E-value=3.4e-06  Score=63.11  Aligned_cols=68  Identities=26%  Similarity=0.422  Sum_probs=48.3

Q ss_pred             ceEEEeCCCCcCcHH----HHHHHHhccC-CeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          280 FRIYVGNLPWEVDNA----RLEQVFSEHG-KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       280 ~~lfV~nLp~~~tee----~L~~~F~~~G-~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      +.|+|.|||...+..    .|++++..+| .|..|  .        .|-|+|.|.+.+.|.+|.+.|+|....|++|.|+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~--------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S--------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e--------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            379999999988764    5677777886 56665  1        4679999999999999999999999999999999


Q ss_pred             Ecc
Q 017842          355 VAE  357 (365)
Q Consensus       355 ~a~  357 (365)
                      |..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            974

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.28  E-value=1.4e-06  Score=85.81  Aligned_cols=158  Identities=22%  Similarity=0.269  Sum_probs=109.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|+|-|||..++..+|+.+|+.||.|..++                               .+-..+|..||+|-+.
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir-------------------------------~t~~~~~~~~v~FyDv  122 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIR-------------------------------ETPNKRGIVFVEFYDV  122 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhh-------------------------------cccccCceEEEEEeeh
Confidence            578999999999999999999999999998865                               3556789999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCC------------------CCCcCCCCceEEEeCCCCcCcHHHHHHH
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER------------------APRVFEPGFRIYVGNLPWEVDNARLEQV  299 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~------------------~~~~~~~~~~lfV~nLp~~~tee~L~~~  299 (365)
                      .+|++|++.|++..|.|+.|..    +.......                  .+...-+...+|. .|+......-++.+
T Consensus       123 R~A~~Alk~l~~~~~~~~~~k~----~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g-~l~P~~s~~~~~~~  197 (549)
T KOG4660|consen  123 RDAERALKALNRREIAGKRIKR----PGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFG-MLSPTRSSILLEHI  197 (549)
T ss_pred             HhHHHHHHHHHHHHhhhhhhcC----CCcccccchhcccchhhhhccchhhcCCCCCCcCCccee-eeccchhhhhhhcc
Confidence            9999999999999999999982    22211110                  0000011123333 38888888777788


Q ss_pred             HhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          300 FSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       300 F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      +.-+|.+.. +-.     +.-+---|+.|.+..++..++... |..+.+....++++.+
T Consensus       198 ~~~~~~~~~-~~~-----~~~~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  198 SSVDGSSPG-RET-----PLLNHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             hhccCcccc-ccc-----cchhhhhhhhhccccchhhcccCC-ceecCCCCceEEecCC
Confidence            888887766 322     111224567777777775555533 5666666666666544

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.28  E-value=2.5e-07  Score=87.22  Aligned_cols=173  Identities=13%  Similarity=0.109  Sum_probs=124.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      ..|.|.||.+.++.++++.+|.-.|+|..+.+.     ++                  +.+-...-....|||-|.+...
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrly-----p~------------------~~d~~~pv~sRtcyVkf~d~~s   64 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLY-----PN------------------VDDSKIPVISRTCYVKFLDSQS   64 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhcccccccccc-----CC------------------CCCccCcceeeeEEEeccCCcc
Confidence            489999999999999999999999999987743     10                  1111222345679999999988


Q ss_pred             HHHHHHHHccCcccCeeEEEeecCCCCCCC----------C----------------------CCCC--cC---------
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKAAPRGTQP----------E----------------------RAPR--VF---------  276 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a~~~~~~~----------~----------------------~~~~--~~---------  276 (365)
                      +..|- .|.+++|-|+.|.|..+.......          .                      ..+.  ..         
T Consensus        65 v~vaQ-hLtntvfvdraliv~p~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~  143 (479)
T KOG4676|consen   65 VTVAQ-HLTNTVFVDRALIVRPYGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAA  143 (479)
T ss_pred             eeHHh-hhccceeeeeeEEEEecCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhh
Confidence            87654 458888888888886543221000          0                      0000  00         


Q ss_pred             -----CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeE
Q 017842          277 -----EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAI  351 (365)
Q Consensus       277 -----~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l  351 (365)
                           .-..+++|++|+..+...++.+.|..+|.|.+.++.-    +-..-+|.|.|....+...|+. ++|..+.-...
T Consensus       144 A~kleeirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~as----k~~s~~c~~sf~~qts~~halr-~~gre~k~qhs  218 (479)
T KOG4676|consen  144 AKKLEEIRRTREVQSLISAAILPESGESFERKGEVSYAHTAS----KSRSSSCSHSFRKQTSSKHALR-SHGRERKRQHS  218 (479)
T ss_pred             hhhhHHHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhc----cCCCcchhhhHhhhhhHHHHHH-hcchhhhhhhh
Confidence                 0124799999999999999999999999999998863    3335688899999999999999 78887765555


Q ss_pred             EEEEcccccc
Q 017842          352 RVNVAEDRQR  361 (365)
Q Consensus       352 ~V~~a~~~~~  361 (365)
                      ++..-++..+
T Consensus       219 r~ai~kP~kK  228 (479)
T KOG4676|consen  219 RRAIIKPHKK  228 (479)
T ss_pred             hhhhcCcccc
Confidence            5555554443

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.27  E-value=9.5e-08  Score=90.73  Aligned_cols=151  Identities=25%  Similarity=0.406  Sum_probs=120.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      ..+|+|||...++..+|..+|...-                                +.....--...|||||.+.+...
T Consensus         2 nklyignL~p~~~psdl~svfg~ak--------------------------------~~~~g~fl~k~gyafvd~pdq~w   49 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAK--------------------------------IPGSGQFLVKSGYAFVDCPDQQW   49 (584)
T ss_pred             CcccccccCCCCChHHHHHHhcccc--------------------------------CCCCcceeeecceeeccCCchhh
Confidence            3689999999999999999996531                                00000011247899999999999


Q ss_pred             HHHHHHHHcc-CcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEE-eeCCC
Q 017842          240 AEKAVEMFHR-YDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVV-YDRET  317 (365)
Q Consensus       240 a~~Al~~lng-~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~-~d~~~  317 (365)
                      |.+|++.++| ..+.|..+.|....++..+..          .+-|+|+|....++.|..+...||.|..|..+ .+.. 
T Consensus        50 a~kaie~~sgk~elqGkr~e~~~sv~kkqrsr----------k~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e-  118 (584)
T KOG2193|consen   50 ANKAIETLSGKVELQGKRQEVEHSVPKKQRSR----------KIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE-  118 (584)
T ss_pred             hhhhHHhhchhhhhcCceeeccchhhHHHHhh----------hhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH-
Confidence            9999999998 568999999998877654321          58899999999999999999999999999764 2322 


Q ss_pred             CCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          318 GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       318 ~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                         ....-|+|.+.+.+..||..|+|..|....+.|.|-
T Consensus       119 ---tavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen  119 ---TAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             ---HHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccC
Confidence               233458899999999999999999998888888774

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.26  E-value=1.5e-06  Score=87.50  Aligned_cols=86  Identities=23%  Similarity=0.362  Sum_probs=74.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      .+..+.||||||++.++++.|...|..||+|..++|.|.                       ...-...+.+.+|||-|.
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwp-----------------------RtEeEk~r~r~cgfvafm  227 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWP-----------------------RTEEEKRRERNCGFVAFM  227 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecc-----------------------cchhhhccccccceeeeh
Confidence            345678999999999999999999999999999987642                       223345677889999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      +..+|.+|++.|+|..+.+..+++-|...
T Consensus       228 nR~D~era~k~lqg~iv~~~e~K~gWgk~  256 (877)
T KOG0151|consen  228 NRADAERALKELQGIIVMEYEMKLGWGKA  256 (877)
T ss_pred             hhhhHHHHHHHhcceeeeeeeeeeccccc
Confidence            99999999999999999999999988743

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.25  E-value=1.5e-06  Score=77.80  Aligned_cols=84  Identities=25%  Similarity=0.462  Sum_probs=73.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +..+.+||+|-|..+++.+-|...|.+|-.-...+                          ++++..+|+++||+||.|.
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~ak--------------------------viRdkRTgKSkgygfVSf~  240 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAK--------------------------VIRDKRTGKSKGYGFVSFR  240 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhcc--------------------------ccccccccccccceeeeec
Confidence            33577999999999999999999999986554444                          8889999999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      +..++..|+..++|.-++.|+|.+....-+
T Consensus       241 ~pad~~rAmrem~gkyVgsrpiklRkS~wk  270 (290)
T KOG0226|consen  241 DPADYVRAMREMNGKYVGSRPIKLRKSEWK  270 (290)
T ss_pred             CHHHHHHHHHhhcccccccchhHhhhhhHH
Confidence            999999999999999999999998765443

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.21  E-value=1.3e-05  Score=62.60  Aligned_cols=79  Identities=14%  Similarity=0.274  Sum_probs=62.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHcc--CCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKA--GTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~--G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +||+|+|||...+.+.|.+++...  |...-+.                          +..|..++.+.|||||-|.+.
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~Y--------------------------LPiDf~~~~N~GYAFVNf~~~   55 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFY--------------------------LPIDFKNKCNLGYAFVNFTSP   55 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEE--------------------------eeeeccCCCceEEEEEEcCCH
Confidence            689999999999999999999653  4433333                          556677888999999999999


Q ss_pred             HHHHHHHHHHccCccc----CeeEEEeecCC
Q 017842          238 EEAEKAVEMFHRYDID----GRLLTVNKAAP  264 (365)
Q Consensus       238 e~a~~Al~~lng~~~~----gr~l~V~~a~~  264 (365)
                      +.|.+....++|..+.    .+...|.+|.-
T Consensus        56 ~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAri   86 (97)
T PF04059_consen   56 QAAIRFYKAFNGKKWPNFNSKKVCEISYARI   86 (97)
T ss_pred             HHHHHHHHHHcCCccccCCCCcEEEEehhHh
Confidence            9999999999998874    45555655543

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.20  E-value=3.8e-06  Score=84.64  Aligned_cols=84  Identities=23%  Similarity=0.385  Sum_probs=74.1

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCC---CCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE---TGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR  352 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~---~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~  352 (365)
                      .+..+.|||+||+..++++.|...|..||.|..|+|...+.   ..+.+-+|||-|.+..+|.+|++.|+|..+.++.++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            34556899999999999999999999999999999975532   356677899999999999999999999999999999


Q ss_pred             EEEcccc
Q 017842          353 VNVAEDR  359 (365)
Q Consensus       353 V~~a~~~  359 (365)
                      +-|++.-
T Consensus       251 ~gWgk~V  257 (877)
T KOG0151|consen  251 LGWGKAV  257 (877)
T ss_pred             ecccccc
Confidence            9998643

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.16  E-value=8.2e-07  Score=77.81  Aligned_cols=75  Identities=17%  Similarity=0.273  Sum_probs=68.6

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+|||+|+-..++++-|.++|-..|.|..|.|+.++. +..+ ||||.|.+..++.-|+..|||-.+.++.|.|.+-
T Consensus        10 rtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen   10 RTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             hHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            4899999999999999999999999999999987754 5556 9999999999999999999999999998888764

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=98.16  E-value=2.2e-06  Score=76.87  Aligned_cols=85  Identities=15%  Similarity=0.192  Sum_probs=60.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ....||++|||+.+...-|+++|+.||.|-.|.+.-...+.       .++       +.......+..-.-|+|+|.+.
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~-------~~~-------r~~~~~n~~~~y~EGWvEF~~K  138 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSK-------RAA-------RKRKGGNYKKLYSEGWVEFISK  138 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHH-------HHH-------HhhcCCCccccchhHHHHHHHH
Confidence            35689999999999999999999999999988754221110       000       0000001111222389999999


Q ss_pred             HHHHHHHHHHccCcccCee
Q 017842          238 EEAEKAVEMFHRYDIDGRL  256 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~  256 (365)
                      ..|+++...|||..|+|+.
T Consensus       139 rvAK~iAe~Lnn~~Iggkk  157 (278)
T KOG3152|consen  139 RVAKRIAELLNNTPIGGKK  157 (278)
T ss_pred             HHHHHHHHHhCCCccCCCC
Confidence            9999999999999999875

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.02  E-value=1.2e-05  Score=80.86  Aligned_cols=169  Identities=17%  Similarity=0.083  Sum_probs=123.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +...+-+.+.+++....+++++|...- |....                          +..+...+...|.+||.|...
T Consensus       310 d~~y~~~~gm~fn~~~nd~rkfF~g~~-~~~~~--------------------------l~~~~v~~~~tG~~~v~f~~~  362 (944)
T KOG4307|consen  310 DKYYNNYKGMEFNNDFNDGRKFFPGRN-AQSTD--------------------------LSENRVAPPQTGRKTVMFTPQ  362 (944)
T ss_pred             hhheeeecccccccccchhhhhcCccc-ccccc--------------------------hhhhhcCCCcCCceEEEecCc
Confidence            345566789999999999999985321 22221                          333434444588999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC--------CC-----------------------CCCCCcCCCCceEEEeC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT--------QP-----------------------ERAPRVFEPGFRIYVGN  286 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~--------~~-----------------------~~~~~~~~~~~~lfV~n  286 (365)
                      ..+.+|+.. |...+-.|.+.|..+....-        ..                       ...+....-+..|||..
T Consensus       363 ~~~q~A~~r-n~~~~~~R~~q~~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~  441 (944)
T KOG4307|consen  363 APFQNAFTR-NPSDDVNRPFQTGPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQ  441 (944)
T ss_pred             chHHHHHhc-CchhhhhcceeecCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEecc
Confidence            999999998 88888888888854422110        00                       00111223356999999


Q ss_pred             CCCcCcHHHHHHHHhccCCeEE-EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          287 LPWEVDNARLEQVFSEHGKVVN-ARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       287 Lp~~~tee~L~~~F~~~G~V~~-v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ||+.++...+-.+|...-.|+. |.|.+- -+++.++.|||.|....++..|+..-+.+.++-|.|+|.-
T Consensus       442 lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~s  510 (944)
T KOG4307|consen  442 LPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDS  510 (944)
T ss_pred             CCccccccchhhhhhhhhhhhheeEeccC-CcccccchhhheeccccccchhhhcccccccCceEEEeec
Confidence            9999999999999998878887 555554 4678899999999999999988886667777889999864

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.96  E-value=4.6e-05  Score=57.13  Aligned_cols=69  Identities=28%  Similarity=0.366  Sum_probs=47.4

Q ss_pred             CeEEEcCCCCCCCHHH----HHHHHHccC-CeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          160 AKLFVGNLPYDVDSEK----LAMLFEKAG-TVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~----L~~~F~~~G-~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      ..|||.|||.+.....    |+.++..|| .|..+                                    ..+.|+|.|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v------------------------------------~~~tAilrF   46 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV------------------------------------SGGTAILRF   46 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE--------------------------------------TT-EEEEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE------------------------------------eCCEEEEEe
Confidence            4699999999997765    556667776 44332                                    257899999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      .+.+.|.+|.+.|+|..+.|+.|.|.+...
T Consensus        47 ~~~~~A~RA~KRmegEdVfG~kI~v~~~~~   76 (90)
T PF11608_consen   47 PNQEFAERAQKRMEGEDVFGNKISVSFSPK   76 (90)
T ss_dssp             SSHHHHHHHHHHHTT--SSSS--EEESS--
T ss_pred             CCHHHHHHHHHhhcccccccceEEEEEcCC
Confidence            999999999999999999999999987743

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.88  E-value=6.2e-07  Score=92.01  Aligned_cols=163  Identities=18%  Similarity=0.138  Sum_probs=121.3

Q ss_pred             CCCeEEEcCCCCCCCHH-HHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          158 EDAKLFVGNLPYDVDSE-KLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~-~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ..+...+.|+-+....+ ..+..|..+|.|+.+++.                          ..........++++++..
T Consensus       570 ~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p--------------------------~~g~k~h~q~~~~~~~s~  623 (881)
T KOG0128|consen  570 ERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGP--------------------------KRGFKAHEQPQQQKVQSK  623 (881)
T ss_pred             hhhhhcccCCCcchhhHHhhHHHhhcccccccccCc--------------------------cccccccccchhhhhhcc
Confidence            34567777887777665 577888999999887742                          101111122278899999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCc--CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEee
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRV--FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYD  314 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~--~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d  314 (365)
                      ..+++.|... .|.-+.++.+.|..+.+...........  ...-.++||+||+..+.+.+|...|..+|.+..++|.-.
T Consensus       624 ~~~~esat~p-a~~~~a~~~~av~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h  702 (881)
T KOG0128|consen  624 HGSAESATVP-AGGALANRSAAVGLADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIH  702 (881)
T ss_pred             ccchhhcccc-cccccCCccccCCCCCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHH
Confidence            9999988876 8888899999998877666433222211  123358999999999999999999999999988888766


Q ss_pred             CCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 017842          315 RETGRSRGFGFVTMSSETELNDAIAALDGQNLDG  348 (365)
Q Consensus       315 ~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g  348 (365)
                      ...++.+|+||+.|....++.+|+.. +...+.|
T Consensus       703 ~n~~~~rG~~Y~~F~~~~~~~aaV~f-~d~~~~g  735 (881)
T KOG0128|consen  703 KNEKRFRGKAYVEFLKPEHAGAAVAF-RDSCFFG  735 (881)
T ss_pred             hhccccccceeeEeecCCchhhhhhh-hhhhhhh
Confidence            66789999999999999999999984 4433333

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.76  E-value=5.7e-05  Score=60.21  Aligned_cols=71  Identities=17%  Similarity=0.322  Sum_probs=44.8

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCC-----CccCCeeEEE
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDG-----QNLDGRAIRV  353 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~-----~~l~gr~l~V  353 (365)
                      ++.|+|.|++..++.++|+..|+.||.|.+|.+.+.      -.-|||.|.+.+.|.+|+..+..     ..+.+..+.+
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~   74 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTL   74 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEE
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEE
Confidence            357999999999999999999999999999988754      33699999999999999987743     3566666665


Q ss_pred             EE
Q 017842          354 NV  355 (365)
Q Consensus       354 ~~  355 (365)
                      +.
T Consensus        75 ~v   76 (105)
T PF08777_consen   75 EV   76 (105)
T ss_dssp             E-
T ss_pred             EE
Confidence            54

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.63  E-value=5.3e-05  Score=71.27  Aligned_cols=83  Identities=25%  Similarity=0.364  Sum_probs=75.7

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeE--------EEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCee
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVV--------NARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRA  350 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~--------~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~  350 (365)
                      ..+|||-+||..++..+|..+|..+|.|.        .|.|.++++|+++||-|.|.|.+..+|+.|+..++++.+.|.+
T Consensus        66 ~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~  145 (351)
T KOG1995|consen   66 NETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNT  145 (351)
T ss_pred             cccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCCC
Confidence            34899999999999999999999998553        4677889999999999999999999999999999999999999


Q ss_pred             EEEEEcccccc
Q 017842          351 IRVNVAEDRQR  361 (365)
Q Consensus       351 l~V~~a~~~~~  361 (365)
                      |.|..|..++.
T Consensus       146 ikvs~a~~r~~  156 (351)
T KOG1995|consen  146 IKVSLAERRTG  156 (351)
T ss_pred             chhhhhhhccC
Confidence            99999987764

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.60  E-value=4.2e-05  Score=68.76  Aligned_cols=70  Identities=21%  Similarity=0.379  Sum_probs=60.4

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCC--------CCcce----EEEEEecCHHHHHHHHHHhCCCccCC
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRET--------GRSRG----FGFVTMSSETELNDAIAALDGQNLDG  348 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~--------~~~kG----~afV~F~s~~~a~~Al~~l~~~~l~g  348 (365)
                      .||++|||+.+....|+++|+.||.|-.|.+.....+        |..++    -|+|+|.+...|..+...|||..|+|
T Consensus        76 VvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Igg  155 (278)
T KOG3152|consen   76 VVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIGG  155 (278)
T ss_pred             EEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccCC
Confidence            8999999999999999999999999999999765443        22222    27999999999999999999999998


Q ss_pred             ee
Q 017842          349 RA  350 (365)
Q Consensus       349 r~  350 (365)
                      ++
T Consensus       156 kk  157 (278)
T KOG3152|consen  156 KK  157 (278)
T ss_pred             CC
Confidence            74

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.57  E-value=0.00021  Score=70.80  Aligned_cols=77  Identities=31%  Similarity=0.478  Sum_probs=63.4

Q ss_pred             eEEEeCCCCcCc------HHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CeeEEE
Q 017842          281 RIYVGNLPWEVD------NARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD-GRAIRV  353 (365)
Q Consensus       281 ~lfV~nLp~~~t------ee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~-gr~l~V  353 (365)
                      .|+|.|+|---.      ..-|..+|+++|.|..+.++.+.++| .+||.|++|.+..+|..|++.|||+.|+ .++..|
T Consensus        60 vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v  138 (698)
T KOG2314|consen   60 VVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFV  138 (698)
T ss_pred             EEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceEEe
Confidence            899999985332      23477899999999999999887655 8999999999999999999999999885 566666


Q ss_pred             EEccc
Q 017842          354 NVAED  358 (365)
Q Consensus       354 ~~a~~  358 (365)
                      ..-++
T Consensus       139 ~~f~d  143 (698)
T KOG2314|consen  139 RLFKD  143 (698)
T ss_pred             ehhhh
Confidence            54433

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.51  E-value=0.0003  Score=71.17  Aligned_cols=75  Identities=21%  Similarity=0.371  Sum_probs=65.7

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeE-EEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVV-NARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~-~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      +.|-+.|+||.++-++|.++|..|--+- +|++.+. +.|++.|-|.|-|.+.+.|..|...|+++.|..|+|.|.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3788999999999999999999996443 4545444 6799999999999999999999999999999999998865

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.49  E-value=0.00014  Score=68.57  Aligned_cols=91  Identities=23%  Similarity=0.334  Sum_probs=75.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...+|||.+||..++...|..+|.+||.|..-+-     -..++             +.+.+++.|+..+|-|.|.|.+.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~-----t~kPk-------------i~~y~dkeT~~~KGeatvS~~D~  126 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKR-----TGKPK-------------IKIYTDKETGAPKGEATVSYEDP  126 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCC-----CCCcc-------------hhccccccccCcCCceeeeecCh
Confidence            4669999999999999999999999998754220     00112             22788889999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      -.|+.|+..+++..|.|..|+|..+..+.
T Consensus       127 ~~akaai~~~agkdf~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  127 PAAKAAIEWFAGKDFCGNTIKVSLAERRT  155 (351)
T ss_pred             hhhhhhhhhhccccccCCCchhhhhhhcc
Confidence            99999999999999999999998776554

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.39  E-value=0.00049  Score=62.07  Aligned_cols=99  Identities=27%  Similarity=0.299  Sum_probs=81.4

Q ss_pred             HHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCC
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR  319 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~  319 (365)
                      |..|...|++....|+.|+|.++.+.               .|+|.||...+..+.|.+-|+.||.|....++-| ..++
T Consensus         7 ae~ak~eLd~~~~~~~~lr~rfa~~a---------------~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k   70 (275)
T KOG0115|consen    7 AEIAKRELDGRFPKGRSLRVRFAMHA---------------ELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGK   70 (275)
T ss_pred             HHHHHHhcCCCCCCCCceEEEeeccc---------------eEEEEecchhhhhHHHHHhhhhcCccchheeeec-cccc
Confidence            55566778999999999999998762               7999999999999999999999999998776666 3477


Q ss_pred             cceEEEEEecCHHHHHHHHHHhCCC----ccCCeeEEEE
Q 017842          320 SRGFGFVTMSSETELNDAIAALDGQ----NLDGRAIRVN  354 (365)
Q Consensus       320 ~kG~afV~F~s~~~a~~Al~~l~~~----~l~gr~l~V~  354 (365)
                      +.|-++|.|.....+.+|+..++..    ...+++.-|.
T Consensus        71 ~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~Ve  109 (275)
T KOG0115|consen   71 PTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVE  109 (275)
T ss_pred             ccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCC
Confidence            8888999999999999999977433    3345555544

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.36  E-value=0.00013  Score=68.65  Aligned_cols=82  Identities=24%  Similarity=0.469  Sum_probs=72.0

Q ss_pred             CCeEE-EcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          159 DAKLF-VGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       159 ~~tvf-VgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++| |+||+++++.++|+.+|..+|.|..++                          +..+..++..+|||||.|.+.
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r--------------------------~~~~~~s~~~kg~a~~~~~~~  237 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVR--------------------------LPTDEESGDSKGFAYVDFSAG  237 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeec--------------------------cCCCCCccchhhhhhhhhhhc
Confidence            34555 999999999999999999999998887                          666778999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ..+..++.. +...+.|+.+.+....+...
T Consensus       238 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  238 NSKKLALND-QTRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             hhHHHHhhc-ccCcccCcccccccCCCCcc
Confidence            999999887 88899999999988776643

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.33  E-value=0.00053  Score=63.99  Aligned_cols=77  Identities=23%  Similarity=0.374  Sum_probs=58.6

Q ss_pred             CCeEEEcCCCCCCCHHH----H--HHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCC---CCccc-
Q 017842          159 DAKLFVGNLPYDVDSEK----L--AMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRET---DRSRG-  228 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~----L--~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~g-  228 (365)
                      ..-|||-+||+.+..++    |  .++|.+||.|..|.+.                            +.+   +...+ 
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvN----------------------------kkt~s~nst~~h  165 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVN----------------------------KKTSSLNSTASH  165 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEec----------------------------cccccccccccc
Confidence            34699999999886665    2  3789999999776432                            211   11122 


Q ss_pred             e-EEEEeCCHHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          229 F-GFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       229 ~-afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      + .||.|.+.++|.+||...+|..++||.|+..+-.
T Consensus       166 ~gvYITy~~kedAarcIa~vDgs~~DGr~lkatYGT  201 (480)
T COG5175         166 AGVYITYSTKEDAARCIAEVDGSLLDGRVLKATYGT  201 (480)
T ss_pred             ceEEEEecchHHHHHHHHHhccccccCceEeeecCc
Confidence            2 3999999999999999999999999999997654

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.24  E-value=0.00039  Score=65.07  Aligned_cols=74  Identities=23%  Similarity=0.561  Sum_probs=65.9

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccC--CeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHG--KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G--~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      .++|||||-|.+|+++|.+.+...|  .+..+++..++.+|.+||||+|...+..++.+.+..|--+.|.|..-.|
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            4899999999999999999998877  6777888888888999999999999999999999999888998874444

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.23  E-value=0.00082  Score=62.75  Aligned_cols=78  Identities=24%  Similarity=0.413  Sum_probs=61.8

Q ss_pred             ceEEEeCCCCcCcHHH----H--HHHHhccCCeEEEEEEeeCCC-CCcceE--EEEEecCHHHHHHHHHHhCCCccCCee
Q 017842          280 FRIYVGNLPWEVDNAR----L--EQVFSEHGKVVNARVVYDRET-GRSRGF--GFVTMSSETELNDAIAALDGQNLDGRA  350 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~----L--~~~F~~~G~V~~v~i~~d~~~-~~~kG~--afV~F~s~~~a~~Al~~l~~~~l~gr~  350 (365)
                      +-+||-+||..+..++    |  .++|..||.|..|.|-+...+ +...+.  .||+|.+.++|.+||...+|..++||.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            3688889988877766    2  479999999999987654311 222332  399999999999999999999999999


Q ss_pred             EEEEEcc
Q 017842          351 IRVNVAE  357 (365)
Q Consensus       351 l~V~~a~  357 (365)
                      |+..|..
T Consensus       195 lkatYGT  201 (480)
T COG5175         195 LKATYGT  201 (480)
T ss_pred             EeeecCc
Confidence            9999864

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.17  E-value=0.0015  Score=52.06  Aligned_cols=59  Identities=25%  Similarity=0.320  Sum_probs=38.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      ..|+|.+++..++.++|+..|..||.|..|.+.                                +....|||.|.+.++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~--------------------------------~G~~~g~VRf~~~~~   49 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFS--------------------------------RGDTEGYVRFKTPEA   49 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE----------------------------------TT-SEEEEEESS---
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEec--------------------------------CCCCEEEEEECCcch
Confidence            468899999999999999999999988776531                                345579999999999


Q ss_pred             HHHHHHHHccC
Q 017842          240 AEKAVEMFHRY  250 (365)
Q Consensus       240 a~~Al~~lng~  250 (365)
                      |++|+..+...
T Consensus        50 A~~a~~~~~~~   60 (105)
T PF08777_consen   50 AQKALEKLKEA   60 (105)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHhc
Confidence            99999887654

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.14  E-value=0.0025  Score=53.24  Aligned_cols=72  Identities=28%  Similarity=0.400  Sum_probs=52.8

Q ss_pred             CCCceEEEeCCC------CcCcH---HHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 017842          277 EPGFRIYVGNLP------WEVDN---ARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD  347 (365)
Q Consensus       277 ~~~~~lfV~nLp------~~~te---e~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~  347 (365)
                      ++--||.|.=+.      ...++   .+|-+.|..||.|.-||++-+        --+|+|.+-++|.+|+. |+|..++
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~   95 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVN   95 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEET
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEEC
Confidence            333477665554      12222   367788899999999998843        48999999999999999 9999999


Q ss_pred             CeeEEEEEcc
Q 017842          348 GRAIRVNVAE  357 (365)
Q Consensus       348 gr~l~V~~a~  357 (365)
                      |+.|+|+.-.
T Consensus        96 g~~l~i~LKt  105 (146)
T PF08952_consen   96 GRTLKIRLKT  105 (146)
T ss_dssp             TEEEEEEE--
T ss_pred             CEEEEEEeCC
Confidence            9999998743

; PDB: 1UFW_A 2DNR_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.94  E-value=0.0025  Score=44.13  Aligned_cols=52  Identities=17%  Similarity=0.327  Sum_probs=41.7

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHH
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI  338 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al  338 (365)
                      +.|-|.|.+....+ .+..+|..||.|..+.+...      .-+.||+|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            36889999876554 45558889999999988722      347999999999999986

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=96.88  E-value=0.00068  Score=63.52  Aligned_cols=78  Identities=22%  Similarity=0.394  Sum_probs=64.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      ..+|||||-|.+|.++|.+.+...|--..+.|+                        ...++..|.++|||.|...+..+
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmK------------------------FFENR~NGQSKG~AL~~~~SdAa  136 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMK------------------------FFENRTNGQSKGYALLVLNSDAA  136 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhh------------------------hhhcccCCcccceEEEEecchHH
Confidence            459999999999999999999887754333322                        44566789999999999999999


Q ss_pred             HHHHHHHHccCcccCeeEEEee
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNK  261 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~  261 (365)
                      +++.++.|-...|+|+.-.|..
T Consensus       137 ~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen  137 VKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             HHHHHHhcccceecCCCCeeec
Confidence            9999999999999998877753

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.88  E-value=0.0038  Score=61.63  Aligned_cols=63  Identities=30%  Similarity=0.401  Sum_probs=56.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHH-ccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFE-KAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~-~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      +.+|||||+||--++..+|..+|. -||.|..+-                          |-+|..-+..+|-|=|.|.+
T Consensus       369 prrTVFVGgvprpl~A~eLA~imd~lyGgV~yaG--------------------------IDtD~k~KYPkGaGRVtFsn  422 (520)
T KOG0129|consen  369 PRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVG--------------------------IDTDPKLKYPKGAGRVTFSN  422 (520)
T ss_pred             ccceEEecCCCCcchHHHHHHHHHHhcCceEEEE--------------------------eccCcccCCCCCcceeeecc
Confidence            578999999999999999999998 599998876                          66677778899999999999


Q ss_pred             HHHHHHHHHH
Q 017842          237 VEEAEKAVEM  246 (365)
Q Consensus       237 ~e~a~~Al~~  246 (365)
                      -.+-.+||.+
T Consensus       423 qqsYi~AIsa  432 (520)
T KOG0129|consen  423 QQAYIKAISA  432 (520)
T ss_pred             cHHHHHHHhh
Confidence            9999999987

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.86  E-value=0.0025  Score=61.44  Aligned_cols=66  Identities=21%  Similarity=0.322  Sum_probs=55.2

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEee---CCC--CCc--------ceEEEEEecCHHHHHHHHHHhCC
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYD---RET--GRS--------RGFGFVTMSSETELNDAIAALDG  343 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d---~~~--~~~--------kG~afV~F~s~~~a~~Al~~l~~  343 (365)
                      +.++|.+.|||-+-.-+.|.++|..+|.|..|||+..   +..  +.+        +-.|+|+|.....|.+|...|+.
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            4569999999999889999999999999999999866   222  222        34589999999999999997744

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.78  E-value=0.0043  Score=61.74  Aligned_cols=77  Identities=22%  Similarity=0.298  Sum_probs=58.6

Q ss_pred             CCCeEEEcCCCCCC--CH----HHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEE
Q 017842          158 EDAKLFVGNLPYDV--DS----EKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGF  231 (365)
Q Consensus       158 ~~~tvfVgnLp~~~--t~----~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~af  231 (365)
                      -+..|+|.|+|---  .-    .-|..+|+++|+|....                          +..+. .|..+||.|
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~--------------------------~P~~e-~ggtkG~lf  109 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMY--------------------------YPIDE-EGGTKGYLF  109 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhcccccee--------------------------eccCc-cCCeeeEEE
Confidence            46689999999643  22    34667899999987765                          22233 445999999


Q ss_pred             EEeCCHHHHHHHHHHHccCccc-CeeEEEee
Q 017842          232 VTMSTVEEAEKAVEMFHRYDID-GRLLTVNK  261 (365)
Q Consensus       232 V~f~~~e~a~~Al~~lng~~~~-gr~l~V~~  261 (365)
                      ++|++...|..|++.|||..|+ .|...|..
T Consensus       110 ~E~~~~~~A~~aVK~l~G~~ldknHtf~v~~  140 (698)
T KOG2314|consen  110 VEYASMRDAKKAVKSLNGKRLDKNHTFFVRL  140 (698)
T ss_pred             EEecChhhHHHHHHhcccceecccceEEeeh
Confidence            9999999999999999999985 45556643

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=96.77  E-value=0.0065  Score=47.82  Aligned_cols=78  Identities=14%  Similarity=0.200  Sum_probs=52.7

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEE-EEeeC------CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe-eE
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNAR-VVYDR------ETGRSRGFGFVTMSSETELNDAIAALDGQNLDGR-AI  351 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~-i~~d~------~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr-~l  351 (365)
                      +-|.|=|.|.. .-..|-++|+.||.|.... +.++.      ..........|+|.+..+|.+||. .||..+.|. -+
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mv   84 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLMV   84 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEEE
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEEE
Confidence            36888888877 5567778999999998775 11110      001235588999999999999999 799999885 56


Q ss_pred             EEEEcccc
Q 017842          352 RVNVAEDR  359 (365)
Q Consensus       352 ~V~~a~~~  359 (365)
                      -|.++++.
T Consensus        85 GV~~~~~~   92 (100)
T PF05172_consen   85 GVKPCDPA   92 (100)
T ss_dssp             EEEE-HHH
T ss_pred             EEEEcHHh
Confidence            68888543

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.55  E-value=0.0022  Score=64.16  Aligned_cols=78  Identities=18%  Similarity=0.238  Sum_probs=65.0

Q ss_pred             CcCCCCceEEEeCCCCcCcHHHHHHHHh-ccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc---CCe
Q 017842          274 RVFEPGFRIYVGNLPWEVDNARLEQVFS-EHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL---DGR  349 (365)
Q Consensus       274 ~~~~~~~~lfV~nLp~~~tee~L~~~F~-~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l---~gr  349 (365)
                      ......+.|+|.||-..+|.-+|+.++. ..|.|+...|  |    +-|-.|||.|.+.++|.....+|||..+   +++
T Consensus       439 sR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--D----kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK  512 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--D----KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPK  512 (718)
T ss_pred             CCCCccceEeeecccccchHHHHHHHHhhccCchHHHHH--H----HhhcceeEecccHHHHHHHHHHHhccccCCCCCc
Confidence            3455667999999999999999999998 5567777733  3    2366899999999999999999999977   788


Q ss_pred             eEEEEEcc
Q 017842          350 AIRVNVAE  357 (365)
Q Consensus       350 ~l~V~~a~  357 (365)
                      .|.+.|+.
T Consensus       513 ~L~adf~~  520 (718)
T KOG2416|consen  513 HLIADFVR  520 (718)
T ss_pred             eeEeeecc
Confidence            99999875

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.47  E-value=0.0091  Score=41.28  Aligned_cols=52  Identities=23%  Similarity=0.316  Sum_probs=41.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      +.|-|.+.+.+..+. +..+|..||.|..+.+                                .....+.||.|.+..+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~--------------------------------~~~~~~~~l~y~~~~~   48 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYV--------------------------------PESTNWMYLKYKSRKD   48 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEc--------------------------------CCCCcEEEEEECCHHH
Confidence            568888888777755 5558889999987652                                1346789999999999


Q ss_pred             HHHHH
Q 017842          240 AEKAV  244 (365)
Q Consensus       240 a~~Al  244 (365)
                      |++|+
T Consensus        49 ae~Al   53 (53)
T PF14605_consen   49 AEKAL   53 (53)
T ss_pred             HHhhC
Confidence            99885

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.43  E-value=0.0016  Score=58.87  Aligned_cols=63  Identities=17%  Similarity=0.273  Sum_probs=51.6

Q ss_pred             HHHHHHHh-ccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          294 ARLEQVFS-EHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       294 e~L~~~F~-~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ++|...|+ +||.|+.+.|..+. .-.-+|=+||.|...++|.+|+..|||..+.|++|...++-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            44445555 89999999776553 34558889999999999999999999999999999988753

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.12  E-value=0.017  Score=53.21  Aligned_cols=65  Identities=17%  Similarity=0.169  Sum_probs=52.7

Q ss_pred             HHHHHHHHhccCCeEEEEEEeeCCCCCc-ceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          293 NARLEQVFSEHGKVVNARVVYDRETGRS-RGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       293 ee~L~~~F~~~G~V~~v~i~~d~~~~~~-kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +.++++-|++||.|..|.|.-.+..-.. .--.||+|....+|.+|+-.|||..|+||.++.-|..
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            4578899999999999988766432211 2247999999999999999999999999999887654

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.01  E-value=0.0078  Score=58.15  Aligned_cols=81  Identities=20%  Similarity=0.180  Sum_probs=55.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      -+.+||.+-|||.+-.-+.|.++|+.+|.|..|+|--.-     .+...+        ..+......-..+-+|+|+|..
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPg-----aip~d~--------r~~~~~~~~~~tk~~AlvEye~  295 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPG-----AIPEDV--------RGFPKKYFELQTKECALVEYEE  295 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCC-----CCCccc--------ccCCccchhhhhhhhhhhhhhh
Confidence            368899999999999999999999999999998842110     000000        0000000000125569999999


Q ss_pred             HHHHHHHHHHHccC
Q 017842          237 VEEAEKAVEMFHRY  250 (365)
Q Consensus       237 ~e~a~~Al~~lng~  250 (365)
                      .++|.+|.++++..
T Consensus       296 ~~~A~KA~e~~~~e  309 (484)
T KOG1855|consen  296 VEAARKARELLNPE  309 (484)
T ss_pred             hHHHHHHHHhhchh
Confidence            99999999998643

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=95.98  E-value=0.013  Score=61.48  Aligned_cols=82  Identities=21%  Similarity=0.375  Sum_probs=70.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....+.+|||+|+.++....|...|..||.|..|.++                                +...||||.|.
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~--------------------------------hgq~yayi~ye  499 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR--------------------------------HGQPYAYIQYE  499 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeecc--------------------------------cCCcceeeecc
Confidence            3456789999999999999999999999999876633                                45679999999


Q ss_pred             CHHHHHHHHHHHccCcccC--eeEEEeecCCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDG--RLLTVNKAAPRGTQP  269 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~g--r~l~V~~a~~~~~~~  269 (365)
                      +...++.|+..+-|..|+|  +.|+|+++......+
T Consensus       500 s~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~~~P  535 (975)
T KOG0112|consen  500 SPPAAQAATHDMRGAPLGGPPRRLRVDLASPPGATP  535 (975)
T ss_pred             cCccchhhHHHHhcCcCCCCCcccccccccCCCCCh
Confidence            9999999999999999965  789999987765443

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.98  E-value=0.0041  Score=56.30  Aligned_cols=63  Identities=24%  Similarity=0.296  Sum_probs=50.6

Q ss_pred             HHHHHHHH-ccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHHHHHHHHHccCcc
Q 017842          174 EKLAMLFE-KAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI  252 (365)
Q Consensus       174 ~~L~~~F~-~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~~Al~~lng~~~  252 (365)
                      ++|...|. +||.|+.+.                           +.+...-.-.|.+||.|...++|++|+..|||..+
T Consensus        83 Ed~f~E~~~kygEiee~~---------------------------Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~  135 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELN---------------------------VCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWY  135 (260)
T ss_pred             HHHHHHHHHHhhhhhhhh---------------------------hhcccchhhhhhhhhhcccHHHHHHHHHHHcCccc
Confidence            45555565 899998864                           22333456789999999999999999999999999


Q ss_pred             cCeeEEEeecC
Q 017842          253 DGRLLTVNKAA  263 (365)
Q Consensus       253 ~gr~l~V~~a~  263 (365)
                      .|++|....+.
T Consensus       136 ~G~pi~ae~~p  146 (260)
T KOG2202|consen  136 NGRPIHAELSP  146 (260)
T ss_pred             cCCcceeeecC
Confidence            99999987664

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=95.97  E-value=0.023  Score=44.72  Aligned_cols=83  Identities=16%  Similarity=0.125  Sum_probs=51.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .+.|.|=+.|.. ....+...|++||.|....-..+.   ..                -+..........+..|.|.++.
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~---~~----------------~~~~~~~~~~~NWi~I~Y~~~~   65 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRS---SS----------------GINPYPIPSGGNWIHITYDNPL   65 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG-----------------------------E-CCTTEEEEEESSHH
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeeccccc---cc----------------ccccccCCCCCCEEEEECCCHH
Confidence            557888888888 556788999999998654300000   00                0000011234678999999999


Q ss_pred             HHHHHHHHHccCcccCeeEE-Eeec
Q 017842          239 EAEKAVEMFHRYDIDGRLLT-VNKA  262 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~-V~~a  262 (365)
                      +|.+||.. ||..|.|..+- |.++
T Consensus        66 ~A~rAL~~-NG~i~~g~~mvGV~~~   89 (100)
T PF05172_consen   66 SAQRALQK-NGTIFSGSLMVGVKPC   89 (100)
T ss_dssp             HHHHHHTT-TTEEETTCEEEEEEE-
T ss_pred             HHHHHHHh-CCeEEcCcEEEEEEEc
Confidence            99999998 99999886554 5544

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=95.80  E-value=0.041  Score=55.32  Aligned_cols=74  Identities=24%  Similarity=0.303  Sum_probs=59.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHc-cCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEK-AGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~-~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ....|+|.||---.|...|+.++.. +|.|... +                               ..+-+..|||.|.+
T Consensus       443 ~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-W-------------------------------mDkIKShCyV~yss  490 (718)
T KOG2416|consen  443 PSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-W-------------------------------MDKIKSHCYVSYSS  490 (718)
T ss_pred             ccceEeeecccccchHHHHHHHHhhccCchHHH-H-------------------------------HHHhhcceeEeccc
Confidence            4567999999999999999999985 6655543 1                               11335679999999


Q ss_pred             HHHHHHHHHHHccCcc---cCeeEEEeecC
Q 017842          237 VEEAEKAVEMFHRYDI---DGRLLTVNKAA  263 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~---~gr~l~V~~a~  263 (365)
                      .+.|.....+|+|+.+   ++++|.+++..
T Consensus       491 ~eEA~atr~AlhnV~WP~sNPK~L~adf~~  520 (718)
T KOG2416|consen  491 VEEAAATREALHNVQWPPSNPKHLIADFVR  520 (718)
T ss_pred             HHHHHHHHHHHhccccCCCCCceeEeeecc
Confidence            9999999999999988   78899887663

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=95.74  E-value=0.012  Score=56.30  Aligned_cols=77  Identities=18%  Similarity=0.196  Sum_probs=64.7

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeC---CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR---ETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~---~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      .|-|.||...+|.++++.+|...|.|..+++....   .-......|||.|.+.+++..|-. |.+..+-|+.|.|..+-
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~~   87 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPYG   87 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEecC
Confidence            79999999999999999999999999999987532   224456689999999999999888 88888888888876554


Q ss_pred             c
Q 017842          358 D  358 (365)
Q Consensus       358 ~  358 (365)
                      .
T Consensus        88 ~   88 (479)
T KOG4676|consen   88 D   88 (479)
T ss_pred             C
Confidence            3

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=95.70  E-value=0.015  Score=50.79  Aligned_cols=79  Identities=14%  Similarity=0.209  Sum_probs=51.4

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhc-cCCe---EEEEEEeeCCC--CCcceEEEEEecCHHHHHHHHHHhCCCccC---C-
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSE-HGKV---VNARVVYDRET--GRSRGFGFVTMSSETELNDAIAALDGQNLD---G-  348 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~-~G~V---~~v~i~~d~~~--~~~kG~afV~F~s~~~a~~Al~~l~~~~l~---g-  348 (365)
                      ++.|.|++||+.+|++++++.+.. ++.-   .++.-......  ...-..|||.|.+.+++......++|+.|.   | 
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~   86 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN   86 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence            458999999999999999997776 5554   34442222222  112345999999999999999999998773   2 


Q ss_pred             -eeEEEEEcc
Q 017842          349 -RAIRVNVAE  357 (365)
Q Consensus       349 -r~l~V~~a~  357 (365)
                       .+..|.||-
T Consensus        87 ~~~~~VE~Ap   96 (176)
T PF03467_consen   87 EYPAVVEFAP   96 (176)
T ss_dssp             EEEEEEEE-S
T ss_pred             CcceeEEEcc
Confidence             255566654

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.64  E-value=0.031  Score=46.82  Aligned_cols=73  Identities=22%  Similarity=0.314  Sum_probs=50.8

Q ss_pred             CCCCeEEEcCCCCC-----CCH----HHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCcc
Q 017842          157 PEDAKLFVGNLPYD-----VDS----EKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSR  227 (365)
Q Consensus       157 ~~~~tvfVgnLp~~-----~t~----~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (365)
                      |++.||.|.=+...     .-.    .+|...|..||.+.-+|+                          +        .
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRf--------------------------v--------~   70 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRF--------------------------V--------G   70 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEE--------------------------E--------T
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEE--------------------------e--------C
Confidence            45678777766521     122    367788999998866552                          1        3


Q ss_pred             ceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          228 GFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       228 g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      +.-+|+|.+-..|.+|+.+ +|..+.|+.|+|..-.+
T Consensus        71 ~~mwVTF~dg~sALaals~-dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   71 DTMWVTFRDGQSALAALSL-DGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             TCEEEEESSCHHHHHHHHG-CCSEETTEEEEEEE---
T ss_pred             CeEEEEECccHHHHHHHcc-CCcEECCEEEEEEeCCc
Confidence            4679999999999999997 99999999999986544

; PDB: 1UFW_A 2DNR_A.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=95.58  E-value=0.01  Score=57.21  Aligned_cols=76  Identities=28%  Similarity=0.500  Sum_probs=60.6

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCC-ccCCeeEEEEEcccc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQ-NLDGRAIRVNVAEDR  359 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~-~l~gr~l~V~~a~~~  359 (365)
                      .+|++||...++..+|..+|...-.-.+-.++.      -.||+||.+.+..-|.+|+..++|+ .+.|.++.|.+.-++
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~k   76 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK   76 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH
Confidence            699999999999999999997652111111111      1689999999999999999999998 789999999988776


Q ss_pred             ccC
Q 017842          360 QRR  362 (365)
Q Consensus       360 ~~~  362 (365)
                      ..+
T Consensus        77 kqr   79 (584)
T KOG2193|consen   77 KQR   79 (584)
T ss_pred             HHH
Confidence            654

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=95.45  E-value=0.21  Score=40.04  Aligned_cols=65  Identities=9%  Similarity=0.169  Sum_probs=51.3

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhcc-CCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEH-GKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD  347 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~-G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~  347 (365)
                      .+.+...|+.++-..|..+.+.+ ..|..+||++|..  .++-.++++|.+..+|..-...+||+.++
T Consensus        15 ~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   15 LCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             EEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            55566667777777787666665 4788999998843  35667999999999999999999999885

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.03  E-value=0.13  Score=36.70  Aligned_cols=53  Identities=19%  Similarity=0.206  Sum_probs=45.0

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhcc---CCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHh
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEH---GKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL  341 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~---G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l  341 (365)
                      .|.|+|++ +++-++|+.+|..|   .....|..+-|.       .|=|.|.+...|.+||.+|
T Consensus         7 avhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    7 AVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            79999997 58889999999998   246688888774       4889999999999999864

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.40  E-value=0.22  Score=41.40  Aligned_cols=73  Identities=18%  Similarity=0.175  Sum_probs=55.1

Q ss_pred             CCCceEEEeCCCCcCc----HHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEE
Q 017842          277 EPGFRIYVGNLPWEVD----NARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR  352 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~t----ee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~  352 (365)
                      ++..+|.|+=|..++.    -..+-..++.||.|.+|...       ++--|.|.|.+..+|-+|+.++.. ..-|.-+.
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-------GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~q  155 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-------GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQ  155 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-------CCceEEEEehhhHHHHHHHHhhcC-CCCCceEE
Confidence            4456888876655543    34455666889999999765       245799999999999999998765 66788888


Q ss_pred             EEEcc
Q 017842          353 VNVAE  357 (365)
Q Consensus       353 V~~a~  357 (365)
                      ++|-.
T Consensus       156 CsWqq  160 (166)
T PF15023_consen  156 CSWQQ  160 (166)
T ss_pred             eeccc
Confidence            88743

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=93.79  E-value=0.2  Score=46.39  Aligned_cols=64  Identities=22%  Similarity=0.098  Sum_probs=47.3

Q ss_pred             HHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHHHHHHHHHccCccc
Q 017842          174 EKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDID  253 (365)
Q Consensus       174 ~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~~Al~~lng~~~~  253 (365)
                      .+++....+||.|..|.|..+.                         ...-.-.--.||+|...+.|.+|+-.|||..|+
T Consensus       301 de~keEceKyg~V~~viifeip-------------------------~~p~deavRiFveF~r~e~aiKA~VdlnGRyFG  355 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIP-------------------------SQPEDEAVRIFVEFERVESAIKAVVDLNGRYFG  355 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecC-------------------------CCccchhheeeeeeccHHHHHHHHHhcCCceec
Confidence            4566778999999887643221                         111112334799999999999999999999999


Q ss_pred             CeeEEEeec
Q 017842          254 GRLLTVNKA  262 (365)
Q Consensus       254 gr~l~V~~a  262 (365)
                      ||.++..+.
T Consensus       356 Gr~v~A~Fy  364 (378)
T KOG1996|consen  356 GRVVSACFY  364 (378)
T ss_pred             ceeeeheec
Confidence            999887654

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=93.43  E-value=0.067  Score=46.72  Aligned_cols=74  Identities=11%  Similarity=0.100  Sum_probs=43.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHc-cCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEK-AGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~-~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...+|-|++||+++|++++...+.. ++....    |..+.|.                 .-..........-|||.|.+
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~----w~y~~g~-----------------~~~~~~~~~~~SRaYi~F~~   64 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWD----WYYFQGK-----------------YGKKSFKPPTYSRAYINFKN   64 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE-------EEEEEE-----------------ES-SSSTTS--EEEEEEESS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccc----eEEEecC-----------------CCCccCCCCcceEEEEEeCC
Confidence            4568999999999999999887765 554411    1111110                 11111111234569999999


Q ss_pred             HHHHHHHHHHHccCcc
Q 017842          237 VEEAEKAVEMFHRYDI  252 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~  252 (365)
                      .+++......++|..|
T Consensus        65 ~~~~~~F~~~~~g~~F   80 (176)
T PF03467_consen   65 PEDLLEFRDRFDGHVF   80 (176)
T ss_dssp             CHHHHHHHHHCTTEEE
T ss_pred             HHHHHHHHHhcCCcEE
Confidence            9999999999999777

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.25  E-value=0.38  Score=44.78  Aligned_cols=74  Identities=23%  Similarity=0.249  Sum_probs=56.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      .+..|-|=+.|..... -|..+|.+||.|....                                +++...+-+|.|.+.
T Consensus       196 ~D~WVTVfGFppg~~s-~vL~~F~~cG~Vvkhv--------------------------------~~~ngNwMhirYssr  242 (350)
T KOG4285|consen  196 ADTWVTVFGFPPGQVS-IVLNLFSRCGEVVKHV--------------------------------TPSNGNWMHIRYSSR  242 (350)
T ss_pred             ccceEEEeccCccchh-HHHHHHHhhCeeeeee--------------------------------cCCCCceEEEEecch
Confidence            3567888888887654 4778999999885543                                446667899999999


Q ss_pred             HHHHHHHHHHccCcccCee-EEEeecCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRL-LTVNKAAPR  265 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~-l~V~~a~~~  265 (365)
                      -.|.+||.. ||..|+|.. |-|..+..+
T Consensus       243 ~~A~KALsk-ng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  243 THAQKALSK-NGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             hHHHHhhhh-cCeeeccceEEeeeecCCH
Confidence            999999998 999997754 455554443

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=93.11  E-value=0.095  Score=53.52  Aligned_cols=72  Identities=22%  Similarity=0.306  Sum_probs=63.3

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ..++..++||+|+-..+..+-++.+...+|.|..+....         |||..|..+....+|+..|+-..++|.++.+.
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~  106 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIEN  106 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhcc
Confidence            345556999999999999999999999999998886542         89999999999999999999999999988776


Q ss_pred             E
Q 017842          355 V  355 (365)
Q Consensus       355 ~  355 (365)
                      .
T Consensus       107 ~  107 (668)
T KOG2253|consen  107 V  107 (668)
T ss_pred             c
Confidence            5

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=92.64  E-value=0.66  Score=34.25  Aligned_cols=59  Identities=19%  Similarity=0.374  Sum_probs=36.3

Q ss_pred             CcCcHHHHHHHHhccC-----CeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          289 WEVDNARLEQVFSEHG-----KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       289 ~~~tee~L~~~F~~~G-----~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ..++..+|-.++...+     .|-.|+|..+        |+||+-... .|..++..|++..+.|++|+|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            3567778877777664     5777877633        899998874 889999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=92.24  E-value=0.29  Score=43.03  Aligned_cols=61  Identities=23%  Similarity=0.238  Sum_probs=45.7

Q ss_pred             cHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC--CCccCCeeEEEEEccc
Q 017842          292 DNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD--GQNLDGRAIRVNVAED  358 (365)
Q Consensus       292 tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~--~~~l~gr~l~V~~a~~  358 (365)
                      ....|+.+|..|+.+.....++.      =+-..|.|.+.+.|.+|...|+  +..+.|..|+|-|+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            45789999999999888877744      3358999999999999999999  9999999999999853

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=92.04  E-value=0.013  Score=59.49  Aligned_cols=147  Identities=19%  Similarity=0.271  Sum_probs=94.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ++..+|||||+.+.+...-++.....||-|.+..                                  + --|||..|..
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~k----------------------------------r-~~fgf~~f~~   82 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWK----------------------------------R-DKFGFCEFLK   82 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhh----------------------------------h-hhhcccchhh
Confidence            3567999999999999999999999999886543                                  1 1199999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCC-------CCCCCCcCCC---CceEEEeCCCCcCcHHHHHHHHhccCCe
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ-------PERAPRVFEP---GFRIYVGNLPWEVDNARLEQVFSEHGKV  306 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~-------~~~~~~~~~~---~~~lfV~nLp~~~tee~L~~~F~~~G~V  306 (365)
                      ......|+..++-..++|..+.+..-......       .........+   .+-.+|+|+|..+........+.-.+..
T Consensus        83 ~~~~~ra~r~~t~~~~~~~kl~~~~d~q~~~n~~k~~~~~~~~~~~f~p~~srr~e~i~~k~~~l~~~~~~~~~~is~s~  162 (668)
T KOG2253|consen   83 HIGDLRASRLLTELNIDDQKLIENVDEQTIENADKEKSIANKESHKFVPSSSRRQESIQNKPLSLDEQIHKKSLQISSSA  162 (668)
T ss_pred             HHHHHHHHHHhcccCCCcchhhccchhhhhcCccccccchhhhhcccCCchhHHHHHhhccccchhHHHHHHHHhccchh
Confidence            99999999999999999988887642111000       0000011111   3467889998888877777777655444


Q ss_pred             EEEEEEeeCCCCCcceEEEEEecCHHHHHHHHH
Q 017842          307 VNARVVYDRETGRSRGFGFVTMSSETELNDAIA  339 (365)
Q Consensus       307 ~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~  339 (365)
                      ...+.+... .+...-++|-.|.+......++.
T Consensus       163 ~s~~~~~e~-d~h~~e~~~~~~~s~~~~~~~~~  194 (668)
T KOG2253|consen  163 ASRRQIAEA-DDHCLELEKTETESNSALSKEAE  194 (668)
T ss_pred             hhhhhhHHH-HHHHHHHHHhhcccccccCcccc
Confidence            444333321 12223344444544444433333

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=91.61  E-value=0.076  Score=50.09  Aligned_cols=79  Identities=24%  Similarity=0.418  Sum_probs=60.4

Q ss_pred             eEEEeCCCCcCcHHHHH---HHHhccCCeEEEEEEeeCC-CCCcce--EEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          281 RIYVGNLPWEVDNARLE---QVFSEHGKVVNARVVYDRE-TGRSRG--FGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~---~~F~~~G~V~~v~i~~d~~-~~~~kG--~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      -+||-+|+..+..+.+.   ++|..||.|..|.+-++.. .....|  -+||+|...++|..||...+|..+.|+.|+..
T Consensus        79 lvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka~  158 (327)
T KOG2068|consen   79 LVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKAS  158 (327)
T ss_pred             hhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHHh
Confidence            57777888776665543   5788899999999988762 111111  37999999999999999999999999998877


Q ss_pred             Ecccc
Q 017842          355 VAEDR  359 (365)
Q Consensus       355 ~a~~~  359 (365)
                      +...+
T Consensus       159 ~gttk  163 (327)
T KOG2068|consen  159 LGTTK  163 (327)
T ss_pred             hCCCc
Confidence            76543

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=91.38  E-value=0.78  Score=34.67  Aligned_cols=57  Identities=16%  Similarity=0.336  Sum_probs=40.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      .+...+|+ .|......+|.++|+.||.|..-=                           +       +-..|||.....
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~VsW---------------------------i-------~dTSAfV~l~~r   52 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSW---------------------------I-------NDTSAFVALHNR   52 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEEEEE---------------------------E-------CTTEEEEEECCC
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEEEEE---------------------------E-------cCCcEEEEeecH
Confidence            34455565 999999999999999999985321                           1       234699999999


Q ss_pred             HHHHHHHHHHcc
Q 017842          238 EEAEKAVEMFHR  249 (365)
Q Consensus       238 e~a~~Al~~lng  249 (365)
                      +.|..++..++.
T Consensus        53 ~~~~~v~~~~~~   64 (87)
T PF08675_consen   53 DQAKVVMNTLKK   64 (87)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHHHhcc
Confidence            999998888653

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=91.35  E-value=0.12  Score=50.84  Aligned_cols=72  Identities=24%  Similarity=0.347  Sum_probs=58.6

Q ss_pred             eEEEeCCCCcC-cHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          281 RIYVGNLPWEV-DNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       281 ~lfV~nLp~~~-tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      .|-+.-.|+.. |-.+|..+|..||.|..|.|-+.      .-.|.|+|.+..+|.+|.. .++..|++|.|.|.|.++.
T Consensus       374 ~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  374 PLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             hhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEEecCC
Confidence            44444445554 45889999999999999988654      2358999999999999988 7999999999999998764

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.25  E-value=3.3  Score=42.04  Aligned_cols=35  Identities=11%  Similarity=0.196  Sum_probs=29.8

Q ss_pred             eEEEEEecCHHHHHHHHHHhCCCccC--CeeEEEEEc
Q 017842          322 GFGFVTMSSETELNDAIAALDGQNLD--GRAIRVNVA  356 (365)
Q Consensus       322 G~afV~F~s~~~a~~Al~~l~~~~l~--gr~l~V~~a  356 (365)
                      -||.|+|.+...|......++|..|.  |..|-++|-
T Consensus       269 YyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFI  305 (650)
T KOG2318|consen  269 YYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFI  305 (650)
T ss_pred             EEEEEEecCchHHHHHHHhcCcceeccccceeeeeec
Confidence            38999999999999999999999884  567777664

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=91.07  E-value=0.14  Score=53.67  Aligned_cols=72  Identities=25%  Similarity=0.307  Sum_probs=61.0

Q ss_pred             EEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc--CCeeEEEEEcccc
Q 017842          282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL--DGRAIRVNVAEDR  359 (365)
Q Consensus       282 lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l--~gr~l~V~~a~~~  359 (365)
                      ..+.|.+-..+-..|..+|..||.|...+.+|+-      ..|.|.|.+.+.|..|+.+|+|+.+  .|.+.+|.+|+.-
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            3444556677778899999999999999999884      3799999999999999999999965  6889999998753

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=91.01  E-value=0.98  Score=32.66  Aligned_cols=55  Identities=18%  Similarity=0.279  Sum_probs=42.5

Q ss_pred             cCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          290 EVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       290 ~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      .++-++++..+..|+ -.  +|..|+     .|| ||.|.+..+|.+|....+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~-~~--~I~~d~-----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WD--RIRDDR-----TGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCC-cc--eEEecC-----CEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            467789999999994 23  344443     344 99999999999999999999888777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=90.90  E-value=0.74  Score=45.19  Aligned_cols=67  Identities=10%  Similarity=0.215  Sum_probs=57.8

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccC-CeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHG-KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD  347 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G-~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~  347 (365)
                      ++.|+|-.+|..++--+|-.|+..+- .|..++|+||..  -.+-.++|.|.+..+|......+||+.|.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            56899999999999999999998764 789999999732  22456899999999999999999999884

>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins

Probab=90.42  E-value=0.37  Score=47.26  Aligned_cols=9  Identities=11%  Similarity=0.257  Sum_probs=3.9

Q ss_pred             CCeEEEcCC
Q 017842          159 DAKLFVGNL  167 (365)
Q Consensus       159 ~~tvfVgnL  167 (365)
                      ...+|.-+.
T Consensus       121 d~~~WtP~~  129 (458)
T PF10446_consen  121 DYEFWTPGA  129 (458)
T ss_pred             cceeecccc
Confidence            344444443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=90.39  E-value=1.9  Score=36.05  Aligned_cols=75  Identities=17%  Similarity=0.255  Sum_probs=56.0

Q ss_pred             CCCCCCeEEEcCCCCCCC-HHH---HHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceE
Q 017842          155 EPPEDAKLFVGNLPYDVD-SEK---LAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFG  230 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t-~~~---L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~a  230 (365)
                      ..++-.||.|+=|..++. .++   +...++.||+|.++..                                 -.+..|
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~---------------------------------cGrqsa  128 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTL---------------------------------CGRQSA  128 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeee---------------------------------cCCceE
Confidence            455677999998888773 334   4455688999998762                                 245679


Q ss_pred             EEEeCCHHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          231 FVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       231 fV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      .|+|.+..+|=+|+.++.. ...|..+.+.+..
T Consensus       129 vVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWqq  160 (166)
T PF15023_consen  129 VVVFKDITSACKAVSAFQS-RAPGTMFQCSWQQ  160 (166)
T ss_pred             EEEehhhHHHHHHHHhhcC-CCCCceEEeeccc
Confidence            9999999999999998554 6677888777643

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=90.08  E-value=0.65  Score=43.30  Aligned_cols=72  Identities=24%  Similarity=0.311  Sum_probs=54.5

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe-eEEEEEcccc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGR-AIRVNVAEDR  359 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr-~l~V~~a~~~  359 (365)
                      =|-|-+.|.. .-.-|..+|..||.|........      -.+-+|.|.++.+|.+||. .||+.|+|- -|-|..|.++
T Consensus       199 WVTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~~n------gNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  199 WVTVFGFPPG-QVSIVLNLFSRCGEVVKHVTPSN------GNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             eEEEeccCcc-chhHHHHHHHhhCeeeeeecCCC------CceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecCCH
Confidence            4566677654 34567789999999988865522      3489999999999999999 799999875 5667776655


Q ss_pred             c
Q 017842          360 Q  360 (365)
Q Consensus       360 ~  360 (365)
                      .
T Consensus       271 s  271 (350)
T KOG4285|consen  271 S  271 (350)
T ss_pred             H
Confidence            4

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=90.05  E-value=0.15  Score=48.12  Aligned_cols=85  Identities=16%  Similarity=0.262  Sum_probs=59.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHH---HHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          158 EDAKLFVGNLPYDVDSEKLA---MLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~---~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      ...-+||-+|+.....+.+.   ..|.+||.|..+.+.-..-                      . ........-+||+|
T Consensus        76 qknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S----------------------~-~s~~~~~~s~yITy  132 (327)
T KOG2068|consen   76 QKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPS----------------------S-SSSSGGTCSVYITY  132 (327)
T ss_pred             hhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcc----------------------c-ccCCCCCCcccccc
Confidence            44678999999888655544   4688899988775321100                      0 00111223389999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      ...++|..||...+|....|+.|+..+...+
T Consensus       133 ~~~eda~rci~~v~g~~~dg~~lka~~gttk  163 (327)
T KOG2068|consen  133 EEEEDADRCIDDVDGFVDDGRALKASLGTTK  163 (327)
T ss_pred             cchHhhhhHHHHhhhHHhhhhhhHHhhCCCc
Confidence            9999999999999999999999877655444

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=89.99  E-value=0.4  Score=43.71  Aligned_cols=74  Identities=24%  Similarity=0.311  Sum_probs=58.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      ..|||.||+.-+.-+.|...|+.||+|....                          ++.+ ..++..+-++|.|...-.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av--------------------------~~vD-~r~k~t~eg~v~~~~k~~   84 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAV--------------------------AKVD-DRGKPTREGIVEFAKKPN   84 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchhe--------------------------eeec-ccccccccchhhhhcchh
Confidence            5799999999999999999999999998764                          3333 466778889999999999


Q ss_pred             HHHHHHHHcc----CcccCeeEEEe
Q 017842          240 AEKAVEMFHR----YDIDGRLLTVN  260 (365)
Q Consensus       240 a~~Al~~lng----~~~~gr~l~V~  260 (365)
                      +.+|+..++-    ....+++.-|.
T Consensus        85 a~~a~rr~~~~g~~~~~~~~p~~Ve  109 (275)
T KOG0115|consen   85 ARKAARRCREGGFGGTTGGRPVGVE  109 (275)
T ss_pred             HHHHHHHhccCccccCCCCCccCCC
Confidence            9999988742    33345555553

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=89.83  E-value=0.88  Score=45.81  Aligned_cols=97  Identities=14%  Similarity=0.198  Sum_probs=68.5

Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhc--cCCeEEEEEEee
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSE--HGKVVNARVVYD  314 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~--~G~V~~v~i~~d  314 (365)
                      .+-...+|....++.++.+-.+|....              ..|.|.++-||.....++++.+|..  +-.+.+|.+..+
T Consensus       147 vdLI~Evlresp~VqvDekgekVrp~~--------------kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N  212 (684)
T KOG2591|consen  147 VDLIVEVLRESPNVQVDEKGEKVRPNH--------------KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN  212 (684)
T ss_pred             hHHHHHHHhcCCCceeccCccccccCc--------------ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec
Confidence            334444555555666666666665322              2357888999999999999999975  557888877654


Q ss_pred             CCCCCcceEEEEEecCHHHHHHHHHHhCC--CccCCeeEEEE
Q 017842          315 RETGRSRGFGFVTMSSETELNDAIAALDG--QNLDGRAIRVN  354 (365)
Q Consensus       315 ~~~~~~kG~afV~F~s~~~a~~Al~~l~~--~~l~gr~l~V~  354 (365)
                      .       -=||+|.+..+|..|.+.|..  +.|.|+.|-.+
T Consensus       213 ~-------nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  213 D-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             C-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            2       158999999999999998754  36667665443

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=88.74  E-value=0.25  Score=48.70  Aligned_cols=75  Identities=23%  Similarity=0.277  Sum_probs=59.4

Q ss_pred             CCeEEEcCCCCCC-CHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          159 DAKLFVGNLPYDV-DSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       159 ~~tvfVgnLp~~~-t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      .+.+-+.-.|+.. +..+|..+|.+||.|..|.+.                                .+.--|.|+|.+.
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~--------------------------------~~~~~a~vTF~t~  419 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVD--------------------------------YSSLHAVVTFKTR  419 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCcccccccc--------------------------------Cchhhheeeeecc
Confidence            4556666667666 678899999999999887632                                2245689999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ..|-.|... .+.+|++|.|+|.|..+..
T Consensus       420 aeag~a~~s-~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  420 AEAGEAYAS-HGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             ccccchhcc-ccceecCceeEEEEecCCc
Confidence            999878766 9999999999999987644

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=88.40  E-value=1.8  Score=32.74  Aligned_cols=54  Identities=19%  Similarity=0.308  Sum_probs=39.8

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDG  343 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~  343 (365)
                      ..+|. .|..+...+|.++|+.||.|. |..+.|       ..|||...+.+.|..|+..++-
T Consensus        11 VFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   11 VFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             EEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             EEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhcc
Confidence            44454 999999999999999999875 444434       2699999999999999987753

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=87.86  E-value=1.9  Score=33.11  Aligned_cols=71  Identities=10%  Similarity=0.055  Sum_probs=45.8

Q ss_pred             EEEEeCCHHHHHHHHHHHc-cCcccCeeEEEeecCCCCCCCC-CCCCcCCCCceEEEeCCCCcCcHHHHHHHH
Q 017842          230 GFVTMSTVEEAEKAVEMFH-RYDIDGRLLTVNKAAPRGTQPE-RAPRVFEPGFRIYVGNLPWEVDNARLEQVF  300 (365)
Q Consensus       230 afV~f~~~e~a~~Al~~ln-g~~~~gr~l~V~~a~~~~~~~~-~~~~~~~~~~~lfV~nLp~~~tee~L~~~F  300 (365)
                      |.|+|.+...|.+.+++-. ...+++..+.|........... -......++++|-|.|||...++++|+..+
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeE
Confidence            6899999999999887621 2445666666643322111111 111233455699999999999999998654

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=86.39  E-value=0.58  Score=43.06  Aligned_cols=79  Identities=23%  Similarity=0.437  Sum_probs=53.0

Q ss_pred             ceEEEeCCCCc------------CcHHHHHHHHhccCCeEEEEEEee-----CCCCCc-----ceE---------EEEEe
Q 017842          280 FRIYVGNLPWE------------VDNARLEQVFSEHGKVVNARVVYD-----RETGRS-----RGF---------GFVTM  328 (365)
Q Consensus       280 ~~lfV~nLp~~------------~tee~L~~~F~~~G~V~~v~i~~d-----~~~~~~-----kG~---------afV~F  328 (365)
                      -||++.+||-.            .++..|+..|+.||.|..|.|+.-     .-+|+.     .||         |||+|
T Consensus       150 dti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipicdplr~~mn~kisgiq~~gfg~g~dlffeayvqf  229 (445)
T KOG2891|consen  150 DTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPICDPLREEMNGKISGIQFHGFGFGGDLFFEAYVQF  229 (445)
T ss_pred             CceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcccchhHHHhcCccccceeeccccCcchhHHHHHHH
Confidence            48888888832            356889999999999999988532     112332     333         36777


Q ss_pred             cCHHHHHHHHHHhCCCcc----CCe----eEEEEEccc
Q 017842          329 SSETELNDAIAALDGQNL----DGR----AIRVNVAED  358 (365)
Q Consensus       329 ~s~~~a~~Al~~l~~~~l----~gr----~l~V~~a~~  358 (365)
                      ...-....|+..|.|..+    .|+    .+.|.|..+
T Consensus       230 meykgfa~amdalr~~k~akk~d~~ffqanvkvdfdrs  267 (445)
T KOG2891|consen  230 MEYKGFAQAMDALRGMKLAKKGDDGFFQANVKVDFDRS  267 (445)
T ss_pred             HHHHhHHHHHHHHhcchHHhhcCCcccccccccccchh
Confidence            777777788888888755    333    555555443

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=84.91  E-value=2.4  Score=37.21  Aligned_cols=62  Identities=21%  Similarity=0.229  Sum_probs=43.5

Q ss_pred             CHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHHHHHHHHHc--c
Q 017842          172 DSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFH--R  249 (365)
Q Consensus       172 t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~~Al~~ln--g  249 (365)
                      ....|+.+|..|+.+..+.                          .+      ++-+-..|.|.+.++|.+|...|+  +
T Consensus         8 ~~~~l~~l~~~~~~~~~~~--------------------------~L------~sFrRi~v~f~~~~~A~~~r~~l~~~~   55 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFS--------------------------PL------KSFRRIRVVFESPESAQRARQLLHWDG   55 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEE--------------------------EE------TTTTEEEEE-SSTTHHHHHHHTST--T
T ss_pred             hHHHHHHHHHhcCCceEEE--------------------------Ec------CCCCEEEEEeCCHHHHHHHHHHhcccc
Confidence            4578999999999876653                          11      334558899999999999999999  9


Q ss_pred             CcccCeeEEEeecCCC
Q 017842          250 YDIDGRLLTVNKAAPR  265 (365)
Q Consensus       250 ~~~~gr~l~V~~a~~~  265 (365)
                      ..+.|..|+|.++...
T Consensus        56 ~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen   56 TSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             SEETTEE-EEE----S
T ss_pred             cccCCCceEEEEcccc
Confidence            9999999999887544

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production []

Probab=84.80  E-value=1.4  Score=47.93  Aligned_cols=21  Identities=24%  Similarity=0.447  Sum_probs=14.7

Q ss_pred             EcCCCCCC----CHHHHHHHHHccC
Q 017842          164 VGNLPYDV----DSEKLAMLFEKAG  184 (365)
Q Consensus       164 VgnLp~~~----t~~~L~~~F~~~G  184 (365)
                      -..||+..    +.++|..++..+.
T Consensus       415 ~~elPftf~~P~s~eel~~lL~~~~  439 (840)
T PF04147_consen  415 KSELPFTFPCPSSHEELLELLDGYS  439 (840)
T ss_pred             ccCCCceecCCCCHHHHHHHHhcCC
Confidence            44566553    7788999998765

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=84.66  E-value=5.7  Score=39.22  Aligned_cols=77  Identities=14%  Similarity=0.206  Sum_probs=59.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHcc-CCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKA-GTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~-G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ..+.|+|-.+|..++..+|..|...+ -.|..++                          ++++..  .++=...|.|.+
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~ir--------------------------ivRd~~--pnrymvLIkFr~  124 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIR--------------------------IVRDGM--PNRYMVLIKFRD  124 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeE--------------------------EeecCC--CceEEEEEEecc
Confidence            37899999999999999999998764 3455544                          666432  234457999999


Q ss_pred             HHHHHHHHHHHccCcccC------eeEEEeec
Q 017842          237 VEEAEKAVEMFHRYDIDG------RLLTVNKA  262 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~g------r~l~V~~a  262 (365)
                      .++|......+||..|+.      +.|.|..+
T Consensus       125 q~da~~Fy~efNGk~Fn~le~e~Chll~V~~v  156 (493)
T KOG0804|consen  125 QADADTFYEEFNGKQFNSLEPEVCHLLYVDRV  156 (493)
T ss_pred             chhHHHHHHHcCCCcCCCCCccceeEEEEEEE
Confidence            999999999999999865      55666543

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=84.35  E-value=6.2  Score=28.14  Aligned_cols=53  Identities=15%  Similarity=0.218  Sum_probs=38.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHcc----CCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKA----GTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~----G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ..|+|.++. +++.++++.+|..|    ++. .+.                          .+-       -..|=|+|.
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~-~IE--------------------------WId-------DtScNvvf~   50 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPF-RIE--------------------------WID-------DTSCNVVFK   50 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCc-eEE--------------------------Eec-------CCcEEEEEC
Confidence            479999984 47888999999998    432 222                          221       123679999


Q ss_pred             CHHHHHHHHHHH
Q 017842          236 TVEEAEKAVEMF  247 (365)
Q Consensus       236 ~~e~a~~Al~~l  247 (365)
                      +.+.|.+|+..|
T Consensus        51 d~~~A~~AL~~L   62 (62)
T PF10309_consen   51 DEETAARALVAL   62 (62)
T ss_pred             CHHHHHHHHHcC
Confidence            999999998753

>PF12220 U1snRNP70_N: U1 small nuclear ribonucleoprotein of 70kDa MW N terminal; InterPro: IPR022023 This domain is found in eukaryotes

Probab=83.74  E-value=0.095  Score=40.80  Aligned_cols=43  Identities=23%  Similarity=0.137  Sum_probs=30.6

Q ss_pred             cCCCCcccc-cCCCCccCCCCCCc-ee-eeccccccCCCccccccc
Q 017842           21 LLSPPSIFA-RNPYFSIHPRPRPI-KL-HLSDSSLSSKGFSFKLKK   63 (365)
Q Consensus        21 ~~~~~~~f~-~~~~~~~~~~~~p~-~~-~~~~~~~~~~~~~~~~~~   63 (365)
                      .+.++.||. ||+..|+++.+.|. +. ...+++++.+...|....
T Consensus         6 Pp~ll~LF~PRPPL~y~pP~d~~p~~r~t~~itGvs~~l~~~~~~~   51 (94)
T PF12220_consen    6 PPNLLALFAPRPPLPYLPPIDYPPEKRKTPPITGVSQYLSEFEDYK   51 (94)
T ss_pred             CHHHHHHcCCCCCCCCCCccccCcccccCCCCCcHHHHHHHHhccc
Confidence            455779999 99999999988876 32 223777777765555444

This domain is about 90 amino acids in length. This domain is found associated with PF00076 from PFAM. This domain is part of U1 snRNP, which is the pre-mRNA binding protein of the penta-snRNP spliceosome complex. It extends over a distance of 180 A from its RNA binding domain, wraps around the core domain of U1 snRNP consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition.

>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar

Probab=81.95  E-value=0.87  Score=49.17  Aligned_cols=7  Identities=43%  Similarity=0.852  Sum_probs=3.3

Q ss_pred             HHHHHHc
Q 017842          176 LAMLFEK  182 (365)
Q Consensus       176 L~~~F~~  182 (365)
                      |.++|..
T Consensus       741 La~~Fk~  747 (784)
T PF04931_consen  741 LAAIFKE  747 (784)
T ss_pred             HHHHHHH
Confidence            4445543

The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=81.70  E-value=16  Score=29.31  Aligned_cols=36  Identities=17%  Similarity=0.251  Sum_probs=28.5

Q ss_pred             EEecCCCCCccceEEEEeCCHHHHHHHHHHHccCcccC
Q 017842          217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDG  254 (365)
Q Consensus       217 ~~~~~~~~~~~g~afV~f~~~e~a~~Al~~lng~~~~g  254 (365)
                      ++++.  ..++-.+.+.|.+..+|......+||..|+.
T Consensus        46 iird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   46 IIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             EeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            55543  2356678999999999999999999988854

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=81.11  E-value=7.6  Score=28.04  Aligned_cols=55  Identities=15%  Similarity=0.104  Sum_probs=41.5

Q ss_pred             CCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHHHHHHHHHcc
Q 017842          170 DVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHR  249 (365)
Q Consensus       170 ~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~~Al~~lng  249 (365)
                      .++-.+++..+..|+-..                             |+ ...+    | -||+|.+..+|+++....+|
T Consensus        11 ~~~v~d~K~~Lr~y~~~~-----------------------------I~-~d~t----G-fYIvF~~~~Ea~rC~~~~~~   55 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWDR-----------------------------IR-DDRT----G-FYIVFNDSKEAERCFRAEDG   55 (66)
T ss_pred             CccHHHHHHHHhcCCcce-----------------------------EE-ecCC----E-EEEEECChHHHHHHHHhcCC
Confidence            457789999999987542                             12 1123    3 49999999999999999999


Q ss_pred             CcccCeeEEE
Q 017842          250 YDIDGRLLTV  259 (365)
Q Consensus       250 ~~~~gr~l~V  259 (365)
                      ..+.+-.|.+
T Consensus        56 ~~~f~y~m~M   65 (66)
T PF11767_consen   56 TLFFTYRMQM   65 (66)
T ss_pred             CEEEEEEEEe
Confidence            9888776654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	365
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		2e-15
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		6e-15
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-05
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		7e-15
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-14
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		3e-04
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		3e-14
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		6e-14
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		5e-06
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		6e-14
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		6e-14
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		7e-06
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		6e-14
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		7e-06
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		9e-14
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		7e-06
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		9e-14
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		6e-06
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		6e-13
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		1e-12
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		4e-04
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-12
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		3e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-12
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		3e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-11
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		4e-11
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		8e-11
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		1e-10
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		5e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-10
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		8e-10
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-09
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		3e-09
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		3e-09
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		6e-09
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		1e-08
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-08
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		3e-04
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		1e-08
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		1e-04
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		1e-08
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		2e-08
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-08
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		2e-08
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		2e-08
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		2e-08
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		2e-08
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		3e-08
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		5e-08
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		9e-08
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		1e-07
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-07
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		6e-05
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		2e-07
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		2e-07
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		2e-07
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		2e-07
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-07
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		2e-07
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		2e-07
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		2e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		3e-07
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		3e-07
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		3e-07
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		4e-07
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		4e-07
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		4e-07
2dng_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		4e-07
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		4e-07
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		5e-07
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		7e-07
1sxl_A	97	Resonance Assignments And Solution Structure Of The		7e-07
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		1e-06
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-06
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		1e-06
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		1e-06
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		2e-06
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		2e-06
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		2e-06
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		3e-06
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		6e-06
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		8e-06
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		8e-06
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		9e-06
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		9e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		1e-05
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		2e-05
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		2e-05
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		2e-05
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		3e-05
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		3e-05
1x5o_A	114	Solution Structure Of Rrm Domain In Rna Binding Mot		3e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		3e-05
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		4e-05
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		4e-05
2dnp_A	90	Solution Structure Of Rna Binding Domain 2 In Rna-B		5e-05
2khc_A	118	Bruno Rrm3+ Length = 118		6e-05
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		6e-05
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		6e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		6e-05
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		6e-05
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		6e-05
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		8e-05
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		8e-05
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		1e-04
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		2e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		2e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		2e-04
1wf2_A	98	Solution Structure Of Rrm Domain In Hnrpc Protein L		2e-04
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		3e-04
2kt5_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		3e-04
2yka_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		3e-04
3n9u_C	156	Crystal Structure Of The Complex Between The 25 Kda		4e-04
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		4e-04
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		5e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		6e-04
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		6e-04
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		6e-04
2f3j_A	177	The Solution Structure Of The Ref2-I Mrna Export Fa		6e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		6e-04
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		6e-04
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		8e-04
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		8e-04

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 80.1 bits (196), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 94/201 (46%), Gaps = 37/201 (18%)
Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
            K+F+G L +D   + L   F K GTV                          + L+++ 
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTV--------------------------TDLKIMK 37
Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPG 279
           +  T RSRGFGF++       ++ V+  H   +DG+++   +A PR  Q +         
Sbjct: 38  DPATGRSRGFGFLSFEKPSSVDEVVKTQHI--LDGKVIDPKRAIPRDEQDKTG------- 88
Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
            +I+VG +  +V     E+ FS+ G +++A+++ D++TG+SRGFGFVT  S   + D + 
Sbjct: 89  -KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV-DRVC 146
Query: 340 ALDGQNLDGRAIRVNVAEDRQ 360
                +   R I +  AE R 
Sbjct: 147 QNKFIDFKDRKIEIKRAEPRH 167

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 78.2 bits (191), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 47/163 (28%), Positives = 81/163 (49%), Gaps = 17/163 (10%)
Query: 193 FHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI 252
           F  LFG+ G  +  C        +++ ++ T +S G+GFV  S   +A+KA+   +   +
Sbjct: 21  FKSLFGSIG-DIESC--------KLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKL 71
Query: 253 DGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVV 312
             + + V+ A P       A         +YV  LP  +    +EQ+FS++G+++ +R++
Sbjct: 72  QTKTIKVSYARPSSASIRDA--------NLYVSGLPKTMSQKEMEQLFSQYGRIITSRIL 123
Query: 313 YDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV 355
            D+ TG SRG GF+      E  +AI  L+GQ   G A  + V
Sbjct: 124 LDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITV 166

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 40/75 (53%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP  +     + +F   G + + ++V D+ TG+S G+GFV  S   + + AI  L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 342 DGQNLDGRAIRVNVA 356
           +G  L  + I+V+ A
Sbjct: 67  NGLKLQTKTIKVSYA 81

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 78.2 bits (191), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 55/76 (72%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG L ++ +   LEQVFS++G++    VV DRET RSRGFGFVT  +  +  DA+ A
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 341 LDGQNLDGRAIRVNVA 356
           ++G+++DGR IRV+ A
Sbjct: 74  MNGKSVDGRQIRVDQA 89

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 77.4 bits (189), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 46/156 (29%), Positives = 78/156 (50%), Gaps = 17/156 (10%)
Query: 193 FHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI 252
           F  LFG+ G  +  C        +++ ++ T +S G+GFV     ++AEKA+   +   +
Sbjct: 19  FRSLFGSIG-EIESC--------KLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL 69
Query: 253 DGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVV 312
             + + V+ A P       A         +YV  LP  +    LEQ+FS++G+++ +R++
Sbjct: 70  QTKTIKVSYARPSSASIRDA--------NLYVSGLPKTMTQKELEQLFSQYGRIITSRIL 121
Query: 313 YDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDG 348
            D+ TG SRG GF+      E  +AI  L+GQ   G
Sbjct: 122 VDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 38/75 (50%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP  +       +F   G++ + ++V D+ TG+S G+GFV      +   AI  L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 342 DGQNLDGRAIRVNVA 356
           +G  L  + I+V+ A
Sbjct: 65  NGLRLQTKTIKVSYA 79

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 75.9 bits (185), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 55/79 (69%), Gaps = 1/79 (1%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           IYVGNL +   + +++++FS+ GKV N +++YDRET + +GFGFV M  E+ +++AIA L
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKL 62
Query: 342 DGQNLDGRAIRVNVAEDRQ 360
           D  +  GR IRV  A  ++
Sbjct: 63  DNTDFMGRTIRVTEANPKK 81

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 91/204 (44%), Gaps = 30/204 (14%)
Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLF+G L ++   E L   FE+ GT                  +  C V        + +
Sbjct: 16  KLFIGGLSFETTDESLRSHFEQWGT------------------LTDCVV--------MRD 49
Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGF 280
             T RSRGFGFVT +TVEE + A+     + +DGR++   +A  R  +  + P       
Sbjct: 50  PNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR--EDSQRPGAHLTVK 106
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG +  + +   L   F ++GK+    ++ DR +G+ RGF FVT      + D I  
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV-DKIVI 165
Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
                ++G    V  A  +Q  +S
Sbjct: 166 QKYHTVNGHNCEVRKALSKQEMAS 189

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 48.9 bits (115), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 32/99 (32%), Positives = 51/99 (51%), Gaps = 4/99 (4%)
Query: 266 GTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGF 325
           G     +P+  E   ++++G L +E  +  L   F + G + +  V+ D  T RSRGFGF
Sbjct: 1   GGSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 60
Query: 326 VTMSSETELNDAIAALDGQNLDGRAI---RVNVAEDRQR 361
           VT ++  E++ A+ A     +DGR +   R    ED QR
Sbjct: 61  VTYATVEEVDAAMNARP-HKVDGRVVEPKRAVSREDSQR 98

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 91/204 (44%), Gaps = 30/204 (14%)
Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLF+G L ++   E L   FE+ GT                  +  C V        + +
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGT------------------LTDCVV--------MRD 41
Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGF 280
             T RSRGFGFVT +TVEE + A+     + +DGR++   +A  R  +  + P       
Sbjct: 42  PNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR--EDSQRPGAHLTVK 98
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG +  + +   L   F ++GK+    ++ DR +G+ RGF FVT      + D I  
Sbjct: 99  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV-DKIVI 157
Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
                ++G    V  A  +Q  +S
Sbjct: 158 QKYHTVNGHNCEVRKALSKQEMAS 181

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 91/204 (44%), Gaps = 30/204 (14%)
Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLF+G L ++   E L   FE+ GT                  +  C V        + +
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGT------------------LTDCVV--------MRD 48
Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGF 280
             T RSRGFGFVT +TVEE + A+     + +DGR++   +A  R  +  + P       
Sbjct: 49  PNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR--EDSQRPGAHLTVK 105
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG +  + +   L   F ++GK+    ++ DR +G+ RGF FVT      + D I  
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV-DKIVI 164
Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
                ++G    V  A  +Q  +S
Sbjct: 165 QKYHTVNGHNCEVRKALSKQEMAS 188

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 31/93 (33%), Positives = 50/93 (53%), Gaps = 4/93 (4%)
Query: 272 APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
           +P+  E   ++++G L +E  +  L   F + G + +  V+ D  T RSRGFGFVT ++ 
Sbjct: 6   SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 65
Query: 332 TELNDAIAALDGQNLDGRAI---RVNVAEDRQR 361
            E++ A+ A     +DGR +   R    ED QR
Sbjct: 66  EEVDAAMNARP-HKVDGRVVEPKRAVSREDSQR 97

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 91/204 (44%), Gaps = 30/204 (14%)
Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLF+G L ++   E L   FE+ GT                  +  C V        + +
Sbjct: 14  KLFIGGLSFETTDESLRSHFEQWGT------------------LTDCVV--------MRD 47
Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGF 280
             T RSRGFGFVT +TVEE + A+     + +DGR++   +A  R  +  + P       
Sbjct: 48  PNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR--EDSQRPGAHLTVK 104
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG +  + +   L   F ++GK+    ++ DR +G+ RGF FVT      + D I  
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV-DKIVI 163
Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
                ++G    V  A  +Q  +S
Sbjct: 164 QKYHTVNGHNCEVRKALSKQEMAS 187

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 31/93 (33%), Positives = 50/93 (53%), Gaps = 4/93 (4%)
Query: 272 APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
           +P+  E   ++++G L +E  +  L   F + G + +  V+ D  T RSRGFGFVT ++ 
Sbjct: 5   SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 64
Query: 332 TELNDAIAALDGQNLDGRAI---RVNVAEDRQR 361
            E++ A+ A     +DGR +   R    ED QR
Sbjct: 65  EEVDAAMNARP-HKVDGRVVEPKRAVSREDSQR 96

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 74.3 bits (181), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 56/200 (28%), Positives = 89/200 (44%), Gaps = 30/200 (15%)
Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLF+G L ++   E L   FE+ GT                  +  C V        + +
Sbjct: 13  KLFIGGLSFETTDESLRSHFEQWGT------------------LTDCVV--------MRD 46
Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGF 280
             T RSRGFGFVT +TVEE + A+     + +DGR++   +A  R  +  + P       
Sbjct: 47  PNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR--EDSQRPGAHLTVK 103
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG +  + +   L   F ++GK+    ++ DR +G+ RGF FVT      + D I  
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV-DKIVI 162
Query: 341 LDGQNLDGRAIRVNVAEDRQ 360
                ++G    V  A  +Q
Sbjct: 163 QKYHTVNGHNCEVRKALSKQ 182

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 31/93 (33%), Positives = 50/93 (53%), Gaps = 4/93 (4%)
Query: 272 APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
           +P+  E   ++++G L +E  +  L   F + G + +  V+ D  T RSRGFGFVT ++ 
Sbjct: 4   SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 63
Query: 332 TELNDAIAALDGQNLDGRAI---RVNVAEDRQR 361
            E++ A+ A     +DGR +   R    ED QR
Sbjct: 64  EEVDAAMNARP-HKVDGRVVEPKRAVSREDSQR 95

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 74.3 bits (181), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 56/200 (28%), Positives = 89/200 (44%), Gaps = 30/200 (15%)
Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLF+G L ++   E L   FE+ GT                  +  C V        + +
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGT------------------LTDCVV--------MRD 48
Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGF 280
             T RSRGFGFVT +TVEE + A+     + +DGR++   +A  R  +  + P       
Sbjct: 49  PNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR--EDSQRPGAHLTVK 105
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG +  + +   L   F ++GK+    ++ DR +G+ RGF FVT      + D I  
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV-DKIVI 164
Query: 341 LDGQNLDGRAIRVNVAEDRQ 360
                ++G    V  A  +Q
Sbjct: 165 QKYHTVNGHNCEVRKALSKQ 184

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 31/93 (33%), Positives = 50/93 (53%), Gaps = 4/93 (4%)
Query: 272 APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
           +P+  E   ++++G L +E  +  L   F + G + +  V+ D  T RSRGFGFVT ++ 
Sbjct: 6   SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 65
Query: 332 TELNDAIAALDGQNLDGRAI---RVNVAEDRQR 361
            E++ A+ A     +DGR +   R    ED QR
Sbjct: 66  EEVDAAMNARP-HKVDGRVVEPKRAVSREDSQR 97

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 71.6 bits (174), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 33/81 (40%), Positives = 53/81 (65%), Gaps = 1/81 (1%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGN+P+E    +L+ +FSE G VV+ R+VYDRETG+ +G+GF     +     A+  L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 342 DGQNLDGRAIRV-NVAEDRQR 361
           +G+   GRA+RV N A ++ +
Sbjct: 71  NGREFSGRALRVDNAASEKNK 91

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 93/195 (47%), Gaps = 33/195 (16%)
Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L+VGNL   +  + L   F+  G   IA +K                         I   
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGP--IANIK-------------------------IMID 35
Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFR 281
           + +++  + FV      +A  A++  +   I+  ++ +N A     Q +++    +  F 
Sbjct: 36  KNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWA----FQSQQSSS--DDTFN 89
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VG+L   VD+  L   F +    ++  V++D +TG SRG+GFV+ +S+ +  +A+ ++
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 342 DGQNLDGRAIRVNVA 356
            GQ+L+GR +R+N A
Sbjct: 150 QGQDLNGRPLRINWA 164

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/83 (26%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVGNL   +    L+Q F   G + N +++ D+   ++  + FV      + N A+  L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQTL 61
Query: 342 DGQNLDGRAIRVNVAEDRQRRSS 364
           +G+ ++   +++N A   Q+ SS
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSS 84

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 47/187 (25%), Positives = 82/187 (43%), Gaps = 34/187 (18%)
Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L V  LP ++  ++L  LF   G VE A                          ++I ++
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESA--------------------------KLIRDK 38
Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFR 281
               S G+GFV   T ++AE+A+   +   +  + + V+ A P     + A         
Sbjct: 39  VAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDA--------N 90
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+  LP  +    +E +FS  G+++N+RV+ D+ TG SRG  F+     +E  +AI + 
Sbjct: 91  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 342 DGQNLDG 348
           +G    G
Sbjct: 151 NGHKPPG 157

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 40/75 (53%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP  +    L  +FS  G+V +A+++ D+  G S G+GFV   +  +   AI  L
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 342 DGQNLDGRAIRVNVA 356
           +G  L  + I+V+ A
Sbjct: 65  NGLRLQSKTIKVSYA 79

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 47/187 (25%), Positives = 82/187 (43%), Gaps = 34/187 (18%)
Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L V  LP ++  ++L  LF   G VE A                          ++I ++
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESA--------------------------KLIRDK 38
Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFR 281
               S G+GFV   T ++AE+A+   +   +  + + V+ A P     + A         
Sbjct: 39  VAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDA--------N 90
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+  LP  +    +E +FS  G+++N+RV+ D+ TG SRG  F+     +E  +AI + 
Sbjct: 91  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 342 DGQNLDG 348
           +G    G
Sbjct: 151 NGHKPPG 157

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 40/75 (53%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP  +    L  +FS  G+V +A+++ D+  G S G+GFV   +  +   AI  L
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 342 DGQNLDGRAIRVNVA 356
           +G  L  + I+V+ A
Sbjct: 65  NGLRLQSKTIKVSYA 79

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/77 (40%), Positives = 49/77 (63%)
Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           F ++VG+L  E+    ++  F+  GK+ +ARVV D  TG+S+G+GFV+  ++ +  +AI 
Sbjct: 16  FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 75
Query: 340 ALDGQNLDGRAIRVNVA 356
            + GQ L GR IR N A
Sbjct: 76  HMGGQWLGGRQIRTNWA 92

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 65.5 bits (158), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 51/77 (66%)
Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           F ++VG+L   VD+  L   F +    ++  V++D +TG SRG+GFV+ +S+ +  +A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 340 ALDGQNLDGRAIRVNVA 356
           ++ GQ+L+GR +R+N A
Sbjct: 62  SMQGQDLNGRPLRINWA 78

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 64.7 bits (156), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 49/77 (63%)
Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           F ++VG+L  E+    ++  F+  G++ +ARVV D  TG+S+G+GFV+  ++ +  +AI 
Sbjct: 16  FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
Query: 340 ALDGQNLDGRAIRVNVA 356
            + GQ L GR IR N A
Sbjct: 76  QMGGQWLGGRQIRTNWA 92

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 80/184 (43%), Gaps = 34/184 (18%)
Query: 159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVI 218
           +  L V  LP D+   +L  LF   G +    +   +                       
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY----------------------- 39
Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEP 278
              +T  S G+ FV  ++  ++++A+++ +   +  + L V+ A P G   +        
Sbjct: 40  ---KTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDT------ 90
Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
              +YV NLP  + + +L+ +F ++G +V   ++ D+ TGR RG  FV  +   E  +AI
Sbjct: 91  --NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Query: 339 AALD 342
           +AL+
Sbjct: 149 SALN 152

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 40/75 (53%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP ++ +  L  +F   G +   R++ D +TG S G+ FV  +SE +   AI  L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 342 DGQNLDGRAIRVNVA 356
           +G  +  + ++V+ A
Sbjct: 66  NGITVRNKRLKVSYA 80

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 79/184 (42%), Gaps = 34/184 (18%)
Query: 159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVI 218
           +  L V  LP D    +L  LF   G +    +   +                       
Sbjct: 14  NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDY----------------------- 50
Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEP 278
              +T  S G+ FV  ++  ++++A+++ +   +  + L V+ A P G   +        
Sbjct: 51  ---KTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDT------ 101
Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
              +YV NLP  + + +L+ +F ++G +V   ++ D+ TGR RG  FV  +   E  +AI
Sbjct: 102 --NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
Query: 339 AALD 342
           +AL+
Sbjct: 160 SALN 163

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 61.2 bits (147), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 48/81 (59%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  +P  VD  +L Q+F  +G + + ++V DRET +SRG+GFV   S +    AIA L
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 342 DGQNLDGRAIRVNVAEDRQRR 362
           +G N+  + ++V +A    +R
Sbjct: 105 NGFNILNKRLKVALAASGHQR 125

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 39/140 (27%), Positives = 69/140 (49%), Gaps = 9/140 (6%)
Query: 223 TDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK------AAPRGTQPERAPRVF 276
           T + +GF FV     E A+ A+E  +   + GR + V +      A P   Q     R F
Sbjct: 66  TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF 125
Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
               RIYV ++  ++ +  ++ VF   GK+ +A +  D  TG+ +G+GF+         D
Sbjct: 126 N---RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQD 182
Query: 337 AIAALDGQNLDGRAIRVNVA 356
           A+++++  +L G+ +RV  A
Sbjct: 183 AVSSMNLFDLGGQYLRVGKA 202

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 44/74 (59%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV  LP  +    +EQ+FS++G+++ +R++ D+ TG SRG GF+      E  +AI  L
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 342 DGQNLDGRAIRVNV 355
           +GQ   G A  + V
Sbjct: 64  NGQKPLGAAEPITV 77

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 38/140 (27%), Positives = 68/140 (48%), Gaps = 9/140 (6%)
Query: 223 TDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK------AAPRGTQPERAPRVF 276
           T + +GF FV     E A+ A+E  +   + GR + V +      A P   Q     R F
Sbjct: 51  TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF 110
Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
               RIYV ++  ++ +  ++ VF   GK+ +  +  D  TG+ +G+GF+         D
Sbjct: 111 N---RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQD 167
Query: 337 AIAALDGQNLDGRAIRVNVA 356
           A+++++  +L G+ +RV  A
Sbjct: 168 AVSSMNLFDLGGQYLRVGKA 187

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 58.5 bits (140), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 38/140 (27%), Positives = 67/140 (47%), Gaps = 9/140 (6%)
Query: 223 TDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK------AAPRGTQPERAPRVF 276
           T + +GF FV     E A+ A+E  +   + GR + V +      A P   Q     R F
Sbjct: 50  TXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF 109
Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
               RIYV ++  ++ +  ++ VF   GK+ +  +  D  TG+ +G+GF+         D
Sbjct: 110 N---RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQD 166
Query: 337 AIAALDGQNLDGRAIRVNVA 356
           A+++ +  +L G+ +RV  A
Sbjct: 167 AVSSXNLFDLGGQYLRVGKA 186

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 24/75 (32%), Positives = 46/75 (61%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV NLP+ + N  L ++FS++GKVV   ++ D++T +S+G  F+    +    +   A+
Sbjct: 19  VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 342 DGQNLDGRAIRVNVA 356
           + + L GR I+ ++A
Sbjct: 79  NNKQLFGRVIKASIA 93

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/206 (26%), Positives = 93/206 (45%), Gaps = 36/206 (17%)
Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
           A L+VG+L  DV     AML+EK              F   G          +  ++V  
Sbjct: 11  ASLYVGDLHPDVTE---AMLYEK--------------FSPAG---------PILSIRVCR 44
Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPG 279
           +  T RS G+ +V      +AE+A++  +   I G+ + +          +R P + + G
Sbjct: 45  DMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRI-------MWSQRDPSLRKSG 97
Query: 280 F-RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
              I++ NL   +DN  L   FS  G +++ +VV D E G S+G+GFV   ++     AI
Sbjct: 98  VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAI 155
Query: 339 AALDGQNLDGRAIRVNVAEDRQRRSS 364
             ++G  L+ R + V   + R+ R +
Sbjct: 156 EKMNGMLLNDRKVFVGRFKSRKEREA 181

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
           P   +YVG+L  +V  A L + FS  G +++ RV  D  T RS G+ +V         DA
Sbjct: 9   PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA---DA 65
Query: 338 IAALDGQNLD---GRAIRV 353
             ALD  N D   G+ +R+
Sbjct: 66  ERALDTMNFDVIKGKPVRI 84

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 53/206 (25%), Positives = 89/206 (43%), Gaps = 36/206 (17%)
Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
           A L+VG+L  DV    L   F  AG +                 + VC            
Sbjct: 16  ASLYVGDLHPDVTEAMLYEKFSPAGPI---------------LSIRVCR----------- 49
Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPG 279
           +  T RS G+ +V      +AE+A++  +   I G+ + +          +R P + + G
Sbjct: 50  DMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRI-------MWSQRDPSLRKSG 102
Query: 280 F-RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
              I++ NL   +DN  L   FS  G +++ +VV D E G S+G+GFV   ++     AI
Sbjct: 103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAI 160
Query: 339 AALDGQNLDGRAIRVNVAEDRQRRSS 364
             ++G  L+ R + V   + R+ R +
Sbjct: 161 EKMNGMLLNDRKVFVGRFKSRKEREA 186

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 32/94 (34%), Positives = 45/94 (47%), Gaps = 8/94 (8%)
Query: 263 APRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRG 322
            P G+    AP    P   +YVG+L  +V  A L + FS  G +++ RV  D  T RS G
Sbjct: 1   GPLGSMNPSAPSY--PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLG 58
Query: 323 FGFVTMSSETELNDAIAALDGQNLD---GRAIRV 353
           + +V         DA  ALD  N D   G+ +R+
Sbjct: 59  YAYVNFQQPA---DAERALDTMNFDVIKGKPVRI 89

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 50/83 (60%), Gaps = 2/83 (2%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV NL   +D+ RL + FS  G + +A+V+   E GRS+GFGFV  SS  E   A+  +
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 342 DGQNLDGRAIRVNVAEDRQRRSS 364
           +G+ +  + + V +A+ ++ R S
Sbjct: 76  NGRIVATKPLYVALAQRKEERQS 98

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 32/83 (38%), Positives = 46/83 (55%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVG L  +V    L ++F + G VVN  +  DR TG+ +G+GFV   SE + + AI  +
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 342 DGQNLDGRAIRVNVAEDRQRRSS 364
           D   L G+ IRVN A    +  S
Sbjct: 78  DMIKLYGKPIRVNKASAHNKNLS 100

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 27/79 (34%), Positives = 46/79 (58%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R+YVG+L + +    L  +F   G++ + +++ D ETGRS+G+GF+T S       A+  
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 341 LDGQNLDGRAIRVNVAEDR 359
           L+G  L GR ++V    +R
Sbjct: 88  LNGFELAGRPMKVGHVTER 106

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/77 (40%), Positives = 49/77 (63%)
Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           F ++VG+L  E+  A +   F+  G++ +ARVV D  TG+S+G+GFV+  ++ +  +AI 
Sbjct: 7   FHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
Query: 340 ALDGQNLDGRAIRVNVA 356
            + GQ L GR IR N A
Sbjct: 67  QMGGQWLGGRQIRTNWA 83

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 43/75 (57%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V NL +      L +VF ++G+V +  +  DR T  SRGF FV    + +  DA+ A+
Sbjct: 50  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 342 DGQNLDGRAIRVNVA 356
           DG  LDGR +RV +A
Sbjct: 110 DGAVLDGRELRVQMA 124

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG LP+   +A L + F   G +  A V+ DR+TG+SRG+GFVTM+       A   
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 341 LDGQNLDGRAIRVNVA 356
            +   +DGR   VN+A
Sbjct: 79  PN-PIIDGRKANVNLA 93

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 43/75 (57%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V NL +      L +VF ++G+V +  +  DR T  SRGF FV    + +  DA+ A+
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 342 DGQNLDGRAIRVNVA 356
           DG  LDGR +RV +A
Sbjct: 133 DGAVLDGRELRVQMA 147

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 56/179 (31%), Positives = 79/179 (44%), Gaps = 47/179 (26%)
Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
            +LFVGNLP D+  E    LFE+ G  E +EV   F+                       
Sbjct: 23  CRLFVGNLPTDITEEDFKRLFERYG--EPSEV---FI----------------------- 54
Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPG 279
               +R RGFGF+ + +   AE A     + ++DG +L         ++P R  R    G
Sbjct: 55  ----NRDRGFGFIRLESRTLAEIA-----KAELDGTILK--------SRPLRI-RFATHG 96
Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
             + V NL   V N  LEQ FS+ G V  A VV D + GR+ G GFV  +++     A+
Sbjct: 97  AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKAL 154

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++VGNLP ++     +++F  +G+     +       R RGFGF+ + S T    A A 
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 341 LDGQNLDGRAIRVNVA 356
           LDG  L  R +R+  A
Sbjct: 78  LDGTILKSRPLRIRFA 93

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 55.5 bits (132), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 44/78 (56%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVG+L + +    L  +F   GK+ N  ++ D +TGRS+G+GF+T S       A+  L
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 342 DGQNLDGRAIRVNVAEDR 359
           +G  L GR +RV    +R
Sbjct: 68  NGFELAGRPMRVGHVTER 85

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 54.7 bits (130), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 44/84 (52%), Gaps = 1/84 (1%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG +P       L + F + G V    ++YD E  R RGFGF+T   E  ++ A+  
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-N 70
Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
           +   ++ G+ + V  AE R  +SS
Sbjct: 71  MHFHDIMGKKVEVKRAEPRDSKSS 94

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/95 (34%), Positives = 51/95 (53%), Gaps = 1/95 (1%)
Query: 270 ERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMS 329
           ER  R  E   ++++G L +E     L   + + GK+ +  V+ D  + RSRGFGFVT S
Sbjct: 18  ERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS 77
Query: 330 SETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           S  E++ A+AA    ++DGR +    A  R+   S
Sbjct: 78  SMAEVDAAMAARP-HSIDGRVVEPKRAVAREESGS 111

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 70/179 (39%), Gaps = 47/179 (26%)
Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
           ++LFVGNLP D+  E++  LFEK G     EV  H                         
Sbjct: 23  SRLFVGNLPPDITEEEMRKLFEKYGKA--GEVFIH------------------------- 55
Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPG 279
                + +GFGF+ + T   AE A        + G+ L V  A    +            
Sbjct: 56  -----KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS------------ 98
Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
             + V NLP  V N  LE+ FS  G+V  A V+ D + GR  G G V  S +     A+
Sbjct: 99  --LTVRNLPQYVSNELLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARKAL 154

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++VGNLP ++    + ++F ++GK     +  D      +GFGF+ + + T    A   
Sbjct: 24  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 341 LDGQNLDGRAIRVNVA 356
           LD   L G+ +RV  A
Sbjct: 78  LDNMPLRGKQLRVRFA 93

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/132 (28%), Positives = 60/132 (45%), Gaps = 14/132 (10%)
Query: 223 TDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRI 282
            D+ +G  FVT+   E+AE A+  FH+  +  R L+V        QP  A         +
Sbjct: 53  VDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQ------LQPTDA--------LL 98
Query: 283 YVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD 342
            V NLP  +   + E++    G +    +VY   TG+S+G+GF     +     A + L 
Sbjct: 99  CVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL 158
Query: 343 GQNLDGRAIRVN 354
           G+ L  R + V+
Sbjct: 159 GKPLGPRTLYVH 170

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/132 (28%), Positives = 60/132 (45%), Gaps = 14/132 (10%)
Query: 223 TDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRI 282
            D+ +G  FVT+   E+AE A+  FH+  +  R L+V        QP  A         +
Sbjct: 51  VDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQ------LQPTDA--------LL 96
Query: 283 YVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD 342
            V NLP  +   + E++    G +    +VY   TG+S+G+GF     +     A + L 
Sbjct: 97  CVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL 156
Query: 343 GQNLDGRAIRVN 354
           G+ L  R + V+
Sbjct: 157 GKPLGPRTLYVH 168

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/132 (28%), Positives = 60/132 (45%), Gaps = 14/132 (10%)
Query: 223 TDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRI 282
            D+ +G  FVT+   E+AE A+  FH+  +  R L+V        QP  A         +
Sbjct: 53  VDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQ------LQPTDA--------LL 98
Query: 283 YVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD 342
            V NLP  +   + E++    G +    +VY   TG+S+G+GF     +     A + L 
Sbjct: 99  CVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL 158
Query: 343 GQNLDGRAIRVN 354
           G+ L  R + V+
Sbjct: 159 GKPLGPRTLYVH 170

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 48/79 (60%), Gaps = 2/79 (2%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++V N+P+   +  L Q+F + GK+++  ++++ E G S+GFGFVT  +  + + A   
Sbjct: 17  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERG-SKGFGFVTFENSADADRAREK 74
Query: 341 LDGQNLDGRAIRVNVAEDR 359
           L G  ++GR I VN A  R
Sbjct: 75  LHGTVVEGRKIEVNNATAR 93

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 36/87 (41%), Positives = 48/87 (55%), Gaps = 8/87 (9%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL-NDAIAA 340
           +YVG L  EVD+  L   F   G + + ++  D ET + RGF FV    E EL  DA AA
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV----EFELAEDAAAA 70
Query: 341 LDGQN---LDGRAIRVNVAEDRQRRSS 364
           +D  N   L GR IRVN+A+  + + S
Sbjct: 71  IDNMNESELFGRTIRVNLAKPMRIKES 97

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 48/79 (60%), Gaps = 2/79 (2%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++V N+P+   +  L Q+F + GK+++  ++++ E G S+GFGFVT  +  + + A   
Sbjct: 31  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERG-SKGFGFVTFENSADADRAREK 88
Query: 341 LDGQNLDGRAIRVNVAEDR 359
           L G  ++GR I VN A  R
Sbjct: 89  LHGTVVEGRKIEVNNATAR 107

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 44/79 (55%), Gaps = 8/79 (10%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL-NDAIAA 340
           +YVG L  EVD+  L   F   G + + ++  D ET + RGF FV    E EL  DA AA
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV----EFELAEDAAAA 121
Query: 341 LDGQN---LDGRAIRVNVA 356
           +D  N   L GR IRVN+A
Sbjct: 122 IDNMNESELFGRTIRVNLA 140

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/80 (43%), Positives = 45/80 (56%), Gaps = 8/80 (10%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL-NDAIAA 340
           +YVG L  EVD+  L   F   G + + ++  D ET + RGF FV    E EL  DA AA
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV----EFELAEDAAAA 65
Query: 341 LDGQN---LDGRAIRVNVAE 357
           +D  N   L GR IRVN+A+
Sbjct: 66  IDNMNESELFGRTIRVNLAK 85

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 27/80 (33%), Positives = 49/80 (61%), Gaps = 2/80 (2%)
Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
           PG ++++G L  E +   L+ VF +HG +    ++ DR T +SRGF F+T  +  +  +A
Sbjct: 7   PG-KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNA 64
Query: 338 IAALDGQNLDGRAIRVNVAE 357
              ++G++L G+AI+V  A+
Sbjct: 65  AKDMNGKSLHGKAIKVEQAK 84

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 35/80 (43%), Positives = 45/80 (56%), Gaps = 8/80 (10%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL-NDAIAA 340
           +YVG L  EVD+  L   F   G + + ++  D ET + RGF FV    E EL  DA AA
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV----EFELAEDAAAA 63
Query: 341 LDGQN---LDGRAIRVNVAE 357
           +D  N   L GR IRVN+A+
Sbjct: 64  IDNMNESELFGRTIRVNLAK 83

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 44/79 (55%), Gaps = 8/79 (10%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL-NDAIAA 340
           +YVG L  EVD+  L   F   G + + ++  D ET + RGF FV    E EL  DA AA
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV----EFELAEDAAAA 60
Query: 341 LDGQN---LDGRAIRVNVA 356
           +D  N   L GR IRVN+A
Sbjct: 61  IDNMNESELFGRTIRVNLA 79

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 4/71 (5%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG L W      L   FS++G+VV+  ++ D+ T +SRGFGFV       +   +A+
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 341 ----LDGQNLD 347
               LDG+N+D
Sbjct: 78  RPHTLDGRNID 88

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 39/61 (63%)
Query: 296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV 355
           L +VFS++G + +  +VYD+++ RSRGF FV   +  +  +A    +G  LDGR IRV+ 
Sbjct: 29  LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 88
Query: 356 A 356
           +
Sbjct: 89  S 89

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 40/75 (53%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V NL +      L +VF ++G+V +  +  +  T   RGF FV      +  DA AA+
Sbjct: 16  LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 342 DGQNLDGRAIRVNVA 356
           DG  LDGR +RV VA
Sbjct: 76  DGAELDGRELRVQVA 90

>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 4h Length = 103

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 50/88 (56%), Gaps = 2/88 (2%)
Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           EP +  YVGNLP+      ++ +F +   + + R+V D++T + +GF +V       L +
Sbjct: 13  EPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71
Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           A+   DG  L  R++RV++AE R++  S
Sbjct: 72  AL-TYDGALLGDRSLRVDIAEGRKQDKS 98

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 41/168 (24%), Positives = 77/168 (45%), Gaps = 20/168 (11%)
Query: 193 FHFLFGNQGFH-------MWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVE 245
           F+   GN  F+         +  VF  + L V+  R    +R FG+V   + E+ EKA+E
Sbjct: 8   FNLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVR-IGMTRKFGYVDFESAEDLEKALE 66
Query: 246 MFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGK 305
           +     + G  + + K   + ++ ER  R       +   NLP++V    L++VF +  +
Sbjct: 67  L-TGLKVFGNEIKLEKPKGKDSKKERDART------LLAKNLPYKVTQDELKEVFEDAAE 119
Query: 306 VVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV 353
           +   R+V   + G+S+G  ++   +E +         G  +DGR+I +
Sbjct: 120 I---RLV--SKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISL 162

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 39/61 (63%)
Query: 296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV 355
           L +VFS++G + +  +VYD+++ RSRGF FV   +  +  +A    +G  LDGR IRV+ 
Sbjct: 32  LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 91
Query: 356 A 356
           +
Sbjct: 92  S 92

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 51.6 bits (122), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 20/78 (25%), Positives = 43/78 (55%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++V  + ++   ++L + F  +G +    +VY + +G+ RG+ F+    E +++ A    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 342 DGQNLDGRAIRVNVAEDR 359
           DG+ +DGR + V+V   R
Sbjct: 165 DGKKIDGRRVLVDVERGR 182

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 51.6 bits (122), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 38/61 (62%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV NLP  + + +L+ +F ++G +V   ++ D+ TGR RG  FV  +   E  +AI+AL
Sbjct: 16  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 342 D 342
           +
Sbjct: 76  N 76

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 39/61 (63%)
Query: 296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV 355
           L +VFS++G + +  +VYD+++ RSRGF FV   +  +  +A    +G  LDGR IRV+ 
Sbjct: 63  LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122
Query: 356 A 356
           +
Sbjct: 123 S 123

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 38/59 (64%)
Query: 296 LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN 354
           L +VFS++G + +  +VYD+++ RSRGF FV   +  +  +A    +G  LDGR IRV+
Sbjct: 32  LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS 90

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G  ++V NL ++V   +L++VFS  G VV A ++ D++ G+SRG G VT     E   AI
Sbjct: 15  GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAI 73
Query: 339 AALDGQNLDGRAIRVNVAE 357
           +  +GQ L  R + V + E
Sbjct: 74  SMFNGQLLFDRPMHVKMDE 92

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 47/210 (22%), Positives = 90/210 (42%), Gaps = 38/210 (18%)
Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +L+VGN+P+ +  E +   F        A+++   L   Q     V AV           
Sbjct: 6   RLYVGNIPFGITEEAMMDFFN-------AQMRLGGL--TQAPGNPVLAV----------- 45
Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP----ERAPRVF 276
            + ++ + F F+   +V+E  +A+  F      G+ L + +  P   QP       P V+
Sbjct: 46  -QINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRR--PHDYQPLPGMSENPSVY 101
Query: 277 EPGF----------RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFV 326
            PG           ++++G LP  +++ +++++ +  G +    +V D  TG S+G+ F 
Sbjct: 102 VPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 161
Query: 327 TMSSETELNDAIAALDGQNLDGRAIRVNVA 356
                   + AIA L+G  L  + + V  A
Sbjct: 162 EYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 1/84 (1%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNA-RVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           I++GNL  E+D   L   FS  G ++   +++ D +TG S+G+ F+  +S    + AI A
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
           ++GQ L  R I V+ A  +  + S
Sbjct: 68  MNGQYLCNRPITVSYAFKKDSKGS 91

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/90 (32%), Positives = 44/90 (48%), Gaps = 1/90 (1%)
Query: 271 RAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSS 330
           R   +   G ++++G L W+     L + F + G+V    V+ D  T RSRGFGFVT   
Sbjct: 17  RGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 76
Query: 331 ETELNDAIAALDGQNLDGRAIRVNVAEDRQ 360
           +  + D + A     LD + I   VA  R+
Sbjct: 77  QAGV-DKVLAQSRHELDSKTIDPKVAFPRR 105

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/78 (25%), Positives = 43/78 (55%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++V  + ++   ++L + F  +G +    +VY + +G+ RG+ F+    E +++ A    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 342 DGQNLDGRAIRVNVAEDR 359
           DG+ +DGR + V+V   R
Sbjct: 165 DGKKIDGRRVLVDVERGR 182

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +++G L W+     L+  FS+ G+VV+  +  D  TGRSRGFGFV +  E+E  D +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFV-LFKESESVDKVMDQ 60
Query: 342 DGQNLDGRAI 351
               L+G+ I
Sbjct: 61  KEHKLNGKVI 70

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           E   + +VG L W+     L+  F++ G+VV+  +  D  TGRSRGFGF+       +  
Sbjct: 9   EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEK 68
Query: 337 AIAALDGQNLDGRAI 351
            +   +   LDGR I
Sbjct: 69  VLDQKE-HRLDGRVI 82

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 45/197 (22%), Positives = 87/197 (44%), Gaps = 32/197 (16%)
Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +L+VGN+P+ +  E +   F        A+++   L   Q     V AV           
Sbjct: 8   RLYVGNIPFGITEEAMMDFFN-------AQMRLGGL--TQAPGNPVLAV----------- 47
Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPG- 279
            + ++ + F F+   +V+E  +A+  F      G+ L + +  P   QP        PG 
Sbjct: 48  -QINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRR--PHDYQP-------LPGA 96
Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
            ++++G LP  +++ +++++ +  G +    +V D  TG S+G+ F         + AIA
Sbjct: 97  HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 156
Query: 340 ALDGQNLDGRAIRVNVA 356
            L+G  L  + + V  A
Sbjct: 157 GLNGMQLGDKKLLVQRA 173

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 45/197 (22%), Positives = 87/197 (44%), Gaps = 32/197 (16%)
Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +L+VGN+P+ +  E +   F        A+++   L   Q     V AV           
Sbjct: 6   RLYVGNIPFGITEEAMMDFFN-------AQMRLGGL--TQAPGNPVLAV----------- 45
Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPG- 279
            + ++ + F F+   +V+E  +A+  F      G+ L + +  P   QP        PG 
Sbjct: 46  -QINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRR--PHDYQP-------LPGA 94
Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
            ++++G LP  +++ +++++ +  G +    +V D  TG S+G+ F         + AIA
Sbjct: 95  HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154
Query: 340 ALDGQNLDGRAIRVNVA 356
            L+G  L  + + V  A
Sbjct: 155 GLNGMQLGDKKLLVQRA 171

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L W+     L + F + G+V    V+ D  T RSRGFGFVT   +  + D + A
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV-DKVLA 60
Query: 341 LDGQNLDGRAIRVNVA 356
                LD + I   VA
Sbjct: 61  QSRHELDSKTIDPKVA 76

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           +P   ++V  L  +     L++ F      V AR+V DRETG S+GFGFV  +SE +   
Sbjct: 13  QPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKA 69
Query: 337 AIAALDGQNLDGRAIRVNVAE 357
           A  A++   +DG  + ++ A+
Sbjct: 70  AKEAMEDGEIDGNKVTLDWAK 90

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/108 (27%), Positives = 53/108 (49%), Gaps = 5/108 (4%)
Query: 257 LTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE 316
           LT       G+Q E  P     G  +++ +LP E  +  L Q+F   G VV+A+V  D++
Sbjct: 8   LTQQSIGAAGSQKE-GPE----GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ 62
Query: 317 TGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           T  S+ FGFV+  +      AI +++G  +  + ++V +   +    S
Sbjct: 63  TNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKS 110

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 20/75 (26%), Positives = 42/75 (56%)
Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
           P   +Y+G++P++    ++  + S  G V+N ++++D +TGRS+G+ F+          A
Sbjct: 2   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 338 IAALDGQNLDGRAIR 352
           +  L+G  L  R ++
Sbjct: 62  VRNLNGYQLGSRFLK 76

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 39/168 (23%), Positives = 75/168 (44%), Gaps = 20/168 (11%)
Query: 193 FHFLFGNQG-------FHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVE 245
           F+   GN           + +  +F  + L V+  R T  +R FG+V   + E+ EKA+E
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALE 72
Query: 246 MFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGK 305
           +     + G  + + K   R ++  RA R       +   NL + +    L++VF +   
Sbjct: 73  LTG-LKVFGNEIKLEKPKGRDSKKVRAART------LLAKNLSFNITEDELKEVFED--- 122
Query: 306 VVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV 353
            +  R+V   + G+S+G  ++   SE +    +    G  +DGR++ +
Sbjct: 123 ALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 35/73 (47%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++V NL +      LE++FS +G +       D  T + +GF FVT         A A 
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 341 LDGQNLDGRAIRV 353
           +DGQ   GR + V
Sbjct: 70  VDGQVFQGRMLHV 82

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 20/75 (26%), Positives = 42/75 (56%)
Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
           P   +Y+G++P++    ++  + S  G V+N ++++D +TGRS+G+ F+          A
Sbjct: 3   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 338 IAALDGQNLDGRAIR 352
           +  L+G  L  R ++
Sbjct: 63  VRNLNGYQLGSRFLK 77

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 20/75 (26%), Positives = 42/75 (56%)
Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
           P   +Y+G++P++    ++  + S  G V+N ++++D +TGRS+G+ F+          A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 338 IAALDGQNLDGRAIR 352
           +  L+G  L  R ++
Sbjct: 61  VRNLNGYQLGSRFLK 75

>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 1 Length = 114

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 266 GTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGF 325
           G Q + A +  +    +Y+ NLP  +D   LE +    G+V++ R++ D  +G SRG GF
Sbjct: 12  GVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGF 70
Query: 326 VTMSSETELNDAIAALDGQ 344
             M S  +    I   +G+
Sbjct: 71  ARMESTEKCEAVIGHFNGK 89

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/78 (32%), Positives = 40/78 (51%)
Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G  + V  LP       L  +FS  G+V +A+++ D+  G S G+GFV   +  +   AI
Sbjct: 19  GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 78
Query: 339 AALDGQNLDGRAIRVNVA 356
             L+G  L  + I+V+ A
Sbjct: 79  NTLNGLRLQSKTIKVSYA 96

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 2/83 (2%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I++ NL   +DN  L   FS  G +++ +VV D E G S+G+GFV   ++     AI  +
Sbjct: 14  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 342 DGQNLDGRAIRVNVAEDRQRRSS 364
           +G  L+ R + V   + R+ R +
Sbjct: 72  NGMLLNDRKVFVGRFKSRKEREA 94

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 2/83 (2%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I++ NL   +DN  L   FS  G +++ +VV D E G S+G+GFV   ++     AI  +
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 342 DGQNLDGRAIRVNVAEDRQRRSS 364
           +G  L+ R + V   + R+ R +
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREA 88

>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding Protein 14 Length = 90

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 8/84 (9%)
Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           ++I+VGN+     +  L  +F   G+V+   VV D        + FV M  E +   AIA
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIA 61
Query: 340 ALDGQNLDGRAIRVNVAEDRQRRS 363
            L+G+ + G+ I V ++   Q++S
Sbjct: 62  QLNGKEVKGKRINVELSTKGQKKS 85

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 22/79 (27%), Positives = 43/79 (54%)
Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G  +++ +LP E  +  L   F   G V++A+V  D++T  S+ FGFV+  +      AI
Sbjct: 40  GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAI 99
Query: 339 AALDGQNLDGRAIRVNVAE 357
            A++G  +  + ++V + +
Sbjct: 100 KAMNGFQVGTKRLKVQLKK 118

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 24/75 (32%), Positives = 40/75 (53%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP  +    L  +FS  G+V +A+++ D+  G S G+GFV   +  +   AI  L
Sbjct: 7   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 342 DGQNLDGRAIRVNVA 356
           +G  L  + I+V+ A
Sbjct: 67  NGLRLQSKTIKVSYA 81

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 8/84 (9%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++GNLP E     +  +F ++GKV+   ++        + +GFV +  +T   DAI  
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61
Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
           L    L G  I V  ++++ + SS
Sbjct: 62  LHHYKLHGVNINVEASKNKSKASS 85

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 40/75 (53%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP  +     + +F   G + + ++V D+ TG+S G+GFV  S   + + AI  L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 342 DGQNLDGRAIRVNVA 356
           +G  L  + I+V+ A
Sbjct: 67  NGLKLQTKTIKVSYA 81

>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous Cell Carcinoma Antigen Recognized By T Cells 3 Length = 100

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 19/76 (25%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++  LP+      LE++   HG V + R+V +R  G+ +G  +V   +E++ + A+  
Sbjct: 19  KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMK 77
Query: 341 LDGQNLDGRAIRVNVA 356
           +DG  +    I+V ++
Sbjct: 78  MDGMTIKENIIKVAIS 93

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++VGNLP ++    + ++F ++GK     +  D      +GFGF+ + + T    A   
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 341 LDGQNLDGRAIRVNVA 356
           LD   L G+ +RV  A
Sbjct: 71  LDNMPLRGKQLRVRFA 86

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 5/86 (5%)
Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
            ++YVGNL        LE+ FS +G +    +  +       GF FV      +  DA+ 
Sbjct: 1   MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVR 55
Query: 340 ALDGQNLDGRAIRVNVAEDRQRRSSF 365
            LDG+ + G  +RV ++    RRS F
Sbjct: 56  GLDGKVICGSRVRVELSTGMPRRSRF 81

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 21/50 (42%), Positives = 30/50 (60%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
           I+VG L        ++  F + GKV +A +++D+ T R RGFGFVT  SE
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VGNL   V    L ++F + G +    +  DRE G+ + FGFV       ++ AIA L
Sbjct: 19  VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALL 77
Query: 342 DGQNLDGRAIRVN 354
           +G  L GR I V+
Sbjct: 78  NGIRLYGRPINVS 90

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 4/79 (5%)
Query: 287 LPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL 346
           LPW+     L++ FS  G+V+  +V  D +TG S+GFGFV     TE    +  +  +++
Sbjct: 23  LPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF---TEYETQVKVMSQRHM 79
Query: 347 -DGRAIRVNVAEDRQRRSS 364
            DGR     +   +Q + S
Sbjct: 80  IDGRWCDCKLPNSKQSQDS 98

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/85 (28%), Positives = 43/85 (50%)
Query: 270 ERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMS 329
           E  P+    G+ ++V  +  E     +   F+E+G++ N  +  DR TG  +G+  V   
Sbjct: 14  EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 73
Query: 330 SETELNDAIAALDGQNLDGRAIRVN 354
           +  E   A+  L+GQ+L G+ I V+
Sbjct: 74  TYKEAQAAMEGLNGQDLMGQPISVD 98

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/85 (28%), Positives = 43/85 (50%)
Query: 270 ERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMS 329
           E  P+    G+ ++V  +  E     +   F+E+G++ N  +  DR TG  +G+  V   
Sbjct: 13  EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72
Query: 330 SETELNDAIAALDGQNLDGRAIRVN 354
           +  E   A+  L+GQ+L G+ I V+
Sbjct: 73  TYKEAQAAMEGLNGQDLMGQPISVD 97

>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein Length = 98

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/94 (28%), Positives = 48/94 (51%), Gaps = 11/94 (11%)
Query: 266 GTQPERAPRVFEPGFRIYVGNL-PWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFG 324
           G+  +  PR      R+++GNL    V  + +E +FS++GK+V   V         +GF 
Sbjct: 4   GSSGKTDPRSMNS--RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFA 53
Query: 325 FVTMSSETELNDAIAALDGQNLDGRAIRVNVAED 358
           FV   +E     A+A  DG+ + G+ + +N+A +
Sbjct: 54  FVQYVNERNARAAVAGEDGRMIAGQVLDINLAAE 87

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++ V NL + V +A ++++F+E G +  A V YDR +GRS G   V    + +   A+  
Sbjct: 30  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 88
Query: 341 LDGQNLDGRAIRVNV 355
            +G  LDGR + + +
Sbjct: 89  YNGVPLDGRPMNIQL 103

>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1 Icp27 Peptide Length = 124

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           E G ++ V NL + V +A ++++F+E G +  A V YDR +GRS G   V      +   
Sbjct: 33  ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALK 91
Query: 337 AIAALDGQNLDGRAIRVNV 355
           A+    G  LDGR + + +
Sbjct: 92  AMKQYKGVPLDGRPMDIQL 110

>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs Orf57 Peptide Length = 124

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           E G ++ V NL + V +A ++++F+E G +  A V YDR +GRS G   V      +   
Sbjct: 33  ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALK 91
Query: 337 AIAALDGQNLDGRAIRVNV 355
           A+    G  LDGR + + +
Sbjct: 92  AMKQYKGVPLDGRPMDIQL 110

>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda Subunit And The 59 Kda Subunit (Rrm Domain) Of Human Cleavage Factor Im Length = 156

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 3/86 (3%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHG--KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           +YVG+  W   + +L QV    G   VV  +   +R  G+S+G+  V ++SE  ++  + 
Sbjct: 58  VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 340 ALDGQNLDGRAIRVNVAEDRQRRSSF 365
            L G+ L+G  + V  A  RQ  S F
Sbjct: 118 LLPGKVLNGEKVDVRPA-TRQNLSQF 142

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           RIYVGNLP ++    +E VF ++G + +  +  +R  G    F FV      +  DA+  
Sbjct: 24  RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK-NRRGGPP--FAFVEFEDPRDAEDAVYG 80
Query: 341 LDGQNLDGRAIRV 353
            DG + DG  +RV
Sbjct: 81  RDGYDYDGYRLRV 93

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 40/76 (52%)
Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G+ ++V  +  E     +   F+E+G++ N  +  DR TG  +G+  V   +  E   A+
Sbjct: 7   GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 339 AALDGQNLDGRAIRVN 354
             L+GQ+L G+ I V+
Sbjct: 67  EGLNGQDLMGQPISVD 82

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 23/83 (27%), Positives = 42/83 (50%)
Query: 272 APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
            P+    G+ ++V  +  E     +   F+E+G++ N  +  DR TG  +G+  V   + 
Sbjct: 2   GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
Query: 332 TELNDAIAALDGQNLDGRAIRVN 354
            E   A+  L+GQ+L G+ I V+
Sbjct: 62  KEAQAAMEGLNGQDLMGQPISVD 84

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 40/76 (52%)
Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G+ ++V  +  E     +   F+E+G++ N  +  DR TG  +G+  V   +  E   A+
Sbjct: 7   GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 339 AALDGQNLDGRAIRVN 354
             L+GQ+L G+ I V+
Sbjct: 67  EGLNGQDLMGQPISVD 82

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 31/128 (24%), Positives = 58/128 (45%), Gaps = 14/128 (10%)
Query: 227 RGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGN 286
           +G GF + S   EA  + E     D D              + E  P+    G+ ++V +
Sbjct: 34  KGRGFGSDSNTREAIHSYERVRNEDDD--------------ELEPGPQRSVEGWILFVTS 79
Query: 287 LPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL 346
           +  E     +++ F ++G++ N  +  DR TG S+G+  V   +  +   A  AL+G  +
Sbjct: 80  IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEI 139
Query: 347 DGRAIRVN 354
            G+ I+V+
Sbjct: 140 MGQTIQVD 147

>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor (Residues 1-155) Length = 177

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           E G ++ V NL + V +A ++++F+E G +  A V YDR +GRS G   V      +   
Sbjct: 86  ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALK 144
Query: 337 AIAALDGQNLDGRAIRVNV 355
           A+    G  LDGR + + +
Sbjct: 145 AMKQYKGVPLDGRPMDIQL 163

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 40/76 (52%)
Query: 279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI 338
           G+ ++V  +  E     +   F+E+G++ N  +  DR TG  +G+  V   +  E   A+
Sbjct: 7   GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 339 AALDGQNLDGRAIRVN 354
             L+GQ+L G+ I V+
Sbjct: 67  EGLNGQDLMGQPISVD 82

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 22/75 (29%), Positives = 40/75 (53%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP ++ +  L  +F   G +   R++ D +TG S G+ FV  +SE +   AI  L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 342 DGQNLDGRAIRVNVA 356
           +G  +  + ++V+ A
Sbjct: 66  NGITVRNKRLKVSYA 80

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 22/85 (25%), Positives = 45/85 (52%)
Query: 270 ERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMS 329
           E  P+    G+ ++V ++  E     +++ F ++G++ N  +  DR TG S+G+  V   
Sbjct: 17  EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 76
Query: 330 SETELNDAIAALDGQNLDGRAIRVN 354
           +  +   A  AL+G  + G+ I+V+
Sbjct: 77  THKQALAAKEALNGAEIMGQTIQVD 101

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 20/84 (23%), Positives = 46/84 (54%), Gaps = 3/84 (3%)
Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VG +   +D   +   F+ +G V   +++ DR TG S+G+GFV+  ++ ++   + + 
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES- 69
Query: 342 DGQNLDGRAIRVNVAEDRQRRSSF 365
              N  G+ +++  A  +Q  S++
Sbjct: 70  -QINFHGKKLKLGPAIRKQNLSTY 92

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	365
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-70
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-31
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-20
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-67
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-25
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-14
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-67
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	9e-28
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-16
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-66
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-26
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-62
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-23
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-21
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-61
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-24
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-18
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-61
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-23
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-61
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-23
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-18
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-59
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	8e-26
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-19
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-56
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-52
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-17
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-54
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-42
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-15
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-53
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	7e-21
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-50
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-23
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-13
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-45
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-27
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-44
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-23
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-42
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-13
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	7e-41
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	5e-24
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	8e-41
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-27
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-40
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-23
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-40
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-24
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-40
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	9e-26
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-40
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-24
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	6e-40
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	8e-24
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-39
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-24
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-39
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-23
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	7e-39
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	7e-25
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	9e-39
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	4e-25
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-38
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	9e-22
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-38
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-24
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-38
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-24
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-37
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-23
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-37
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	6e-28
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-37
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-22
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-37
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-23
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-36
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-24
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	7e-36
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-24
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	8e-36
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-24
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	9e-36
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	7e-24
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-35
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-23
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-35
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-22
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-35
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-22
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-35
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-23
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	4e-35
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-24
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-35
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	9e-26
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-34
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-21
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-34
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-18
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-34
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-22
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-34
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-22
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-34
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-25
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-34
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-20
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-34
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	9e-24
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	4e-34
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-19
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	5e-34
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-18
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	6e-34
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	8e-26
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	7e-34
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	9e-24
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-33
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	9e-21
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-33
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-21
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-32
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-21
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-32
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-23
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	8e-32
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-22
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-31
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	7e-21
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-31
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-23
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-31
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-22
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-31
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-22
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-31
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-20
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	4e-31
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-27
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-30
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-18
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-30
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-25
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-30
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-18
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-30
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	9e-10
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-30
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	7e-19
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	5e-30
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-20
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-29
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-22
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	3e-29
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-16
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-29
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-27
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	6e-29
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-25
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-28
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-20
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-28
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-18
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-28
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-19
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-28
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-28
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-19
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	9e-28
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-23
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-27
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-19
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-27
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-17
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-27
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-24
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-27
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-18
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-27
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-23
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-27
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-21
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	7e-27
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-19
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	9e-27
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-17
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	9e-27
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-23
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-25
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-17
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-25
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	6e-18
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-25
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-09
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	8e-25
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-19
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	9e-25
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-15
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-24
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	6e-20
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-24
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-15
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-24
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-13
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-24
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-21
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	6e-24
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-17
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-23
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	9e-20
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-23
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	8e-15
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-23
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	7e-20
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-23
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	7e-18
2div_A	99	TRNA selenocysteine associated protein; structural	3e-22
2div_A	99	TRNA selenocysteine associated protein; structural	1e-14
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	4e-22
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-17
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-21
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-12
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-21
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	5e-15
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	5e-21
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-16
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	5e-21
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-17
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-20
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	6e-13
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-20
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	8e-14
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-20
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	7e-18
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-20
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-16
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	4e-20
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-11
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	7e-20
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-11
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	8e-20
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	8e-15
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	9e-20
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-12
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-19
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-16
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-19
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-11
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-19
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-11
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-19
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	4e-15
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-19
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-15
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-18
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-14
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	4e-18
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-13
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-17
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	6e-11
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-17
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-15
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-17
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	4e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-17
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-13
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	5e-17
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	9e-15
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	6e-17
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	6e-11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	9e-17
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-16
2dis_A	109	Unnamed protein product; structural genomics, RRM	7e-13
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-16
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	7e-12
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-16
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-10
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	5e-16
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-11
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-16
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-11
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-15
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-14
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-15
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	9e-10
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	6e-15
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-15
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-14
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	8e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-14
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	5e-10
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-14
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-11
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	9e-14
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-09
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-09
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	7e-13
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-08
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-12
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	8e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	8e-09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-11
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	6e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-11
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-11
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	4e-11
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-06
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-10
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-10
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-06
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	6e-10
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-05
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	8e-10
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	5e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	6e-06
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-09
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	7e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	5e-07
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	4e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	6e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	5e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	6e-06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-05
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	2e-05
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	1e-04
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-04
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	7e-04
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	6e-04

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  217 bits (554), Expect = 8e-70
 Identities = 41/213 (19%), Positives = 90/213 (42%), Gaps = 29/213 (13%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                ++++VG++ Y++  + +   F   G ++  ++                       
Sbjct: 24  ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM----------------------- 60

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
               ++  T + +GF FV     E A+ A+E  +   + GR + V + +  G       +
Sbjct: 61  ---SWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQ 117

Query: 275 VFE---PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
           + E      RIYV ++  ++ +  ++ VF   GK+ +A +  D  TG+ +G+GF+     
Sbjct: 118 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKA 177

Query: 332 TELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
               DA+++++  +L G+ +RV  A        
Sbjct: 178 QSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLL 210

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  116 bits (293), Expect = 3e-31
 Identities = 24/108 (22%), Positives = 48/108 (44%), Gaps = 1/108 (0%)

Query: 257 LTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE 316
           +T  +   RG+  +R   +     R+YVG++ +E+    + Q F+  G + +  + +D  
Sbjct: 7   MTGGQQMGRGSAAQRQGALAIMS-RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSV 65

Query: 317 TGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           T + +GF FV          A+  ++   L GR I+V    +  +   
Sbjct: 66  TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQP 113

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 87.4 bits (217), Expect = 2e-20
 Identities = 23/136 (16%), Positives = 50/136 (36%), Gaps = 27/136 (19%)

Query: 138 RQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLF 197
           R    G+     ++   E     +++V ++  D+  + +  +FE  G ++ A        
Sbjct: 104 RPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSA-------- 155

Query: 198 GNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLL 257
                              +  +  T + +G+GF+     + ++ AV   + +D+ G+ L
Sbjct: 156 ------------------TLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 197

Query: 258 TVNKAAPRGTQPERAP 273
            V KA      P   P
Sbjct: 198 RVGKAVTPP-MPLLTP 212

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score =  208 bits (532), Expect = 3e-67
 Identities = 43/196 (21%), Positives = 89/196 (45%), Gaps = 33/196 (16%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L+VGNL   +  + L   F+  G +   ++                          + ++
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKI--------------------------MIDK 36

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFR 281
             +++  + FV      +A  A++  +   I+  ++ +N A              +  F 
Sbjct: 37  -NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSS------DDTFN 89

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           ++VG+L   VD+  L   F +    ++  V++D +TG SRG+GFV+ +S+ +  +A+ ++
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149

Query: 342 DGQNLDGRAIRVNVAE 357
            GQ+L+GR +R+N A 
Sbjct: 150 QGQDLNGRPLRINWAA 165

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 98.0 bits (245), Expect = 8e-25
 Identities = 22/83 (26%), Positives = 43/83 (51%), Gaps = 1/83 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVGNL   +    L+Q F   G + N +++ D+   ++  + FV      + N A+  L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 342 DGQNLDGRAIRVNVAEDRQRRSS 364
           +G+ ++   +++N A   Q+ SS
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSS 84

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 69.9 bits (172), Expect = 1e-14
 Identities = 27/105 (25%), Positives = 47/105 (44%), Gaps = 26/105 (24%)

Query: 159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVI 218
              LFVG+L  +VD E L   F+   +                               V+
Sbjct: 87  TFNLFVGDLNVNVDDETLRNAFKDFPS--YLSGH------------------------VM 120

Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAA 263
           ++ +T  SRG+GFV+ ++ ++A+ A++     D++GR L +N AA
Sbjct: 121 WDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score =  207 bits (530), Expect = 6e-67
 Identities = 45/201 (22%), Positives = 87/201 (43%), Gaps = 36/201 (17%)

Query: 158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
            +  L V  LP D+   +L  LF   G +    +                          
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRI-------------------------- 35

Query: 218 IYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFE 277
           + + +T  S G+ FV  ++  ++++A+++ +   +  + L V+ A P G           
Sbjct: 36  MRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGES--------I 87

Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
               +YV NLP  + + +L+ +F ++G +V   ++ D+ TGR RG  FV  +   E  +A
Sbjct: 88  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147

Query: 338 IAALDGQNLDG--RAIRVNVA 356
           I+AL+    +G  + + V +A
Sbjct: 148 ISALNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score =  106 bits (266), Expect = 9e-28
 Identities = 22/82 (26%), Positives = 40/82 (48%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP ++ +  L  +F   G +   R++ D +TG S G+ FV  +SE +   AI  L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 342 DGQNLDGRAIRVNVAEDRQRRS 363
           +G  +  + ++V+ A       
Sbjct: 66  NGITVRNKRLKVSYARPGGESI 87

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 75.7 bits (187), Expect = 1e-16
 Identities = 26/110 (23%), Positives = 46/110 (41%), Gaps = 28/110 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           E  +D  L+V NLP  +  ++L  +F K G+  I +                        
Sbjct: 85  ESIKDTNLYVTNLPRTITDDQLDTIFGKYGS--IVQKN---------------------- 120

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDG--RLLTVNKA 262
             ++ ++ T R RG  FV  +  EEA++A+   +    +G  + L+V  A
Sbjct: 121 --ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score =  206 bits (527), Expect = 2e-66
 Identities = 51/199 (25%), Positives = 85/199 (42%), Gaps = 36/199 (18%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
             L V  LP ++  E+   LF   G +E  ++                          + 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKL--------------------------VR 36

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPG 279
           ++ T +S G+GFV     ++AEKA+   +   +  + + V+ A P               
Sbjct: 37  DKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSAS--------IRD 88

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
             +YV  LP  +    LEQ+FS++G+++ +R++ D+ TG SRG GF+      E  +AI 
Sbjct: 89  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148

Query: 340 ALDGQNLDG--RAIRVNVA 356
            L+GQ   G    I V  A
Sbjct: 149 GLNGQKPSGATEPITVKFA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score =  102 bits (257), Expect = 2e-26
 Identities = 22/82 (26%), Positives = 38/82 (46%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LP  +       +F   G++ + ++V D+ TG+S G+GFV      +   AI  L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 342 DGQNLDGRAIRVNVAEDRQRRS 363
           +G  L  + I+V+ A       
Sbjct: 65  NGLRLQTKTIKVSYARPSSASI 86

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 73.0 bits (180), Expect = 1e-15
 Identities = 24/110 (21%), Positives = 42/110 (38%), Gaps = 28/110 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
               DA L+V  LP  +  ++L  LF + G +  +                         
Sbjct: 84  ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITS------------------------- 118

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDG--RLLTVNKA 262
            +++ ++ T  SRG GF+      EAE+A++  +     G    +TV  A
Sbjct: 119 -RILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score =  197 bits (503), Expect = 2e-62
 Identities = 35/215 (16%), Positives = 81/215 (37%), Gaps = 34/215 (15%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +L+VGN+P+ +  E +   F     +                          +    +  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQ---------------------APGNPVLA 44

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR------ 274
            + ++ + F F+   +V+E  +A+         G+ L + +       P  +        
Sbjct: 45  VQINQDKNFAFLEFRSVDETTQAMAF-DGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVP 103

Query: 275 ------VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTM 328
                 V +   ++++G LP  +++ +++++ +  G +    +V D  TG S+G+ F   
Sbjct: 104 GVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY 163

Query: 329 SSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRS 363
                 + AIA L+G  L  + + V  A    + +
Sbjct: 164 VDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNA 198

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 95.9 bits (239), Expect = 1e-23
 Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 6/89 (6%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVN-----ARVVYDRETGRSRGFGFVTMSSETELN 335
           R+YVGN+P+ +    +   F+   ++          V   +  + + F F+   S  E  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 336 DAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
            A+A  DG    G+++++    D Q    
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQPLPG 93

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 88.5 bits (220), Expect = 6e-21
 Identities = 20/132 (15%), Positives = 43/132 (32%), Gaps = 26/132 (19%)

Query: 137 ERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFL 196
               E+    V      V P    KLF+G LP  ++ +++  L    G ++         
Sbjct: 92  PGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF------- 144

Query: 197 FGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRL 256
                               ++ +  T  S+G+ F     +   ++A+   +   +  + 
Sbjct: 145 -------------------NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185

Query: 257 LTVNKAAPRGTQ 268
           L V +A+     
Sbjct: 186 LLVQRASVGAKN 197

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  194 bits (495), Expect = 1e-61
 Identities = 55/203 (27%), Positives = 92/203 (45%), Gaps = 37/203 (18%)

Query: 158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
           E  K+F+G L +D   + L   F K GTV   ++                          
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIM------------------------- 36

Query: 218 IYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFE 277
             +  T RSRGFGF++       ++ V+  H   +DG+++   +A PR  Q        +
Sbjct: 37  -KDPATGRSRGFGFLSFEKPSSVDEVVKTQHI--LDGKVIDPKRAIPRDEQ--------D 85

Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
              +I+VG +  +V     E+ FS+ G +++A+++ D++TG+SRGFGFVT  S  +  D 
Sbjct: 86  KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA-DAVDR 144

Query: 338 IAALDGQNLDGRAIRVNVAEDRQ 360
           +      +   R I +  AE R 
Sbjct: 145 VCQNKFIDFKDRKIEIKRAEPRH 167

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 96.8 bits (242), Expect = 3e-24
 Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 2/82 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L W+     L + F ++G V + +++ D  TGRSRGFGF++    + +++ +  
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64

Query: 341 LDGQNLDGRAIRVNVAEDRQRR 362
                LDG+ I    A  R  +
Sbjct: 65  --QHILDGKVIDPKRAIPRDEQ 84

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 81.4 bits (202), Expect = 1e-18
 Identities = 25/111 (22%), Positives = 47/111 (42%), Gaps = 27/111 (24%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           E  +  K+FVG +  DV  ++    F + GT+  A+                        
Sbjct: 83  EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ------------------------ 118

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
             ++ +++T +SRGFGFVT  + +  ++  +     D   R + + +A PR
Sbjct: 119 --LMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIKRAEPR 166

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score =  194 bits (494), Expect = 4e-61
 Identities = 58/210 (27%), Positives = 91/210 (43%), Gaps = 30/210 (14%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           EP +  KLF+G L ++   E L   FE+ GT+    V                       
Sbjct: 9   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV----------------------- 45

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
              + +  T RSRGFGFVT +TVEE + A+     + +DGR++   +A  R       P 
Sbjct: 46  ---MRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQR--PG 99

Query: 275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL 334
                 +I+VG +  + +   L   F ++GK+    ++ DR +G+ RGF FVT      +
Sbjct: 100 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159

Query: 335 NDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
            D I       ++G    V  A  +Q  +S
Sbjct: 160 -DKIVIQKYHTVNGHNCEVRKALSKQEMAS 188

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 95.4 bits (238), Expect = 2e-23
 Identities = 28/93 (30%), Positives = 48/93 (51%), Gaps = 1/93 (1%)

Query: 272 APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
           +P+  E   ++++G L +E  +  L   F + G + +  V+ D  T RSRGFGFVT ++ 
Sbjct: 6   SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 65

Query: 332 TELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
            E++ A+ A     +DGR +    A  R+    
Sbjct: 66  EEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQR 97

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 80.8 bits (200), Expect = 4e-18
 Identities = 24/114 (21%), Positives = 42/114 (36%), Gaps = 27/114 (23%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG +  D +   L   FE+ G +E+ E+                          + +
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEI--------------------------MTD 139

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
           R + + RGF FVT    +  +K V     + ++G    V KA  +      +  
Sbjct: 140 RGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMASASSS 192

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score =  192 bits (491), Expect = 6e-61
 Identities = 33/200 (16%), Positives = 75/200 (37%), Gaps = 30/200 (15%)

Query: 157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQ 216
               +L+VGN+P+ +  E +   F     +                          +   
Sbjct: 2   GSARRLYVGNIPFGITEEAMMDFFNAQMRL---------------------GGLTQAPGN 40

Query: 217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVF 276
            +   + ++ + F F+   +V+E  +A+         G+ L + +               
Sbjct: 41  PVLAVQINQDKNFAFLEFRSVDETTQAMAF-DGIIFQGQSLKIRRPHDYQPL-------- 91

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
               ++++G LP  +++ +++++ +  G +    +V D  TG S+G+ F         + 
Sbjct: 92  PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151

Query: 337 AIAALDGQNLDGRAIRVNVA 356
           AIA L+G  L  + + V  A
Sbjct: 152 AIAGLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 95.4 bits (238), Expect = 1e-23
 Identities = 19/90 (21%), Positives = 37/90 (41%), Gaps = 6/90 (6%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVN-----ARVVYDRETGRSRGFGFVTMSSETELN 335
           R+YVGN+P+ +    +   F+   ++          V   +  + + F F+   S  E  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 336 DAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
            A+A  DG    G+++++    D Q     
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQPLPGA 94

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 81.5 bits (202), Expect = 1e-18
 Identities = 17/109 (15%), Positives = 39/109 (35%), Gaps = 26/109 (23%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
             P   KLF+G LP  ++ +++  L    G ++                           
Sbjct: 90  PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF------------------------- 124

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAA 263
             ++ +  T  S+G+ F     +   ++A+   +   +  + L V +A+
Sbjct: 125 -NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  187 bits (478), Expect = 5e-59
 Identities = 36/205 (17%), Positives = 74/205 (36%), Gaps = 39/205 (19%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           E      LF+GNL  +    +L +   +        V                       
Sbjct: 9   ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV---------------------- 46

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
                +  T  +R FG+V   + E+ EKA+E+     + G  + + K   R ++  R   
Sbjct: 47  -----DVRTGTNRKFGYVDFESAEDLEKALEL-TGLKVFGNEIKLEKPKGRDSKKVR--- 97

Query: 275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL 334
                  +   NL + +    L++VF +  ++         + G+S+G  ++   SE + 
Sbjct: 98  ---AARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADA 149

Query: 335 NDAIAALDGQNLDGRAIRVNVAEDR 359
              +    G  +DGR++ +    ++
Sbjct: 150 EKNLEEKQGAEIDGRSVSLYYTGEK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  101 bits (253), Expect = 8e-26
 Identities = 24/96 (25%), Positives = 38/96 (39%), Gaps = 3/96 (3%)

Query: 270 ERAPRVFEPGFR-IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTM 328
                        +++GNL      A L+   SE     +  VV D  TG +R FG+V  
Sbjct: 3   HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDF 61

Query: 329 SSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
            S  +L  A+  L G  + G  I++   + R  +  
Sbjct: 62  ESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSKKV 96

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 83.8 bits (208), Expect = 2e-19
 Identities = 18/119 (15%), Positives = 42/119 (35%), Gaps = 31/119 (26%)

Query: 148 FEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVC 207
            +  +  +      L   NL +++  ++L  +FE A  + +                   
Sbjct: 88  PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV------------------ 129

Query: 208 AVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG 266
                         +  +S+G  ++   +  +AEK +E     +IDGR +++     +G
Sbjct: 130 -------------SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 175

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  185 bits (472), Expect = 1e-56
 Identities = 39/210 (18%), Positives = 69/210 (32%), Gaps = 33/210 (15%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
            P DA L V NLP  +  ++   L    G++E   +                        
Sbjct: 92  QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFL------------------------ 127

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRV 275
             +Y+  T +S+G+GF      + A +A        +  R L V+        P      
Sbjct: 128 --VYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLH-- 183

Query: 276 FEPGFRIYVGNLPWEVDNA-RLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL 334
                 + V  LP   ++   L +  S        ++    + G+ +GF  +   +    
Sbjct: 184 ---SRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVLEYETAEMA 239

Query: 335 NDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
            +A    DG +L G  +RV+         S
Sbjct: 240 EEAQQQADGLSLGGSHLRVSFCAPGPPGRS 269

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  173 bits (441), Expect = 4e-52
 Identities = 41/210 (19%), Positives = 73/210 (34%), Gaps = 47/210 (22%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +     K+ +  LP DV ++++  L                                   
Sbjct: 18  QFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYC-------------------------- 51

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
                    D+ +G  FVT+   E+AE A+  FH+  +  R L+V               
Sbjct: 52  -------FVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ------------ 92

Query: 275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL 334
                  + V NLP  +   + E++    G +    +VY   TG+S+G+GF     +   
Sbjct: 93  --PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 150

Query: 335 NDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
             A + L G+ L  R + V+  +  Q   +
Sbjct: 151 ARAKSDLLGKPLGPRTLYVHWTDAGQLTPA 180

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 80.4 bits (199), Expect = 2e-17
 Identities = 19/94 (20%), Positives = 35/94 (37%), Gaps = 7/94 (7%)

Query: 264 PRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGF 323
               + E   R F    +I +  LP +V N  +  + S++        +      + +G 
Sbjct: 7   EIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGT 59

Query: 324 GFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE 357
            FVT+ +  +   AI A     L  R + V +  
Sbjct: 60  AFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP 93

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 73.5 bits (181), Expect = 5e-15
 Identities = 18/112 (16%), Positives = 30/112 (26%), Gaps = 28/112 (25%)

Query: 155 EPPEDAKLFVGNLPYDV-DSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVS 213
                  L V  LP    D + L        +    ++                      
Sbjct: 180 ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG------------------- 220

Query: 214 LLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                   +  + +GF  +   T E AE+A +      + G  L V+  AP 
Sbjct: 221 --------QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG 264

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  179 bits (456), Expect = 3e-54
 Identities = 37/215 (17%), Positives = 76/215 (35%), Gaps = 30/215 (13%)

Query: 147 VFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWV 206
           V + E  V    +  L++ N P       +  L +    V ++                 
Sbjct: 105 VGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIR--------------- 149

Query: 207 CAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG 266
                      + +   + SR F ++ +++ E+A   VE  +   I+G  L    + P  
Sbjct: 150 -----------LPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPL- 197

Query: 267 TQPERAPRVFEPGFRIYVGNLPWEV-DNARLEQVFSEHGKVVNARVVYDR-ETGRSRGFG 324
            + +R       G  I + NL  E+ D   L + F   G +    +   + E   +    
Sbjct: 198 EKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCA 257

Query: 325 FVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR 359
           F+   ++     A+  ++   L  R I V++A+ +
Sbjct: 258 FMVFENKDSAERAL-QMNRSLLGNREISVSLADKK 291

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  148 bits (377), Expect = 1e-42
 Identities = 27/226 (11%), Positives = 66/226 (29%), Gaps = 44/226 (19%)

Query: 137 ERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFL 196
                +G       E      E   + V NLP   +  K+   F+  G +          
Sbjct: 19  GSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPI---------- 68

Query: 197 FGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRL 256
                             + V       ++  F  +  +  + A  A+   H+  +    
Sbjct: 69  ------------------IHVDVADSLKKNFRFARIEFARYDGALAAITKTHKV-VGQNE 109

Query: 257 LTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE 316
           + V+                     +++ N P       +  +  +   V  +  +    
Sbjct: 110 IIVSHLTEC---------------TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR 154

Query: 317 TGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
              SR F ++ ++S+ +    +  L+G  ++G  +   V+   ++ 
Sbjct: 155 FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKS 200

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 75.0 bits (185), Expect = 2e-15
 Identities = 24/140 (17%), Positives = 48/140 (34%), Gaps = 34/140 (24%)

Query: 127 EGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEK-LAMLFEKAGT 185
           EG   V +     E+S       +       E  ++ + NL  ++  E  L   FE  G+
Sbjct: 185 EGYTLVTKVSNPLEKS-------KRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGS 237

Query: 186 VEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVE 245
           +E   +                             +E   +    F+     + AE+A++
Sbjct: 238 IEKINI-------------------------PAGQKEHSFNNCCAFMVFENKDSAERALQ 272

Query: 246 MFHRYDIDGRLLTVNKAAPR 265
           M +R  +  R ++V+ A  +
Sbjct: 273 M-NRSLLGNREISVSLADKK 291

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score =  176 bits (447), Expect = 3e-53
 Identities = 58/216 (26%), Positives = 81/216 (37%), Gaps = 48/216 (22%)

Query: 148 FEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVC 207
           F +       +  +LFVGNLP D+  E    LFE+ G  E +EV              + 
Sbjct: 11  FLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYG--EPSEVF-------------IN 55

Query: 208 AVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT 267
                            R RGFGF+ + +   AE A        +  R L +  A     
Sbjct: 56  -----------------RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA----- 93

Query: 268 QPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVT 327
                      G  + V NL   V N  LEQ FS+ G V  A VV D + GR+ G GFV 
Sbjct: 94  ---------THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVE 143

Query: 328 MSSETELNDAIAAL-DGQNLDGRAIRVNVAEDRQRR 362
            +++     A+    DG  L     R  + E  ++ 
Sbjct: 144 FAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF 179

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 89.7 bits (223), Expect = 7e-21
 Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 6/99 (6%)

Query: 259 VNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETG 318
           +       +  +   + +    R++VGNLP ++     +++F  +G+     +       
Sbjct: 2   MGFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------ 55

Query: 319 RSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE 357
           R RGFGF+ + S T    A A LDG  L  R +R+  A 
Sbjct: 56  RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT 94

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 65.5 bits (160), Expect = 2e-12
 Identities = 23/114 (20%), Positives = 32/114 (28%), Gaps = 28/114 (24%)

Query: 159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVI 218
            A L V NL   V +E L   F + G VE A V            +              
Sbjct: 96  GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVV------------VV------------- 130

Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAV-EMFHRYDIDGRLLTVNKAAPRGTQPER 271
              +  R+ G GFV  +    A KA+        +           P     + 
Sbjct: 131 --DDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDE 182

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score =  165 bits (421), Expect = 5e-50
 Identities = 49/210 (23%), Positives = 84/210 (40%), Gaps = 34/210 (16%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                A L+VG+L  DV    L   F  AG   I  ++                      
Sbjct: 11  PSYPMASLYVGDLHPDVTEAMLYEKFSPAG--PILSIR---------------------- 46

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
             V  +  T RS G+ +V      +AE+A++  +   I G+ + +  +  R     +   
Sbjct: 47  --VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS-QRDPSLRK--- 100

Query: 275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL 334
                  I++ NL   +DN  L   FS  G +++ +VV D     S+G+GFV   ++   
Sbjct: 101 --SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAA 156

Query: 335 NDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
             AI  ++G  L+ R + V   + R+ R +
Sbjct: 157 ERAIEKMNGMLLNDRKVFVGRFKSRKEREA 186

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 96.6 bits (241), Expect = 1e-23
 Identities = 29/103 (28%), Positives = 49/103 (47%), Gaps = 3/103 (2%)

Query: 263 APRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRG 322
            P G+    AP    P   +YVG+L  +V  A L + FS  G +++ RV  D  T RS G
Sbjct: 1   GPLGSMNPSAPS--YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLG 58

Query: 323 FGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE-DRQRRSS 364
           + +V      +   A+  ++   + G+ +R+  ++ D   R S
Sbjct: 59  YAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKS 101

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 67.7 bits (166), Expect = 2e-13
 Identities = 26/130 (20%), Positives = 47/130 (36%), Gaps = 31/130 (23%)

Query: 159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVI 218
              +F+ NL   +D++ L   F   G +   +V                           
Sbjct: 103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV-------------------------- 136

Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEP 278
              + + S+G+GFV   T E AE+A+E  +   ++ R + V +   R    ER   +   
Sbjct: 137 --CDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR---KEREAELGAR 191

Query: 279 GFRIYVGNLP 288
               Y  ++P
Sbjct: 192 AKEFYPYDVP 201

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score =  151 bits (384), Expect = 2e-45
 Identities = 34/125 (27%), Positives = 62/125 (49%), Gaps = 3/125 (2%)

Query: 244 VEMFHRYDIDGRLLTVNKAAPRGTQ---PERAPRVFEPGFRIYVGNLPWEVDNARLEQVF 300
           + +  +YD  G+   + +   +  Q   P +     +    + V  +P  VD  +L Q+F
Sbjct: 4   IPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLF 63

Query: 301 SEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ 360
             +G + + ++V DRET +SRG+GFV   S +    AIA L+G N+  + ++V +A    
Sbjct: 64  ERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH 123

Query: 361 RRSSF 365
           +R   
Sbjct: 124 QRPGI 128

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score =  102 bits (257), Expect = 6e-27
 Identities = 32/121 (26%), Positives = 51/121 (42%), Gaps = 26/121 (21%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           EP     L V  +P  VD  +L  LFE+ G +E                           
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESV------------------------- 72

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
            +++ +RET +SRG+GFV   +   A++A+   + ++I  + L V  AA    +P  A  
Sbjct: 73  -KIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGA 131

Query: 275 V 275
           V
Sbjct: 132 V 132

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score =  148 bits (376), Expect = 5e-44
 Identities = 40/149 (26%), Positives = 61/149 (40%), Gaps = 10/149 (6%)

Query: 227 RGFGFVTMSTVE-----EAEKAVEMFHRYDIDGRLLTVNKA-----APRGTQPERAPRVF 276
            G      +T E      AEK  + +   +      T + A        G+         
Sbjct: 8   NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           E    + V NL +      L +VF ++G+V +  +  DR T  SRGF FV    + +  D
Sbjct: 68  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
           A+ A+DG  LDGR +RV +A   +   S 
Sbjct: 128 AMDAMDGAVLDGRELRVQMARYGRPPDSH 156

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 94.1 bits (234), Expect = 2e-23
 Identities = 36/163 (22%), Positives = 54/163 (33%), Gaps = 28/163 (17%)

Query: 109 ENQGADETEGNLSDWGEPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLP 168
           +   A++     ++    +GE T  +A +    +           VE      L V NL 
Sbjct: 22  DAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGM--TSLKVDNLT 79

Query: 169 YDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRG 228
           Y    + L  +FEK G V   +V                         +  +R T  SRG
Sbjct: 80  YRTSPDTLRRVFEKYGRVG--DVY------------------------IPRDRYTKESRG 113

Query: 229 FGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
           F FV      +AE A++      +DGR L V  A         
Sbjct: 114 FAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 156

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  144 bits (365), Expect = 4e-42
 Identities = 41/205 (20%), Positives = 76/205 (37%), Gaps = 36/205 (17%)

Query: 158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
           +  K+FVG +P     + L  LFE+ G   + E+                         V
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYG--AVYEIN------------------------V 35

Query: 218 IYNRET--DRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRV 275
           + +R     +S+G  FVT  T + A +A    H   +   +    +  P  ++   A   
Sbjct: 36  LRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVE- 94

Query: 276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELN 335
                ++++G +  +     +  +FS  G++   R++     G SRG  FVT ++     
Sbjct: 95  ---DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQ 150

Query: 336 DAIAALDGQNL---DGRAIRVNVAE 357
            AI A+            + V  A+
Sbjct: 151 TAIKAMHQAQTMEGCSSPMVVKFAD 175

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 66.1 bits (162), Expect = 4e-13
 Identities = 25/116 (21%), Positives = 39/116 (33%), Gaps = 30/116 (25%)

Query: 150 EEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAV 209
           + E     ED KLF+G +        + ++F   G +E   +    L G  G        
Sbjct: 86  DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRI----LRGPDG-------- 133

Query: 210 FYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI---DGRLLTVNKA 262
                           SRG  FVT +T   A+ A++  H+          + V  A
Sbjct: 134 ---------------LSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score =  139 bits (352), Expect = 7e-41
 Identities = 32/122 (26%), Positives = 56/122 (45%), Gaps = 8/122 (6%)

Query: 247 FHRYDIDGRLL--------TVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQ 298
            H +   G +         T  +   RG++        +P   + V  L        L +
Sbjct: 6   HHHHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLRE 65

Query: 299 VFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED 358
           VFS++G + +  +VYD+++ RSRGF FV   +  +  +A    +G  LDGR IRV+ +  
Sbjct: 66  VFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSIT 125

Query: 359 RQ 360
           ++
Sbjct: 126 KR 127

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 94.8 bits (236), Expect = 5e-24
 Identities = 24/111 (21%), Positives = 44/111 (39%), Gaps = 26/111 (23%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
            P  +  L V  L        L  +F K G +                            
Sbjct: 42  NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADV------------------------- 76

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
             ++Y++++ RSRGF FV    V++A++A E  +  ++DGR + V+ +  +
Sbjct: 77  -SIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score =  138 bits (349), Expect = 8e-41
 Identities = 37/88 (42%), Positives = 56/88 (63%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
               +++VG L ++ +   LEQVFS++G++    VV DRET RSRGFGFVT  +  +  D
Sbjct: 10  SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           A+ A++G+++DGR IRV+ A       S
Sbjct: 70  AMMAMNGKSVDGRQIRVDQAGKSSDNRS 97

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score =  101 bits (255), Expect = 6e-27
 Identities = 32/120 (26%), Positives = 51/120 (42%), Gaps = 27/120 (22%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
              ++ KLFVG L +D + + L  +F K G +                            
Sbjct: 8   MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEV------------------------- 42

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
             V+ +RET RSRGFGFVT   +++A+ A+   +   +DGR + V++A          P 
Sbjct: 43  -VVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNR-SGPS 100

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score =  139 bits (351), Expect = 1e-40
 Identities = 33/106 (31%), Positives = 49/106 (46%)

Query: 260 NKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR 319
            +         R P   E    + V NL +      L +VF ++G+V +  +  DR T  
Sbjct: 28  QQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE 87

Query: 320 SRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
           SRGF FV    + +  DA+ A+DG  LDGR +RV +A   +   S 
Sbjct: 88  SRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 133

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 93.7 bits (233), Expect = 2e-23
 Identities = 31/140 (22%), Positives = 47/140 (33%), Gaps = 28/140 (20%)

Query: 135 AGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFH 194
           +    ++ G   +       +      L V NL Y    + L  +FEK G V   +V   
Sbjct: 23  SMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVG--DVY-- 78

Query: 195 FLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDG 254
                                 +  +R T  SRGF FV      +AE A++      +DG
Sbjct: 79  ----------------------IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG 116

Query: 255 RLLTVNKAAPRGTQPERAPR 274
           R L V  A     +P  +  
Sbjct: 117 RELRVQMARYG--RPPDSHH 134

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score =  137 bits (348), Expect = 1e-40
 Identities = 30/94 (31%), Positives = 45/94 (47%)

Query: 271 RAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSS 330
            +    +    + V NL +      L +VF ++G+V +  +  +  T   RGF FV    
Sbjct: 5   SSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64

Query: 331 ETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
             +  DA AA+DG  LDGR +RV VA   +R  S
Sbjct: 65  RRDAQDAEAAMDGAELDGRELRVQVARYGRRDLS 98

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 94.6 bits (236), Expect = 3e-24
 Identities = 26/117 (22%), Positives = 35/117 (29%), Gaps = 26/117 (22%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +      L V NL Y    + L  +FEK G V   +V                       
Sbjct: 9   DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVG--DVY---------------------- 44

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
             +     T   RGF FV      +A+ A       ++DGR L V  A         
Sbjct: 45  --IPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSG 99

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score =  137 bits (347), Expect = 2e-40
 Identities = 29/88 (32%), Positives = 45/88 (51%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                +YVG+L + +    L  +F   GK+ N  ++ D +TGRS+G+GF+T S       
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           A+  L+G  L GR +RV    +R    S
Sbjct: 63  ALEQLNGFELAGRPMRVGHVTERLDGGS 90

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 98.4 bits (246), Expect = 9e-26
 Identities = 24/115 (20%), Positives = 48/115 (41%), Gaps = 26/115 (22%)

Query: 157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQ 216
              + L+VG+L +++  + L  +FE  G ++                             
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNI--------------------------V 36

Query: 217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
           ++ + +T RS+G+GF+T S  E A +A+E  + +++ GR + V     R      
Sbjct: 37  LMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDGGSG 91

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score =  135 bits (343), Expect = 4e-40
 Identities = 28/81 (34%), Positives = 52/81 (64%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
           F ++VG+L   VD+  L   F +    ++  V++D +TG SRG+GFV+ +S+ +  +A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 340 ALDGQNLDGRAIRVNVAEDRQ 360
           ++ GQ+L+GR +R+N A   +
Sbjct: 62  SMQGQDLNGRPLRINWAAKLE 82

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 94.1 bits (235), Expect = 2e-24
 Identities = 27/106 (25%), Positives = 47/106 (44%), Gaps = 26/106 (24%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
             LFVG+L  +VD E L   F+   +                               V++
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSG--------------------------HVMW 35

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
           + +T  SRG+GFV+ ++ ++A+ A++     D++GR L +N AA  
Sbjct: 36  DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL 81

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score =  135 bits (343), Expect = 6e-40
 Identities = 29/101 (28%), Positives = 51/101 (50%), Gaps = 3/101 (2%)

Query: 260 NKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR 319
           + AA      ++         R+YVG+L + +    L  +F   G++ + +++ D ETGR
Sbjct: 10  HMAAAMANNLQKGS---AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGR 66

Query: 320 SRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ 360
           S+G+GF+T S       A+  L+G  L GR ++V    +R 
Sbjct: 67  SKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT 107

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 93.5 bits (233), Expect = 8e-24
 Identities = 28/110 (25%), Positives = 50/110 (45%), Gaps = 26/110 (23%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
                +L+VG+L +++  + L  +FE  G +E                            
Sbjct: 23  SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESI-------------------------- 56

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
           Q++ + ET RS+G+GF+T S  E A+KA+E  + +++ GR + V     R
Sbjct: 57  QLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER 106

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score =  133 bits (337), Expect = 5e-39
 Identities = 34/90 (37%), Positives = 54/90 (60%)

Query: 273 PRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSET 332
           P V      ++VGN+P+E    +L+ +FSE G VV+ R+VYDRETG+ +G+GF     + 
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 333 ELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
               A+  L+G+   GRA+RV+ A   + +
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKNK 91

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 94.6 bits (236), Expect = 3e-24
 Identities = 28/115 (24%), Positives = 46/115 (40%), Gaps = 26/115 (22%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
             +FVGN+PY+   E+L  +F + G V                             +++Y
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSF--------------------------RLVY 42

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
           +RET + +G+GF      E A  A+   +  +  GR L V+ AA    + E    
Sbjct: 43  DRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSL 97

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score =  133 bits (337), Expect = 6e-39
 Identities = 30/97 (30%), Positives = 52/97 (53%)

Query: 267 TQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFV 326
           +      +     F ++VG+L  E+    ++  F+  G++ +ARVV D  TG+S+G+GFV
Sbjct: 3   SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62

Query: 327 TMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRS 363
           +  ++ +  +AI  + GQ L GR IR N A  +    
Sbjct: 63  SFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAP 99

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 93.6 bits (233), Expect = 1e-23
 Identities = 23/120 (19%), Positives = 45/120 (37%), Gaps = 26/120 (21%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +      +FVG+L  ++ +E +   F   G +  A                         
Sbjct: 11  DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDA------------------------- 45

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
            +V+ +  T +S+G+GFV+     +AE A++      + GR +  N A  +   P+    
Sbjct: 46  -RVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYE 104

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score =  132 bits (335), Expect = 7e-39
 Identities = 35/84 (41%), Positives = 54/84 (64%), Gaps = 1/84 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            IYVGNL +   + +++++FS+ GKV N +++YDRET + +GFGFV M  E+  ++AIA 
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAIAK 61

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
           LD  +  GR IRV  A  ++    
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEH 85

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 95.7 bits (239), Expect = 7e-25
 Identities = 30/114 (26%), Positives = 46/114 (40%), Gaps = 27/114 (23%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            ++VGNL Y   SE++  LF + G V                             ++IY+
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNV--------------------------KLIYD 36

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
           RET + +GFGFV M   E   +A+      D  GR + V +A P+ +       
Sbjct: 37  RETKKPKGFGFVEMQE-ESVSEAIAKLDNTDFMGRTIRVTEANPKKSLEHHHHH 89

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score =  132 bits (335), Expect = 9e-39
 Identities = 30/92 (32%), Positives = 47/92 (51%), Gaps = 2/92 (2%)

Query: 265 RGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFG 324
            G+   RA    +P   + V  L        L +VFS++G + +  +VYD+++ RSRGF 
Sbjct: 3   SGSSGNRANP--DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60

Query: 325 FVTMSSETELNDAIAALDGQNLDGRAIRVNVA 356
           FV   +  +  +A    +G  LDGR IRV+  
Sbjct: 61  FVYFENVDDAKEAKERANGMELDGRRIRVSGP 92

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 96.9 bits (242), Expect = 4e-25
 Identities = 24/109 (22%), Positives = 43/109 (39%), Gaps = 26/109 (23%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
            P  +  L V  L        L  +F K G +                            
Sbjct: 11  NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADV------------------------- 45

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAA 263
             ++Y++++ RSRGF FV    V++A++A E  +  ++DGR + V+  +
Sbjct: 46  -SIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPS 93

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score =  130 bits (330), Expect = 4e-38
 Identities = 31/82 (37%), Positives = 50/82 (60%)

Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
             F ++VG+L  E+  A +   F+  G++ +ARVV D  TG+S+G+GFV+  ++ +  +A
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64

Query: 338 IAALDGQNLDGRAIRVNVAEDR 359
           I  + GQ L GR IR N A  +
Sbjct: 65  IQQMGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 87.2 bits (217), Expect = 9e-22
 Identities = 22/107 (20%), Positives = 42/107 (39%), Gaps = 26/107 (24%)

Query: 159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVI 218
              +FVG+L  ++ +  +A  F   G +  A                          +V+
Sbjct: 6   HFHVFVGDLSPEITTAAIAAAFAPFGRISDA--------------------------RVV 39

Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
            +  T +S+G+GFV+     +AE A++      + GR +  N A  +
Sbjct: 40  KDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score =  131 bits (331), Expect = 4e-38
 Identities = 29/88 (32%), Positives = 43/88 (48%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                +YVG L  EVD+  L   F   G + + ++  D ET + RGF FV      +   
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           AI  ++   L GR IRVN+A+  + + S
Sbjct: 70  AIDNMNESELFGRTIRVNLAKPMRIKES 97

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 95.7 bits (239), Expect = 1e-24
 Identities = 26/115 (22%), Positives = 42/115 (36%), Gaps = 26/115 (22%)

Query: 157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQ 216
                L+VG L  +VD + L   F   G +                             Q
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI--------------------------Q 43

Query: 217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
           +  + ET++ RGF FV     E+A  A++  +  ++ GR + VN A P   +   
Sbjct: 44  IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESG 98

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score =  130 bits (330), Expect = 4e-38
 Identities = 24/80 (30%), Positives = 46/80 (57%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                +YV NLP+ + N  L ++FS++GKVV   ++ D++T +S+G  F+    +    +
Sbjct: 14  PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73

Query: 337 AIAALDGQNLDGRAIRVNVA 356
              A++ + L GR I+ ++A
Sbjct: 74  CTRAINNKQLFGRVIKASIA 93

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 95.4 bits (238), Expect = 1e-24
 Identities = 18/108 (16%), Positives = 40/108 (37%), Gaps = 26/108 (24%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
             P  + ++V NLP+ + +  L  +F K G V                            
Sbjct: 12  LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKV------------------------- 46

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
             ++ +++T +S+G  F+     + A+      +   + GR++  + A
Sbjct: 47  -TIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score =  129 bits (327), Expect = 1e-37
 Identities = 20/100 (20%), Positives = 44/100 (44%), Gaps = 1/100 (1%)

Query: 263 APRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRG 322
              G+             ++++  LP+      LE++   HG V + R+V +R  G+ +G
Sbjct: 1   GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKG 59

Query: 323 FGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
             +V   +E++ + A+  +DG  +    I+V ++      
Sbjct: 60  LAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 92.0 bits (229), Expect = 2e-23
 Identities = 22/123 (17%), Positives = 40/123 (32%), Gaps = 27/123 (21%)

Query: 143 GEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGF 202
           G  G      +    E  KLF+  LP+    E+L  + +  GTV+               
Sbjct: 1   GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDL------------- 47

Query: 203 HMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
                        +++ NR   + +G  +V      +A +AV       I   ++ V  +
Sbjct: 48  -------------RLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS 93

Query: 263 APR 265
              
Sbjct: 94  NSG 96

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score =  128 bits (324), Expect = 4e-37
 Identities = 19/88 (21%), Positives = 35/88 (39%), Gaps = 2/88 (2%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHG--KVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
             +Y+GNL W   +  L +     G   ++  +   +R  G+S+GF  V + SE      
Sbjct: 2   IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61

Query: 338 IAALDGQNLDGRAIRVNVAEDRQRRSSF 365
           +  L  + L G+   V  +   +     
Sbjct: 62  MDLLPKRELHGQNPVVTPSNKLEHHHHH 89

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score =  103 bits (260), Expect = 6e-28
 Identities = 20/111 (18%), Positives = 39/111 (35%), Gaps = 24/111 (21%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            L++GNL +    E L       G  +I E+KF                          N
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKF------------------------FEN 38

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
           R   +S+GF  V + +   ++K +++  + ++ G+   V  +         
Sbjct: 39  RANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEHHHHH 89

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score =  128 bits (323), Expect = 4e-37
 Identities = 28/81 (34%), Positives = 40/81 (49%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                +YVG L  EVD+  L   F   G + + ++  D ET + RGF FV      +   
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64

Query: 337 AIAALDGQNLDGRAIRVNVAE 357
           AI  ++   L GR IRVN+A+
Sbjct: 65  AIDNMNESELFGRTIRVNLAK 85

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 89.9 bits (224), Expect = 1e-22
 Identities = 25/106 (23%), Positives = 40/106 (37%), Gaps = 26/106 (24%)

Query: 157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQ 216
                L+VG L  +VD + L   F   G +                             Q
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI--------------------------Q 38

Query: 217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           +  + ET++ RGF FV     E+A  A++  +  ++ GR + VN A
Sbjct: 39  IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score =  129 bits (326), Expect = 6e-37
 Identities = 28/80 (35%), Positives = 39/80 (48%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                +YVG L  EVD+  L   F   G + + ++  D ET + RGF FV      +   
Sbjct: 61  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 120

Query: 337 AIAALDGQNLDGRAIRVNVA 356
           AI  ++   L GR IRVN+A
Sbjct: 121 AIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 92.5 bits (230), Expect = 5e-23
 Identities = 25/108 (23%), Positives = 40/108 (37%), Gaps = 26/108 (24%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                  L+VG L  +VD + L   F   G +                            
Sbjct: 59  SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI------------------------- 93

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
            Q+  + ET++ RGF FV     E+A  A++  +  ++ GR + VN A
Sbjct: 94  -QIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score =  126 bits (318), Expect = 3e-36
 Identities = 30/100 (30%), Positives = 49/100 (49%), Gaps = 4/100 (4%)

Query: 266 GTQPERAPRV-FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFG 324
           G+     P    +P   ++V  L  +     L++ F      V AR+V DRETG S+GFG
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFG 57

Query: 325 FVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           FV  +SE +   A  A++   +DG  + ++ A+ +    S
Sbjct: 58  FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGS 97

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 95.0 bits (237), Expect = 2e-24
 Identities = 28/120 (23%), Positives = 44/120 (36%), Gaps = 29/120 (24%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                  LFV  L  D   E L   F+ +                               
Sbjct: 11  RSQPSKTLFVKGLSEDTTEETLKESFDGSVRA---------------------------- 42

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
            +++ +RET  S+GFGFV  ++ E+A+ A E     +IDG  +T++ A P+G        
Sbjct: 43  -RIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score =  125 bits (316), Expect = 7e-36
 Identities = 22/97 (22%), Positives = 38/97 (39%)

Query: 269 PERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTM 328
                R  +    I V NL  +     L+++F   G +    +  D+ TG+S+GF F++ 
Sbjct: 5   SSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64

Query: 329 SSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
               +   AIA + G   D   + V  A+        
Sbjct: 65  HRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPS 101

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 94.2 bits (235), Expect = 4e-24
 Identities = 23/120 (19%), Positives = 40/120 (33%), Gaps = 29/120 (24%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
              ++A + V NL  D     L  LF   G++                            
Sbjct: 11  RADDNATIRVTNLSEDTRETDLQELFRPFGSISRI------------------------- 45

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
             +  ++ T +S+GF F++    E+A +A+     +  D  +L V  A P        P 
Sbjct: 46  -YLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS---TNSGPS 101

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score =  125 bits (316), Expect = 8e-36
 Identities = 26/88 (29%), Positives = 50/88 (56%), Gaps = 1/88 (1%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           +   ++++G L  E +   L+ VF +HG +    ++ DR T +SRGF F+T  +  +  +
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKN 63

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           A   ++G++L G+AI+V  A+    +S 
Sbjct: 64  AAKDMNGKSLHGKAIKVEQAKKPSFQSG 91

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 95.1 bits (237), Expect = 2e-24
 Identities = 29/126 (23%), Positives = 47/126 (37%), Gaps = 27/126 (21%)

Query: 154 VEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVS 213
           VE     KLF+G L  + + + L  +F K G +   EV                      
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPIS--EVL--------------------- 38

Query: 214 LLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAP 273
              +I +R T +SRGF F+T     +A+ A +  +   + G+ + V +A     Q     
Sbjct: 39  ---LIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRR 94

Query: 274 RVFEPG 279
           R     
Sbjct: 95  RPPASS 100

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score =  125 bits (315), Expect = 9e-36
 Identities = 28/103 (27%), Positives = 51/103 (49%), Gaps = 7/103 (6%)

Query: 262 AAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSR 321
           +   G    +         R++V N+P+   +  L Q+F + GK+++  ++++     S+
Sbjct: 3   SGSSGNSESK-----STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSK 55

Query: 322 GFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           GFGFVT  +  + + A   L G  ++GR I VN A  R   +S
Sbjct: 56  GFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNS 98

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 93.5 bits (233), Expect = 7e-24
 Identities = 26/117 (22%), Positives = 42/117 (35%), Gaps = 28/117 (23%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                 +L V N+P+      L  +F + G +                            
Sbjct: 11  SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDV------------------------- 45

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
            ++I+N     S+GFGFVT     +A++A E  H   ++GR + VN A  R      
Sbjct: 46  -EIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSG 99

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score =  124 bits (314), Expect = 2e-35
 Identities = 32/88 (36%), Positives = 46/88 (52%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                +YVG L  +V    L ++F + G VVN  +  DR TG+ +G+GFV   SE + + 
Sbjct: 13  NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           AI  +D   L G+ IRVN A    +  S
Sbjct: 73  AIKIMDMIKLYGKPIRVNKASAHNKNLS 100

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 91.2 bits (227), Expect = 5e-23
 Identities = 27/117 (23%), Positives = 46/117 (39%), Gaps = 26/117 (22%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           E  +DA ++VG L   V    L  LF +AG V                            
Sbjct: 11  ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNT------------------------- 45

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
             +  +R T + +G+GFV   + E+A+ A+++     + G+ + VNKA+        
Sbjct: 46  -HMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score =  124 bits (313), Expect = 2e-35
 Identities = 20/87 (22%), Positives = 44/87 (50%)

Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
           P   +Y+G++P++    ++  + S  G V+N ++++D +TGRS+G+ F+          A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 338 IAALDGQNLDGRAIRVNVAEDRQRRSS 364
           +  L+G  L  R ++   + +      
Sbjct: 61  VRNLNGYQLGSRFLKCGYSSNSDISGV 87

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 88.1 bits (219), Expect = 5e-22
 Identities = 19/115 (16%), Positives = 41/115 (35%), Gaps = 26/115 (22%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
             +++G++PYD   E++  L    G V                             ++++
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINL--------------------------KMMF 36

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
           + +T RS+G+ F+    +E +  AV   + Y +  R L    ++           
Sbjct: 37  DPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDISGVSLEH 91

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  124 bits (312), Expect = 3e-35
 Identities = 28/115 (24%), Positives = 52/115 (45%), Gaps = 5/115 (4%)

Query: 243 AVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSE 302
           +        +    L+   AA  G Q E        G  +++ +LP E  +  L   F  
Sbjct: 9   SASALSTSPLASVALSAAAAAAAGKQIEG-----PEGCNLFIYHLPQEFTDTDLASTFLP 63

Query: 303 HGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE 357
            G V++A+V  D++T  S+ FGFV+  +      AI A++G  +  + ++V + +
Sbjct: 64  FGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 89.7 bits (223), Expect = 3e-22
 Identities = 24/109 (22%), Positives = 42/109 (38%), Gaps = 26/109 (23%)

Query: 154 VEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVS 213
           +E PE   LF+ +LP +     LA  F   G V  A                        
Sbjct: 35  IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISA------------------------ 70

Query: 214 LLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
             +V  +++T  S+ FGFV+    + A+ A++  + + +  + L V   
Sbjct: 71  --KVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score =  124 bits (313), Expect = 4e-35
 Identities = 26/101 (25%), Positives = 43/101 (42%), Gaps = 1/101 (0%)

Query: 264 PRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGF 323
                        E G ++ V NL + V +A ++++F+E G +  A V YDR +GRS G 
Sbjct: 20  DLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGT 78

Query: 324 GFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
             V      +   A+    G  LDGR + + +   +     
Sbjct: 79  ADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEH 119

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 91.7 bits (228), Expect = 7e-23
 Identities = 26/119 (21%), Positives = 42/119 (35%), Gaps = 30/119 (25%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
               AKL V NL + V    +  LF + GT++ A                          
Sbjct: 32  VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA-------------------------- 65

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
            V Y+R + RS G   V      +A KA++ +    +DGR + +   A +    +    
Sbjct: 66  AVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ---IDLEHH 120

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  123 bits (311), Expect = 4e-35
 Identities = 29/97 (29%), Positives = 51/97 (52%), Gaps = 4/97 (4%)

Query: 263 APRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRG 322
            PRG+      +      R++V N+P+   +  L Q+F + GK+++  ++++     S+G
Sbjct: 15  VPRGSHMNTENK--SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKG 70

Query: 323 FGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR 359
           FGFVT  +  + + A   L G  ++GR I VN A  R
Sbjct: 71  FGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 94.3 bits (235), Expect = 5e-24
 Identities = 28/128 (21%), Positives = 45/128 (35%), Gaps = 28/128 (21%)

Query: 138 RQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLF 197
               SG              +  +L V N+P+      L  +F + G +           
Sbjct: 8   HHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDV-------- 59

Query: 198 GNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLL 257
                             ++I+N     S+GFGFVT     +A++A E  H   ++GR +
Sbjct: 60  ------------------EIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKI 99

Query: 258 TVNKAAPR 265
            VN A  R
Sbjct: 100 EVNNATAR 107

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score =  123 bits (311), Expect = 5e-35
 Identities = 32/96 (33%), Positives = 50/96 (52%), Gaps = 1/96 (1%)

Query: 270 ERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMS 329
             A +    G  ++V NL ++V   +L++VFS  G VV A ++ D++ G+SRG G VT  
Sbjct: 6   SGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFE 64

Query: 330 SETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
              E   AI+  +GQ L  R + V + E    +  F
Sbjct: 65  QSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDF 100

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 98.9 bits (247), Expect = 9e-26
 Identities = 27/120 (22%), Positives = 45/120 (37%), Gaps = 27/120 (22%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                + +FV NL Y V  +KL  +F  AG V  A++                       
Sbjct: 11  AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADI----------------------- 47

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
              + +++  +SRG G VT     EA +A+ MF+   +  R + V        + +  P 
Sbjct: 48  ---LEDKD-GKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPP 103

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score =  122 bits (308), Expect = 1e-34
 Identities = 32/95 (33%), Positives = 53/95 (55%), Gaps = 4/95 (4%)

Query: 270 ERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMS 329
           +R  R       +YV NL   +D+ RL + FS  G + +A+V+   E GRS+GFGFV  S
Sbjct: 8   DRITR--YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFS 63

Query: 330 SETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           S  E   A+  ++G+ +  + + V +A+ ++ R S
Sbjct: 64  SPEEATKAVTEMNGRIVATKPLYVALAQRKEERQS 98

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 87.3 bits (217), Expect = 2e-21
 Identities = 31/114 (27%), Positives = 45/114 (39%), Gaps = 28/114 (24%)

Query: 152 EFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFY 211
           + +   +   L+V NL   +D E+L   F   GT+  A+V            M       
Sbjct: 8   DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKV------------M------- 48

Query: 212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                     E  RS+GFGFV  S+ EEA KAV   +   +  + L V  A  +
Sbjct: 49  ---------MEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRK 93

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score =  121 bits (307), Expect = 1e-34
 Identities = 30/102 (29%), Positives = 54/102 (52%), Gaps = 4/102 (3%)

Query: 263 APRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRG 322
              G+  +  P   EP +  YVGNLP+      ++ +F +   + + R+V D++T + +G
Sbjct: 1   GSSGSSGKELPT--EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKG 57

Query: 323 FGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           F +V       L +A+   DG  L  R++RV++AE R++  S
Sbjct: 58  FCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQDKS 98

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 78.8 bits (195), Expect = 2e-18
 Identities = 24/129 (18%), Positives = 47/129 (36%), Gaps = 30/129 (23%)

Query: 143 GEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGF 202
           G  G   +E   EPP     +VGNLP++     +  +F+      +              
Sbjct: 1   GSSGSSGKELPTEPPY--TAYVGNLPFNTVQGDIDAIFKDLSIRSV-------------- 44

Query: 203 HMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
                        +++ +++TD+ +GF +V    V+  ++A+       +  R L V+ A
Sbjct: 45  -------------RLVRDKDTDKFKGFCYVEFDEVDSLKEALTY-DGALLGDRSLRVDIA 90

Query: 263 APRGTQPER 271
             R      
Sbjct: 91  EGRKQDKSG 99

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score =  122 bits (307), Expect = 1e-34
 Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 1/90 (1%)

Query: 268 QPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVT 327
                    E G ++ V NL + V +A ++++F+E G +  A V YDR +GRS G   V 
Sbjct: 18  SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVH 76

Query: 328 MSSETELNDAIAALDGQNLDGRAIRVNVAE 357
              + +   A+   +G  LDGR + + +  
Sbjct: 77  FERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 90.4 bits (225), Expect = 1e-22
 Identities = 27/132 (20%), Positives = 47/132 (35%), Gaps = 32/132 (24%)

Query: 136 GERQEESGEEGV---FEE--EEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAE 190
           G R ++  ++     F+             KL V NL + V    +  LF + GT++ A 
Sbjct: 1   GSRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKA- 59

Query: 191 VKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRY 250
                                     V Y+R + RS G   V      +A KA++ ++  
Sbjct: 60  -------------------------AVHYDR-SGRSLGTADVHFERKADALKAMKQYNGV 93

Query: 251 DIDGRLLTVNKA 262
            +DGR + +   
Sbjct: 94  PLDGRPMNIQLV 105

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score =  121 bits (305), Expect = 2e-34
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 1/83 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR-ETGRSRGFGFVTMSSETELNDAIA 339
           ++++G L   V    + ++FS +GK+    +  +R     S+G+ +V   +  E   A+ 
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 340 ALDGQNLDGRAIRVNVAEDRQRR 362
            +DG  +DG+ I          R
Sbjct: 66  HMDGGQIDGQEITATAVLAPWPR 88

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 89.1 bits (222), Expect = 2e-22
 Identities = 19/110 (17%), Positives = 38/110 (34%), Gaps = 27/110 (24%)

Query: 157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQ 216
            +  K+ +G L  +V  + +  +F   G +++                            
Sbjct: 2   MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMI--------------------------D 35

Query: 217 VIYNR-ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
           +   R     S+G+ +V     +EAEKA++      IDG+ +T       
Sbjct: 36  MPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAP 85

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score =  120 bits (304), Expect = 3e-34
 Identities = 25/84 (29%), Positives = 39/84 (46%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++V NL +      LE++FS +G +       D  T + +GF FVT         A A 
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
           +DGQ   GR + V  +  ++  S 
Sbjct: 70  VDGQVFQGRMLHVLPSTIKKEASQ 93

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 98.1 bits (245), Expect = 1e-25
 Identities = 27/120 (22%), Positives = 37/120 (30%), Gaps = 26/120 (21%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                 +LFV NL Y    E L  LF   G +   E+                       
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLS--ELH---------------------- 39

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
                +  T + +GF FVT    E A KA          GR+L V  +  +    +  P 
Sbjct: 40  --YPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPS 97

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score =  120 bits (304), Expect = 4e-34
 Identities = 24/88 (27%), Positives = 43/88 (48%)

Query: 272 APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
            P+    G+ ++V  +  E     +   F+E+G++ N  +  DR TG  +G+  V   + 
Sbjct: 16  GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 75

Query: 332 TELNDAIAALDGQNLDGRAIRVNVAEDR 359
            E   A+  L+GQ+L G+ I V+    R
Sbjct: 76  KEAQAAMEGLNGQDLMGQPISVDWCFVR 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 85.0 bits (211), Expect = 1e-20
 Identities = 21/111 (18%), Positives = 40/111 (36%), Gaps = 26/111 (23%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
             E   LFV  +  +   E +   F + G ++                            
Sbjct: 20  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNI-------------------------- 53

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG 266
            +  +R T   +G+  V   T +EA+ A+E  +  D+ G+ ++V+    RG
Sbjct: 54  HLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG 104

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score =  121 bits (305), Expect = 4e-34
 Identities = 24/107 (22%), Positives = 50/107 (46%)

Query: 258 TVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRET 317
             +    +      + +    G  +++ +LP E  +  L Q+F   G VV+A+V  D++T
Sbjct: 4   GSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 63

Query: 318 GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
             S+ FGFV+  +      AI +++G  +  + ++V +   +    S
Sbjct: 64  NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKS 110

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 93.5 bits (233), Expect = 9e-24
 Identities = 25/117 (21%), Positives = 44/117 (37%), Gaps = 26/117 (22%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           E PE A LF+ +LP +   + L  +F   G V  A                         
Sbjct: 21  EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSA------------------------- 55

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
            +V  +++T+ S+ FGFV+      A+ A++  + + I  + L V     +      
Sbjct: 56  -KVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSG 111

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score =  120 bits (304), Expect = 4e-34
 Identities = 22/98 (22%), Positives = 48/98 (48%)

Query: 265 RGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFG 324
              + E  P+    G+ ++V ++  E     +++ F ++G++ N  +  DR TG S+G+ 
Sbjct: 12  DDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYA 71

Query: 325 FVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
            V   +  +   A  AL+G  + G+ I+V+    +  +
Sbjct: 72  LVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK 109

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 82.3 bits (204), Expect = 1e-19
 Identities = 19/111 (17%), Positives = 40/111 (36%), Gaps = 26/111 (23%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
             E   LFV ++  +   +++   F   G ++                           +
Sbjct: 23  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIK--------------------------NI 56

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG 266
            +  +R T  S+G+  V   T ++A  A E  +  +I G+ + V+    +G
Sbjct: 57  HLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG 107

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score =  119 bits (302), Expect = 5e-34
 Identities = 28/88 (31%), Positives = 47/88 (53%), Gaps = 1/88 (1%)

Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVN-ARVVYDRETGRSRGFGFVTMSSETELND 336
               I++GNL  E+D   L   FS  G ++   +++ D +TG S+G+ F+  +S    + 
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           AI A++GQ L  R I V+ A  +  + S
Sbjct: 64  AIEAMNGQYLCNRPITVSYAFKKDSKGS 91

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 79.2 bits (196), Expect = 1e-18
 Identities = 18/113 (15%), Positives = 47/113 (41%), Gaps = 25/113 (22%)

Query: 157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQ 216
              + +F+GNL  ++D + L   F   G +                         +   +
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVI-------------------------LQTPK 37

Query: 217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP 269
           ++ + +T  S+G+ F+  ++ + ++ A+E  +   +  R +TV+ A  + ++ 
Sbjct: 38  IMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKG 90

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score =  122 bits (307), Expect = 6e-34
 Identities = 26/106 (24%), Positives = 44/106 (41%), Gaps = 4/106 (3%)

Query: 260 NKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHG--KVVNARVVYDRET 317
           N   P         R       +YVG+  W   + +L QV    G   VV  +   +R  
Sbjct: 38  NNKTPAILYTYSGLR--NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRAN 95

Query: 318 GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRS 363
           G+S+G+  V ++SE  ++  +  L G+ L+G  + V  A  +    
Sbjct: 96  GQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQ 141

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score =  100 bits (251), Expect = 8e-26
 Identities = 20/130 (15%), Positives = 43/130 (33%), Gaps = 34/130 (26%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                A ++VG+  +    ++L  +    G  ++ E+K                      
Sbjct: 51  LRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELK---------------------- 88

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR--------- 265
                NR   +S+G+  V +++     K +E+     ++G  + V  A  +         
Sbjct: 89  --FAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQA 146

Query: 266 -GTQPERAPR 274
              +  R PR
Sbjct: 147 RKRECVRVPR 156

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score =  120 bits (303), Expect = 7e-34
 Identities = 25/104 (24%), Positives = 45/104 (43%), Gaps = 6/104 (5%)

Query: 267 TQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFV 326
           +     P     G  +++ NL ++ +   L +V  + G +   RVV   +T  S+G  F 
Sbjct: 3   SGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 62

Query: 327 TMSSETELNDAIAALD------GQNLDGRAIRVNVAEDRQRRSS 364
              ++      +AA        G  LDGR ++V++A  R   +S
Sbjct: 63  QFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 93.6 bits (233), Expect = 9e-24
 Identities = 24/124 (19%), Positives = 44/124 (35%), Gaps = 32/124 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +  E   +F+ NL +D + E L  + ++ G ++                           
Sbjct: 11  DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYV------------------------- 45

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHR------YDIDGRLLTVNKAAPRGTQ 268
            +V+ + +T+ S+G  F    T E A+K +             +DGR L V+ A  R   
Sbjct: 46  -RVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA 104

Query: 269 PERA 272
               
Sbjct: 105 ASGP 108

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score =  120 bits (303), Expect = 1e-33
 Identities = 25/95 (26%), Positives = 44/95 (46%)

Query: 270 ERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMS 329
           E  P+    G+ ++V  +  E     +   F+E+G++ N  +  DR TG  +G+  V   
Sbjct: 13  EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72

Query: 330 SETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           +  E   A+  L+GQ+L G+ I V+    R     
Sbjct: 73  TYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKG 107

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 85.9 bits (213), Expect = 9e-21
 Identities = 21/118 (17%), Positives = 41/118 (34%), Gaps = 26/118 (22%)

Query: 154 VEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVS 213
               E   LFV  +  +   E +   F + G ++                          
Sbjct: 17  QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNI------------------------ 52

Query: 214 LLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
              +  +R T   +G+  V   T +EA+ A+E  +  D+ G+ ++V+    RG    +
Sbjct: 53  --HLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGK 108

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score =  121 bits (306), Expect = 2e-33
 Identities = 26/101 (25%), Positives = 43/101 (42%), Gaps = 1/101 (0%)

Query: 264 PRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGF 323
                        E G ++ V NL + V +A ++++F+E G +  A V YDR +GRS G 
Sbjct: 73  DLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGT 131

Query: 324 GFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
             V      +   A+    G  LDGR + + +   +     
Sbjct: 132 ADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEH 172

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 88.4 bits (219), Expect = 4e-21
 Identities = 26/117 (22%), Positives = 41/117 (35%), Gaps = 27/117 (23%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                AKL V NL + V    +  LF + GT++ A V                       
Sbjct: 84  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAV----------------------- 120

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
               Y+R + RS G   V      +A KA++ +    +DGR + +   A +      
Sbjct: 121 ---DYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHH 173

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score =  116 bits (293), Expect = 1e-32
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 3/87 (3%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETG---RSRGFGFVTMSSETELNDA 337
            +++ NL +      L+ VFS+ G + +  +   +       S GFGFV      +   A
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 338 IAALDGQNLDGRAIRVNVAEDRQRRSS 364
           +  L G  +DG  + V ++E   + +S
Sbjct: 67  LKQLQGHTVDGHKLEVRISERATKPAS 93

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 86.9 bits (216), Expect = 2e-21
 Identities = 26/122 (21%), Positives = 42/122 (34%), Gaps = 30/122 (24%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
               + LF+ NL +    E L  +F K G ++                            
Sbjct: 2   SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSC-------------------------- 35

Query: 216 QVIYNRET---DRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERA 272
            +   +       S GFGFV     E+A+KA++    + +DG  L V  +    T+P   
Sbjct: 36  TISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERA-TKPASG 94

Query: 273 PR 274
           P 
Sbjct: 95  PS 96

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score =  114 bits (289), Expect = 5e-32
 Identities = 27/88 (30%), Positives = 41/88 (46%), Gaps = 2/88 (2%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
               +I+V NLP++     L+  F+E G V+ A +    E G+S+G G V   S      
Sbjct: 6   SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAER 63

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           A   ++G  L GR I V +  +    SS
Sbjct: 64  ACRMMNGMKLSGREIDVRIDRNASGPSS 91

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 90.7 bits (226), Expect = 6e-23
 Identities = 25/112 (22%), Positives = 39/112 (34%), Gaps = 28/112 (25%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
                ++FV NLP+D   + L   F + G V  A++K                       
Sbjct: 5   SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIK----------------------- 41

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT 267
                 E  +S+G G V   + E AE+A  M +   + GR + V        
Sbjct: 42  -----MENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASG 88

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score =  114 bits (287), Expect = 8e-32
 Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 1/90 (1%)

Query: 267 TQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFV 326
                 P   E    ++VGNL   V    L ++F + G +    +  DRE G+ + FGFV
Sbjct: 4   GSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFV 62

Query: 327 TMSSETELNDAIAALDGQNLDGRAIRVNVA 356
                  ++ AIA L+G  L GR I V+  
Sbjct: 63  CFKHPESVSYAIALLNGIRLYGRPINVSGP 92

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 88.5 bits (220), Expect = 4e-22
 Identities = 29/122 (23%), Positives = 45/122 (36%), Gaps = 31/122 (25%)

Query: 142 SGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQG 201
           SG  G+F  +E      D  +FVGNL   V  E L  LF +AG +               
Sbjct: 3   SGSSGMFPAQE----EADRTVFVGNLEARVREEILYELFLQAGPLTKV------------ 46

Query: 202 FHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK 261
                          +  +RE  + + FGFV     E    A+ + +   + GR + V+ 
Sbjct: 47  --------------TICKDREG-KPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG 91

Query: 262 AA 263
            +
Sbjct: 92  PS 93

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score =  116 bits (292), Expect = 1e-31
 Identities = 27/132 (20%), Positives = 57/132 (43%), Gaps = 3/132 (2%)

Query: 236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPR---GTQPERAPRVFEPGFRIYVGNLPWEVD 292
             E+A+         D + R    +    R     + E  P+    G+ ++V ++  E  
Sbjct: 26  LKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQ 85

Query: 293 NARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR 352
              +++ F ++G++ N  +  DR TG S+G+  V   +  +   A  AL+G  + G+ I+
Sbjct: 86  EDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ 145

Query: 353 VNVAEDRQRRSS 364
           V+    +  +  
Sbjct: 146 VDWCFVKGPKRV 157

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 87.6 bits (217), Expect = 7e-21
 Identities = 29/183 (15%), Positives = 58/183 (31%), Gaps = 28/183 (15%)

Query: 94  LEQEQEENGEEEPNWENQGADETEGNLSDWGEPEGEDTVVEAGERQEESGEEGVFEEEEF 153
           L+ +  E  E + + +       E      G   G D+         E       +E E 
Sbjct: 5   LDIDNAEEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEP 64

Query: 154 --VEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFY 211
                 E   LFV ++  +   +++   F   G ++                        
Sbjct: 65  GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNI---------------------- 102

Query: 212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
                +  +R T  S+G+  V   T ++A  A E  +  +I G+ + V+    +G +  +
Sbjct: 103 ----HLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVK 158

Query: 272 APR 274
              
Sbjct: 159 KSE 161

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score =  113 bits (285), Expect = 1e-31
 Identities = 16/74 (21%), Positives = 36/74 (48%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            +Y+  L     +  L ++   +GK+V+ + + D+ T + +G+GFV   S +    A+ A
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 341 LDGQNLDGRAIRVN 354
           L    +  +  + +
Sbjct: 67  LKASGVQAQMAKQS 80

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 91.4 bits (228), Expect = 2e-23
 Identities = 16/107 (14%), Positives = 34/107 (31%), Gaps = 26/107 (24%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
               + L++  L      + L  L +  G +     K                       
Sbjct: 2   SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIV--STK----------------------- 36

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
             I ++ T++ +G+GFV   +   A+KAV       +  ++   +  
Sbjct: 37  -AILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP 82

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score =  113 bits (286), Expect = 2e-31
 Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 2/86 (2%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
              F +++GNL      A L+   SE     +  VV D  TG +R FG+V   S  +L  
Sbjct: 15  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEK 73

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRR 362
           A+  L G  + G  I++   + R   
Sbjct: 74  AL-ELTGLKVFGNEIKLEKPKGRDGT 98

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 90.0 bits (224), Expect = 1e-22
 Identities = 22/123 (17%), Positives = 40/123 (32%), Gaps = 28/123 (22%)

Query: 143 GEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGF 202
           G   + +  E  E      LF+GNL  +    +L +   +                    
Sbjct: 1   GSHMLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL------------- 47

Query: 203 HMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
                          + +  T  +R FG+V   + E+ EKA+E+     + G  + + K 
Sbjct: 48  --------------AVVDVRTGTNRKFGYVDFESAEDLEKALEL-TGLKVFGNEIKLEKP 92

Query: 263 APR 265
             R
Sbjct: 93  KGR 95

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score =  113 bits (284), Expect = 3e-31
 Identities = 18/101 (17%), Positives = 41/101 (40%), Gaps = 11/101 (10%)

Query: 263 APRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRG 322
            P  ++  RA R       +   NL + +    L++VF +  ++         + G+S+G
Sbjct: 6   DPCTSKKVRAAR------TLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKG 54

Query: 323 FGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRS 363
             ++   SE +    +    G  +DGR++ +    ++    
Sbjct: 55  IAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 88.9 bits (221), Expect = 3e-22
 Identities = 18/122 (14%), Positives = 42/122 (34%), Gaps = 31/122 (25%)

Query: 145 EGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHM 204
             + +     +      L   NL +++  ++L  +FE A                     
Sbjct: 2   HMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-------------------- 41

Query: 205 WVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP 264
                      ++    +  +S+G  ++   +  +AEK +E     +IDGR +++     
Sbjct: 42  -----------EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 90

Query: 265 RG 266
           +G
Sbjct: 91  KG 92

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score =  112 bits (283), Expect = 4e-31
 Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 1/84 (1%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                IYVGN+ +      LE  F   G V    ++ D+ +G  +GF ++  S +  +  
Sbjct: 4   ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQ 360
           ++ ALD     GR I+V      +
Sbjct: 64  SL-ALDESLFRGRQIKVIPKRTNR 86

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 83.7 bits (208), Expect = 2e-20
 Identities = 17/105 (16%), Positives = 35/105 (33%), Gaps = 27/105 (25%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            ++VGN+ Y   +E+L   F   G+V    V                         ++ +
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVN--RVT------------------------ILCD 41

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
           + +   +GF ++  S  E    ++ +       GR + V      
Sbjct: 42  KFSGHPKGFAYIEFSDKESVRTSLAL-DESLFRGRQIKVIPKRTN 85

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score =  112 bits (283), Expect = 4e-31
 Identities = 19/88 (21%), Positives = 43/88 (48%), Gaps = 4/88 (4%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                + + NL +      L++VF +   +     V   + G+S+G+ F+  +S  +  +
Sbjct: 13  GESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKE 68

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           A+ + + + ++GRAIR+ +   R   +S
Sbjct: 69  ALNSCNKREIEGRAIRLELQGPRGSPNS 96

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score =  103 bits (258), Expect = 2e-27
 Identities = 23/120 (19%), Positives = 45/120 (37%), Gaps = 30/120 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
              E   L + NL Y    E L  +FEKA  +                            
Sbjct: 11  WSGESKTLVLSNLSYSATEETLQEVFEKATFI---------------------------- 42

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
              +   +  +S+G+ F+  ++ E+A++A+   ++ +I+GR + +    PRG+       
Sbjct: 43  --KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSS 100

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score =  111 bits (279), Expect = 2e-30
 Identities = 26/103 (25%), Positives = 50/103 (48%), Gaps = 5/103 (4%)

Query: 263 APRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYD-RETGRSR 321
              G+   R P+   P +  ++GNLP++V    +++ F     +   R+  +     R +
Sbjct: 1   GSSGSSGSRLPK--SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLK 57

Query: 322 GFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           GFG+        L  A+ +L+ ++L  + IRV+VA+  Q + S
Sbjct: 58  GFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKDS 99

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 78.1 bits (193), Expect = 4e-18
 Identities = 19/120 (15%), Positives = 36/120 (30%), Gaps = 29/120 (24%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
            PP     F+GNLPYDV  E +   F       +   +                      
Sbjct: 13  SPP--YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPR---------------------- 48

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
                    +R +GFG+     ++    A+ + +   +  + + V+ A     +      
Sbjct: 49  ----EPSNPERLKGFGYAEFEDLDSLLSALSL-NEESLGNKRIRVDVADQAQDKDSGPSS 103

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score =  115 bits (288), Expect = 2e-30
 Identities = 23/107 (21%), Positives = 39/107 (36%), Gaps = 2/107 (1%)

Query: 258 TVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHG--KVVNARVVYDR 315
           TV     +G  P            +Y+GNL W   +  L +     G   ++  +   +R
Sbjct: 47  TVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENR 106

Query: 316 ETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
             G+S+GF  V + SE      +  L  + L G+   V     +   
Sbjct: 107 ANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLS 153

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score =  100 bits (250), Expect = 5e-25
 Identities = 31/191 (16%), Positives = 64/191 (33%), Gaps = 34/191 (17%)

Query: 82  DQEEDKDNTTITLEQEQEENGEEEPNWENQGADETEGNLSDWGEPEGEDTVVEAGERQEE 141
           D  E+ +       QE E  G ++ +  +   D    + ++   PE  D +        +
Sbjct: 1   DVGEEFN-------QEAEYGGHDQIDLYD---DVISPSANNGDAPEDRDYMDTLPPTVGD 50

Query: 142 SGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQG 201
              +G      +    +   L++GNL +    E L       G  +I E+KF        
Sbjct: 51  DVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKF-------- 102

Query: 202 FHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK 261
                             NR   +S+GF  V + +   ++K +++  + ++ G+   V  
Sbjct: 103 ----------------FENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP 146

Query: 262 AAPRGTQPERA 272
              +       
Sbjct: 147 VNKQFLSQFEM 157

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score =  111 bits (279), Expect = 2e-30
 Identities = 27/102 (26%), Positives = 42/102 (41%), Gaps = 1/102 (0%)

Query: 263 APRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRG 322
           +P     +           ++   L   +    LE  FS  GKV + R++ DR + RS+G
Sbjct: 9   SPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG 68

Query: 323 FGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
             +V       +  AI  L GQ L G  I V  ++  + R S
Sbjct: 69  IAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNRLS 109

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 80.1 bits (198), Expect = 1e-18
 Identities = 19/139 (13%), Positives = 37/139 (26%), Gaps = 29/139 (20%)

Query: 136 GERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHF 195
           G   +    E V       E  +   +F   L   +    L   F   G V         
Sbjct: 4   GSSGKSPVREPVDNLSP--EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDV------ 55

Query: 196 LFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGR 255
                               ++I +R + RS+G  +V    ++    A+ +     + G 
Sbjct: 56  --------------------RIISDRNSRRSKGIAYVEFCEIQSVPLAIGL-TGQRLLGV 94

Query: 256 LLTVNKAAPRGTQPERAPR 274
            + V  +     +      
Sbjct: 95  PIIVQASQAEKNRLSGPSS 113

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score =  114 bits (286), Expect = 2e-30
 Identities = 39/227 (17%), Positives = 75/227 (33%), Gaps = 64/227 (28%)

Query: 162 LFVGNL-PYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           L V NL P  V  + L +LF   G V+  ++ F                           
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF--------------------------- 38

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERA-------- 272
                 +    V M+   +A+ A+   + + + G+ + +  +  +  Q  R         
Sbjct: 39  ----NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLT 94

Query: 273 -------------------PRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVY 313
                                +F P   +++ N+P  V    L+ +FS +G VV     +
Sbjct: 95  KDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF 154

Query: 314 DRETGRSRGFGFVTMSSETELNDAIAALDGQNL-DGRAIRVNVAEDR 359
                + R    + M S  E   A+  L   +L +   +RV+ ++  
Sbjct: 155 Q----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 197

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 56.8 bits (137), Expect = 9e-10
 Identities = 24/105 (22%), Positives = 37/105 (35%), Gaps = 31/105 (29%)

Query: 157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQ 216
           P  A L + N+P  V  E L +LF   G V                              
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGV------------------------------ 147

Query: 217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI-DGRLLTVN 260
           V   +   + R    + M +VEEA +A+   H +D+ +   L V+
Sbjct: 148 VKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS 192

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score =  111 bits (279), Expect = 3e-30
 Identities = 22/88 (25%), Positives = 43/88 (48%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           EP   +Y+ NL   V    L  +F+   +     + +   TGR RG  F+T  ++     
Sbjct: 23  EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           A+  ++G  L G+ + +   +++++RSS
Sbjct: 83  ALHLVNGYKLYGKILVIEFGKNKKQRSS 110

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 80.4 bits (199), Expect = 7e-19
 Identities = 19/105 (18%), Positives = 35/105 (33%), Gaps = 26/105 (24%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            L++ NL   V    L  LF +    +                             + + 
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGP--------------------------PIQFR 60

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
             T R RG  F+T    E A +A+ + + Y + G++L +     +
Sbjct: 61  MMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNK 105

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score =  110 bits (276), Expect = 5e-30
 Identities = 26/99 (26%), Positives = 42/99 (42%), Gaps = 3/99 (3%)

Query: 269 PERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTM 328
              +        ++++G +P  +D   L+ +F E GK+    V+ DR TG  +G  F+T 
Sbjct: 3   SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62

Query: 329 SSETELNDAIAALDGQNL---DGRAIRVNVAEDRQRRSS 364
                   A +AL  Q       R I+V  A+   R  S
Sbjct: 63  CERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGS 101

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 85.1 bits (211), Expect = 1e-20
 Identities = 26/120 (21%), Positives = 41/120 (34%), Gaps = 29/120 (24%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +  +  KLF+G +P ++D + L  LFE+ G +   E+                       
Sbjct: 9   KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIY--ELT---------------------- 44

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI---DGRLLTVNKAAPRGTQPER 271
             V+ +R T   +G  F+T    E A KA    H         R + V  A         
Sbjct: 45  --VLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSG 102

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score =  108 bits (273), Expect = 2e-29
 Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 1/98 (1%)

Query: 265 RGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFG 324
            G Q + A +  +    +Y+ NLP  +D   LE +    G+V++ R++ D  +G SRG G
Sbjct: 11  SGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVG 69

Query: 325 FVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
           F  M S  +    I   +G+ +          E    +
Sbjct: 70  FARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCK 107

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 89.2 bits (222), Expect = 4e-22
 Identities = 21/131 (16%), Positives = 40/131 (30%), Gaps = 27/131 (20%)

Query: 135 AGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFH 194
                      GV  +    +  +   L++ NLP  +D ++L  + +  G V        
Sbjct: 1   GSSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVIST----- 55

Query: 195 FLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDG 254
                                +++ +  +  SRG GF  M + E+ E  +  F+   I  
Sbjct: 56  ---------------------RILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKT 93

Query: 255 RLLTVNKAAPR 265
                    P 
Sbjct: 94  PPGVSAPTEPL 104

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score =  107 bits (270), Expect = 3e-29
 Identities = 24/99 (24%), Positives = 45/99 (45%), Gaps = 3/99 (3%)

Query: 263 APRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRET-GRSR 321
                   R+     P +  ++GNLP++V    +++ F     +   R+  +     R +
Sbjct: 3   GSHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLK 61

Query: 322 GFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ 360
           GFG+        L  A+ +L+ ++L  R IRV+VA+  Q
Sbjct: 62  GFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQ 99

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 73.0 bits (180), Expect = 2e-16
 Identities = 22/111 (19%), Positives = 38/111 (34%), Gaps = 29/111 (26%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
            PP     F+GNLPYDV  E +   F     + I+ V+                      
Sbjct: 17  SPP--YTAFLGNLPYDVTEESIKEFFRG---LNISAVRL--------------------- 50

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                    +R +GFG+     ++    A+ + +   +  R + V+ A   
Sbjct: 51  --PREPSNPERLKGFGYAEFEDLDSLLSALSL-NEESLGNRRIRVDVADQA 98

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score =  107 bits (270), Expect = 5e-29
 Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I++ NL   +DN  L   FS  G +++ +VV D     S+G+GFV   ++     AI  +
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 65

Query: 342 DGQNLDGRAIRVNVAEDRQRRSS 364
           +G  L+ R + V   + R+ R +
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREA 88

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score =  103 bits (259), Expect = 2e-27
 Identities = 26/139 (18%), Positives = 48/139 (34%), Gaps = 28/139 (20%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
           P     +F+ NL   +D++ L   F   G +   +V                        
Sbjct: 2   PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV----------------------- 38

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRV 275
                 + + S+G+GFV   T E AE+A+E  +   ++ R + V +   R  +       
Sbjct: 39  -----CDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAR 93

Query: 276 FEPGFRIYVGNLPWEVDNA 294
            +    +Y+ N       A
Sbjct: 94  AKEFTNVYIKNFGPGSTRA 112

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score =  107 bits (269), Expect = 6e-29
 Identities = 31/84 (36%), Positives = 45/84 (53%), Gaps = 1/84 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG LP+   +A L + F   G +  A V+ DR+TG+SRG+GFVTM+       A   
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
                +DGR   VN+A    +  S
Sbjct: 79  -PNPIIDGRKANVNLAYLGAKPRS 101

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 97.0 bits (242), Expect = 5e-25
 Identities = 41/135 (30%), Positives = 52/135 (38%), Gaps = 34/135 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +     K+FVG LPY      L   FE  G  +I E                        
Sbjct: 13  KDTTFTKIFVGGLPYHTTDASLRKYFEGFG--DIEEAV---------------------- 48

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVE-MFHRYDIDGRLLTVNKAAPRGTQPERAP 273
             VI +R+T +SRG+GFVTM+    AE+A +       IDGR   VN A          P
Sbjct: 49  --VITDRQTGKSRGYGFVTMADRAAAERACKDPNP--IIDGRKANVNLAYLGAK-----P 99

Query: 274 RVFEPGFRIYVGNLP 288
           R  + GF I V    
Sbjct: 100 RSLQTGFAIGVSGPS 114

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score =  107 bits (270), Expect = 1e-28
 Identities = 22/96 (22%), Positives = 44/96 (45%)

Query: 270 ERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMS 329
           E   ++ +    +YVGNL +     ++ ++FS+ G +    +  D+    + GF FV   
Sbjct: 30  EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYY 89

Query: 330 SETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
           S  +  +A+  ++G  LD R IR +     +    +
Sbjct: 90  SRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQY 125

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 86.0 bits (213), Expect = 2e-20
 Identities = 22/116 (18%), Positives = 43/116 (37%), Gaps = 26/116 (22%)

Query: 150 EEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAV 209
           EE+     +   L+VGNL +    E++  LF K+G ++                      
Sbjct: 30  EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKI-------------------- 69

Query: 210 FYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                  +  ++    + GF FV   +  +AE A+   +   +D R++  +  A  
Sbjct: 70  ------IMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGF 119

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score =  105 bits (264), Expect = 2e-28
 Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 8/88 (9%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
              ++I+VGN+     +  L  +F   G+V+   VV        + + FV M  E +   
Sbjct: 7   GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKA 58

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           AIA L+G+ + G+ I V ++   Q++S 
Sbjct: 59  AIAQLNGKEVKGKRINVELSTKGQKKSG 86

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 77.2 bits (191), Expect = 5e-18
 Identities = 22/119 (18%), Positives = 40/119 (33%), Gaps = 36/119 (30%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
                K+FVGN+     S++L  LFE+ G V   +V                        
Sbjct: 6   SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV----------------------- 42

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
                      + + FV M    +A+ A+   +  ++ G+ + V  +     Q +  P 
Sbjct: 43  -----------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG--QKKSGPS 88

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score =  105 bits (265), Expect = 2e-28
 Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 2/90 (2%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE-TGRSRGFGFVTMSSETELN 335
           +   +I V N+P++ +   + ++FS  G++   R+      TG  RGFGFV   ++ +  
Sbjct: 13  QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 72

Query: 336 DAIAAL-DGQNLDGRAIRVNVAEDRQRRSS 364
            A  AL    +L GR + +  A+      S
Sbjct: 73  KAFNALCHSTHLYGRRLVLEWADSEVTVQS 102

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 82.0 bits (203), Expect = 2e-19
 Identities = 25/120 (20%), Positives = 43/120 (35%), Gaps = 28/120 (23%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +    +K+ V N+P+  +  ++  LF   G ++   V+                      
Sbjct: 11  KKQTTSKILVRNIPFQANQREIRELFSTFGELK--TVR---------------------- 46

Query: 215 LQVIYNRE-TDRSRGFGFVTMSTVEEAEKAVE-MFHRYDIDGRLLTVNKAAPRGTQPERA 272
             +      T   RGFGFV   T ++A+KA   + H   + GR L +  A    T     
Sbjct: 47  --LPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGP 104

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score =  109 bits (273), Expect = 3e-28
 Identities = 39/235 (16%), Positives = 78/235 (33%), Gaps = 64/235 (27%)

Query: 154 VEPPEDAKLFVGNL-PYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYV 212
           +    ++ L V NL P  V  + L +LF   G V+  ++ F                   
Sbjct: 29  LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF------------------- 69

Query: 213 SLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERA 272
                         +    V M+   +A+ A+   + + + G+ + +  +  +  Q  R 
Sbjct: 70  ------------NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPRE 117

Query: 273 ---------------------------PRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGK 305
                                        +F P   +++ N+P  V    L+ +FS +G 
Sbjct: 118 GQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG 177

Query: 306 VVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL-DGRAIRVNVAEDR 359
           VV     +     + R    + M S  E   A+  L   +L +   +RV+ ++  
Sbjct: 178 VVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score =  105 bits (264), Expect = 4e-28
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 1/84 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            +YVGN+ +      LE  FS  G +    ++ D+ +G  +G+ ++  +    ++ A+ A
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-A 96

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
           +D     GR I+V          S
Sbjct: 97  MDETVFRGRTIKVLPKRTNMPGIS 120

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 82.5 bits (204), Expect = 2e-19
 Identities = 16/141 (11%), Positives = 40/141 (28%), Gaps = 30/141 (21%)

Query: 137 ERQEESGEEGVFEEEEFVEPPEDA---KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKF 193
            +           +    E  ++     ++VGN+ Y   ++ L   F   G++    +  
Sbjct: 11  SKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSIN--RIT- 67

Query: 194 HFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDID 253
                                  ++ ++ +   +G+ ++  +     + AV M       
Sbjct: 68  -----------------------ILCDKFSGHPKGYAYIEFAERNSVDAAVAM-DETVFR 103

Query: 254 GRLLTVNKAAPRGTQPERAPR 274
           GR + V              R
Sbjct: 104 GRTIKVLPKRTNMPGISSTDR 124

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score =  104 bits (261), Expect = 9e-28
 Identities = 23/104 (22%), Positives = 38/104 (36%), Gaps = 8/104 (7%)

Query: 269 PERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKV--------VNARVVYDRETGRS 320
               P        IYV  L   V    L   F + G V            +  D+ETG+ 
Sbjct: 5   SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKP 64

Query: 321 RGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           +G   V+         A+   DG++  G  ++V++A  +   +S
Sbjct: 65  KGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 108

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 92.9 bits (231), Expect = 2e-23
 Identities = 25/123 (20%), Positives = 48/123 (39%), Gaps = 20/123 (16%)

Query: 143 GEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGF 202
           G  G   + +  E  +++ ++V  L   V  + LA  F++ G V++ +     +      
Sbjct: 1   GSSGSSGDPD--EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMI----- 53

Query: 203 HMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
                         +  ++ET + +G   V+      A+ AVE F   D  G  L V+ A
Sbjct: 54  -------------HIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 100

Query: 263 APR 265
             +
Sbjct: 101 RKK 103

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score =  103 bits (259), Expect = 1e-27
 Identities = 24/99 (24%), Positives = 44/99 (44%), Gaps = 6/99 (6%)

Query: 266 GTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGF 325
            +      + F    R++VGNLP ++    + ++F ++GK     +       + +GFGF
Sbjct: 2   SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGF 55

Query: 326 VTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           + + + T    A   LD   L G+ +RV  A      +S
Sbjct: 56  IRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTS 94

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 81.2 bits (201), Expect = 2e-19
 Identities = 30/119 (25%), Positives = 43/119 (36%), Gaps = 33/119 (27%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
              + ++LFVGNLP D+  E++  LFEK G  +  EV  H                    
Sbjct: 11  TFTQRSRLFVGNLPPDITEEEMRKLFEKYG--KAGEVFIH-------------------- 48

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAP 273
                     + +GFGF+ + T   AE A        + G+ L V  A          P
Sbjct: 49  ----------KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS-ASLTSGP 96

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score =  103 bits (258), Expect = 1e-27
 Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 8/88 (9%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           +   +++VGN+     N  L   F E+G V+   +V        + + FV M    +  +
Sbjct: 8   KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVE 59

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           AI  LD     G+ + V ++  R R +S
Sbjct: 60  AIRGLDNTEFQGKRMHVQLSTSRLRTAS 87

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 76.5 bits (189), Expect = 1e-17
 Identities = 19/118 (16%), Positives = 35/118 (29%), Gaps = 34/118 (28%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
                KL VGN+     +++L   FE+ G V   ++                        
Sbjct: 7   GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV----------------------- 43

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAP 273
                      + + FV M   E+A +A+      +  G+ + V  +  R        
Sbjct: 44  -----------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTASGPS 90

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score =  102 bits (257), Expect = 3e-27
 Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 1/84 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG +P       L + F + G V    ++YD E  R RGFGF+T   E  ++ A+  
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
               ++ G+ + V  AE R  +SS
Sbjct: 72  -HFHDIMGKKVEVKRAEPRDSKSS 94

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 95.0 bits (237), Expect = 2e-24
 Identities = 31/117 (26%), Positives = 50/117 (42%), Gaps = 27/117 (23%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
              +  K+FVG +P++    +L   F+K G V    +                       
Sbjct: 6   SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVM----------------------- 42

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
              IY+ E  R RGFGF+T    +  ++AV M H +DI G+ + V +A PR ++   
Sbjct: 43  ---IYDAEKQRPRGFGFITFEDEQSVDQAVNM-HFHDIMGKKVEVKRAEPRDSKSSG 95

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score =  102 bits (256), Expect = 3e-27
 Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 5/85 (5%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++YVGNL        LE+ FS +G +    +  +       GF FV      +  DA+  
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSSF 365
           LDG+ + G  +RV ++    RRS F
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRSRF 81

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 78.5 bits (194), Expect = 2e-18
 Identities = 25/129 (19%), Positives = 39/129 (30%), Gaps = 33/129 (25%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K++VGNL       +L   F   G +    +                             
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIA---------------------------- 33

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA--APRGTQPERAPRVFEP 278
                  GF FV      +AE AV       I G  + V  +   PR ++ +R P   + 
Sbjct: 34  ---RNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPARRKL 90

Query: 279 GFRIYVGNL 287
              ++ G L
Sbjct: 91  LEVLFNGPL 99

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score =  101 bits (255), Expect = 4e-27
 Identities = 21/84 (25%), Positives = 32/84 (38%), Gaps = 8/84 (9%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNA--------RVVYDRETGRSRGFGFVTMSSET 332
            I+V  L   V    +   F + G +            +  DRETG+ +G   V+     
Sbjct: 15  TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74

Query: 333 ELNDAIAALDGQNLDGRAIRVNVA 356
               AI   DG+   G  I+V+ A
Sbjct: 75  SAKAAIDWFDGKEFSGNPIKVSFA 98

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 92.4 bits (230), Expect = 1e-23
 Identities = 19/109 (17%), Positives = 41/109 (37%), Gaps = 18/109 (16%)

Query: 154 VEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVS 213
               ++  +FV  L  +V  E +A  F++ G ++  +     +                 
Sbjct: 8   HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMI---------------- 51

Query: 214 LLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
              +  +RET + +G   V+      A+ A++ F   +  G  + V+ A
Sbjct: 52  --NLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score =  102 bits (255), Expect = 6e-27
 Identities = 15/86 (17%), Positives = 31/86 (36%)

Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
           P   +    L   V    L+ +  ++G+V    ++    T +  G   V  +S     + 
Sbjct: 5   PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKET 64

Query: 338 IAALDGQNLDGRAIRVNVAEDRQRRS 363
           +  L   ++ G  I   +    Q+R 
Sbjct: 65  VKNLHLTSVMGNIIHAQLDIKGQQRM 90

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 87.8 bits (218), Expect = 1e-21
 Identities = 19/124 (15%), Positives = 39/124 (31%), Gaps = 27/124 (21%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
                ++    L  +V    L  +  K G VE  EV+                       
Sbjct: 3   QIPLKEVTFARLNDNVRETFLKDMCRKYGEVE--EVE----------------------- 37

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRV 275
            ++ +  T +  G   V  ++   A++ V+  H   + G ++       +G Q  +   +
Sbjct: 38  -ILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL-DIKGQQRMKYYEL 95

Query: 276 FEPG 279
              G
Sbjct: 96  IVNG 99

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score =  101 bits (254), Expect = 7e-27
 Identities = 20/85 (23%), Positives = 45/85 (52%), Gaps = 3/85 (3%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            ++VG +   +D   +   F+ +G V   +++ DR TG S+G+GFV+  ++ ++   +  
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE- 68

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSSF 365
               N  G+ +++  A  +Q  S++
Sbjct: 69  -SQINFHGKKLKLGPAIRKQNLSTY 92

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 81.5 bits (202), Expect = 2e-19
 Identities = 23/120 (19%), Positives = 44/120 (36%), Gaps = 33/120 (27%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            +FVG +   +D  ++   F + G+V+                            ++I +
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEV--------------------------KIITD 44

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERA----PRVF 276
           R T  S+G+GFV+     + +K VE     +  G+ L +  A  +           P +F
Sbjct: 45  R-TGVSKGYGFVSFYNDVDVQKIVESQI--NFHGKKLKLGPAIRKQNLSTYHVQPRPLIF 101

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score =  100 bits (252), Expect = 9e-27
 Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 8/84 (9%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++GNLP E     +  +F ++GKV+   ++        + +GFV +  +T   DAI  
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
           L    L G  I V  ++++ + SS
Sbjct: 62  LHHYKLHGVNINVEASKNKSKASS 85

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 74.5 bits (184), Expect = 5e-17
 Identities = 22/111 (19%), Positives = 38/111 (34%), Gaps = 34/111 (30%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLF+GNLP +   +++  LFE+ G V   ++                             
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII---------------------------- 41

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
                 + +GFV +     AE A+   H Y + G  + V  +  +      
Sbjct: 42  ------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASSG 86

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score =  101 bits (254), Expect = 9e-27
 Identities = 22/92 (23%), Positives = 34/92 (36%), Gaps = 8/92 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNA--------RVVYDRETGRSRGFGFVTMSSET 332
            I+V  L   V    +   F + G +            +  DRETG+ +G   V+     
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 333 ELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
               AI   DG+   G  I+V+ A  R   + 
Sbjct: 69  SAKAAIDWFDGKEFSGNPIKVSFATRRADFNR 100

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 92.8 bits (231), Expect = 2e-23
 Identities = 20/119 (16%), Positives = 43/119 (36%), Gaps = 18/119 (15%)

Query: 154 VEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVS 213
            +  ++  +FV  L  +V  E +A  F++ G ++  +     +                 
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMI---------------- 45

Query: 214 LLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERA 272
              +  +RET + +G   V+      A+ A++ F   +  G  + V+ A  R       
Sbjct: 46  --NLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGG 102

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 98.1 bits (245), Expect = 1e-25
 Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 7/85 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++Y+GNL   V    L Q+F +    +        +     G+ FV    +     AI  
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIET 63

Query: 341 LDGQ-NLDGRAIRVNVAEDRQRRSS 364
           L G+  L G+ + V+ +  ++ RSS
Sbjct: 64  LSGKVELHGKIMEVDYSVSKKLRSS 88

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 75.4 bits (186), Expect = 2e-17
 Identities = 17/110 (15%), Positives = 36/110 (32%), Gaps = 33/110 (30%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KL++GNL   V ++ L  LF                                    +   
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDRK--------------------------------LPLA 37

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFH-RYDIDGRLLTVNKAAPRGTQP 269
            +     G+ FV       A +A+E    + ++ G+++ V+ +  +  + 
Sbjct: 38  GQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLRS 87

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 97.4 bits (243), Expect = 3e-25
 Identities = 28/102 (27%), Positives = 41/102 (40%), Gaps = 4/102 (3%)

Query: 263 APRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRG 322
              G    R P       RIYVGNLP ++    +E VF ++G + +  +   R       
Sbjct: 7   GMSGGGVIRGPAG-NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPP 62

Query: 323 FGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           F FV      +  DA+   DG + DG  +RV      +   S
Sbjct: 63  FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGS 104

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 77.7 bits (192), Expect = 6e-18
 Identities = 24/119 (20%), Positives = 36/119 (30%), Gaps = 29/119 (24%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
              D +++VGNLP D+ ++ +  +F K G +   ++K                       
Sbjct: 19  GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK----------------------- 55

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
                        F FV      +AE AV     YD DG  L V               
Sbjct: 56  ------NRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPSS 108

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score =  100 bits (249), Expect = 5e-25
 Identities = 29/223 (13%), Positives = 60/223 (26%), Gaps = 61/223 (27%)

Query: 162 LFVGNLPYD-VDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           L V  L    ++ +++  +F   G VE  +VKF                           
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVE--KVKFMK------------------------- 39

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAP------- 273
                  G   V M+     ++A+   +   + G+ + V  +      P ++        
Sbjct: 40  ----SKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSC 95

Query: 274 ----------------------RVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARV 311
                                 R+  P   ++  N P EV      ++  E G      V
Sbjct: 96  SYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSV 155

Query: 312 VYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN 354
                       G +   S+++  + +  L+   +        
Sbjct: 156 KVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP 198

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 62.4 bits (151), Expect = 1e-11
 Identities = 11/104 (10%), Positives = 22/104 (21%), Gaps = 26/104 (25%)

Query: 157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQ 216
                L   N P +V  E    + ++ G      VK                        
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVF---------------------- 158

Query: 217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
                        G +   +  +A + +   + Y +        
Sbjct: 159 ----SGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP 198

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 55.1 bits (132), Expect = 4e-09
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 278 PGFRIYVGNL-PWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
               + V  L   +++  R+  VF  +G V   + +  +      G   V M+    ++ 
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDR 57

Query: 337 AIAALDGQNLDGRAIRVNVA 356
           AI  L+   + G+ + V V+
Sbjct: 58  AITHLNNNFMFGQKMNVCVS 77

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 96.2 bits (240), Expect = 8e-25
 Identities = 30/113 (26%), Positives = 48/113 (42%), Gaps = 12/113 (10%)

Query: 248 HRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVV 307
           H +             PRG+    +        ++++G L W+     L + F + G+V 
Sbjct: 5   HHHHHHSS-----GLVPRGSHMGSSGC------KMFIGGLSWQTTQEGLREYFGQFGEVK 53

Query: 308 NARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ 360
              V+ D  T RSRGFGFVT   +  ++  +A      LD + I   VA  R+
Sbjct: 54  ECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTIDPKVAFPRR 105

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 82.3 bits (204), Expect = 1e-19
 Identities = 29/116 (25%), Positives = 42/116 (36%), Gaps = 29/116 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                 K+F+G L +    E L   F + G  E+ E                        
Sbjct: 21  MGSSGCKMFIGGLSWQTTQEGLREYFGQFG--EVKECL---------------------- 56

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEM-FHRYDIDGRLLTVNKAAPRGTQP 269
             V+ +  T RSRGFGFVT       +K +    H  ++D + +    A PR  QP
Sbjct: 57  --VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRH--ELDSKTIDPKVAFPRRAQP 108

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 95.8 bits (239), Expect = 9e-25
 Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVGNL  +V    + Q+FS+ G   + +++ +  +     + FV      +   A+AA+
Sbjct: 18  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 75

Query: 342 DGQNLDGRAIRVNVAEDRQRRSS 364
           +G+ + G+ ++VN A     + S
Sbjct: 76  NGRKILGKEVKVNWATTPSSQKS 98

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 69.2 bits (170), Expect = 5e-15
 Identities = 22/118 (18%), Positives = 37/118 (31%), Gaps = 28/118 (23%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +  +   L+VGNL  DV    +  LF + G       K                      
Sbjct: 11  DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPC--KSCK---------------------- 46

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERA 272
             +I    +  +  + FV      +A  A+   +   I G+ + VN A    +Q    
Sbjct: 47  --MITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGP 100

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 95.5 bits (238), Expect = 1e-24
 Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 6/88 (6%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGK--VVNARVVYDRETGRSRGFGFVTMSSETEL 334
                I + N+        +    S +    V N R++ D++T ++RGF FV +SS  + 
Sbjct: 7   HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDA 66

Query: 335 NDAIAALDGQ----NLDGRAIRVNVAED 358
           +  +  L        +DG+ I V+ A+ 
Sbjct: 67  SQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 82.8 bits (205), Expect = 6e-20
 Identities = 15/112 (13%), Positives = 41/112 (36%), Gaps = 28/112 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                  + + N+      + +        ++ +  ++                      
Sbjct: 5   HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIR---------------------- 42

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVE----MFHRYDIDGRLLTVNKA 262
             +I +++T ++RGF FV +S+  +A + ++    +     IDG+ + V+ A
Sbjct: 43  --LIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 95.0 bits (237), Expect = 2e-24
 Identities = 27/87 (31%), Positives = 46/87 (52%), Gaps = 3/87 (3%)

Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEH-GKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           P + ++VG+L  +VD+  L + F +        +VV D +TG S+G+GFV  + E E   
Sbjct: 8   PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKR 66

Query: 337 AIAALDGQ-NLDGRAIRVNVAEDRQRR 362
           A+    G   L  + +R++VA  +  R
Sbjct: 67  ALTECQGAVGLGSKPVRLSVAIPKASR 93

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 70.4 bits (173), Expect = 2e-15
 Identities = 23/115 (20%), Positives = 44/115 (38%), Gaps = 29/115 (25%)

Query: 159 DAKLFVGNLPYDVDSEKLAMLFEKA-GTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
           +  LFVG+L  DVD   L   F K   +    +V            +             
Sbjct: 9   EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKV------------VL------------ 44

Query: 218 IYNRETDRSRGFGFVTMSTVEEAEKAV-EMFHRYDIDGRLLTVNKAAPRGTQPER 271
               +T  S+G+GFV  +   E ++A+ E      +  + + ++ A P+ ++ + 
Sbjct: 45  ---DQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKP 96

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 95.7 bits (238), Expect = 4e-24
 Identities = 30/136 (22%), Positives = 49/136 (36%), Gaps = 10/136 (7%)

Query: 231 FVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT-----QPERAPRVFEPGFRIYVG 285
            V  +T E+  K     +  D +       K                        ++YVG
Sbjct: 20  AVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVG 79

Query: 286 NLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQN 345
           NL    +   LE+ F  +G + +  V  +       GF FV      +  DA+  LDG+ 
Sbjct: 80  NLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRT 134

Query: 346 LDGRAIRVNVAEDRQR 361
           L G  +RV ++   +R
Sbjct: 135 LCGCRVRVELSNGEKR 150

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 65.7 bits (160), Expect = 3e-13
 Identities = 20/110 (18%), Positives = 30/110 (27%), Gaps = 31/110 (28%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
            P D K++VGNL  + +  +L   F   G +    V                        
Sbjct: 70  CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR---------------------- 107

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                       GF FV      +A  AV       + G  + V  +   
Sbjct: 108 ---------NPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE 148

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 93.8 bits (234), Expect = 5e-24
 Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V  LPW+     L++ FS  G+V+  +V  D +TG S+GFGFV  +        ++  
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-- 75

Query: 342 DGQNLDGRAIRVNVAEDRQRRSS 364
               +DGR     +   +Q + S
Sbjct: 76  QRHMIDGRWCDCKLPNSKQSQDS 98

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 87.3 bits (217), Expect = 1e-21
 Identities = 25/115 (21%), Positives = 37/115 (32%), Gaps = 28/115 (24%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
              + + L V  LP+    + L   F   G V +                          
Sbjct: 11  AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMV------------------------- 45

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP 269
            QV  + +T  S+GFGFV  +  E   K +   H   IDGR         + +Q 
Sbjct: 46  -QVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQD 97

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 92.9 bits (232), Expect = 6e-24
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L W+     L + F + G+V    V+ D  T RSRGFGFVT   +  ++  +A 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 341 LDGQNLDGRAIRVNVA 356
                LD + I   VA
Sbjct: 62  -SRHELDSKTIDPKVA 76

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 74.8 bits (185), Expect = 2e-17
 Identities = 24/103 (23%), Positives = 37/103 (35%), Gaps = 29/103 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+F+G L +    E L   F + G V+                             V+ +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKEC--------------------------LVMRD 35

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEM-FHRYDIDGRLLTVNKA 262
             T RSRGFGFVT       +K +    H  ++D + +    A
Sbjct: 36  PLTKRSRGFGFVTFMDQAGVDKVLAQSRH--ELDSKTIDPKVA 76

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 93.5 bits (233), Expect = 1e-23
 Identities = 30/104 (28%), Positives = 51/104 (49%), Gaps = 5/104 (4%)

Query: 261 KAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRS 320
           +  P   +     +      ++++G L +E     L   + + GK+ +  V+ D  + RS
Sbjct: 13  ETVPLERKKREKEQFR----KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRS 68

Query: 321 RGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           RGFGFVT SS  E++ A+AA    ++DGR +    A  R+   S
Sbjct: 69  RGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREESGS 111

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 82.7 bits (205), Expect = 9e-20
 Identities = 35/136 (25%), Positives = 54/136 (39%), Gaps = 29/136 (21%)

Query: 135 AGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFH 194
           +G    E   E V  E +  E  +  KLF+G L ++   E L   +E+ G +        
Sbjct: 3   SGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDC----- 57

Query: 195 FLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEM-FHRYDID 253
                                 V+ +  + RSRGFGFVT S++ E + A+    H   ID
Sbjct: 58  ---------------------VVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPH--SID 94

Query: 254 GRLLTVNKAAPRGTQP 269
           GR++   +A  R    
Sbjct: 95  GRVVEPKRAVAREESG 110

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 94.1 bits (234), Expect = 1e-23
 Identities = 29/133 (21%), Positives = 51/133 (38%), Gaps = 8/133 (6%)

Query: 240 AEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGF---RIYVGNLPWEVDNARL 296
                +      I  R L   + +    +     R +EPG    RIYV NL   V    L
Sbjct: 3   LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDL 62

Query: 297 EQVFSEHGKV--VNARVVYD---RETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAI 351
           + +F  +        R+++D    + GR +G  F+ + +E     A+   +G  L G+ +
Sbjct: 63  KYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM 122

Query: 352 RVNVAEDRQRRSS 364
            V  A   + +  
Sbjct: 123 VVQFARSARPKQD 135

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 69.9 bits (171), Expect = 8e-15
 Identities = 18/111 (16%), Positives = 38/111 (34%), Gaps = 21/111 (18%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +++V NL   V  + L  +F +         +  F                      I  
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFD---------------------IRL 85

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
            +  R +G  F+ +   + A KA++  + Y + G+ + V  A     + + 
Sbjct: 86  MKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQDP 136

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 92.7 bits (231), Expect = 2e-23
 Identities = 27/84 (32%), Positives = 42/84 (50%), Gaps = 1/84 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG L W      L   FS++G+VV+  ++ D+ T +SRGFGFV       +   +A+
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
                LDGR I       R  + S
Sbjct: 78  -RPHTLDGRNIDPKPCTPRGMQPS 100

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 82.7 bits (205), Expect = 7e-20
 Identities = 29/116 (25%), Positives = 42/116 (36%), Gaps = 29/116 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
              E  KLFVG L +    E L   F + G  E+ +                        
Sbjct: 12  GADEIGKLFVGGLDWSTTQETLRSYFSQYG--EVVDCV---------------------- 47

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEM-FHRYDIDGRLLTVNKAAPRGTQP 269
             ++ ++ T++SRGFGFV           +    H   +DGR +      PRG QP
Sbjct: 48  --IMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPH--TLDGRNIDPKPCTPRGMQP 99

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 91.0 bits (227), Expect = 3e-23
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG L        ++  F + GKV +A +++D+ T R RGFGFVT  SE  + + +  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIV-EKVCE 59

Query: 341 LDGQNLDGRAIRVNVA 356
           +    ++ + +    A
Sbjct: 60  IHFHEINNKMVECKKA 75

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 76.4 bits (189), Expect = 7e-18
 Identities = 27/102 (26%), Positives = 47/102 (46%), Gaps = 27/102 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG L  +   E +   FE+ G V+ A +                          +++
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAML--------------------------MFD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           + T+R RGFGFVT  + +  EK  E+ H ++I+ +++   KA
Sbjct: 35  KTTNRHRGFGFVTFESEDIVEKVCEI-HFHEINNKMVECKKA 75

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 89.3 bits (222), Expect = 3e-22
 Identities = 18/92 (19%), Positives = 41/92 (44%), Gaps = 5/92 (5%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHG-KVVNARVVYDRETGRSRGFGFVTMSSETELN 335
                +++G+L   +D   + + F+  G  V++ +++ +R TG   G+ FV  +      
Sbjct: 7   GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAE 66

Query: 336 DAIAALDGQNLDG----RAIRVNVAEDRQRRS 363
             +  ++G+ L G    +  ++N A      S
Sbjct: 67  KCLHKINGKPLPGATPAKRFKLNYATYSGPSS 98

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 68.1 bits (167), Expect = 1e-14
 Identities = 23/116 (19%), Positives = 39/116 (33%), Gaps = 29/116 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                A L++G+L   +D   ++  F   G   +  VK                      
Sbjct: 5   SSGMAASLWMGDLEPYMDENFISRAFATMG-ETVMSVK---------------------- 41

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDG----RLLTVNKAAPRG 266
             +I NR T    G+ FV  + +  AEK +   +   + G    +   +N A   G
Sbjct: 42  --IIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSG 95

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 88.4 bits (220), Expect = 4e-22
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG L W+     L+  F++ G+VV+  +  D  TGRSRGFGF+       +   +  
Sbjct: 13  KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ 72

Query: 341 LDGQNLDGRAIRVNVA 356
            +   LDGR I    A
Sbjct: 73  KE-HRLDGRVIDPKKA 87

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 75.3 bits (186), Expect = 2e-17
 Identities = 27/109 (24%), Positives = 39/109 (35%), Gaps = 29/109 (26%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
              +  K+FVG L +D   + L   F K G V                            
Sbjct: 7   NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDC------------------------- 41

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVE-MFHRYDIDGRLLTVNKA 262
             +  +  T RSRGFGF+        EK ++   H   +DGR++   KA
Sbjct: 42  -TIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEH--RLDGRVIDPKKA 87

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 87.1 bits (216), Expect = 2e-21
 Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 283 YVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD 342
            + +    V    L  +FS+ GKVVN     D  TG+++GF FV   S  +    I +  
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 343 GQNLDGR-AIRVNVAEDRQRRSS 364
           G+ LD +  + +   +D +R +S
Sbjct: 76  GKRLDLKHRLFLYTMKDVERYNS 98

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 62.4 bits (152), Expect = 1e-12
 Identities = 20/106 (18%), Positives = 37/106 (34%), Gaps = 27/106 (25%)

Query: 159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVI 218
           +    + +    V  + L  LF KAG V   E                            
Sbjct: 12  NGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEF--------------------------P 45

Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRL-LTVNKAA 263
            +  T +++GF FV   ++ +A+K ++ FH   +D +  L +    
Sbjct: 46  IDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMK 91

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 86.6 bits (215), Expect = 2e-21
 Identities = 22/86 (25%), Positives = 36/86 (41%), Gaps = 4/86 (4%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG L  +     + ++F   G +    V+     G S+G  FV  SS TE   AI A
Sbjct: 17  KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSSHTEAQAAIHA 75

Query: 341 LDGQNL---DGRAIRVNVAEDRQRRS 363
           L G         ++ V  A+  +   
Sbjct: 76  LHGSQTMPGASSSLVVKFADTDKESG 101

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 69.6 bits (171), Expect = 5e-15
 Identities = 29/123 (23%), Positives = 37/123 (30%), Gaps = 33/123 (26%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
               D KLFVG L      E +  LF+  G ++   V    L G  G             
Sbjct: 11  RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTV----LRGPDG------------- 53

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFH---RYDIDGRLLTVNKAAPRGTQPER 271
                      S+G  FV  S+  EA+ A+   H           L V  A       E 
Sbjct: 54  ----------SSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTD---KES 100

Query: 272 APR 274
            P 
Sbjct: 101 GPS 103

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 84.9 bits (211), Expect = 5e-21
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG L  +    ++ + F   G+V +  +  D +T + RGF F+T   E  +   +  
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 341 LDGQNLDGRAIRVNVA 356
               N+      + VA
Sbjct: 61  -KYHNVGLSKCEIKVA 75

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 72.5 bits (179), Expect = 2e-16
 Identities = 24/103 (23%), Positives = 38/103 (36%), Gaps = 29/103 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG L  D   EK+   F   G VE  E+                            +
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIEL--------------------------PMD 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEM-FHRYDIDGRLLTVNKA 262
            +T++ RGF F+T    E  +K +E  +H  ++      +  A
Sbjct: 35  NKTNKRRGFCFITFKEEEPVKKIMEKKYH--NVGLSKCEIKVA 75

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 86.3 bits (214), Expect = 5e-21
 Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 3/87 (3%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           E    +Y+ NLP+++    +  +F ++G +   RV     T  +RG  +V      +  +
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKN 62

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRS 363
           A+  L G N+  R + V      +   
Sbjct: 63  AVDHLSGFNVSNRYLVVLYYNANRAFQ 89

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 75.9 bits (187), Expect = 3e-17
 Identities = 23/116 (19%), Positives = 42/116 (36%), Gaps = 30/116 (25%)

Query: 156 PPE-DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           PPE +  L++ NLPY + +E++  +F K G +    V                       
Sbjct: 4   PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---------------------- 41

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPE 270
                   T  +RG  +V    + +A+ AV+    +++  R L V          +
Sbjct: 42  -------NTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQK 90

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 84.8 bits (210), Expect = 1e-20
 Identities = 28/101 (27%), Positives = 46/101 (45%), Gaps = 11/101 (10%)

Query: 269 PERAPRVFEPGFRIYVGNLPWEVDNAR-------LEQVFSEHGKVVNARVVYDRETGRSR 321
            +R          I V N+P +V   R       + ++FS+ GK+ N    Y  E G+++
Sbjct: 5   KDRPQEADGIDSVIVVDNVP-QVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEEDGKTK 61

Query: 322 GFGFVTMSSETELNDAIAALDGQNLDGR-AIRVNVAEDRQR 361
           G+ F+  +S     DA+   DG  LD +   RVN+  D  +
Sbjct: 62  GYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFDK 102

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 63.6 bits (155), Expect = 6e-13
 Identities = 22/125 (17%), Positives = 40/125 (32%), Gaps = 37/125 (29%)

Query: 147 VFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAML-------FEKAGTVEIAEVKFHFLFGN 199
           V ++        D+ + V N+P  V  ++L  L       F K G +             
Sbjct: 3   VLKDRPQEADGIDSVIVVDNVPQ-VGPDRLEKLKNVIHKIFSKFGKIT------------ 49

Query: 200 QGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRL-LT 258
                              Y  E  +++G+ F+  ++   A  AV+    Y +D +    
Sbjct: 50  ----------------NDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR 93

Query: 259 VNKAA 263
           VN   
Sbjct: 94  VNLFT 98

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 84.5 bits (209), Expect = 2e-20
 Identities = 23/101 (22%), Positives = 34/101 (33%), Gaps = 8/101 (7%)

Query: 262 AAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSR 321
             PRG+   + P      +RI + NLP       L+ +  E+             T    
Sbjct: 14  LVPRGSHMSKLPA---KRYRITMKNLPEGCSWQDLKDLARENSLET---TFSSVNTRDFD 67

Query: 322 GFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
           G G +   SE  L +A+  L+     G  I V    D    
Sbjct: 68  GTGALEFPSEEILVEALERLNNIEFRGSVITVE--RDDNPP 106

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 66.0 bits (161), Expect = 8e-14
 Identities = 17/120 (14%), Positives = 34/120 (28%), Gaps = 35/120 (29%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
           P +  ++ + NLP     + L  L  +                                 
Sbjct: 25  PAKRYRITMKNLPEGCSWQDLKDLARENSLE----------------------------- 55

Query: 216 QVIYNR-ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
              ++   T    G G +   + E   +A+E  +  +  G ++TV +       P    R
Sbjct: 56  -TTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD----DNPPPIRR 110

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 83.9 bits (208), Expect = 2e-20
 Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 6/83 (7%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YV NL        +E+ F+        RV       + R + FV  S+  +  +A+ AL
Sbjct: 18  LYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKAL 71

Query: 342 DGQNLDGRAIRVNVAEDRQRRSS 364
           +G+ LDG  I V +A+   + SS
Sbjct: 72  NGKVLDGSPIEVTLAKPVDKDSS 94

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 76.9 bits (190), Expect = 7e-18
 Identities = 20/109 (18%), Positives = 32/109 (29%), Gaps = 32/109 (29%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            L+V NL      E +   F       +  VK                            
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---------------------------- 48

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP 269
               + R + FV  S  E+A +A++  +   +DG  + V  A P     
Sbjct: 49  ----KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDS 93

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 83.9 bits (208), Expect = 3e-20
 Identities = 17/84 (20%), Positives = 37/84 (44%), Gaps = 8/84 (9%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            ++V NL   V    LE+ FS+ GK+   + +        + + F+          A+  
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEE 64

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
           ++G++L+G  I +  A+   ++  
Sbjct: 65  MNGKDLEGENIEIVFAKPPDQKRK 88

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 71.9 bits (177), Expect = 6e-16
 Identities = 22/119 (18%), Positives = 37/119 (31%), Gaps = 34/119 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            LFV NL   V  E L   F + G +E   VK                            
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLE--RVKK--------------------------- 43

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPG 279
                 + + F+     + A KA+E  +  D++G  + +  A P   + +      +  
Sbjct: 44  -----LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAA 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 83.3 bits (206), Expect = 4e-20
 Identities = 23/102 (22%), Positives = 40/102 (39%), Gaps = 6/102 (5%)

Query: 262 AAPRGTQPERAPRVFEP-GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRS 320
            +   + P   P    P    +YVGNLP +   + L++   E G  V  R+ +       
Sbjct: 1   GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELG-SVPLRLTWQG----P 55

Query: 321 RGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
           R   F+          A++ L G  L    +RV +A  ++ +
Sbjct: 56  RRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRDK 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 58.7 bits (142), Expect = 2e-11
 Identities = 19/111 (17%), Positives = 29/111 (26%), Gaps = 31/111 (27%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
             P  A ++VGNLP D     L     + G+V +                          
Sbjct: 15  GAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLT----------------------- 51

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                       R   F+       A++AV       +    L V  A  +
Sbjct: 52  --------WQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 82.9 bits (205), Expect = 7e-20
 Identities = 25/107 (23%), Positives = 32/107 (29%), Gaps = 13/107 (12%)

Query: 262 AAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSR 321
            APRG      P       R+ V  LP       L+    E G V  A V          
Sbjct: 2   GAPRG---RYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRD 51

Query: 322 GFGFVTMSSETELNDAIAALDGQNLDGRAIRVN---VAEDRQRRSSF 365
           G G V    + ++  A+  LD               V  D  R  S+
Sbjct: 52  GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSY 98

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 60.2 bits (146), Expect = 1e-11
 Identities = 16/119 (13%), Positives = 23/119 (19%), Gaps = 33/119 (27%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           ++ V  LP     + L     +AG V  A+V                             
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDVCYADV----------------------------- 48

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPG 279
                  G G V     E+   AV                    +   P          
Sbjct: 49  ----YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRS 103

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 82.4 bits (204), Expect = 8e-20
 Identities = 15/91 (16%), Positives = 32/91 (35%)

Query: 266 GTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGF 325
            +    +         I V N+P+ V    +   F  +  +  +  +   E G   G   
Sbjct: 2   SSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 326 VTMSSETELNDAIAALDGQNLDGRAIRVNVA 356
           V   S  E   A+  L+ + +  R ++++  
Sbjct: 62  VAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 68.5 bits (168), Expect = 8e-15
 Identities = 15/107 (14%), Positives = 31/107 (28%), Gaps = 26/107 (24%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
            P    + V N+P+ V  +++   F     +  +       +  +G              
Sbjct: 12  KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGS---VCLKYNEKG-------------- 54

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
                       G   V   + +EA  AV   +   I  R + ++  
Sbjct: 55  ---------MPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 82.5 bits (204), Expect = 9e-20
 Identities = 21/103 (20%), Positives = 29/103 (28%), Gaps = 10/103 (9%)

Query: 266 GTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGF 325
            +     P       R+ V  LP       L+    E G V  A V  D       G G 
Sbjct: 2   SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGV 54

Query: 326 VTMSSETELNDAIAALDGQNLDGRAIRVNVA---EDRQRRSSF 365
           V    + ++  A+  LD                  D  R  S+
Sbjct: 55  VEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSY 97

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 62.5 bits (152), Expect = 1e-12
 Identities = 16/114 (14%), Positives = 23/114 (20%), Gaps = 33/114 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           ++ V  LP     + L     +AG V  A+V                             
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGDVCYADV----------------------------- 47

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
                  G G V     E+   AV                    +   P     
Sbjct: 48  ----YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSY 97

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 82.3 bits (204), Expect = 1e-19
 Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 8/103 (7%)

Query: 260 NKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR 319
           +   PRG+             R++V   P +V  + L ++F   G +   +++       
Sbjct: 12  SGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL------- 64

Query: 320 SRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
             GF FV          AI  + G++   + + V  ++   +R
Sbjct: 65  -NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR 106

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 72.7 bits (179), Expect = 3e-16
 Identities = 22/129 (17%), Positives = 33/129 (25%), Gaps = 34/129 (26%)

Query: 137 ERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFL 196
                    G            + +LFV   P DV   +L  +F   G ++  ++     
Sbjct: 9   HHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---- 64

Query: 197 FGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRL 256
                                          GF FV     E A KA+E  H      + 
Sbjct: 65  ------------------------------NGFAFVEFEEAESAAKAIEEVHGKSFANQP 94

Query: 257 LTVNKAAPR 265
           L V  +   
Sbjct: 95  LEVVYSKLP 103

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 82.0 bits (203), Expect = 2e-19
 Identities = 23/90 (25%), Positives = 44/90 (48%), Gaps = 9/90 (10%)

Query: 276 FEPGFRIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL 334
                R+++GNL    V  + +E +FS++G+V    V         +G+ FV  S+E   
Sbjct: 24  KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHA 75

Query: 335 NDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
             A+   +G+ L G+ + +N+A + +   S
Sbjct: 76  RAAVLGENGRVLAGQTLDINMAGEPKPDRS 105

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 60.1 bits (146), Expect = 1e-11
 Identities = 20/110 (18%), Positives = 36/110 (32%), Gaps = 35/110 (31%)

Query: 157 PEDAKLFVGNLPYDVDSEK-LAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
             ++++F+GNL   +  +  +  +F K G   +A    H                     
Sbjct: 25  SINSRVFIGNLNTALVKKSDVETIFSKYG--RVAGCSVH--------------------- 61

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                      +G+ FV  S    A  AV   +   + G+ L +N A   
Sbjct: 62  -----------KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP 100

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 81.1 bits (201), Expect = 2e-19
 Identities = 21/97 (21%), Positives = 41/97 (42%), Gaps = 13/97 (13%)

Query: 267 TQPERAPRVFEPGFRIYVGNLPWEVDNAR-LEQVFSEHGKVVNARVVYDRETGRSRGFGF 325
           T+    P    P  R+++GNLP +  +   L ++FS +G ++   +           FGF
Sbjct: 2   TEMHNIP----PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGF 49

Query: 326 VTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
           +   +   + DAI     +   G+ + + V+    R 
Sbjct: 50  IQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARP 86

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 20/122 (16%), Positives = 37/122 (30%), Gaps = 36/122 (29%)

Query: 155 EPPEDAKLFVGNLPY-DVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVS 213
             P  ++LF+GNLP  +V  E L  +F   G +                           
Sbjct: 6   NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHI--------------------------- 38

Query: 214 LLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA-APRGTQPERA 272
                   + +    FGF+     +    A+E   +    G+ L +  + +    Q +  
Sbjct: 39  -------MQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQFDHG 91

Query: 273 PR 274
             
Sbjct: 92  DH 93

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 81.2 bits (201), Expect = 2e-19
 Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 1/92 (1%)

Query: 266 GTQPERAPRVFEPG-FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFG 324
           G+         +PG   I V N+P+ V    +   F  +  +  +  +   E G   G  
Sbjct: 1   GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 325 FVTMSSETELNDAIAALDGQNLDGRAIRVNVA 356
            V   S  E   A+  L+ + +  R +++ + 
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 92

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 69.6 bits (171), Expect = 4e-15
 Identities = 15/109 (13%), Positives = 31/109 (28%), Gaps = 26/109 (23%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
            P    + V N+P+ V  +++   F     +  +       +  +G              
Sbjct: 12  KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGS---VCLKYNEKG-------------- 54

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP 264
                       G   V   + +EA  AV   +   I  R + +   + 
Sbjct: 55  ---------MPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 80.2 bits (198), Expect = 5e-19
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 3/80 (3%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++ + N+P  +    L+ +  ++G V +   V             VT SS+ +   A+  
Sbjct: 17  KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQALDK 73

Query: 341 LDGQNLDGRAIRVNVAEDRQ 360
           L+G  L+   ++V    D  
Sbjct: 74  LNGFQLENFTLKVAYIPDEM 93

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 69.4 bits (170), Expect = 4e-15
 Identities = 20/111 (18%), Positives = 35/111 (31%), Gaps = 29/111 (26%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +     KL + N+P  +  E L  L  + G VE  E                        
Sbjct: 11  KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV---------------------- 48

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                   TD       VT S+ ++A +A++  + + ++   L V      
Sbjct: 49  -------NTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE 92

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 78.5 bits (194), Expect = 3e-18
 Identities = 21/106 (19%), Positives = 39/106 (36%), Gaps = 14/106 (13%)

Query: 262 AAPRGTQPERAPRVFEPGFR--------IYVGNLPWEVDNARLEQVFSEHGKVVNARVVY 313
           +   G  P+  P+  +   R         Y+GN+P     A L  +F   G +++ +   
Sbjct: 2   SQTIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKH-- 59

Query: 314 DRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR 359
                  +G  F+   +  +    I AL      GR +R    ++R
Sbjct: 60  ----YPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER 101

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 66.6 bits (163), Expect = 5e-14
 Identities = 20/110 (18%), Positives = 32/110 (29%), Gaps = 32/110 (29%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
           PP     ++GN+P+      L  LF+  G   I + K +                     
Sbjct: 24  PPRVTTAYIGNIPHFATEADLIPLFQNFG--FILDFKHY--------------------- 60

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                      +G  F+   T E+A   +     +   GR L       R
Sbjct: 61  ---------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER 101

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 77.1 bits (190), Expect = 4e-18
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 6/79 (7%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARV-----VYDRETGRSRGFGFVTMSSETELN 335
           R+YVGN+P+ +    +   F+   ++          V   +  + + F F+   S  E  
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 336 DAIAALDGQNLDGRAIRVN 354
            A+ A DG    G+++++ 
Sbjct: 68  QAM-AFDGIIFQGQSLKIR 85

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 64.4 bits (157), Expect = 2e-13
 Identities = 14/101 (13%), Positives = 34/101 (33%), Gaps = 22/101 (21%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +L+VGN+P+ +  E +   F     +                               +  
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPG---------------------NPVLA 46

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK 261
            + ++ + F F+   +V+E  +A+         G+ L + +
Sbjct: 47  VQINQDKNFAFLEFRSVDETTQAMAF-DGIIFQGQSLKIRR 86

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 77.6 bits (191), Expect = 1e-17
 Identities = 24/99 (24%), Positives = 45/99 (45%), Gaps = 1/99 (1%)

Query: 262 AAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSR 321
            +P G +  R+    E GF +Y+  LP+E +N  +   F +   V ++  +     G++ 
Sbjct: 8   KSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT 67

Query: 322 GFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ 360
           G GFV   +E +   A+     Q +  R I+V+    + 
Sbjct: 68  GEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKG 105

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 58.3 bits (141), Expect = 6e-11
 Identities = 17/128 (13%), Positives = 40/128 (31%), Gaps = 27/128 (21%)

Query: 138 RQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLF 197
                   G               +++  LP++ +++ +   F+K   VE +    +  +
Sbjct: 4   GSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDS---IYIAY 60

Query: 198 GNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLL 257
           G  G                       ++ G GFV      + + A+   H+  +  R +
Sbjct: 61  GPNG-----------------------KATGEGFVEFRNEADYKAALCR-HKQYMGNRFI 96

Query: 258 TVNKAAPR 265
            V+    +
Sbjct: 97  QVHPITKK 104

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 75.9 bits (187), Expect = 1e-17
 Identities = 14/84 (16%), Positives = 30/84 (35%), Gaps = 7/84 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            I V NLP + +   +  +  ++               R++   FVT+ +  +  +AI  
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLKY-------CYVDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
               +  G+ + V +        S
Sbjct: 60  FHQYSFRGKDLIVQLQPTDALLCS 83

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 70.5 bits (173), Expect = 1e-15
 Identities = 23/113 (20%), Positives = 39/113 (34%), Gaps = 34/113 (30%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            + V NLP D + +++  L +                                       
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLKYC-------------------------------- 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAP 273
              DR++   FVT+   E+A+ A++MFH+Y   G+ L V +  P        P
Sbjct: 35  -YVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIV-QLQPTDALLCSGP 85

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 76.2 bits (188), Expect = 2e-17
 Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 9/90 (10%)

Query: 273 PRVFEPGFRIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
           PR      R+++GNLP + V    L ++FS +G ++   +           FGF+   + 
Sbjct: 16  PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNP 67

Query: 332 TELNDAIAALDGQNLDGRAIRVNVAEDRQR 361
             + DAI     +   G+ + + V+    R
Sbjct: 68  QSVRDAIEXESQEMNFGKKLILEVSSSNAR 97

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 58.1 bits (141), Expect = 4e-11
 Identities = 19/111 (17%), Positives = 34/111 (30%), Gaps = 35/111 (31%)

Query: 156 PPEDAKLFVGNLPY-DVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
               ++LF+GNLP  +V  E L  +F   G   I ++                       
Sbjct: 19  SHMKSRLFIGNLPLKNVSKEDLFRIFSPYG--HIMQINIK-------------------- 56

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                         FGF+     +    A+E   +    G+ L +  ++  
Sbjct: 57  ------------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN 95

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 75.4 bits (186), Expect = 3e-17
 Identities = 17/84 (20%), Positives = 39/84 (46%), Gaps = 6/84 (7%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            +Y G +   + +  + Q FS  G+++  RV  ++      G+ FV  S+      AI +
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVS 80

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
           ++G  ++G  ++    ++    +S
Sbjct: 81  VNGTTIEGHVVKCYWGKESPDMTS 104

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.9 bits (156), Expect = 4e-13
 Identities = 18/127 (14%), Positives = 40/127 (31%), Gaps = 32/127 (25%)

Query: 139 QEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFG 198
              + ++  FE+      P++  ++ G +   +  + +   F   G  +I E++      
Sbjct: 5   SSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFG--QIMEIRVF---- 58

Query: 199 NQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLT 258
                                       +G+ FV  ST E A  A+   +   I+G ++ 
Sbjct: 59  --------------------------PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVK 92

Query: 259 VNKAAPR 265
                  
Sbjct: 93  CYWGKES 99

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 74.2 bits (183), Expect = 5e-17
 Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 7/84 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            ++VG    ++    L + FS++G V++  +         R F FVT + +         
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQSLCG- 60

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
            +   + G ++ ++ AE +   +S
Sbjct: 61  -EDLIIKGISVHISNAEPKHNSNS 83

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 68.0 bits (167), Expect = 9e-15
 Identities = 18/114 (15%), Positives = 32/114 (28%), Gaps = 33/114 (28%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
               + +FVG    D+  ++L   F + G V    +                        
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI------------------------ 37

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP 269
                      R F FVT +  + A+          I G  + ++ A P+    
Sbjct: 38  -------PKPFRAFAFVTFADDQIAQSLCGEDL--IIKGISVHISNAEPKHNSN 82

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 74.6 bits (184), Expect = 6e-17
 Identities = 19/91 (20%), Positives = 40/91 (43%), Gaps = 10/91 (10%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQ----VFSEHGKVVNARVVYDRETGRSRGFGFVTMSSET 332
            P   IY+ NL  ++    L++    +FS  G++++  V     + + RG  FV     +
Sbjct: 6   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVS 62

Query: 333 ELNDAIAALDGQNLDGRAIRVNVAEDRQRRS 363
              +A+ ++ G     + +R+  A   +  S
Sbjct: 63  SATNALRSMQGFPFYDKPMRIQYA---KTDS 90

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 57.6 bits (140), Expect = 6e-11
 Identities = 16/101 (15%), Positives = 35/101 (34%), Gaps = 25/101 (24%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +++ NL   +  ++L             +   H +F   G            +L ++ +R
Sbjct: 11  IYINNLNEKIKKDEL-------------KKSLHAIFSRFG-----------QILDILVSR 46

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
            + + RG  FV    V  A  A+     +    + + +  A
Sbjct: 47  -SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 74.4 bits (183), Expect = 9e-17
 Identities = 19/99 (19%), Positives = 33/99 (33%), Gaps = 2/99 (2%)

Query: 266 GTQPERAPR-VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFG 324
           G+        V       ++ N+P+ +    + Q         NA  V     G+  G  
Sbjct: 1   GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60

Query: 325 FVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRS 363
            V   +E +   +   L  + L+GR   V+V      R 
Sbjct: 61  LVQFKNEDDARKSE-RLHRKKLNGREAFVHVVTLEDMRE 98

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 57.8 bits (140), Expect = 7e-11
 Identities = 19/119 (15%), Positives = 33/119 (27%), Gaps = 27/119 (22%)

Query: 151 EEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVF 210
            E           + N+P+ +    +    E     E A    H L  N G         
Sbjct: 7   GEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENA---VHVLVDNNG--------- 54

Query: 211 YVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP 269
                         +  G   V     ++A K+  + HR  ++GR   V+       + 
Sbjct: 55  --------------QGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTLEDMRE 98

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 73.7 bits (181), Expect = 1e-16
 Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 4/86 (4%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVY--DRETGRSRGFGFVTMSSETELNDAI 338
           R+++G +P       + +  ++  + V   +VY    +  ++RGF FV   S      A 
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 339 AAL--DGQNLDGRAIRVNVAEDRQRR 362
             L      L G  I V+ AE     
Sbjct: 70  RKLMPGRIQLWGHQIAVDWAEPEIDV 95

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.3 bits (154), Expect = 7e-13
 Identities = 20/117 (17%), Positives = 37/117 (31%), Gaps = 26/117 (22%)

Query: 157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQ 216
             + +LF+G +P     E++     K     + +V  +    ++                
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEIAKVTEG-VLDVIVYASAADKM--------------- 49

Query: 217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFH--RYDIDGRLLTVNKAAPRGTQPER 271
                   ++RGF FV   +   A  A       R  + G  + V+ A P     E 
Sbjct: 50  --------KNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDED 98

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 73.1 bits (180), Expect = 2e-16
 Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 6/84 (7%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            ++V   P  VD+A+L + F   G V  A VV D++ G    F  V M       +A+ +
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPV--ASVVMDKDKGV---FAIVEMGDVGAR-EAVLS 63

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
               +L G  +RV   E ++ +S 
Sbjct: 64  QSQHSLGGHRLRVRPREQKEFQSP 87

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 60.0 bits (146), Expect = 7e-12
 Identities = 21/116 (18%), Positives = 36/116 (31%), Gaps = 34/116 (29%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            +FV   P  VDS +L+  F   G V                              V+ +
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVA----------------------------SVVMD 41

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ--PERAPR 274
           ++      F  V M  V   E  +    ++ + G  L V     +  Q    ++P+
Sbjct: 42  KDK---GVFAIVEMGDVGAREAVLSQ-SQHSLGGHRLRVRPREQKEFQSPASKSPK 93

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 72.2 bits (177), Expect = 5e-16
 Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 6/79 (7%)

Query: 282 IYVGNLPWEV---DNARLEQVFSEHGKVVNARVVYDRETGRSR---GFGFVTMSSETELN 335
           ++V  L   +   +  +  + F + GK+    +        S+      +VT     +  
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 336 DAIAALDGQNLDGRAIRVN 354
            AI  ++   +DGR ++ +
Sbjct: 78  RAIQCVNNVVVDGRTLKAS 96

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 54.9 bits (132), Expect = 9e-10
 Identities = 17/99 (17%), Positives = 33/99 (33%), Gaps = 20/99 (20%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +FV  L   +   ++              +K    FG  G       +  V +       
Sbjct: 18  VFVVGLSQRLADPEV--------------LKRPEYFGKFG------KIHKVVINNSTSYA 57

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
            +       +VT    E+A +A++  +   +DGR L  +
Sbjct: 58  GSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS 96

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 71.9 bits (177), Expect = 5e-16
 Identities = 22/99 (22%), Positives = 39/99 (39%), Gaps = 10/99 (10%)

Query: 266 GTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGF 325
           G+  ER       G  +YV     ++    L   FS  G +++  +         R   F
Sbjct: 4   GSSGERRAP--RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM------DPPRNCAF 53

Query: 326 VTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           VT       + A+A L+G  ++   ++VN+A  +    S
Sbjct: 54  VTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDS 92

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 57.7 bits (140), Expect = 6e-11
 Identities = 21/111 (18%), Positives = 33/111 (29%), Gaps = 34/111 (30%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
            P +   L+V     D+    L   F   G   I ++                       
Sbjct: 11  APRKGNTLYVYGE--DMTPTLLRGAFSPFG--NIIDLS---------------------- 44

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                    D  R   FVT   +E A++AV   +   ++   L VN A  +
Sbjct: 45  --------MDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ 87

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 70.3 bits (173), Expect = 2e-15
 Identities = 16/84 (19%), Positives = 38/84 (45%), Gaps = 7/84 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG    ++    L+Q F ++G+VV+  +         R F FVT + +         
Sbjct: 13  KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG- 66

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
            +   + G ++ ++ AE +  + +
Sbjct: 67  -EDLIIKGISVHISNAEPKHNKLN 89

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 66.5 bits (163), Expect = 3e-14
 Identities = 20/114 (17%), Positives = 35/114 (30%), Gaps = 33/114 (28%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                +K+FVG    D+ +E+L   F + G V    +                       
Sbjct: 7   HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI----------------------- 43

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ 268
                       R F FVT +  + A+          I G  + ++ A P+  +
Sbjct: 44  --------PKPFRAFAFVTFADDKVAQSLCGEDL--IIKGISVHISNAEPKHNK 87

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 69.7 bits (171), Expect = 2e-15
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 11/81 (13%)

Query: 282 IYVGNLPWEVDNAR-------LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL 334
           I V N+P +V   R       + ++FS+ GK+ N    Y  E G+++G+ F+  +S    
Sbjct: 4   IVVDNVP-QVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLEYASPAHA 60

Query: 335 NDAIAALDGQNLDGR-AIRVN 354
            DA+   DG  LD +   RVN
Sbjct: 61  VDAVKNADGYKLDKQHTFRVN 81

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 53.9 bits (130), Expect = 9e-10
 Identities = 18/109 (16%), Positives = 35/109 (32%), Gaps = 35/109 (32%)

Query: 159 DAKLFVGNLP------YDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYV 212
           D+ + V N+P       +     +  +F K G +                          
Sbjct: 1   DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT------------------------- 35

Query: 213 SLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGR-LLTVN 260
                 Y  E  +++G+ F+  ++   A  AV+    Y +D +    VN
Sbjct: 36  ---NDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVN 81

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 70.3 bits (172), Expect = 6e-15
 Identities = 18/94 (19%), Positives = 34/94 (36%), Gaps = 3/94 (3%)

Query: 260 NKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR 319
            +   RG+           G  +++  LP++     +   FS     V   +    + GR
Sbjct: 27  GQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GR 84

Query: 320 SRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV 353
             G   V  ++  E   A+ + D  N+  R I +
Sbjct: 85  VTGEADVEFATHEEAVAAM-SKDRANMQHRYIEL 117

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 54.8 bits (132), Expect = 2e-09
 Identities = 26/143 (18%), Positives = 40/143 (27%), Gaps = 32/143 (22%)

Query: 126 PEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGT 185
           P G       G +Q   G     + E  V+      + +  LPY      +   F     
Sbjct: 16  PRGSHMASMTGGQQMGRGSG---DSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNP 72

Query: 186 VEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVE 245
           V +     H   G  G                       R  G   V  +T EEA  A+ 
Sbjct: 73  VRV-----HIEIGPDG-----------------------RVTGEADVEFATHEEAVAAMS 104

Query: 246 MFHRYDIDGRLLTVNKAAPRGTQ 268
              R ++  R + +   +  G  
Sbjct: 105 K-DRANMQHRYIELFLNSTTGAS 126

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 73.4 bits (179), Expect = 7e-15
 Identities = 18/90 (20%), Positives = 40/90 (44%), Gaps = 7/90 (7%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQ----VFSEHGKVVNARVVYDRETGRSRGFGFVTMSSET 332
            P   IY+ NL  ++    L++    +FS+ G++++  V     + + RG  FV     +
Sbjct: 7   RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVS 63

Query: 333 ELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
              +A+ ++ G     + +R+  A+     
Sbjct: 64  SATNALRSMQGFPFYDKPMRIQYAKTDSDI 93

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 63.7 bits (154), Expect = 9e-12
 Identities = 22/183 (12%), Positives = 46/183 (25%), Gaps = 25/183 (13%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +++ NL   +  ++L                 + +F   G            +L ++ +R
Sbjct: 12  IYINNLNEKIKKDELKKSL-------------YAIFSQFG-----------QILDILVSR 47

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFR 281
            + + RG  FV    V  A  A+     +    + + +  A        +    F    R
Sbjct: 48  -SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDR 106

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
                 P   +    ++     G       V     G         +             
Sbjct: 107 KREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPP 166

Query: 342 DGQ 344
            G 
Sbjct: 167 PGM 169

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 58.3 bits (140), Expect = 7e-10
 Identities = 21/98 (21%), Positives = 38/98 (38%), Gaps = 6/98 (6%)

Query: 260 NKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR 319
            +  P    P +      P   +++ NLP E +   L  +F++       R+V  R    
Sbjct: 188 QQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR---- 243

Query: 320 SRGFGFVTMSSETELNDAIAALDGQNL-DGRAIRVNVA 356
                FV   +E +   A  AL G  +    A++++ A
Sbjct: 244 -HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFA 280

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 68.4 bits (167), Expect = 2e-14
 Identities = 14/97 (14%), Positives = 35/97 (36%), Gaps = 7/97 (7%)

Query: 267 TQPERAPRVFEPGFRIYVGNLPWEVDNARLEQ----VFSEHGKVVNARVVYDRETGRSRG 322
                 P   EP   + + N+  EV   +L+     + S  G +++   +    +  + G
Sbjct: 17  PDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLSDDNSG 73

Query: 323 FGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR 359
             ++  +++      + A  G    G  + +  +E  
Sbjct: 74  KAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETP 110

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 52.6 bits (126), Expect = 8e-09
 Identities = 23/141 (16%), Positives = 42/141 (29%), Gaps = 36/141 (25%)

Query: 129 EDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLA----MLFEKAG 184
           ++T     ERQ     +                + + N+  +V  EKL      L    G
Sbjct: 2   KETAAAKFERQHMDSPD---LGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQG 58

Query: 185 TVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAV 244
            +                            L ++ +  +D + G  ++  +T E A+  V
Sbjct: 59  DI----------------------------LDIVVDL-SDDNSGKAYIVFATQESAQAFV 89

Query: 245 EMFHRYDIDGRLLTVNKAAPR 265
           E F  Y   G  L +  +   
Sbjct: 90  EAFQGYPFQGNPLVITFSETP 110

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 67.9 bits (166), Expect = 2e-14
 Identities = 19/100 (19%), Positives = 38/100 (38%), Gaps = 4/100 (4%)

Query: 266 GTQPERAPRVFEPG-FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFG 324
            +     P    P    + V  +P+      +   F    +V    ++ D   GR+ G G
Sbjct: 2   SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNG 59

Query: 325 FVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
            V   S  +  +A+   +   +  R + V+ A +RQ  ++
Sbjct: 60  LVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATERQWVAA 98

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 55.5 bits (134), Expect = 5e-10
 Identities = 19/124 (15%), Positives = 37/124 (29%), Gaps = 29/124 (23%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
             P+D  + V  +P+      +   F       +     H L  + G             
Sbjct: 12  INPDDLYVSVHGMPFSAMENDVRDFFHGLRVDAV-----HLLKDHVG------------- 53

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
                     R+ G G V   + ++  +A++  +R  +  R + V+ A  R         
Sbjct: 54  ----------RNNGNGLVKFLSPQDTFEALKR-NRMLMIQRYVEVSPATERQWVAAGGHI 102

Query: 275 VFEP 278
              P
Sbjct: 103 TSGP 106

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 68.0 bits (166), Expect = 3e-14
 Identities = 21/104 (20%), Positives = 36/104 (34%), Gaps = 3/104 (2%)

Query: 262 AAPRGTQPERAPRVFEP--GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR 319
           +   G Q  R     +      + +  LP+      + Q FS    V N   +     G+
Sbjct: 23  SMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK 82

Query: 320 SRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRS 363
             G  FV  +S+     A+     + +  R I V  +   + RS
Sbjct: 83  ITGEAFVQFASQELAEKAL-GKHKERIGHRYIEVFKSSQEEVRS 125

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 58.7 bits (142), Expect = 4e-11
 Identities = 22/142 (15%), Positives = 40/142 (28%), Gaps = 27/142 (19%)

Query: 124 GEPEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKA 183
                   V         +G + +       +   D  + +  LP+    E++   F   
Sbjct: 7   HHHHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGL 66

Query: 184 GTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKA 243
             V             +G                       +  G  FV  ++ E AEKA
Sbjct: 67  EIVPNG---ITLPVDPEG-----------------------KITGEAFVQFASQELAEKA 100

Query: 244 VEMFHRYDIDGRLLTVNKAAPR 265
           +   H+  I  R + V K++  
Sbjct: 101 LGK-HKERIGHRYIEVFKSSQE 121

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 65.9 bits (161), Expect = 9e-14
 Identities = 23/101 (22%), Positives = 38/101 (37%), Gaps = 6/101 (5%)

Query: 264 PRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGF 323
             G  P+ A   F     + +  LP+      + Q FS    V N   +     GRS G 
Sbjct: 5   SSGNSPDTANDGF-----VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGE 59

Query: 324 GFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
            FV  +S+     A+     + +  R I +  +   + R+S
Sbjct: 60  AFVQFASQEIAEKAL-KKHKERIGHRYIEIFKSSRAEVRTS 99

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 54.0 bits (130), Expect = 1e-09
 Identities = 20/114 (17%), Positives = 37/114 (32%), Gaps = 27/114 (23%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +   D  + +  LP+    E++   F     V                            
Sbjct: 11  DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG------------------------- 45

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ 268
              +      RS G  FV  ++ E AEKA++  H+  I  R + + K++    +
Sbjct: 46  -MTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSRAEVR 97

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 65.0 bits (159), Expect = 2e-13
 Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 8/84 (9%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++VG L      A L + F   G +     V      +   F ++   S      A A 
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACAK 72

Query: 341 LDGQNLDG--RAIRVNVAEDRQRR 362
           + G  L G  R +RV+ A+     
Sbjct: 73  MRGFPLGGPDRRLRVDFAKSGPSS 96

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 51.9 bits (125), Expect = 6e-09
 Identities = 16/116 (13%), Positives = 36/116 (31%), Gaps = 34/116 (29%)

Query: 152 EFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFY 211
            + +     +L+VG L  +     LA  F++ G++    +                    
Sbjct: 10  GYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIR--TIDH------------------ 49

Query: 212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDG--RLLTVNKAAPR 265
                        +   F ++   +++ A+ A      + + G  R L V+ A   
Sbjct: 50  ------------VKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG 93

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 63.2 bits (154), Expect = 7e-13
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 3/77 (3%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
             G  +++  LP+      +   FS     +   +    + GR  G   V  ++  +   
Sbjct: 13  TTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPD-GRVTGEADVEFATHEDAVA 70

Query: 337 AIAALDGQNLDGRAIRV 353
           A+ A D  N+  R + +
Sbjct: 71  AM-AKDKANMQHRYVEL 86

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 17/120 (14%), Positives = 32/120 (26%), Gaps = 29/120 (24%)

Query: 149 EEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCA 208
                 +      + +  LPY      +   F     + +     H   G  G       
Sbjct: 5   SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRV-----HIEIGPDG------- 52

Query: 209 VFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ 268
                           R  G   V  +T E+A  A+    + ++  R + +   +  GT 
Sbjct: 53  ----------------RVTGEADVEFATHEDAVAAMAK-DKANMQHRYVELFLNSTAGTS 95

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 61.6 bits (150), Expect = 2e-12
 Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                + +   P+ V    + +  +   K V  R+V +   G   G+ FV  S+E E+  
Sbjct: 8   TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAH-GNKTGYIFVDFSNEEEVKQ 65

Query: 337 AIAALDGQNLDGRAIRV 353
           A+   + + + GR I V
Sbjct: 66  AL-KCNREYMGGRYIEV 81

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 48.5 bits (116), Expect = 8e-08
 Identities = 18/112 (16%), Positives = 34/112 (30%), Gaps = 31/112 (27%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                  + +   P++V  + +         V I       +    G             
Sbjct: 6   SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAI-----RIVRNAHG------------- 47

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV--NKAAP 264
                        G+ FV  S  EE ++A++  +R  + GR + V   K+ P
Sbjct: 48  ----------NKTGYIFVDFSNEEEVKQALKC-NREYMGGRYIEVFREKSGP 88

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 61.3 bits (149), Expect = 4e-12
 Identities = 12/81 (14%), Positives = 29/81 (35%), Gaps = 2/81 (2%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+   P +     +++   + G+V+N ++         +G  FV   S       +   
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFV-ET 71

Query: 342 DGQNLDGRAIRVNVAEDRQRR 362
            GQ      + +   +D   +
Sbjct: 72  PGQKYKETDLLILFKDDYFAK 92

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 51.7 bits (124), Expect = 8e-09
 Identities = 14/102 (13%), Positives = 29/102 (28%), Gaps = 28/102 (27%)

Query: 158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
           ++  +++   P D   + +    E  G V   +++                         
Sbjct: 10  KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT----------------------- 46

Query: 218 IYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
                    +G  FV   ++E A+K VE           L +
Sbjct: 47  ----LHKAFKGSIFVVFDSIESAKKFVET-PGQKYKETDLLI 83

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 60.7 bits (147), Expect = 1e-11
 Identities = 16/100 (16%), Positives = 30/100 (30%), Gaps = 6/100 (6%)

Query: 258 TVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNA----RVVY 313
           +   +    +         E    + +  LP+      +   F +H  +         V 
Sbjct: 2   SSGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVT 61

Query: 314 DRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV 353
             + GR  G  FV  + E    +A+       L  R I +
Sbjct: 62  YPD-GRPTGDAFVLFACEEYAQNAL-RKHKDLLGKRYIEL 99

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 55.7 bits (134), Expect = 6e-10
 Identities = 18/120 (15%), Positives = 39/120 (32%), Gaps = 24/120 (20%)

Query: 149 EEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCA 208
           E  +F+       + +  LP+   +E++   F +   +   +    F+    G       
Sbjct: 13  EVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDG------- 65

Query: 209 VFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ 268
                           R  G  FV  +  E A+ A+   H+  +  R + + ++     Q
Sbjct: 66  ----------------RPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFRSTAAEVQ 108

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 58.7 bits (142), Expect = 3e-11
 Identities = 13/75 (17%), Positives = 20/75 (26%), Gaps = 6/75 (8%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I   NLP     A +++ FS  G +    +              V      E   A   L
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFRHL 66

Query: 342 DGQNLDGRAIRVNVA 356
                    + +  A
Sbjct: 67  AYSKFHHVPLYLEWA 81

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 51.7 bits (124), Expect = 1e-08
 Identities = 14/117 (11%), Positives = 24/117 (20%), Gaps = 33/117 (28%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +   NLP    + ++   F + G++    +                              
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLP----------------------------- 43

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEP 278
                     V      EA KA             L +   AP G       +    
Sbjct: 44  ---EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEW-APIGVFGAAPQKKDSQ 96

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 58.8 bits (142), Expect = 4e-11
 Identities = 19/107 (17%), Positives = 42/107 (39%), Gaps = 8/107 (7%)

Query: 260 NKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR 319
           +   PRG+    +     P   I++  LP +V    +  +    GKV N  ++      +
Sbjct: 12  SGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------K 65

Query: 320 SRGFGFVTMSSETELNDAI--AALDGQNLDGRAIRVNVAEDRQRRSS 364
            +   F+ M++E   N  +         L G+ I +  +  ++ ++ 
Sbjct: 66  GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD 112

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 45.3 bits (107), Expect = 3e-06
 Identities = 16/114 (14%), Positives = 34/114 (29%), Gaps = 34/114 (29%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           + +  LP DV   ++  L    G V                                 N 
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVT--------------------------------NL 61

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHR--YDIDGRLLTVNKAAPRGTQPERAP 273
              + +   F+ M+T E A   V  +      + G+ + +  +  +  + + +P
Sbjct: 62  LMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSP 115

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 58.8 bits (142), Expect = 4e-11
 Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 8/94 (8%)

Query: 266 GTQPERAPRVF---EPGFRIYVGNLPWEVDNARLEQVFSE---HGKVVNARVVYDRETGR 319
           G+       +      G+ + +  LPW      ++   S+   H  V     +Y RE GR
Sbjct: 1   GSSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GR 59

Query: 320 SRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV 353
             G  FV + SE ++  A+   D +++  R I V
Sbjct: 60  QSGEAFVELESEDDVKLAL-KKDRESMGHRYIEV 92

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 45.7 bits (108), Expect = 1e-06
 Identities = 20/124 (16%), Positives = 39/124 (31%), Gaps = 28/124 (22%)

Query: 142 SGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQG 201
           SG  G+    E     E   + +  LP+    E +          +      HF++  +G
Sbjct: 3   SGSSGMMLGPE---GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHD-GVAGVHFIYTREG 58

Query: 202 FHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK 261
                                  R  G  FV + + ++ + A++   R  +  R + V K
Sbjct: 59  -----------------------RQSGEAFVELESEDDVKLALKK-DRESMGHRYIEVFK 94

Query: 262 AAPR 265
           +   
Sbjct: 95  SHRT 98

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 62.6 bits (151), Expect = 6e-11
 Identities = 23/96 (23%), Positives = 48/96 (50%), Gaps = 1/96 (1%)

Query: 269 PERAPRVFEPGFR-IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVT 327
           P   P      F+ ++V  + ++   ++L + F  +G +    +VY + +G+ RG+ F+ 
Sbjct: 91  PHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIE 150

Query: 328 MSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRS 363
              E +++ A    DG+ +DGR + V+V   R  + 
Sbjct: 151 YEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKG 186

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 48.7 bits (115), Expect = 1e-06
 Identities = 35/213 (16%), Positives = 67/213 (31%), Gaps = 38/213 (17%)

Query: 122 DWGEPEGEDTVVEAGERQE----ESGEEGVFEEEEFVEPPEDAK--------LFVGNLPY 169
           D   P   +T  E  ER+     E  ++ V  E +  +P  D          LFV  + Y
Sbjct: 53  DAPPPTRAETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNY 112

Query: 170 DVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGF 229
           D    KL   FE  G ++                           + ++Y++ + + RG+
Sbjct: 113 DTTESKLRREFEVYGPIK--------------------------RIHMVYSKRSGKPRGY 146

Query: 230 GFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPW 289
            F+      +   A +      IDGR + V+    R  +  R  R+         G    
Sbjct: 147 AFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADV 206

Query: 290 EVDNARLEQVFSEHGKVVNARVVYDRETGRSRG 322
            + ++  +       +   + + +         
Sbjct: 207 NIRHSGRDDTSRYDERPGPSPLPHRDRDRDRER 239

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 57.3 bits (139), Expect = 7e-11
 Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 7/74 (9%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAI-AA 340
           +YVG L   +    L   F + G++    VV        +   F+  ++      A   +
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68

Query: 341 LDGQNLDGRAIRVN 354
            +   ++GR + V 
Sbjct: 69  FNKLIVNGRRLNVK 82

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 55.4 bits (134), Expect = 3e-10
 Identities = 22/109 (20%), Positives = 35/109 (32%), Gaps = 36/109 (33%)

Query: 156 PPEDA---KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYV 212
             ED     L+VG L   +    L   F + G  EI  +                     
Sbjct: 6   SGEDKTITTLYVGGLGDTITETDLRNHFYQFG--EIRTITVV------------------ 45

Query: 213 SLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVE-MFHRYDIDGRLLTVN 260
                       + +   F+  +T + AE A E  F++  ++GR L V 
Sbjct: 46  ------------QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK 82

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 56.9 bits (137), Expect = 2e-10
 Identities = 23/95 (24%), Positives = 36/95 (37%), Gaps = 5/95 (5%)

Query: 262 AAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSE---HGKVVNARVVYDRETG 318
               G            GF + +  LPW      ++   S+   H        +Y RE G
Sbjct: 27  GQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-G 85

Query: 319 RSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV 353
           R  G  FV + SE ++  A+   D +++  R I V
Sbjct: 86  RQSGEAFVELGSEDDVKMAL-KKDRESMGHRYIEV 119

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 45.4 bits (107), Expect = 3e-06
 Identities = 22/137 (16%), Positives = 42/137 (30%), Gaps = 30/137 (21%)

Query: 126 PEGEDTVVEAGERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGT 185
           P G       G +Q   G   +  E       E   + +  LP+    E +         
Sbjct: 16  PRGSHMASMTGGQQMGRGSMMLGPE-----GGEGFVVKLRGLPWSCSVEDVQNFLSDCTI 70

Query: 186 VEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVE 245
            +      HF++  +G                       R  G  FV + + ++ + A++
Sbjct: 71  HD-GAAGVHFIYTREG-----------------------RQSGEAFVELGSEDDVKMALK 106

Query: 246 MFHRYDIDGRLLTVNKA 262
              R  +  R + V K+
Sbjct: 107 K-DRESMGHRYIEVFKS 122

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 55.9 bits (135), Expect = 3e-10
 Identities = 13/84 (15%), Positives = 23/84 (27%), Gaps = 8/84 (9%)

Query: 273 PRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSET 332
           P        +++  L   V  A L +   E G +    V+        +    V      
Sbjct: 15  PHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVL 68

Query: 333 ELNDAIAALDGQN--LDGRAIRVN 354
              +A+         + G    VN
Sbjct: 69  GACNAVNYAADNQIYIAGHPAFVN 92

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 16/108 (14%), Positives = 25/108 (23%), Gaps = 34/108 (31%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           + P    + +  L   V    L    ++ G +                        YV +
Sbjct: 17  KTPASPVVHIRGLIDGVVEADLVEALQEFGPIS-----------------------YVVV 53

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHR--YDIDGRLLTVN 260
           +           +    V    V  A  AV         I G    VN
Sbjct: 54  M---------PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN 92

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 54.9 bits (132), Expect = 6e-10
 Identities = 16/79 (20%), Positives = 28/79 (35%), Gaps = 3/79 (3%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVY--DRETGRSRGFGFVTMSSETEL 334
           +  F I    LPW      +   FS+         ++      G+ RG   + M SE ++
Sbjct: 9   DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDV 68

Query: 335 NDAIAALDGQNLDGRAIRV 353
             A+       +  R + V
Sbjct: 69  QKAL-EKHRMYMGQRYVEV 86

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 20/111 (18%), Positives = 34/111 (30%), Gaps = 25/111 (22%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           E  +   +    LP+    E +   F         E   HFL    G             
Sbjct: 7   EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRN-GENGIHFLLNRDG------------- 52

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                     + RG   + M + ++ +KA+E  HR  +  R + V +    
Sbjct: 53  ----------KRRGDALIEMESEQDVQKALEK-HRMYMGQRYVEVYEINNE 92

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 54.9 bits (132), Expect = 8e-10
 Identities = 18/102 (17%), Positives = 39/102 (38%), Gaps = 8/102 (7%)

Query: 265 RGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFG 324
           RG+          P   I++  LP +V    +  +    GKV N  ++      + +   
Sbjct: 2   RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQA 55

Query: 325 FVTMSSETELNDAIAAL--DGQNLDGRAIRVNVAEDRQRRSS 364
           F+ M++E   N  +         L G+ I +  +  ++ ++ 
Sbjct: 56  FIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD 97

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 46.8 bits (111), Expect = 5e-07
 Identities = 16/114 (14%), Positives = 34/114 (29%), Gaps = 34/114 (29%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           + +  LP DV   ++  L    G V                                 N 
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVT--------------------------------NL 46

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYD--IDGRLLTVNKAAPRGTQPERAP 273
              + +   F+ M+T E A   V  +      + G+ + +  +  +  + + +P
Sbjct: 47  LMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSP 100

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 53.6 bits (129), Expect = 2e-09
 Identities = 10/89 (11%), Positives = 26/89 (29%), Gaps = 14/89 (15%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                ++V  L   V  A L +   + G +    ++        +    V   +    + 
Sbjct: 13  SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM------PFKRQALVEFENI---DS 63

Query: 337 AIAALD-----GQNLDGRAIRVNVAEDRQ 360
           A   +         + G+    N +  ++
Sbjct: 64  AKECVTFAADVPVYIAGQQAFFNYSTSKR 92

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 43.6 bits (103), Expect = 6e-06
 Identities = 14/101 (13%), Positives = 22/101 (21%), Gaps = 34/101 (33%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           + V  L   V    L    EK GT+                                   
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTIC--------------------------------YV 45

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMF--HRYDIDGRLLTVN 260
                +    V    ++ A++ V         I G+    N
Sbjct: 46  MMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN 86

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 53.1 bits (127), Expect = 2e-09
 Identities = 19/90 (21%), Positives = 36/90 (40%), Gaps = 7/90 (7%)

Query: 279 GFRIYVGNLPWEVDNARLEQ----VFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL 334
           G  + V N+ + +    L+Q     F+ HGKV +  +         +    V M +  + 
Sbjct: 9   GADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPH---TDYQLKAVVQMENLQDA 65

Query: 335 NDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
             A+ +L    +  + I V++A      SS
Sbjct: 66  IGAVNSLHRYKIGSKKILVSLATGASGPSS 95

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 43.4 bits (102), Expect = 7e-06
 Identities = 21/119 (17%), Positives = 35/119 (29%), Gaps = 33/119 (27%)

Query: 155 EPPEDAKLFVGNLPYDVDS----EKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVF 210
                A + V N+ Y +      + L   F + G V+  E+  H                
Sbjct: 5   SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT--------------- 49

Query: 211 YVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP 269
                           +    V M  +++A  AV   HRY I  + + V+ A       
Sbjct: 50  --------------DYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGASGPS 94

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 52.9 bits (127), Expect = 4e-09
 Identities = 14/90 (15%), Positives = 37/90 (41%), Gaps = 8/90 (8%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
            P   +++  LP EV    +  +    GKV N  ++      + +   F+ +++E     
Sbjct: 13  APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELATEEAAIT 66

Query: 337 AIA--ALDGQNLDGRAIRVNVAEDRQRRSS 364
            +   +    +L  + I +  +  ++ ++S
Sbjct: 67  MVNYYSAVTPHLRNQPIYIQYSNHKELKTS 96

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 13/101 (12%), Positives = 27/101 (26%), Gaps = 34/101 (33%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L +  LP +V   ++  L    G V                                 N 
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVT--------------------------------NI 45

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYD--IDGRLLTVN 260
              + +   F+ ++T E A   V  +      +  + + + 
Sbjct: 46  LMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ 86

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 51.5 bits (123), Expect = 1e-08
 Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 2/62 (3%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYD--RETGRSRGFGFVTMSSETELNDAI 338
           +++VG LP ++D   +   F   G +V         +     +G+ F+    E+ +   I
Sbjct: 10  KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69

Query: 339 AA 340
            A
Sbjct: 70  DA 71

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 46.9 bits (111), Expect = 5e-07
 Identities = 13/96 (13%), Positives = 29/96 (30%), Gaps = 24/96 (25%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
                K+FVG LP D+D +++   F + G + +                           
Sbjct: 5   SSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWP------------------------ 40

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYD 251
               ++     +G+ F+        +  ++     D
Sbjct: 41  HKAESKSYFPPKGYAFLLFQEESSVQALIDACLEED 76

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 49.9 bits (119), Expect = 4e-08
 Identities = 19/105 (18%), Positives = 45/105 (42%), Gaps = 9/105 (8%)

Query: 263 APRGTQPERAPRVFEPGFRIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSR 321
            P G   ++  +  E G  I++ NLP     ++ + ++   +GK+ N  ++      R +
Sbjct: 9   KPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM------RMK 62

Query: 322 GFGFVTMSSETELNDAIA--ALDGQNLDGRAIRVNVAEDRQRRSS 364
              F+ M +  +    +           GR ++V+++E  ++  S
Sbjct: 63  SQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVS 107

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 48.3 bits (114), Expect = 6e-07
 Identities = 12/79 (15%), Positives = 28/79 (35%), Gaps = 2/79 (2%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
             +Y+   P +     +++   + G+V+N ++         +G  FV   S       + 
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE 168

Query: 340 ALDGQNLDGRAIRVNVAED 358
              GQ      + +   +D
Sbjct: 169 TP-GQKYKETDLLILFKDD 186

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 45.5 bits (107), Expect = 5e-06
 Identities = 25/122 (20%), Positives = 42/122 (34%), Gaps = 9/122 (7%)

Query: 235 STVEEAEKAVEMFHRYDIDGRLLTVNKAA-PRGTQPERAPRVFEPGFRIYVGNLPWEVDN 293
                A+ A++  +        L  + AA   G        V     RI V NL + V  
Sbjct: 5   HHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVL----RIIVENLFYPVTL 60

Query: 294 ARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV 353
             L Q+FS+ G V+            ++    +  +       A  +LDGQN+      +
Sbjct: 61  DVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL 116

Query: 354 NV 355
            +
Sbjct: 117 RI 118

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 44.2 bits (104), Expect = 6e-06
 Identities = 21/94 (22%), Positives = 33/94 (35%), Gaps = 8/94 (8%)

Query: 262 AAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSR 321
           A   G        V     RI V NL + V    L Q+FS+ G V+            ++
Sbjct: 15  AVDAGMAMAGQSPVL----RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQ 66

Query: 322 GFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV 355
               +  +       A  +LDGQN+      + +
Sbjct: 67  FQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI 100

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 45.2 bits (106), Expect = 1e-05
 Identities = 22/125 (17%), Positives = 36/125 (28%), Gaps = 21/125 (16%)

Query: 248 HRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFR-IYVGNLPWEVDNAR---------LE 297
              D  GR    +     G         F    + +YVG +   +++           + 
Sbjct: 107 EVLDCFGREKFADYREDMGGIGS-----FRKKNKTLYVGGIDGALNSKHLKPAQIESRIR 161

Query: 298 QVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE 357
            VFS  G +   R V       S+  GFV    +     A  A+  Q L   + +     
Sbjct: 162 FVFSRLGDIDRIRYV------ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDR 215

Query: 358 DRQRR 362
                
Sbjct: 216 REGTG 220

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 22/134 (16%), Positives = 35/134 (26%), Gaps = 42/134 (31%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                  + V  LP  V  E L + FE         V                       
Sbjct: 4   GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVL---------------------- 41

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
                     R    G +T     +AE+ +     +++ G  L++  A PR         
Sbjct: 42  -------SWQRLGCGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAPPRAPA------ 87

Query: 275 VFEPGFRIYVGNLP 288
                 R+ +  LP
Sbjct: 88  ------RLLLQGLP 95

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 17/83 (20%), Positives = 26/83 (31%), Gaps = 4/83 (4%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
             G  + V  LP  V +  L   F    +     V+      R    G +T     +   
Sbjct: 6   SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVL---SWQRLGCGGVLTFREPADAER 62

Query: 337 AIAALDGQNLDGRAIRVNVAEDR 359
            +A  D   L G  + +  A  R
Sbjct: 63  VLAQAD-HELHGAQLSLRPAPPR 84

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 39.1 bits (91), Expect = 3e-04
 Identities = 12/62 (19%), Positives = 21/62 (33%), Gaps = 6/62 (9%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +  G L   V   +L  V  + G V    +        ++ + F    +  E   A   L
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMP------PNKPYSFARYRTTEESKRAYVTL 83

Query: 342 DG 343
           +G
Sbjct: 84  NG 85

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 38.0 bits (88), Expect = 7e-04
 Identities = 13/91 (14%), Positives = 27/91 (29%), Gaps = 32/91 (35%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +  G L   V   +L  + EK G V+   +                              
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVD--ALLM---------------------------- 59

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI 252
               ++ + F    T EE+++A    +  ++
Sbjct: 60  --PPNKPYSFARYRTTEESKRAYVTLNGKEV 88

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 38.5 bits (89), Expect = 6e-04
 Identities = 14/75 (18%), Positives = 25/75 (33%), Gaps = 5/75 (6%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            + + N  + +    L  V +  GKV            R+     V   S      A AA
Sbjct: 27  LLSIQNPLYPITVDVLYTVCNPVGKVQRI-----VIFKRNGIQAMVEFESVLCAQKAKAA 81

Query: 341 LDGQNLDGRAIRVNV 355
           L+G ++      + +
Sbjct: 82  LNGADIYAGCCTLKI 96

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	365
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.98
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.97
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.91
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.89
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.86
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.85
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.82
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.82
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.81
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.81
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.81
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.81
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.8
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.8
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.8
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.8
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.8
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.79
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.79
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.79
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.79
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.79
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.79
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.79
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.79
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.79
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.79
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.79
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.79
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.79
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.78
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.78
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.78
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.78
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.78
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.78
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.78
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.78
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.78
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.78
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.77
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.77
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.77
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.77
2div_A	99	TRNA selenocysteine associated protein; structural	99.77
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.77
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.77
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.76
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.76
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.76
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.76
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.76
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.76
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.76
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.76
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.76
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.76
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.76
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.76
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.75
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.75
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.75
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.75
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.75
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.75
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.75
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.75
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.75
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.75
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.75
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.75
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.75
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.74
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.74
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.74
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.74
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.74
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.74
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.74
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.74
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.74
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.74
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.74
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.73
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.73
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.73
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.73
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.73
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.73
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.73
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.73
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.73
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.73
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.72
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.72
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.72
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.72
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.72
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.72
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.72
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.72
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.72
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.72
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.72
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.72
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.72
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.72
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.72
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.72
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.72
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.72
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.71
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.71
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.71
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.71
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.71
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.71
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.71
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.71
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.71
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.71
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.71
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.71
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.71
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.71
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.71
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.71
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.71
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.7
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.7
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.7
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.7
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.7
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.7
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.7
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.7
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.7
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.7
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.7
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.7
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.7
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.7
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.7
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.7
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.7
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.7
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.7
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.7
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.7
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.7
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.69
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.69
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.69
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.69
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.69
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.69
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.69
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.69
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.69
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.69
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.69
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.69
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.69
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.69
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.52
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.69
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.69
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.69
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.69
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.69
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.68
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.68
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.68
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.68
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.68
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.68
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.68
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.68
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.68
2div_A	99	TRNA selenocysteine associated protein; structural	99.68
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.68
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.68
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.67
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.67
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.67
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.67
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.67
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.67
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.67
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.67
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.67
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.67
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.67
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.67
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.67
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.67
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.67
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.66
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.66
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.66
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.66
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.66
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.66
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.66
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.66
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.66
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.66
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.66
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.66
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.65
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.65
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.65
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.65
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.65
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.65
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.65
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.65
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.65
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.65
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.65
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.65
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.65
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.64
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.64
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.64
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.64
1x5p_A	97	Negative elongation factor E; structure genomics,	99.64
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.64
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.64
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.64
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.64
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.64
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.64
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.64
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.64
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.64
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.64
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.63
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.63
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.63
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.63
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.63
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.63
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.63
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.63
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.63
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.63
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.63
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.63
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.62
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.62
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.62
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.62
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.62
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.62
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.62
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.62
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.62
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.62
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.61
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.61
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.61
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.61
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.61
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.61
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.61
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.61
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.61
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.61
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.61
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.61
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.61
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.61
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.61
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.61
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.61
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.6
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.6
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.6
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.6
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.6
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.6
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.6
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.59
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.59
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.59
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.59
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.59
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.59
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.58
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.58
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.58
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.58
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.35
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.57
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.57
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.57
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.57
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.56
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.56
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.56
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.56
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.56
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.56
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.56
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.56
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.55
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.55
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.54
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.54
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.54
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.54
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.54
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.54
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.53
1x5p_A	97	Negative elongation factor E; structure genomics,	99.53
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.52
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.52
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.52
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.52
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.51
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.51
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.51
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.51
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.51
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.51
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.5
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.49
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.49
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.48
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.48
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.47
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.47
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.46
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.46
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.45
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.45
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.45
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.44
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.44
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.43
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.37
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.35
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.34
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.3
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.28
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.26
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.25
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.22
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.11
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.09
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.05
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.03
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.97
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.95
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.84
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.8
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.72
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.69
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.54
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.46
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.92
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.91
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.57
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.33
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.27
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.98
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.86
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.52
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.52
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.17
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.08
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.92
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.79
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.04
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	94.47
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.14
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	93.59
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.87
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.5

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=9.5e-35  Score=260.92  Aligned_cols=169  Identities=27%  Similarity=0.402  Sum_probs=153.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +.+||||||||+++++++|+++|++||.|..++                          ++++..+++++|||||+|.+.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~--------------------------i~~d~~tg~~~G~afV~F~~~   67 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIR--------------------------VCRDMITRRSLGYAYVNFQQP   67 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTCCEEEEEEEEESSH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEE--------------------------EecccCCCCccccccceeCCH
Confidence            568999999999999999999999999999987                          788889999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRET  317 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~  317 (365)
                      ++|.+|+..+++..+.|+.|+|.++......      ......+|||+|||+.+++++|+++|+.||.|..|+|+++.  
T Consensus        68 ~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~~~------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--  139 (213)
T 4f02_A           68 ADAERALDTMNFDVIKGKPVRIMWSQRDPSL------RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--  139 (213)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEEECCCCTHH------HHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--
T ss_pred             HHHHHHHHHhhhhhcCCcccccccccccccc------cccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--
Confidence            9999999999999999999999987654321      12233589999999999999999999999999999999985  


Q ss_pred             CCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccc
Q 017842          318 GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       318 ~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      +.++|||||+|.+.++|.+||..|||..|+||+|+|.||.++.
T Consensus       140 ~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          140 NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHH
T ss_pred             CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            4579999999999999999999999999999999999998764

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=100.00  E-value=5.3e-34  Score=244.99  Aligned_cols=165  Identities=27%  Similarity=0.536  Sum_probs=153.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +.++|||+|||+++++++|+++|+.||.|..+.                          ++.+..+++++|||||+|.+.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~~   55 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCR--------------------------IMRDYKTGYSYGYAFVDFTSE   55 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCEETTTTEECSEEEEEESSH
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE--------------------------EEEeCCCCccceEEEEEECCH
Confidence            468999999999999999999999999998887                          677778999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRET  317 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~  317 (365)
                      ++|.+|+..|+|..+.|+.|+|.++.+....        .+.++|||+|||..+++++|+++|+.||.|..++++++..+
T Consensus        56 ~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~--------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~  127 (168)
T 1b7f_A           56 MDSQRAIKVLNGITVRNKRLKVSYARPGGES--------IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLT  127 (168)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEEECCCCSST--------TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTT
T ss_pred             HHHHHHHHhcCCCEeCCcEEEEEecCCCccc--------CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCC
Confidence            9999999999999999999999998765432        23459999999999999999999999999999999999889


Q ss_pred             CCcceEEEEEecCHHHHHHHHHHhCCCccCC--eeEEEEEc
Q 017842          318 GRSRGFGFVTMSSETELNDAIAALDGQNLDG--RAIRVNVA  356 (365)
Q Consensus       318 ~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g--r~l~V~~a  356 (365)
                      |+++|||||+|.+.++|.+|+..|||..+.|  ++|+|.||
T Consensus       128 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          128 GRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            9999999999999999999999999999988  99999986

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=4.7e-34  Score=244.40  Aligned_cols=166  Identities=26%  Similarity=0.550  Sum_probs=151.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      |+|||+|||+++++++|+++|+.||.|..+.                          ++.+. .++++|||||+|.+.++
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~--------------------------i~~~~-~~~~~g~afV~f~~~~~   53 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIK--------------------------IMIDK-NNKNVNYAFVEYHQSHD   53 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEE--------------------------EECCC-C-CCEEEEEEEESSHHH
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEE--------------------------EEECC-CCCCCCEEEEEeCCHHH
Confidence            6899999999999999999999999999887                          55554 46789999999999999


Q ss_pred             HHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCC
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR  319 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~  319 (365)
                      |.+|+..|+|..+.|+.|+|.++.+....      ...+.++|||+|||+.+++++|+++|+.||.|..++++++..+|.
T Consensus        54 a~~A~~~l~~~~~~g~~i~v~~~~~~~~~------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~  127 (166)
T 3md3_A           54 ANIALQTLNGKQIENNIVKINWAFQSQQS------SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGS  127 (166)
T ss_dssp             HHHHHHHHTTCEETTEECEEEECCCCCCC------CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCC
T ss_pred             HHHHHHHcCCCccCCCeeEEEEcCCCCCC------CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCC
Confidence            99999999999999999999998765432      234566999999999999999999999999999999999999999


Q ss_pred             cceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          320 SRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       320 ~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      ++|||||+|.+.++|.+|+..|||..++|++|+|.||+.
T Consensus       128 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          128 SRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             EEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             cceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            999999999999999999999999999999999999863

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=100.00  E-value=8.4e-34  Score=243.08  Aligned_cols=164  Identities=31%  Similarity=0.562  Sum_probs=152.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||+|||+++++++|+++|+.||.|..+.                          ++.+..++.++|||||+|.+.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~--------------------------~~~~~~~~~~~g~afV~f~~~~   55 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCK--------------------------LVRDKITGQSLGYGFVNYIDPK   55 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------EEECTTTCCEEEEEEEEESSHH
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEeCCCCCcceeEEEEEECCHH
Confidence            57999999999999999999999999999887                          7778789999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETG  318 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~  318 (365)
                      +|.+|+..|+|..+.|+.|+|.++.+...        ....++|||+|||+.+++++|+++|+.||.|..++++++..+|
T Consensus        56 ~A~~a~~~l~~~~~~g~~l~v~~~~~~~~--------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g  127 (167)
T 1fxl_A           56 DAEKAINTLNGLRLQTKTIKVSYARPSSA--------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTG  127 (167)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEECCCCCG--------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTC
T ss_pred             HHHHHHHHcCCCccCCceEEEEecCCCcc--------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCC
Confidence            99999999999999999999999876542        2234589999999999999999999999999999999998899


Q ss_pred             CcceEEEEEecCHHHHHHHHHHhCCCccCCee--EEEEEc
Q 017842          319 RSRGFGFVTMSSETELNDAIAALDGQNLDGRA--IRVNVA  356 (365)
Q Consensus       319 ~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~--l~V~~a  356 (365)
                      +++|||||+|.+.++|.+|+..|||..+.|+.  |+|.||
T Consensus       128 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          128 VSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             CEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            99999999999999999999999999999975  888886

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=6.9e-34  Score=250.57  Aligned_cols=177  Identities=31%  Similarity=0.535  Sum_probs=152.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+++|+.||.|..+.                          ++.+..++.++|||||+|.
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~~~~~g~~~g~afV~f~   63 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV--------------------------VMRDPNTKRSRGFGFVTYA   63 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTCCEEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE--------------------------EEEcCCCCCccceEEEEeC
Confidence            34578999999999999999999999999999887                          7788889999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR  315 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~  315 (365)
                      +.++|.+|+.. ++..+.|+.|.|.++.+......  +....+.++|||+|||+.+++++|+++|+.||.|..|+|+++.
T Consensus        64 ~~~~A~~A~~~-~~~~~~g~~l~v~~~~~~~~~~~--~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~  140 (196)
T 1l3k_A           64 TVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQR--PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR  140 (196)
T ss_dssp             SHHHHHHHHHT-CSCEETTEECEEEECCC-------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECT
T ss_pred             CHHHHHHHHhc-CCCEECCEEeeeecccCcccccc--cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecC
Confidence            99999999987 99999999999999876543321  2233455799999999999999999999999999999999999


Q ss_pred             CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccccC
Q 017842          316 ETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR  362 (365)
Q Consensus       316 ~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~~  362 (365)
                      .+|.++|||||+|.+.++|.+|+.. +|..|+|+.|.|.||.++...
T Consensus       141 ~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          141 GSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             CCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence            8999999999999999999999984 899999999999999987654

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=100.00  E-value=6.3e-34  Score=254.62  Aligned_cols=179  Identities=22%  Similarity=0.424  Sum_probs=156.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|+.||.|..+.                          ++.+..+++++|||||.|.+.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~--------------------------i~~~~~~g~~~g~afV~f~~~   80 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSID--------------------------MSWDSVTMKHKGFAFVEYEVP   80 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEE--------------------------ECCC-CC-CCCSEEEEEESSH
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEE--------------------------EeecCCCCccCceEEEEeCCH
Confidence            367999999999999999999999999999887                          667777899999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCC---CCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEee
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER---APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYD  314 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~---~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d  314 (365)
                      ++|.+|+..|+|..|.|+.|+|.++.........   ........++|||+|||+.+++++|+++|+.||.|..|+|+++
T Consensus        81 ~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~  160 (216)
T 2qfj_A           81 EAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARD  160 (216)
T ss_dssp             HHHHHHHHHHSSCCCC-CCCEEECCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEEC
T ss_pred             HHHHHHHHHccCCeeCCeeEEEecCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEec
Confidence            9999999999999999999999887654321100   0011234569999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccccC
Q 017842          315 RETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR  362 (365)
Q Consensus       315 ~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~~  362 (365)
                      ..+|+++|||||+|.+.++|.+|+..|||..|+|++|+|.|+.+++.+
T Consensus       161 ~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          161 PTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             TTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSST
T ss_pred             CCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCCC
Confidence            999999999999999999999999999999999999999999988654

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=100.00  E-value=2.9e-34  Score=246.59  Aligned_cols=166  Identities=31%  Similarity=0.584  Sum_probs=151.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +.++|||+|||+++++++|+++|+.||.|..+.                          ++.+..+|+++|||||+|.+.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~g~~~g~afV~f~~~   55 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLK--------------------------IMKDPATGRSRGFGFLSFEKP   55 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEE--------------------------CCCCTTTSSCCSCEEEEESST
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE--------------------------EEECCCCCCccceEEEEEccH
Confidence            467999999999999999999999999999887                          777878999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRET  317 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~  317 (365)
                      ++|.+|+.  ++..++|+.|.|.++.+...        ..+.++|||+|||+.+++++|+++|+.||.|..|++++++.+
T Consensus        56 ~~a~~A~~--~~~~~~g~~i~v~~~~~~~~--------~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~  125 (167)
T 2cjk_A           56 SSVDEVVK--TQHILDGKVIDPKRAIPRDE--------QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDT  125 (167)
T ss_dssp             HHHHHHHH--SCCEETTEECCCEECCCHHH--------HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSS
T ss_pred             HHHHHHHh--cccccCCeEcccccccchhh--------ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCC
Confidence            99999998  46789999999998765432        223459999999999999999999999999999999999889


Q ss_pred             CCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccc
Q 017842          318 GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       318 ~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      |.++|||||+|.+.++|.+|+. ++|..++|++|+|.||.+|.
T Consensus       126 g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk~  167 (167)
T 2cjk_A          126 GQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPRH  167 (167)
T ss_dssp             STTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCCC
T ss_pred             CccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCCC
Confidence            9999999999999999999998 89999999999999998863

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=100.00  E-value=1.4e-32  Score=242.65  Aligned_cols=183  Identities=20%  Similarity=0.391  Sum_probs=150.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|+.||.|..+.+.    .                 ...+.+...++++|||||+|.+.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~----~-----------------~~~v~~~~~~~~~g~afV~F~~~   61 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQA----P-----------------GNPVLAVQINQDKNFAFLEFRSV   61 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSS----S-----------------SCSEEEEEEETTTTEEEEEESCS
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccC----C-----------------CCceEEeEecCCCCEEEEEeCCH
Confidence            46899999999999999999999999533211000    0                 00011111346799999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCC------------CCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER------------APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGK  305 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~------------~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~  305 (365)
                      ++|.+|+ .|||..|.|+.|+|.++.........            ......+.++|||+|||+.+++++|+++|+.||.
T Consensus        62 ~~A~~Al-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~  140 (198)
T 2yh0_A           62 DETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGP  140 (198)
T ss_dssp             HHHHHHG-GGTTEEETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSC
T ss_pred             HHHHHHH-HhcCCEEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCC
Confidence            9999999 78999999999999988765332211            1112245689999999999999999999999999


Q ss_pred             eEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccccC
Q 017842          306 VVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR  362 (365)
Q Consensus       306 V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~~  362 (365)
                      |..|++.+++.+|.++|||||+|.+.++|.+|+..|||..++|++|+|.||.++.++
T Consensus       141 v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  197 (198)
T 2yh0_A          141 LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN  197 (198)
T ss_dssp             EEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCCC
T ss_pred             ccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            999999999889999999999999999999999999999999999999999988765

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=100.00  E-value=2.9e-32  Score=235.44  Aligned_cols=166  Identities=24%  Similarity=0.399  Sum_probs=147.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCC--CccceEEEEeC
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETD--RSRGFGFVTMS  235 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~g~afV~f~  235 (365)
                      +.++|||+|||+++++++|+++|++||.|..++                          ++.+..++  +++|||||+|.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~~~g~afV~f~   55 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEIN--------------------------VLRDRSQNPPQSKGCCFVTFY   55 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------EEEECSSSSCEEEEEEEEEES
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE--------------------------EEecCCCCCCCcceEEEEEEC
Confidence            468999999999999999999999999999887                          66777676  89999999999


Q ss_pred             CHHHHHHHHHHHccCccc---CeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEE
Q 017842          236 TVEEAEKAVEMFHRYDID---GRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVV  312 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~---gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~  312 (365)
                      +.++|.+|+..|+|..+.   ++.+.+.++.+....       ....++|||+|||+.+++++|+++|+.||.|..|+++
T Consensus        56 ~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~  128 (175)
T 3nmr_A           56 TRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNN-------AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRIL  128 (175)
T ss_dssp             SHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGGCCS-------CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE
T ss_pred             CHHHHHHHHHHhcCcEEccCCccceEEccccccccc-------cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEE
Confidence            999999999999998876   688888877654332       2234599999999999999999999999999999999


Q ss_pred             eeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC---CeeEEEEEcc
Q 017842          313 YDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD---GRAIRVNVAE  357 (365)
Q Consensus       313 ~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~---gr~l~V~~a~  357 (365)
                      ++. +|.++|||||+|.+.++|.+|+..|||..+.   ||+|+|.||.
T Consensus       129 ~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          129 RGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             ECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             ECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            995 5899999999999999999999999998775   4999999984

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=100.00  E-value=2.5e-32  Score=235.63  Aligned_cols=159  Identities=23%  Similarity=0.491  Sum_probs=142.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHcc----C-------CeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCc
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKA----G-------TVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRS  226 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~----G-------~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  226 (365)
                      +.++|||+|||+++++++|+++|+.|    |       .|..+.                                .+++
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~--------------------------------~~~~   50 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ--------------------------------INQD   50 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEE--------------------------------EETT
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeE--------------------------------ecCC
Confidence            46899999999999999999999999    5       444433                                2356


Q ss_pred             cceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCe
Q 017842          227 RGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKV  306 (365)
Q Consensus       227 ~g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V  306 (365)
                      +|||||+|.+.++|.+|+ .+||..+.|+.|+|.++......        ...++|||+|||+.+++++|+++|+.||.|
T Consensus        51 ~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~~~~~~~~~--------~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v  121 (172)
T 2g4b_A           51 KNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPL--------PGAHKLFIGGLPNYLNDDQVKELLTSFGPL  121 (172)
T ss_dssp             TTEEEEEESSHHHHHHHG-GGTTCEETTEECEEECCSSCCCC--------TTTTCEEEECCCTTCCHHHHHHHHHTTSCE
T ss_pred             CCEEEEEeCCHHHHHHHH-HhCCcEecCceeeecCCcccCCC--------CCCCEEEEEcCCCcCCHHHHHHHHHhcCCc
Confidence            899999999999999999 78999999999999987654332        224599999999999999999999999999


Q ss_pred             EEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          307 VNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       307 ~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..|++++++.+|+++|||||+|.+.++|.+|+..|||..++|++|+|.||.
T Consensus       122 ~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          122 KAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             EEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             eEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            999999998899999999999999999999999999999999999999974

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.98  E-value=1.4e-32  Score=238.22  Aligned_cols=167  Identities=20%  Similarity=0.406  Sum_probs=146.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .+...++|||+|||+++++++|+++|..||.+..+                           ++.+..+++++|||||+|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~---------------------------~~~~~~~~~~~g~afV~f   61 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL---------------------------AVVDVRTGTNRKFGYVDF   61 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC---------------------------CCCEEEEETTTTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE---------------------------EEEECCCCccccEEEEEE
Confidence            34568899999999999999999999999876541                           344445788999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEee
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYD  314 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d  314 (365)
                      .+.++|.+|++ |||..+.|+.|+|.++.+....      ...+.++|||+|||+.+++++|+++|+.||.|..+     
T Consensus        62 ~~~~~a~~A~~-l~g~~~~g~~l~v~~~~~~~~~------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----  129 (175)
T 1fje_B           62 ESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSK------KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----  129 (175)
T ss_dssp             SSHHHHHHHHH-GGGEEETTEEEEEECCCCSSCS------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----
T ss_pred             CCHHHHHHHHh-cCCCEeCCeEEEEecCCCcccc------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----
Confidence            99999999995 8999999999999998765432      22345699999999999999999999999988766     


Q ss_pred             CCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccc
Q 017842          315 RETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       315 ~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      ..++.++|||||+|.+.++|.+|+..|||..|.||+|+|.||.+|+
T Consensus       130 ~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k~  175 (175)
T 1fje_B          130 SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG  175 (175)
T ss_dssp             CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSCC
T ss_pred             cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCCC
Confidence            4678999999999999999999999999999999999999998874

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.97  E-value=4.5e-31  Score=246.58  Aligned_cols=172  Identities=22%  Similarity=0.322  Sum_probs=157.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|+.||.|..+.                          ++.+..+|.++|||||.|.+.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~--------------------------i~~~~~~g~~~g~afV~f~~~  147 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCF--------------------------LVYSERTGQSKGYGFAEYMKK  147 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTCCEEEEEEEEESSH
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEE--------------------------EEeeCCCCccceEEEEEECCH
Confidence            467999999999999999999999999999887                          777888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcC-cHHHHHHHHhccCCeEEEEEEeeCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEV-DNARLEQVFSEHGKVVNARVVYDRE  316 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~-tee~L~~~F~~~G~V~~v~i~~d~~  316 (365)
                      ++|.+|+..|+|..++|+.|.|.++.+......     ..+.++|||+|||+.+ ++++|+++|+.||.|..|+|.++. 
T Consensus       148 ~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~-----~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-  221 (284)
T 3smz_A          148 DSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPA-----LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-  221 (284)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEEECCGGGCCTT-----TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-
T ss_pred             HHHHHHHHHhCCCEeCCcEEEEEECCCCCCCcc-----cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-
Confidence            999999999999999999999999987654322     2345699999999995 999999999999999999999986 


Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccccc
Q 017842          317 TGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR  361 (365)
Q Consensus       317 ~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~  361 (365)
                      +|+++|||||+|.+.++|.+|+..|||..++|++|+|.|+.++..
T Consensus       222 ~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          222 DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            789999999999999999999999999999999999999987764

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.97  E-value=4.9e-31  Score=247.29  Aligned_cols=174  Identities=18%  Similarity=0.308  Sum_probs=146.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccC-CeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAG-TVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G-~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ..++|||+|||+++++++|+.+|..|| .|..+.                          ++.+.. +.++|||||.|.+
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~--------------------------i~~~~~-~~~~g~afV~f~~  168 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIR--------------------------LPSLRF-NTSRRFAYIDVTS  168 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEE--------------------------CC--------CCEEEEECSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEE--------------------------EEeCCC-CCcceEEEEEECC
Confidence            478999999999999999999999999 998887                          444443 7789999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCc-CcHHHHHHHHhccCCeEEEEEEeeC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDR  315 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~-~tee~L~~~F~~~G~V~~v~i~~d~  315 (365)
                      .++|.+|+..|+|..+.|+.|.|.++.+....... .....+.++|||+|||+. +++++|+++|+.||.|..|+|+++.
T Consensus       169 ~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~-~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~  247 (292)
T 2ghp_A          169 KEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRT-DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQ  247 (292)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEEECCCC----------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCC
T ss_pred             HHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccc-cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecC
Confidence            99999999999999999999999998876543322 123445679999999999 9999999999999999999999987


Q ss_pred             C-CCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccc
Q 017842          316 E-TGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       316 ~-~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      . +|.++|||||+|.+.++|.+|+ .|||..|+|++|+|.||.+++
T Consensus       248 ~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k~  292 (292)
T 2ghp_A          248 KEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKKP  292 (292)
T ss_dssp             C---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCCC
T ss_pred             CcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCCC
Confidence            6 5999999999999999999999 899999999999999999874

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.97  E-value=2e-30  Score=231.59  Aligned_cols=166  Identities=16%  Similarity=0.257  Sum_probs=141.1

Q ss_pred             CCCeEEEcCCC-CCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          158 EDAKLFVGNLP-YDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp-~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      +.++|||+||| +.+++++|+++|+.||.|..++                          ++.+     .+|||||+|.+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~--------------------------i~~~-----~~g~afV~f~~   51 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVK--------------------------FMKS-----KPGAAMVEMAD   51 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEE--------------------------ECTT-----STTCEEEEESS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEE--------------------------EecC-----CCCEEEEEECC
Confidence            46899999999 8999999999999999999887                          3322     47999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCCC---------------------C--------CCCcCCCCceEEEeCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPE---------------------R--------APRVFEPGFRIYVGNL  287 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~---------------------~--------~~~~~~~~~~lfV~nL  287 (365)
                      .++|.+|+..|||..+.|+.|+|.++......+.                     +        ......+..+|||+||
T Consensus        52 ~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NL  131 (205)
T 3tyt_A           52 GYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNA  131 (205)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEE
T ss_pred             HHHHHHHHHHhCCCEECCceEEEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCC
Confidence            9999999999999999999999998864432110                     0        0011245678999999


Q ss_pred             CCcCcHHHHHHHHhccCCe--EEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe----eEEEEEc
Q 017842          288 PWEVDNARLEQVFSEHGKV--VNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGR----AIRVNVA  356 (365)
Q Consensus       288 p~~~tee~L~~~F~~~G~V--~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr----~l~V~~a  356 (365)
                      |+.+++++|+++|+.||.|  ..|++..+.  +.++|||||+|.+.++|.+||..|||..|.|+    ++.|.||
T Consensus       132 p~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          132 PLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            9999999999999999999  899998774  45579999999999999999999999999876    6888776

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.97  E-value=5.3e-30  Score=232.44  Aligned_cols=167  Identities=22%  Similarity=0.394  Sum_probs=144.6

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          157 PEDAKLFVGNLPY-DVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       157 ~~~~tvfVgnLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ++.++|||+|||+ ++++++|+++|+.||.|..++                          ++.+.     +|||||+|.
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~--------------------------i~~~~-----~g~afV~F~   80 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVK--------------------------ILFNK-----KENALVQMA   80 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEE--------------------------ECCTT-----SCCEEEEES
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEE--------------------------EEECC-----CCEEEEEEC
Confidence            4678999999999 999999999999999999887                          44332     789999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCC---------------------------CCcCCCCceEEEeCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERA---------------------------PRVFEPGFRIYVGNLP  288 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~---------------------------~~~~~~~~~lfV~nLp  288 (365)
                      +.++|.+|+..|+|..|.|+.|+|.++.+......+.                           .....+.++|||+|||
T Consensus        81 ~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp  160 (229)
T 2adc_A           81 DGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIP  160 (229)
T ss_dssp             CHHHHHHHHHHHTTCBCSSSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCC
T ss_pred             CHHHHHHHHHHhCCCeECCeEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCC
Confidence            9999999999999999999999999887553211110                           0113456899999999


Q ss_pred             CcCcHHHHHHHHhccC-CeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CeeEEEEEcccc
Q 017842          289 WEVDNARLEQVFSEHG-KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD-GRAIRVNVAEDR  359 (365)
Q Consensus       289 ~~~tee~L~~~F~~~G-~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~-gr~l~V~~a~~~  359 (365)
                      +.+++++|+++|+.|| .|..|++..+     .+|||||+|.+.++|.+|+..|||..+. |++|+|.|++++
T Consensus       161 ~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          161 PSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             TTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             ccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            9999999999999999 9999999653     3789999999999999999999999999 999999999865

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.97  E-value=8e-30  Score=237.83  Aligned_cols=168  Identities=20%  Similarity=0.334  Sum_probs=145.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEE
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLA----MLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGF  231 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~----~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~af  231 (365)
                      ..+.++|||+|||+++++++|+    .+|+.||.|..++                          +..   +++++||||
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~--------------------------~~~---~~~~~g~af   56 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDIL--------------------------VSR---SLKMRGQAF   56 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEE--------------------------EcC---CCCcceEEE
Confidence            3468899999999999999966    8999999998876                          332   778999999


Q ss_pred             EEeCCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCC-----------------------------------------
Q 017842          232 VTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPE-----------------------------------------  270 (365)
Q Consensus       232 V~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~-----------------------------------------  270 (365)
                      |+|.+.++|.+|+..|||..|.|+.|+|.++........                                         
T Consensus        57 V~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  136 (282)
T 3pgw_A           57 VIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGA  136 (282)
T ss_pred             EEECCHHHHHHHHHHhcCCeeCCcEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCC
Confidence            999999999999999999999999999998865442000                                         


Q ss_pred             --------------------------------------------------------------CCCCcCCCCceEEEeCCC
Q 017842          271 --------------------------------------------------------------RAPRVFEPGFRIYVGNLP  288 (365)
Q Consensus       271 --------------------------------------------------------------~~~~~~~~~~~lfV~nLp  288 (365)
                                                                                    .......+.++|||+|||
T Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~  216 (282)
T 3pgw_A          137 VQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLP  216 (282)
T ss_pred             CCCCCCCCCcccccccccccCCCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCC
Confidence                                                                          000122356789999999


Q ss_pred             CcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CeeEEEEEcc
Q 017842          289 WEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD-GRAIRVNVAE  357 (365)
Q Consensus       289 ~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~-gr~l~V~~a~  357 (365)
                      +.+++++|+++|+.||.|..|+|++++     +|||||+|.+.++|.+|+..|||..|. |+.|+|.||+
T Consensus       217 ~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          217 EETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            999999999999999999999999663     689999999999999999999999999 9999999986

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.97  E-value=1.4e-29  Score=236.40  Aligned_cols=157  Identities=27%  Similarity=0.429  Sum_probs=145.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|+.|| |..+.                          +      ++++|||||+|.+.
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~--------------------------~------~~~~g~afV~f~~~   67 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCF--------------------------V------DKYKGTAFVTLLNG   67 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEE--------------------------E------ETTTTEEEEEESSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEE--------------------------E------ecCCCEEEEEeCCH
Confidence            468999999999999999999999999 77765                          2      46789999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRET  317 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~  317 (365)
                      ++|.+|+..|||..+.|+.|+|.++..              .++|||+|||+.+++++|+++|+.||.|..++++++..+
T Consensus        68 ~~A~~A~~~l~~~~~~g~~i~v~~~~~--------------~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~  133 (284)
T 3smz_A           68 EQAEAAINAFHQSRLRERELSVQLQPT--------------DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERT  133 (284)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEEECCC--------------SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTT
T ss_pred             HHHHHHHHHcCCCeeCCeEEEEEecCC--------------CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCC
Confidence            999999999999999999999997432              249999999999999999999999999999999999999


Q ss_pred             CCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccccc
Q 017842          318 GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR  361 (365)
Q Consensus       318 ~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~  361 (365)
                      |.++|||||+|.+.++|.+|+..|+|..+.|++|+|.|+.++..
T Consensus       134 g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~  177 (284)
T 3smz_A          134 GQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQL  177 (284)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGC
T ss_pred             CccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            99999999999999999999999999999999999999987664

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.97  E-value=3.8e-30  Score=227.57  Aligned_cols=165  Identities=22%  Similarity=0.395  Sum_probs=143.0

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          159 DAKLFVGNLPY-DVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       159 ~~tvfVgnLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      .++|||+|||+ ++++++|+++|+.||.|..++                          ++.+.     +|||||+|.+.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~--------------------------i~~~~-----~g~afV~f~~~   51 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVK--------------------------ILFNK-----KENALVQMADG   51 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEE--------------------------CSTTC-----SSCCEEECTTT
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEE--------------------------EEeCC-----CCEEEEEECCH
Confidence            57999999999 999999999999999998877                          33322     78999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCC---------------------------CCCcCCCCceEEEeCCCCc
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER---------------------------APRVFEPGFRIYVGNLPWE  290 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~---------------------------~~~~~~~~~~lfV~nLp~~  290 (365)
                      ++|.+|+..|||..+.|+.|+|.++.+......+                           ......+.++|||+|||+.
T Consensus        52 ~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~  131 (198)
T 1qm9_A           52 NQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPS  131 (198)
T ss_dssp             HHHHHHHHHHTTCCCSSCCCEEEECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTT
T ss_pred             HHHHHHHHHhCCCeecCeEEEEEEecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCC
Confidence            9999999999999999999999988754311100                           0112345789999999999


Q ss_pred             CcHHHHHHHHhccC-CeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC-CeeEEEEEcccc
Q 017842          291 VDNARLEQVFSEHG-KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD-GRAIRVNVAEDR  359 (365)
Q Consensus       291 ~tee~L~~~F~~~G-~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~-gr~l~V~~a~~~  359 (365)
                      +++++|+++|+.|| .|..|++.++     .+|||||+|.+.++|.+|+..|||..++ |++|+|.|++++
T Consensus       132 ~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          132 VSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             CCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             CCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            99999999999999 9999999754     2799999999999999999999999999 999999999864

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.97  E-value=1.9e-29  Score=233.24  Aligned_cols=157  Identities=34%  Similarity=0.460  Sum_probs=142.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++|+++|+.+|+.||.|..+.+                          .      +++|||||.|.+
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i--------------------------~------~~kg~afV~f~~   67 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI--------------------------N------RDRGFGFIRLES   67 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEE--------------------------E------TTTTEEEEECSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEE--------------------------e------CCCcEEEEEECC
Confidence            35679999999999999999999999999988763                          2      458999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE  316 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~  316 (365)
                      .++|.+|+..|||..|.|+.|+|.++.+              +++|||+|||+.+|+++|+++|+.||.|..|+|+++ .
T Consensus        68 ~~~A~~A~~~l~g~~i~g~~l~v~~a~~--------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~  132 (261)
T 3sde_A           68 RTLAEIAKAELDGTILKSRPLRIRFATH--------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-D  132 (261)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEEECCC--------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-T
T ss_pred             HHHHHHHHHHcCCcEECCceeEeeeccc--------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-C
Confidence            9999999999999999999999998864              348999999999999999999999999999999999 5


Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHhCC-CccC---CeeEEEEEccccc
Q 017842          317 TGRSRGFGFVTMSSETELNDAIAALDG-QNLD---GRAIRVNVAEDRQ  360 (365)
Q Consensus       317 ~~~~kG~afV~F~s~~~a~~Al~~l~~-~~l~---gr~l~V~~a~~~~  360 (365)
                      +|+++|||||+|.+.++|.+|+..||+ ..+.   ||+|+|.++....
T Consensus       133 ~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          133 RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             TSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             CCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            899999999999999999999999955 4444   9999999998654

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.97  E-value=1.6e-29  Score=236.87  Aligned_cols=162  Identities=15%  Similarity=0.276  Sum_probs=137.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .+...++|||+|||+++++++|+.+|+.||.|..+.                          ++.+...  ++|||||+|
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~--~~g~afV~f   88 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVD--------------------------VADSLKK--NFRFARIEF   88 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTS--SSEEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEECCCC--CcEEEEEEE
Confidence            445688999999999999999999999999999887                          5554433  589999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccC-CeEEEEEEe
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHG-KVVNARVVY  313 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G-~V~~v~i~~  313 (365)
                      .+.++|.+|+. ++|..+.|+.|.|.++.               .++|||+|||+.+++++|+++|+.|| .|..|+|++
T Consensus        89 ~~~~~A~~A~~-~~~~~~~g~~i~v~~~~---------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~  152 (292)
T 2ghp_A           89 ARYDGALAAIT-KTHKVVGQNEIIVSHLT---------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPS  152 (292)
T ss_dssp             SSHHHHHHHHT-TTTCEETTEECEEEECC---------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-
T ss_pred             CCHHHHHHHHH-hCCcEeCCcEEEEEECC---------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEe
Confidence            99999999996 79999999999999763               34999999999999999999999999 999999998


Q ss_pred             eCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccccc
Q 017842          314 DRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR  361 (365)
Q Consensus       314 d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~  361 (365)
                      +.. |.++|||||+|.+.++|.+|+..|+|..+.|++|+|.|+.++.+
T Consensus       153 ~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  199 (292)
T 2ghp_A          153 LRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK  199 (292)
T ss_dssp             -------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC--
T ss_pred             CCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcc
Confidence            865 78899999999999999999999999999999999999987654

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.91  E-value=1.1e-23  Score=179.82  Aligned_cols=144  Identities=27%  Similarity=0.362  Sum_probs=114.6

Q ss_pred             EEecCCCCCccceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecCCC-----CCCCCCCCCcCCCCceEEEeCCCCcC
Q 017842          217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR-----GTQPERAPRVFEPGFRIYVGNLPWEV  291 (365)
Q Consensus       217 ~~~~~~~~~~~g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~-----~~~~~~~~~~~~~~~~lfV~nLp~~~  291 (365)
                      ++.+..  .++|||||+|.+.++|.+|+..+++....+..+.+......     ............+.++|||+|||+.+
T Consensus         5 l~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~   82 (158)
T 2kn4_A            5 LILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRT   82 (158)
T ss_dssp             EEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTC
T ss_pred             EEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCCC
Confidence            444543  68999999999999999999988864433333333222111     00111122233456799999999999


Q ss_pred             cHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccccC
Q 017842          292 DNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR  362 (365)
Q Consensus       292 tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~~  362 (365)
                      ++++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|+..|||..|.|++|+|.||+++..+
T Consensus        83 ~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  153 (158)
T 2kn4_A           83 SPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  153 (158)
T ss_dssp             CHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCC
T ss_pred             CHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            99999999999999999999999989999999999999999999999999999999999999999977544

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.89  E-value=1.1e-22  Score=172.26  Aligned_cols=133  Identities=25%  Similarity=0.370  Sum_probs=115.6

Q ss_pred             CCCccceEEEEeCCHHHHHHHHHHH-ccCcccCeeEEEeecCCCCC--------CCCCCCCcCCCCceEEEeCCCCcCcH
Q 017842          223 TDRSRGFGFVTMSTVEEAEKAVEMF-HRYDIDGRLLTVNKAAPRGT--------QPERAPRVFEPGFRIYVGNLPWEVDN  293 (365)
Q Consensus       223 ~~~~~g~afV~f~~~e~a~~Al~~l-ng~~~~gr~l~V~~a~~~~~--------~~~~~~~~~~~~~~lfV~nLp~~~te  293 (365)
                      ....+|+++|+|.+.++|.+|+..+ ||..++| .|+++.+.....        ..........+.++|||+|||+.+++
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~   87 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNK   87 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSC
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCH
Confidence            4467899999999999999999999 9999999 999998765321        11122334456679999999999999


Q ss_pred             HHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccccc
Q 017842          294 ARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR  361 (365)
Q Consensus       294 e~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~  361 (365)
                      ++|+++|+.||.|..|+|+++     ++|||||+|.+.++|.+|+..|||..+.|++|+|.|+.++.+
T Consensus        88 ~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~r  150 (150)
T 2i2y_A           88 TELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEKR  150 (150)
T ss_dssp             HHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCCC
T ss_pred             HHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCCC
Confidence            999999999999999999876     589999999999999999999999999999999999988754

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.86  E-value=7.5e-22  Score=159.69  Aligned_cols=110  Identities=23%  Similarity=0.351  Sum_probs=73.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||||||+++++++|+++|+.||.|..++                          ++.+.  +.++|||||+|.+.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~--------------------------i~~d~--~~~kg~afV~f~~~   55 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCK--------------------------VVCDE--NGSKGYGFVHFETQ   55 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEEET--TEEEEEEEEEESCH
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEE--------------------------EeecC--CCCCceEEEEECCH
Confidence            457899999999999999999999999999887                          55553  45799999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHH
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNAR  295 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~  295 (365)
                      ++|.+|+..|+|..|+|+.|+|.++.++..+...........++|||+|||+.+|++.
T Consensus        56 ~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           56 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEEESSCCCC----------------------------
T ss_pred             HHHHHHHHHcCCCEECCEEEEEEECCCccccccccccccCCCCceEeCCCCCCccccc
Confidence            9999999999999999999999999877655444333444456899999999999863

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.85  E-value=3.6e-21  Score=151.52  Aligned_cols=83  Identities=30%  Similarity=0.556  Sum_probs=79.1

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ...+++|||+|||+.+|+++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|+..|||..|.||+|+|.|
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34467999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 017842          356 AED  358 (365)
Q Consensus       356 a~~  358 (365)
                      |+|
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            975

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.82  E-value=7.6e-21  Score=147.27  Aligned_cols=84  Identities=19%  Similarity=0.383  Sum_probs=78.4

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccC-CeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC-CCccCCeeEEEEEcc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHG-KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD-GQNLDGRAIRVNVAE  357 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G-~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~-~~~l~gr~l~V~~a~  357 (365)
                      ++|||+|||+.+|+++|+++|+.|| .|..|+|++++.+|.++|||||+|.+.++|.+||..|+ +..++||+|+|.||.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            4899999999999999999999999 89999999999999999999999999999999999774 567999999999999


Q ss_pred             ccccCC
Q 017842          358 DRQRRS  363 (365)
Q Consensus       358 ~~~~~~  363 (365)
                      ++++..
T Consensus        82 ~~~~~~   87 (91)
T 2lxi_A           82 PKPKIN   87 (91)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            888753

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.82  E-value=1.8e-20  Score=156.01  Aligned_cols=127  Identities=28%  Similarity=0.359  Sum_probs=84.3

Q ss_pred             ceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeE
Q 017842          228 GFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVV  307 (365)
Q Consensus       228 g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~  307 (365)
                      -++|++|.+...+..|+..++|....|+.- +...        ..+....+.++|||+|||+.+++++|+++|+.||.|.
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~--------~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~   75 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYG--------RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVG   75 (135)
T ss_dssp             -------------------------------CCSC--------CSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCS
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCCC-CCcC--------CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE
Confidence            467889999999999999988877666542 1111        1223334567999999999999999999999999999


Q ss_pred             EEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccccCC
Q 017842          308 NARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRS  363 (365)
Q Consensus       308 ~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~~~  363 (365)
                      .|+|++++.+++++|||||+|.+.++|.+|+..|||..|.|++|+|.|++++..+.
T Consensus        76 ~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~~  131 (135)
T 2lea_A           76 DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD  131 (135)
T ss_dssp             EEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCCT
T ss_pred             EEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCCc
Confidence            99999998899999999999999999999999999999999999999999776543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.81  E-value=8.9e-20  Score=146.33  Aligned_cols=84  Identities=17%  Similarity=0.211  Sum_probs=79.7

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|++|+.+++++|||||+|.+.++|.+|+..|||..|.||+|+|.+|
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34569999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 017842          357 EDRQ  360 (365)
Q Consensus       357 ~~~~  360 (365)
                      ....
T Consensus        84 ~~~~   87 (110)
T 3s8s_A           84 IKGQ   87 (110)
T ss_dssp             STTH
T ss_pred             CCCc
Confidence            7654

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.81  E-value=1.8e-19  Score=136.49  Aligned_cols=82  Identities=34%  Similarity=0.731  Sum_probs=79.2

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      ++|||+|||+.+++++|+++|+.||.|..|++++++.+++++|||||+|.+.++|.+|+..|||..+.|++|+|.||.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cc
Q 017842          360 QR  361 (365)
Q Consensus       360 ~~  361 (365)
                      .+
T Consensus        82 ~~   83 (83)
T 3md1_A           82 EH   83 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.81  E-value=1.7e-19  Score=137.81  Aligned_cols=83  Identities=37%  Similarity=0.671  Sum_probs=77.2

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +.++|||+|||+.+++++|+++|+.||.|..|++++++.++.++|||||+|.+.++|.+|+..|||..+.|++|+|.||+
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            45699999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             ccc
Q 017842          358 DRQ  360 (365)
Q Consensus       358 ~~~  360 (365)
                      +++
T Consensus        85 ~kp   87 (87)
T 3bs9_A           85 RKP   87 (87)
T ss_dssp             ---
T ss_pred             CCC
Confidence            764

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.81  E-value=1.5e-19  Score=155.40  Aligned_cols=130  Identities=19%  Similarity=0.337  Sum_probs=81.5

Q ss_pred             EEeCCHHHHHHHHHHHccCccc--CeeEEEeecCCCCC-----------C-CCCCCCcCCCCceEEEeCCCCcCcHHHHH
Q 017842          232 VTMSTVEEAEKAVEMFHRYDID--GRLLTVNKAAPRGT-----------Q-PERAPRVFEPGFRIYVGNLPWEVDNARLE  297 (365)
Q Consensus       232 V~f~~~e~a~~Al~~lng~~~~--gr~l~V~~a~~~~~-----------~-~~~~~~~~~~~~~lfV~nLp~~~tee~L~  297 (365)
                      .+|.+.+++..|+..+++....  |+.+.+........           . ....+....++++|||+|||+.+++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            6889999999999998887664  77776654322110           0 11123344556799999999999999999


Q ss_pred             HHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccccc
Q 017842          298 QVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR  361 (365)
Q Consensus       298 ~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~  361 (365)
                      .+|+.||.|..|.|++++.+|.++|||||+|.+..+|.+||..|||..|.|++|+|.||.++..
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            9999999999999999999999999999999999999999999999999999999999987654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.80  E-value=3.6e-20  Score=144.62  Aligned_cols=80  Identities=26%  Similarity=0.396  Sum_probs=75.3

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCC--eEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCC----ccCCeeEE
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGK--VVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQ----NLDGRAIR  352 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~--V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~----~l~gr~l~  352 (365)
                      -.+|||+|||+.+|+++|+++|+.||.  |..|+|++|+.+|+++|||||+|.+.++|.+|++.|||.    .++||+|+
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~   88 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIG   88 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEE
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEE
Confidence            349999999999999999999999995  679999999999999999999999999999999999997    48999999


Q ss_pred             EEEccc
Q 017842          353 VNVAED  358 (365)
Q Consensus       353 V~~a~~  358 (365)
                      |.||++
T Consensus        89 V~~Aks   94 (95)
T 2lkz_A           89 VDFAKS   94 (95)
T ss_dssp             EEECCC
T ss_pred             EEEccC
Confidence            999985

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=3.4e-19  Score=138.57  Aligned_cols=86  Identities=33%  Similarity=0.596  Sum_probs=81.8

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +.++|||+|||+.+++++|+++|+.||.|..|+|.+++.+++++|||||+|.+.++|.+|+..|||..+.|++|+|.|+.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   83 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            45699999999999999999999999999999999999899999999999999999999999999999999999999999


Q ss_pred             ccccCC
Q 017842          358 DRQRRS  363 (365)
Q Consensus       358 ~~~~~~  363 (365)
                      ++...+
T Consensus        84 ~~~~~~   89 (95)
T 2dnz_A           84 ERLDGG   89 (95)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            887654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3.6e-19  Score=141.38  Aligned_cols=87  Identities=26%  Similarity=0.412  Sum_probs=81.9

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...++++|||+|||+.+++++|+++|+.||.|..|+|++++.+|.++|||||+|.+.++|.+|+..|||..+.|++|+|.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            34456799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Ecccccc
Q 017842          355 VAEDRQR  361 (365)
Q Consensus       355 ~a~~~~~  361 (365)
                      ||.+++.
T Consensus        99 ~a~~~~~  105 (106)
T 1p27_B           99 WCFVRGP  105 (106)
T ss_dssp             ESEESSC
T ss_pred             eecCCCC
Confidence            9988764

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=4.5e-19  Score=140.12  Aligned_cols=88  Identities=24%  Similarity=0.405  Sum_probs=83.1

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|++++.++.++|||||+|.+.++|.+|+..|||..|.|++|+|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            44567999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ccccccCC
Q 017842          356 AEDRQRRS  363 (365)
Q Consensus       356 a~~~~~~~  363 (365)
                      +.++.++.
T Consensus        92 a~~~~~~~   99 (103)
T 2cq0_A           92 AKPSTNSG   99 (103)
T ss_dssp             SSCCCCSC
T ss_pred             CCCCCCCC
Confidence            99887654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=7.5e-19  Score=138.05  Aligned_cols=87  Identities=22%  Similarity=0.531  Sum_probs=81.4

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|++++ +++++|||||+|.+.++|.+|+..|||..+.|++|+|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34456799999999999999999999999999999999997 89999999999999999999999999999999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      |+++++.+
T Consensus        92 ~a~~~~~~   99 (100)
T 2do4_A           92 ISNSGPSS   99 (100)
T ss_dssp             ECCCCSCC
T ss_pred             ECCCCCCC
Confidence            99988764

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.79  E-value=6.5e-19  Score=142.07  Aligned_cols=87  Identities=26%  Similarity=0.484  Sum_probs=82.0

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..|||..|.|++|+|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ccccccC
Q 017842          356 AEDRQRR  362 (365)
Q Consensus       356 a~~~~~~  362 (365)
                      ++++..+
T Consensus       102 a~~~~~~  108 (115)
T 2cpz_A          102 KRSKNDS  108 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCcC
Confidence            9987654

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.79  E-value=6.8e-20  Score=141.43  Aligned_cols=83  Identities=23%  Similarity=0.485  Sum_probs=73.1

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccC--CeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHG--KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G--~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      .+|||+|||+.+++++|+++|+.||  .|..|+|++++.+|+++|||||+|.+.++|.+|+..|||..+.||+|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4899999999999999999999999  99999999999999999999999999999999999999999999999999999


Q ss_pred             ccccC
Q 017842          358 DRQRR  362 (365)
Q Consensus       358 ~~~~~  362 (365)
                      +.+.+
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            87654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=6.9e-19  Score=138.01  Aligned_cols=86  Identities=30%  Similarity=0.627  Sum_probs=80.8

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+. |++..|.|++|+|.++
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEEC
Confidence            445699999999999999999999999999999999999999999999999999999999999 9999999999999999


Q ss_pred             cccccCC
Q 017842          357 EDRQRRS  363 (365)
Q Consensus       357 ~~~~~~~  363 (365)
                      .++..++
T Consensus        87 ~~~~~~~   93 (99)
T 2dgs_A           87 EPRDSKS   93 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCcccC
Confidence            9877543

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.79  E-value=4.7e-19  Score=138.24  Aligned_cols=84  Identities=24%  Similarity=0.571  Sum_probs=80.1

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      |.++|||+|||+.+++++|+++|+.||.|..|+|.+++.+|+++|||||+|.+.++|.+|+..|||..++|+.|+|.||.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            34699999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 017842          358 DRQR  361 (365)
Q Consensus       358 ~~~~  361 (365)
                      ++..
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            8764

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.79  E-value=1.1e-19  Score=143.27  Aligned_cols=83  Identities=31%  Similarity=0.446  Sum_probs=79.4

Q ss_pred             CceEEEeCCCC------cCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC-eeE
Q 017842          279 GFRIYVGNLPW------EVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDG-RAI  351 (365)
Q Consensus       279 ~~~lfV~nLp~------~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g-r~l  351 (365)
                      .++|||+|||+      .+++++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|+..|||..|.| |+|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            45999999999      99999999999999999999999999999999999999999999999999999999999 999


Q ss_pred             EEEEcccccc
Q 017842          352 RVNVAEDRQR  361 (365)
Q Consensus       352 ~V~~a~~~~~  361 (365)
                      +|.+|.++.+
T Consensus        86 ~V~~a~~~~~   95 (100)
T 3ns6_A           86 FLYTMKDVER   95 (100)
T ss_dssp             EEEESHHHHH
T ss_pred             EEEECchhhh
Confidence            9999987654

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.79  E-value=5.2e-19  Score=139.12  Aligned_cols=81  Identities=30%  Similarity=0.558  Sum_probs=76.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++|+++|+++|++||.|..++                          +++++.+|+++|||||+|.+.
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~--------------------------i~~d~~tg~~kG~afV~f~~~   71 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAK--------------------------LIRDKVAGHSLGYGFVNYVTA   71 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------EEECSSSCCEEEEEEEEESSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeE--------------------------eeecCCCCcccccEEEEECCH
Confidence            467999999999999999999999999999887                          788888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      ++|.+|+..|||..|+|+.|+|.++.|
T Consensus        72 ~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           72 KDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             HHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            999999999999999999999999875

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=7.6e-19  Score=139.23  Aligned_cols=88  Identities=35%  Similarity=0.516  Sum_probs=82.7

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..|||..|.|++|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34456799999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      ||.++.+.
T Consensus        91 ~a~~~~~~   98 (105)
T 1x5u_A           91 KASAHNKN   98 (105)
T ss_dssp             ETTTTSCC
T ss_pred             ECCCCCcC
Confidence            99987764

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=6.7e-19  Score=138.02  Aligned_cols=86  Identities=28%  Similarity=0.416  Sum_probs=81.4

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..|||..+.|++|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            34569999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cccccC
Q 017842          357 EDRQRR  362 (365)
Q Consensus       357 ~~~~~~  362 (365)
                      .++..+
T Consensus        86 ~~~~~~   91 (99)
T 1whw_A           86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCccc
Confidence            987754

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.79  E-value=1.4e-18  Score=140.03  Aligned_cols=88  Identities=34%  Similarity=0.601  Sum_probs=82.3

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|++++.++.++|||||+|.+.++|.+||..|||..|.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34456799999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      |+.++..+
T Consensus        91 ~a~~~~~~   98 (115)
T 2dgo_A           91 WATRKPPA   98 (115)
T ss_dssp             ESSCCCCC
T ss_pred             EccCCCCC
Confidence            99977653

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.79  E-value=5.8e-19  Score=134.27  Aligned_cols=81  Identities=35%  Similarity=0.551  Sum_probs=77.5

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..|||..+.|++|+|.||
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            34569999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             c
Q 017842          357 E  357 (365)
Q Consensus       357 ~  357 (365)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.79  E-value=1.1e-18  Score=139.47  Aligned_cols=87  Identities=31%  Similarity=0.629  Sum_probs=81.8

Q ss_pred             CcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          274 RVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       274 ~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      ....+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|+..|+|..+.|++|+|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456679999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEccccc
Q 017842          354 NVAEDRQ  360 (365)
Q Consensus       354 ~~a~~~~  360 (365)
                      .+++++.
T Consensus       101 ~~a~~k~  107 (108)
T 2jrs_A          101 GHVTERT  107 (108)
T ss_dssp             ECSCSSC
T ss_pred             EEcccCC
Confidence            9998764

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=5.4e-19  Score=138.30  Aligned_cols=86  Identities=23%  Similarity=0.460  Sum_probs=80.2

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCC---CCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE---TGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~---~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      +.++|||+|||+.+++++|+++|+.||.|..|+|.+++.   ++.++|||||+|.+.++|.+|+..|||..|.|++|+|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            456999999999999999999999999999999999876   66899999999999999999999999999999999999


Q ss_pred             EccccccCC
Q 017842          355 VAEDRQRRS  363 (365)
Q Consensus       355 ~a~~~~~~~  363 (365)
                      |++++.++.
T Consensus        84 ~a~~~~~~~   92 (98)
T 2cpf_A           84 ISERATKPA   92 (98)
T ss_dssp             CSSCSSCCC
T ss_pred             EccCCCCCC
Confidence            999877643

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=5.6e-19  Score=139.58  Aligned_cols=88  Identities=33%  Similarity=0.519  Sum_probs=82.1

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|++++.++.++|||||+|.+.++|.+|+..|||..|.|++|+|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34456799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      ||+.+.++
T Consensus        89 ~a~~~~~~   96 (103)
T 2dnm_A           89 VARYGRRD   96 (103)
T ss_dssp             ECSSCCSC
T ss_pred             ECCcCCCC
Confidence            99976553

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=3.7e-19  Score=138.60  Aligned_cols=85  Identities=32%  Similarity=0.542  Sum_probs=81.0

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEE-EEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNA-RVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v-~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      +.++|||+|||+.+++++|+++|+.||.|..| +|++++.++.++|||||+|.+.++|.+|+..|||..+.|++|+|.|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45699999999999999999999999999999 99999899999999999999999999999999999999999999999


Q ss_pred             cccccC
Q 017842          357 EDRQRR  362 (365)
Q Consensus       357 ~~~~~~  362 (365)
                      .++..+
T Consensus        84 ~~~~~~   89 (96)
T 1x5t_A           84 FKKDSK   89 (96)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            987754

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.78  E-value=1.8e-18  Score=137.06  Aligned_cols=86  Identities=26%  Similarity=0.385  Sum_probs=80.4

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC---eeEEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDG---RAIRV  353 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g---r~l~V  353 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|++++ +++++|||||+|.+.++|.+|+..|||..+.|   ++|+|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            456799999999999999999999999999999999997 79999999999999999999999999999988   99999


Q ss_pred             EEccccccCC
Q 017842          354 NVAEDRQRRS  363 (365)
Q Consensus       354 ~~a~~~~~~~  363 (365)
                      .||.++..+.
T Consensus        92 ~~a~~~~~~~  101 (105)
T 2dnh_A           92 KFADTDKESG  101 (105)
T ss_dssp             EESCSSCCCS
T ss_pred             EECccCcccC
Confidence            9999877543

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=1.1e-18  Score=139.55  Aligned_cols=89  Identities=26%  Similarity=0.506  Sum_probs=82.9

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC------CCccCC
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD------GQNLDG  348 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~------~~~l~g  348 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|++++.++.++|||||+|.+.++|.+|+..||      +..|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            34456799999999999999999999999999999999999999999999999999999999999999      999999


Q ss_pred             eeEEEEEccccccCC
Q 017842          349 RAIRVNVAEDRQRRS  363 (365)
Q Consensus       349 r~l~V~~a~~~~~~~  363 (365)
                      ++|+|.|+.++....
T Consensus        91 ~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           91 RQLKVDLAVTRDEAA  105 (111)
T ss_dssp             CEEEEECCCCCCCCC
T ss_pred             EEEEEEECCCCccCC
Confidence            999999999877643

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=6.7e-19  Score=138.77  Aligned_cols=86  Identities=42%  Similarity=0.709  Sum_probs=81.3

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|++++.++.++|||||+|.+.++|.+|+..|||..|.|++|+|.|+
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   89 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   89 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45569999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             cccccC
Q 017842          357 EDRQRR  362 (365)
Q Consensus       357 ~~~~~~  362 (365)
                      +++...
T Consensus        90 ~~~~~~   95 (102)
T 1x5s_A           90 GKSSDN   95 (102)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            987654

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.78  E-value=7.8e-19  Score=140.41  Aligned_cols=88  Identities=23%  Similarity=0.406  Sum_probs=82.5

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+|.++|||||+|.+.++|.+|+..|||..|.|++|+|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34456799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      ||.++..+
T Consensus       102 ~a~~~~~~  109 (110)
T 1oo0_B          102 WCFVKGPK  109 (110)
T ss_dssp             ESEESSCC
T ss_pred             EcccCCCC
Confidence            99987654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.5e-18  Score=134.88  Aligned_cols=83  Identities=33%  Similarity=0.528  Sum_probs=79.0

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..|||..+.|++|+|.|
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 017842          356 AED  358 (365)
Q Consensus       356 a~~  358 (365)
                      |++
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            875

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=1.6e-18  Score=136.96  Aligned_cols=86  Identities=31%  Similarity=0.657  Sum_probs=80.3

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.|| |..|+|++++.+++++|||||+|.+.++|.+|+ .|||..|.|++|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            345567999999999999999999999997 999999999999999999999999999999999 799999999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      |+.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2dng_A           89 IAEGRKQD   96 (103)
T ss_dssp             ECCCCCCC
T ss_pred             EecCCCCC
Confidence            99987754

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.78  E-value=1e-18  Score=141.17  Aligned_cols=81  Identities=30%  Similarity=0.532  Sum_probs=75.7

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|+|+++.  +.++|||||+|.+.++|.+||..|+|..|.||+|+|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            3489999999999999999999999999999999985  55899999999999999999999999999999999999987


Q ss_pred             ccc
Q 017842          359 RQR  361 (365)
Q Consensus       359 ~~~  361 (365)
                      +..
T Consensus        83 ~~~   85 (115)
T 4f25_A           83 RKE   85 (115)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.78  E-value=1.3e-18  Score=136.44  Aligned_cols=83  Identities=25%  Similarity=0.379  Sum_probs=78.6

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEE--------EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVN--------ARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL  346 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~--------v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l  346 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..        |+|++++.+|+++|||||+|.+.++|.+|+..|||..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3455679999999999999999999999999999        99999999999999999999999999999999999999


Q ss_pred             CCeeEEEEEcc
Q 017842          347 DGRAIRVNVAE  357 (365)
Q Consensus       347 ~gr~l~V~~a~  357 (365)
                      .|++|+|.+|+
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999984

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=4.8e-19  Score=139.62  Aligned_cols=87  Identities=32%  Similarity=0.511  Sum_probs=82.0

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..|||..|.|++|+|.|+
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCC
Q 017842          357 EDRQRRS  363 (365)
Q Consensus       357 ~~~~~~~  363 (365)
                      .++..+.
T Consensus        90 ~~~~~~~   96 (102)
T 2cqb_A           90 KPMRIKE   96 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9877543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=2.1e-18  Score=137.05  Aligned_cols=88  Identities=26%  Similarity=0.479  Sum_probs=81.8

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEee-CCCCCcceEEEEEecCHHHHHHHHHHh-CCCccCCeeEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYD-RETGRSRGFGFVTMSSETELNDAIAAL-DGQNLDGRAIR  352 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d-~~~~~~kG~afV~F~s~~~a~~Al~~l-~~~~l~gr~l~  352 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|+++ +.++.++|||||+|.+.++|.+|+..| |+..|.|++|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3445679999999999999999999999999999999999 788999999999999999999999999 99999999999


Q ss_pred             EEEccccccC
Q 017842          353 VNVAEDRQRR  362 (365)
Q Consensus       353 V~~a~~~~~~  362 (365)
                      |.||.++...
T Consensus        91 v~~a~~~~~~  100 (107)
T 2cph_A           91 LEWADSEVTV  100 (107)
T ss_dssp             EEECCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999987653

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.77  E-value=1.1e-18  Score=138.48  Aligned_cols=87  Identities=29%  Similarity=0.483  Sum_probs=81.5

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc---CCeeEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL---DGRAIR  352 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l---~gr~l~  352 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..|||..+   .|++|+
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            34567999999999999999999999999999999999999999999999999999999999999999987   899999


Q ss_pred             EEEccccccC
Q 017842          353 VNVAEDRQRR  362 (365)
Q Consensus       353 V~~a~~~~~~  362 (365)
                      |.|+.++.+.
T Consensus        90 v~~a~~~~~~   99 (106)
T 2dgp_A           90 VKPADSESRG   99 (106)
T ss_dssp             EEECCCCSCC
T ss_pred             EEECCccccc
Confidence            9999987754

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.5e-18  Score=135.43  Aligned_cols=84  Identities=20%  Similarity=0.311  Sum_probs=78.4

Q ss_pred             CCCceEEEeCCCCcCcHHHHH----HHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLE----QVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR  352 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~----~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~  352 (365)
                      ..+++|||+|||+.+++++|+    ++|+.||.|..|+|++++.+   +|||||+|.+.++|.+|+..|||..+.||+|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            345799999999999999999    99999999999999988765   89999999999999999999999999999999


Q ss_pred             EEEccccccCC
Q 017842          353 VNVAEDRQRRS  363 (365)
Q Consensus       353 V~~a~~~~~~~  363 (365)
                      |.+|++++.++
T Consensus        84 V~~a~~~~~~~   94 (96)
T 2dgx_A           84 VSLATGASGPS   94 (96)
T ss_dssp             EEECCCSSCCC
T ss_pred             EEEcCCCCCCC
Confidence            99999887765

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=2.5e-18  Score=135.78  Aligned_cols=84  Identities=33%  Similarity=0.611  Sum_probs=79.4

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|+++  ++.++|||||+|.+.++|.+|+..|||..|.|++|+|.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             SSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            45679999999999999999999999999999999998  7999999999999999999999999999999999999999


Q ss_pred             cccccC
Q 017842          357 EDRQRR  362 (365)
Q Consensus       357 ~~~~~~  362 (365)
                      .++..+
T Consensus        91 ~~~~~~   96 (103)
T 2d9p_A           91 QRKEER   96 (103)
T ss_dssp             SSCCCC
T ss_pred             cccccC
Confidence            987654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.8e-18  Score=134.11  Aligned_cols=82  Identities=29%  Similarity=0.551  Sum_probs=78.1

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..|||..|.|++|+|.|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q 017842          356 AE  357 (365)
Q Consensus       356 a~  357 (365)
                      |+
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=136.82  Aligned_cols=87  Identities=21%  Similarity=0.406  Sum_probs=81.8

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeE-EEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCee----E
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVV-NARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRA----I  351 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~-~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~----l  351 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|. .|+|++++.+++++|||||+|.+.++|.+|+..|||..+.|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            3456999999999999999999999999999 9999999999999999999999999999999999999999999    9


Q ss_pred             EEEEccccccCC
Q 017842          352 RVNVAEDRQRRS  363 (365)
Q Consensus       352 ~V~~a~~~~~~~  363 (365)
                      +|.||++...++
T Consensus        87 ~v~~a~~~~~~s   98 (99)
T 2div_A           87 KLNYATYSGPSS   98 (99)
T ss_dssp             CEEETTCCSSSC
T ss_pred             EEeecCCCCCCC
Confidence            999999877654

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=2e-18  Score=136.64  Aligned_cols=86  Identities=26%  Similarity=0.554  Sum_probs=80.1

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRET-GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~-~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      ...+.++|||+|||+.+++++|+++|+.|| |..|+|++++.+ ++++|||||+|.+.++|.+|| .||+..|.|++|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            345567999999999999999999999999 999999999887 999999999999999999999 79999999999999


Q ss_pred             EEccccccC
Q 017842          354 NVAEDRQRR  362 (365)
Q Consensus       354 ~~a~~~~~~  362 (365)
                      .++.++..+
T Consensus        89 ~~a~~~~~~   97 (104)
T 1wi8_A           89 DVADQAQDK   97 (104)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCCCCC
Confidence            999987653

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.77  E-value=2.9e-18  Score=132.47  Aligned_cols=85  Identities=29%  Similarity=0.513  Sum_probs=79.3

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|.++  +++++|||||+|.+.++|.+|+..|||..+.|++|+|.|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45679999999999999999999999999999999974  7899999999999999999999999999999999999999


Q ss_pred             cccccCC
Q 017842          357 EDRQRRS  363 (365)
Q Consensus       357 ~~~~~~~  363 (365)
                      +++..++
T Consensus        84 ~~~~~~~   90 (92)
T 2dgv_A           84 RNASGPS   90 (92)
T ss_dssp             SCCSSCC
T ss_pred             CCCCCCC
Confidence            9877654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.7e-18  Score=137.94  Aligned_cols=87  Identities=24%  Similarity=0.370  Sum_probs=81.6

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeE--------EEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVV--------NARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD  347 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~--------~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~  347 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|.        .|+|++++.+++++|||||+|.+.++|.+||..|||..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            34567999999999999999999999999999        6999999999999999999999999999999999999999


Q ss_pred             CeeEEEEEccccccC
Q 017842          348 GRAIRVNVAEDRQRR  362 (365)
Q Consensus       348 gr~l~V~~a~~~~~~  362 (365)
                      |++|+|.+++++...
T Consensus        92 g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           92 GSKLKVSLARKKPPM  106 (113)
T ss_dssp             TEECEEECSSCCCCS
T ss_pred             CCEEEEEECCCCCCC
Confidence            999999999987754

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=8.8e-18  Score=132.64  Aligned_cols=87  Identities=30%  Similarity=0.579  Sum_probs=79.4

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|+++..  .++|||||+|.+.++|.+|+..|||..|.|++|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   88 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            344567999999999999999999999999999999998854  389999999999999999999999999999999999


Q ss_pred             EccccccCC
Q 017842          355 VAEDRQRRS  363 (365)
Q Consensus       355 ~a~~~~~~~  363 (365)
                      |+.++..+.
T Consensus        89 ~a~~~~~~~   97 (103)
T 2cq3_A           89 NATARVMTN   97 (103)
T ss_dssp             ECCSSCCCC
T ss_pred             EcccCCCCC
Confidence            999887643

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.76  E-value=5.4e-18  Score=141.23  Aligned_cols=88  Identities=33%  Similarity=0.550  Sum_probs=82.6

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ....++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..|||..|.|++|+|.|
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34557999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccCC
Q 017842          356 AEDRQRRS  363 (365)
Q Consensus       356 a~~~~~~~  363 (365)
                      |+++.++.
T Consensus       119 a~~~~~~~  126 (139)
T 1u6f_A          119 AASGHQRP  126 (139)
T ss_dssp             SSCCCCCC
T ss_pred             CCCCCCCC
Confidence            99877653

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.76  E-value=2.6e-18  Score=131.45  Aligned_cols=82  Identities=22%  Similarity=0.423  Sum_probs=77.1

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCC-cceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR-SRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~-~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|+|+++..++. ++|||||+|.+.++|.+|+..|||..+.|++|+|.++.
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   83 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVL   83 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECC
Confidence            45999999999999999999999999999999999987665 89999999999999999999999999999999999998


Q ss_pred             ccc
Q 017842          358 DRQ  360 (365)
Q Consensus       358 ~~~  360 (365)
                      +..
T Consensus        84 ~~~   86 (88)
T 4a8x_A           84 APW   86 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=2.8e-18  Score=135.69  Aligned_cols=85  Identities=32%  Similarity=0.585  Sum_probs=79.7

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhc-cCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCc-cCCeeEEEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSE-HGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQN-LDGRAIRVN  354 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~-~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~-l~gr~l~V~  354 (365)
                      .+.++|||+|||+.+++++|+++|+. ||.|..|+|+++. +++++|||||+|.+.++|.+|+..|||.. +.|++|+|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            34569999999999999999999999 9999999999998 89999999999999999999999999999 999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      ++.++..+
T Consensus        86 ~a~~~~~~   93 (104)
T 2dhg_A           86 VAIPKASR   93 (104)
T ss_dssp             BCCCCCSC
T ss_pred             EccCCCcC
Confidence            99876643

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.76  E-value=2.3e-18  Score=142.02  Aligned_cols=86  Identities=31%  Similarity=0.531  Sum_probs=81.2

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||..|||..|.|++|+|.|
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            44567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 017842          356 AEDRQR  361 (365)
Q Consensus       356 a~~~~~  361 (365)
                      +.++..
T Consensus       123 a~~~~p  128 (129)
T 2kxn_B          123 SITKRP  128 (129)
T ss_dssp             CSSSSC
T ss_pred             ecCCCC
Confidence            987653

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=5.3e-18  Score=136.92  Aligned_cols=87  Identities=34%  Similarity=0.541  Sum_probs=80.2

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||..|++ .|.|++|+|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            345567999999999999999999999999999999999999999999999999999999999999898 8999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      ||..+.++
T Consensus        92 ~a~~~~~~   99 (116)
T 2cqd_A           92 LAYLGAKP   99 (116)
T ss_dssp             ESTTTCCC
T ss_pred             EcccCCCc
Confidence            99765443

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.76  E-value=3.1e-18  Score=138.56  Aligned_cols=84  Identities=30%  Similarity=0.595  Sum_probs=79.2

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||+|||+.+++++|+++|+.||.|..|+|.++. ++.++|||||+|.+.++|.+|+..|||..+.|++|+|.|++
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   84 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK   84 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            34599999999999999999999999999999999997 89999999999999999999999999999999999999998


Q ss_pred             ccccC
Q 017842          358 DRQRR  362 (365)
Q Consensus       358 ~~~~~  362 (365)
                      ++...
T Consensus        85 ~~~~~   89 (116)
T 2fy1_A           85 KPSFQ   89 (116)
T ss_dssp             CSSCS
T ss_pred             CCCCC
Confidence            77643

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.76  E-value=4.7e-18  Score=129.93  Aligned_cols=79  Identities=33%  Similarity=0.675  Sum_probs=74.8

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|+. +++..|.|++|+|.+|
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            445699999999999999999999999999999999999999999999999999999999997 6889999999999986

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=9e-19  Score=138.48  Aligned_cols=84  Identities=38%  Similarity=0.742  Sum_probs=79.8

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +.++|||+|||+.+++++|+++|+.||.|..|+|.+++.+|.++|||||+|.+.++|.+|+..|||..+.|++|+|.||.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            34599999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 017842          358 DRQR  361 (365)
Q Consensus       358 ~~~~  361 (365)
                      ++..
T Consensus        87 ~~~~   90 (104)
T 1p1t_A           87 SEKN   90 (104)
T ss_dssp             CTTH
T ss_pred             Cccc
Confidence            7654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=5.6e-18  Score=130.67  Aligned_cols=83  Identities=22%  Similarity=0.369  Sum_probs=78.2

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ...++|||+|||+.+++++|+++|+.| .|..|+|+++ .+|+++|||||+|.+.++|.+|+. |||..|.||.|+|.+|
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            345699999999999999999999999 9999999999 789999999999999999999999 9999999999999999


Q ss_pred             cccccC
Q 017842          357 EDRQRR  362 (365)
Q Consensus       357 ~~~~~~  362 (365)
                      .+++++
T Consensus        85 ~~~~~s   90 (91)
T 2dgw_A           85 KSGPSS   90 (91)
T ss_dssp             SSCCCC
T ss_pred             CcCCCC
Confidence            988764

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.76  E-value=3.8e-18  Score=130.83  Aligned_cols=79  Identities=28%  Similarity=0.526  Sum_probs=76.3

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      ++|||+|||+.+++++|+++|+.||.|..|++++++.+++++|||||+|.+.++|.+|+ .|||..+.|++|+|.+++++
T Consensus         7 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A            7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCC
Confidence            59999999999999999999999999999999999989999999999999999999999 79999999999999999864

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.75  E-value=4e-18  Score=132.44  Aligned_cols=81  Identities=33%  Similarity=0.547  Sum_probs=76.7

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|++++. ++++|||||+|.+.++|.+|+..|||..+.|++|+|.||
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            4456999999999999999999999999999999999975 899999999999999999999999999999999999998


Q ss_pred             cc
Q 017842          357 ED  358 (365)
Q Consensus       357 ~~  358 (365)
                      ++
T Consensus        93 ~~   94 (95)
T 2ywk_A           93 SS   94 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.75  E-value=6.5e-18  Score=134.28  Aligned_cols=83  Identities=31%  Similarity=0.545  Sum_probs=78.3

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|+++. +++++|||||+|.+.++|.+|+..|||..|.|++|+|.
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34566799999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             Eccc
Q 017842          355 VAED  358 (365)
Q Consensus       355 ~a~~  358 (365)
                      ||.+
T Consensus       104 ~a~s  107 (107)
T 3ulh_A          104 LVTS  107 (107)
T ss_dssp             EECC
T ss_pred             EeCC
Confidence            9863

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.75  E-value=3.9e-18  Score=139.68  Aligned_cols=88  Identities=26%  Similarity=0.404  Sum_probs=82.0

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+.+|+.||.|..|.|+++..++.++|||||+|.+.++|.+|+..|||..|.|+.|+|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34456799999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      ||.++..+
T Consensus        98 ~a~~~~~~  105 (126)
T 3ex7_B           98 WCFVRGPP  105 (126)
T ss_dssp             ESEESSSC
T ss_pred             EecCCCCC
Confidence            99876643

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.1e-17  Score=131.97  Aligned_cols=85  Identities=24%  Similarity=0.424  Sum_probs=77.9

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|++++.  .++|||||+|.+.++|.+|+..|||..|.|++|+|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            34567999999999999999999999999999999999854  3689999999999999999999999999999999999


Q ss_pred             ccccccC
Q 017842          356 AEDRQRR  362 (365)
Q Consensus       356 a~~~~~~  362 (365)
                      +.++..+
T Consensus        90 a~~~~~~   96 (103)
T 2cqi_A           90 ATTPSSQ   96 (103)
T ss_dssp             CCCTTCC
T ss_pred             CCCCccc
Confidence            9977654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.75  E-value=1e-17  Score=136.85  Aligned_cols=87  Identities=30%  Similarity=0.505  Sum_probs=81.5

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|+++. +|+++|||||+|.+.++|.+|+..|||..+.|++|+|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            44567899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      ||......
T Consensus       110 ~a~~~~~~  117 (124)
T 2kt5_A          110 LVASQIDL  117 (124)
T ss_dssp             EECCTTCC
T ss_pred             EeCCCCCC
Confidence            99876654

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.75  E-value=3.4e-18  Score=145.62  Aligned_cols=81  Identities=28%  Similarity=0.532  Sum_probs=77.6

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccC--CeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHG--KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G--~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .++|||+|||+.+++++|+++|+.||  .|..|+|++|+.+|+++|||||+|.+.++|.+||..|||..|.||+|+|.+|
T Consensus        55 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a  134 (156)
T 3n9u_C           55 RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA  134 (156)
T ss_dssp             -CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEc
Confidence            45999999999999999999999999  9999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 017842          357 EDR  359 (365)
Q Consensus       357 ~~~  359 (365)
                      .++
T Consensus       135 ~~~  137 (156)
T 3n9u_C          135 TRQ  137 (156)
T ss_dssp             CHH
T ss_pred             CCC
Confidence            764

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=3e-18  Score=134.03  Aligned_cols=85  Identities=18%  Similarity=0.240  Sum_probs=79.4

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ....++|||+|||+.+++++|+++|..||.|..+++++++.+++++|||||+|.+.++|.+|+..|||..|.||+|+|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            34457999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 017842          356 AEDRQ  360 (365)
Q Consensus       356 a~~~~  360 (365)
                      +..+.
T Consensus        92 a~~~~   96 (98)
T 2cqp_A           92 GSGPS   96 (98)
T ss_dssp             SSCSS
T ss_pred             cCCCC
Confidence            98654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.75  E-value=2.8e-18  Score=138.90  Aligned_cols=82  Identities=27%  Similarity=0.509  Sum_probs=77.7

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..|||..+.|++|+|.|
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            44567999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cc
Q 017842          356 AE  357 (365)
Q Consensus       356 a~  357 (365)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            85

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.75  E-value=6e-18  Score=135.59  Aligned_cols=84  Identities=18%  Similarity=0.227  Sum_probs=78.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +++.++|||+|||+++++++|+++|++||.|..+.                          ++++..+++++|||||+|.
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~--------------------------i~~d~~tg~~rG~aFV~f~   56 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVE--------------------------ILLHPRTRKHLGLARVLFT   56 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEE--------------------------EEECTTTCCEEEEEEEEES
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEE--------------------------EEECCCCCceeeEEEEEEC
Confidence            34678999999999999999999999999999988                          8888899999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      +.++|.+|+..|||..|.|+.|+|.++...
T Consensus        57 ~~~~A~~Ai~~lng~~~~gr~i~V~~a~~~   86 (110)
T 3s8s_A           57 STRGAKETVKNLHLTSVMGNIIHAQLDIKG   86 (110)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEECSTT
T ss_pred             CHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            999999999999999999999999988644

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.75  E-value=1.3e-18  Score=143.80  Aligned_cols=86  Identities=23%  Similarity=0.349  Sum_probs=80.4

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEE--EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCC----ccCC
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVN--ARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQ----NLDG  348 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~--v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~----~l~g  348 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..  |+|++|+.+|+++|||||+|.+. +|.+|+..|||.    .+.|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3455679999999999999999999999999977  99999999999999999999999 999999999999    9999


Q ss_pred             eeEEEEEcccccc
Q 017842          349 RAIRVNVAEDRQR  361 (365)
Q Consensus       349 r~l~V~~a~~~~~  361 (365)
                      |+|+|.||+++.+
T Consensus        98 r~l~V~~a~~~~~  110 (131)
T 2m2b_A           98 KTINVEFAKGSKR  110 (131)
T ss_dssp             CCCCCEECCCSCC
T ss_pred             EEEEEEECCCCCC
Confidence            9999999988754

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=1.3e-17  Score=134.06  Aligned_cols=84  Identities=36%  Similarity=0.542  Sum_probs=78.2

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|..||.|..|+|++++ +++++|||||+|.+.++|.+|+..|||..|.|++|+|.|+
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            456799999999999999999999999999999999997 5999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 017842          357 EDRQR  361 (365)
Q Consensus       357 ~~~~~  361 (365)
                      +....
T Consensus        92 ~~~~~   96 (114)
T 2do0_A           92 ERALP   96 (114)
T ss_dssp             SCCCC
T ss_pred             ccCCC
Confidence            75443

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=3.7e-18  Score=135.29  Aligned_cols=87  Identities=30%  Similarity=0.525  Sum_probs=81.2

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||.. ++..|.|++|+|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            345567999999999999999999999999999999999999999999999999999999999997 9999999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      ++.++...
T Consensus        91 ~a~~~~~~   98 (105)
T 2dh8_A           91 PCTPRGMQ   98 (105)
T ss_dssp             CSCCSSCC
T ss_pred             EccCCCCC
Confidence            99987654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=3e-18  Score=135.74  Aligned_cols=79  Identities=15%  Similarity=0.267  Sum_probs=74.9

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||+|||+.+|+++|+++|+.||.|..|+|++++. |+++|||||+|.+.++|.+|+. ++|..+.|+.|+|.++.
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            345999999999999999999999999999999999987 9999999999999999999999 99999999999999876


Q ss_pred             c
Q 017842          358 D  358 (365)
Q Consensus       358 ~  358 (365)
                      +
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            5

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.74  E-value=5.4e-18  Score=133.35  Aligned_cols=98  Identities=23%  Similarity=0.270  Sum_probs=82.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      ++|||+|||+++++++|+.+|++||.|..+.                          +..+     ++|||||+|.+.++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~-----~~g~afV~f~~~~~   49 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVW--------------------------IARN-----PPGFAFVEFEDPRD   49 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEE--------------------------EESS-----SSSEEEEECSSHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EeeC-----CCCEEEEEECCHHH
Confidence            4899999999999999999999999998887                          4433     78999999999999


Q ss_pred             HHHHHHHHccCcccCeeEEEeecCCCCCCCCCC--CCcCCCCceEEEeCCC
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERA--PRVFEPGFRIYVGNLP  288 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~--~~~~~~~~~lfV~nLp  288 (365)
                      |.+|+..|+|..+.|+.|+|.++.++.......  +.......+||||||+
T Consensus        50 a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           50 AEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             HHHHHHHHHHSCSSSCCCEEEESSSCCCSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             HHHHHHHHCCCeECCcEEEEEEccCCCCcccCCCCCccccCCCceecCCCC
Confidence            999999999999999999999998776443222  2222335689999997

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.74  E-value=1.3e-18  Score=136.87  Aligned_cols=84  Identities=27%  Similarity=0.572  Sum_probs=76.4

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeC-CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR-ETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~-~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ....++|||+|||+.+++++|+++|+.|| |..|+|++++ .+|+++|||||+|.+.++|.+|+ .|||..|.|+.|+|.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            34567999999999999999999999999 9999999998 68999999999999999999999 799999999999999


Q ss_pred             Ecccccc
Q 017842          355 VAEDRQR  361 (365)
Q Consensus       355 ~a~~~~~  361 (365)
                      +|+++.+
T Consensus        94 ~a~~~~~  100 (100)
T 2j76_E           94 VADQAQD  100 (100)
T ss_dssp             ECCCSCC
T ss_pred             eccCCCC
Confidence            9988753

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3.8e-18  Score=135.02  Aligned_cols=80  Identities=20%  Similarity=0.329  Sum_probs=72.9

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCC--CccCCeeEEEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDG--QNLDGRAIRVN  354 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~--~~l~gr~l~V~  354 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|+++      ||||||+|.+.++|.+|+..|++  ..|.||+|+|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            34569999999999999999999999999999999865      79999999999999999998864  78999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      ||+.+...
T Consensus        88 ~A~~~~~~   95 (105)
T 1sjq_A           88 FSNHKELK   95 (105)
T ss_dssp             CCSSSSCC
T ss_pred             EcCCCCCC
Confidence            99987654

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.74  E-value=2.5e-18  Score=133.60  Aligned_cols=81  Identities=19%  Similarity=0.265  Sum_probs=76.3

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +.++|||+|||+.+++++|+++|+.||.|..+++++++.+++++|||||+|.+.++|.+|+..|||..|.||+|+|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            45699999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             c
Q 017842          358 D  358 (365)
Q Consensus       358 ~  358 (365)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            4

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.74  E-value=1.4e-17  Score=141.64  Aligned_cols=87  Identities=24%  Similarity=0.435  Sum_probs=81.8

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|++++.++.++|||||+|.+.++|.+||..||+..|.|++|+|.||
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45579999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCC
Q 017842          357 EDRQRRS  363 (365)
Q Consensus       357 ~~~~~~~  363 (365)
                      .++....
T Consensus       117 ~~~~~~~  123 (156)
T 1h2v_Z          117 AGFKEGR  123 (156)
T ss_dssp             SCCCTTC
T ss_pred             CCCCCcC
Confidence            8766543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.74  E-value=5.2e-18  Score=135.70  Aligned_cols=86  Identities=31%  Similarity=0.577  Sum_probs=77.6

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|+..+ |..|+|+.|+|.+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            345579999999999999999999999999999999999999999999999999999999999965 6999999999999


Q ss_pred             ccccccC
Q 017842          356 AEDRQRR  362 (365)
Q Consensus       356 a~~~~~~  362 (365)
                      +.++..+
T Consensus       101 a~~~~~~  107 (109)
T 2rs2_A          101 AFPRRAQ  107 (109)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9987654

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=2.3e-17  Score=130.23  Aligned_cols=85  Identities=27%  Similarity=0.495  Sum_probs=78.9

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||.  ++..|.|++|+|.|
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            3455699999999999999999999999999999999999999999999999999999999999  57899999999999


Q ss_pred             ccccccC
Q 017842          356 AEDRQRR  362 (365)
Q Consensus       356 a~~~~~~  362 (365)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cqg_A           90 PNSKQSQ   96 (103)
T ss_dssp             CCTTCCC
T ss_pred             cCCCCcC
Confidence            9987653

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=2.2e-17  Score=131.80  Aligned_cols=85  Identities=27%  Similarity=0.454  Sum_probs=77.4

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|..+   +.++|||||+|.+.++|.+|+..||+..|.|++|+|.|
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            345679999999999999999999999999999999654   56899999999999999999999999999999999999


Q ss_pred             ccccccCC
Q 017842          356 AEDRQRRS  363 (365)
Q Consensus       356 a~~~~~~~  363 (365)
                      ++++.++.
T Consensus        96 a~~~~~~~  103 (109)
T 1x4a_A           96 PRSGRGTG  103 (109)
T ss_dssp             CCCCCCCC
T ss_pred             cccCCCCC
Confidence            99877643

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.74  E-value=2.8e-18  Score=132.77  Aligned_cols=83  Identities=20%  Similarity=0.410  Sum_probs=75.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccC-CeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAG-TVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G-~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      .++|||+|||+++|+++|+++|++|| .|..++                          +++++.+++++|||||+|.+.
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~--------------------------i~~d~~t~~~rg~aFV~F~~~   54 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVR--------------------------LMRNKSSGQSRGFAFVEFSHL   54 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCC--------------------------SSSCSSSCCCSSEEEEECSSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEE--------------------------EEecCCCCCcCceEEEEecCH
Confidence            36899999999999999999999999 788776                          788888999999999999999


Q ss_pred             HHHHHHHHHH-ccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMF-HRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~l-ng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|.+|+..+ ++..++|+.|+|.++.++..
T Consensus        55 ~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~~   85 (91)
T 2lxi_A           55 QDATRWMEANQHSLNILGQKVSMHYSDPKPK   85 (91)
T ss_dssp             HHHHHHHHTTTTEEEETTEEEEEECCCSCCC
T ss_pred             HHHHHHHHhcCCCeEECCEEEEEEEcCCCCC
Confidence            9999999876 56789999999999987654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.74  E-value=2.5e-18  Score=140.46  Aligned_cols=82  Identities=23%  Similarity=0.491  Sum_probs=78.0

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|+|++++.++.++|||||+|.+.++|.+|+ .|||..|.|++|+|.+++.
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            469999999999999999999999999999999999999999999999999999999999 6999999999999999986


Q ss_pred             ccc
Q 017842          359 RQR  361 (365)
Q Consensus       359 ~~~  361 (365)
                      ...
T Consensus       115 ~~~  117 (124)
T 2jwn_A          115 NMP  117 (124)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            554

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.74  E-value=2.7e-18  Score=127.50  Aligned_cols=75  Identities=29%  Similarity=0.570  Sum_probs=72.6

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      +|||+|||+.+++++|+++|+.||.|..|++++++.+++++|||||+|.+.++|.+|+. |||..++|++|+|.+|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            59999999999999999999999999999999998899999999999999999999998 9999999999999986

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=7.1e-18  Score=134.52  Aligned_cols=84  Identities=23%  Similarity=0.296  Sum_probs=78.5

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCC-eEEEEEE-eeCCCCCcceEEEEEecCHHHHHHHHHHhC--CCccCCeeEEE
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGK-VVNARVV-YDRETGRSRGFGFVTMSSETELNDAIAALD--GQNLDGRAIRV  353 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~-V~~v~i~-~d~~~~~~kG~afV~F~s~~~a~~Al~~l~--~~~l~gr~l~V  353 (365)
                      +.++|||+|||+.+++++|+++|..||. |..|+|+ ++..+++++|||||+|.+.++|.+|+..|+  +..+.|++|+|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V   86 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   86 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEE
Confidence            4569999999999999999999999998 9999998 888889999999999999999999999996  58999999999


Q ss_pred             EEcccccc
Q 017842          354 NVAEDRQR  361 (365)
Q Consensus       354 ~~a~~~~~  361 (365)
                      .||.++..
T Consensus        87 ~~a~~~~~   94 (109)
T 2dis_A           87 DWAEPEID   94 (109)
T ss_dssp             EESCSSCS
T ss_pred             EEcCCCCC
Confidence            99998765

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.73  E-value=9.8e-18  Score=131.36  Aligned_cols=79  Identities=15%  Similarity=0.141  Sum_probs=71.9

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCc--cCCeeEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQN--LDGRAIRV  353 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~--l~gr~l~V  353 (365)
                      ..|+.+|||+|||+.+++++|+++|+.||.|..|++++      .||||||+|.+.++|.+|+..|++..  +.||+|+|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            34566999999999999999999999999999999985      37999999999999999999999885  78999999


Q ss_pred             EEccccc
Q 017842          354 NVAEDRQ  360 (365)
Q Consensus       354 ~~a~~~~  360 (365)
                      +|++.+.
T Consensus        92 ~~S~~k~   98 (100)
T 3r27_A           92 NYSTSQK   98 (100)
T ss_dssp             EECSCSC
T ss_pred             Eeccccc
Confidence            9998763

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.73  E-value=7.8e-18  Score=135.65  Aligned_cols=105  Identities=22%  Similarity=0.375  Sum_probs=92.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+.+|+.||.|..+.                          +..   .+.++|||||+|.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~--------------------------i~~---~~~~~g~afV~f~   55 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIR--------------------------VGN---TPETRGTAYVVYE   55 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------EEC---STTTTTCEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------Eee---CCCCCcEEEEEEC
Confidence            44678999999999999999999999999999887                          443   3456999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGK  305 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~  305 (365)
                      +.++|.+|+..|||..++|+.|+|.++.+....                ++++...++++|.++|+.||.
T Consensus        56 ~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~----------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           56 DIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAF----------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             SHHHHHHHHHHHTTCBSSSCBCEEEECCHHHHT----------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             CHHHHHHHHHHcCCCEECCeEEEEEEecCChhh----------------hhhhHhHhHHHHHHHHHHhCC
Confidence            999999999999999999999999998765432                477888999999999999974

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.73  E-value=8.7e-18  Score=133.38  Aligned_cols=84  Identities=29%  Similarity=0.414  Sum_probs=77.2

Q ss_pred             CCCceEEEeCCCCcC------cHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe-
Q 017842          277 EPGFRIYVGNLPWEV------DNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGR-  349 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~------tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr-  349 (365)
                      ...++|||+|||+.+      ++++|+++|+.||.|..|+|+  +.+|+++|||||+|.+.++|.+|+..|||..|.|| 
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            345699999999999      889999999999999999998  36789999999999999999999999999999999 


Q ss_pred             eEEEEEccccccC
Q 017842          350 AIRVNVAEDRQRR  362 (365)
Q Consensus       350 ~l~V~~a~~~~~~  362 (365)
                      +|+|.+|.+..+-
T Consensus        91 ~l~V~~a~~~~k~  103 (105)
T 2nlw_A           91 TFRVNLFTDFDKY  103 (105)
T ss_dssp             EEEEECSCCCCCC
T ss_pred             eEEEEEcchHhhh
Confidence            9999999877653

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=3.3e-18  Score=137.68  Aligned_cols=82  Identities=29%  Similarity=0.456  Sum_probs=78.2

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|+|++++.++.++|||||+|.+.++|.+|| .|||..|.|+.|+|.++.+
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            469999999999999999999999999999999999999999999999999999999999 8999999999999999987


Q ss_pred             ccc
Q 017842          359 RQR  361 (365)
Q Consensus       359 ~~~  361 (365)
                      +..
T Consensus       104 ~~~  106 (114)
T 2cq4_A          104 EKN  106 (114)
T ss_dssp             HHH
T ss_pred             Ccc
Confidence            654

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=1e-17  Score=132.16  Aligned_cols=79  Identities=15%  Similarity=0.226  Sum_probs=71.7

Q ss_pred             CCCceEEEeCCCC-cCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCC--ccCCeeEEE
Q 017842          277 EPGFRIYVGNLPW-EVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQ--NLDGRAIRV  353 (365)
Q Consensus       277 ~~~~~lfV~nLp~-~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~--~l~gr~l~V  353 (365)
                      .+.++|||+|||+ .+++++|+++|+.||.|..|+|+++      +|||||+|.+.++|.+|+..|++.  .|.||+|+|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            4567999999999 9999999999999999999999865      689999999999999999998864  599999999


Q ss_pred             EEcccccc
Q 017842          354 NVAEDRQR  361 (365)
Q Consensus       354 ~~a~~~~~  361 (365)
                      .||+.+++
T Consensus        87 ~~a~~~~~   94 (102)
T 1x4d_A           87 HLSQKYKR   94 (102)
T ss_dssp             EEECCCTT
T ss_pred             EECCCCCC
Confidence            99996553

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=3.2e-17  Score=131.83  Aligned_cols=83  Identities=25%  Similarity=0.512  Sum_probs=77.7

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc--------C
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL--------D  347 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l--------~  347 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|++++ ++.++|||||+|.+.++|.+|+..|||..+        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            3456799999999999999999999999999999999998 899999999999999999999999999999        6


Q ss_pred             CeeEEEEEcccc
Q 017842          348 GRAIRVNVAEDR  359 (365)
Q Consensus       348 gr~l~V~~a~~~  359 (365)
                      |++|+|.||.++
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            888999999865

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.7e-18  Score=131.83  Aligned_cols=80  Identities=20%  Similarity=0.417  Sum_probs=76.1

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +.++|||+|||+.+++++|+++|+.||.|..|+|++++.++.++|||||+|.+.++|.+|+..|||..+.|+.|+++++.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            45699999999999999999999999999999999999999999999999999999999999999999999999988754

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=8.9e-18  Score=135.59  Aligned_cols=85  Identities=34%  Similarity=0.591  Sum_probs=79.9

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||.. ++..|.|++|+|.++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            3446999999999999999999999999999999999999999999999999999999999996 999999999999999


Q ss_pred             cccccC
Q 017842          357 EDRQRR  362 (365)
Q Consensus       357 ~~~~~~  362 (365)
                      .++...
T Consensus       104 ~~~~~~  109 (116)
T 1x4b_A          104 VAREES  109 (116)
T ss_dssp             SSCCCC
T ss_pred             CCCccC
Confidence            988754

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.73  E-value=1.5e-18  Score=133.59  Aligned_cols=82  Identities=43%  Similarity=0.785  Sum_probs=74.2

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      ++|||+|||+.+++++|+++|+.||.|..|++.+++.+|+++|||||+|.+.+ |.+|+..|||..++|++|+|.+|.++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            48999999999999999999999999999999999999999999999999999 99999999999999999999999877


Q ss_pred             ccC
Q 017842          360 QRR  362 (365)
Q Consensus       360 ~~~  362 (365)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            654

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=3.7e-17  Score=128.00  Aligned_cols=88  Identities=28%  Similarity=0.394  Sum_probs=80.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      .+.++|||+|||+++++++|+.+|+.||.|..+.                          ++.+..+++++|||||+|.+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~   59 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELH--------------------------YPIDSLTKKPKGFAFVTFMF   59 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCCCTTTCCCCSEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEE--------------------------EEecCCCCCcCeEEEEEECC
Confidence            3578999999999999999999999999998887                          77777789999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPE  270 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~  270 (365)
                      .++|.+|+..|||..|.|+.|+|.++.++.....
T Consensus        60 ~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~   93 (99)
T 1whw_A           60 PEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQ   93 (99)
T ss_dssp             HHHHHHHHHHTTTEESSSCEEEEEECCCCSTTCC
T ss_pred             HHHHHHHHHHhCCCEECCcEEEEEEcCCCccccc
Confidence            9999999999999999999999999988765443

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.72  E-value=2.1e-18  Score=170.20  Aligned_cols=85  Identities=24%  Similarity=0.559  Sum_probs=80.4

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+|+++|+.+|+.||.|..|.|+.+..++.++|||||+|.+..+|.+||..|||..|.|+.|.|.||
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            44569999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 017842          357 EDRQR  361 (365)
Q Consensus       357 ~~~~~  361 (365)
                      ..+..
T Consensus       180 ~~~~~  184 (437)
T 3pgw_S          180 RGRTV  184 (437)
T ss_pred             CCCCC
Confidence            87653

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=3.8e-18  Score=127.23  Aligned_cols=76  Identities=33%  Similarity=0.636  Sum_probs=73.4

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ++|||+|||+.+++++|+++|+.||.|..|++++++.+|+++|||||+|.+.++|.+|+..++ ..++|++|+|.+|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            379999999999999999999999999999999999899999999999999999999999888 9999999999987

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.72  E-value=7.4e-18  Score=129.88  Aligned_cols=82  Identities=20%  Similarity=0.370  Sum_probs=71.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccC--CeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAG--TVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G--~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      .+|||||||+++++++|+++|+.||  .|..++                          ++.++.+|+++|||||+|.+.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~--------------------------i~~~~~~g~~kG~afV~f~~~   55 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIK--------------------------FFENRANGQSKGFALVGVGSE   55 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEE--------------------------EEECTTTCCEEEEEEECC-CH
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEE--------------------------EEecCCCCccCcEEEEEECCH
Confidence            4899999999999999999999999  888877                          788888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|.+|+..|||..|+|+.|+|.++.+...
T Consensus        56 ~~a~~Ai~~l~g~~~~gr~i~V~~~~~~~~   85 (90)
T 3p5t_L           56 ASSKKLMDLLPKRELHGQNPVVTPSNKLEH   85 (90)
T ss_dssp             HHHHHHHHHGGGSCSSSCCCEECCC-----
T ss_pred             HHHHHHHHHcCCCeeCCEEEEEEECCCCcc
Confidence            999999999999999999999999887654

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=2.4e-17  Score=130.65  Aligned_cols=81  Identities=11%  Similarity=0.101  Sum_probs=72.5

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCC--ccCCeeEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQ--NLDGRAIRV  353 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~--~l~gr~l~V  353 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|+++      ||||||+|.+.++|.+|+..|++.  .+.||+|+|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345679999999999999999999999999999999853      799999999999999999988654  599999999


Q ss_pred             EEccccccC
Q 017842          354 NVAEDRQRR  362 (365)
Q Consensus       354 ~~a~~~~~~  362 (365)
                      .|++.+...
T Consensus        86 ~~a~~~~~~   94 (104)
T 1wex_A           86 NYSTSKRIT   94 (104)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCcccc
Confidence            999876643

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.72  E-value=1.3e-17  Score=126.48  Aligned_cols=73  Identities=21%  Similarity=0.300  Sum_probs=69.5

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ...|||+||++.+|+++|+++|..||.|..+++..      ++|||||+|.+.++|.+|++.|||..+.||+|+|.+|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            45899999999999999999999999999999964      59999999999999999999999999999999999985

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=6.9e-17  Score=125.38  Aligned_cols=86  Identities=28%  Similarity=0.566  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|++||.|..+.                          +..+..+++++|||||+|.+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~--------------------------i~~~~~~~~~~g~afV~f~~   56 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIV--------------------------LMKDSDTGRSKGYGFITFSD   56 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEE--------------------------EECCSSSCCCCSEEEEEESC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEE--------------------------EeecCCCCceeeEEEEEECC
Confidence            4678999999999999999999999999999887                          77787889999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      .++|.+|+..|||..|+|+.|+|.++.++...
T Consensus        57 ~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   88 (95)
T 2dnz_A           57 SECARRALEQLNGFELAGRPMRVGHVTERLDG   88 (95)
T ss_dssp             HHHHHHHHHHHTTCCSSSSCCEEEESSCCCCC
T ss_pred             HHHHHHHHHHhCCCeeCCcEEEEEEcccccCC
Confidence            99999999999999999999999999877554

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=4.3e-17  Score=125.46  Aligned_cols=79  Identities=28%  Similarity=0.596  Sum_probs=73.8

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|.        +|||||+|.+.++|.+|+..|||..+.|++|+|.|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            456799999999999999999999999999999997        689999999999999999999999999999999999


Q ss_pred             cccccCC
Q 017842          357 EDRQRRS  363 (365)
Q Consensus       357 ~~~~~~~  363 (365)
                      +++.+++
T Consensus        78 ~~~~~~~   84 (90)
T 2dnq_A           78 KNKSKAS   84 (90)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            9887653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.5e-17  Score=129.52  Aligned_cols=84  Identities=21%  Similarity=0.472  Sum_probs=76.2

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|   +++++ .+++++|||||+|.+.++|.+|+..|||..|.|++|+|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            3456799999999999999999999999977   56666 6789999999999999999999999999999999999999


Q ss_pred             ccccccCC
Q 017842          356 AEDRQRRS  363 (365)
Q Consensus       356 a~~~~~~~  363 (365)
                      +.++.+++
T Consensus        88 a~~~~~~~   95 (101)
T 2fc9_A           88 QGPRGSPN   95 (101)
T ss_dssp             CSSCCCCC
T ss_pred             cCCCCCCC
Confidence            99887654

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=1.7e-17  Score=133.10  Aligned_cols=84  Identities=14%  Similarity=0.251  Sum_probs=77.7

Q ss_pred             CCceEEEeCCCCcCcHHHHH---HHHhccCCeEEEEEEeeCCCC---CcceEEEEEecCHHHHHHHHHHhCCCccCCeeE
Q 017842          278 PGFRIYVGNLPWEVDNARLE---QVFSEHGKVVNARVVYDRETG---RSRGFGFVTMSSETELNDAIAALDGQNLDGRAI  351 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~---~~F~~~G~V~~v~i~~d~~~~---~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l  351 (365)
                      ..++|||+|||+.+++++|+   ++|+.||.|..|+|+++..++   +++|||||+|.+.++|.+|+..|||..|.||+|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l   93 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   93 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEE
Confidence            34599999999999999999   999999999999999887643   567999999999999999999999999999999


Q ss_pred             EEEEcccccc
Q 017842          352 RVNVAEDRQR  361 (365)
Q Consensus       352 ~V~~a~~~~~  361 (365)
                      +|.||.++..
T Consensus        94 ~V~~a~~k~~  103 (111)
T 2cpi_A           94 KASLGTTKYC  103 (111)
T ss_dssp             EEESCCCCSC
T ss_pred             EEEecccccc
Confidence            9999998874

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=5.5e-17  Score=126.67  Aligned_cols=80  Identities=25%  Similarity=0.377  Sum_probs=74.2

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC--CeeEEEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD--GRAIRVN  354 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~--gr~l~V~  354 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|++.++      +|||||+|.+.++|.+|+..|||..+.  |++|+|.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            45569999999999999999999999999999999754      789999999999999999999999999  9999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      |+++++.+
T Consensus        89 ~a~~~~~~   96 (97)
T 1why_A           89 FAKSGPSS   96 (97)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCCCC
Confidence            99988764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.72  E-value=5.6e-18  Score=132.11  Aligned_cols=81  Identities=19%  Similarity=0.385  Sum_probs=72.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeE--EEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVE--IAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~--~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      .-.||||+|||+++|+++|+++|++||.+.  .++                          +++++.+++++|||||+|.
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~--------------------------i~~d~~tg~srG~aFV~f~   61 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIR--------------------------LIKDKQTQQNRGFAFVQLS   61 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEE--------------------------CCCCSSSSSCSSEEEEECS
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEE--------------------------EEecCCCCCCceEeEEEEC
Confidence            356999999999999999999999999653  444                          7888999999999999999


Q ss_pred             CHHHHHHHHHHHccCc----ccCeeEEEeecCC
Q 017842          236 TVEEAEKAVEMFHRYD----IDGRLLTVNKAAP  264 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~----~~gr~l~V~~a~~  264 (365)
                      +.++|.+|+..|||..    ++||.|.|.++..
T Consensus        62 ~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           62 SAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             SSHHHHHHHHHHHSSSSCEEETTEEEEEEECCC
T ss_pred             CHHHHHHHHHHhcCCCCCceECCEEEEEEEccC
Confidence            9999999999999974    8999999999864

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.72  E-value=2.6e-17  Score=135.24  Aligned_cols=82  Identities=18%  Similarity=0.372  Sum_probs=74.3

Q ss_pred             CCCCceEEEeCCCCcCcHHHHH----HHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLE----QVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAI  351 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~----~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l  351 (365)
                      ..+.++|||+|||+.+++++|+    ++|+.||.|..|.+.+   +++++|||||+|.+.++|.+|+..|||..|.||+|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            3456799999999999999866    7999999999998853   57889999999999999999999999999999999


Q ss_pred             EEEEccccc
Q 017842          352 RVNVAEDRQ  360 (365)
Q Consensus       352 ~V~~a~~~~  360 (365)
                      +|.||+.+.
T Consensus       103 ~V~~a~~~~  111 (127)
T 2a3j_A          103 VITFSETPQ  111 (127)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCcc
Confidence            999998765

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.72  E-value=3.1e-17  Score=125.17  Aligned_cols=82  Identities=27%  Similarity=0.453  Sum_probs=75.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +.++|||+|||+++++++|+.+|+.||.|..+.                          +..+..++.++|||||+|.+.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~~   58 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDAR--------------------------VVKDMATGKSKGYGFVSFFNK   58 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTCCEEEEEEEEESSH
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEE--------------------------EEecCCCCccceEEEEEECCH
Confidence            568999999999999999999999999999887                          777878999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      ++|.+|+..|||..++|+.|+|.++.++
T Consensus        59 ~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A           59 WDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             HHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            9999999999999999999999998764

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.8e-17  Score=132.51  Aligned_cols=84  Identities=31%  Similarity=0.593  Sum_probs=77.5

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      .....++|||+|||+.+++++|+++|+.||.|..|+|.++.  +.++|||||+|.+.++|.+|+..|||..++|++|+|.
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34556799999999999999999999999999999999885  4589999999999999999999999999999999999


Q ss_pred             Eccccc
Q 017842          355 VAEDRQ  360 (365)
Q Consensus       355 ~a~~~~  360 (365)
                      +|+++.
T Consensus       103 ~a~~~~  108 (109)
T 2err_A          103 NATARV  108 (109)
T ss_dssp             ECCCSC
T ss_pred             ECCCCc
Confidence            998764

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=5.4e-17  Score=127.94  Aligned_cols=81  Identities=16%  Similarity=0.230  Sum_probs=72.9

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHh--CCCccCCeeEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL--DGQNLDGRAIRV  353 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l--~~~~l~gr~l~V  353 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|+++      +|||||+|.+.++|.+|+..|  ++..+.||+|+|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            345679999999999999999999999999999999864      899999999999999999977  567899999999


Q ss_pred             EEccccccC
Q 017842          354 NVAEDRQRR  362 (365)
Q Consensus       354 ~~a~~~~~~  362 (365)
                      .||+.+...
T Consensus        86 ~~a~~~~~~   94 (101)
T 2cq1_A           86 QYSNHKELK   94 (101)
T ss_dssp             EECSCSSCC
T ss_pred             EEcCcccCc
Confidence            999977643

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=6.6e-17  Score=126.62  Aligned_cols=87  Identities=34%  Similarity=0.645  Sum_probs=79.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||+|||+++++++|+.+|..||.|..+.                          ++.+..+++++|||||+|.
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~   60 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVV--------------------------MIYDAEKQRPRGFGFITFE   60 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEE--------------------------ECCCTTTCSCCSEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEeCCCCCCCCceEEEEEC
Confidence            34578999999999999999999999999999887                          7778888999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      +.++|.+|+. |+|..|+|+.|+|.++.++....
T Consensus        61 ~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~~~~   93 (99)
T 2dgs_A           61 DEQSVDQAVN-MHFHDIMGKKVEVKRAEPRDSKS   93 (99)
T ss_dssp             SHHHHHHHHH-HCCCBSSSCBCEEEECCCCCCCC
T ss_pred             CHHHHHHHHH-hCCCEECCeEEEEEECCCCcccC
Confidence            9999999999 79999999999999998776543

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=7.8e-18  Score=135.59  Aligned_cols=87  Identities=23%  Similarity=0.402  Sum_probs=75.6

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|.+..+..+++++|||||+|.+.++|.+|+..|||..|.|++|+|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34567999999999999999999999999985443333333788999999999999999999999999999999999999


Q ss_pred             ccccccC
Q 017842          356 AEDRQRR  362 (365)
Q Consensus       356 a~~~~~~  362 (365)
                      |.++..+
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9987654

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.71  E-value=4.5e-17  Score=126.91  Aligned_cols=84  Identities=23%  Similarity=0.520  Sum_probs=77.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +.++|||+|||+++++++|+.+|++||.|..++                          +..+..+++++|||||+|.+.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~g~~~g~afV~f~~~   54 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLK--------------------------MMFDPQTGRSKGYAFIEFRDL   54 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCBCTTTCCBCSEEEEEESSH
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEeCCCCCccceEEEEEECCH
Confidence            367999999999999999999999999999887                          777778899999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|.+|+..|||..|+|+.|+|.++.++..
T Consensus        55 ~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   84 (96)
T 2x1f_A           55 ESSASAVRNLNGYQLGSRFLKCGYSSNSDI   84 (96)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEEECSCSSG
T ss_pred             HHHHHHHHHhCCCeECCeEEEEEEcCCCCC
Confidence            999999999999999999999999987653

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=5.1e-17  Score=127.89  Aligned_cols=84  Identities=32%  Similarity=0.570  Sum_probs=77.1

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+++++|+++|+.|   ..|++++++.+++++|||||+|.+.++|.+||..|||..|.|++|+|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4456799999999999999999999977   3788888888999999999999999999999999999999999999999


Q ss_pred             ccccccC
Q 017842          356 AEDRQRR  362 (365)
Q Consensus       356 a~~~~~~  362 (365)
                      |+++..+
T Consensus        89 a~~~~~~   95 (102)
T 2fc8_A           89 AKPKGEG   95 (102)
T ss_dssp             CCCCCSS
T ss_pred             ecCCCCC
Confidence            9988764

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.71  E-value=4e-17  Score=123.98  Aligned_cols=82  Identities=29%  Similarity=0.481  Sum_probs=76.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ..+.++|||+|||+++++++|+++|++||.|..+.                          ++.+..+++++|||||+|.
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~   57 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQ--------------------------IPLDYETEKHRGFAFVEFE   57 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEE--------------------------CCEETTTTEECSEEEEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEE--------------------------EEECCCCCccccEEEEEEC
Confidence            34678999999999999999999999999999887                          7777789999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      +.++|.+|+..|||..++|+.|+|.++.
T Consensus        58 ~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A           58 LAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            9999999999999999999999999863

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.71  E-value=9.9e-17  Score=129.13  Aligned_cols=88  Identities=26%  Similarity=0.455  Sum_probs=81.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||+|||+++++++|+.+|..||.|..+.                          ++.+..++.++|||||+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~   65 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDAR--------------------------VVKDMATGKSKGYGFVSFF   65 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTCCEEEEEEEEES
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEEcCCCCCcceEEEEEEC
Confidence            44678999999999999999999999999998887                          7778789999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      +.++|.+|+..|||..|.|+.|+|.++.++....
T Consensus        66 ~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   99 (115)
T 2dgo_A           66 NKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAP   99 (115)
T ss_dssp             SHHHHHHHHHHTTTCEETTEECEEEESSCCCCCS
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEEccCCCCCC
Confidence            9999999999999999999999999998776544

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.71  E-value=4.1e-17  Score=135.75  Aligned_cols=82  Identities=34%  Similarity=0.526  Sum_probs=77.1

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..|||..|.|++|+|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34456799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Ec
Q 017842          355 VA  356 (365)
Q Consensus       355 ~a  356 (365)
                      ||
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            86

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.71  E-value=5.2e-17  Score=122.75  Aligned_cols=81  Identities=33%  Similarity=0.566  Sum_probs=76.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      .+|||+|||+++++++|+.+|+.||.|..+.                          ++.+..+++++|||||+|.+.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~--------------------------i~~~~~~~~~~g~afV~f~~~~~   55 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGH--------------------------VMWDMQTGSSRGYGFVSFTSQDD   55 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEE--------------------------EEECTTTCCEEEEEEEEESCHHH
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE--------------------------EEEcCCCCCccceEEEEECCHHH
Confidence            5899999999999999999999999999887                          77788899999999999999999


Q ss_pred             HHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      |.+|+..|||..++|+.|+|.++.++.
T Consensus        56 a~~a~~~l~g~~~~g~~l~v~~a~~~~   82 (83)
T 3md1_A           56 AQNAMDSMQGQDLNGRPLRINWAAKLE   82 (83)
T ss_dssp             HHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             HHHHHHHhcCCeeCCcEEEEEecCcCC
Confidence            999999999999999999999988653

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=2.6e-17  Score=133.34  Aligned_cols=81  Identities=20%  Similarity=0.298  Sum_probs=73.7

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC--CCccCCeeEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD--GQNLDGRAIRV  353 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~--~~~l~gr~l~V  353 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|+|+++      ||||||+|.+.++|.+|+..|+  +..|.||+|+|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            345679999999999999999999999999999999875      8999999999999999999887  46899999999


Q ss_pred             EEccccccC
Q 017842          354 NVAEDRQRR  362 (365)
Q Consensus       354 ~~a~~~~~~  362 (365)
                      .||+.+...
T Consensus       102 ~~a~~k~~~  110 (119)
T 2ad9_A          102 QFSNHKELK  110 (119)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCCCCC
Confidence            999987654

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=8.5e-18  Score=137.48  Aligned_cols=83  Identities=25%  Similarity=0.465  Sum_probs=76.9

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ....++|||+|||+.+++++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|.+||. |||..|+||.|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3456799999999999999999999999999997777777899999999999999999999999 999999999999999


Q ss_pred             cccc
Q 017842          356 AEDR  359 (365)
Q Consensus       356 a~~~  359 (365)
                      |..+
T Consensus       101 a~~~  104 (124)
T 1wel_A          101 ITKK  104 (124)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8764

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.6e-17  Score=131.24  Aligned_cols=84  Identities=17%  Similarity=0.270  Sum_probs=76.4

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ...++|||+|||+.+++++|+++|+.||. ..|+|++++ +++++|||||+|.+.++|.+||. +|+..|.||.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            34569999999999999999999999994 599999997 89999999999999999999996 8999999999999999


Q ss_pred             cccccCC
Q 017842          357 EDRQRRS  363 (365)
Q Consensus       357 ~~~~~~~  363 (365)
                      ....+.+
T Consensus        90 ~~~~~~~   96 (102)
T 1wez_A           90 STAGTSG   96 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8776543

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.71  E-value=9.8e-17  Score=129.21  Aligned_cols=89  Identities=28%  Similarity=0.471  Sum_probs=81.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      ..+..++|||+|||+++++++|+.+|..||.|..++                          ++.+..+++++|||||+|
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~g~~~g~afV~f   74 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAK--------------------------VFIDKQTNLSKCFGFVSY   74 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEE--------------------------EEECSSSCSEEEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEECCCCCCcCccEEEEE
Confidence            334578999999999999999999999999999887                          777888999999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      .+.++|.+|+..|||..|.|+.|+|.++.++....
T Consensus        75 ~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~  109 (115)
T 2cpz_A           75 DNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK  109 (115)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEECCCCSCCCC
T ss_pred             CCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCcCC
Confidence            99999999999999999999999999998776543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=5.8e-17  Score=127.89  Aligned_cols=87  Identities=29%  Similarity=0.355  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|+.||.|..+.                          +..+..++.++|||||+|.+
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~   64 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVY--------------------------IPREPHTKAPRGFAFVRFHD   64 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEE--------------------------CCBCSSSCSBCSCEEEEESS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEeCCCCCCCCeEEEEEECC
Confidence            4578999999999999999999999999998887                          77788889999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      .++|.+|+..|||..|+|+.|+|.++.+.....
T Consensus        65 ~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   97 (103)
T 2dnm_A           65 RRDAQDAEAAMDGAELDGRELRVQVARYGRRDL   97 (103)
T ss_dssp             SSHHHHHHHHHSSCCBTTBCCEEEECSSCCSCC
T ss_pred             HHHHHHHHHHcCCCEECCcEEEEEECCcCCCCC
Confidence            999999999999999999999999998765443

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=6.3e-17  Score=126.44  Aligned_cols=87  Identities=26%  Similarity=0.433  Sum_probs=77.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCC---CCCccceEEEE
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRE---TDRSRGFGFVT  233 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~g~afV~  233 (365)
                      .+.++|||+|||+++++++|+.+|+.||.|..+.                          +..+..   +++++|||||+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~gt~~~~g~afV~   56 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCT--------------------------ISKKKNKAGVLLSMGFGFVE   56 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------EEEEECTTCCEEEEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEecCCCCCCcCcccEEEEE
Confidence            3578999999999999999999999999999887                          555554   56899999999


Q ss_pred             eCCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      |.+.++|.+|+..|||..|+|+.|+|.++.++....
T Consensus        57 f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   92 (98)
T 2cpf_A           57 YKKPEQAQKALKQLQGHTVDGHKLEVRISERATKPA   92 (98)
T ss_dssp             ESSHHHHHHHHHHSTTCEETTEECEEECSSCSSCCC
T ss_pred             ECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCCCCC
Confidence            999999999999999999999999999998765443

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=4.5e-17  Score=126.68  Aligned_cols=87  Identities=21%  Similarity=0.424  Sum_probs=79.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEE-EEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIA-EVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      .+.++|||+|||+++++++|+.+|+.||.|..+ +                          ++.+..++.++|||||+|.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~--------------------------i~~~~~~g~~~g~afV~f~   56 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPK--------------------------IMRDPDTGNSKGYAFINFA   56 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCE--------------------------ECCCTTTCSCCSEEEEEBS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE--------------------------EEEcCCCCCcCeEEEEEEC
Confidence            357899999999999999999999999999876 6                          7777789999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      +.++|.+|+..|||..|.|+.|+|.++.++....
T Consensus        57 ~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   90 (96)
T 1x5t_A           57 SFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKG   90 (96)
T ss_dssp             SHHHHHHHHHTTTTCEETTEECEEEESCCCCCCC
T ss_pred             CHHHHHHHHHHcCCCEECCEEEEEEEecccCCCC
Confidence            9999999999999999999999999998776543

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=1.2e-16  Score=127.73  Aligned_cols=88  Identities=27%  Similarity=0.489  Sum_probs=80.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||+|||+++++++|+.+|..||.|..++                          ++.+..++.++|||||+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~g~~~g~afV~f~   65 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVR--------------------------VVLHPDTEHSKGCAFAQFM   65 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCBCSSSCCBCSEEEEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEecCCCCCCccEEEEEEC
Confidence            34678999999999999999999999999998887                          7778889999999999999


Q ss_pred             CHHHHHHHHHHHc------cCcccCeeEEEeecCCCCCCC
Q 017842          236 TVEEAEKAVEMFH------RYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       236 ~~e~a~~Al~~ln------g~~~~gr~l~V~~a~~~~~~~  269 (365)
                      +.++|.+|+..||      |..|+|+.|+|.++.++....
T Consensus        66 ~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           66 TQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA  105 (111)
T ss_dssp             SHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCCCC
T ss_pred             CHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCccCC
Confidence            9999999999999      999999999999998775543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=4.2e-17  Score=128.39  Aligned_cols=87  Identities=29%  Similarity=0.472  Sum_probs=80.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|+.||.|..+.                          ++.+..+++++|||||+|.+
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~   63 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQ--------------------------IPLDYETEKHRGFAFVEFEL   63 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEE--------------------------CCCCSSSCCCSSEEEECCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEE--------------------------EEecCCCCCcceEEEEEECC
Confidence            4578999999999999999999999999998887                          77777889999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      .++|.+|+..|||..|.|+.|+|.++.++....
T Consensus        64 ~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   96 (102)
T 2cqb_A           64 AEDAAAAIDNMNESELFGRTIRVNLAKPMRIKE   96 (102)
T ss_dssp             HHHHHHHHHHHTTEEETTEEEEEEECCCCCCCC
T ss_pred             HHHHHHHHHHhCCCEECCcEEEEEeCCCCCCCC
Confidence            999999999999999999999999998776544

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=7.9e-17  Score=125.81  Aligned_cols=80  Identities=25%  Similarity=0.459  Sum_probs=73.0

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ...++|||+|||+.+++++|+++|+.||.|. ++++.+    +++|||||+|.+.++|.+|+..|||..+.|++|+|.++
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            4456999999999999999999999999997 677654    56999999999999999999999999999999999999


Q ss_pred             ccccc
Q 017842          357 EDRQR  361 (365)
Q Consensus       357 ~~~~~  361 (365)
                      +++.+
T Consensus        92 ~~~~~   96 (97)
T 2e5j_A           92 RQQRD   96 (97)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98764

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=6.8e-17  Score=127.19  Aligned_cols=87  Identities=36%  Similarity=0.682  Sum_probs=79.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ..+.++|||+|||+++++++|+.+|+.||.|..+.                          ++.+..++.++|||||+|.
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~   62 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVV--------------------------VVKDRETQRSRGFGFVTFE   62 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEE--------------------------ECCCSSSCSCCSEEEEECS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEeCCCCCCcccEEEEEEC
Confidence            34578999999999999999999999999999887                          7777788999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..|||..|.|+.|+|.++.++...
T Consensus        63 ~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   95 (102)
T 1x5s_A           63 NIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN   95 (102)
T ss_dssp             SHHHHHHHHHHHTTCCTTSCCCEEEEEECCCCC
T ss_pred             CHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            999999999999999999999999999876544

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.71  E-value=1e-17  Score=131.87  Aligned_cols=82  Identities=28%  Similarity=0.391  Sum_probs=76.8

Q ss_pred             CCCeEEEcCCCC------CCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEE
Q 017842          158 EDAKLFVGNLPY------DVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGF  231 (365)
Q Consensus       158 ~~~tvfVgnLp~------~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~af  231 (365)
                      ..++|||+|||+      ++++++|+.+|++||.|..++                          ++++..+++++||||
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~--------------------------i~~d~~tg~~kG~af   58 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNME--------------------------FPIDEATGKTKGFLF   58 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEE--------------------------CCEETTTTEECSEEE
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEE--------------------------EEEcCCCCccceEEE
Confidence            367999999999      999999999999999999887                          788888999999999


Q ss_pred             EEeCCHHHHHHHHHHHccCcccC-eeEEEeecCCC
Q 017842          232 VTMSTVEEAEKAVEMFHRYDIDG-RLLTVNKAAPR  265 (365)
Q Consensus       232 V~f~~~e~a~~Al~~lng~~~~g-r~l~V~~a~~~  265 (365)
                      |+|.+.++|.+|+..|||..|.| +.|+|.++.++
T Consensus        59 V~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~~   93 (100)
T 3ns6_A           59 VECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDV   93 (100)
T ss_dssp             EEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHHH
T ss_pred             EEECCHHHHHHHHHHhCCcccCCCeEEEEEECchh
Confidence            99999999999999999999999 99999988654

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.1e-16  Score=126.56  Aligned_cols=88  Identities=31%  Similarity=0.481  Sum_probs=80.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .+...++|||+|||+++++++|+.+|+.||.|..+.                          +..+..++.++|||||+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f   64 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTH--------------------------MPKDRVTGQHQGYGFVEF   64 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCBCSSSCSBCSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEecCCCCcCCcEEEEEE
Confidence            344678999999999999999999999999998887                          777778899999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      .+.++|.+|+..|||..|.|+.|+|.++.++...
T Consensus        65 ~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (105)
T 1x5u_A           65 LSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKN   98 (105)
T ss_dssp             SSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSCC
T ss_pred             CCHHHHHHHHHHhCCCeECCeEEEEEECCCCCcC
Confidence            9999999999999999999999999999876543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=5.8e-17  Score=127.90  Aligned_cols=87  Identities=25%  Similarity=0.414  Sum_probs=80.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ..+.++|||+|||+++++++|+.+|+.||.|..+.                          ++.+..++.++|||||+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~   65 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIY--------------------------LAKDKTTGQSKGFAFISFH   65 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEE--------------------------EEECSSSCSEEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEE--------------------------EeecCCCCceeeEEEEEEC
Confidence            34578999999999999999999999999999887                          7778889999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..|||..|.|+.|+|.++.++...
T Consensus        66 ~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (103)
T 2cq0_A           66 RREDAARAIAGVSGFGYDHLILNVEWAKPSTNS   98 (103)
T ss_dssp             SHHHHHHHHHHTTTCEETTEECEEEESSCCCCS
T ss_pred             CHHHHHHHHHHcCCCeeCCcEEEEEECCCCCCC
Confidence            999999999999999999999999999876543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=1.5e-16  Score=124.87  Aligned_cols=85  Identities=24%  Similarity=0.428  Sum_probs=77.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||+|||+++++++|+.+|..||.|..++                          +..+. +++++|||||+|.
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~-~g~~~g~afV~f~   66 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLR--------------------------LVTNR-AGKPKGLAYVEYE   66 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEE--------------------------EEECT-TSCEEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEE--------------------------EEECC-CCCEEeEEEEEEC
Confidence            44678999999999999999999999999999887                          66666 8899999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      +.++|.+|+..|||..|+|+.|+|.++.++..
T Consensus        67 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   98 (100)
T 2do4_A           67 NESQASQAVMKMDGMTIKENIIKVAISNSGPS   98 (100)
T ss_dssp             SHHHHHHHHHHHTTEESSSCEEEEEECCCCSC
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            99999999999999999999999999987653

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=6.5e-17  Score=128.92  Aligned_cols=79  Identities=28%  Similarity=0.354  Sum_probs=73.6

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC-----eeE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDG-----RAI  351 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g-----r~l  351 (365)
                      ...++|||+|||+.+++++|+++|..||.|..|+|+++       |||||+|.+.++|.+||..|||..|.|     ++|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            34579999999999999999999999999999999865       899999999999999999999999999     999


Q ss_pred             EEEEccccccC
Q 017842          352 RVNVAEDRQRR  362 (365)
Q Consensus       352 ~V~~a~~~~~~  362 (365)
                      +|.+|.++.+.
T Consensus        86 ~V~~a~~~~~~   96 (108)
T 1x4c_A           86 RVKVDGPRSPS   96 (108)
T ss_dssp             EEEESSCCSCC
T ss_pred             EEEeCCCCCCC
Confidence            99999987653

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=7.6e-17  Score=124.57  Aligned_cols=79  Identities=27%  Similarity=0.515  Sum_probs=73.1

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|.        +|||||+|.+.++|.+|+..|||..+.|++|+|.|+
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            455699999999999999999999999999999997        459999999999999999999999999999999999


Q ss_pred             cccccCC
Q 017842          357 EDRQRRS  363 (365)
Q Consensus       357 ~~~~~~~  363 (365)
                      +++.+..
T Consensus        80 ~~~~~~~   86 (92)
T 2dgt_A           80 TSRLRTA   86 (92)
T ss_dssp             SCCCSCC
T ss_pred             cCCCCCC
Confidence            9877643

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=5.9e-17  Score=128.34  Aligned_cols=82  Identities=22%  Similarity=0.271  Sum_probs=76.0

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEE-EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVN-ARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~-v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ...++|||+|||+.+++++|+++|+.||.|.. |+|+++ .+|+++|||||+|.+.++|.+||.. |+..|+||.|+|.+
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            44569999999999999999999999999997 889888 7899999999999999999999996 99999999999999


Q ss_pred             ccccc
Q 017842          356 AEDRQ  360 (365)
Q Consensus       356 a~~~~  360 (365)
                      +..+.
T Consensus        91 ~~~~~   95 (104)
T 1wg5_A           91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            87654

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=6.6e-17  Score=129.02  Aligned_cols=80  Identities=20%  Similarity=0.488  Sum_probs=74.7

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ...++|||+|||+.+++++|+.+|+.||.|..|+|.++      +|||||+|.+.++|.+|+..|||..|.|++|+|.|+
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            34569999999999999999999999999999999866      899999999999999999999999999999999999


Q ss_pred             cccccC
Q 017842          357 EDRQRR  362 (365)
Q Consensus       357 ~~~~~~  362 (365)
                      ++++..
T Consensus        97 ~~~~~~  102 (109)
T 1x4g_A           97 KESPDM  102 (109)
T ss_dssp             CCCCSS
T ss_pred             CCCCCC
Confidence            987754

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.70  E-value=8.5e-17  Score=125.81  Aligned_cols=79  Identities=24%  Similarity=0.446  Sum_probs=72.2

Q ss_pred             cCCCCceEEEeCCCC-cCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          275 VFEPGFRIYVGNLPW-EVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~-~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      ...+.++|||+|||+ .+++++|+++|+.||.|..|+|.        +|||||+|.+.++|.+|+..|||..+.|++|+|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344567999999998 99999999999999999999983        899999999999999999999999999999999


Q ss_pred             EEcccccc
Q 017842          354 NVAEDRQR  361 (365)
Q Consensus       354 ~~a~~~~~  361 (365)
                      .|++.+.|
T Consensus        90 ~~a~~~~r   97 (97)
T 2xnq_A           90 EVSSSNAR   97 (97)
T ss_dssp             EECCCCC-
T ss_pred             EecCCCCC
Confidence            99987754

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.8e-17  Score=133.52  Aligned_cols=82  Identities=17%  Similarity=0.252  Sum_probs=76.7

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCe-EEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKV-VNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V-~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      .+.++|||+|||+.+++++|+++|+.||.| ..|+|++++ +++++|||||+|.+.++|.+||.. |+..|.||.|+|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            445699999999999999999999999999 899999998 899999999999999999999995 99999999999999


Q ss_pred             ccccc
Q 017842          356 AEDRQ  360 (365)
Q Consensus       356 a~~~~  360 (365)
                      +..+.
T Consensus        91 a~~~~   95 (114)
T 2cpy_A           91 VTLED   95 (114)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            98654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.6e-16  Score=124.49  Aligned_cols=81  Identities=27%  Similarity=0.460  Sum_probs=73.9

Q ss_pred             CcCCCCceEEEeCCCCcCcHHHHHHHHhcc--CCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeE
Q 017842          274 RVFEPGFRIYVGNLPWEVDNARLEQVFSEH--GKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAI  351 (365)
Q Consensus       274 ~~~~~~~~lfV~nLp~~~tee~L~~~F~~~--G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l  351 (365)
                      ....+.++|||+|||+.+++++|+++|+.|  |.|..|++.        +|||||+|.+.++|.+|+..|||..|.|++|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (99)
T 2cpd_A           10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPI   81 (99)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEE
T ss_pred             cccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            344566799999999999999999999999  999999875        6799999999999999999999999999999


Q ss_pred             EEEEccccccC
Q 017842          352 RVNVAEDRQRR  362 (365)
Q Consensus       352 ~V~~a~~~~~~  362 (365)
                      +|.|++++.+.
T Consensus        82 ~v~~a~~~~~~   92 (99)
T 2cpd_A           82 EVTLAKPVDKD   92 (99)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEEECCCCCCC
Confidence            99999987764

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=9.9e-17  Score=124.42  Aligned_cols=84  Identities=29%  Similarity=0.489  Sum_probs=77.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .+.+.++|||+|||+++++++|+.+|+.||.|..+.                          ++.+..+++++|||||+|
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~--------------------------i~~~~~~~~~~g~afV~f   64 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVS--------------------------IVYDQQSRRSRGFAFVYF   64 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEE--------------------------EEECSSSSSEEEEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEE--------------------------EEEcCCCCCcccEEEEEE
Confidence            345678999999999999999999999999999887                          777888899999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      .+.++|.+|+..|||..|+|+.|+|.++..
T Consensus        65 ~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           65 ENVDDAKEAKERANGMELDGRRIRVSGPSS   94 (95)
T ss_dssp             SSHHHHHHHHHHHTTEEETTEEEEEECCSC
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEecCC
Confidence            999999999999999999999999998764

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=7.8e-17  Score=127.75  Aligned_cols=83  Identities=25%  Similarity=0.362  Sum_probs=77.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|+.||.|..+.                          +..+..++.++|||||+|.+.
T Consensus        22 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~~   75 (106)
T 1p27_B           22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIH--------------------------LNLDRRTGYLKGYTLVEYETY   75 (106)
T ss_dssp             TBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTSSEEEEEEEEESCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEE--------------------------EEecCCCCceeeEEEEEECCH
Confidence            467999999999999999999999999999887                          778888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ++|.+|+..|||..|+|+.|+|.++.++.
T Consensus        76 ~~a~~A~~~l~g~~~~g~~l~V~~a~~~~  104 (106)
T 1p27_B           76 KEAQAAMEGLNGQDLMGQPISVDWCFVRG  104 (106)
T ss_dssp             HHHHHHHHHHTTCBSSSSBCEEEESEESS
T ss_pred             HHHHHHHHHhcCCEECCcEEEEEeecCCC
Confidence            99999999999999999999999987654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=1.7e-16  Score=125.88  Aligned_cols=88  Identities=27%  Similarity=0.459  Sum_probs=79.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEec-CCCCCccceEEEEe
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN-RETDRSRGFGFVTM  234 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~g~afV~f  234 (365)
                      ....++|||+|||+++++++|+.+|..||.|..++                          ++.+ ..++.++|||||+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~~g~afV~f   65 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVR--------------------------LPKKMTGTGAHRGFGFVDF   65 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCCCCSSSCSSCSEEEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEE--------------------------EecCCCCCCCcCceEEEEE
Confidence            34578999999999999999999999999999887                          6666 67899999999999


Q ss_pred             CCHHHHHHHHHHH-ccCcccCeeEEEeecCCCCCCC
Q 017842          235 STVEEAEKAVEMF-HRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       235 ~~~e~a~~Al~~l-ng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      .+.++|.+|+..| ||..|.|+.|+|.++.++....
T Consensus        66 ~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~~~~  101 (107)
T 2cph_A           66 ITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ  101 (107)
T ss_dssp             SSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCCCC
T ss_pred             CCHHHHHHHHHHhccCCeECCCEEEEEeCCCCCCCC
Confidence            9999999999999 9999999999999998775543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.70  E-value=7.2e-18  Score=132.64  Aligned_cols=85  Identities=28%  Similarity=0.434  Sum_probs=77.8

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|.. .++++..+++++|||||+|.+.++|.+|+. |||..+.|++|+|.+|
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            34679999999999999999999999999888 677777789999999999999999999999 9999999999999999


Q ss_pred             cccccCC
Q 017842          357 EDRQRRS  363 (365)
Q Consensus       357 ~~~~~~~  363 (365)
                      .++..++
T Consensus        93 ~~~~~~~   99 (101)
T 1fj7_A           93 KGRDGTR   99 (101)
T ss_dssp             SCCCCSS
T ss_pred             CCCCCCC
Confidence            9877643

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.70  E-value=5.6e-17  Score=130.60  Aligned_cols=81  Identities=21%  Similarity=0.374  Sum_probs=74.9

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ++++|||+|||+.+++++|+.+|+.||.|..|+|+++   +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            4569999999999999999999999999999999976   4569999999999999999999999999999999999998


Q ss_pred             cccc
Q 017842          358 DRQR  361 (365)
Q Consensus       358 ~~~~  361 (365)
                      ++..
T Consensus        84 ~~~~   87 (115)
T 3lqv_A           84 ANRA   87 (115)
T ss_dssp             HHHH
T ss_pred             CChh
Confidence            7543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.70  E-value=7.7e-17  Score=126.28  Aligned_cols=83  Identities=23%  Similarity=0.386  Sum_probs=76.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEE--------EEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCc
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEI--------AEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRS  226 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~--------~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  226 (365)
                      .+...++|||+|||+++++++|+.+|++||.|..        ++                          ++.++.++++
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~--------------------------i~~~~~~g~~   62 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMIN--------------------------LYTDRETGKL   62 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEE--------------------------EEECTTTCSE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEE--------------------------EEecCCCCCe
Confidence            4556889999999999999999999999999988        66                          7788889999


Q ss_pred             cceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          227 RGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       227 ~g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      +|||||+|.+.++|.+|+..|||..|.|+.|+|.++.
T Consensus        63 ~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           63 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             EEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             eeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEecC
Confidence            9999999999999999999999999999999999863

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=9.3e-17  Score=123.57  Aligned_cols=78  Identities=29%  Similarity=0.631  Sum_probs=72.3

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|.        +|||||+|.+.++|.+|+..|||..+.|++|+|.|+
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            345699999999999999999999999999999997        459999999999999999999999999999999999


Q ss_pred             cccccC
Q 017842          357 EDRQRR  362 (365)
Q Consensus       357 ~~~~~~  362 (365)
                      .++.++
T Consensus        79 ~~~~~~   84 (90)
T 2dnp_A           79 TKGQKK   84 (90)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            977654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.6e-16  Score=125.38  Aligned_cols=88  Identities=33%  Similarity=0.441  Sum_probs=79.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .+...++|||+|||+++++++|+.+|..||.|..+.                          ++.+  ++.++|||||+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~--~g~~~g~afV~f   62 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAK--------------------------VMME--GGRSKGFGFVCF   62 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEE--------------------------EEEC--SSSEEEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEcC--CCCcCEEEEEEE
Confidence            344678999999999999999999999999999887                          5555  788999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPE  270 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~  270 (365)
                      .+.++|.+|+..|||..|.|+.|+|.++.++.....
T Consensus        63 ~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~   98 (103)
T 2d9p_A           63 SSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQS   98 (103)
T ss_dssp             SSHHHHHHHHHHHTTCBSSSSBCEEEECSSCCCCCC
T ss_pred             CCHHHHHHHHHHhCCCEeCCcEEEEEEecccccCCC
Confidence            999999999999999999999999999988765443

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.70  E-value=2e-17  Score=134.15  Aligned_cols=81  Identities=26%  Similarity=0.480  Sum_probs=75.6

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCC---eEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGK---VVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~---V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      ...++|||+|||+.+|+++|+++|+.||.   |..|+|++++. |+++|||||+|.+.++|.+||. ||+..|+||.|+|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            34569999999999999999999999998   89999999976 9999999999999999999999 9999999999999


Q ss_pred             EEcccc
Q 017842          354 NVAEDR  359 (365)
Q Consensus       354 ~~a~~~  359 (365)
                      .++..+
T Consensus        93 ~~a~~~   98 (118)
T 2db1_A           93 FKSHRT   98 (118)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998644

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.70  E-value=2.9e-17  Score=129.13  Aligned_cols=78  Identities=31%  Similarity=0.562  Sum_probs=73.8

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      ++|||+|||+.+++++|+++|+.||.|..|+|+++     ++|||||+|.+.++|.+|+..|||..+.|++|+|.|++++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            48999999999999999999999999999999877     6899999999999999999999999999999999999987


Q ss_pred             ccC
Q 017842          360 QRR  362 (365)
Q Consensus       360 ~~~  362 (365)
                      .+.
T Consensus        76 ~~~   78 (101)
T 2hvz_A           76 PRR   78 (101)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            754

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.70  E-value=1.3e-16  Score=127.31  Aligned_cols=85  Identities=32%  Similarity=0.632  Sum_probs=78.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ++..++|||+|||+++++++|+.+|+.||.|..+.                          ++.+..+++++|||||+|.
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~~~~~g~~~g~afV~F~   76 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQ--------------------------LMMDSETGRSKGYGFITFS   76 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEE--------------------------EEEETTTTEEEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEEcCCCCccceEEEEEEC
Confidence            44578999999999999999999999999999887                          7778889999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      +.++|.+|+..|||..|+|+.|+|.++.++.
T Consensus        77 ~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k~  107 (108)
T 2jrs_A           77 DSECAKKALEQLNGFELAGRPMKVGHVTERT  107 (108)
T ss_dssp             CHHHHHHHHHHHTTCCSSSSCCEEECSCSSC
T ss_pred             CHHHHHHHHHHcCCCEECCEEEEEEEcccCC
Confidence            9999999999999999999999999987653

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=6.5e-17  Score=126.72  Aligned_cols=81  Identities=30%  Similarity=0.527  Sum_probs=74.6

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|++.++      +|||||+|.+.++|.+|+..|||..|.|++|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            3455679999999999999999999999999999999854      7999999999999999999999999999999999


Q ss_pred             Ecccccc
Q 017842          355 VAEDRQR  361 (365)
Q Consensus       355 ~a~~~~~  361 (365)
                      |+.++..
T Consensus        85 ~a~~~~~   91 (99)
T 2cpj_A           85 FACHSAS   91 (99)
T ss_dssp             ESSCCSC
T ss_pred             EcCCCCC
Confidence            9998764

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.69  E-value=7.9e-17  Score=123.07  Aligned_cols=83  Identities=23%  Similarity=0.439  Sum_probs=75.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCC-ccceEEEEeCC
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDR-SRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~afV~f~~  236 (365)
                      ..++|||+|||+++++++|+.+|+.||.|..+.                          +..+..++. ++|||||+|.+
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~--------------------------i~~~~~~~~~~~g~afV~f~~   56 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMID--------------------------MPVERMHPHLSKGYAYVEFEN   56 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCEETTEEEEECSEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE--------------------------EEeCCCCCCCCCcEEEEEEec
Confidence            467999999999999999999999999999887                          555655555 89999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      .++|.+|+..|||..++|+.|+|.++.++.
T Consensus        57 ~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (88)
T 4a8x_A           57 PDEAEKALKHMDGGQIDGQEITATAVLAPW   86 (88)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEEEECCCC
T ss_pred             HHHHHHHHHHcCCCeECCeEEEEEECCCCC
Confidence            999999999999999999999999987654

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.69  E-value=1e-17  Score=124.21  Aligned_cols=75  Identities=24%  Similarity=0.457  Sum_probs=72.3

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      +|||+|||+.+++++|+++|+.||.|..|++++++.+++++|||||+|.+.++|.+|+. +++..+.|++|+|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999999 6999999999999986

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.69  E-value=1.9e-17  Score=124.91  Aligned_cols=73  Identities=32%  Similarity=0.479  Sum_probs=68.3

Q ss_pred             ceEEEeCCCCcC------cHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe-eEE
Q 017842          280 FRIYVGNLPWEV------DNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGR-AIR  352 (365)
Q Consensus       280 ~~lfV~nLp~~~------tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr-~l~  352 (365)
                      ++|||+|||+.+      ++++|+++|+.||.|..|+|+  +.+|+++|||||+|.+.++|.+|+..|||..+.|| +|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            589999999999      789999999999999999988  45789999999999999999999999999999999 887


Q ss_pred             EE
Q 017842          353 VN  354 (365)
Q Consensus       353 V~  354 (365)
                      |+
T Consensus        80 V~   81 (81)
T 2krb_A           80 VN   81 (81)
T ss_dssp             CC
T ss_pred             eC
Confidence            63

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.69  E-value=3.1e-17  Score=127.88  Aligned_cols=82  Identities=22%  Similarity=0.451  Sum_probs=75.7

Q ss_pred             CCCceEEEeCCCCcCcHHHHH----HHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLE----QVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR  352 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~----~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~  352 (365)
                      .++++|||+|||+.+++++|+    ++|+.||.|..|++.+   +|.++|||||+|.+.++|.+|+..|||..+.|++|+
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            456699999999999999999    9999999999999874   477899999999999999999999999999999999


Q ss_pred             EEEcccccc
Q 017842          353 VNVAEDRQR  361 (365)
Q Consensus       353 V~~a~~~~~  361 (365)
                      |.|++++..
T Consensus        83 v~~a~~~~~   91 (97)
T 1nu4_A           83 IQYAKTDSD   91 (97)
T ss_dssp             EEECSSCCT
T ss_pred             EEEccCCCc
Confidence            999997654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=1.9e-16  Score=124.99  Aligned_cols=87  Identities=25%  Similarity=0.408  Sum_probs=79.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHc-cCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEK-AGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~-~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      +.+.++|||+|||+++++++|+.+|.. ||.|..+.                          ++.+. +++++|||||+|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~--------------------------i~~~~-~g~~~g~afV~f   58 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGK--------------------------VVLDQ-TGVSKGYGFVKF   58 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEE--------------------------EEECT-TCCEEEEEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEE--------------------------EEECC-CCCccceEEEEE
Confidence            346789999999999999999999999 99998887                          77777 899999999999


Q ss_pred             CCHHHHHHHHHHHccCc-ccCeeEEEeecCCCCCCC
Q 017842          235 STVEEAEKAVEMFHRYD-IDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~-~~gr~l~V~~a~~~~~~~  269 (365)
                      .+.++|.+|+..|+|.. |+|+.|+|.++.++....
T Consensus        59 ~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~~~~   94 (104)
T 2dhg_A           59 TDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRV   94 (104)
T ss_dssp             SCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCCSCC
T ss_pred             CCHHHHHHHHHHccCCcccCCEeEEEEEccCCCcCC
Confidence            99999999999999999 999999999997765543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.3e-16  Score=128.11  Aligned_cols=88  Identities=25%  Similarity=0.403  Sum_probs=79.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeE--------EEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCcc
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVE--------IAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSR  227 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~--------~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (365)
                      ....++|||+|||+++++++|+.+|..||.|.        .++                          +..++.+++++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~--------------------------i~~~~~~g~~~   65 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIH--------------------------IYLDKETGKPK   65 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEE--------------------------CCBCTTTCSBC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEE--------------------------EEEeCCCCCee
Confidence            34578999999999999999999999999997        355                          77788899999


Q ss_pred             ceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          228 GFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       228 g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      |||||+|.+.++|.+|+..|||..|.|+.|+|.++.++....
T Consensus        66 g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  107 (113)
T 2cpe_A           66 GDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN  107 (113)
T ss_dssp             SEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCCST
T ss_pred             eEEEEEECCHHHHHHHHHHcCCCccCCCEEEEEECCCCCCCC
Confidence            999999999999999999999999999999999998776543

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.69  E-value=2.6e-17  Score=136.81  Aligned_cols=80  Identities=26%  Similarity=0.491  Sum_probs=75.5

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCC---eEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGK---VVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~---V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ..++|||+|||+.+|+++|+++|+.||.   |..|+|++++. |+++|||||+|.+.++|.+||. ||+..|+||.|+|.
T Consensus        43 ~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           43 EGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVF  120 (136)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            4569999999999999999999999999   89999999987 9999999999999999999999 99999999999999


Q ss_pred             Ecccc
Q 017842          355 VAEDR  359 (365)
Q Consensus       355 ~a~~~  359 (365)
                      ++..+
T Consensus       121 ~a~~~  125 (136)
T 2hgl_A          121 KSHRT  125 (136)
T ss_dssp             ECCHH
T ss_pred             ECChH
Confidence            98654

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.2e-16  Score=121.42  Aligned_cols=76  Identities=18%  Similarity=0.278  Sum_probs=70.7

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHh-CCCccCCeeEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL-DGQNLDGRAIRVN  354 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l-~~~~l~gr~l~V~  354 (365)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|++.++      +|||||+|.+.++|.+|+..| +|..+.|++|+|.
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            345569999999999999999999999999999999864      899999999999999999988 9999999999999


Q ss_pred             Ecc
Q 017842          355 VAE  357 (365)
Q Consensus       355 ~a~  357 (365)
                      ||+
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            985

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=3.4e-17  Score=131.16  Aligned_cols=80  Identities=19%  Similarity=0.302  Sum_probs=72.0

Q ss_pred             CCCCceEEEeCCCCc-CcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC--CCccCCeeEE
Q 017842          276 FEPGFRIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD--GQNLDGRAIR  352 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~-~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~--~~~l~gr~l~  352 (365)
                      ..+.++|||+|||+. +++++|+++|+.||.|..|+|++      ++|||||+|.+.++|.+|+..|+  +..|.||+|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            456779999999998 99999999999999999999974      38999999999999999999885  4569999999


Q ss_pred             EEEcccccc
Q 017842          353 VNVAEDRQR  361 (365)
Q Consensus       353 V~~a~~~~~  361 (365)
                      |.||..+.+
T Consensus        96 V~~a~~~~~  104 (112)
T 1x4f_A           96 VDLSEKYKK  104 (112)
T ss_dssp             EEEECSCSS
T ss_pred             EEECccccc
Confidence            999987654

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.69  E-value=8.6e-17  Score=128.56  Aligned_cols=96  Identities=25%  Similarity=0.457  Sum_probs=80.3

Q ss_pred             ccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCc-CcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecC
Q 017842          252 IDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSS  330 (365)
Q Consensus       252 ~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~-~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s  330 (365)
                      ..|..|+|..+.......     ...+.++|||+|||+. +++++|+++|+.||.|..|+|        ++|||||+|.+
T Consensus         5 ~~g~~~~~~~s~~~~~~~-----~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~   71 (110)
T 1wf1_A            5 SSGMSLKLQASNVTNKND-----PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSN   71 (110)
T ss_dssp             CCSCCCCCCCCCSCCSCC-----CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSS
T ss_pred             CCCcccccccCCCCCCCC-----CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECC
Confidence            356677776555433221     2234469999999999 999999999999999999998        48999999999


Q ss_pred             HHHHHHHHHHhCCCccCCeeEEEEEccccc
Q 017842          331 ETELNDAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       331 ~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      .++|.+|+..|||..|.|++|+|.|+..+.
T Consensus        72 ~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           72 ERHARAAVLGENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             SHHHHHHHHHHTTCEETTEECCEEESCCCC
T ss_pred             HHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            999999999999999999999999998544

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.69  E-value=2.1e-16  Score=127.68  Aligned_cols=86  Identities=28%  Similarity=0.497  Sum_probs=78.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||+|||+++++++|+.+|+.||.|..+.                          +..+. ++.++|||||+|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~-~g~~~g~afV~F~   56 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVL--------------------------LIKDR-TSKSRGFAFITFE   56 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEE--------------------------EECST-TTTCCCEEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEECC-CCCcccEEEEEEC
Confidence            34578999999999999999999999999999887                          66666 8999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..|||..|+|+.|+|.++.++...
T Consensus        57 ~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~   89 (116)
T 2fy1_A           57 NPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQ   89 (116)
T ss_dssp             SHHHHHHHHHHCSSCBCSSSBCEEEECCCSSCS
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEECCCCCCC
Confidence            999999999999999999999999999876644

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.69  E-value=4e-17  Score=127.08  Aligned_cols=82  Identities=17%  Similarity=0.437  Sum_probs=74.5

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|+..|||..+.|++|+|.++
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            345699999999999999999999999988766     246889999999999999999999999999999999999999


Q ss_pred             cccccCC
Q 017842          357 EDRQRRS  363 (365)
Q Consensus       357 ~~~~~~~  363 (365)
                      .++.+.+
T Consensus        89 ~~~~~~~   95 (96)
T 1fjc_A           89 GEKGGTR   95 (96)
T ss_dssp             SSSCCCC
T ss_pred             CCCCCCC
Confidence            9887654

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.69  E-value=2.6e-16  Score=124.46  Aligned_cols=85  Identities=28%  Similarity=0.371  Sum_probs=77.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|+.||.|..+.                          ++.+. ++.++|||||+|.+
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~-~g~~~g~afV~f~~   65 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECT--------------------------VLRGP-DGSSKGCAFVKFSS   65 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEE--------------------------EEECS-SSCEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEECC-CCCcCcEEEEEeCC
Confidence            3578999999999999999999999999999887                          66665 78899999999999


Q ss_pred             HHHHHHHHHHHccCcccC---eeEEEeecCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDG---RLLTVNKAAPRGTQ  268 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~g---r~l~V~~a~~~~~~  268 (365)
                      .++|.+|+..|||..+.|   +.|+|.++.++..+
T Consensus        66 ~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~~~  100 (105)
T 2dnh_A           66 HTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES  100 (105)
T ss_dssp             HHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSCCC
T ss_pred             HHHHHHHHHHHcCCccCCCCCccEEEEECccCccc
Confidence            999999999999999998   99999999877654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=1e-16  Score=124.17  Aligned_cols=83  Identities=22%  Similarity=0.478  Sum_probs=76.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .++..++|||+|||+++++++|+++|+.||.|..+.                          +..+..+++++|||||+|
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~--------------------------i~~~~~~~~~~g~afV~f   65 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVT--------------------------IMKDKDTRKSKGVAFILF   65 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEE--------------------------ECCCSSSCCCTTCEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEeCCCCCCcccEEEEEE
Confidence            345678999999999999999999999999999887                          777778899999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      .+.++|.+|+..|||..|.|+.|+|.+++
T Consensus        66 ~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           66 LDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             SCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            99999999999999999999999999863

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.52  E-value=1.8e-18  Score=139.77  Aligned_cols=86  Identities=26%  Similarity=0.373  Sum_probs=80.8

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEE--------EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVN--------ARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDG  348 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~--------v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g  348 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..        |+|++++.+++++|||||+|.+.++|.+|+..|||..+.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            34569999999999999999999999999999        9999998899999999999999999999999999999999


Q ss_pred             eeEEEEEccccccC
Q 017842          349 RAIRVNVAEDRQRR  362 (365)
Q Consensus       349 r~l~V~~a~~~~~~  362 (365)
                      ++|+|.+|.++...
T Consensus        85 ~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           85 NPIKVSFATRRADF   98 (116)
Confidence            99999999987654

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.69  E-value=7.6e-17  Score=128.69  Aligned_cols=80  Identities=20%  Similarity=0.448  Sum_probs=73.0

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|.        +|||||+|.+.++|.+|+..|||..+.|++|+|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34556799999999999999999999999999999997        7899999999999999999999999999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      |+++++++
T Consensus        99 ~a~~~~~r  106 (108)
T 2jvo_A           99 YSKLPAKR  106 (108)
T ss_dssp             SCSCCC--
T ss_pred             EecCCCCC
Confidence            99987764

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.69  E-value=4.3e-17  Score=130.70  Aligned_cols=78  Identities=23%  Similarity=0.303  Sum_probs=71.0

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccC-CeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHG-KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G-~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      .++|||+|||+.+++++|+++|+.|| .|..++|..    +.++|||||+|.+.++|.+|+..|||..|.||+|+|.++.
T Consensus        28 ~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~  103 (111)
T 2jvr_A           28 RYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDD  103 (111)
T ss_dssp             CEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            46999999999999999999999999 899999863    2479999999999999999999999999999999999998


Q ss_pred             ccc
Q 017842          358 DRQ  360 (365)
Q Consensus       358 ~~~  360 (365)
                      .++
T Consensus       104 ~~p  106 (111)
T 2jvr_A          104 NPP  106 (111)
T ss_dssp             C--
T ss_pred             CCC
Confidence            664

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.69  E-value=1.8e-16  Score=125.69  Aligned_cols=87  Identities=29%  Similarity=0.419  Sum_probs=79.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+.+|++||.|..++                          ++.+..+++++|||||+|.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~g~~~g~afV~f~   63 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELT--------------------------VLKDRFTGMHKGCAFLTYC   63 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEE--------------------------CCCCSSSCSCCSEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE--------------------------EEecCCCCCcceEEEEEEC
Confidence            34578999999999999999999999999999887                          7778888999999999999


Q ss_pred             CHHHHHHHHHHHccCcc---cCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDI---DGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~---~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..|||..+   .|+.|+|.++.++...
T Consensus        64 ~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~~~   99 (106)
T 2dgp_A           64 ERESALKAQSALHEQKTLPGMNRPIQVKPADSESRG   99 (106)
T ss_dssp             SHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCSCC
T ss_pred             CHHHHHHHHHHhcCCcccCCCCceEEEEECCccccc
Confidence            99999999999999988   8999999999876543

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.69  E-value=1.2e-16  Score=131.71  Aligned_cols=88  Identities=27%  Similarity=0.465  Sum_probs=80.6

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEE
Q 017842          154 VEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVT  233 (365)
Q Consensus       154 ~~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~  233 (365)
                      ..+.+.++|||+|||+++++++|+.+|+.||.|..+.                          ++.+..+++++|||||+
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~--------------------------i~~d~~tg~~~G~afV~   94 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVS--------------------------IVYDQQSRRSRGFAFVY   94 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEE--------------------------EECCSSSSCCCCEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEecCCCCccceEEEEE
Confidence            3455688999999999999999999999999998887                          77788889999999999


Q ss_pred             eCCHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      |.+.++|.+|+..|||..|+|+.|+|.++.++.+
T Consensus        95 F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~~p  128 (129)
T 2kxn_B           95 FENVDDAKEAKERANGMELDGRRIRVDFSITKRP  128 (129)
T ss_dssp             ESCHHHHHHHHHHHTTCCSSSSCCEESCCSSSSC
T ss_pred             ECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            9999999999999999999999999999987653

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.69  E-value=1.4e-16  Score=121.98  Aligned_cols=81  Identities=20%  Similarity=0.434  Sum_probs=75.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||+|||+++++++|+.+|+.||.|..++                          +..+..+++++|||||+|.+.+
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~~~   59 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVT--------------------------ILCDKFSGHPKGFAYIEFSDKE   59 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEE--------------------------EEESCSSSSCCEEEEEEESSTH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE--------------------------EEecCCCCCcceEEEEEECCHH
Confidence            57999999999999999999999999999887                          7778889999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      +|.+|+ .+||..|.|+.|+|.++.+..
T Consensus        60 ~a~~a~-~~~g~~~~g~~l~V~~a~~~~   86 (89)
T 3ucg_A           60 SVRTSL-ALDESLFRGRQIKVIPKRTNR   86 (89)
T ss_dssp             HHHHHG-GGTTCEETTEECEEEETTTTS
T ss_pred             HHHHHH-hcCCCEECCcEEEEEEccCCC
Confidence            999999 889999999999999987643

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.68  E-value=4.2e-17  Score=147.57  Aligned_cols=80  Identities=24%  Similarity=0.502  Sum_probs=77.1

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccC--CeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHG--KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G--~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ++|||+|||+.+|+++|+++|+.||  .|..|+|++++.+++++|||||+|.+.++|.+||..||+..|.||+|+|.+|.
T Consensus        69 ~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~  148 (229)
T 3q2s_C           69 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVN  148 (229)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECC
Confidence            4899999999999999999999999  99999999999999999999999999999999999999999999999999986


Q ss_pred             cc
Q 017842          358 DR  359 (365)
Q Consensus       358 ~~  359 (365)
                      +.
T Consensus       149 ~~  150 (229)
T 3q2s_C          149 KQ  150 (229)
T ss_dssp             HH
T ss_pred             CC
Confidence            43

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=5.4e-17  Score=129.74  Aligned_cols=78  Identities=21%  Similarity=0.333  Sum_probs=73.0

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.| .|..|+|++++. |+++|||||+|.+.++|.+||. ||+..|+||.|+|..+..
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHH-TTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECCc
Confidence            4699999999999999999999999 899999999975 9999999999999999999995 999999999999998865


Q ss_pred             c
Q 017842          359 R  359 (365)
Q Consensus       359 ~  359 (365)
                      +
T Consensus        93 ~   93 (109)
T 2dnn_A           93 R   93 (109)
T ss_dssp             H
T ss_pred             c
Confidence            4

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.68  E-value=1.3e-16  Score=127.34  Aligned_cols=85  Identities=22%  Similarity=0.320  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|+.||.|..+.                          ++.+..++.++|||||+|.+
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~   77 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIH--------------------------LNLDRRTGFSKGYALVEYET   77 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------CCBCTTTSSBCSEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEecCCCCCcceEEEEEECC
Confidence            3568999999999999999999999999998887                          77777899999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      .++|.+|+..|||..|+|+.|+|.++.++..
T Consensus        78 ~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  108 (110)
T 1oo0_B           78 HKQALAAKEALNGAEIMGQTIQVDWCFVKGP  108 (110)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEEESEESSC
T ss_pred             HHHHHHHHHHcCCCEECCcEEEEEEcccCCC
Confidence            9999999999999999999999999876653

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.68  E-value=2.3e-16  Score=124.50  Aligned_cols=85  Identities=21%  Similarity=0.451  Sum_probs=77.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+.+|..|| |..++                          ++.+..+++++|||||+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~--------------------------i~~~~~~g~~~g~afV~f~   64 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVR--------------------------LVRDKDTDKFKGFCYVEFD   64 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEE--------------------------EEECSSSCSEEEEEEEEES
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEE--------------------------EeecCCCCccceEEEEEEC
Confidence            34578999999999999999999999997 88877                          7788889999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+ .|||..|.|+.|+|.++.++...
T Consensus        65 ~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2dng_A           65 EVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQD   96 (103)
T ss_dssp             SHHHHHHHG-GGTTCEETTEECEEEECCCCCCC
T ss_pred             CHHHHHHHH-hhCCCeECCeEEEEEEecCCCCC
Confidence            999999999 78999999999999999876544

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=8.2e-17  Score=127.40  Aligned_cols=81  Identities=17%  Similarity=0.204  Sum_probs=73.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||||||+++|+++|+.+|+.||.|..++                          ++.+.. ++++|||||+|.
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~--------------------------i~~d~~-g~~rG~aFV~F~   60 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ--------------------------MRRTLH-KAFKGSIFVVFD   60 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEE--------------------------EECCCT-TSCCCEEEEEES
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEE--------------------------EEECCC-CCCccEEEEEEC
Confidence            33568999999999999999999999999999987                          666766 899999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      +.++|.+|+. ++|..|+|+.|+|.++..
T Consensus        61 ~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           61 SIESAKKFVE-TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             SHHHHHHHHT-SSCCCCTTTTCEEEEHHH
T ss_pred             CHHHHHHHHH-cCCCEECCEEEEEEEchH
Confidence            9999999999 699999999999987643

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.68  E-value=6.6e-17  Score=127.09  Aligned_cols=76  Identities=22%  Similarity=0.407  Sum_probs=71.3

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||+|||+.+++++|+++|+.||.|..|++.      +++|||||+|.+.++|.+|+..|||..+.|++|+|.||+
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            34699999999999999999999999999999997      348999999999999999999999999999999999998


Q ss_pred             cc
Q 017842          358 DR  359 (365)
Q Consensus       358 ~~  359 (365)
                      ++
T Consensus       100 ~~  101 (101)
T 2la4_A          100 ER  101 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.68  E-value=4.1e-17  Score=128.51  Aligned_cols=81  Identities=23%  Similarity=0.545  Sum_probs=75.8

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||+|||+.+++++|+++|+.||.|..|+|++++ +|+++|||||+|.+.++|.+|+.  ++..|+|++|.|.++.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            34699999999999999999999999999999999998 89999999999999999999999  9999999999999998


Q ss_pred             cccc
Q 017842          358 DRQR  361 (365)
Q Consensus       358 ~~~~  361 (365)
                      .+..
T Consensus        85 ~~~~   88 (102)
T 2xs2_A           85 RKQN   88 (102)
T ss_dssp             ECC-
T ss_pred             cCcc
Confidence            6654

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.68  E-value=9.7e-17  Score=125.10  Aligned_cols=79  Identities=25%  Similarity=0.515  Sum_probs=71.8

Q ss_pred             CCCCceEEEeCCCC-cCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          276 FEPGFRIYVGNLPW-EVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       276 ~~~~~~lfV~nLp~-~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ..+.++|||+|||+ .+++++|+++|+.||.|..|+|.        +|||||+|.+.++|.+|+..|||..+.|++|+|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34567999999999 99999999999999999999984        7899999999999999999999999999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      |++++.++
T Consensus        79 ~a~~~~~~   86 (96)
T 2kvi_A           79 VSSSNARP   86 (96)
T ss_dssp             EEECCCC-
T ss_pred             EcCcCCCC
Confidence            99876654

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.68  E-value=2.2e-17  Score=131.46  Aligned_cols=82  Identities=21%  Similarity=0.378  Sum_probs=76.3

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCC---eEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGK---VVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~---V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      ...++|||+|||+.+|+++|+++|+.||.   |..|+|++++. |+++|||||+|.+.++|.+||. ||+..|+||.|+|
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            34569999999999999999999999988   99999999987 9999999999999999999999 9999999999999


Q ss_pred             EEccccc
Q 017842          354 NVAEDRQ  360 (365)
Q Consensus       354 ~~a~~~~  360 (365)
                      .++.++.
T Consensus        87 ~~a~~~~   93 (107)
T 2lmi_A           87 YEINNED   93 (107)
T ss_dssp             EECCHHH
T ss_pred             EECCHHH
Confidence            9987643

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.7e-16  Score=124.17  Aligned_cols=84  Identities=25%  Similarity=0.370  Sum_probs=78.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeE-EEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVE-IAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~-~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ...++|||+|||+++++++|+.+|++||.|. .++                          ++.++.+++++|||||+|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~--------------------------i~~~~~~g~~~g~afV~f~   60 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVK--------------------------IIRNRLTGIPAGYCFVEFA   60 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEE--------------------------EEECSSSCCEEEEEEEECS
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEE--------------------------EeecCCCCCcCCEEEEEeC
Confidence            3578999999999999999999999999998 877                          7788889999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCee----EEEeecCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRL----LTVNKAAPRG  266 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~----l~V~~a~~~~  266 (365)
                      +.++|.+|+..|||..+.|+.    |+|.++.+..
T Consensus        61 ~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~~   95 (99)
T 2div_A           61 DLATAEKCLHKINGKPLPGATPAKRFKLNYATYSG   95 (99)
T ss_dssp             CHHHHHHHHHTTTTSEESSCSSCEECCEEETTCCS
T ss_pred             CHHHHHHHHHHHcCCccCCCCcceeEEEeecCCCC
Confidence            999999999999999999999    9999987654

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.68  E-value=2.7e-16  Score=124.14  Aligned_cols=78  Identities=22%  Similarity=0.444  Sum_probs=72.2

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..|+|+        +|||||+|.+.++|.+|+..|||..|.|++|+|.|+
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            445699999999999999999999999999999987        569999999999999999999999999999999999


Q ss_pred             cccccC
Q 017842          357 EDRQRR  362 (365)
Q Consensus       357 ~~~~~~  362 (365)
                      .++..+
T Consensus        81 ~~~~~~   86 (103)
T 2dgu_A           81 KPPDQK   86 (103)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            876643

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.68  E-value=1.9e-16  Score=120.91  Aligned_cols=80  Identities=33%  Similarity=0.580  Sum_probs=73.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+.+|++||.|..+.                          ++.+..+++++|||||+|.
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~g~~~g~afV~f~   61 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCT--------------------------IKMDPNTGRSRGFGFILFK   61 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEE--------------------------EEECTTTCCEEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE--------------------------EeecCCCCccccEEEEEEC
Confidence            34678999999999999999999999999999887                          7778889999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeec
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      +.++|.+|+.. ++..|+|+.|+|.++
T Consensus        62 ~~~~a~~A~~~-~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           62 DAASVEKVLDQ-KEHRLDGRVIDPKKA   87 (87)
T ss_dssp             STHHHHHHHHS-SCEEETTEEEEEEEC
T ss_pred             CHHHHHHHHHh-CCCEECCEEEEEEeC
Confidence            99999999976 888899999999875

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=7e-17  Score=122.78  Aligned_cols=81  Identities=19%  Similarity=0.403  Sum_probs=75.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      .+.++|||+|||+++++++|+.+|++||.|..+.                          ++.+..++.++|||||+|.+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~--------------------------i~~~~~~~~~~g~afV~f~~   56 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTK--------------------------AILDKTTNKCKGYGFVDFDS   56 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEE--------------------------EECCSSSCSCCSEEEEEESC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEecCCCCCcCcEEEEEECC
Confidence            4578999999999999999999999999999887                          77788899999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      .++|.+|+..|||..|.|+.|+|.++.
T Consensus        57 ~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A           57 PSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             HHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             HHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            999999999999999999999988654

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.67  E-value=1e-16  Score=158.14  Aligned_cols=84  Identities=25%  Similarity=0.439  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +.++|||+|||+++|+++|..+|..||.|..|.                          |+.+..++.++|||||+|.+.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~--------------------------i~~d~~tg~~kG~aFV~F~~~  154 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIH--------------------------MVYSKRSGKPRGYAFIEYEHE  154 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEE--------------------------eeccCCCCCccceEEEeeccH
Confidence            467999999999999999999999999999887                          777888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|.+||..|||..|.|+.|.|.++.+...
T Consensus       155 e~A~~Ai~~lng~~i~gr~i~V~~a~~~~~  184 (437)
T 3pgw_S          155 RDMHSAYKHADGKKIDGRRVLVDVERGRTV  184 (437)
T ss_pred             HHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            999999999999999999999999986543

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.67  E-value=2.4e-16  Score=140.83  Aligned_cols=84  Identities=26%  Similarity=0.440  Sum_probs=78.6

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..|++..+.|+.|++.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccc
Q 017842          357 EDRQ  360 (365)
Q Consensus       357 ~~~~  360 (365)
                      ....
T Consensus        93 ~~~~   96 (213)
T 4f02_A           93 QRDP   96 (213)
T ss_dssp             CCCT
T ss_pred             cccc
Confidence            7543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.67  E-value=1.7e-16  Score=130.98  Aligned_cols=85  Identities=21%  Similarity=0.381  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEE--EEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEI--AEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~--~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      ...++|||||||+++++++|+.+|..||.|..  ++                          +++++.+++++|||||+|
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~--------------------------i~~d~~tg~~rG~aFV~f   74 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVR--------------------------VIKDKQTQLNRGFAFIQL   74 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEE--------------------------CCBCSSSSSBCSCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEE--------------------------EEEcCCCCCcceEEEEEE
Confidence            35679999999999999999999999999966  66                          888888999999999999


Q ss_pred             CCHHHHHHHHHHHccC----cccCeeEEEeecCCCCCC
Q 017842          235 STVEEAEKAVEMFHRY----DIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~----~~~gr~l~V~~a~~~~~~  268 (365)
                      .+. +|.+|+..|||.    .|+|+.|+|.++.+....
T Consensus        75 ~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           75 STI-EAAQLLQILQALHPPLTIDGKTINVEFAKGSKRD  111 (131)
T ss_dssp             CHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCSCCC
T ss_pred             CCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCCCCC
Confidence            999 999999999999    999999999999876543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1.7e-16  Score=125.60  Aligned_cols=87  Identities=32%  Similarity=0.543  Sum_probs=79.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+.+|..||.|..+.                          ++.++.+++++|||||+|.
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~--------------------------i~~~~~~g~~~g~afV~f~   66 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCV--------------------------IMKDKTTNQSRGFGFVKFK   66 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEE--------------------------EEECSSSCCEEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EeeCCCCCCcceEEEEEEC
Confidence            34678999999999999999999999999999887                          7788889999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      +.++|.+|+.. ++..|+|+.|+|.++.++....
T Consensus        67 ~~~~a~~a~~~-~~~~~~g~~l~V~~a~~~~~~~   99 (105)
T 2dh8_A           67 DPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGMQP   99 (105)
T ss_dssp             STTHHHHHHHH-CSEEETTEEEBCCCSCCSSCCT
T ss_pred             CHHHHHHHHHh-CCCeECCEEEEEEEccCCCCCC
Confidence            99999999999 9999999999999998776543

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=3.4e-16  Score=123.68  Aligned_cols=85  Identities=20%  Similarity=0.421  Sum_probs=77.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCC-CCccceEEEEeC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRET-DRSRGFGFVTMS  235 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~g~afV~f~  235 (365)
                      ...++|||+|||+++++++|+.+|..|| |..+.                          ++.+..+ ++++|||||+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~--------------------------i~~~~~~~g~~~g~afV~f~   65 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVR--------------------------LPREPSNPERLKGFGYAEFE   65 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEE--------------------------CCBCSSCTTSBCSCEEEEES
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEE--------------------------EecCCCCCCCcCeEEEEEEC
Confidence            4568999999999999999999999999 98877                          6777777 899999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      +.++|.+|+ .|||..|.|+.|+|.++.++....
T Consensus        66 ~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~~   98 (104)
T 1wi8_A           66 DLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKD   98 (104)
T ss_dssp             SHHHHHHHH-GGGTCEETTEECEEEECCCCCCCC
T ss_pred             CHHHHHHHH-hcCCCEeCCcEEEEEEccCCCCCC
Confidence            999999999 889999999999999998776543

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=6.9e-16  Score=121.66  Aligned_cols=86  Identities=31%  Similarity=0.563  Sum_probs=76.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||+|||+++++++|+++|..||.|..++                          ++.+..  .++|||||+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~--------------------------i~~~~~--~~~g~afV~f~   63 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE--------------------------IIFNER--GSKGFGFVTFE   63 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEE--------------------------EECCTT--TTCCEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEecCC--CCcEEEEEEEC
Confidence            34578999999999999999999999999999887                          454433  38999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      +.++|.+|+..|||..|+|+.|+|.++.++....
T Consensus        64 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   97 (103)
T 2cq3_A           64 NSADADRAREKLHGTVVEGRKIEVNNATARVMTN   97 (103)
T ss_dssp             CHHHHHHHHHHHTTCEETTEECEEEECCSSCCCC
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEEcccCCCCC
Confidence            9999999999999999999999999998876544

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.67  E-value=1.6e-16  Score=135.22  Aligned_cols=82  Identities=20%  Similarity=0.352  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccC--CeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAG--TVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G--~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ..++|||||||+++++++|+.+|+.||  .|..++                          ++.++.+|+++|||||+|.
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~--------------------------i~~d~~tg~skGfaFV~f~  107 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELK--------------------------FAENRANGQSKGYAEVVVA  107 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEE--------------------------EEECTTTCCEEEEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEE--------------------------EEecCCCCccceEEEEEEC
Confidence            367999999999999999999999999  887776                          8888899999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      +.++|.+|+..|||..|+|+.|+|.++.+.
T Consensus       108 ~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~~  137 (156)
T 3n9u_C          108 SENSVHKLLELLPGKVLNGEKVDVRPATRQ  137 (156)
T ss_dssp             CHHHHHHHHHHSTTCEETTEECEEEECCHH
T ss_pred             CHHHHHHHHHHcCCCEECCeEeEEEEcCCC
Confidence            999999999999999999999999988653

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.9e-16  Score=125.04  Aligned_cols=83  Identities=33%  Similarity=0.607  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|+.||.|..+.                          +..+..++.++|||||+|.+.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~--------------------------i~~~~~~g~~~g~afV~f~~~   60 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFR--------------------------LVYDRETGKPKGYGFCEYQDQ   60 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEE--------------------------EEEETTTTEEEEEEEEECSCH
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEE--------------------------EEeCCCCCccceEEEEEECCH
Confidence            357999999999999999999999999998887                          777878999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ++|.+|+..|||..|.|+.|+|.++.+..
T Consensus        61 ~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   89 (104)
T 1p1t_A           61 ETALSAMRNLNGREFSGRALRVDNAASEK   89 (104)
T ss_dssp             HHHHHHHHHSSSBSCSSSCBEEEETTCTT
T ss_pred             HHHHHHHHHhCCCeeCCcEEEEEeCCCcc
Confidence            99999999999999999999999988664

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=3.1e-16  Score=123.97  Aligned_cols=82  Identities=17%  Similarity=0.227  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +.+.++|||+|||+++++++|+.+|++||.|..++                          ++.      .+|||||+|.
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~--------------------------i~~------~kGfaFVeF~   60 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLL--------------------------MLK------GKNQAFIEMN   60 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEE--------------------------EET------TTTEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEc------CCCEEEEEEC
Confidence            45678999999999999999999999999999987                          332      3899999999


Q ss_pred             CHHHHHHHHHHHc--cCcccCeeEEEeecCCCCCCC
Q 017842          236 TVEEAEKAVEMFH--RYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       236 ~~e~a~~Al~~ln--g~~~~gr~l~V~~a~~~~~~~  269 (365)
                      +.++|.+|+..|+  +..|.|+.|+|.++.++....
T Consensus        61 ~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~~~   96 (105)
T 1sjq_A           61 TEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT   96 (105)
T ss_dssp             SHHHHHHHHHHHTTSCCEETTEECCBCCCSSSSCCC
T ss_pred             CHHHHHHHHHHhccCCceECCEEEEEEEcCCCCCCc
Confidence            9999999999876  478999999999998776544

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=6.8e-16  Score=121.67  Aligned_cols=85  Identities=25%  Similarity=0.359  Sum_probs=75.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||+|||+++++++|+.+|+.||.|..+.                          ++.+.  +.++|||||+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~--~~~~g~afV~f~   63 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCK--------------------------MITEH--TSNDPYCFVEFY   63 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEE--------------------------EECCC--CSSCCEEEEEES
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEE--------------------------EEecC--CCCCCEEEEEEC
Confidence            34578999999999999999999999999999887                          55553  336899999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..|||..|.|+.|+|.++.++...
T Consensus        64 ~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2cqi_A           64 EHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ   96 (103)
T ss_dssp             SHHHHHHHHHHHTTEEETTEEEEEEECCCTTCC
T ss_pred             CHHHHHHHHHHhCCCCcCCCeEEEEECCCCccc
Confidence            999999999999999999999999999876544

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.67  E-value=3.9e-16  Score=132.69  Aligned_cols=83  Identities=27%  Similarity=0.493  Sum_probs=79.0

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|++++++.+|+++|||||+|.+.++|.+|+..|+|..+.|++|+|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            46999999999999999999999999999999999988999999999999999999999999999999999999999986


Q ss_pred             ccc
Q 017842          359 RQR  361 (365)
Q Consensus       359 ~~~  361 (365)
                      ...
T Consensus        82 ~~~   84 (167)
T 1fxl_A           82 SSA   84 (167)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.67  E-value=4.7e-16  Score=119.88  Aligned_cols=83  Identities=29%  Similarity=0.473  Sum_probs=75.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|.+||.|..+.                          +..  .+++++|||||+|.+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~--------------------------i~~--~~g~~~g~afV~f~~   57 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYAD--------------------------IKM--ENGKSKGCGVVKFES   57 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEE--------------------------EEE--SSSCEEEEEEEEESS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEc--cCCCcceEEEEEECC
Confidence            3578999999999999999999999999999887                          443  378899999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      .++|.+|+..|||..|+|+.|+|.++.+...
T Consensus        58 ~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   88 (92)
T 2dgv_A           58 PEVAERACRMMNGMKLSGREIDVRIDRNASG   88 (92)
T ss_dssp             HHHHHHHHHHHTTCCBTTBCCCCEECSCCSS
T ss_pred             HHHHHHHHHHhCCCEECCcEEEEEEcCCCCC
Confidence            9999999999999999999999999887654

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.67  E-value=1.9e-17  Score=138.09  Aligned_cols=82  Identities=20%  Similarity=0.295  Sum_probs=75.1

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ...++|||+|||+.+|+++|+++|+.|| |..|+|++++. ++++|||||+|.+.++|.+|| .+|+..|.||.|+|.++
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            3456999999999999999999999999 77999999976 999999999999999999999 58999999999999999


Q ss_pred             ccccc
Q 017842          357 EDRQR  361 (365)
Q Consensus       357 ~~~~~  361 (365)
                      ..+..
T Consensus       121 ~~~~~  125 (139)
T 2hgn_A          121 STTGA  125 (139)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            87654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.67  E-value=9.2e-16  Score=127.64  Aligned_cols=89  Identities=33%  Similarity=0.548  Sum_probs=81.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+.+|+.||.|..+.                          ++.+..+++++|||||+|.
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~   92 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVK--------------------------IVCDRETRQSRGYGFVKFQ   92 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEE--------------------------EEEETTTTEEEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEEcCCCCCcceEEEEEEC
Confidence            44578999999999999999999999999999887                          7778888999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPE  270 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~  270 (365)
                      +.++|.+|+..|||..|.|+.|+|.++.++..+..
T Consensus        93 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~  127 (139)
T 1u6f_A           93 SGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPG  127 (139)
T ss_dssp             SHHHHHHHHHHTTTEECSSCEEEEEESSCCCCCCC
T ss_pred             CHHHHHHHHHHhCCCEECCeEEEEEECCCCCCCCC
Confidence            99999999999999999999999999988765543

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.66  E-value=3.3e-16  Score=133.58  Aligned_cols=84  Identities=26%  Similarity=0.461  Sum_probs=79.7

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +.++|||+|||+.+++++|+++|+.||.|..|++.+++.+|+++|||||+|.+.++|.+|+..|+|..+.|++|+|.|+.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            35699999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             cccc
Q 017842          358 DRQR  361 (365)
Q Consensus       358 ~~~~  361 (365)
                      ++..
T Consensus        82 ~~~~   85 (168)
T 1b7f_A           82 PGGE   85 (168)
T ss_dssp             CCSS
T ss_pred             CCcc
Confidence            7654

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.66  E-value=2.8e-16  Score=121.96  Aligned_cols=81  Identities=30%  Similarity=0.490  Sum_probs=74.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+++|+.||.|..+.                          +..+.. ++++|||||+|.+
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~--------------------------i~~~~~-g~~~g~afV~f~~   66 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVT--------------------------ICKDRE-GKPKSFGFVCFKH   66 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTT-SCEEEEEEEEESS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEECCC-CCCceEEEEEECC
Confidence            3568999999999999999999999999999887                          666654 8899999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      .++|.+|+..|||..|.|+.|+|.++..
T Consensus        67 ~~~a~~A~~~l~g~~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           67 PESVSYAIALLNGIRLYGRPINVSGPSS   94 (95)
T ss_dssp             THHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             HHHHHHHHHHhCCCEECCCEEEEEEcCC
Confidence            9999999999999999999999998753

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.66  E-value=2.6e-16  Score=125.71  Aligned_cols=86  Identities=31%  Similarity=0.502  Sum_probs=75.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+.+|+.||.|..++                          ++.+..+++++|||||+|.
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~--------------------------i~~~~~tg~~kg~afV~f~   75 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECL--------------------------VMRDPLTKRSRGFGFVTFM   75 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEE--------------------------ECCCTTTCCCTTCEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEE--------------------------EEECCCCCCcCcEEEEEEC
Confidence            34578999999999999999999999999999887                          7778888999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..+ |..|+|+.|+|.++.++..+
T Consensus        76 ~~~~A~~Ai~~~-~~~l~g~~l~V~~a~~~~~~  107 (109)
T 2rs2_A           76 DQAGVDKVLAQS-RHELDSKTIDPKVAFPRRAQ  107 (109)
T ss_dssp             SHHHHHHHHHSS-CEEETTEEEEEEECCCCCCC
T ss_pred             CHHHHHHHHHHC-CCcCCCEEEEEEEccCCCCC
Confidence            999999999985 69999999999999876543

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.6e-16  Score=122.99  Aligned_cols=79  Identities=24%  Similarity=0.431  Sum_probs=70.6

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCC-eEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCC-CccCCeeEEEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGK-VVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDG-QNLDGRAIRVN  354 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~-V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~-~~l~gr~l~V~  354 (365)
                      .+.++|||+|||+.+++++|+++|+.||. |..+.+.       ++|||||+|.+.++|.+|+..||| ..+.|++|+|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            34569999999999999999999999999 6666552       489999999999999999999999 99999999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      |+.++..+
T Consensus        79 ~a~~~~~~   86 (93)
T 2cqh_A           79 YSVSKKLR   86 (93)
T ss_dssp             ECCCCCCC
T ss_pred             EccCcccc
Confidence            99987654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=4.6e-16  Score=125.45  Aligned_cols=85  Identities=41%  Similarity=0.558  Sum_probs=77.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||+|||+++++++|+.+|..||.|..++                          ++.+..+++++|||||+|.
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~   67 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAV--------------------------VITDRQTGKSRGYGFVTMA   67 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEE--------------------------ESCCSSSCCCCSEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEE--------------------------EEEcCCCCccceEEEEEEC
Confidence            34678999999999999999999999999998887                          7778888999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      +.++|.+|+..+++ .|.|+.|+|.++.+...
T Consensus        68 ~~~~a~~Ai~~~~~-~~~g~~l~V~~a~~~~~   98 (116)
T 2cqd_A           68 DRAAAERACKDPNP-IIDGRKANVNLAYLGAK   98 (116)
T ss_dssp             SHHHHHHHHTCSSC-EETTEECEEEESTTTCC
T ss_pred             CHHHHHHHHHhCCC-cCCCEEEEEEEcccCCC
Confidence            99999999999998 89999999999976543

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.66  E-value=2.9e-16  Score=134.76  Aligned_cols=86  Identities=22%  Similarity=0.322  Sum_probs=78.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|..||.|..+.                          ++.+..++.++|||||+|.+
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~--------------------------i~~~~~~g~~~g~afV~f~~  123 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIH--------------------------LNLDRRTGFSKGYALVEYET  123 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTSSEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE--------------------------EEecCCCCcEeeEEEEEECC
Confidence            4567899999999999999999999999999887                          77788899999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      .++|.+||..|||..|.|+.|.|.++.++...
T Consensus       124 ~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  155 (165)
T 1rk8_A          124 HKQALAAKEALNGAEIMGQTIQVDWCFVKGPK  155 (165)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEEESEECC--
T ss_pred             HHHHHHHHHHhCCCEECCEEEEEEEecCCCCC
Confidence            99999999999999999999999999876554

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.66  E-value=1.4e-16  Score=118.18  Aligned_cols=75  Identities=36%  Similarity=0.663  Sum_probs=70.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      +|||+|||+++++++|+.+|++||.|..+.                          +..+..+++++|||||+|.+.++|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~~~~a   54 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAM--------------------------LMFDKTTNRHRGFGFVTFESEDIV   54 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEEC--------------------------CCBCSSSTTSCBEEEEECSCHHHH
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEecCCCCCcCcEEEEEECCHHHH
Confidence            599999999999999999999999998877                          677777899999999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEeec
Q 017842          241 EKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      .+|+. ++|..++|+.|+|.++
T Consensus        55 ~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A           55 EKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             HHHHS-SSCCCSSSCCCEEECC
T ss_pred             HHHHH-CCCCEECCEEEEEEeC
Confidence            99998 7999999999999875

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.66  E-value=6.8e-16  Score=120.84  Aligned_cols=79  Identities=19%  Similarity=0.209  Sum_probs=70.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      .++.++|||+|||+++++++|+.+|++||.|..+.                          ++      +.+|||||+|.
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~--------------------------i~------~~kg~AFVef~   65 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVV--------------------------VM------PKKRQALVEFE   65 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EE------TTTTEEEEEES
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEE--------------------------EE------cCCCEEEEEEC
Confidence            34688999999999999999999999999999887                          33      35899999999


Q ss_pred             CHHHHHHHHHHHccCc--ccCeeEEEeecCCCC
Q 017842          236 TVEEAEKAVEMFHRYD--IDGRLLTVNKAAPRG  266 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~--~~gr~l~V~~a~~~~  266 (365)
                      +.++|.+|+..|+|..  +.|+.|+|.++.++.
T Consensus        66 ~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           66 DVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             SHHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             CHHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence            9999999999999976  789999999987653

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=2.5e-16  Score=126.29  Aligned_cols=76  Identities=17%  Similarity=0.094  Sum_probs=70.9

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|+|++      ++|||||+|.+.++|.+|+..|||..|.|++|+|.||..
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            45999999999999999999999999999999874      488999999999999999999999999999999999976


Q ss_pred             cc
Q 017842          359 RQ  360 (365)
Q Consensus       359 ~~  360 (365)
                      ..
T Consensus        84 ~~   85 (111)
T 1whx_A           84 GV   85 (111)
T ss_dssp             TT
T ss_pred             Cc
Confidence            43

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.66  E-value=4.5e-16  Score=127.29  Aligned_cols=86  Identities=24%  Similarity=0.342  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|..||.|..+.                          ++.+..++.++|||||+|.+
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~   73 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIH--------------------------LNLDRRTGYLKGYTLVEYET   73 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCBCTTTSSBCSCEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEecCCCCccceEEEEEECC
Confidence            3467999999999999999999999999998887                          77777899999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      .++|.+|+..|||..|+|+.|+|.++.++...
T Consensus        74 ~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  105 (126)
T 3ex7_B           74 YKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP  105 (126)
T ss_dssp             HHHHHHHHHHHTTCBSSSSBCEEEESEESSSC
T ss_pred             HHHHHHHHHHhCCCeeCCeEEEEEEecCCCCC
Confidence            99999999999999999999999999776543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=1.4e-15  Score=122.03  Aligned_cols=85  Identities=31%  Similarity=0.413  Sum_probs=76.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+++|..||.|..+.                          ++.+. +++++|||||+|.+
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~--------------------------i~~~~-~g~~~g~afV~f~~   65 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRAD--------------------------ILEDK-DGKSRGIGTVTFEQ   65 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEE--------------------------EEECT-TCSEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEECC-CCCeeeEEEEEECC
Confidence            3578999999999999999999999999998887                          66665 58899999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      .++|.+|+..|||..|+|+.|+|.++......
T Consensus        66 ~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   97 (114)
T 2do0_A           66 SIEAVQAISMFNGQLLFDRPMHVKMDERALPK   97 (114)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEEECSCCCCC
T ss_pred             HHHHHHHHHHhCCCEeCCCEEEEEEcccCCCC
Confidence            99999999999999999999999998765443

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.66  E-value=5.9e-16  Score=122.86  Aligned_cols=80  Identities=30%  Similarity=0.476  Sum_probs=74.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|..||.|..+.                          ++.+. ++.++|||||+|.+
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~-~g~~~g~afV~f~~   79 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAA--------------------------VHYDR-SGRSLGTADVHFER   79 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------EEECT-TSCEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEECC-CCCcceEEEEEECC
Confidence            4578999999999999999999999999998887                          66676 88999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      .++|.+|+..|||..|.|+.|+|.++.
T Consensus        80 ~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           80 KADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            999999999999999999999999875

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=6.5e-16  Score=123.02  Aligned_cols=86  Identities=23%  Similarity=0.313  Sum_probs=77.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCC-eEEEEEeeeeccCCCcccceeeeeeeeeeeeEE-ecCCCCCccceEEEEe
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGT-VEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVI-YNRETDRSRGFGFVTM  234 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~-i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~g~afV~f  234 (365)
                      .+.++|||+|||+++++++|+.+|..||. |..+.                          ++ .+..+++++|||||+|
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~--------------------------i~~~~~~~g~~~g~afV~f   59 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVI--------------------------VYASAADKMKNRGFAFVEY   59 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEE--------------------------CCSSSCTTTTTCCEEEEEE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEE--------------------------EEccCCCCCCcCcEEEEEe
Confidence            45789999999999999999999999998 98887                          55 6777889999999999


Q ss_pred             CCHHHHHHHHHHHc--cCcccCeeEEEeecCCCCCC
Q 017842          235 STVEEAEKAVEMFH--RYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       235 ~~~e~a~~Al~~ln--g~~~~gr~l~V~~a~~~~~~  268 (365)
                      .+.++|.+|+..|+  +..+.|+.|+|.++.++...
T Consensus        60 ~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~~~   95 (109)
T 2dis_A           60 ESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDV   95 (109)
T ss_dssp             SSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCST
T ss_pred             cCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCCCc
Confidence            99999999999996  59999999999999877653

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=5.1e-16  Score=120.99  Aligned_cols=80  Identities=25%  Similarity=0.377  Sum_probs=72.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHH----HHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEE
Q 017842          158 EDAKLFVGNLPYDVDSEKLA----MLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVT  233 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~----~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~  233 (365)
                      ..++|||+|||+++++++|+    .+|++||.|..++                          ++.+..+   +|||||+
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~--------------------------i~~~~~~---rg~afV~   58 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVE--------------------------LSPHTDY---QLKAVVQ   58 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEE--------------------------ECSCCST---TCCEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEE--------------------------EEeCCCC---CeEEEEE
Confidence            46799999999999999999    9999999999887                          5555544   8899999


Q ss_pred             eCCHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      |.+.++|.+|+..|||..|+|+.|+|.++.+..
T Consensus        59 f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~   91 (96)
T 2dgx_A           59 MENLQDAIGAVNSLHRYKIGSKKILVSLATGAS   91 (96)
T ss_dssp             ESSHHHHHHHHHHHTTEEETTEEEEEEECCCSS
T ss_pred             ECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            999999999999999999999999999997654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.65  E-value=1.7e-16  Score=128.40  Aligned_cols=80  Identities=13%  Similarity=0.147  Sum_probs=72.5

Q ss_pred             ceEEEeCC----CCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecC----HHH----HHHHHH--HhCCCc
Q 017842          280 FRIYVGNL----PWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSS----ETE----LNDAIA--ALDGQN  345 (365)
Q Consensus       280 ~~lfV~nL----p~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s----~~~----a~~Al~--~l~~~~  345 (365)
                      +.|||+||    |+.+++..|+.+|+.||.|..|.++.|+.||+++|||||+|.+    ...    |.+|+.  .|+|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            48999999    9999999999999999999999999999999999999999995    322    888888  789999


Q ss_pred             cCCeeEEEEEcccc
Q 017842          346 LDGRAIRVNVAEDR  359 (365)
Q Consensus       346 l~gr~l~V~~a~~~  359 (365)
                      |.||+|+|.+-++.
T Consensus        83 I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           83 IMGFKFEVILNKHS   96 (136)
T ss_dssp             ETTEEEEEEECCTT
T ss_pred             ecCcEEEEEECccc
Confidence            99999999987653

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=1.6e-16  Score=124.02  Aligned_cols=83  Identities=17%  Similarity=0.198  Sum_probs=75.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|..||.|..+.                          ++.+..+++++|||||+|.+.
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~--------------------------~~~~~~~g~~~g~afV~f~~~   67 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSV--------------------------CLKYNEKGMPTGEAMVAFESR   67 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTC--------------------------EEEECSSSCEEEEEEEEESCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccceE--------------------------EEEECCCCCeeeEEEEEECCH
Confidence            467999999999999999999999999987554                          667778999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ++|.+|+..|||..|.|+.|+|.++..+.
T Consensus        68 ~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   96 (98)
T 2cqp_A           68 DEATAAVIDLNDRPIGSRKVKLVLGSGPS   96 (98)
T ss_dssp             HHHHHHHHHTTTCEETTEECEEEESSCSS
T ss_pred             HHHHHHHHHhCCCeeCCeEEEEEEcCCCC
Confidence            99999999999999999999999987543

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.65  E-value=5.9e-16  Score=131.61  Aligned_cols=87  Identities=32%  Similarity=0.402  Sum_probs=79.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|+.||.|..++                          +..+..+++++|||||+|.+
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~--------------------------i~~~~~~g~~~g~afV~f~~  121 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVY--------------------------IPRDRYTKESRGFAFVRFHD  121 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEE--------------------------CCCCSSCTTSCCEEEEEESB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EeecCCCCccceEEEEEECC
Confidence            3478999999999999999999999999998887                          77787899999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      .++|.+|+..|||..|.|+.|+|.++.+.....
T Consensus       122 ~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  154 (158)
T 2kn4_A          122 KRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD  154 (158)
T ss_dssp             HHHHHHHHHHSTTEESSSSEEEEEEECCSSCCC
T ss_pred             HHHHHHHHHHhCCCEECCeEEEEEECCCCCCCC
Confidence            999999999999999999999999998765543

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.65  E-value=1.4e-16  Score=123.63  Aligned_cols=81  Identities=17%  Similarity=0.231  Sum_probs=73.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|.+||.|..+.                          ++.+..+++++|||||+|.+.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~--------------------------~~~~~~~g~~~g~afV~f~~~   67 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSV--------------------------CLKYNEKGMPTGEAMVAFESR   67 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCC--------------------------EEEECTTSCEEEEEEEEESSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceE--------------------------EEEeCCCCCEeeEEEEEECCH
Confidence            468999999999999999999999999987655                          667778899999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      ++|.+|+..|||..|.|+.|+|.++.+
T Consensus        68 ~~a~~Ai~~l~g~~~~gr~l~v~~a~s   94 (95)
T 2ek1_A           68 DEATAAVIDLNDRPIGSRKVKLSGPSS   94 (95)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEECCC-
T ss_pred             HHHHHHHHHhCCCeECCcEEEEEeccC
Confidence            999999999999999999999998753

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.65  E-value=7.5e-17  Score=135.06  Aligned_cols=84  Identities=26%  Similarity=0.410  Sum_probs=72.6

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEE-----EeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARV-----VYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAI  351 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i-----~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l  351 (365)
                      .+.++|||+|||+.+++++|+.+|+.||.|..|.+     ++...+++++|||||+|.+.++|.+|+..|||..|.|+.|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            44569999999999999999999999999877411     1112468899999999999999999999999999999999


Q ss_pred             EEEEccccc
Q 017842          352 RVNVAEDRQ  360 (365)
Q Consensus       352 ~V~~a~~~~  360 (365)
                      +|.||+++.
T Consensus       123 ~V~~a~~~~  131 (143)
T 3egn_A          123 VVQFARSAR  131 (143)
T ss_dssp             EEEECCCSC
T ss_pred             EEEECCCCC
Confidence            999998654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.65  E-value=2.3e-16  Score=127.60  Aligned_cols=82  Identities=28%  Similarity=0.480  Sum_probs=75.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||+|||+++++++|+++|++||.|..++                          ++.+..+++++|||||+|.
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~--------------------------i~~~~~~g~~~g~afV~f~   90 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAK--------------------------VFIDKQTSLSKCFGFVSFD   90 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEE--------------------------ECCCSSSSCCCCEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEeCCCCCCcCcEEEEEEC
Confidence            34578999999999999999999999999998887                          7777788999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      +.++|.+|+..|||..|+|+.|+|.+++
T Consensus        91 ~~~~A~~A~~~l~g~~~~g~~l~V~~ak  118 (118)
T 2khc_A           91 NPDSAQVAIKAMNGFQVGTKRLKVQLKK  118 (118)
T ss_dssp             SSHHHHHHHHHCCCCEETTEECCEEEC-
T ss_pred             CHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            9999999999999999999999998763

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.65  E-value=6e-16  Score=134.43  Aligned_cols=86  Identities=30%  Similarity=0.519  Sum_probs=80.2

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|.|+++. ++.++|||||+|.+.++|.+|+..|||..|.|++|+|.
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34556899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             Ecccccc
Q 017842          355 VAEDRQR  361 (365)
Q Consensus       355 ~a~~~~~  361 (365)
                      ||.....
T Consensus       163 ~a~~~~~  169 (177)
T 2f3j_A          163 LVASQID  169 (177)
T ss_dssp             EESSGGG
T ss_pred             EecCCCC
Confidence            9986543

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.65  E-value=1.6e-16  Score=124.83  Aligned_cols=83  Identities=22%  Similarity=0.434  Sum_probs=73.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecC-CCCCccceEEEEe
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR-ETDRSRGFGFVTM  234 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~g~afV~f  234 (365)
                      ....++|||+|||+++++++|+.+|+.|| |..++                          ++.+. .+++++|||||+|
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~--------------------------i~~~~~~~g~~~g~afV~f   68 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVR--------------------------LPREPSNPERLKGFGYAEF   68 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEE--------------------------CSCCTTTTCCCCSCEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEE--------------------------EEecCCcCCccCeEEEEEE
Confidence            34578999999999999999999999999 98887                          66666 5899999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      .+.++|.+|+ .|||..|+|+.|+|.++.++.
T Consensus        69 ~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~~~~   99 (100)
T 2j76_E           69 EDLDSLLSAL-SLNEESLGNRRIRVDVADQAQ   99 (100)
T ss_dssp             CCHHHHHHHH-HTTTCCBTTBCCCCEECCCSC
T ss_pred             CCHHHHHHHH-hcCCCEECCeEEEEEeccCCC
Confidence            9999999999 789999999999999987653

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.65  E-value=6.8e-16  Score=125.88  Aligned_cols=83  Identities=16%  Similarity=0.392  Sum_probs=76.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||+|||+++++++|+.+|+.||.|..+.                          ++.+..++.++|||||+|.+.+
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~~~   89 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRIT--------------------------ILCDKFSGHPKGYAYIEFAERN   89 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEE--------------------------EEEECTTSSCEEEEEEEESSHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEecCCCCCcccEEEEEECCHH
Confidence            57999999999999999999999999999887                          7778889999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +|.+|+ .|||..|+|+.|+|.++.+....
T Consensus        90 ~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~  118 (124)
T 2jwn_A           90 SVDAAV-AMDETVFRGRTIKVLPKRTNMPG  118 (124)
T ss_dssp             HHHHHH-TTTTCEETTEECEEEESSCCCSS
T ss_pred             HHHHHH-hcCCCeECCeEEEEEECCCCCCC
Confidence            999999 78999999999999998865443

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=1.7e-15  Score=119.40  Aligned_cols=84  Identities=29%  Similarity=0.455  Sum_probs=76.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|..||.|..+.                          ++.+..+++++|||||+|.+
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~g~~~g~afV~f~~   66 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQ--------------------------VKKDLKTGHSKGFGFVRFTE   66 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEE--------------------------EEECSSSCSEEEEEEEEESS
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEE--------------------------EEecCCCCCccceEEEEECC
Confidence            3578999999999999999999999999999887                          77888899999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      .++|.+|+.  ++..|+|+.|+|.++.++...
T Consensus        67 ~~~a~~A~~--~~~~~~g~~l~v~~a~~~~~~   96 (103)
T 2cqg_A           67 YETQVKVMS--QRHMIDGRWCDCKLPNSKQSQ   96 (103)
T ss_dssp             HHHHHHHHH--SCEEETTEEEEEECCCTTCCC
T ss_pred             HHHHHHHHH--cCCeeCCeEEEEEecCCCCcC
Confidence            999999998  578899999999999877554

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=1.1e-16  Score=130.72  Aligned_cols=80  Identities=19%  Similarity=0.241  Sum_probs=73.0

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCe----EEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKV----VNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V----~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      ..++|||+|||+.+|+++|+++|+.||.|    ..|+|+++ .+|+++|||||+|.+.++|.+||. +|+..|.||.|+|
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~-~~~~~l~gR~i~V   99 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALR-KHKDLLGKRYIEL   99 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHT-TTTEESSSCEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHH-hCCCeeCCeEEEE
Confidence            34599999999999999999999999875    68999998 589999999999999999999999 4999999999999


Q ss_pred             EEcccc
Q 017842          354 NVAEDR  359 (365)
Q Consensus       354 ~~a~~~  359 (365)
                      ..+..+
T Consensus       100 ~~a~~~  105 (123)
T 2dha_A          100 FRSTAA  105 (123)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            988643

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.64  E-value=1.7e-16  Score=129.93  Aligned_cols=79  Identities=22%  Similarity=0.304  Sum_probs=72.8

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeE--EEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVV--NARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~--~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..++|||+|||+.+|+++|+++|+.| .|.  .|+|++++. |+++|||||+|.+.++|.+||. +++..|+||.|+|.+
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFK  117 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEE
Confidence            34699999999999999999999999 677  999999977 9999999999999999999999 688999999999999


Q ss_pred             cccc
Q 017842          356 AEDR  359 (365)
Q Consensus       356 a~~~  359 (365)
                      +..+
T Consensus       118 a~~~  121 (126)
T 2hgm_A          118 SSQE  121 (126)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8654

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=4e-16  Score=125.48  Aligned_cols=88  Identities=22%  Similarity=0.349  Sum_probs=75.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ..+.++|||+|||+++++++|+.+|..||.|..+.+                          ..+..+++++|||||+|.
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~--------------------------~~~~~~g~~~g~afV~f~   75 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPI--------------------------QFRMMTGRMRGQAFITFP   75 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCC--------------------------EEEEECSSSCSEEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEE--------------------------EEEcCCCccceEEEEEEC
Confidence            446789999999999999999999999999854431                          112227889999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      +.++|.+|+..|||..|.|+.|+|.++.++....
T Consensus        76 ~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~  109 (115)
T 2cpx_A           76 NKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRS  109 (115)
T ss_dssp             SHHHHHHHHHHSTTCBCSSCBCEEEECCCCSCCC
T ss_pred             CHHHHHHHHHHhCCCEeCCcEEEEEEccCCCCCC
Confidence            9999999999999999999999999998776543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=3.7e-16  Score=125.99  Aligned_cols=85  Identities=33%  Similarity=0.568  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|..||.|..+.                          ++.+..++.++|||||+|.+.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~~~~~g~~~g~afV~f~~~   79 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCV--------------------------VMRDPASKRSRGFGFVTFSSM   79 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEE--------------------------EECCTTTSSCCSEEEEECSSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEECCCCCCcCceEEEEeCCH
Confidence            357999999999999999999999999998887                          777888899999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      ++|.+|+.. +|..|+|+.|+|.++.++....
T Consensus        80 ~~a~~Ai~~-~~~~~~g~~l~V~~a~~~~~~~  110 (116)
T 1x4b_A           80 AEVDAAMAA-RPHSIDGRVVEPKRAVAREESG  110 (116)
T ss_dssp             HHHHHHHTS-CSEEETTEEEEEECCSSCCCCC
T ss_pred             HHHHHHHHh-CCcEECCEEEEEEECCCCccCC
Confidence            999999998 9999999999999998876543

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=8.2e-16  Score=121.68  Aligned_cols=82  Identities=24%  Similarity=0.344  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEE-EEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEI-AEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~-~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ...++|||+|||+++++++|+++|..||.|.. ++                          ++++ .+++++|||||+|.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~--------------------------i~~~-~~g~~~G~afV~F~   65 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMT--------------------------LPVD-FQGRSTGEAFVQFA   65 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEE--------------------------CCBC-SSSCBCSEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEE--------------------------EEEC-CCCCcceEEEEEEC
Confidence            35789999999999999999999999999876 55                          5566 78999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      +.++|.+|+.. ++..++||.|+|.++....
T Consensus        66 ~~~~a~~A~~~-~~~~~~gr~i~v~~~~~~~   95 (104)
T 1wg5_A           66 SQEIAEKALKK-HKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             SHHHHHHHHTT-TTCCSSSSCCEEEEECTTT
T ss_pred             CHHHHHHHHHh-CcchhCCcEEEEEECCHHH
Confidence            99999999998 9999999999999886554

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.6e-15  Score=118.37  Aligned_cols=78  Identities=23%  Similarity=0.410  Sum_probs=71.5

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+||  .+++++|+++|+.||.|..|+|.      +++|||||+|.+.++|.+|+..|||..+.|++|+|.|+
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a   84 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   84 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            45579999996  89999999999999999999984      45899999999999999999999999999999999999


Q ss_pred             cccccC
Q 017842          357 EDRQRR  362 (365)
Q Consensus       357 ~~~~~~  362 (365)
                      .++...
T Consensus        85 ~~~~~~   90 (97)
T 1x5p_A           85 RKQPML   90 (97)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987754

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=6.8e-16  Score=118.26  Aligned_cols=73  Identities=22%  Similarity=0.341  Sum_probs=65.9

Q ss_pred             Cce-EEEeCCCCcCcHHH----HHHHHhcc-CCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEE
Q 017842          279 GFR-IYVGNLPWEVDNAR----LEQVFSEH-GKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR  352 (365)
Q Consensus       279 ~~~-lfV~nLp~~~tee~----L~~~F~~~-G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~  352 (365)
                      ..+ |||+|||+.+++++    |+++|+.| |.|..|       ++   |+|||+|.+.++|.+|++.|+|..+.||+|+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            345 99999999999887    55899999 599999       23   9999999999999999999999999999999


Q ss_pred             EEEcccccc
Q 017842          353 VNVAEDRQR  361 (365)
Q Consensus       353 V~~a~~~~~  361 (365)
                      |+||+.+..
T Consensus        78 v~~A~~~sd   86 (96)
T 2diu_A           78 VSFTPKNRE   86 (96)
T ss_dssp             EESSCCSCC
T ss_pred             EEecCCCcc
Confidence            999998764

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.64  E-value=1.3e-15  Score=124.40  Aligned_cols=85  Identities=31%  Similarity=0.435  Sum_probs=77.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|+.||.|..+.                          +..+. +++++|||||+|.+
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~--------------------------i~~~~-~g~~~g~afV~f~~   85 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA--------------------------VDYDR-SGRSLGTADVHFER   85 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEE--------------------------EECCS-SSSCCSEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE--------------------------EEECC-CCCEeeEEEEEECC
Confidence            3578999999999999999999999999998887                          66676 88999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      .++|.+|+..|||..|+|+.|+|.++.+....
T Consensus        86 ~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  117 (124)
T 2kt5_A           86 RADALKAMKQYKGVPLDGRPMDIQLVASQIDL  117 (124)
T ss_dssp             HHHHHHHHHHHTTEESSSCEEEEEEECCTTCC
T ss_pred             HHHHHHHHHHcCCCEECCcEEEEEEeCCCCCC
Confidence            99999999999999999999999998876543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=2e-16  Score=117.79  Aligned_cols=76  Identities=30%  Similarity=0.500  Sum_probs=71.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      ++|||+|||+++++++|+.+|++||.|..+.                          +..++.+++++|||||+|.+.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~--------------------------i~~~~~~~~~~g~afV~f~~~~~   54 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECL--------------------------VMRDPLTKRSRGFGFVTFMDQAG   54 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEE--------------------------EECCCCSSSCSSEEEECCCCTTH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EecCCCCCCcCceEEEEEcCHHH
Confidence            4899999999999999999999999998877                          77777889999999999999999


Q ss_pred             HHHHHHHHccCcccCeeEEEeec
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      |.+|+..++ ..++|+.|+|.++
T Consensus        55 a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A           55 VDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             HHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             HHHHHHhCC-CccCCEEEEEEec
Confidence            999999988 9999999999876

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.8e-15  Score=120.57  Aligned_cols=84  Identities=27%  Similarity=0.414  Sum_probs=74.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||+|||+++++++|+.+|.+||.|..+.|                          .   ..+.++|||||+|.
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i--------------------------~---~~~~~~g~afV~f~   69 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL--------------------------K---NRRGGPPFAFVEFE   69 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEE--------------------------C---CSSSSSCCEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE--------------------------E---ECCCCCcEEEEEEC
Confidence            446789999999999999999999999999988773                          2   23457999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..||+..|+|+.|+|.++.+....
T Consensus        70 ~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~  102 (109)
T 1x4a_A           70 DPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT  102 (109)
T ss_dssp             CHHHHHHHHHHHTTCEETTEECEEECCCCCCCC
T ss_pred             CHHHHHHHHHHcCCCEECCeEEEEEEcccCCCC
Confidence            999999999999999999999999999876543

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.64  E-value=9.7e-17  Score=123.33  Aligned_cols=81  Identities=36%  Similarity=0.659  Sum_probs=72.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      ++|||+|||+++++++|+++|+.||.|..+.                          +..+..+++++|||||+|.+.+ 
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~~~-   54 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVK--------------------------LIYDRETKKPKGFGFVEMQEES-   54 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEE--------------------------ECCCSSSCCCCEEEEEEECTTH-
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEEcCCCCCcceEEEEEECCHH-
Confidence            5899999999999999999999999999887                          7778888999999999999999 


Q ss_pred             HHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      |.+|+..|||..++|+.|+|.++.+...
T Consensus        55 a~~a~~~l~g~~~~g~~l~V~~a~~~~~   82 (90)
T 2ki2_A           55 VSEAIAKLDNTDFMGRTIRVTEANPKKS   82 (90)
T ss_dssp             HHHHHHTSCSSCCSSSSCSEEEC-----
T ss_pred             HHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            9999999999999999999999887644

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.64  E-value=3.1e-16  Score=118.22  Aligned_cols=74  Identities=23%  Similarity=0.345  Sum_probs=67.0

Q ss_pred             CCeEEEcCCCCCC------CHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEE
Q 017842          159 DAKLFVGNLPYDV------DSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFV  232 (365)
Q Consensus       159 ~~tvfVgnLp~~~------t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV  232 (365)
                      +++|||+|||+++      ++++|+.+|++||.|..+.                          +.  ..+|+++|||||
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~--------------------------i~--~~~g~~~g~afV   52 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDF--------------------------YP--EEDGKTKGYIFL   52 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEE--------------------------CC--CBTTBCCCEEEE
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEE--------------------------ec--CCCCcEeEEEEE
Confidence            3689999999999      7799999999999998876                          33  458899999999


Q ss_pred             EeCCHHHHHHHHHHHccCcccCe-eEEEe
Q 017842          233 TMSTVEEAEKAVEMFHRYDIDGR-LLTVN  260 (365)
Q Consensus       233 ~f~~~e~a~~Al~~lng~~~~gr-~l~V~  260 (365)
                      +|.+.++|.+|+..|||..|+|+ .|+|+
T Consensus        53 ~f~~~~~A~~Ai~~lng~~~~g~~~l~V~   81 (81)
T 2krb_A           53 EYASPAHAVDAVKNADGYKLDKQHTFRVN   81 (81)
T ss_dssp             EESSHHHHHHHHTTSSSCCCSSSSCCCCC
T ss_pred             EECCHHHHHHHHHHhcCcccCCceeEEeC
Confidence            99999999999999999999999 88874

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.64  E-value=1.6e-16  Score=124.80  Aligned_cols=84  Identities=23%  Similarity=0.345  Sum_probs=74.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+.+|..||.|.. .                          ++.+..+++++|||||+|.
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~--------------------------~~~~~~~g~~~g~afV~f~   66 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-L--------------------------AVVDVRTGTNRKFGYVDFE   66 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-C--------------------------CCCEEEEETTTTEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-E--------------------------EEecCCCCCcCcEEEEEEC
Confidence            335789999999999999999999999998865 2                          5556667899999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      +.++|.+|+. |||..|.|+.|+|.++.++..
T Consensus        67 ~~~~a~~A~~-l~g~~~~g~~l~V~~a~~~~~   97 (101)
T 1fj7_A           67 SAEDLEKALE-LTGLKVFGNEIKLEKPKGRDG   97 (101)
T ss_dssp             SHHHHHHHHH-GGGCCBTTBCCEEECCSCCCC
T ss_pred             CHHHHHHHHh-cCCcEECCcEEEEEEcCCCCC
Confidence            9999999999 899999999999999987654

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.64  E-value=2.6e-16  Score=142.34  Aligned_cols=82  Identities=20%  Similarity=0.389  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccC--CeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAG--TVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G--~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ..++|||+|||+++++++|+++|..||  .|..|+                          |++++.+++++|||||+|.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~--------------------------i~~d~~tg~skGfaFV~f~  120 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIK--------------------------FFENRANGQSKGFALVGVG  120 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEE--------------------------EEECTTTCCEEEEEEEEES
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEE--------------------------EEecCCCCccceEEEEEEC
Confidence            467899999999999999999999999  898877                          8888899999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      +.++|.+||..|||..|.|+.|+|.++.+.
T Consensus       121 ~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~~  150 (229)
T 3q2s_C          121 SEASSKKLMDLLPKRELHGQNPVVTPVNKQ  150 (229)
T ss_dssp             CTTHHHHHHTTSTTSCBTTBCCEEEECCHH
T ss_pred             CHHHHHHHHHHcCCCeECCEEeEEEECCCC
Confidence            999999999999999999999999988643

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=9.8e-16  Score=117.98  Aligned_cols=81  Identities=17%  Similarity=0.297  Sum_probs=74.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+++|..| .|..++                          ++++ .+++++|||||+|.+
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~--------------------------i~~~-~~g~~~g~afV~f~~   59 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIR--------------------------IVRN-AHGNKTGYIFVDFSN   59 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEE--------------------------EEEC-TTSCEEEEEEEECSS
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEE--------------------------EEEC-CCCCCceEEEEEECC
Confidence            457899999999999999999999999 888877                          6666 788999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      .++|.+|+. +||..|+|+.|+|.++.++.
T Consensus        60 ~~~a~~A~~-~~g~~~~gr~i~v~~a~~~~   88 (91)
T 2dgw_A           60 EEEVKQALK-CNREYMGGRYIEVFREKSGP   88 (91)
T ss_dssp             HHHHHHHHH-SCSEEETTEEEEEEEESSCC
T ss_pred             HHHHHHHHH-hCCceeCCcEEEEEECCcCC
Confidence            999999999 89999999999999987653

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.64  E-value=1.5e-15  Score=129.05  Aligned_cols=85  Identities=24%  Similarity=0.393  Sum_probs=79.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|+.||.|..|.                          ++.+..++.++|||||+|.+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~   90 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKII--------------------------MGLDKMKKTACGFCFVEYYS   90 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTCCEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEecCCCCccceEEEEEECC
Confidence            3578999999999999999999999999999887                          77888899999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      .++|.+|+..|||..|.|+.|+|.++.+...
T Consensus        91 ~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  121 (156)
T 1h2v_Z           91 RADAENAMRYINGTRLDDRIIRTDWDAGFKE  121 (156)
T ss_dssp             HHHHHHHHHHTTTSEETTEECEEEEESCCCT
T ss_pred             HHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            9999999999999999999999999987654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.63  E-value=9.7e-16  Score=121.49  Aligned_cols=81  Identities=21%  Similarity=0.273  Sum_probs=73.1

Q ss_pred             CCCeEEEcCCCCCC------CHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEE
Q 017842          158 EDAKLFVGNLPYDV------DSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGF  231 (365)
Q Consensus       158 ~~~tvfVgnLp~~~------t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~af  231 (365)
                      ..++|||||||+.+      ++++|+.+|++||.|..+.                          +.  ..+|+++||||
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~--------------------------i~--~~~g~~~G~af   65 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDF--------------------------YP--EEDGKTKGYIF   65 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEE--------------------------CC--CBTTBSCCEEE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEE--------------------------ee--CCCCCeeeEEE
Confidence            46899999999999      7899999999999998876                          43  36889999999


Q ss_pred             EEeCCHHHHHHHHHHHccCcccCe-eEEEeecCCCC
Q 017842          232 VTMSTVEEAEKAVEMFHRYDIDGR-LLTVNKAAPRG  266 (365)
Q Consensus       232 V~f~~~e~a~~Al~~lng~~~~gr-~l~V~~a~~~~  266 (365)
                      |+|.+.++|.+|+..|||..|.|+ .|+|.++....
T Consensus        66 V~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           66 LEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFD  101 (105)
T ss_dssp             EEECSSSHHHHHHHHCSSEECSTTCEEEEECSCCCC
T ss_pred             EEECCHHHHHHHHHHhCCcccCCCceEEEEEcchHh
Confidence            999999999999999999999998 99999987543

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=2e-15  Score=122.15  Aligned_cols=83  Identities=17%  Similarity=0.225  Sum_probs=72.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      ..++.++|||+|||+++++++|+.+|++||.|..++                          ++.      .+|||||+|
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~--------------------------i~~------~kG~AFVeF   74 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLL--------------------------MLK------GKNQAFIEM   74 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEE--------------------------EEG------GGTEEEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EeC------CCCEEEEEE
Confidence            344678999999999999999999999999999887                          432      379999999


Q ss_pred             CCHHHHHHHHHHHcc--CcccCeeEEEeecCCCCCCC
Q 017842          235 STVEEAEKAVEMFHR--YDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       235 ~~~e~a~~Al~~lng--~~~~gr~l~V~~a~~~~~~~  269 (365)
                      .+.++|.+|+..|++  ..|.|+.|+|.++.++....
T Consensus        75 ~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~~~  111 (119)
T 2ad9_A           75 NTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT  111 (119)
T ss_dssp             SCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSSCCC
T ss_pred             CCHHHHHHHHHHhccCCceECCeEEEEEEccCCCCCc
Confidence            999999999998874  68999999999998776554

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=4.5e-16  Score=124.81  Aligned_cols=79  Identities=20%  Similarity=0.248  Sum_probs=71.1

Q ss_pred             CCCceEEE--eCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc-----CCe
Q 017842          277 EPGFRIYV--GNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL-----DGR  349 (365)
Q Consensus       277 ~~~~~lfV--~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l-----~gr  349 (365)
                      .+..+|||  +||++.+++++|+++|+.||.|..|.|+.      ++|||||+|.+.++|.+|+..|||..+     .|+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            34568999  77999999999999999999999998863      379999999999999999999999988     799


Q ss_pred             eEEEEEcccccc
Q 017842          350 AIRVNVAEDRQR  361 (365)
Q Consensus       350 ~l~V~~a~~~~~  361 (365)
                      +|.|.|++..+-
T Consensus        97 ~l~v~~a~~~p~  108 (114)
T 2cq2_A           97 TLYLNFVEKVQW  108 (114)
T ss_dssp             ECEEEEESCCCC
T ss_pred             EEEEEecccCcc
Confidence            999999987653

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=1e-15  Score=118.97  Aligned_cols=79  Identities=24%  Similarity=0.291  Sum_probs=72.0

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEE-EEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNAR-VVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~-i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ..++|||+|||+.+++++|+++|+.||.|..|+ |++++.+    |.|||+|.+.++|.+|+..|||..+.||+|+|.||
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~----~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            346999999999999999999999999999995 8877553    44999999999999999999999999999999999


Q ss_pred             cccc
Q 017842          357 EDRQ  360 (365)
Q Consensus       357 ~~~~  360 (365)
                      .++.
T Consensus        90 ~~~~   93 (96)
T 2e44_A           90 PDEM   93 (96)
T ss_dssp             CCCC
T ss_pred             Cccc
Confidence            9874

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.63  E-value=8.7e-16  Score=118.11  Aligned_cols=77  Identities=26%  Similarity=0.503  Sum_probs=63.2

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc--CCeeEEEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL--DGRAIRVN  354 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l--~gr~l~V~  354 (365)
                      .+.++|||+|||+.+|+++|+++|+.||.|..|+|+++     ++|||||+|.+.++|.+    |+|..+  .|++|.|.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            45569999999999999999999999999999999875     69999999999999883    566654  69999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      +|.++..+
T Consensus        80 ~a~~k~~~   87 (89)
T 3d2w_A           80 NAEPKHNK   87 (89)
T ss_dssp             ECC-----
T ss_pred             EcCCCCcC
Confidence            99987653

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.63  E-value=7.6e-16  Score=123.40  Aligned_cols=81  Identities=20%  Similarity=0.276  Sum_probs=70.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccC-CeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEE
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAG-TVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVT  233 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G-~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~  233 (365)
                      .++..++|||+|||+++++++|+++|++|| .|..+.+                          .    ...++|||||+
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i--------------------------~----~~~~rGfaFV~   73 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSV--------------------------N----TRDFDGTGALE   73 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEEC--------------------------S----SCSSSCCEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEE--------------------------E----cCCCCCEEEEE
Confidence            345578999999999999999999999999 8887662                          2    23579999999


Q ss_pred             eCCHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      |.+.++|.+|+..|||..|+|+.|+|.++..+
T Consensus        74 F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           74 FPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             ESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             ECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            99999999999999999999999999998654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.6e-15  Score=119.12  Aligned_cols=83  Identities=30%  Similarity=0.598  Sum_probs=73.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+.+|.+||.|   +                          ++.+ .+++++|||||+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~--------------------------~~~~-~~g~~~g~afV~f~   61 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---K--------------------------VPQN-QNGKSKGYAFIEFA   61 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---E--------------------------CCBC-SSSCBCSEEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---E--------------------------EEEC-CCCCEeeEEEEEEC
Confidence            3467899999999999999999999999987   2                          3444 57889999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..|||..|.|+.|+|.++.++...
T Consensus        62 ~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   94 (101)
T 2fc9_A           62 SFEDAKEALNSCNKREIEGRAIRLELQGPRGSP   94 (101)
T ss_dssp             SHHHHHHHHHHTSSEEETTEEEEEEECSSCCCC
T ss_pred             CHHHHHHHHHHhCCCEeCCeEEEEEEcCCCCCC
Confidence            999999999999999999999999999877543

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=5.9e-16  Score=124.40  Aligned_cols=80  Identities=19%  Similarity=0.343  Sum_probs=74.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||+|||+++++++|+.+|..||.|..+.                          ++.+..+++++|||||+|.+.+
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~g~~~g~afV~f~~~~   78 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVR--------------------------IISDRNSRRSKGIAYVEFCEIQ   78 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEE--------------------------ECCSCCSSSCCCCEEEEESCGG
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEE--------------------------EEecCCCCccCcEEEEEeCcHH
Confidence            57999999999999999999999999999887                          7778888999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      +|.+|+ .|||..|+|+.|+|.++.++
T Consensus        79 ~a~~A~-~l~g~~~~g~~l~V~~a~~~  104 (114)
T 2cq4_A           79 SVPLAI-GLTGQRLLGVPIIVQASQAE  104 (114)
T ss_dssp             GHHHHH-HHTTEEETTEEEEEEEHHHH
T ss_pred             HHHHHH-HcCCCEeCCeEEEEEecCCC
Confidence            999999 88999999999999987654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=1.2e-15  Score=118.33  Aligned_cols=77  Identities=26%  Similarity=0.453  Sum_probs=69.7

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|  +.++.+++   ||||+|.+.++|.+|+. |||..|.|+.|+|.++.+
T Consensus         8 ~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~   81 (94)
T 2e5g_A            8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQ   81 (94)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCc
Confidence            4599999999999999999999999999987  55655554   99999999999999999 999999999999999986


Q ss_pred             ccc
Q 017842          359 RQR  361 (365)
Q Consensus       359 ~~~  361 (365)
                      +..
T Consensus        82 ~~~   84 (94)
T 2e5g_A           82 KEF   84 (94)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.63  E-value=1.1e-15  Score=127.11  Aligned_cols=80  Identities=30%  Similarity=0.493  Sum_probs=74.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|+.||.|..++                          ++.++.+++++|||||+|.+
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~  114 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQ--------------------------IPLDYETEKHRGFAFVEFEL  114 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEE--------------------------CCCCTTTCCCCSEEEEEESC
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EeecCCCCCcCcEEEEEECC
Confidence            3578999999999999999999999999999887                          77777889999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeec
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      .++|.+|+..|||..|+|+.|+|.++
T Consensus       115 ~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A          115 AEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             HHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             HHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            99999999999999999999999874

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=2.8e-15  Score=120.35  Aligned_cols=82  Identities=24%  Similarity=0.459  Sum_probs=74.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|..||.|..++                          ++.+. ++.++|||||+|.+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~--------------------------i~~~~-~g~~~g~afV~f~~   75 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTR--------------------------ILRDS-SGTSRGVGFARMES   75 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEE--------------------------EEECS-SSCEEEEEEEEESC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEECC-CCCcceEEEEEECC
Confidence            3568999999999999999999999999999887                          66776 88999999999999


Q ss_pred             HHHHHHHHHHHccCcc--------cCeeEEEeecCCC
Q 017842          237 VEEAEKAVEMFHRYDI--------DGRLLTVNKAAPR  265 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~--------~gr~l~V~~a~~~  265 (365)
                      .++|.+|+..|||..|        .+++|+|.++.++
T Consensus        76 ~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           76 TEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             HHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECCCS
T ss_pred             HHHHHHHHHHhCCCEEcCCccccCCCCceeEEccCCC
Confidence            9999999999999999        5788999888754

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.63  E-value=7.1e-16  Score=118.15  Aligned_cols=76  Identities=18%  Similarity=0.294  Sum_probs=70.3

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||+|||+.+++++|+++|+.| .|..|+|.      +++|||||+|.+.++|.+|+..|||..+.|++|+|.|+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            34589999999999999999999999 99999984      569999999999999999999999999999999999987


Q ss_pred             ccc
Q 017842          358 DRQ  360 (365)
Q Consensus       358 ~~~  360 (365)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            653

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=3.6e-15  Score=114.60  Aligned_cols=79  Identities=29%  Similarity=0.582  Sum_probs=71.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+.+|+.||.|..+.                          +.        +|||||+|.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------------------------~~--------~g~afV~f~   50 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECD--------------------------II--------KNYGFVHIE   50 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEE--------------------------EE--------TTEEEEEES
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE--------------------------EE--------CCEEEEEEC
Confidence            34578999999999999999999999999998877                          33        689999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..|||..|+|+.|+|.++.++...
T Consensus        51 ~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   83 (90)
T 2dnq_A           51 DKTAAEDAIRNLHHYKLHGVNINVEASKNKSKA   83 (90)
T ss_dssp             SHHHHHHHHHHHTTCBCSSCBCEEECSSCCCCC
T ss_pred             CHHHHHHHHHHhcCCccCCcEEEEEECCCCCCC
Confidence            999999999999999999999999999876554

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.62  E-value=2.2e-15  Score=123.60  Aligned_cols=76  Identities=26%  Similarity=0.400  Sum_probs=70.1

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceE-EEEEecCHHHHHHHHHHhCCCccCC--eeEEEEEc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGF-GFVTMSSETELNDAIAALDGQNLDG--RAIRVNVA  356 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~-afV~F~s~~~a~~Al~~l~~~~l~g--r~l~V~~a  356 (365)
                      .+|||+||++.+|+++|+++|+.||.|..|+|..+.     +|| |||+|.+.++|.+|+..|||..|.|  +.|+|.|+
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~a  103 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  103 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEEC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEec
Confidence            478999999999999999999999999999998652     688 9999999999999999999999988  99999999


Q ss_pred             cccc
Q 017842          357 EDRQ  360 (365)
Q Consensus       357 ~~~~  360 (365)
                      +.+.
T Consensus       104 k~~~  107 (130)
T 3zzy_A          104 KLTS  107 (130)
T ss_dssp             SCSS
T ss_pred             CCCc
Confidence            8753

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=4.1e-15  Score=117.76  Aligned_cols=81  Identities=17%  Similarity=0.177  Sum_probs=70.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      .++.++|||+|||+++++++|+.+|++||.|..+.                          ++      +.+|||||+|.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~--------------------------i~------~~kg~aFVef~   59 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVM--------------------------MM------PFKRQALVEFE   59 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEE--------------------------EE------TTTTEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE--------------------------EE------CCCCEEEEEEC
Confidence            34678999999999999999999999999999876                          33      24899999999


Q ss_pred             CHHHHHHHHHHHccC--cccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRY--DIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~--~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..|++.  .|.|+.|+|.++.++...
T Consensus        60 ~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~~   94 (104)
T 1wex_A           60 NIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT   94 (104)
T ss_dssp             SHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSCC
T ss_pred             CHHHHHHHHHHhccCCceECCEEEEEEEccCcccc
Confidence            999999999988764  599999999999876544

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.62  E-value=4.8e-16  Score=129.07  Aligned_cols=87  Identities=32%  Similarity=0.402  Sum_probs=79.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|+.||.|..+.                          ++.+..+++++|||||+|.+
T Consensus        45 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~--------------------------i~~~~~~g~~~G~afV~F~~   98 (135)
T 2lea_A           45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVY--------------------------IPRDRYTKESRGFAFVRFHD   98 (135)
T ss_dssp             GGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEE--------------------------CCCCSSSSSCCSCCEEECSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEecCCCCccceEEEEEECC
Confidence            3478999999999999999999999999998887                          67777889999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      .++|.+|+..|||..|.|+.|+|.++.+.....
T Consensus        99 ~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~~  131 (135)
T 2lea_A           99 KRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD  131 (135)
T ss_dssp             HHHHHHHHTTTTTCCSSSSCCEEEECCCCCCCT
T ss_pred             HHHHHHHHHHcCCCEECCEEEEEEECCCCCCCc
Confidence            999999999999999999999999998765543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.62  E-value=1.2e-15  Score=115.65  Aligned_cols=73  Identities=19%  Similarity=0.235  Sum_probs=67.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ....||||||++.+|+++|+.+|.+||+|..+++                          .      .++|||||+|.+.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l--------------------------~------~~kGfaFVey~~~   53 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHP--------------------------Y------LNQGIALCKYTTR   53 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEE--------------------------E------TTTTEEEEEESSH
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEE--------------------------c------CCCcEEEEEECCH
Confidence            3568999999999999999999999999999873                          2      2699999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeec
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      ++|.+|++.|||..+.|+.|+|+.+
T Consensus        54 ~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A           54 EEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             HHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             HHHHHHHHHhcCCEECCcEEEEEEC
Confidence            9999999999999999999999876

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=7.8e-16  Score=123.27  Aligned_cols=84  Identities=18%  Similarity=0.246  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH---HHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCC---CCccceE
Q 017842          157 PEDAKLFVGNLPYDVDSEKLA---MLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRET---DRSRGFG  230 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~---~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~g~a  230 (365)
                      ...++|||+|||+++++++|+   ++|.+||.|..+.                          +..+..+   ++++|||
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~~~~G~a   66 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVV--------------------------INNSTSYAGSQGPSASA   66 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEE--------------------------EECCSSCCSSSCCCEEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEE--------------------------EecCCCcCccCCCCeEE
Confidence            357799999999999999999   9999999999887                          5555543   3566999


Q ss_pred             EEEeCCHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          231 FVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       231 fV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ||+|.+.++|.+|+..|||..|+|+.|+|.++.++.
T Consensus        67 fV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           67 YVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             EEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCS
T ss_pred             EEEECcHHHHHHHHHHhCCCEECCEEEEEEeccccc
Confidence            999999999999999999999999999999998765

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=1.3e-15  Score=120.01  Aligned_cols=78  Identities=17%  Similarity=0.199  Sum_probs=69.0

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          157 PEDAKLFVGNLPY-DVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       157 ~~~~tvfVgnLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      .+.++|||+|||+ ++++++|+.+|++||.|..+.                          ++      +.+|||||+|.
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~--------------------------i~------~~kg~aFVef~   60 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHL--------------------------IL------NKINEAFIEMA   60 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEE--------------------------EC------SSSSCEEEEES
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEE--------------------------EE------cCCCEEEEEEC
Confidence            3678999999999 999999999999999999987                          33      24689999999


Q ss_pred             CHHHHHHHHHHHccC--cccCeeEEEeecCCCC
Q 017842          236 TVEEAEKAVEMFHRY--DIDGRLLTVNKAAPRG  266 (365)
Q Consensus       236 ~~e~a~~Al~~lng~--~~~gr~l~V~~a~~~~  266 (365)
                      +.++|.+|+..||+.  .|.|++|+|.++....
T Consensus        61 ~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~   93 (102)
T 1x4d_A           61 TTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   93 (102)
T ss_dssp             SHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             CHHHHHHHHHHHcCCCceECCcEEEEEECCCCC
Confidence            999999999999875  4999999999988543

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=4.2e-16  Score=125.45  Aligned_cols=83  Identities=16%  Similarity=0.298  Sum_probs=74.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCe-EEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTV-EIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      +...++|||+|||+++++++|+.+|..||.| ..++                          ++++. +++++|||||+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~--------------------------i~~d~-~g~~~G~afV~F   64 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVH--------------------------VLVDN-NGQGLGQALVQF   64 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEE--------------------------ECCCT-TSSCSSCEEEEC
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEE--------------------------EEECC-CCCcceEEEEEE
Confidence            3457899999999999999999999999998 6666                          67777 899999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      .+.++|.+|+.. ||..|+|+.|+|.++.++.
T Consensus        65 ~~~~~a~~Al~~-~~~~~~gr~i~v~~a~~~~   95 (114)
T 2cpy_A           65 KNEDDARKSERL-HRKKLNGREAFVHVVTLED   95 (114)
T ss_dssp             SSHHHHHHHGGG-CSEEETTEEEEEEEECHHH
T ss_pred             CCHHHHHHHHHh-CCCccCCeEEEEEECCHHH
Confidence            999999999998 9999999999999886543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=3.3e-15  Score=116.49  Aligned_cols=80  Identities=24%  Similarity=0.375  Sum_probs=70.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||+|||+++++++|+.+|..||.|. +.                          ++.    ++++|||||+|.
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~--------------------------~~~----~~~~g~afV~f~   64 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LR--------------------------LTW----QGPRRRAFLHYP   64 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SE--------------------------EEE----ETTTTEEEEECS
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EE--------------------------EEc----CCCCcEEEEEEC
Confidence            34578999999999999999999999999985 43                          332    368999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      +.++|.+|+..|||..|+|+.|+|.++.++.
T Consensus        65 ~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           65 DSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             SHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             CHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            9999999999999999999999999988754

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1.3e-15  Score=121.58  Aligned_cols=83  Identities=33%  Similarity=0.611  Sum_probs=73.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .....++|||+|||.++++++|+.+|++||.|..+.                          +..+.  +.++|||||+|
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~~~--~~~kg~afV~f   76 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE--------------------------IIFNE--RGSKGFGFVTF   76 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEE--------------------------ECCBT--TBCTTEEEEEC
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEE--------------------------EEECC--CCCceEEEEEE
Confidence            344678999999999999999999999999998877                          44443  45899999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      .+.++|.+|+..|||..|+|+.|+|.++.++
T Consensus        77 ~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  107 (109)
T 2err_A           77 ENSADADRAREKLHGTVVEGRKIEVNNATAR  107 (109)
T ss_dssp             CCSHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             CCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            9999999999999999999999999998765

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=3.8e-15  Score=117.27  Aligned_cols=82  Identities=15%  Similarity=0.195  Sum_probs=71.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      .++.++|||+|||+++++++|+.+|++||.|..+.                          ++.      .+|||||+|.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~--------------------------i~~------~kg~aFVef~   59 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNIL--------------------------MLK------GKNQAFLELA   59 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEE--------------------------EET------TTTEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEC------CCCEEEEEEC
Confidence            34678999999999999999999999999998876                          332      3899999999


Q ss_pred             CHHHHHHHHHHHc--cCcccCeeEEEeecCCCCCCC
Q 017842          236 TVEEAEKAVEMFH--RYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       236 ~~e~a~~Al~~ln--g~~~~gr~l~V~~a~~~~~~~  269 (365)
                      +.++|.+|+..|+  +..+.|+.|+|.++.++....
T Consensus        60 ~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~~   95 (101)
T 2cq1_A           60 TEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKT   95 (101)
T ss_dssp             SHHHHHHHHHHHHHSCCEETTEECEEEECSCSSCCC
T ss_pred             CHHHHHHHHHHhccCCceECCcEEEEEEcCcccCcC
Confidence            9999999999875  677999999999998766543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.61  E-value=2.3e-15  Score=123.57  Aligned_cols=81  Identities=23%  Similarity=0.325  Sum_probs=71.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEE
Q 017842          157 PEDAKLFVGNLPYDVDSEKLA----MLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFV  232 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~----~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV  232 (365)
                      .+.++|||||||+.+++++|+    .+|++||.|..|.                          +.   .+++++|||||
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~--------------------------i~---~~~~~rG~aFV   77 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIV--------------------------VD---LSDDNSGKAYI   77 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEE--------------------------EC---CCCSSCCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEE--------------------------ec---cCCCcCCEEEE
Confidence            357899999999999999876    6999999997765                          22   36788999999


Q ss_pred             EeCCHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          233 TMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       233 ~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      +|.+.++|.+|+..|||..|.|+.|+|.++..+.
T Consensus        78 ~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~~  111 (127)
T 2a3j_A           78 VFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ  111 (127)
T ss_dssp             EESSHHHHHHHHHHSTTCCCTTSCCEEEECCCCC
T ss_pred             EECCHHHHHHHHHHHCCCEeCCCEEEEEEccCcc
Confidence            9999999999999999999999999999998654

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=7.9e-16  Score=121.48  Aligned_cols=82  Identities=16%  Similarity=0.231  Sum_probs=72.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+++|..||.+ .++                          ++++. +++++|||||+|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~--------------------------i~~d~-~g~~~G~afV~F~   63 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVH--------------------------IEIGP-DGRVTGEADVEFA   63 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEE--------------------------EEESS-SSCEEEEEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEE--------------------------EEECC-CCCEeeEEEEEEC
Confidence            4457899999999999999999999999955 665                          67776 8999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      +.++|.+|+. +|+..|.||.|+|..+.+..
T Consensus        64 ~~~~a~~Al~-~~~~~~~gr~i~V~~~~~~~   93 (102)
T 1wez_A           64 THEDAVAAMA-KDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             SSHHHHHHHT-TSSCCSSSSCCEEEEECCCC
T ss_pred             CHHHHHHHHH-hCCCeECCcEEEEEECCCCC
Confidence            9999999996 59999999999999877654

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=3.9e-15  Score=118.66  Aligned_cols=82  Identities=18%  Similarity=0.350  Sum_probs=73.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .+...++|||+|||.++++++|+.+|..||.|..+.|                          ..      .+|||||+|
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i--------------------------~~------~~g~afV~f   68 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV--------------------------FP------EKGYSFVRF   68 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEE--------------------------ET------TTTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE--------------------------eC------CCCEEEEEE
Confidence            3446789999999999999999999999999988873                          32      289999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      .+.++|.+|+..|+|..|.|+.|+|.++.++...
T Consensus        69 ~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  102 (109)
T 1x4g_A           69 STHESAAHAIVSVNGTTIEGHVVKCYWGKESPDM  102 (109)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEECCCCCCSS
T ss_pred             CCHHHHHHHHHHcCCCEECCcEEEEEecCCCCCC
Confidence            9999999999999999999999999999876543

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.61  E-value=1.9e-15  Score=128.60  Aligned_cols=77  Identities=25%  Similarity=0.344  Sum_probs=70.7

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eeEEEEEcc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDG--RAIRVNVAE  357 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g--r~l~V~~a~  357 (365)
                      .+|||+||++.+++++|+++|+.||.|..|+|..+    .++|||||+|.+.++|.+|+..|||..|.|  ++|+|.|++
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            47999999999999999999999999999999754    258999999999999999999999999965  999999999


Q ss_pred             ccc
Q 017842          358 DRQ  360 (365)
Q Consensus       358 ~~~  360 (365)
                      ++.
T Consensus       123 ~~~  125 (164)
T 1sjr_A          123 LTS  125 (164)
T ss_dssp             SSS
T ss_pred             CCc
Confidence            764

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.61  E-value=4.9e-16  Score=115.07  Aligned_cols=75  Identities=31%  Similarity=0.448  Sum_probs=69.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      +|||+|||+++++++|+.+|++||.|..+.                          +..+..++.++|||||+|.+.++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~~~~~a   54 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIE--------------------------LPMDNKTNKRRGFCFITFKEEEPV   54 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEEC--------------------------CCCSCCCSSSCCCEEEECSSSHHH
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEecCCCCCcCCEEEEEECCHHHH
Confidence            699999999999999999999999998876                          677778899999999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEeec
Q 017842          241 EKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      .+|+.. ++..++|+.|+|.++
T Consensus        55 ~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A           55 KKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             HHHHTT-SSCCBTTBCCCEEEC
T ss_pred             HHHHHh-CCCeECCEEEEEEEC
Confidence            999997 999999999999864

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.61  E-value=2.5e-15  Score=131.48  Aligned_cols=83  Identities=31%  Similarity=0.567  Sum_probs=76.9

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ...++|||+|||+.+|+++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+||. +++..+.|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHh-cCCCEECCEEeeeecc
Confidence            345699999999999999999999999999999999999999999999999999999999998 5999999999999999


Q ss_pred             cccc
Q 017842          357 EDRQ  360 (365)
Q Consensus       357 ~~~~  360 (365)
                      ..+.
T Consensus        90 ~~~~   93 (196)
T 1l3k_A           90 VSRE   93 (196)
T ss_dssp             CC--
T ss_pred             cCcc
Confidence            7654

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.61  E-value=8.7e-16  Score=127.56  Aligned_cols=80  Identities=21%  Similarity=0.336  Sum_probs=72.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCC---eEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEE
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGT---VEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVT  233 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~---i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~  233 (365)
                      ...++|||+|||+++|+++|+++|+.||.   |..++                          ++++.. ++++|||||+
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~--------------------------i~~d~~-g~srG~aFV~   94 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVH--------------------------FIYTRE-GRQSGEAFVE   94 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEE--------------------------EEECSS-SCEEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEE--------------------------EEECCC-CCCCeEEEEE
Confidence            35789999999999999999999999999   77776                          777776 9999999999


Q ss_pred             eCCHHHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      |.+.++|.+|+. +||..|+||.|+|.++.+
T Consensus        95 F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~~  124 (136)
T 2hgl_A           95 LGSEDDVKMALK-KDRESMGHRYIEVFKSHR  124 (136)
T ss_dssp             CSSHHHHHHHHT-TTEEESSSSEEEEEECCH
T ss_pred             ECCHHHHHHHHh-cCCCEECCEEEEEEECCh
Confidence            999999999999 899999999999998753

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.61  E-value=4.4e-15  Score=117.76  Aligned_cols=82  Identities=15%  Similarity=0.116  Sum_probs=72.9

Q ss_pred             CCCceEEEeCCCC-----cCcHHHHHHHHhccCCeEEEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCCccCCee
Q 017842          277 EPGFRIYVGNLPW-----EVDNARLEQVFSEHGKVVNARVVYDRET-GRSRGFGFVTMSSETELNDAIAALDGQNLDGRA  350 (365)
Q Consensus       277 ~~~~~lfV~nLp~-----~~tee~L~~~F~~~G~V~~v~i~~d~~~-~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~  350 (365)
                      .+..+|+|+||..     ..++++|+++|++||.|..|+|++++.+ ++++|||||+|.+.++|.+|+..|||+.+.||.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            3456999999963     2378999999999999999999998654 688999999999999999999999999999999


Q ss_pred             EEEEEccc
Q 017842          351 IRVNVAED  358 (365)
Q Consensus       351 l~V~~a~~  358 (365)
                      |+|.|+..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999974

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.61  E-value=2.1e-15  Score=118.44  Aligned_cols=77  Identities=22%  Similarity=0.355  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||.++++++|+.+|+.||.|..+++                          .      +++|||||+|.+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~--------------------------~------~~~g~afV~f~~   72 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKH--------------------------Y------PEKGCCFIKYDT   72 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEE--------------------------E------TTTTEEEEECSS
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEE--------------------------e------cCCCEEEEEECC
Confidence            35689999999999999999999999999988773                          2      568999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      .++|.+|+..|||..|+|+.|+|.++.++
T Consensus        73 ~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           73 HEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             HHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             HHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            99999999999999999999999998753

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=4.3e-15  Score=115.81  Aligned_cols=80  Identities=19%  Similarity=0.391  Sum_probs=71.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .+.+.++|||+|||+++++++|+++|++||.|..+.+                          .      ..+|||||+|
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~--------------------------~------~~~g~afV~f   60 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH--------------------------V------KGDSFAYIQY   60 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEE--------------------------C------SSSCCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE--------------------------e------CCCCEEEEEE
Confidence            3456789999999999999999999999999988763                          2      1278999999


Q ss_pred             CCHHHHHHHHHHHccCccc--CeeEEEeecCCCC
Q 017842          235 STVEEAEKAVEMFHRYDID--GRLLTVNKAAPRG  266 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~--gr~l~V~~a~~~~  266 (365)
                      .+.++|.+|+..|||..|.  |+.|+|.++.++.
T Consensus        61 ~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           61 ESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             SSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCC
Confidence            9999999999999999999  9999999998764

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.61  E-value=6.9e-15  Score=129.51  Aligned_cols=121  Identities=13%  Similarity=0.204  Sum_probs=92.9

Q ss_pred             CHHHHHHHHHHH--ccCcccCeeEEEeecCCCCCCCCCCC--CcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEE
Q 017842          236 TVEEAEKAVEMF--HRYDIDGRLLTVNKAAPRGTQPERAP--RVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARV  311 (365)
Q Consensus       236 ~~e~a~~Al~~l--ng~~~~gr~l~V~~a~~~~~~~~~~~--~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i  311 (365)
                      +.+.+..|+...  ....+.+...+|.+.... +.+....  ......++|||+|||+.+++++|+++|+.||.|..|+|
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~-p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i  141 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSK-PLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQM  141 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTS-CCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccC-CCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEE
Confidence            567777788775  455666666677655211 1111000  01123469999999999999999999999999999999


Q ss_pred             EeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          312 VYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       312 ~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      +++. +++++|||||+|.+.++|.+|+.. .+..++||+|+|.++++-
T Consensus       142 ~~~~-~~~~kG~aFVeF~~~e~A~~A~~~-~~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          142 RRTL-HKAFKGSIFVVFDSIESAKKFVET-PGQKYKETDLLILFKDDY  187 (193)
T ss_dssp             EECT-TCCEEEEEEEEESSHHHHHHHHHC-TTCEETTEECEEEETTTC
T ss_pred             EECC-CCCcccEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEhHHH
Confidence            9986 589999999999999999999984 566999999999998753

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=7.6e-15  Score=114.82  Aligned_cols=77  Identities=27%  Similarity=0.382  Sum_probs=69.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHcc--CCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKA--GTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~--G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      ...++|||+|||+++++++|+.+|..|  |.|..+.+                                  .+|||||+|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~----------------------------------~~g~afV~f   58 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK----------------------------------IRDYAFVHF   58 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE----------------------------------CSSEEEEEE
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE----------------------------------eCCeEEEEe
Confidence            357899999999999999999999999  88877652                                  368999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      .+.++|.+|+..|||..|.|+.|+|.++.++..
T Consensus        59 ~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpd_A           59 SNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   91 (99)
T ss_dssp             SSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             CCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            999999999999999999999999999987654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=2.4e-15  Score=118.20  Aligned_cols=84  Identities=33%  Similarity=0.535  Sum_probs=74.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+++|+.|+.|   .                          ++.+..+++++|||||+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~---~--------------------------~~~~~~~~~~~g~afV~f~   62 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSVRA---R--------------------------IVTDRETGSSKGFGFVDFN   62 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCSEE---E--------------------------EEECSSSCSEEEEEEEECS
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCeEE---E--------------------------EEecCCCCCcCcEEEEEEC
Confidence            4467899999999999999999999987533   3                          6667778999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..|||..|.|+.|+|.++.++...
T Consensus        63 ~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   95 (102)
T 2fc8_A           63 SEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG   95 (102)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEECCCCCSS
T ss_pred             CHHHHHHHHHHhCCCeECCeEEEEEEecCCCCC
Confidence            999999999999999999999999999877654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.61  E-value=9.4e-16  Score=124.28  Aligned_cols=80  Identities=23%  Similarity=0.343  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCC---eEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEE
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGT---VEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVT  233 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~---i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~  233 (365)
                      ...++|||+|||+++++++|+.+|+.||.   |..++                          ++++.. ++++|||||+
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~--------------------------i~~~~~-g~~~G~afV~   67 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVH--------------------------FIYTRE-GRQSGEAFVE   67 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEE--------------------------EEECSS-SCEEEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEE--------------------------EEECCC-CCCCeEEEEE
Confidence            35789999999999999999999999998   77776                          666766 8999999999


Q ss_pred             eCCHHHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      |.+.++|.+|+. +||..|+||.|+|.++..
T Consensus        68 F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~   97 (118)
T 2db1_A           68 LESEDDVKLALK-KDRESMGHRYIEVFKSHR   97 (118)
T ss_dssp             BSSHHHHHHHGG-GTTEEETTEEEEEEEECH
T ss_pred             ECCHHHHHHHHh-cCCCeECCeEEEEEECCH
Confidence            999999999999 799999999999988754

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=5.8e-15  Score=117.54  Aligned_cols=80  Identities=23%  Similarity=0.304  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+++|.+||.|..+.                          ++.+       |||||+|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~--------------------------i~~~-------g~afV~f~~   59 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYAD--------------------------VYRD-------GTGVVEFVR   59 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEE--------------------------EETT-------TEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEE--------------------------EecC-------CEEEEEECC
Confidence            3578999999999999999999999999998887                          4433       899999999


Q ss_pred             HHHHHHHHHHHccCcccC-----eeEEEeecCCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDG-----RLLTVNKAAPRGTQP  269 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~g-----r~l~V~~a~~~~~~~  269 (365)
                      .++|.+|+..|||..|.|     +.|+|.++.++....
T Consensus        60 ~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~~~~~   97 (108)
T 1x4c_A           60 KEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSY   97 (108)
T ss_dssp             HHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCCSCCC
T ss_pred             HHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCCCCCC
Confidence            999999999999999999     999999998876544

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.61  E-value=1.2e-15  Score=123.13  Aligned_cols=77  Identities=29%  Similarity=0.377  Sum_probs=67.3

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCee-----EE
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRA-----IR  352 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~-----l~  352 (365)
                      ..++|||+|||+.+++++|+++|+.||.|..|.|+.+       |||||+|.+.++|.+||..|||..|.|++     |+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            3469999999999999999999999999999999755       89999999999999999999999999998     88


Q ss_pred             EEEcccccc
Q 017842          353 VNVAEDRQR  361 (365)
Q Consensus       353 V~~a~~~~~  361 (365)
                      |..+.++..
T Consensus        88 v~~~~~~~~   96 (115)
T 3beg_B           88 VKVDGPRSP   96 (115)
T ss_dssp             EEECC----
T ss_pred             eccCCCCCC
Confidence            888776554

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.60  E-value=4.2e-15  Score=116.28  Aligned_cols=80  Identities=33%  Similarity=0.507  Sum_probs=71.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ..+.++|||+|||+++++++|+.+|..||.|..+.+                          .      +++|||||+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~--------------------------~------~~kg~afV~f~   59 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI--------------------------H------KDKGFGFIRLE   59 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEE--------------------------E------TTTTEEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEE--------------------------e------cCCCEEEEEEC
Confidence            346789999999999999999999999999988773                          2      34899999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      +.++|.+|+..|+|..|+|+.|+|.++.++..
T Consensus        60 ~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpj_A           60 TRTLAEIAKVELDNMPLRGKQLRVRFACHSAS   91 (99)
T ss_dssp             SSHHHHHHHHHHTTCCBTTBCCEEEESSCCSC
T ss_pred             CHHHHHHHHHHhCCCEeCCceEEEEEcCCCCC
Confidence            99999999999999999999999999987653

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=5.7e-15  Score=113.47  Aligned_cols=79  Identities=25%  Similarity=0.473  Sum_probs=70.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+.+|++||.|..+.+                          .        ++||||+|.
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~--------------------------~--------~~~afV~f~   51 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDV--------------------------V--------KDYAFVHME   51 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEE--------------------------C--------SSCEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEE--------------------------E--------CCEEEEEEC
Confidence            446789999999999999999999999999988773                          2        459999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..|||..|+|+.|+|.++.+....
T Consensus        52 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   84 (90)
T 2dnp_A           52 KEADAKAAIAQLNGKEVKGKRINVELSTKGQKK   84 (90)
T ss_dssp             CHHHHHHHHHHHTTCEETTEECEEEESCCCCCC
T ss_pred             CHHHHHHHHHHhCCCEECCcEEEEEECCCCCCC
Confidence            999999999999999999999999999876543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.60  E-value=7.1e-15  Score=119.84  Aligned_cols=74  Identities=20%  Similarity=0.255  Sum_probs=67.7

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceE-EEEEecCHHHHHHHHHHhCCCccCC--eeEEEEEcc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGF-GFVTMSSETELNDAIAALDGQNLDG--RAIRVNVAE  357 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~-afV~F~s~~~a~~Al~~l~~~~l~g--r~l~V~~a~  357 (365)
                      .|||+||++.+++++|+++|+.||.|..|+|...      .|| |||+|.+.++|..|+..|||..|.|  +.|+|.||+
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            5789999999999999999999999999999642      386 9999999999999999999999987  699999998


Q ss_pred             ccc
Q 017842          358 DRQ  360 (365)
Q Consensus       358 ~~~  360 (365)
                      ++.
T Consensus       101 ~~~  103 (124)
T 2e5i_A          101 PTR  103 (124)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            764

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.60  E-value=2.7e-15  Score=120.05  Aligned_cols=80  Identities=20%  Similarity=0.257  Sum_probs=70.2

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          156 PPEDAKLFVGNLPYD-VDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      ..+.++|||+|||++ +++++|+.+|++||.|..+.                          ++      +++|||||+|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~--------------------------i~------~~kg~aFVef   69 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYI--------------------------LM------RMKSQAFIEM   69 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEE--------------------------EE------TTTTEEEEEC
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEE--------------------------Ee------cCCCEEEEEE
Confidence            446889999999998 99999999999999999887                          32      4589999999


Q ss_pred             CCHHHHHHHHHHHcc--CcccCeeEEEeecCCCCC
Q 017842          235 STVEEAEKAVEMFHR--YDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       235 ~~~e~a~~Al~~lng--~~~~gr~l~V~~a~~~~~  267 (365)
                      .+.++|.+|+..|++  ..|.||.|+|.++..+..
T Consensus        70 ~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~~  104 (112)
T 1x4f_A           70 ETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKK  104 (112)
T ss_dssp             SSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCSS
T ss_pred             CCHHHHHHHHHHhccCCceECCEEEEEEECccccc
Confidence            999999999998865  569999999999876543

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.60  E-value=1.7e-15  Score=117.87  Aligned_cols=82  Identities=17%  Similarity=0.325  Sum_probs=73.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEE
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLA----MLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGF  231 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~----~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~af  231 (365)
                      .++.++|||+|||+++++++|+    .+|++||.|..+.+                          .   .++.++||||
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i--------------------------~---~~~~~~g~af   55 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV--------------------------S---RSLKMRGQAF   55 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEEC--------------------------C---HHHHHTTCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEE--------------------------E---cCCCcCcEEE
Confidence            3467899999999999999999    99999999988762                          2   2567889999


Q ss_pred             EEeCCHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          232 VTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       232 V~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      |+|.+.++|.+|+..|||..+.|+.|+|.++.+..
T Consensus        56 V~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   90 (97)
T 1nu4_A           56 VIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS   90 (97)
T ss_dssp             EEESSHHHHHHHHHHHTTCEETTEECEEEECSSCC
T ss_pred             EEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCCC
Confidence            99999999999999999999999999999988754

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=4.7e-15  Score=112.49  Aligned_cols=75  Identities=24%  Similarity=0.353  Sum_probs=68.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||.++++++|+++|.+||.|..+.+                          .      +++|||||+|.+
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~--------------------------~------~~kg~afV~f~~   57 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITV--------------------------V------QRQQCAFIQFAT   57 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEE--------------------------E------GGGTEEEEEESS
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEE--------------------------E------CCCCEEEEEECC
Confidence            45789999999999999999999999999988873                          3      258999999999


Q ss_pred             HHHHHHHHHHH-ccCcccCeeEEEeecC
Q 017842          237 VEEAEKAVEMF-HRYDIDGRLLTVNKAA  263 (365)
Q Consensus       237 ~e~a~~Al~~l-ng~~~~gr~l~V~~a~  263 (365)
                      .++|.+|+..| +|..++|+.|+|.+++
T Consensus        58 ~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           58 RQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             HHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             HHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            99999999988 9999999999999863

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1e-15  Score=125.09  Aligned_cols=82  Identities=18%  Similarity=0.320  Sum_probs=73.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||+|||+++++++|+.+|..||.|..+.                          ++.+..+++++|||||+|.
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~--------------------------~~~~~~~g~~~G~afV~F~   75 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSI--------------------------YIAYGPNGKATGEGFVEFR   75 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTC--------------------------EEEECTTSSEEEEEEEEBS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceE--------------------------EEEECCCCCCCeEEEEEEC
Confidence            34568999999999999999999999999986533                          5566679999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      +.++|.+||. +||..|+|+.|+|.++..
T Consensus        76 ~~~~a~~Al~-~~g~~~~gr~i~V~~a~~  103 (124)
T 1wel_A           76 NEADYKAALC-RHKQYMGNRFIQVHPITK  103 (124)
T ss_dssp             SSHHHHHHHT-SCSBCSTTSCBEEEEECH
T ss_pred             CHHHHHHHHH-hCCCeECCcEEEEEECCH
Confidence            9999999999 899999999999998764

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.59  E-value=7.3e-15  Score=114.72  Aligned_cols=78  Identities=23%  Similarity=0.408  Sum_probs=69.9

Q ss_pred             cCCCCCCeEEEcCCCC-CCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEE
Q 017842          154 VEPPEDAKLFVGNLPY-DVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFV  232 (365)
Q Consensus       154 ~~~~~~~tvfVgnLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV  232 (365)
                      ...+..++|||||||+ ++++++|+.+|+.||.|..++                          +        .+|||||
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~--------------------------i--------~~g~afV   62 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQIN--------------------------I--------KNAFGFI   62 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEE--------------------------E--------CSSEEEE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEE--------------------------E--------eCCEEEE
Confidence            3455788999999998 999999999999999998876                          2        2799999


Q ss_pred             EeCCHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          233 TMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       233 ~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      +|.+.++|.+|+..|||..++|+.|+|.++..+
T Consensus        63 ~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           63 QFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             EESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             EECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            999999999999999999999999999998754

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.59  E-value=8.3e-16  Score=122.31  Aligned_cols=81  Identities=20%  Similarity=0.323  Sum_probs=72.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCC---eEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEE
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGT---VEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVT  233 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~---i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~  233 (365)
                      ...++|||+|||+++++++|+.+|..||.   |..++                          ++++.. |+++|||||+
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~--------------------------i~~~~~-g~~~G~afV~   61 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIH--------------------------FLLNRD-GKRRGDALIE   61 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEE--------------------------CCCCTT-STTCSEEEEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEE--------------------------EEECCC-CCEeeEEEEE
Confidence            35789999999999999999999999998   77776                          666766 9999999999


Q ss_pred             eCCHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      |.+.++|.+|+. ++|..++||.|+|.++.+.
T Consensus        62 F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~~~   92 (107)
T 2lmi_A           62 MESEQDVQKALE-KHRMYMGQRYVEVYEINNE   92 (107)
T ss_dssp             BSSHHHHHHHHT-TTTCCSSSSCCCCEECCHH
T ss_pred             ECCHHHHHHHHH-hCcceeCCeEEEEEECCHH
Confidence            999999999999 7999999999999987643

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.59  E-value=4.5e-15  Score=125.96  Aligned_cols=80  Identities=25%  Similarity=0.503  Sum_probs=74.8

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      +|||+|||+.+++++|+++|+.||.|..|++++++. ++++|||||+|.+.++|.+|+..|+|..+.|+.|+|.++.++.
T Consensus         2 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             EEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             EEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            899999999999999999999999999999999864 7799999999999999999999999999999999999998665


Q ss_pred             c
Q 017842          361 R  361 (365)
Q Consensus       361 ~  361 (365)
                      .
T Consensus        81 ~   81 (166)
T 3md3_A           81 Q   81 (166)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.59  E-value=3.5e-15  Score=132.65  Aligned_cols=77  Identities=21%  Similarity=0.285  Sum_probs=71.7

Q ss_pred             CCceEEEeCCC-CcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          278 PGFRIYVGNLP-WEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       278 ~~~~lfV~nLp-~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ++++|||+||| +.+++++|+.+|+.||.|..|+|++++     +|||||+|.+.++|.+|+..|||..+.||+|+|.|+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            45699999999 899999999999999999999998652     799999999999999999999999999999999999


Q ss_pred             ccc
Q 017842          357 EDR  359 (365)
Q Consensus       357 ~~~  359 (365)
                      +.+
T Consensus        78 ~~~   80 (205)
T 3tyt_A           78 KQP   80 (205)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            743

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.59  E-value=3.7e-15  Score=132.41  Aligned_cols=82  Identities=24%  Similarity=0.448  Sum_probs=75.3

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|+|+++..+++++|||||+|.+.++|.+|+..|+|..+.|+.|+|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            35999999999999999999999999999999999988999999999999999999999999999999999999999876


Q ss_pred             cc
Q 017842          359 RQ  360 (365)
Q Consensus       359 ~~  360 (365)
                      +.
T Consensus       108 ~~  109 (216)
T 2qfj_A          108 IG  109 (216)
T ss_dssp             CG
T ss_pred             cc
Confidence            64

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.59  E-value=5.8e-15  Score=117.66  Aligned_cols=78  Identities=27%  Similarity=0.451  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||+|||+++++++|+.+|++||.|..+.                          +.        +|||||+|.
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~--------------------------i~--------kg~afV~f~   73 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK--------------------------IL--------NGFAFVEFE   73 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEE--------------------------EE--------TTEEEEECS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEE--------------------------EE--------CCEEEEEEC
Confidence            44678999999999999999999999999998877                          33        799999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      +.++|.+|+..|||..|+|+.|+|.++.++..
T Consensus        74 ~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  105 (108)
T 2jvo_A           74 EAESAAKAIEEVHGKSFANQPLEVVYSKLPAK  105 (108)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEESCSCCC-
T ss_pred             CHHHHHHHHHHcCCCEECCeEEEEEEecCCCC
Confidence            99999999999999999999999999887643

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=4.8e-15  Score=114.53  Aligned_cols=80  Identities=21%  Similarity=0.385  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCC-eEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGT-VEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~-i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ...++|||+|||+++++++|+.+|++||. |..+.                          +       .++|||||+|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~--------------------------~-------~~~g~afV~f~   52 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV--------------------------L-------LKSGYAFVDYP   52 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCE--------------------------E-------EETTEEEECCS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEE--------------------------E-------cCCCEEEEEEC
Confidence            45789999999999999999999999998 54433                          1       25899999999


Q ss_pred             CHHHHHHHHHHHcc-CcccCeeEEEeecCCCCCCC
Q 017842          236 TVEEAEKAVEMFHR-YDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       236 ~~e~a~~Al~~lng-~~~~gr~l~V~~a~~~~~~~  269 (365)
                      +.++|.+|+..||| ..|+|+.|+|.++.++..+.
T Consensus        53 ~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~~~~   87 (93)
T 2cqh_A           53 DQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLRS   87 (93)
T ss_dssp             CHHHHHHHHHHHTTTCEETTEECEEEECCCCCCCC
T ss_pred             CHHHHHHHHHHccCCeeECCEEEEEEEccCccccC
Confidence            99999999999999 99999999999998775543

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.58  E-value=7.2e-15  Score=117.70  Aligned_cols=77  Identities=16%  Similarity=0.088  Sum_probs=69.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|++||.|..+.|                          .      .++|||||+|.+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i--------------------------~------~~~g~afV~f~~~   56 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL--------------------------P------EGGITAIVEFLEP   56 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC--------------------------C------SSSSCEEEEESCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE--------------------------e------CCCCEEEEEeCCH
Confidence            3579999999999999999999999999988763                          2      3689999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ++|.+|+..|||..|.|++|+|.++....
T Consensus        57 ~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A           57 LEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             HHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             HHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            99999999999999999999999986543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.58  E-value=3.2e-15  Score=116.16  Aligned_cols=79  Identities=23%  Similarity=0.478  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|..||.|..+                               ..++.++|||||+|.+.
T Consensus        15 ~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-------------------------------~~~~~~~g~afV~f~~~   63 (96)
T 1fjc_A           15 AARTLLAKNLSFNITEDELKEVFEDALEIRLV-------------------------------SQDGKSKGIAYIEFKSE   63 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-------------------------------EETTEEEEEEEEEESSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-------------------------------CCCCCcceEEEEEECCH
Confidence            56899999999999999999999999977432                               34788999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|.+|+..|+|..|.|+.|+|.++.++..
T Consensus        64 ~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (96)
T 1fjc_A           64 ADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             HHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             HHHHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            999999999999999999999999987654

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.58  E-value=1.3e-14  Score=114.46  Aligned_cols=78  Identities=26%  Similarity=0.404  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|..||.|..+.+                          .        ++||||+|.+.
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~--------------------------~--------~~~afV~f~~~   55 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK--------------------------L--------KDYAFIHFDER   55 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEE--------------------------C--------SSCEEEEESSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE--------------------------E--------CCEEEEEeCCH
Confidence            4689999999999999999999999999988762                          2        56999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      ++|.+|+..|||..|.|+.|+|.++.++....
T Consensus        56 ~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   87 (103)
T 2dgu_A           56 DGAVKAMEEMNGKDLEGENIEIVFAKPPDQKR   87 (103)
T ss_dssp             HHHHHHHHHHTTEEETTEEEEEEECCCCCCCC
T ss_pred             HHHHHHHHHHCCCccCCCEEEEEEcCCCcccc
Confidence            99999999999999999999999998776544

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.35  E-value=1.6e-16  Score=128.18  Aligned_cols=86  Identities=23%  Similarity=0.383  Sum_probs=78.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEE--------EEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccc
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEI--------AEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRG  228 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~--------~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g  228 (365)
                      .+.++|||+|||+++++++|+.+|+.||.|..        ++                          +..+..+++++|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~--------------------------i~~~~~~g~~~g   58 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMIN--------------------------LYTDRETGKLKG   58 (116)
Confidence            35789999999999999999999999999987        44                          677778899999


Q ss_pred             eEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          229 FGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       229 ~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      ||||+|.+.++|.+|+..|||..|.|+.|+|.++.++...
T Consensus        59 ~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           59 EATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADF   98 (116)
Confidence            9999999999999999999999999999999999876543

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.57  E-value=4.5e-15  Score=113.01  Aligned_cols=71  Identities=27%  Similarity=0.612  Sum_probs=66.1

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhcc----C-------CeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEH----G-------KVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL  346 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~----G-------~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l  346 (365)
                      +.++|||+|||+.+++++|+++|+.|    |       .|..+++.++      +|||||+|.+.++|.+|+ .|||..+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            34699999999999999999999999    8       8999999754      899999999999999999 8999999


Q ss_pred             CCeeEEEEE
Q 017842          347 DGRAIRVNV  355 (365)
Q Consensus       347 ~gr~l~V~~  355 (365)
                      .||+|+|++
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999974

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=1.7e-14  Score=111.17  Aligned_cols=79  Identities=24%  Similarity=0.425  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+.+|+.||.|..+.+                          .        ++||||+|.
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~--------------------------~--------~~~afV~f~   52 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDI--------------------------V--------KDYAFVHME   52 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEE--------------------------C--------SSEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE--------------------------E--------CCEEEEEEC
Confidence            446789999999999999999999999999988773                          2        459999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..|||..|.|+.|+|.++.++...
T Consensus        53 ~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   85 (92)
T 2dgt_A           53 RAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRT   85 (92)
T ss_dssp             CHHHHHHHHHHHTTEEETTEEEEEEESSCCCSC
T ss_pred             CHHHHHHHHHHhCCCeeCCcEEEEEEccCCCCC
Confidence            999999999999999999999999999876543

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.57  E-value=1.3e-14  Score=124.23  Aligned_cols=83  Identities=24%  Similarity=0.430  Sum_probs=76.2

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCC--CcceEEEEEecCHHHHHHHHHHhCCCccC---CeeEEE
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETG--RSRGFGFVTMSSETELNDAIAALDGQNLD---GRAIRV  353 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~--~~kG~afV~F~s~~~a~~Al~~l~~~~l~---gr~l~V  353 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|+|++++.++  +++|||||+|.+.++|.+|+..|+|..+.   ++.|.+
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~   82 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQM   82 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEE
Confidence            4699999999999999999999999999999999998887  89999999999999999999999998775   688999


Q ss_pred             EEcccccc
Q 017842          354 NVAEDRQR  361 (365)
Q Consensus       354 ~~a~~~~~  361 (365)
                      .++.....
T Consensus        83 ~~~~~~~~   90 (175)
T 3nmr_A           83 KPADSEKN   90 (175)
T ss_dssp             EECGGGCC
T ss_pred             cccccccc
Confidence            88876553

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=5.8e-15  Score=117.87  Aligned_cols=77  Identities=18%  Similarity=0.289  Sum_probs=69.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||+|||+++++++|+++|+.| .|..++                          ++++.. |+++|||||+|.+.+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~--------------------------i~~d~~-g~~~G~afV~F~~~~   67 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVH--------------------------LLKDHV-GRNNGNGLVKFLSPQ   67 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEE--------------------------ECCCTT-CCCCSEEEEECSSHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEE--------------------------EEECCC-CCCCeEEEEEECCHH
Confidence            4689999999999999999999999 787776                          666665 899999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      +|.+|+ .+||..|+||.|.|..+..
T Consensus        68 ~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           68 DTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             HHHHHH-hcCCCeECCeEEEEEECCc
Confidence            999999 5699999999999987754

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.56  E-value=7.4e-15  Score=114.33  Aligned_cols=78  Identities=24%  Similarity=0.457  Sum_probs=69.8

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          156 PPEDAKLFVGNLPY-DVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       156 ~~~~~tvfVgnLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .++.++|||+|||+ ++++++|+.+|++||.|..+.                          +        .+|||||+|
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~--------------------------i--------~~g~afV~f   52 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQIN--------------------------I--------KNAFGFIQF   52 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEE--------------------------E--------ETTEEEEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEE--------------------------E--------eCCEEEEEE
Confidence            34678999999999 999999999999999998876                          2        278999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      .+.++|.+|+..|||..+.|+.|+|.++.+...
T Consensus        53 ~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   85 (96)
T 2kvi_A           53 DNPQSVRDAIECESQEMNFGKKLILEVSSSNAR   85 (96)
T ss_dssp             SCHHHHHHHHHHHTCSSCBTTTBCEEEEECCCC
T ss_pred             CCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCCC
Confidence            999999999999999999999999999876544

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=3.6e-15  Score=119.93  Aligned_cols=74  Identities=22%  Similarity=0.374  Sum_probs=63.6

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCC---CCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRET---GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~---~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ..++|||+|||+.+++++|+++|+.||.|. ++++.+..+   |+++|||||+|.+.++|.+||..|++  ++|+.|.+.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~~G~~~~~~   83 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--EDGKLYLCV   83 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--ETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--cCCcEEEec
Confidence            346999999999999999999999999999 888888777   79999999999999999999998832  444444443

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=2e-14  Score=111.35  Aligned_cols=79  Identities=24%  Similarity=0.365  Sum_probs=68.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|..||.|..+                            +.+..+++   ||||+|.+.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v----------------------------~~~~~~g~---~afV~f~~~   55 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV----------------------------VMDKDKGV---FAIVEMGDV   55 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE----------------------------EECSSSCC---EEEEEESSH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE----------------------------EEcCCCCc---EEEEEECCH
Confidence            46799999999999999999999999999764                            33444554   999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      ++|.+|+. |||..|+|+.|+|.++.++...
T Consensus        56 ~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~~   85 (94)
T 2e5g_A           56 GAREAVLS-QSQHSLGGHRLRVRPREQKEFQ   85 (94)
T ss_dssp             HHHHHHHT-CSCCEETTEECCCBCSCCSCCC
T ss_pred             HHHHHHHh-cCCeEECCEEEEEEECCcCCCC
Confidence            99999999 8999999999999988765543

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=2.6e-15  Score=114.91  Aligned_cols=78  Identities=19%  Similarity=0.360  Sum_probs=66.3

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +.++|||+|||+.+++++|+++|+.||.|..|+|+++     ++|||||+|.+.++|.+|+.  .+..+.|++|+|.++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecC
Confidence            3469999999999999999999999999999999865     58999999999999975432  1335599999999999


Q ss_pred             ccccC
Q 017842          358 DRQRR  362 (365)
Q Consensus       358 ~~~~~  362 (365)
                      ++...
T Consensus        77 ~~~~~   81 (88)
T 1wf0_A           77 PKHNS   81 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.56  E-value=2.6e-15  Score=125.64  Aligned_cols=92  Identities=18%  Similarity=0.267  Sum_probs=74.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ..+.++|||+|||+++++++|+.+|+.||.|..+.++..                     .-+....+++++|||||+|.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~---------------------~di~~~~~g~~~g~afV~f~  100 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIM---------------------FDIRLMKEGRMKGQAFIGLP  100 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHH---------------------CEEEEEEETTTEEEEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccce---------------------eeEEeccCCCcccEEEEEeC
Confidence            446789999999999999999999999999866310000                     01112247889999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..|||..|.|+.|+|.++.+...+
T Consensus       101 ~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~~  133 (143)
T 3egn_A          101 NEKAAAKALKEANGYVLFGKPMVVQFARSARPK  133 (143)
T ss_dssp             SHHHHHHHHHHHTTBEETTEECEEEECCCSCC-
T ss_pred             CHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCc
Confidence            999999999999999999999999999876543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=4.1e-15  Score=121.29  Aligned_cols=80  Identities=18%  Similarity=0.286  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCe----EEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEE
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTV----EIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFV  232 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i----~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV  232 (365)
                      ...++|||+|||+++|+++|+++|+.||.|    ..|+                          ++++ .+++++|||||
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~--------------------------i~~d-~~gr~~G~aFV   73 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGIL--------------------------FVTY-PDGRPTGDAFV   73 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEE--------------------------EEEC-TTSCEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEE--------------------------EEEC-CCCCEeeEEEE
Confidence            357899999999999999999999999975    4555                          6666 48999999999


Q ss_pred             EeCCHHHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          233 TMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       233 ~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      +|.+.++|.+|+.. |+..|+||.|.|..+.+
T Consensus        74 ~F~~~~~A~~Al~~-~~~~l~gR~i~V~~a~~  104 (123)
T 2dha_A           74 LFACEEYAQNALRK-HKDLLGKRYIELFRSTA  104 (123)
T ss_dssp             CCSSHHHHHHHHTT-TTEESSSCEECCEEECH
T ss_pred             EECCHHHHHHHHHh-CCCeeCCeEEEEEECCH
Confidence            99999999999997 99999999999987643

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.56  E-value=1.9e-14  Score=114.87  Aligned_cols=76  Identities=28%  Similarity=0.405  Sum_probs=69.6

Q ss_pred             CCCeEEEcCCCCC-CCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          158 EDAKLFVGNLPYD-VDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ..++|||+|||++ +++++|+.+|.+||.|..+.                          +        .+|||||+|.+
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~--------------------------i--------~~g~afV~f~~   71 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCS--------------------------V--------HKGYAFVQYSN   71 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEE--------------------------E--------ETTEEEEECSS
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEE--------------------------E--------eCCEEEEEECC
Confidence            4689999999999 99999999999999998876                          3        58999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      .++|.+|+..|+|..|+|+.|+|.++.++..
T Consensus        72 ~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~  102 (110)
T 1wf1_A           72 ERHARAAVLGENGRVLAGQTLDINMAGEPKP  102 (110)
T ss_dssp             SHHHHHHHHHHTTCEETTEECCEEESCCCCS
T ss_pred             HHHHHHHHHHcCCCEECCeEEEEEECCCCCC
Confidence            9999999999999999999999999975543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=1.6e-14  Score=112.16  Aligned_cols=80  Identities=25%  Similarity=0.277  Sum_probs=69.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|..||.|..++.                         ++.+..    .|.|||+|.+.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~-------------------------i~~~~~----~~~afV~f~~~   64 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQ-------------------------VNTDSE----TAVVNVTYSSK   64 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEE-------------------------ECCSSS----SEEEEEEESSH
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEE-------------------------eecCCC----CCEEEEEECCH
Confidence            4689999999999999999999999999988731                         333333    33499999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ++|.+|+..|||..|+|+.|+|.++.++.
T Consensus        65 ~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           65 DQARQALDKLNGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             HHHHHHHHHHTTCBCSSCBCEEEECCCCC
T ss_pred             HHHHHHHHHhCCCEECCcEEEEEEcCccc
Confidence            99999999999999999999999998764

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.55  E-value=1.5e-14  Score=121.99  Aligned_cols=79  Identities=27%  Similarity=0.354  Sum_probs=71.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ....++|||||||+++++++|+.+|+.||.|..++                          +..+     ++|||||+|.
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~-----~~g~afV~f~  118 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVW--------------------------VARN-----PPGFAFVEFE  118 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEE--------------------------ECSS-----SCSEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEE--------------------------EeeC-----CCcEEEEEEC
Confidence            34578999999999999999999999999998887                          3332     5899999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      +.++|.+|+..|||..|.|+.|+|.++.++
T Consensus       119 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A          119 DPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             SHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             CHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            999999999999999999999999998765

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.54  E-value=6e-15  Score=125.65  Aligned_cols=80  Identities=29%  Similarity=0.655  Sum_probs=74.9

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+|+++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|+.  ++..+.|+.|.|.++.+
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEcccccccc
Confidence            4699999999999999999999999999999999999999999999999999999999999  47899999999999876


Q ss_pred             cc
Q 017842          359 RQ  360 (365)
Q Consensus       359 ~~  360 (365)
                      +.
T Consensus        81 ~~   82 (167)
T 2cjk_A           81 RD   82 (167)
T ss_dssp             HH
T ss_pred             hh
Confidence            43

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.54  E-value=4.9e-15  Score=116.49  Aligned_cols=81  Identities=26%  Similarity=0.508  Sum_probs=73.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|+.||.|..+.                          +..+. +++++|||||+|.+.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~~~-~g~~~g~afV~f~~~   60 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVK--------------------------IITDR-TGVSKGYGFVSFYND   60 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECT-TSCEEEEEEEEESSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEE--------------------------EEECC-CCCccceEEEEECCH
Confidence            357999999999999999999999999998887                          67776 899999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|.+|+.  +|..++|+.|.|.++.++..
T Consensus        61 ~~a~~Ai~--~~~~~~g~~l~v~~a~~~~~   88 (102)
T 2xs2_A           61 VDVQKIVE--SQINFHGKKLKLGPAIRKQN   88 (102)
T ss_dssp             CCHHHHTT--CCCEETTEECEEEEEEECC-
T ss_pred             HHHHHHHh--CCCeECCEEEEEEECCcCcc
Confidence            99999999  99999999999998876543

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.54  E-value=7.3e-15  Score=120.24  Aligned_cols=79  Identities=24%  Similarity=0.349  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeE--EEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVE--IAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~--~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      ...++|||+|||+++++++|+++|+.| .|.  .|+                          ++++.. |+++|||||+|
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~--------------------------i~~d~~-GrsrGfaFV~F   91 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGIT--------------------------LPVDPE-GKITGEAFVQF   91 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEE--------------------------CCCCSS-SSSCSEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEE--------------------------EEECCC-CCCceEEEEEE
Confidence            457899999999999999999999999 455  555                          677776 99999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      .+.++|.+|+.. ++..|+||.|+|..+..
T Consensus        92 ~~~e~A~~Al~~-~~~~l~gR~I~V~~a~~  120 (126)
T 2hgm_A           92 ASQELAEKALGK-HKERIGHRYIEVFKSSQ  120 (126)
T ss_dssp             SSTTHHHHHHTT-TTCCBTTBCCCCEEECH
T ss_pred             CCHHHHHHHHHH-CCCEECCEEEEEEECCH
Confidence            999999999997 88999999999987754

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.54  E-value=1.4e-14  Score=125.72  Aligned_cols=83  Identities=31%  Similarity=0.452  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+.+|+.||.|..+.                          +.++. ++.++|||||+|.+
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~--------------------------i~~d~-~g~~kG~afV~F~~  138 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA--------------------------VDYDR-SGRSLGTADVHFER  138 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEE--------------------------ECCCT-TSSCSCCEEEEESC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEECC-CCCEeeEEEEEeCC
Confidence            3568999999999999999999999999998887                          66666 88999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      .++|.+|+..|||..|+|+.|+|.++....
T Consensus       139 ~~~A~~Ai~~lng~~l~Gr~l~V~~a~~~~  168 (177)
T 2f3j_A          139 RADALKAMKQYKGVPLDGRPMDIQLVASQI  168 (177)
T ss_dssp             HHHHHHHHHHSTTCBCSSSBCEEEEESSGG
T ss_pred             HHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            999999999999999999999999987643

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.54  E-value=3.6e-15  Score=124.21  Aligned_cols=82  Identities=18%  Similarity=0.236  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+++|+.|| |..++                          ++++.. ++++|||||+|.+
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~--------------------------i~~d~~-g~srGfaFV~F~~   95 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVH--------------------------IEIGPD-GRVTGEADVEFAT   95 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEE--------------------------CCCSSS-SCSSCCCEEECSH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEE--------------------------EEECCC-CCCceEEEEEeCC
Confidence            3567999999999999999999999999 55666                          667765 8999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      .++|.+|| .+|+..|.||.|.|..+.+...
T Consensus        96 ~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           96 HEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             HHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             HHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence            99999999 6699999999999998876543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.54  E-value=1.7e-14  Score=130.50  Aligned_cols=105  Identities=23%  Similarity=0.289  Sum_probs=78.7

Q ss_pred             ccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcC---------cHHHHHHHHhccCCeEEEEEEeeCCCC
Q 017842          248 HRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEV---------DNARLEQVFSEHGKVVNARVVYDRETG  318 (365)
Q Consensus       248 ng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~---------tee~L~~~F~~~G~V~~v~i~~d~~~~  318 (365)
                      +...+.|+.....+......    ........++|||+||+..+         ++++|+.+|+.||.|..|+|+.+    
T Consensus       107 ~~~D~fGr~k~~~~~d~~~g----~gs~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~----  178 (240)
T 3u1l_A          107 EVLDCFGREKFADYREDMGG----IGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES----  178 (240)
T ss_dssp             SSBCTTSSBCGGGTC-------------CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG----
T ss_pred             cCcccccchhcccchhcccC----cCccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC----
Confidence            44556677644433322111    11123456699999999998         89999999999999999999853    


Q ss_pred             CcceEEEEEecCHHHHHHHHHHhCCCcc------------CCeeEEEEEccccccC
Q 017842          319 RSRGFGFVTMSSETELNDAIAALDGQNL------------DGRAIRVNVAEDRQRR  362 (365)
Q Consensus       319 ~~kG~afV~F~s~~~a~~Al~~l~~~~l------------~gr~l~V~~a~~~~~~  362 (365)
                        +|||||+|.+.++|..|+..|+|..|            .|+.|.|.||...+.+
T Consensus       179 --kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          179 --KNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             --GTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC-----
T ss_pred             --CCEEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCCCCH
Confidence              89999999999999999999999999            8999999999977653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.53  E-value=1e-14  Score=118.08  Aligned_cols=78  Identities=14%  Similarity=0.115  Sum_probs=70.0

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          160 AKLFVGNL----PYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       160 ~tvfVgnL----p~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ..||||||    |+.+++..|+++|+.||.|..+.                          ++.|+.||+++|||||+|.
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~--------------------------li~Dp~Tg~slGfgfVef~   56 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFE--------------------------AFNDPNSALPLHVYLIKYA   56 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEE--------------------------EEECTTTCCEEEEEEEECC
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EEecCCCCceeeEEEEEEC
Confidence            58999999    99999999999999999999988                          8999999999999999999


Q ss_pred             C----HHH----HHHHHH--HHccCcccCeeEEEeecC
Q 017842          236 T----VEE----AEKAVE--MFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       236 ~----~e~----a~~Al~--~lng~~~~gr~l~V~~a~  263 (365)
                      +    ++.    |.+|+.  .+||..|+|+.|+|..-.
T Consensus        57 d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln~   94 (136)
T 2j8a_A           57 SSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILNK   94 (136)
T ss_dssp             ------CCHHHHHHHHHHHTTTTCEEETTEEEEEEECC
T ss_pred             CCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEECc
Confidence            5    322    788888  789999999999998654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=9.2e-14  Score=108.23  Aligned_cols=79  Identities=25%  Similarity=0.320  Sum_probs=70.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+||  ++++++|+.+|.+||.|..+.                          +      ++++|||||+|.
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~--------------------------i------~~~~g~afV~f~   57 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLS--------------------------M------DPPRNCAFVTYE   57 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEE--------------------------E------ETTTTEEEEEES
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEE--------------------------e------cCCCCEEEEEEC
Confidence            345789999996  999999999999999998876                          3      267899999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      +.++|.+|+..|||..|.|+.|+|.++.++...
T Consensus        58 ~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~   90 (97)
T 1x5p_A           58 KMESADQAVAELNGTQVESVQLKVNIARKQPML   90 (97)
T ss_dssp             SHHHHHHHHHHTTTEEETTEEEEEECCSSCCCC
T ss_pred             CHHHHHHHHHHhCCCeECCeEEEEEECCCCCCC
Confidence            999999999999999999999999999876543

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.52  E-value=2.5e-14  Score=109.48  Aligned_cols=75  Identities=28%  Similarity=0.467  Sum_probs=68.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|++| .|..++                          +.      +++|||||+|.+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~--------------------------i~------~~~g~afV~f~~~   50 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCY--------------------------VD------RNKRTAFVTLLNG   50 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEE--------------------------EE------GGGTEEEECCSCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEE--------------------------Ee------CCCcEEEEEECCH
Confidence            46899999999999999999999999 887766                          31      6789999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      ++|.+|+..|||..++|+.|+|.++...
T Consensus        51 ~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A           51 EQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             HHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             HHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            9999999999999999999999998644

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.52  E-value=4.2e-14  Score=131.18  Aligned_cols=81  Identities=22%  Similarity=0.463  Sum_probs=74.8

Q ss_pred             CCCceEEEeCCCCcCcHHHHH----HHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLE----QVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR  352 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~----~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~  352 (365)
                      .+.++|||+|||+.+++++|+    ++|+.||.|..|+|.+   +++++|||||+|.+.++|.+|+..|||..|.|+.|+
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   83 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   83 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            456699999999999999976    8999999999999985   578999999999999999999999999999999999


Q ss_pred             EEEccccc
Q 017842          353 VNVAEDRQ  360 (365)
Q Consensus       353 V~~a~~~~  360 (365)
                      |.|++.+.
T Consensus        84 v~~a~~~~   91 (282)
T 3pgw_A           84 IQYAKTDS   91 (282)
T ss_pred             EEEeccCc
Confidence            99997655

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.52  E-value=2.6e-14  Score=108.75  Aligned_cols=71  Identities=24%  Similarity=0.579  Sum_probs=64.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHcc----C-------CeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCc
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKA----G-------TVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRS  226 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~----G-------~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  226 (365)
                      ..++|||+|||+++++++|+.+|++|    |       .|..+++                          .      ++
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~--------------------------~------~~   52 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI--------------------------N------QD   52 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE--------------------------C------SS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEe--------------------------c------CC
Confidence            46899999999999999999999999    8       7877662                          2      34


Q ss_pred             cceEEEEeCCHHHHHHHHHHHccCcccCeeEEEee
Q 017842          227 RGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNK  261 (365)
Q Consensus       227 ~g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~  261 (365)
                      +|||||+|.+.++|.+|+ .|||..++|+.|+|.+
T Consensus        53 kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           53 KNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             SSEEEEEESSHHHHHHHG-GGTTCEETTEECEEEC
T ss_pred             CcEEEEEcCCHHHHHHHH-hcCCCEECCeEEEEeC
Confidence            899999999999999999 8999999999999975

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=8.9e-14  Score=111.41  Aligned_cols=81  Identities=21%  Similarity=0.329  Sum_probs=70.2

Q ss_pred             CCCceEEEeCCCCcCc-----------HHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCc
Q 017842          277 EPGFRIYVGNLPWEVD-----------NARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQN  345 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~t-----------ee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~  345 (365)
                      .+..+|+|+||....+           +++|+++|+.||.|..|.| .++   .++|||||+|.+.++|.+|+..|||..
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            4556999999944332           6899999999999999966 453   379999999999999999999999999


Q ss_pred             cCCeeEEEEEcccccc
Q 017842          346 LDGRAIRVNVAEDRQR  361 (365)
Q Consensus       346 l~gr~l~V~~a~~~~~  361 (365)
                      |.||+|+|.|+.++.+
T Consensus        89 ~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           89 FGGRQITAQAWDGTTD  104 (112)
T ss_dssp             ETTEECEEEECCSCCC
T ss_pred             ECCcEEEEEEeCCCCC
Confidence            9999999999988664

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.51  E-value=5.3e-14  Score=120.32  Aligned_cols=79  Identities=20%  Similarity=0.442  Sum_probs=74.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|++||.|..+.                          +..+..++.++|||||.|.+.
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~--------------------------i~~~~~~g~~~g~afV~f~~~  146 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFN--------------------------LVKDSATGLSKGYAFCEYVDI  146 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEE--------------------------EEECTTTCSEEEEEEEEESST
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEE--------------------------EEecCCCCCcceEEEEEeCCH
Confidence            478999999999999999999999999998887                          777778999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeec
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      ++|.+|+..|||..++|+.|+|.++
T Consensus       147 ~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          147 NVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             THHHHHHHHHTTCEETTEECEEEEC
T ss_pred             HHHHHHHHHcCCCEECCeEEEEEeC
Confidence            9999999999999999999999986

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.51  E-value=2.9e-14  Score=113.02  Aligned_cols=81  Identities=19%  Similarity=0.215  Sum_probs=71.2

Q ss_pred             CCceEEEeCC--CCcC--------cHHHHHHHHhccCCeEEEEEEeeCCC--CCcceEEEEEecCHHHHHHHHHHhCCCc
Q 017842          278 PGFRIYVGNL--PWEV--------DNARLEQVFSEHGKVVNARVVYDRET--GRSRGFGFVTMSSETELNDAIAALDGQN  345 (365)
Q Consensus       278 ~~~~lfV~nL--p~~~--------tee~L~~~F~~~G~V~~v~i~~d~~~--~~~kG~afV~F~s~~~a~~Al~~l~~~~  345 (365)
                      |.+.|++.|+  |..+        .+++|++.|++||.|..|+|++++.+  +.++|||||+|.+.++|.+|+..|||+.
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4568999998  3333        34799999999999999999988765  4689999999999999999999999999


Q ss_pred             cCCeeEEEEEccc
Q 017842          346 LDGRAIRVNVAED  358 (365)
Q Consensus       346 l~gr~l~V~~a~~  358 (365)
                      ++||+|+|.|+..
T Consensus        84 f~GR~i~v~~~~~   96 (105)
T 3v4m_A           84 FANRVVVTKYCDP   96 (105)
T ss_dssp             ETTEECEEEEECH
T ss_pred             eCCCEEEEEEeCH
Confidence            9999999999864

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=6.6e-14  Score=107.22  Aligned_cols=73  Identities=23%  Similarity=0.268  Sum_probs=63.9

Q ss_pred             CCe-EEEcCCCCCCCHHH----HHHHHHcc-CCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEE
Q 017842          159 DAK-LFVGNLPYDVDSEK----LAMLFEKA-GTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFV  232 (365)
Q Consensus       159 ~~t-vfVgnLp~~~t~~~----L~~~F~~~-G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV  232 (365)
                      ..| |||+|||+.+++++    |+.+|+.| |+|..|                                 ++   |+|||
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V---------------------------------tg---G~AfV   51 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI---------------------------------TG---CSAIL   51 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC---------------------------------CT---TCEEE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE---------------------------------ec---CEEEE
Confidence            445 99999999999887    55899999 598653                                 22   99999


Q ss_pred             EeCCHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          233 TMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       233 ~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      +|.+.++|.+|++.|+|..+.||+|+|.++..+..
T Consensus        52 ~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~sd   86 (96)
T 2diu_A           52 RFINQDSAERAQKRMENEDVFGNRIIVSFTPKNRE   86 (96)
T ss_dssp             EESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSCC
T ss_pred             EECCHHHHHHHHHHhcCCccCCceEEEEecCCCcc
Confidence            99999999999999999999999999999987654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.51  E-value=6.9e-14  Score=122.42  Aligned_cols=86  Identities=20%  Similarity=0.432  Sum_probs=79.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||+|||+++++++|+++|+.||.|..++                          +..+..++.++|||||+|.
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~--------------------------~~~~~~~~~~~g~afV~f~  164 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFN--------------------------LVKDSATGLSKGYAFCEYV  164 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEE--------------------------EEECTTTCSEEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEE--------------------------EeecCCCCCcceEEEEEEC
Confidence            34678999999999999999999999999998887                          7777789999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      +.++|.+|+..|||..|+|+.|+|.++.++..
T Consensus       165 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          165 DINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             SSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            99999999999999999999999999987653

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=5.4e-14  Score=112.70  Aligned_cols=77  Identities=22%  Similarity=0.288  Sum_probs=67.3

Q ss_pred             CCCCeEEE--cCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          157 PEDAKLFV--GNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       157 ~~~~tvfV--gnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .+.++|||  |||++++++++|+++|++||.|..+.|                          .      ..+|||||+|
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i--------------------------~------~~rgfaFV~f   70 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM--------------------------P------PNKPYSFARY   70 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEEC--------------------------C------TTCSCEEEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEE--------------------------e------CCCCEEEEEE
Confidence            35788999  779999999999999999999988762                          2      2479999999


Q ss_pred             CCHHHHHHHHHHHccCcc-----cCeeEEEeecCCC
Q 017842          235 STVEEAEKAVEMFHRYDI-----DGRLLTVNKAAPR  265 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~-----~gr~l~V~~a~~~  265 (365)
                      .+.++|.+|+..|||..+     .|++|+|.++...
T Consensus        71 ~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~~  106 (114)
T 2cq2_A           71 RTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKV  106 (114)
T ss_dssp             SSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESCC
T ss_pred             CCHHHHHHHHHHhCCCEEccccCCCcEEEEEecccC
Confidence            999999999999999988     7899999887643

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.51  E-value=5.3e-14  Score=108.03  Aligned_cols=76  Identities=26%  Similarity=0.381  Sum_probs=61.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +++..+|||||||+++++++|+++|++||.|..++                          +++     .++|||||+|.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~--------------------------i~~-----~srGfaFV~F~   56 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVF--------------------------IPK-----PFRAFAFVTFA   56 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEE--------------------------CCS-----SCCSEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEE--------------------------Eee-----CCCCEEEEEEC
Confidence            45678999999999999999999999999999887                          333     27999999999


Q ss_pred             CHHHHHHHHHHHccCcc--cCeeEEEeecCCCC
Q 017842          236 TVEEAEKAVEMFHRYDI--DGRLLTVNKAAPRG  266 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~--~gr~l~V~~a~~~~  266 (365)
                      +.++|.+    ++|..+  .|+.|.|.++.++.
T Consensus        57 ~~~~A~~----~~~~~~~~~g~~v~v~~a~~k~   85 (89)
T 3d2w_A           57 DDKVAQS----LCGEDLIIKGISVHISNAEPKH   85 (89)
T ss_dssp             CHHHHHH----HTTCEEEETTEEEEEEECC---
T ss_pred             CHHHHHH----HcCCCcccCCEEEEEEEcCCCC
Confidence            9999883    466554  59999999988764

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.50  E-value=4.3e-14  Score=113.84  Aligned_cols=77  Identities=23%  Similarity=0.326  Sum_probs=64.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|.+||.|..+.                          ++.+       |||||+|.+.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~--------------------------i~~~-------g~afV~f~~~   61 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYAD--------------------------VYRD-------GTGVVEFVRK   61 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEE--------------------------ECTT-------SEEEEEESSH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------EecC-------CEEEEEECCH
Confidence            467999999999999999999999999998877                          3322       9999999999


Q ss_pred             HHHHHHHHHHccCcccCee-----EEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRL-----LTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~-----l~V~~a~~~~~  267 (365)
                      ++|.+||..|||..|+|+.     |+|....++..
T Consensus        62 ~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~~~~   96 (115)
T 3beg_B           62 EDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSP   96 (115)
T ss_dssp             HHHHHHHHHHTTCBCCCTTSCCCBCEEEECC----
T ss_pred             HHHHHHHHHhCCCEECCcEeeeEEEEeccCCCCCC
Confidence            9999999999999999998     77776665543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=8.7e-14  Score=111.80  Aligned_cols=77  Identities=21%  Similarity=0.418  Sum_probs=65.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCC---CCccceEEEEe
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRET---DRSRGFGFVTM  234 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~g~afV~f  234 (365)
                      ..++|||+|||+++++++|+.+|++||.|. +.                          ++.+..+   |+++|||||+|
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~--------------------------~~~~~~~~~~g~~~G~aFV~f   59 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VD--------------------------WPHKAESKSYFPPKGYAFLLF   59 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EE--------------------------CTTSSSSCCCSCTTSEEEECC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EE--------------------------EeecCCCCCCCCcccEEEEEE
Confidence            468999999999999999999999999998 55                          4555555   79999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      .+.++|.+|+..|++  ++|+.|.+..+.
T Consensus        60 ~~~~~a~~Ai~~~~~--~~G~~~~~~~~~   86 (114)
T 2dnl_A           60 QEESSVQALIDACLE--EDGKLYLCVSSP   86 (114)
T ss_dssp             SSHHHHHHHHHHSEE--ETTEEEEEECCS
T ss_pred             CCHHHHHHHHHhhhh--cCCcEEEeccCC
Confidence            999999999998854  678877776543

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.49  E-value=6.4e-14  Score=126.36  Aligned_cols=78  Identities=22%  Similarity=0.408  Sum_probs=73.2

Q ss_pred             CCCceEEEeCCCC-cCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          277 EPGFRIYVGNLPW-EVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       277 ~~~~~lfV~nLp~-~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      .+.++|||+|||+ .+++++|+++|+.||.|..|+|.+++     +|||||+|.+.++|.+|+..|+|..+.|++|+|.+
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4556999999999 99999999999999999999999874     79999999999999999999999999999999999


Q ss_pred             cccc
Q 017842          356 AEDR  359 (365)
Q Consensus       356 a~~~  359 (365)
                      +..+
T Consensus       107 a~~~  110 (229)
T 2adc_A          107 SKHQ  110 (229)
T ss_dssp             CSCC
T ss_pred             ecCc
Confidence            9865

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.48  E-value=1.5e-13  Score=111.22  Aligned_cols=81  Identities=19%  Similarity=0.217  Sum_probs=71.0

Q ss_pred             CCceEEEeCCCC-----cCcHHHHHHHHhccCCeEEEEEEeeCC----CCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 017842          278 PGFRIYVGNLPW-----EVDNARLEQVFSEHGKVVNARVVYDRE----TGRSRGFGFVTMSSETELNDAIAALDGQNLDG  348 (365)
Q Consensus       278 ~~~~lfV~nLp~-----~~tee~L~~~F~~~G~V~~v~i~~d~~----~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g  348 (365)
                      +..+|+|+|+-.     ...+++|++.|++||.|..|+|++++.    +++++|||||+|.+.++|.+|+..|||+.+.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            445999999932     224689999999999999999999865    35778999999999999999999999999999


Q ss_pred             eeEEEEEccc
Q 017842          349 RAIRVNVAED  358 (365)
Q Consensus       349 r~l~V~~a~~  358 (365)
                      |.|+|.|+..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999863

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.48  E-value=1.8e-13  Score=116.31  Aligned_cols=79  Identities=19%  Similarity=0.154  Sum_probs=69.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      -.+|||+||++.+++++|+.+|++||.|..+.|                          ..    .+.+|||||+|.+.+
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i--------------------------~~----k~~rgfAFVeF~d~~   95 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIIT--------------------------FT----KNNQFQALLQYADPV   95 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEE--------------------------EE----SSSCEEEEEEESCHH
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEE--------------------------Ee----CCCCCEEEEEECCHH
Confidence            456999999999999999999999999998873                          22    235789999999999


Q ss_pred             HHHHHHHHHccCcccC--eeEEEeecCCCCC
Q 017842          239 EAEKAVEMFHRYDIDG--RLLTVNKAAPRGT  267 (365)
Q Consensus       239 ~a~~Al~~lng~~~~g--r~l~V~~a~~~~~  267 (365)
                      +|.+|+..|||..|.|  +.|+|.++.++..
T Consensus        96 ~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~l  126 (164)
T 1sjr_A           96 SAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  126 (164)
T ss_dssp             HHHHHHHHSTTBCSSSSCSCEEEEECSSSSC
T ss_pred             HHHHHHHHhCCCEecCCCcEEEEEEecCCcc
Confidence            9999999999999965  9999999987743

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.47  E-value=2.8e-14  Score=112.89  Aligned_cols=72  Identities=17%  Similarity=0.317  Sum_probs=64.7

Q ss_pred             EeCCCCcCcHHHHHHHH------------hccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeE
Q 017842          284 VGNLPWEVDNARLEQVF------------SEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAI  351 (365)
Q Consensus       284 V~nLp~~~tee~L~~~F------------~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l  351 (365)
                      +.|||+.+++++|+++|            ++||.|..|+|+++.. ++++|||||+|.+.++|.+|+..|||+.++||+|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56788888888777666            9999999999998854 7899999999999999999999999999999999


Q ss_pred             EEEEc
Q 017842          352 RVNVA  356 (365)
Q Consensus       352 ~V~~a  356 (365)
                      +|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.47  E-value=2.6e-13  Score=111.18  Aligned_cols=78  Identities=21%  Similarity=0.218  Sum_probs=68.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccce-EEEEeCCH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGF-GFVTMSTV  237 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~-afV~f~~~  237 (365)
                      -..|||+||++.+|+++|+.+|++||.|..|.+                          ..     +.+|| |||+|.+.
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i--------------------------~~-----~~~gfqAFVef~~~   76 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIIT--------------------------FT-----KNNQFQALLQYADP   76 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEE--------------------------EE-----ETTEEEEEEEESCH
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEE--------------------------Ec-----CCCCcEEEEEECCH
Confidence            346889999999999999999999999998863                          32     23677 99999999


Q ss_pred             HHHHHHHHHHccCcccC--eeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDG--RLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~g--r~l~V~~a~~~~~  267 (365)
                      ++|.+|+..|||..|.|  +.|+|.++.+..-
T Consensus        77 ~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l  108 (130)
T 3zzy_A           77 VSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  108 (130)
T ss_dssp             HHHHHHHHHHTTCEEETTEEEEEEEECSCSSC
T ss_pred             HHHHHHHHHcCCCeecCCCcEEEEEecCCCce
Confidence            99999999999999988  9999999987653

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.46  E-value=1.7e-14  Score=124.02  Aligned_cols=83  Identities=29%  Similarity=0.449  Sum_probs=72.7

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|..||.+.. .++++..+++++|||||+|.+.++|.+|++ |||..+.|++|+|.++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecC
Confidence            34569999999999999999999999997766 344455678899999999999999999995 9999999999999999


Q ss_pred             ccccc
Q 017842          357 EDRQR  361 (365)
Q Consensus       357 ~~~~~  361 (365)
                      .++..
T Consensus        89 ~~~~~   93 (175)
T 1fje_B           89 KGRDS   93 (175)
T ss_dssp             CCSSC
T ss_pred             CCccc
Confidence            86543

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=7.6e-14  Score=106.64  Aligned_cols=78  Identities=23%  Similarity=0.329  Sum_probs=64.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|++||.|..++                          ++.     .++|||||+|.+.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~-----~~~g~afV~f~~~   52 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVF--------------------------IPK-----PFRAFAFVTFADD   52 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEE--------------------------CCS-----SCCSCCEEECSCH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEE--------------------------Eec-----CCCCEEEEEECCH
Confidence            468999999999999999999999999998877                          332     2789999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      ++|++|+.  .+..+.|+.|+|.++.++...
T Consensus        53 ~~a~~~~~--~~~~~~g~~l~v~~a~~~~~~   81 (88)
T 1wf0_A           53 QIAQSLCG--EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             HHHHHTTT--CEEEETTEEEEEECCCCCCCC
T ss_pred             HHHHHHhc--CCceeCCEEEEEEecCCCCCC
Confidence            99976432  134559999999998877554

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.45  E-value=8.5e-14  Score=122.23  Aligned_cols=76  Identities=22%  Similarity=0.425  Sum_probs=71.7

Q ss_pred             CceEEEeCCCC-cCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          279 GFRIYVGNLPW-EVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       279 ~~~lfV~nLp~-~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +++|||+|||+ .+++++|+++|+.||.|..|++++++     +|||||+|.+.++|.+|+..|||..+.|++|+|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            35999999999 99999999999999999999998774     7899999999999999999999999999999999998


Q ss_pred             cc
Q 017842          358 DR  359 (365)
Q Consensus       358 ~~  359 (365)
                      .+
T Consensus        78 ~~   79 (198)
T 1qm9_A           78 HQ   79 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.45  E-value=4.9e-13  Score=105.88  Aligned_cols=83  Identities=18%  Similarity=0.053  Sum_probs=71.5

Q ss_pred             CCCCCeEEEcCCCC-----CCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCC-CCCccce
Q 017842          156 PPEDAKLFVGNLPY-----DVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRE-TDRSRGF  229 (365)
Q Consensus       156 ~~~~~tvfVgnLp~-----~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~g~  229 (365)
                      +.+.++|+|+||..     +-++++|+.+|++||.|..+.                          +..++. +++++||
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~--------------------------i~~~~~~~~~~~G~   58 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCV--------------------------IFEIPGAPDDEAVR   58 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEE--------------------------EEECSSCCTTTSEE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEE--------------------------EecCCCCCCCCcEE
Confidence            34678999999973     237899999999999999987                          666554 3688999


Q ss_pred             EEEEeCCHHHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          230 GFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       230 afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      |||+|.+.++|.+|+..|||..|+||.|+|.++..
T Consensus        59 ~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           59 IFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNL   93 (105)
T ss_dssp             EEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             EEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCH
Confidence            99999999999999999999999999999998754

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.45  E-value=6.8e-13  Score=108.08  Aligned_cols=75  Identities=24%  Similarity=0.286  Sum_probs=66.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccce-EEEEeCCHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGF-GFVTMSTVEE  239 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~-afV~f~~~e~  239 (365)
                      .|||+|||+.+++++|+.+|++||.|..+.                          +.. +     .|| |||+|.+.++
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~--------------------------i~~-~-----~Gf~aFVef~~~~~   74 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIV--------------------------IFK-R-----NGIQAMVEFESVLC   74 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEE--------------------------EEE-S-----SSEEEEEEESSHHH
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEE--------------------------EEe-C-----CCCEEEEEECCHHH
Confidence            478999999999999999999999999887                          322 1     286 9999999999


Q ss_pred             HHHHHHHHccCcccC--eeEEEeecCCCCC
Q 017842          240 AEKAVEMFHRYDIDG--RLLTVNKAAPRGT  267 (365)
Q Consensus       240 a~~Al~~lng~~~~g--r~l~V~~a~~~~~  267 (365)
                      |..|+..|||..|.|  +.|+|.++.++..
T Consensus        75 A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~l  104 (124)
T 2e5i_A           75 AQKAKAALNGADIYAGCCTLKIEYARPTRL  104 (124)
T ss_dssp             HHHHHHHHTTCCCBTTBSEEEEECCSCSCC
T ss_pred             HHHHHHHhCCCEecCCCeEEEEEEecCCcc
Confidence            999999999999987  6999999987753

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.44  E-value=2.4e-13  Score=125.06  Aligned_cols=78  Identities=32%  Similarity=0.583  Sum_probs=71.8

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||+.+|+++|+++|+.||.|..|+|.++      +|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            345579999999999999999999999999999999643      89999999999999999999999999999999999


Q ss_pred             cccc
Q 017842          356 AEDR  359 (365)
Q Consensus       356 a~~~  359 (365)
                      +.+.
T Consensus        93 a~~~   96 (261)
T 3sde_A           93 ATHG   96 (261)
T ss_dssp             CCCS
T ss_pred             cccC
Confidence            8753

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.43  E-value=3.6e-13  Score=118.45  Aligned_cols=79  Identities=18%  Similarity=0.199  Sum_probs=70.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||+|||+++++++|+.+|++||.|..++                          +.++. +++++|||||+|.+.+
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~--------------------------i~~~~-~~~~kG~aFVeF~~~e  161 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ--------------------------MRRTL-HKAFKGSIFVVFDSIE  161 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEE--------------------------EEECT-TCCEEEEEEEEESSHH
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEE--------------------------EEECC-CCCcccEEEEEECCHH
Confidence            57999999999999999999999999999987                          45544 5889999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      +|.+|+..+ +..++|+.|+|.+....
T Consensus       162 ~A~~A~~~~-~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          162 SAKKFVETP-GQKYKETDLLILFKDDY  187 (193)
T ss_dssp             HHHHHHHCT-TCEETTEECEEEETTTC
T ss_pred             HHHHHHHhC-CCeECCEEEEEEEhHHH
Confidence            999999875 56899999999987654

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.37  E-value=1.2e-12  Score=118.42  Aligned_cols=78  Identities=22%  Similarity=0.364  Sum_probs=69.0

Q ss_pred             CCCCeEEEcCCCCCC---------CHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCcc
Q 017842          157 PEDAKLFVGNLPYDV---------DSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSR  227 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~---------t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (365)
                      ...++|||||||..+         ++++|+.+|++||.|..|+                          ++      .++
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~--------------------------v~------~~k  179 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIR--------------------------YV------ESK  179 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEE--------------------------EE------GGG
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEE--------------------------EE------CCC
Confidence            357899999999998         7999999999999999987                          33      358


Q ss_pred             ceEEEEeCCHHHHHHHHHHHccCcc------------cCeeEEEeecCCCC
Q 017842          228 GFGFVTMSTVEEAEKAVEMFHRYDI------------DGRLLTVNKAAPRG  266 (365)
Q Consensus       228 g~afV~f~~~e~a~~Al~~lng~~~------------~gr~l~V~~a~~~~  266 (365)
                      |||||.|.+.++|..|+..|+|..|            .|+.|.|.++....
T Consensus       180 G~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          180 NCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             TEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             CEEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCCC
Confidence            9999999999999999999999999            89999999997543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=5.6e-12  Score=98.77  Aligned_cols=67  Identities=13%  Similarity=0.178  Sum_probs=59.5

Q ss_pred             CcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccccC
Q 017842          289 WEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR  362 (365)
Q Consensus       289 ~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~~  362 (365)
                      ..+++++|+++|+.||.|..|+|+     ++++|||||+|.+.++|.+|+..++  .+.|++|+|.|+++++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~V~~a~~~~~~   93 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV--GLVDNPLKISWLEGQPQD   93 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCEEECSSCCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEEEEEccCCCCC
Confidence            468999999999999999999998     4679999999999999999999644  478999999999977643

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.34  E-value=6.4e-12  Score=100.49  Aligned_cols=84  Identities=18%  Similarity=0.243  Sum_probs=70.6

Q ss_pred             cCCCCCCeEEEcCCCCCCC-----------HHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCC
Q 017842          154 VEPPEDAKLFVGNLPYDVD-----------SEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRE  222 (365)
Q Consensus       154 ~~~~~~~tvfVgnLp~~~t-----------~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  222 (365)
                      ..+.+.++|+|.||.....           +++|+.+|++||.|..+.                          + .+. 
T Consensus        10 ~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~--------------------------i-~~~-   61 (112)
T 2dit_A           10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLL--------------------------L-FDR-   61 (112)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEE--------------------------E-ETT-
T ss_pred             CCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEE--------------------------E-ecC-
Confidence            3566789999999944432           579999999999998875                          3 222 


Q ss_pred             CCCccceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          223 TDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       223 ~~~~~g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                        .++|||||+|.+.++|.+|+..|||..|+|+.|+|.++.++..
T Consensus        62 --~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           62 --HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             --CTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCCC
T ss_pred             --CCCEEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCC
Confidence              3799999999999999999999999999999999999987654

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.30  E-value=6.5e-12  Score=100.83  Aligned_cols=77  Identities=18%  Similarity=0.166  Sum_probs=66.0

Q ss_pred             CCceEEEeCCCCc----------CcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccC
Q 017842          278 PGFRIYVGNLPWE----------VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLD  347 (365)
Q Consensus       278 ~~~~lfV~nLp~~----------~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~  347 (365)
                      +..+|.+.|+-..          ..+++|++.|++||.|..|.|.++.    ++|||||+|.+.++|.+|+..|||+.++
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            3458999998321          2247899999999999999997653    5999999999999999999999999999


Q ss_pred             CeeEEEEEccc
Q 017842          348 GRAIRVNVAED  358 (365)
Q Consensus       348 gr~l~V~~a~~  358 (365)
                      ||.|+|.|+..
T Consensus        82 GR~i~v~~~~~   92 (114)
T 3s6e_A           82 GKMITAAYVPL   92 (114)
T ss_dssp             TEECEEEEECH
T ss_pred             CEEEEEEEEcH
Confidence            99999999863

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.28  E-value=6.9e-12  Score=119.25  Aligned_cols=77  Identities=21%  Similarity=0.264  Sum_probs=67.0

Q ss_pred             CCCCceEEEeC--CCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc---CCe-
Q 017842          276 FEPGFRIYVGN--LPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL---DGR-  349 (365)
Q Consensus       276 ~~~~~~lfV~n--Lp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l---~gr-  349 (365)
                      ..++.+|||+|  |++.+|+++|+++|++||.|..|++.+      +||||||+|.+.++|.+|+..|||..+   .|+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            34566999999  589999999999999999999988763      489999999999999999999999977   355 


Q ss_pred             -eEEEEEccc
Q 017842          350 -AIRVNVAED  358 (365)
Q Consensus       350 -~l~V~~a~~  358 (365)
                       .|.|.|+..
T Consensus        89 ~~ly~~~~~~   98 (345)
T 3tht_A           89 ITLYLNFVEK   98 (345)
T ss_dssp             EECEEEECSS
T ss_pred             eEEEEEEeec
Confidence             688888853

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.26  E-value=1.4e-11  Score=97.40  Aligned_cols=80  Identities=19%  Similarity=0.186  Sum_probs=67.7

Q ss_pred             CCCeEEEcCC--CCCCC--------HHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCC--CC
Q 017842          158 EDAKLFVGNL--PYDVD--------SEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRET--DR  225 (365)
Q Consensus       158 ~~~tvfVgnL--p~~~t--------~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~  225 (365)
                      +.+.|.|.|+  |.+..        .++|+..|++||.|..+.                          +..+..+  ++
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~--------------------------i~~~~~~~~~~   57 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE--------------------------IPRPVDGVEVP   57 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEE--------------------------CCCCBTTBCCT
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEE--------------------------EeccCCCCCcC
Confidence            5789999998  44443        368999999999999987                          5545433  47


Q ss_pred             ccceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          226 SRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       226 ~~g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      ++|+|||+|.+.++|.+|+..|||..|+||.|+|.++.
T Consensus        58 ~~G~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~   95 (105)
T 3v4m_A           58 GCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD   95 (105)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CcEEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeC
Confidence            89999999999999999999999999999999998764

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.25  E-value=3.3e-12  Score=100.91  Aligned_cols=72  Identities=26%  Similarity=0.268  Sum_probs=61.8

Q ss_pred             EcCCCCCCCHHHHHHHH------------HccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEE
Q 017842          164 VGNLPYDVDSEKLAMLF------------EKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGF  231 (365)
Q Consensus       164 VgnLp~~~t~~~L~~~F------------~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~af  231 (365)
                      ++|||+.+++++|+.+|            ++||.|..+.                          +..+. .++++||||
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~--------------------------i~~~~-~~~~~G~~f   72 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMN--------------------------VCDNL-GDHLVGNVY   72 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEE--------------------------ECCSS-SSSSEEEEE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEE--------------------------EEeCC-CCCccEEEE
Confidence            67788888888777666            9999999987                          55444 478999999


Q ss_pred             EEeCCHHHHHHHHHHHccCcccCeeEEEeec
Q 017842          232 VTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       232 V~f~~~e~a~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      |.|.+.++|.+|+..|||..|+||.|+|.++
T Consensus        73 V~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           73 VKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             EEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             EEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            9999999999999999999999999999875

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.22  E-value=2.9e-11  Score=97.61  Aligned_cols=81  Identities=17%  Similarity=0.138  Sum_probs=68.7

Q ss_pred             CCCCeEEEcCCCC--C---CCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCC----CCCcc
Q 017842          157 PEDAKLFVGNLPY--D---VDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRE----TDRSR  227 (365)
Q Consensus       157 ~~~~tvfVgnLp~--~---~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~  227 (365)
                      ++.++|+|.|+-.  +   -.+++|+..|++||.|..+.                          |..+..    +++++
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~--------------------------I~~~~~~~~~~~~~~   71 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVI--------------------------IYQEKQGEEEDAEII   71 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEE--------------------------EEEEEESSSTTCEEE
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEE--------------------------EeecCCCcccCCcce
Confidence            3688999999942  2   24689999999999999988                          444433    46788


Q ss_pred             ceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          228 GFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       228 g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      |+|||+|.+.++|.+|+..|||..|+||.|+|.++.
T Consensus        72 G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~  107 (118)
T 3ue2_A           72 VKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  107 (118)
T ss_dssp             EEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcC
Confidence            999999999999999999999999999999998764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.11  E-value=8.1e-10  Score=86.39  Aligned_cols=76  Identities=21%  Similarity=0.117  Sum_probs=62.0

Q ss_pred             CCeEEEcCCC-------CCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEE
Q 017842          159 DAKLFVGNLP-------YDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGF  231 (365)
Q Consensus       159 ~~tvfVgnLp-------~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~af  231 (365)
                      ..+|.|.-..       .++++++|+.+|++||.|..+.                          ++     ++++||||
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~--------------------------i~-----~~~rGfaF   58 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLV--------------------------LS-----SKKPGTAV   58 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEE--------------------------EE-----SSSSSEEE
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEE--------------------------Ec-----cCCCCEEE
Confidence            3455555544       4689999999999999999887                          33     36899999


Q ss_pred             EEeCCHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          232 VTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       232 V~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      |+|.+.++|.+|+..+++  +.|++|+|.++.++..
T Consensus        59 VeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           59 VEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             EEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             EEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            999999999999997554  6899999999887654

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.09  E-value=2.1e-10  Score=109.00  Aligned_cols=76  Identities=24%  Similarity=0.327  Sum_probs=64.4

Q ss_pred             CCCCCeEEEcC--CCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEE
Q 017842          156 PPEDAKLFVGN--LPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVT  233 (365)
Q Consensus       156 ~~~~~tvfVgn--Lp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~  233 (365)
                      ..+.++|||||  |++.+++++|+++|++||.|..+.                          +.      .++|||||+
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~--------------------------~~------~~kgfaFV~   62 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL--------------------------MP------PNKPYSFAR   62 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEE--------------------------CC------TTCSEEEEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEE--------------------------Ee------CCCCEEEEE
Confidence            44678999999  589999999999999999998765                          21      258999999


Q ss_pred             eCCHHHHHHHHHHHccCccc---Ce--eEEEeecC
Q 017842          234 MSTVEEAEKAVEMFHRYDID---GR--LLTVNKAA  263 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~---gr--~l~V~~a~  263 (365)
                      |.+.++|++|+..|||..+.   |+  .|+|.++.
T Consensus        63 f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~   97 (345)
T 3tht_A           63 YRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE   97 (345)
T ss_dssp             ESSHHHHHHHHHHTTTCEEECTTSCEEECEEEECS
T ss_pred             ECCHHHHHHHHHHhCCCccccccCCceEEEEEEee
Confidence            99999999999999998873   45  68888764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.05  E-value=4.2e-10  Score=90.70  Aligned_cols=78  Identities=15%  Similarity=0.133  Sum_probs=69.0

Q ss_pred             CcCCCCceEEEeCCCCc-CcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecC-HHHHHHHHHHhC--CCccCCe
Q 017842          274 RVFEPGFRIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSS-ETELNDAIAALD--GQNLDGR  349 (365)
Q Consensus       274 ~~~~~~~~lfV~nLp~~-~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s-~~~a~~Al~~l~--~~~l~gr  349 (365)
                      ...++++.|+|+||++. ++.++|+++|+.||.|.+|.+.++..      .|||+|.+ ..+|..|+..|+  +..|+|.
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~   86 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNK   86 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCc
Confidence            34567889999999999 99999999999999999999988754      59999999 899999999995  6788999


Q ss_pred             eEEEEEcc
Q 017842          350 AIRVNVAE  357 (365)
Q Consensus       350 ~l~V~~a~  357 (365)
                      .+++++..
T Consensus        87 ~~~~evL~   94 (121)
T 1owx_A           87 EVTWEVLE   94 (121)
T ss_dssp             SEEEEECC
T ss_pred             EEEEEECC
Confidence            88887653

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.03  E-value=6.2e-10  Score=84.39  Aligned_cols=74  Identities=23%  Similarity=0.318  Sum_probs=62.6

Q ss_pred             CCCceEEEeCCC----CcCcH----HHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 017842          277 EPGFRIYVGNLP----WEVDN----ARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDG  348 (365)
Q Consensus       277 ~~~~~lfV~nLp----~~~te----e~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g  348 (365)
                      +|..||+|.-.+    ..+-.    .+|.+.|..||.|..+||+.++        +||+|.+.++|.+|+. |||..++|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCC
Confidence            445588888776    22323    6799999999999999999763        8999999999999999 99999999


Q ss_pred             eeEEEEEcccc
Q 017842          349 RAIRVNVAEDR  359 (365)
Q Consensus       349 r~l~V~~a~~~  359 (365)
                      |.|+|+++.+.
T Consensus        76 r~LkV~lkt~d   86 (91)
T 2dnr_A           76 RTITIALKSPS   86 (91)
T ss_dssp             EEEEEEECCCS
T ss_pred             eEEEEEeCCCC
Confidence            99999998754

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.97  E-value=1.9e-09  Score=86.31  Aligned_cols=78  Identities=19%  Similarity=0.173  Sum_probs=63.8

Q ss_pred             CCCCCeEEEcCCCCCC----------CHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCC
Q 017842          156 PPEDAKLFVGNLPYDV----------DSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDR  225 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~----------t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  225 (365)
                      +.+.+.|.+.|+=...          .+++|+..|++||.|..+.                          +..+    .
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~--------------------------i~~~----~   53 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIY--------------------------VDKN----S   53 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEE--------------------------ECTT----C
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEE--------------------------EecC----C
Confidence            4467789999884322          2357899999999998876                          3222    2


Q ss_pred             ccceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          226 SRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       226 ~~g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      .+|+|||.|.+.++|.+|+..|||..|+||.|+|.++.
T Consensus        54 ~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~   91 (114)
T 3s6e_A           54 AQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVP   91 (114)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEc
Confidence            58999999999999999999999999999999998874

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.95  E-value=4.1e-09  Score=94.18  Aligned_cols=68  Identities=21%  Similarity=0.261  Sum_probs=62.0

Q ss_pred             cCcHHHHHHHHhccCCeEEEEEEeeCCC----CCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          290 EVDNARLEQVFSEHGKVVNARVVYDRET----GRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       290 ~~tee~L~~~F~~~G~V~~v~i~~d~~~----~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ...+++|++.|++||.|..+.|+++..+    ++++|++||+|.+.++|.+|+..|||+.+.||.|++.|+.
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            3467899999999999999999966544    4899999999999999999999999999999999999986

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.84  E-value=7.4e-09  Score=78.49  Aligned_cols=74  Identities=15%  Similarity=0.196  Sum_probs=61.0

Q ss_pred             CCCCeEEEcCCCC----CCCH----HHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccc
Q 017842          157 PEDAKLFVGNLPY----DVDS----EKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRG  228 (365)
Q Consensus       157 ~~~~tvfVgnLp~----~~t~----~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g  228 (365)
                      +++.||+|..+|.    +.-.    .+|.+.|.+||.|..++                          ++.+        
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr--------------------------~~~d--------   50 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIR--------------------------FVED--------   50 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEE--------------------------ECSS--------
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEE--------------------------EecC--------
Confidence            5678999998873    3333    67999999999998877                          4433        


Q ss_pred             eEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          229 FGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       229 ~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      .+||+|.+.++|.+|+. |||..+.||.|+|+.+.+.
T Consensus        51 ~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           51 KMWVTFLEGSSALNVLS-LNGKELLNRTITIALKSPS   86 (91)
T ss_dssp             SEEEEESSHHHHHHGGG-GTTCEETTEEEEEEECCCS
T ss_pred             CEEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCCCC
Confidence            28999999999999999 7999999999999987753

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.80  E-value=3.7e-09  Score=80.53  Aligned_cols=72  Identities=18%  Similarity=0.201  Sum_probs=61.2

Q ss_pred             CCCCceEEEeCCCCc-----CcH----HHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 017842          276 FEPGFRIYVGNLPWE-----VDN----ARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL  346 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~-----~te----e~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l  346 (365)
                      .+|..||+|.-++..     +-.    .+|.+.|..||.|..+||+.++        +||+|.+.++|.+||. |||..+
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeee
Confidence            345569999988742     222    5699999999999999999773        9999999999999999 999999


Q ss_pred             CCeeEEEEEc
Q 017842          347 DGRAIRVNVA  356 (365)
Q Consensus       347 ~gr~l~V~~a  356 (365)
                      +||.|+|++-
T Consensus        83 ~Gr~L~V~~k   92 (95)
T 1ufw_A           83 KGRAVKISGP   92 (95)
T ss_dssp             TTEEEEEECC
T ss_pred             CCeEEEEecc
Confidence            9999999974

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.72  E-value=4.5e-08  Score=78.74  Aligned_cols=74  Identities=15%  Similarity=0.146  Sum_probs=62.0

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          157 PEDAKLFVGNLPYD-VDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       157 ~~~~tvfVgnLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +....|||+||+++ ++.++|+.+|+.||.|..|.+                          ..      ....|||.|.
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~--------------------------~~------g~~tgfVrf~   63 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDF--------------------------VR------GAKEGIILFK   63 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEEC--------------------------CT------TCSEEEEEES
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEE--------------------------ec------CCCEEEEEEC
Confidence            45789999999999 999999999999999988763                          22      2336999999


Q ss_pred             C-HHHHHHHHHHHc--cCcccCeeEEEeec
Q 017842          236 T-VEEAEKAVEMFH--RYDIDGRLLTVNKA  262 (365)
Q Consensus       236 ~-~e~a~~Al~~ln--g~~~~gr~l~V~~a  262 (365)
                      + ..+|..|+..+|  |..|.|..+++...
T Consensus        64 ~~~~~A~~av~~ln~~~~~i~g~~~~~evL   93 (121)
T 1owx_A           64 EKAKEALGKAKDANNGNLQLRNKEVTWEVL   93 (121)
T ss_dssp             SCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             CChHHHHHHHHHhhcCCcEEeCcEEEEEEC
Confidence            9 889999999984  78889988887643

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.69  E-value=3.7e-08  Score=75.02  Aligned_cols=73  Identities=16%  Similarity=0.225  Sum_probs=60.1

Q ss_pred             CCCCCeEEEcCCCCC-----CCH----HHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCc
Q 017842          156 PPEDAKLFVGNLPYD-----VDS----EKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRS  226 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~-----~t~----~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  226 (365)
                      -+++.||+|..++.+     .-.    .+|.+.|..||.|..++                          ++.++     
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr--------------------------~v~d~-----   60 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVR--------------------------INQGQ-----   60 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEE--------------------------EETTE-----
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEE--------------------------EecCc-----
Confidence            356789999999754     222    56899999999988877                          44333     


Q ss_pred             cceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          227 RGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       227 ~g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                         +||+|.+.++|.+|+. |||..+.||.|+|++..
T Consensus        61 ---~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           61 ---MLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             ---EEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             ---EEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccC
Confidence               9999999999999999 79999999999998754

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.54  E-value=1.6e-07  Score=83.72  Aligned_cols=70  Identities=17%  Similarity=0.063  Sum_probs=58.4

Q ss_pred             CHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHHHHHHHHHccCc
Q 017842          172 DSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYD  251 (365)
Q Consensus       172 t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~~Al~~lng~~  251 (365)
                      .+++|+..|++||.|..+.|...                      ...+..+++++|++||+|.+.++|.+|+..|||..
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~----------------------~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~  199 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQE----------------------KQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRW  199 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEE----------------------ECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCB
T ss_pred             HHHHHHHHHHccCCeEEEEEecC----------------------CCCcccCcCceeEEEEEECCHHHHHHHHHHhcCce
Confidence            56789999999999999873211                      11234466899999999999999999999999999


Q ss_pred             ccCeeEEEeecC
Q 017842          252 IDGRLLTVNKAA  263 (365)
Q Consensus       252 ~~gr~l~V~~a~  263 (365)
                      |+||.|+|.++.
T Consensus       200 ~~gr~i~~~~~~  211 (222)
T 3dxb_A          200 FAGRKVVAEVYD  211 (222)
T ss_dssp             SSSSBCEEEECC
T ss_pred             ECCeEEEEEEcC
Confidence            999999998764

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.46  E-value=7.1e-07  Score=69.37  Aligned_cols=71  Identities=17%  Similarity=0.187  Sum_probs=65.5

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhcc-----CCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEH-----GKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~-----G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      .++|-+-|||-.+++..|+.+.+.+     |.+..+.+..|      -|-|+|+|.+...|.+|..+|+|..|.||+|++
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD------H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~   94 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD------FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRS   94 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT------TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC------CCceEEEEccchhhHHHHhhcCCeeecCeEEEe
Confidence            3489999999999999999999999     99999999887      446999999999999999999999999999998


Q ss_pred             EE
Q 017842          354 NV  355 (365)
Q Consensus       354 ~~  355 (365)
                      .=
T Consensus        95 gT   96 (117)
T 2l9w_A           95 GT   96 (117)
T ss_dssp             EC
T ss_pred             cC
Confidence            63

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.92  E-value=6.8e-05  Score=57.73  Aligned_cols=88  Identities=25%  Similarity=0.341  Sum_probs=70.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHc-----cCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEE
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEK-----AGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFV  232 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~-----~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV  232 (365)
                      ...+|.|.|||..+.++.|.-+|+.     -|.|..+.                            +.      .+-|+|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~----------------------------~~------~~~AvI   52 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ----------------------------RL------GCGGVL   52 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEE----------------------------EE------TTEEEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEE----------------------------Ec------CCcEEE
Confidence            4679999999999999999999976     25776654                            11      167999


Q ss_pred             EeCCHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCc
Q 017842          233 TMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVD  292 (365)
Q Consensus       233 ~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~t  292 (365)
                      +|.+...|++.++. ....|+|..|.|....++...            +|++.||+..++
T Consensus        53 tF~d~~va~rVL~k-~~H~L~~~~LsV~P~~~~~~~------------r~ll~gl~~~t~   99 (104)
T 2dhx_A           53 TFREPADAERVLAQ-ADHELHGAQLSLRPAPPRAPA------------RLLLQGLPPGTS   99 (104)
T ss_dssp             EESSHHHHHHHHTC-SCCBSSSSBCEEEECCCCCCC------------CCCCCSCCCCCC
T ss_pred             EEcChHHHHHHhcC-CcceecCeEEEEEcCCCCCcc------------eEeeecCCCCCC
Confidence            99999999999885 588999999999876655432            788999987653

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.91  E-value=5.8e-05  Score=58.67  Aligned_cols=72  Identities=7%  Similarity=0.114  Sum_probs=63.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHcc-----CCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEE
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKA-----GTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFV  232 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~-----G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV  232 (365)
                      ..++|=+-|||-.++...++.+...+     |.+..+.++                                ...+-|+|
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~--------------------------------pDH~GAiv   67 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLV--------------------------------SDFNGAII   67 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEE--------------------------------TTTTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEe--------------------------------cCCCceEE
Confidence            47899999999999999999999999     888776533                                23566999


Q ss_pred             EeCCHHHHHHHHHHHccCcccCeeEEEee
Q 017842          233 TMSTVEEAEKAVEMFHRYDIDGRLLTVNK  261 (365)
Q Consensus       233 ~f~~~e~a~~Al~~lng~~~~gr~l~V~~  261 (365)
                      +|.+...|-+|.-.|+|..|.||.|++..
T Consensus        68 ef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           68 IFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             ECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             EEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            99999999999988999999999999953

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.57  E-value=0.00036  Score=52.86  Aligned_cols=78  Identities=10%  Similarity=0.103  Sum_probs=62.4

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCC--cceEEEEEecCHHHHHHHHHHhCCCccC---C--eeEE
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGR--SRGFGFVTMSSETELNDAIAALDGQNLD---G--RAIR  352 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~--~kG~afV~F~s~~~a~~Al~~l~~~~l~---g--r~l~  352 (365)
                      ++|.|++||..+|++++++.+.....+...+.+....+..  .-..|||.|.+.+++....+.++|..+.   |  .+..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            3799999999999999999999999888877766544322  2346999999999999999999999883   2  2445


Q ss_pred             EEEcc
Q 017842          353 VNVAE  357 (365)
Q Consensus       353 V~~a~  357 (365)
                      |.||-
T Consensus        82 VE~AP   86 (91)
T 1uw4_A           82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66664

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.33  E-value=0.00054  Score=52.93  Aligned_cols=75  Identities=15%  Similarity=0.100  Sum_probs=62.1

Q ss_pred             CceEEEeCCCCcC-c----HHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          279 GFRIYVGNLPWEV-D----NARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       279 ~~~lfV~nLp~~~-t----ee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      .++|+|.||+..+ .    .+.++.+|..|+.+......+.-      .-..|.|.+.++|.+|...||+..+.|++|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            3589999998654 2    36789999999988877666432      24789999999999999999999999999999


Q ss_pred             EEcccc
Q 017842          354 NVAEDR  359 (365)
Q Consensus       354 ~~a~~~  359 (365)
                      -|+.+-
T Consensus        79 YFgq~~   84 (104)
T 1wey_A           79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             EecCCC
Confidence            998743

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.27  E-value=0.0028  Score=48.77  Aligned_cols=73  Identities=22%  Similarity=0.304  Sum_probs=60.7

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhcc-----CCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEH-----GKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~-----G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      +.+|.|.|||..+.++.|.-+|+.-     |.|..+....        +-|+|+|.+...|.+.|+ -..+.|.|..|.|
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV   78 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLA-QADHELHGAQLSL   78 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhc-CCcceecCeEEEE
Confidence            4599999999999999999999872     5788887652        469999999999999998 3488999999999


Q ss_pred             EEccccc
Q 017842          354 NVAEDRQ  360 (365)
Q Consensus       354 ~~a~~~~  360 (365)
                      .-.-++.
T Consensus        79 ~P~~~~~   85 (104)
T 2dhx_A           79 RPAPPRA   85 (104)
T ss_dssp             EECCCCC
T ss_pred             EcCCCCC
Confidence            7665544

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=96.98  E-value=0.0034  Score=48.40  Aligned_cols=76  Identities=17%  Similarity=0.093  Sum_probs=60.7

Q ss_pred             CCeEEEcCCCCCC-C----HHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEE
Q 017842          159 DAKLFVGNLPYDV-D----SEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVT  233 (365)
Q Consensus       159 ~~tvfVgnLp~~~-t----~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~  233 (365)
                      ..+|+|.||+.++ .    ...++.+|..|+++....                          ..      ++-.-.-|.
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~--------------------------~l------kSFRRirv~   52 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQ--------------------------YF------KSFKRVRIN   52 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEE--------------------------EE------TTTTEEEEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCccee--------------------------ec------CcceEEEEE
Confidence            4689999998876 2    257899999999886643                          11      222346789


Q ss_pred             eCCHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      |.+.++|.+|-..|++..|+|+.|+|..+.+..
T Consensus        53 F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~~   85 (104)
T 1wey_A           53 FSNPLSAADARLRLHKTEFLGKEMKLYFAQTLH   85 (104)
T ss_dssp             CSSTTHHHHHHHTSTTSEETTEECEEECCCCSS
T ss_pred             eCChHHHHHHHHHhccceecCceeEEEecCCCC
Confidence            999999999999999999999999999887443

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.86  E-value=0.0036  Score=47.30  Aligned_cols=70  Identities=13%  Similarity=0.150  Sum_probs=51.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      .+|-|++||+.+|++++.+.+..+..+.....    ..|.                 +-   ......+-|||.|.+.++
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~f----v~G~-----------------~s---~~~~~~SRaYi~f~~~e~   57 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEF----FSND-----------------TS---LYPHMYARAYINFKNQED   57 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEE----EESC-----------------CS---STTCCCEEEEEEESSSHH
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEE----eCCc-----------------cC---CCCCcceEEEEEeCCHHH
Confidence            47899999999999999999998876543321    1111                 00   011234569999999999


Q ss_pred             HHHHHHHHccCccc
Q 017842          240 AEKAVEMFHRYDID  253 (365)
Q Consensus       240 a~~Al~~lng~~~~  253 (365)
                      +......++|..|.
T Consensus        58 v~~f~~~~~g~~F~   71 (91)
T 1uw4_A           58 IILFRDRFDGYVFL   71 (91)
T ss_dssp             HHHHHHHHTTCEEE
T ss_pred             HHHHHHHhCCcEEE
Confidence            99999999998874

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.52  E-value=0.014  Score=46.23  Aligned_cols=71  Identities=14%  Similarity=0.187  Sum_probs=57.8

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC-eeEEEEEcc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDG-RAIRVNVAE  357 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g-r~l~V~~a~  357 (365)
                      .+-|.|-+.|... -..|..+|+.||.|......      ....+..|+|.+..+|.+||. .||..+.| --|-|..+.
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECC
Confidence            3478898998874 66777899999999988762      124589999999999999999 79999975 677777764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.52  E-value=0.003  Score=48.13  Aligned_cols=78  Identities=12%  Similarity=0.064  Sum_probs=56.6

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCc--ceEEEEEecCHHHHHHHHHHhCCCccC---C--eeEE
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRS--RGFGFVTMSSETELNDAIAALDGQNLD---G--RAIR  352 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~--kG~afV~F~s~~~a~~Al~~l~~~~l~---g--r~l~  352 (365)
                      .+|.|+.||..+|++++++.+...-.+.....+....+.++  -..|||.|.+.+++....+.++|..+.   |  -+..
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a~   89 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPAV   89 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeeeE
Confidence            37999999999999999998887655544443332222111  235899999999999999999999873   2  2556


Q ss_pred             EEEcc
Q 017842          353 VNVAE  357 (365)
Q Consensus       353 V~~a~  357 (365)
                      |.||-
T Consensus        90 VE~AP   94 (97)
T 2l08_A           90 VEFAP   94 (97)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            66663

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.17  E-value=0.012  Score=44.71  Aligned_cols=58  Identities=28%  Similarity=0.464  Sum_probs=45.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +.....++| +.|......+|.++|+.||.|.   |++                        +       +-.-|||.|.
T Consensus        13 p~r~HVf~l-~FP~ewKt~DI~~lFs~fggv~---I~W------------------------i-------dDTsAlvvf~   57 (100)
T 1whv_A           13 PKRDHVLHV-TFPKEWKTSDLYQLFSAFGNIQ---ISW------------------------I-------DDTSAFVSLS   57 (100)
T ss_dssp             CCCCSEEEE-ECCTTCCHHHHHHHHTTTCSCC---CEE------------------------E-------ETTEEEEECS
T ss_pred             CCCCeEEEE-eCChhhhhHHHHHHhhccCCEE---EEE------------------------E-------cCCeEEEEec
Confidence            334555666 9999999999999999999553   332                        2       2346999999


Q ss_pred             CHHHHHHHHHHHc
Q 017842          236 TVEEAEKAVEMFH  248 (365)
Q Consensus       236 ~~e~a~~Al~~ln  248 (365)
                      +++.|..|+..++
T Consensus        58 ~~~~a~~al~~i~   70 (100)
T 1whv_A           58 QPEQVQIAVNTSK   70 (100)
T ss_dssp             CHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhcc
Confidence            9999999999764

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.08  E-value=0.014  Score=46.27  Aligned_cols=71  Identities=13%  Similarity=0.147  Sum_probs=57.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .+.|.|-+.|... ...+...|++||.|....                          .      .....+-+|.|.++.
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~--------------------------~------~~~~NWihI~Y~s~~   70 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHV--------------------------M------SNTGNWMHIRYQSKL   70 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEE--------------------------E------CSSSSEEEEEESSHH
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEec--------------------------c------CCCCCeEEEEeCCHH
Confidence            5689999999885 667889999999997654                          1      134678999999999


Q ss_pred             HHHHHHHHHccCcccC-eeEEEeecC
Q 017842          239 EAEKAVEMFHRYDIDG-RLLTVNKAA  263 (365)
Q Consensus       239 ~a~~Al~~lng~~~~g-r~l~V~~a~  263 (365)
                      +|++||.. ||..|.| -.|-|.+..
T Consensus        71 ~A~rAL~k-NG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           71 QARKALSK-DGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             HHHHHHTT-TTCEETTTEECEEEECC
T ss_pred             HHHHHHHh-CCeEecCCEEEEEEECC
Confidence            99999998 9999975 667776654

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=95.92  E-value=0.01  Score=45.20  Aligned_cols=53  Identities=25%  Similarity=0.345  Sum_probs=45.3

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD  342 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~  342 (365)
                      .++| +.|..+.-.+|.++|+.|| -..|+.+-|.       .|||.|.+...|..|+..++
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            4555 9999999999999999999 5567777653       69999999999999999764

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=95.79  E-value=0.026  Score=42.86  Aligned_cols=53  Identities=25%  Similarity=0.363  Sum_probs=44.8

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD  342 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~  342 (365)
                      .++| +.|..+.-.+|.++|+.||. ..|+.+.|.       .|||.|.+...|..|+..++
T Consensus        18 Vf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           18 VLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             EEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             EEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            5556 99999999999999999994 456666553       69999999999999999663

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.04  E-value=0.016  Score=44.05  Aligned_cols=71  Identities=11%  Similarity=0.168  Sum_probs=47.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .-+|-|++||+.+|++++.+.++.+-.+..    +....|...                    .....-.-|||.|.+.+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~----~~fv~G~~s--------------------~~~~~~SRAYI~F~~~e   64 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDY----FEFFAADLS--------------------LYPHLYSRAYINFRNPD   64 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEE----CCCCCCCSS--------------------SCCSCCCCCEEEESCHH
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccce----EEEeCCccC--------------------CCCCcceEEEEEeCCHH
Confidence            347999999999999998877766433211    001111100                    01122356999999999


Q ss_pred             HHHHHHHHHccCccc
Q 017842          239 EAEKAVEMFHRYDID  253 (365)
Q Consensus       239 ~a~~Al~~lng~~~~  253 (365)
                      ++......++|..|.
T Consensus        65 dv~~F~~~f~g~~F~   79 (97)
T 2l08_A           65 DILLFRDRFDGYIFL   79 (97)
T ss_dssp             HHHHHHHHSTTEEEE
T ss_pred             HHHHHHHHcCCcEEE
Confidence            999999999998773

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=94.47  E-value=0.041  Score=41.91  Aligned_cols=53  Identities=25%  Similarity=0.394  Sum_probs=42.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      .++| +.|......+|.++|+.||.|   .|+|.                               +-.-|||.|.+++.|
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv---~I~Wi-------------------------------dDTsAlvvf~~~~~a   52 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNI---QISWI-------------------------------DDTSAFVSLSQPEQV   52 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEE---EEEEE-------------------------------ETTEEEEEEEEECHH
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCE---EEEEE-------------------------------cCCeEEEEecCHHHH
Confidence            3455 999999999999999999943   44432                               234699999999999


Q ss_pred             HHHHHHHc
Q 017842          241 EKAVEMFH  248 (365)
Q Consensus       241 ~~Al~~ln  248 (365)
                      ..|+..++
T Consensus        53 ~~al~~i~   60 (101)
T 3ctr_A           53 KIAVNTSK   60 (101)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHhcc
Confidence            99999765

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.14  E-value=0.056  Score=43.36  Aligned_cols=76  Identities=17%  Similarity=0.248  Sum_probs=54.7

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEE-EEEEee--------CCCC-----CcceEEEEEecCHHHHHHHHHHhCCCcc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVN-ARVVYD--------RETG-----RSRGFGFVTMSSETELNDAIAALDGQNL  346 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~-v~i~~d--------~~~~-----~~kG~afV~F~s~~~a~~Al~~l~~~~l  346 (365)
                      -|.|-+.|.... ..+-+.|++||.|.. +.+.+.        +...     .+..+..|+|.+..+|.+||. .||..|
T Consensus         9 ~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~ii   86 (132)
T 3p3d_A            9 AILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAVF   86 (132)
T ss_dssp             EEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCEE
T ss_pred             EEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeEe
Confidence            677878876544 456678999998876 222110        0001     135678999999999999999 799999


Q ss_pred             CCeeEEEEEccc
Q 017842          347 DGRAIRVNVAED  358 (365)
Q Consensus       347 ~gr~l~V~~a~~  358 (365)
                      .|.-|-|..+.+
T Consensus        87 ~G~mIGV~Py~~   98 (132)
T 3p3d_A           87 NGVLLGVIPYTK   98 (132)
T ss_dssp             TTEECEEEECCH
T ss_pred             CcEEEEEEECCH
Confidence            999888887754

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=93.59  E-value=0.1  Score=41.91  Aligned_cols=90  Identities=17%  Similarity=0.111  Sum_probs=54.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCC-CccceEEEEeCCH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETD-RSRGFGFVTMSTV  237 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~g~afV~f~~~  237 (365)
                      +..|.|=+.|.+.+. .+...|++||.|..-.-+.+   +...     .+   ...  ....+... ...++..|.|.+.
T Consensus         7 e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~---~~~~-----~~---~~~--~~~k~yP~f~g~NWikItYds~   72 (132)
T 3p3d_A            7 ELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLR---KPQA-----MT---VGL--QDRQFVPIFSGNSWTKITYDNP   72 (132)
T ss_dssp             -CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGC---CC---------------------CCCCCEETTEEEEEBSSH
T ss_pred             ceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccc---cccc-----cc---ccc--ccccccCccCCCcEEEEEcCCH
Confidence            456778788776655 57788999999854110000   0000     00   000  00000111 1367889999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      .+|.+||.. ||..|+|..|-|.++.
T Consensus        73 ~~A~rAL~~-NG~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           73 ASAVDALLE-NGAVFNGVLLGVIPYT   97 (132)
T ss_dssp             HHHHHHHTT-TTCEETTEECEEEECC
T ss_pred             HHHHHHHHh-CCeEeCcEEEEEEECC
Confidence            999999998 9999999888887654

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.87  E-value=0.054  Score=53.03  Aligned_cols=57  Identities=9%  Similarity=0.110  Sum_probs=40.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..|+|||. +|...++.+|.++|++||+|..+.+                            +.   ....||.|+|.+.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~----------------------------~~---~~g~~~~vef~~~   99 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFF----------------------------YE---SFGLYAVVEFCQK   99 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEE----------------------------EC---SSSEEEEEECC--
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEE----------------------------Ec---cCCeEEEEEeCCH
Confidence            46899997 7999999999999999999988652                            11   2237999999999


Q ss_pred             HHHHHHHHH
Q 017842          238 EEAEKAVEM  246 (365)
Q Consensus       238 e~a~~Al~~  246 (365)
                      +++..++..
T Consensus       100 ~~~~~~~~~  108 (464)
T 3pq1_A          100 ESIGSLQNG  108 (464)
T ss_dssp             -CCHHHHSS
T ss_pred             HHHHHHHhc
Confidence            998866543

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.50  E-value=0.066  Score=52.44  Aligned_cols=53  Identities=9%  Similarity=0.174  Sum_probs=40.5

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHH
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA  339 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~  339 (365)
                      +|+|. .|...++.+|.++|+.||.|..+.+..+.     .-||.|+|.+.+++..++.
T Consensus        55 sv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           55 TVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             EEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHS
T ss_pred             eEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHh
Confidence            89997 68899999999999999999999887542     3599999999999887765

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	365
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-27
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-18
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	7e-15
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-18
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-13
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-18
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-14
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-18
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-14
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-18
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-18
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-14
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-17
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-17
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-13
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-17
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-17
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-13
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-17
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	9e-17
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	6e-14
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-16
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-16
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-16
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-16
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-14
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-16
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-12
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-16
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-13
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	7e-16
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-16
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-13
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	8e-16
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-13
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	9e-16
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-15
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-13
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-15
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-15
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-15
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-11
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-15
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-07
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-15
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-13
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-15
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-13
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-15
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	7e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-15
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-15
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-15
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	5e-15
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	8e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	6e-15
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-12
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-14
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-12
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-14
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-11
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-14
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-11
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-14
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-11
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	4e-14
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-10
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	5e-14
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	5e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	8e-14
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	6e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-13
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	6e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-13
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-12
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-13
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	4e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-12
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-13
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	7e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-13
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-11
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	5e-13
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	8e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-13
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	7e-13
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-10
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-12
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-08
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-12
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-10
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-10
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-12
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-07
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	5e-12
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	6e-12
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	7e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-11
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-11
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-10
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-11
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 3e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-11
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	4e-06
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-10
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-10
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	6e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-10
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	9e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	8e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	1e-09
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	1e-07
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	8e-09
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	8e-06
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-08
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	6e-05
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-08
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-08
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	7e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	8e-08
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-07
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	4e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-07
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	3e-07
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.003
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	6e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.004
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	3e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	2e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	3e-06
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	5e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	4e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	6e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-06
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	7e-04

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  104 bits (259), Expect = 3e-27
 Identities = 52/210 (24%), Positives = 82/210 (39%), Gaps = 30/210 (14%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           EP +  KLF+G L ++   E L   FE+ GT+    V                       
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP------------------- 42

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
                   T RSRGFGFVT +TVEE + A+              V        +  + P 
Sbjct: 43  -------NTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRV---VEPKRAVSREDSQRPG 92

Query: 275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL 334
                 +I+VG +  + +   L   F ++GK+    ++ DR +G+ RGF FVT      +
Sbjct: 93  AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 152

Query: 335 NDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           +  +       ++G    V  A  +Q  +S
Sbjct: 153 DKIV-IQKYHTVNGHNCEVRKALSKQEMAS 181

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.7 bits (191), Expect = 1e-18
 Identities = 21/76 (27%), Positives = 40/76 (52%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +YVG+L  +V  A L + FS  G +++ RV  D  T RS G+ +V      +   A+  +
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 342 DGQNLDGRAIRVNVAE 357
           +   + G+ +R+  ++
Sbjct: 63  NFDVIKGKPVRIMWSQ 78

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.9 bits (163), Expect = 7e-15
 Identities = 22/103 (21%), Positives = 38/103 (36%), Gaps = 26/103 (25%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
           A L+VG+L  DV    L   F  AG +                             +V  
Sbjct: 1   ASLYVGDLHPDVTEAMLYEKFSPAGPILSI--------------------------RVCR 34

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           +  T RS G+ +V      +AE+A++  +   I G+ + +  +
Sbjct: 35  DMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS 77

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 78.2 bits (192), Expect = 1e-18
 Identities = 31/98 (31%), Positives = 49/98 (50%), Gaps = 1/98 (1%)

Query: 265 RGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFG 324
                ER  R  E   ++++G L +E     L   + + GK+ +  V+ D  + RSRGFG
Sbjct: 6   ETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 65

Query: 325 FVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
           FVT SS  E++ A+ A    ++DGR +    A  R+  
Sbjct: 66  FVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVAREES 102

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.3 bits (156), Expect = 1e-13
 Identities = 32/121 (26%), Positives = 50/121 (41%), Gaps = 27/121 (22%)

Query: 145 EGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHM 204
           E V  E +  E  +  KLF+G L ++   E L   +E+ G                    
Sbjct: 6   ETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGK----------------LTD 49

Query: 205 WVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP 264
            V           + +  + RSRGFGFVT S++ E + A+     + IDGR++   +A  
Sbjct: 50  CVV----------MRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA 98

Query: 265 R 265
           R
Sbjct: 99  R 99

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 76.9 bits (189), Expect = 1e-18
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L W+     L + F + G+V    V+ D  T RSRGFGFVT   +  ++  + A
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 60

Query: 341 LDGQNLDGRAIRVNVA 356
                LD + I   VA
Sbjct: 61  QSRHELDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.0 bits (158), Expect = 3e-14
 Identities = 23/102 (22%), Positives = 37/102 (36%), Gaps = 27/102 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+F+G L +    E L   F +              FG     + +             +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQ--------------FGEVKECLVMR------------D 35

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
             T RSRGFGFVT       +K +    R+++D + +    A
Sbjct: 36  PLTKRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTIDPKVA 76

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 77.7 bits (191), Expect = 1e-18
 Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 2/84 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE-TGRSRGFGFVTMSSETELNDAIA 339
           +I V N+P++ +   + ++FS  G++   R+      TG  RGFGFV   ++ +   A  
Sbjct: 10  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 340 AL-DGQNLDGRAIRVNVAEDRQRR 362
           AL    +L GR + +  A+     
Sbjct: 70  ALCHSTHLYGRRLVLEWADSEVTV 93

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 66.1 bits (161), Expect = 2e-14
 Identities = 24/114 (21%), Positives = 41/114 (35%), Gaps = 26/114 (22%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +    +K+ V N+P+  +  ++  LF   G ++   +                       
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKM------------------- 44

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVE-MFHRYDIDGRLLTVNKAAPRGT 267
                   T   RGFGFV   T ++A+KA   + H   + GR L +  A    T
Sbjct: 45  ------TGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT 92

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 77.0 bits (189), Expect = 2e-18
 Identities = 15/79 (18%), Positives = 30/79 (37%)

Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
               I V N+P+ V    +   F  +  +  +  +   E G   G   V   S  E   A
Sbjct: 8   GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 67

Query: 338 IAALDGQNLDGRAIRVNVA 356
           +  L+ + +  R +++ + 
Sbjct: 68  VIDLNDRPIGSRKVKLVLG 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.9 bits (142), Expect = 7e-12
 Identities = 16/107 (14%), Positives = 30/107 (28%), Gaps = 26/107 (24%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
            P    + V N+P+ V  +++   F                      + +      V   
Sbjct: 6   KPGPTIIKVQNMPFTVSIDEILDFF----------------------YGYQVIPGSV--- 40

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
             +   E     G   V   + +EA  AV   +   I  R + +   
Sbjct: 41  -CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 86

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.0 bits (189), Expect = 2e-18
 Identities = 19/83 (22%), Positives = 42/83 (50%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G LP  +++ +++++ +  G +    +V D  TG S+G+ F         + AIA 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 341 LDGQNLDGRAIRVNVAEDRQRRS 363
           L+G  L  + + V  A    + +
Sbjct: 63  LNGMQLGDKKLLVQRASVGAKNA 85

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.0 bits (158), Expect = 4e-14
 Identities = 15/108 (13%), Positives = 36/108 (33%), Gaps = 26/108 (24%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KLF+G LP  ++ +++  L                        +            ++ +
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSF------------------GPLKAF--------NLVKD 36

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ 268
             T  S+G+ F     +   ++A+   +   +  + L V +A+     
Sbjct: 37  SATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 84

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.4 bits (185), Expect = 1e-17
 Identities = 21/92 (22%), Positives = 43/92 (46%)

Query: 274 RVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETE 333
           ++ +    +YVGNL +     ++ ++FS+ G +    +  D+    + GF FV   S  +
Sbjct: 2   KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRAD 61

Query: 334 LNDAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
             +A+  ++G  LD R IR +     +    +
Sbjct: 62  AENAMRYINGTRLDDRIIRTDWDAGFKEGRQY 93

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.1 bits (148), Expect = 1e-12
 Identities = 20/108 (18%), Positives = 38/108 (35%), Gaps = 26/108 (24%)

Query: 158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
           +   L+VGNL +    E++  LF K               G+    +             
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSK--------------SGDIKKIIMGL---------- 41

Query: 218 IYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
             ++    + GF FV   +  +AE A+   +   +D R++  +  A  
Sbjct: 42  --DKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGF 87

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.8 bits (183), Expect = 1e-17
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 6/85 (7%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARV-----VYDRETGRSRGFGFVTMSSETELN 335
           R+YVGN+P+ +    +   F+   ++          V   +  + + F F+   S  E  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 336 DAIAALDGQNLDGRAIRVNVAEDRQ 360
            A+ A DG    G+++++    D Q
Sbjct: 63  QAM-AFDGIIFQGQSLKIRRPHDYQ 86

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.8 bits (152), Expect = 3e-13
 Identities = 17/109 (15%), Positives = 37/109 (33%), Gaps = 24/109 (22%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +L+VGN+P+ +  E +   F     +                               +  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPG---------------------NPVLA 41

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP 269
            + ++ + F F+   +V+E  +A+         G+ L + +  P   QP
Sbjct: 42  VQINQDKNFAFLEFRSVDETTQAMAF-DGIIFQGQSLKIRR--PHDYQP 87

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.1 bits (184), Expect = 2e-17
 Identities = 28/106 (26%), Positives = 51/106 (48%), Gaps = 5/106 (4%)

Query: 257 LTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE 316
           LT       G+Q E        G  +++ +LP E  +  L Q+F   G VV+A+V  D++
Sbjct: 1   LTQQSIGAAGSQKEG-----PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ 55

Query: 317 TGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
           T  S+ FGFV+  +      AI +++G  +  + ++V +   +   
Sbjct: 56  TNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 101

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.9 bits (147), Expect = 2e-12
 Identities = 24/111 (21%), Positives = 39/111 (35%), Gaps = 26/111 (23%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           E PE A LF+ +LP +   + L  +F   G V  A+V                       
Sbjct: 14  EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN---------------- 57

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                      S+ FGFV+      A+ A++  + + I  + L V     +
Sbjct: 58  ----------LSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSK 98

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.2 bits (182), Expect = 2e-17
 Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 4/90 (4%)

Query: 274 RVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETE 333
           R  +    + V  LPW+     L++ FS  G+V+  +V  D +TG S+GFGFV  +    
Sbjct: 3   RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY-- 60

Query: 334 LNDAIAALDGQN-LDGRAIRVNVAEDRQRR 362
               +  +  ++ +DGR     +   +Q +
Sbjct: 61  -ETQVKVMSQRHMIDGRWCDCKLPNSKQSQ 89

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.1 bits (153), Expect = 3e-13
 Identities = 25/111 (22%), Positives = 37/111 (33%), Gaps = 28/111 (25%)

Query: 158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
           + + L V  LP+    + L   F   G V +                           QV
Sbjct: 7   KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMV--------------------------QV 40

Query: 218 IYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ 268
             + +T  S+GFGFV  +  E   K +   H   IDGR         + +Q
Sbjct: 41  KKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQ 89

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 72.8 bits (178), Expect = 6e-17
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 3/85 (3%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE---TGRSRGFGFVTMSSETELNDAI 338
           +++ NL +      L+ VFS+ G + +  +   +       S GFGFV      +   A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 339 AALDGQNLDGRAIRVNVAEDRQRRS 363
             L G  +DG  + V ++E   + +
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKPA 85

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.6 bits (149), Expect = 6e-13
 Identities = 23/104 (22%), Positives = 34/104 (32%), Gaps = 23/104 (22%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           LF+ NL +    E L  +F K G +                                   
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAI------------KSCTISKKK-----------NKA 37

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
               S GFGFV     E+A+KA++    + +DG  L V  +   
Sbjct: 38  GVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERA 81

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 72.3 bits (177), Expect = 9e-17
 Identities = 25/78 (32%), Positives = 45/78 (57%), Gaps = 2/78 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            +YV NLP  + + +L+ +F ++G +V   ++ D+ TGR RG  FV  +   E  +AI+A
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 341 LDGQNLDG--RAIRVNVA 356
           L+    +G  + + V +A
Sbjct: 68  LNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 64.6 bits (157), Expect = 6e-14
 Identities = 25/110 (22%), Positives = 42/110 (38%), Gaps = 28/110 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           E  +D  L+V NLP  +  ++L  +F K G++    +                       
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK------------------- 42

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDG--RLLTVNKA 262
                   T R RG  FV  +  EEA++A+   +    +G  + L+V  A
Sbjct: 43  -------LTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 85

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.0 bits (176), Expect = 1e-16
 Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 7/84 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++Y+GNL   V    L Q+F +    +        +     G+ FV    +     AI  
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 341 LDGQ-NLDGRAIRVNVAEDRQRRS 363
           L G+  L G+ + V+ +  ++ RS
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKLRS 80

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 2e-09
 Identities = 17/107 (15%), Positives = 34/107 (31%), Gaps = 33/107 (30%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KL++GNL   V ++ L  LF                                        
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKL--------------------------------PLA 30

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFH-RYDIDGRLLTVNKAAPRG 266
            +     G+ FV       A +A+E    + ++ G+++ V+ +  + 
Sbjct: 31  GQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK 77

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.0 bits (176), Expect = 1e-16
 Identities = 28/82 (34%), Positives = 42/82 (51%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            +YVG L  EVD+  L   F   G + + ++  D ET + RGF FV      +   AI  
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 341 LDGQNLDGRAIRVNVAEDRQRR 362
           ++   L GR IRVN+A+  + +
Sbjct: 67  MNESELFGRTIRVNLAKPMRIK 88

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 1e-11
 Identities = 26/105 (24%), Positives = 41/105 (39%), Gaps = 26/105 (24%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            L+VG L  +VD + L   F   G +                             Q+  +
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDI--------------------------QIPLD 40

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
            ET++ RGF FV     E+A  A++  +  ++ GR + VN A P 
Sbjct: 41  YETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPM 85

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.4 bits (175), Expect = 3e-16
 Identities = 28/100 (28%), Positives = 49/100 (49%), Gaps = 11/100 (11%)

Query: 266 GTQPERAPRVFEPGFRIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFG 324
           G+  +  PR      R+++GNL    V  + +E +FS++GK+V   V          GF 
Sbjct: 4   GSSGKTDPR--SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFA 53

Query: 325 FVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           FV   +E     A+A  DG+ + G+ + +N+A + +   S
Sbjct: 54  FVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRS 93

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.0 bits (135), Expect = 9e-11
 Identities = 21/112 (18%), Positives = 33/112 (29%), Gaps = 35/112 (31%)

Query: 155 EPPEDAKLFVGNL-PYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVS 213
               ++++F+GNL    V    +  +F K G +                           
Sbjct: 11  PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKI--------------------------- 43

Query: 214 LLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                        +GF FV       A  AV       I G++L +N AA  
Sbjct: 44  -------VGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP 88

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.2 bits (174), Expect = 3e-16
 Identities = 31/85 (36%), Positives = 45/85 (52%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                +YVG L  +V    L ++F + G VVN  +  DR TG+ +G+GFV   SE + + 
Sbjct: 7   NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 66

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQR 361
           AI  +D   L G+ IRVN A    +
Sbjct: 67  AIKIMDMIKLYGKPIRVNKASAHNK 91

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.4 bits (159), Expect = 4e-14
 Identities = 25/111 (22%), Positives = 43/111 (38%), Gaps = 26/111 (23%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           E  +DA ++VG L   V    L  LF +               G                
Sbjct: 5   ERNQDATVYVGGLDEKVSEPLLWELFLQ--------------AGPVVNTHMPK------- 43

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                +R T + +G+GFV   + E+A+ A+++     + G+ + VNKA+  
Sbjct: 44  -----DRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAH 89

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 70.7 bits (173), Expect = 3e-16
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++ V NL + V +A ++++F+E G +  A V YDR +GRS G   V    + +   A+  
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 60

Query: 341 LDGQNLDGRAIRVNVA 356
            +G  LDGR + + + 
Sbjct: 61  YNGVPLDGRPMNIQLV 76

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.6 bits (144), Expect = 3e-12
 Identities = 22/102 (21%), Positives = 37/102 (36%), Gaps = 27/102 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           KL V NL + V    +  LF + GT++ A V +                           
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR------------------------- 36

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
             + RS G   V      +A KA++ ++   +DGR + +   
Sbjct: 37  --SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 76

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.4 bits (172), Expect = 3e-16
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG L  +    ++ + F   G+V +  +  D +T + RGF F+T   E  +   +  
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 341 LDGQNLDGRAIRVNVA 356
               N+      + VA
Sbjct: 61  -KYHNVGLSKCEIKVA 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.4 bits (154), Expect = 1e-13
 Identities = 21/102 (20%), Positives = 35/102 (34%), Gaps = 27/102 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG L  D   EK+   F                FG                     +
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGG--------------FGEVESIELPM------------D 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
            +T++ RGF F+T    E  +K +E  + +++      +  A
Sbjct: 35  NKTNKRRGFCFITFKEEEPVKKIMEKKY-HNVGLSKCEIKVA 75

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.5 bits (172), Expect = 7e-16
 Identities = 24/99 (24%), Positives = 45/99 (45%), Gaps = 3/99 (3%)

Query: 266 GTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGF 325
           G+   R P+   P +  ++GNLP++V    +++ F                  R +GFG+
Sbjct: 4   GSSGSRLPK--SPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGY 61

Query: 326 VTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
                   L  +  +L+ ++L  + IRV+VA+  Q + S
Sbjct: 62  AEFEDLDSL-LSALSLNEESLGNKRIRVDVADQAQDKDS 99

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 2e-09
 Identities = 21/120 (17%), Positives = 39/120 (32%), Gaps = 30/120 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
            PP     F+GNLPYDV  E +   F                   +G ++          
Sbjct: 13  SPP--YTAFLGNLPYDVTEESIKEFF-------------------RGLNISAVR------ 45

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
                    +R +GFG+     ++    A+ + +   +  + + V+ A     +    P 
Sbjct: 46  -LPREPSNPERLKGFGYAEFEDLDSLLSALSL-NEESLGNKRIRVDVADQAQDKD-SGPS 102

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.6 bits (170), Expect = 8e-16
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L W+     L+  FS+ G+VV+  +  D  TGRSRGFGFV       ++  +  
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-D 59

Query: 341 LDGQNLDGRAIRVNVA 356
                L+G+ I    A
Sbjct: 60  QKEHKLNGKVIDPKRA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.9 bits (150), Expect = 4e-13
 Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 27/102 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+F+G L +D   + L   F K              FG                     +
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSK--------------FGEVVDCTLKL------------D 34

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
             T RSRGFGFV     E  +K ++    + ++G+++   +A
Sbjct: 35  PITGRSRGFGFVLFKESESVDKVMDQ-KEHKLNGKVIDPKRA 75

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.8 bits (170), Expect = 8e-16
 Identities = 27/82 (32%), Positives = 46/82 (56%), Gaps = 1/82 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNA-RVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           I++GNL  E+D   L   FS  G ++   +++ D +TG S+G+ F+  +S    + AI A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 341 LDGQNLDGRAIRVNVAEDRQRR 362
           ++GQ L  R I V+ A  +  +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.5 bits (151), Expect = 3e-13
 Identities = 18/107 (16%), Positives = 44/107 (41%), Gaps = 25/107 (23%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           +F+GNL  ++D + L   F   G +                              ++ + 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPK-------------------------IMRDP 35

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ 268
           +T  S+G+ F+  ++ + ++ A+E  +   +  R +TV+ A  + ++
Sbjct: 36  DTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK 82

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.1 bits (171), Expect = 9e-16
 Identities = 27/104 (25%), Positives = 42/104 (40%), Gaps = 7/104 (6%)

Query: 259 VNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETG 318
           V +     +  ER  R       ++   L   +    LE  FS  GKV + R++ DR + 
Sbjct: 4   VREPVDNLSPEERDAR------TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSR 57

Query: 319 RSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
           RS+G  +V       +      L GQ L G  I V  ++  + R
Sbjct: 58  RSKGIAYVEFCEIQSV-PLAIGLTGQRLLGVPIIVQASQAEKNR 100

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 1e-10
 Identities = 16/111 (14%), Positives = 30/111 (27%), Gaps = 27/111 (24%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           E  +   +F   L   +    L   F                         V  V     
Sbjct: 14  EERDARTVFCMQLAARIRPRDLEDFFSA--------------------VGKVRDVRI--- 50

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
              I +R + RS+G  +V    ++    A+ +     + G  + V  +   
Sbjct: 51  ---ISDRNSRRSKGIAYVEFCEIQSVPLAIGL-TGQRLLGVPIIVQASQAE 97

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 69.7 bits (170), Expect = 1e-15
 Identities = 25/83 (30%), Positives = 39/83 (46%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R++V NL +      LE++FS +G +       D  T + +GF FVT         A A 
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 341 LDGQNLDGRAIRVNVAEDRQRRS 363
           +DGQ   GR + V  +  ++  S
Sbjct: 70  VDGQVFQGRMLHVLPSTIKKEAS 92

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 62.4 bits (151), Expect = 4e-13
 Identities = 26/119 (21%), Positives = 35/119 (29%), Gaps = 26/119 (21%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
                +LFV NL Y    E L                   LF   G    +         
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDL-----------------EKLFSAYGPLSELH-------- 39

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
               +  T + +GF FVT    E A KA          GR+L V  +  +    +  P 
Sbjct: 40  -YPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPS 97

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.8 bits (170), Expect = 1e-15
 Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 8/92 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVV--------YDRETGRSRGFGFVTMSSET 332
            IYV  L   V    L   F + G V   +           D+ETG+ +G   V+     
Sbjct: 10  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 69

Query: 333 ELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
               A+   DG++  G  ++V++A  +   +S
Sbjct: 70  TAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 101

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.0 bits (155), Expect = 1e-13
 Identities = 23/111 (20%), Positives = 44/111 (39%), Gaps = 18/111 (16%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           E  +++ ++V  L   V  + LA  F++ G V++ +     +                  
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMI----------------- 46

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
             +  ++ET + +G   V+      A+ AVE F   D  G  L V+ A  +
Sbjct: 47  -HIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 68.9 bits (168), Expect = 1e-15
 Identities = 22/76 (28%), Positives = 40/76 (52%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            + V  LP ++ +  L  +F   G +   R++ D +TG S G+ FV  +SE +   AI  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 341 LDGQNLDGRAIRVNVA 356
           L+G  +  + ++V+ A
Sbjct: 64  LNGITVRNKRLKVSYA 79

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 60.8 bits (147), Expect = 1e-12
 Identities = 16/106 (15%), Positives = 37/106 (34%), Gaps = 26/106 (24%)

Query: 159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVI 218
           +  L V  LP D+   +L  LF   G +    +   +  G    + +V            
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVD----------- 50

Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP 264
                           ++  ++++A+++ +   +  + L V+ A P
Sbjct: 51  ---------------FTSEMDSQRAIKVLNGITVRNKRLKVSYARP 81

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.9 bits (168), Expect = 1e-15
 Identities = 29/78 (37%), Positives = 44/78 (56%), Gaps = 2/78 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            +YV  LP  +    LEQ+FS++G+++ +R++ D+ TG SRG GF+      E  +AI  
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 341 LDGQNLDGR--AIRVNVA 356
           L+GQ   G    I V  A
Sbjct: 68  LNGQKPSGATEPITVKFA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 1e-11
 Identities = 24/106 (22%), Positives = 39/106 (36%), Gaps = 28/106 (26%)

Query: 159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVI 218
           DA L+V  LP  +  ++L  LF +              +G       +            
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQ--------------YGRIITSRILV----------- 40

Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRL--LTVNKA 262
            ++ T  SRG GF+      EAE+A++  +     G    +TV  A
Sbjct: 41  -DQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 85

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.4 bits (169), Expect = 2e-15
 Identities = 21/87 (24%), Positives = 42/87 (48%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           EP   +Y+ NL   V    L  +F+   +     + +   TGR RG  F+T  ++     
Sbjct: 16  EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 75

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRS 363
           A+  ++G  L G+ + +   +++++RS
Sbjct: 76  ALHLVNGYKLYGKILVIEFGKNKKQRS 102

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.5 bits (112), Expect = 1e-07
 Identities = 19/105 (18%), Positives = 32/105 (30%), Gaps = 26/105 (24%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            L++ NL   V    L  LF                                      + 
Sbjct: 20  VLYLKNLSPRVTERDLVSLFA--------------------RFQEKKGPPI------QFR 53

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
             T R RG  F+T    E A +A+ + + Y + G++L +     +
Sbjct: 54  MMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNK 98

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.3 bits (169), Expect = 2e-15
 Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 3/87 (3%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           E    +Y+ NLP+++    +  +F ++G +     +    T  +RG  +V      +  +
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKN 61

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRS 363
           A   L G N+  R + V      +   
Sbjct: 62  ACDHLSGFNVCNRYLVVLYYNANRAFQ 88

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.1 bits (153), Expect = 4e-13
 Identities = 21/117 (17%), Positives = 39/117 (33%), Gaps = 30/117 (25%)

Query: 156 PPEDAK-LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           PPE  + L++ NLPY + +E++  +F K G +    V                       
Sbjct: 3   PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET----------------- 45

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
                       RG  +V    + +A+ A +    +++  R L V          + 
Sbjct: 46  ------------RGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKM 90

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.5 bits (167), Expect = 2e-15
 Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           ++++G L +E  +  L   F + G + +  V+ D  T RSRGFGFVT ++  E++ A+ A
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 341 LDGQNLDGRAIRVNVA 356
                +DGR +    A
Sbjct: 68  -RPHKVDGRVVEPKRA 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.7 bits (152), Expect = 3e-13
 Identities = 31/108 (28%), Positives = 48/108 (44%), Gaps = 27/108 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           EP +  KLF+G L ++   E L   FE+              +G     + +        
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQ--------------WGTLTDCVVMR------- 40

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
                +  T RSRGFGFVT +TVEE + A+     + +DGR++   +A
Sbjct: 41  -----DPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA 82

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.8 bits (168), Expect = 3e-15
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 6/82 (7%)

Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
               +Y G +   + +  + Q FS  G+++  RV         +G+ FV  S+      A
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHA 70

Query: 338 IAALDGQNLDGRAIRVNVAEDR 359
           I +++G  ++G  ++    ++ 
Sbjct: 71  IVSVNGTTIEGHVVKCYWGKES 92

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.8 bits (142), Expect = 7e-12
 Identities = 17/118 (14%), Positives = 34/118 (28%), Gaps = 32/118 (27%)

Query: 148 FEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVC 207
           FE+      P++  ++ G +   +  + +   F   G +    V                
Sbjct: 7   FEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF--------------- 51

Query: 208 AVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                              +G+ FV  ST E A  A+   +   I+G ++        
Sbjct: 52  -----------------PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 92

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.5 bits (167), Expect = 3e-15
 Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 2/82 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            I++ NL   +DN  L   FS  G +++ +VV D     S+G+GFV   ++     AI  
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 67

Query: 341 LDGQNLDGRAIRVNVAEDRQRR 362
           ++G  L+ R + V   + R+ R
Sbjct: 68  MNGMLLNDRKVFVGRFKSRKER 89

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 4e-11
 Identities = 22/106 (20%), Positives = 39/106 (36%), Gaps = 28/106 (26%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
             +F+ NL   +D++ L   F   G +   +V                            
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE------------------------ 44

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
               + S+G+GFV   T E AE+A+E  +   ++ R + V +   R
Sbjct: 45  ----NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 86

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.2 bits (166), Expect = 3e-15
 Identities = 27/77 (35%), Positives = 42/77 (54%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           +P   + V  L        L +VFS++G + +  +VYD+++ RSRGF FV   +  +  +
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 337 AIAALDGQNLDGRAIRV 353
           A    +G  LDGR IRV
Sbjct: 67  AKERANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 1e-10
 Identities = 24/105 (22%), Positives = 39/105 (37%), Gaps = 26/105 (24%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
            P  +  L V  L        L  +F K              +G       V        
Sbjct: 5   NPDPNCCLGVFGLSLYTTERDLREVFSK--------------YGPIADVSIVY------- 43

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
                ++++ RSRGF FV    V++A++A E  +  ++DGR + V
Sbjct: 44  -----DQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.2 bits (166), Expect = 4e-15
 Identities = 37/84 (44%), Positives = 56/84 (66%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++VG L ++ +   LEQVFS++G++    VV DRET RSRGFGFVT  +  +  DA+ A
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
           ++G+++DGR IRV+ A       S
Sbjct: 67  MNGKSVDGRQIRVDQAGKSSDNRS 90

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (143), Expect = 4e-12
 Identities = 29/108 (26%), Positives = 48/108 (44%), Gaps = 26/108 (24%)

Query: 158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
           ++ KLFVG L +D + + L                                   +S + V
Sbjct: 4   DEGKLFVGGLSFDTNEQSL--------------------------EQVFSKYGQISEVVV 37

Query: 218 IYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
           + +RET RSRGFGFVT   +++A+ A+   +   +DGR + V++A   
Sbjct: 38  VKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS 85

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.8 bits (165), Expect = 5e-15
 Identities = 28/94 (29%), Positives = 41/94 (43%), Gaps = 6/94 (6%)

Query: 271 RAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSS 330
           R P       RIYVGNLP ++    +E VF ++G + +  +   R       F FV    
Sbjct: 7   RGPAG-NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFED 62

Query: 331 ETELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
             +  DA+   DG + DG  +RV     R  R +
Sbjct: 63  PRDAEDAVYGRDGYDYDGYRLRVEFP--RSGRGT 94

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 8e-12
 Identities = 27/114 (23%), Positives = 38/114 (33%), Gaps = 30/114 (26%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
               D +++VGNLP D+ ++ +  +F K G +                            
Sbjct: 10  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRD-------------------------- 43

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP-RGT 267
              I  +       F FV      +AE AV     YD DG  L V      RGT
Sbjct: 44  ---IDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 94

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.4 bits (164), Expect = 6e-15
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            +YV NL        +E+ F+        RV       + R + FV  S+  +  +A+ A
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKA 63

Query: 341 LDGQNLDGRAIRVNVAEDRQRRS 363
           L+G+ LDG  I V +A+   + S
Sbjct: 64  LNGKVLDGSPIEVTLAKPVDKDS 86

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.0 bits (145), Expect = 2e-12
 Identities = 20/105 (19%), Positives = 32/105 (30%), Gaps = 32/105 (30%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            L+V NL      E +   F       +  VK                            
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---------------------------- 41

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
               + R + FV  S  E+A +A++  +   +DG  + V  A P 
Sbjct: 42  ----KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV 82

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.3 bits (161), Expect = 2e-14
 Identities = 31/84 (36%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG LP+   +A L + F   G +  A V+ DR+TG+SRG+GFVTM+       A   
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
            +   +DGR   VN+A    +  S
Sbjct: 72  PNPI-IDGRKANVNLAYLGAKPRS 94

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.3 bits (148), Expect = 1e-12
 Identities = 37/124 (29%), Positives = 47/124 (37%), Gaps = 32/124 (25%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG LPY      L   FE                        V             +
Sbjct: 12  KIFVGGLPYHTTDASLRKYFE---------------GFGDIEEAVVI-----------TD 45

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGF 280
           R+T +SRG+GFVTM+    AE+A +  +   IDGR   VN A          PR  + GF
Sbjct: 46  RQTGKSRGYGFVTMADRAAAERACKDPNPI-IDGRKANVNLA-----YLGAKPRSLQTGF 99

Query: 281 RIYV 284
            I V
Sbjct: 100 AIGV 103

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.1 bits (158), Expect = 3e-14
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG L        ++  F + GKV +A +++D+ T R RGFGFVT  SE  +      
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 341 LDGQNLDGRAIRVNVA 356
           +    ++ + +    A
Sbjct: 60  IHFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.4 bits (138), Expect = 1e-11
 Identities = 28/102 (27%), Positives = 44/102 (43%), Gaps = 27/102 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG L  +   E +   FE+ G V+ A + F                           
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDK------------------------- 35

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
             T+R RGFGFVT  + +  EK  E+ H ++I+ +++   KA
Sbjct: 36  -TTNRHRGFGFVTFESEDIVEKVCEI-HFHEINNKMVECKKA 75

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.1 bits (158), Expect = 4e-14
 Identities = 22/77 (28%), Positives = 38/77 (49%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            + V  LP  +       +F   G++ + ++V D+ TG+S G+GFV      +   AI  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 341 LDGQNLDGRAIRVNVAE 357
           L+G  L  + I+V+ A 
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.3 bits (135), Expect = 4e-11
 Identities = 22/104 (21%), Positives = 37/104 (35%), Gaps = 26/104 (25%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            L V  LP ++  E+   LF                 G       V             +
Sbjct: 4   NLIVNYLPQNMTQEEFRSLF--------------GSIGEIESCKLVR------------D 37

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP 264
           + T +S G+GFV     ++AEKA+   +   +  + + V+ A P
Sbjct: 38  KITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP 81

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 65.1 bits (158), Expect = 4e-14
 Identities = 22/91 (24%), Positives = 47/91 (51%), Gaps = 4/91 (4%)

Query: 269 PERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTM 328
           P+R+      G+ ++V ++  E     +++ F ++G++ N  +  DR TG S+G+  V  
Sbjct: 1   PQRSV----EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 56

Query: 329 SSETELNDAIAALDGQNLDGRAIRVNVAEDR 359
            +  +   A  AL+G  + G+ I+V+    +
Sbjct: 57  ETHKQALAAKEALNGAEIMGQTIQVDWCFVK 87

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 57.8 bits (139), Expect = 1e-11
 Identities = 19/110 (17%), Positives = 37/110 (33%), Gaps = 26/110 (23%)

Query: 157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQ 216
            E   LFV ++  +   +++   F                +G                  
Sbjct: 5   VEGWILFVTSIHEEAQEDEIQEKFCD--------------YGEIKNIHLNL--------- 41

Query: 217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG 266
              +R T  S+G+  V   T ++A  A E  +  +I G+ + V+    +G
Sbjct: 42  ---DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG 88

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.7 bits (157), Expect = 4e-14
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +I+VG +  + +   L   F ++GK+    ++ DR +G+ RGF FVT     +  D I  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIVI 62

Query: 341 LDGQNLDGRAIRVNVA 356
                ++G    V  A
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.7 bits (131), Expect = 2e-10
 Identities = 22/102 (21%), Positives = 36/102 (35%), Gaps = 27/102 (26%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           K+FVG +  D +   L   FE+              +G       +             +
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQ--------------YGKIEVIEIMT------------D 37

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
           R + + RGF FVT    +  +K V     + ++G    V KA
Sbjct: 38  RGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA 78

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.8 bits (157), Expect = 5e-14
 Identities = 13/79 (16%), Positives = 29/79 (36%), Gaps = 6/79 (7%)

Query: 281 RIYVGNLPWEVDNA---RLEQVFSEHGKVVNARVVYDRETGRS---RGFGFVTMSSETEL 334
            ++V  L   + +    +  + F + GK+    +        S       +VT     + 
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 335 NDAIAALDGQNLDGRAIRV 353
             AI  ++   +DGR ++ 
Sbjct: 70  LRAIQCVNNVVVDGRTLKA 88

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.2 bits (106), Expect = 5e-07
 Identities = 17/99 (17%), Positives = 31/99 (31%), Gaps = 20/99 (20%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            +FV  L   +   ++    E  G            FG     +   +  Y         
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGK-----------FGKIHKVVINNSTSY--------- 49

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTV 259
             +       +VT    E+A +A++  +   +DGR L  
Sbjct: 50  AGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA 88

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 64.3 bits (156), Expect = 8e-14
 Identities = 18/100 (18%), Positives = 40/100 (40%), Gaps = 11/100 (11%)

Query: 264 PRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGF 323
           P  ++  RA R       +   NL + +    L++VF +        +    + G+S+G 
Sbjct: 7   PCTSKKVRAAR------TLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGI 55

Query: 324 GFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRRS 363
            ++   SE +    +    G  +DGR++ +    ++    
Sbjct: 56  AYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 59.3 bits (143), Expect = 6e-12
 Identities = 17/115 (14%), Positives = 38/115 (33%), Gaps = 31/115 (26%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +      L   NL +++  ++L                   +F +      V        
Sbjct: 12  KVRAARTLLAKNLSFNITEDEL-----------------KEVFEDALEIRLVS------- 47

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP 269
                  +  +S+G  ++   +  +AEK +E     +IDGR +++     +G   
Sbjct: 48  -------QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.3 bits (156), Expect = 1e-13
 Identities = 26/87 (29%), Positives = 47/87 (54%), Gaps = 2/87 (2%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
               R++V N+P+   +  L Q+F + GK+++  ++++     S+GFGFVT  +  + + 
Sbjct: 9   STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADR 66

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRS 363
           A   L G  ++GR I VN A  R   +
Sbjct: 67  AREKLHGTVVEGRKIEVNNATARVMTN 93

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 6e-11
 Identities = 24/111 (21%), Positives = 37/111 (33%), Gaps = 28/111 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
                 +L V N+P+      L  +F +                       +        
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQ--------------------FGKIL------- 39

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
             V        S+GFGFVT     +A++A E  H   ++GR + VN A  R
Sbjct: 40  -DVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 89

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 1e-13
 Identities = 21/83 (25%), Positives = 37/83 (44%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
           +    I V NL  +     L+++F   G +    +  D+ TG+S+GF F++     +   
Sbjct: 6   DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 65

Query: 337 AIAALDGQNLDGRAIRVNVAEDR 359
           AIA + G   D   + V  A+  
Sbjct: 66  AIAGVSGFGYDHLILNVEWAKPS 88

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 7e-12
 Identities = 23/111 (20%), Positives = 38/111 (34%), Gaps = 26/111 (23%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
              ++A + V NL  D     L  LF                FG+               
Sbjct: 4   RADDNATIRVTNLSEDTRETDLQELFRP--------------FGSISRIYL--------- 40

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                ++ T +S+GF F++    E+A +A+     +  D  +L V  A P 
Sbjct: 41  ---AKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS 88

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 63.6 bits (154), Expect = 2e-13
 Identities = 21/93 (22%), Positives = 28/93 (30%), Gaps = 7/93 (7%)

Query: 272 APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
            P      FR+ V  LP       L+    E G V  A V  D         G V    +
Sbjct: 8   GPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MGMVEYLRK 60

Query: 332 TELNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
            ++  A+  LD           +       RSS
Sbjct: 61  EDMEYALRKLDDTKFRSHEGETSYIRVYPERSS 93

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.5 bits (107), Expect = 4e-07
 Identities = 10/120 (8%), Positives = 18/120 (15%), Gaps = 33/120 (27%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
               D ++ V  LP     + L     +                                
Sbjct: 11  TRRSDFRVLVSGLPPSGSWQDLKDHMRE----------------AGDVCYADVQKDG--- 51

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
                          G V     E+ E A+               +       +      
Sbjct: 52  --------------MGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERSSGPSS 97

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.6 bits (154), Expect = 2e-13
 Identities = 18/86 (20%), Positives = 31/86 (36%), Gaps = 4/86 (4%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNA--RVVYDRETGRSRGFGFVTMSSETELNDAI 338
           R+++G +P       + +  ++  + V          +  ++RGF FV   S      A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 339 AALDGQN--LDGRAIRVNVAEDRQRR 362
             L      L G  I V+ AE     
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDV 88

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 1e-12
 Identities = 19/107 (17%), Positives = 32/107 (29%), Gaps = 26/107 (24%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +LF+G +P     E++     K                     + V              
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEG----------------VLDVI--------VYASA 38

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMF--HRYDIDGRLLTVNKAAPR 265
            +  ++RGF FV   +   A  A       R  + G  + V+ A P 
Sbjct: 39  ADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPE 85

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.9 bits (155), Expect = 2e-13
 Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 4/85 (4%)

Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
           P  RI V NL + V    L Q+FS+ G V+            ++    +  +       A
Sbjct: 6   PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHA 61

Query: 338 IAALDGQNLDGRAIRVNVAEDRQRR 362
             +LDGQN+      + +   +   
Sbjct: 62  KLSLDGQNIYNACCTLRIDFSKLTS 86

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 7e-09
 Identities = 15/113 (13%), Positives = 29/113 (25%), Gaps = 32/113 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           ++ V NL Y V  + L  +F K GTV                                  
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-------------------------- 42

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI--DGRLLTVNKAAPRGTQPER 271
                ++    +  +    A+ A       +I      L ++ +       + 
Sbjct: 43  ----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKY 91

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 64.2 bits (155), Expect = 3e-13
 Identities = 35/132 (26%), Positives = 62/132 (46%), Gaps = 4/132 (3%)

Query: 234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDN 293
           MS +      V  +  Y    +L  + +   +   P +     +    + V  +P  VD 
Sbjct: 1   MSQIP----LVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDE 56

Query: 294 ARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV 353
            +L Q+F  +G + + ++V DRET +SRG+GFV   S +    AIA L+G N+  + ++V
Sbjct: 57  VQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV 116

Query: 354 NVAEDRQRRSSF 365
            +A    +R   
Sbjct: 117 ALAASGHQRPGI 128

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 59.1 bits (142), Expect = 2e-11
 Identities = 24/139 (17%), Positives = 49/139 (35%), Gaps = 26/139 (18%)

Query: 137 ERQEESGEEGVFEEEEFVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFL 196
           ++ ++  ++ +   +   EP     L V  +P  VD  +L  LFE+ G +E  ++     
Sbjct: 20  QQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE 79

Query: 197 FGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRL 256
                 + +V                             +   A++A+   + ++I  + 
Sbjct: 80  TRQSRGYGFVK--------------------------FQSGSSAQQAIAGLNGFNILNKR 113

Query: 257 LTVNKAAPRGTQPERAPRV 275
           L V  AA    +P  A  V
Sbjct: 114 LKVALAASGHQRPGIAGAV 132

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 61.7 bits (149), Expect = 5e-13
 Identities = 11/78 (14%), Positives = 31/78 (39%)

Query: 280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
             +++ N P       +  +  +   V  +  +       SR F ++ ++S+ +    + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 340 ALDGQNLDGRAIRVNVAE 357
            L+G  ++G  +   V+ 
Sbjct: 62  KLNGLKIEGYTLVTKVSN 79

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 58.3 bits (140), Expect = 8e-12
 Identities = 14/106 (13%), Positives = 30/106 (28%), Gaps = 26/106 (24%)

Query: 159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVI 218
           +  L++ N P       +  L +    V ++       F       ++            
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYID----------- 49

Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP 264
                          +++ E+A   VE  +   I+G  L    + P
Sbjct: 50  ---------------VTSKEDARYCVEKLNGLKIEGYTLVTKVSNP 80

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.9 bits (150), Expect = 5e-13
 Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 6/83 (7%)

Query: 274 RVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETE 333
           + F    R++VGNLP ++    + ++F ++GK     +  D+       FGF+ + + T 
Sbjct: 3   KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTL 56

Query: 334 LNDAIAALDGQNLDGRAIRVNVA 356
              A   LD   L G+ +RV  A
Sbjct: 57  AEIAKVELDNMPLRGKQLRVRFA 79

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.6 bits (131), Expect = 2e-10
 Identities = 25/107 (23%), Positives = 36/107 (33%), Gaps = 32/107 (29%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           +LFVGNLP D+  E++  LFEK              +G  G         +         
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEK--------------YGKAGEVFIHKDKGF--------- 46

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT 267
                    GF+ + T   AE A        + G+ L V  A    +
Sbjct: 47  ---------GFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS 84

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 7e-13
 Identities = 20/86 (23%), Positives = 42/86 (48%), Gaps = 2/86 (2%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                +YVGNL  +V    + Q+FS+ G   + +++ +     +  + FV      +   
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAA 63

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRR 362
           A+AA++G+ + G+ ++VN A     +
Sbjct: 64  ALAAMNGRKILGKEVKVNWATTPSSQ 89

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 3e-10
 Identities = 21/114 (18%), Positives = 35/114 (30%), Gaps = 28/114 (24%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +  +   L+VGNL  DV    +  LF + G  +                           
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCK--------------------------- 36

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ 268
                  E   +  + FV      +A  A+   +   I G+ + VN A    +Q
Sbjct: 37  -SCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ 89

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 1e-12
 Identities = 18/91 (19%), Positives = 39/91 (42%), Gaps = 7/91 (7%)

Query: 278 PGFRIYVGNLPWEVDNARLEQ----VFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETE 333
           P   IY+ NL  ++    L++    +FS  G++++  V       + RG  FV     + 
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSS 58

Query: 334 LNDAIAALDGQNLDGRAIRVNVAEDRQRRSS 364
             +A+ ++ G     + +R+  A+      +
Sbjct: 59  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIA 89

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (129), Expect = 4e-10
 Identities = 15/105 (14%), Positives = 31/105 (29%), Gaps = 25/105 (23%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            +++ NL   +  ++L             +   H +F   G  +             I  
Sbjct: 5   TIYINNLNEKIKKDEL-------------KKSLHAIFSRFGQILD------------ILV 39

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
             + + RG  FV    V  A  A+     +    + + +  A   
Sbjct: 40  SRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD 84

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.4 bits (148), Expect = 1e-12
 Identities = 24/97 (24%), Positives = 43/97 (44%), Gaps = 6/97 (6%)

Query: 273 PRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSET 332
           P     G  +++ NL ++ +   L +V  + G +   RVV   +T  S+G  F    ++ 
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 333 ELNDAIAAL------DGQNLDGRAIRVNVAEDRQRRS 363
                +AA        G  LDGR ++V++A  R   +
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 98

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.0 bits (116), Expect = 2e-08
 Identities = 23/117 (19%), Positives = 41/117 (35%), Gaps = 32/117 (27%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +  E   +F+ NL +D + E L  + ++                       +  V     
Sbjct: 4   DVTEGKTVFIRNLSFDSEEEALGEVLQQ--------------------FGDLKYVRV--- 40

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHR------YDIDGRLLTVNKAAPR 265
              + + +T+ S+G  F    T E A+K +             +DGR L V+ A  R
Sbjct: 41  ---VLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTR 94

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.9 bits (147), Expect = 2e-12
 Identities = 32/82 (39%), Positives = 52/82 (63%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            ++VGN+P+E    +L+ +FSE G VV+ R+VYDRETG+ +G+GF     +     A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 341 LDGQNLDGRAIRVNVAEDRQRR 362
           L+G+   GRA+RV+ A   + +
Sbjct: 70  LNGREFSGRALRVDNAASEKNK 91

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 2e-10
 Identities = 29/120 (24%), Positives = 46/120 (38%), Gaps = 29/120 (24%)

Query: 155 EPPEDA---KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFY 211
           +P  D     +FVGN+PY+   E+L                                V  
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQL--------------------------KDIFSEVGP 34

Query: 212 VSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPER 271
           V   +++Y+RET + +G+GF      E A  A+   +  +  GR L V+ AA    + E 
Sbjct: 35  VVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEEL 94

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 2e-12
 Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 7/84 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            ++VG    ++    L + FS++G V++  +         R F FVT + +         
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLCG- 60

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
            +   + G ++ ++ AE +   +S
Sbjct: 61  -EDLIIKGISVHISNAEPKHNSNS 83

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 3e-10
 Identities = 19/110 (17%), Positives = 33/110 (30%), Gaps = 33/110 (30%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
           + +FVG    D+  ++L   F + G V    +   F                        
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF------------------------ 41

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP 269
                  R F FVT +  + A+          I G  + ++ A P+    
Sbjct: 42  -------RAFAFVTFADDQIAQSLCGEDL--IIKGISVHISNAEPKHNSN 82

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.9 bits (144), Expect = 4e-12
 Identities = 17/86 (19%), Positives = 30/86 (34%), Gaps = 1/86 (1%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                 ++ N+P+ +    + Q         NA  V     G+  G   V   +E +   
Sbjct: 6   SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 65

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRR 362
           +   L  + L+GR   V+V      R
Sbjct: 66  SE-RLHRKKLNGREAFVHVVTLEDMR 90

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.8 bits (110), Expect = 2e-07
 Identities = 11/114 (9%), Positives = 28/114 (24%), Gaps = 27/114 (23%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
              + N+P+ +                                 ++  +        +  
Sbjct: 10  CAHITNIPFSITKMD--------------------------VLQFLEGIPVDENAVHVLV 43

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
               +  G   V     ++A K+  + HR  ++GR   V+       +      
Sbjct: 44  DNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTLEDMREIEKNP 96

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 59.2 bits (142), Expect = 5e-12
 Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
              F +++GNL      A L+   SE     +  VV  R TG +R FG+V   S  +L  
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEK 69

Query: 337 AIAALDGQNLDGRAIRVNVAEDR 359
           A+  L G  + G  I++   + R
Sbjct: 70  AL-ELTGLKVFGNEIKLEKPKGR 91

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 52.6 bits (125), Expect = 1e-09
 Identities = 20/111 (18%), Positives = 36/111 (32%), Gaps = 28/111 (25%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           E      LF+GNL  +    +L +   +                                
Sbjct: 9   ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-------------------------- 42

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
              + +  T  +R FG+V   + E+ EKA+E+     + G  + + K   R
Sbjct: 43  -LAVVDVRTGTNRKFGYVDFESAEDLEKALEL-TGLKVFGNEIKLEKPKGR 91

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 6e-12
 Identities = 22/88 (25%), Positives = 34/88 (38%), Gaps = 11/88 (12%)

Query: 272 APRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE 331
           APR    G  +YV      +    L   FS  G +       D      R   FVT    
Sbjct: 1   APR---KGNTLYVYGED--MTPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKM 49

Query: 332 TELNDAIAALDGQNLDGRAIRVNVAEDR 359
              + A+A L+G  ++   ++VN+A  +
Sbjct: 50  ESADQAVAELNGTQVESVQLKVNIARKQ 77

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.2 bits (104), Expect = 7e-07
 Identities = 21/110 (19%), Positives = 32/110 (29%), Gaps = 34/110 (30%)

Query: 156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLL 215
           P +   L+V     D+    L   F   G                               
Sbjct: 2   PRKGNTLYVYGE--DMTPTLLRGAFSPFGN------------------------------ 29

Query: 216 QVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
             I +   D  R   FVT   +E A++AV   +   ++   L VN A  +
Sbjct: 30  --IIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ 77

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 1e-11
 Identities = 14/84 (16%), Positives = 30/84 (35%), Gaps = 7/84 (8%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            I V NLP + +   +  +  ++               R++   FVT+ +  +  +AI  
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 341 LDGQNLDGRAIRVNVAEDRQRRSS 364
               +  G+ + V +        S
Sbjct: 60  FHQYSFRGKDLIVQLQPTDALLCS 83

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 1e-07
 Identities = 20/106 (18%), Positives = 40/106 (37%), Gaps = 33/106 (31%)

Query: 160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
           + + V NLP D + +++  L +               +  +  ++               
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKD--------------YDLKYCYVD-------------- 37

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                R++   FVT+   E+A+ A++MFH+Y   G+ L V      
Sbjct: 38  -----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD 78

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 57.4 bits (138), Expect = 2e-11
 Identities = 17/108 (15%), Positives = 36/108 (33%), Gaps = 25/108 (23%)

Query: 158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
           E  ++ + NL  ++  E L                    F   G    +           
Sbjct: 3   EGREIMIRNLSTELLDENL----------------LRESFEGFGSIEKIN--------IP 38

Query: 218 IYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
              +E   +    F+     + AE+A++M +R  +  R ++V+ A  +
Sbjct: 39  AGQKEHSFNNCCAFMVFENKDSAERALQM-NRSLLGNREISVSLADKK 85

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 54.4 bits (130), Expect = 2e-10
 Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 3/83 (3%)

Query: 279 GFRIYVGNLPWEV-DNARLEQVFSEHGKVVNARVVYD-RETGRSRGFGFVTMSSETELND 336
           G  I + NL  E+ D   L + F   G +    +    +E   +    F+   ++     
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 337 AIAALDGQNLDGRAIRVNVAEDR 359
           A+  ++   L  R I V++A+ +
Sbjct: 64  ALQ-MNRSLLGNREISVSLADKK 85

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 2e-11
 Identities = 11/73 (15%), Positives = 26/73 (35%), Gaps = 1/73 (1%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + +     E       ++  ++G+V    V  +       G  +V    E +   A+  L
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 342 DGQNLDGRAIRVN 354
           + +  +G+ I   
Sbjct: 89  NNRWFNGQPIHAE 101

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 3e-05
 Identities = 17/100 (17%), Positives = 29/100 (29%), Gaps = 27/100 (27%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            + +     +   E    + EK G VE  E+                            +
Sbjct: 29  DVEMQEHYDEFFEEVFTEMEEKYGEVE--EMNVC-------------------------D 61

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVN 260
              D   G  +V     E+AEKAV   +    +G+ +   
Sbjct: 62  NLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.4 bits (140), Expect = 2e-11
 Identities = 24/100 (24%), Positives = 45/100 (45%), Gaps = 1/100 (1%)

Query: 263 APRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRG 322
           +P G +  R+    E GF +Y+  LP+E +N  +   F +   V ++  +     G++ G
Sbjct: 2   SPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATG 61

Query: 323 FGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQRR 362
            GFV   +E +   A+     Q +  R I+V+    +   
Sbjct: 62  EGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKGML 100

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (100), Expect = 4e-06
 Identities = 13/76 (17%), Positives = 26/76 (34%), Gaps = 1/76 (1%)

Query: 193 FHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI 252
             F   N+    +   +  V     I      ++ G GFV      + + A+    +Y +
Sbjct: 26  LPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQY-M 84

Query: 253 DGRLLTVNKAAPRGTQ 268
             R + V+    +G  
Sbjct: 85  GNRFIQVHPITKKGML 100

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 1e-10
 Identities = 15/87 (17%), Positives = 29/87 (33%), Gaps = 3/87 (3%)

Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
            G  +++  LP+      +   FS    +           GR  G   V  ++  +   A
Sbjct: 14  TGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGRVTGEADVEFATHEDAVAA 71

Query: 338 IAALDGQNLDGRAIRVNVAEDRQRRSS 364
           + A D  N+  R + + +        S
Sbjct: 72  M-AKDKANMQHRYVELFLNSTAGTSGS 97

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 1e-06
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 29/116 (25%)

Query: 154 VEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVS 213
            +      + +  LPY      +   F     + +                         
Sbjct: 10  FQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD------------------ 51

Query: 214 LLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP 269
                      R  G   V  +T E+A  A+    + ++  R + +   +  GT  
Sbjct: 52  ----------GRVTGEADVEFATHEDAVAAMAK-DKANMQHRYVELFLNSTAGTSG 96

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.2 bits (132), Expect = 2e-10
 Identities = 23/93 (24%), Positives = 39/93 (41%), Gaps = 1/93 (1%)

Query: 265 RGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFG 324
            G Q + A +  +    +Y+ NLP  +D   LE +    G+V++   +    +G SRG G
Sbjct: 4   SGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVIS-TRILRDSSGTSRGVG 62

Query: 325 FVTMSSETELNDAIAALDGQNLDGRAIRVNVAE 357
           F  M S  +    I   +G+ +          E
Sbjct: 63  FARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 95

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.9 bits (113), Expect = 6e-08
 Identities = 17/110 (15%), Positives = 30/110 (27%), Gaps = 27/110 (24%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +  +   L++ NLP  +D ++L  +                                   
Sbjct: 14  QEQDPTNLYISNLPLSMDEQELENML----------------KPFGQVISTRI------- 50

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAP 264
                   +  SRG GF  M + E+ E  +  F+   I           P
Sbjct: 51  ----LRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP 96

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.6 bits (128), Expect = 3e-10
 Identities = 16/71 (22%), Positives = 35/71 (49%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +Y+  L     +  L ++   +GK+V+ + + D+ T + +G+GFV   S +    A+ AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 342 DGQNLDGRAIR 352
               +  +  +
Sbjct: 61  KASGVQAQMAK 71

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 9e-07
 Identities = 13/96 (13%), Positives = 29/96 (30%), Gaps = 26/96 (27%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           L++  L      + L  L +            +    +    +                 
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQP-----------YGKIVSTKAILDKT-------------- 35

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLL 257
            T++ +G+GFV   +   A+KAV       +  ++ 
Sbjct: 36  -TNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA 70

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.1 bits (127), Expect = 8e-10
 Identities = 21/87 (24%), Positives = 30/87 (34%), Gaps = 6/87 (6%)

Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
           P  R++VG L      A L + F   G +     V          F ++   S      A
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAA 69

Query: 338 IAALDGQNLDGRAIRVNVAEDRQRRSS 364
            A + G  L G   R+ V   +   SS
Sbjct: 70  CAKMRGFPLGGPDRRLRVDFAKSGPSS 96

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 17/115 (14%), Positives = 34/115 (29%), Gaps = 34/115 (29%)

Query: 153 FVEPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYV 212
           + +     +L+VG L  +     LA  F++                  G    +  V   
Sbjct: 11  YGKANPTTRLWVGGLGPNTSLAALAREFDR-----------------FGSIRTIDHVKG- 52

Query: 213 SLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDG--RLLTVNKAAPR 265
                           F ++   +++ A+ A      + + G  R L V+ A   
Sbjct: 53  --------------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG 93

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 1e-09
 Identities = 18/83 (21%), Positives = 40/83 (48%), Gaps = 6/83 (7%)

Query: 281 RIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA 339
            + V NL  E V    L  +F  +G V   +++++++         V M+   +   A++
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAMS 58

Query: 340 ALDGQNLDGRAIRVNVAEDRQRR 362
            L+G  L G+ IR+ +++ +  +
Sbjct: 59  HLNGHKLHGKPIRITLSKHQNVQ 81

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 1e-07
 Identities = 20/127 (15%), Positives = 42/127 (33%), Gaps = 32/127 (25%)

Query: 161 KLFVGNL-PYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIY 219
            L V NL P  V  + L +LF   G V+  ++ F+                         
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE---------------------- 41

Query: 220 NRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPG 279
                       V M+   +A+ A+   + + + G+ + +  +  +  Q  R  +  +  
Sbjct: 42  ---------NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGL 92

Query: 280 FRIYVGN 286
            + Y  +
Sbjct: 93  TKDYGNS 99

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.3 bits (119), Expect = 8e-09
 Identities = 19/88 (21%), Positives = 26/88 (29%), Gaps = 10/88 (11%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           R+ V  LP       L+    E G V  A V  D         G V    + ++  A+  
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAVRK 54

Query: 341 LDGQNLDGRAIRVNVA---EDRQRRSSF 365
           LD                  D  R  S+
Sbjct: 55  LDNTKFRSHEGETAYIRVKVDGPRSPSY 82

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.8 bits (97), Expect = 8e-06
 Identities = 8/114 (7%), Positives = 13/114 (11%), Gaps = 33/114 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
           ++ V  LP     + L                                            
Sbjct: 2   RVVVSGLPPSGSWQDLKDHM------------REAGDVCYADVYRDGTGVV--------- 40

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPR 274
                            E+   AV                    +   P     
Sbjct: 41  ------------EFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSY 82

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.2 bits (119), Expect = 1e-08
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 1/88 (1%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                + +  LP+      + Q FS    V N   +     GRS G  FV  +S+     
Sbjct: 13  ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEK 72

Query: 337 AIAALDGQNLDGRAIRVNVAEDRQRRSS 364
           A+     + +  R I +  +   + R+S
Sbjct: 73  AL-KKHKERIGHRYIEIFKSSRAEVRTS 99

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (95), Expect = 2e-05
 Identities = 20/111 (18%), Positives = 37/111 (33%), Gaps = 27/111 (24%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +   D  + +  LP+    E++   F                    G  +    +     
Sbjct: 11  DTANDGFVRLRGLPFGCSKEEIVQFF-------------------SGLEIVPNGMTLP-- 49

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                     RS G  FV  ++ E AEKA++  H+  I  R + + K++  
Sbjct: 50  -----VDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSRA 94

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 48.7 bits (115), Expect = 2e-08
 Identities = 11/73 (15%), Positives = 26/73 (35%), Gaps = 3/73 (4%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V NLP   +  ++ + F   G +++  V       ++  F  +  +       A    
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDG-ALAAITK 59

Query: 342 DGQNLDGRAIRVN 354
             + +    I V+
Sbjct: 60  THKVVGQNEIIVS 72

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.7 bits (89), Expect = 6e-05
 Identities = 13/102 (12%), Positives = 29/102 (28%), Gaps = 29/102 (28%)

Query: 161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYN 220
            + V NLP   +  K+   F+  G +   +V                             
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL------------------------- 36

Query: 221 RETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
               ++  F  +  +  + A  A+   H+  +    + V+  
Sbjct: 37  ---KKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVSHL 74

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (116), Expect = 2e-08
 Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 5/86 (5%)

Query: 275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETEL 334
           +F P   +++ N+P  V    L+ +FS +G VV     + ++    R    + M S  E 
Sbjct: 6   IFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEA 61

Query: 335 NDAIAALDGQNL-DGRAIRVNVAEDR 359
             A+  L   +L +   +RV+ ++  
Sbjct: 62  VQALIDLHNHDLGENHHLRVSFSKST 87

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 2e-06
 Identities = 25/110 (22%), Positives = 38/110 (34%), Gaps = 31/110 (28%)

Query: 157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQ 216
           P  A L + N+P  V  E L +LF   G      V   F F  +   M            
Sbjct: 8   PPSATLHLSNIPPSVSEEDLKVLFSSNG-----GVVKGFKFFQKDRKMA----------- 51

Query: 217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI-DGRLLTVNKAAPR 265
                          + M +VEEA +A+   H +D+ +   L V+ +   
Sbjct: 52  --------------LIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 87

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.4 bits (117), Expect = 2e-08
 Identities = 13/90 (14%), Positives = 27/90 (30%), Gaps = 11/90 (12%)

Query: 281 RIYVGNLPWEVDNAR-----LEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELN 335
            +       +V +        E +F  + K    +        +S     +  S+     
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF------KSFKRVRINFSNPLSAA 60

Query: 336 DAIAALDGQNLDGRAIRVNVAEDRQRRSSF 365
           DA   L      G+ +++  A+     SS 
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTLHIGSSH 90

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.2 bits (106), Expect = 7e-07
 Identities = 16/109 (14%), Positives = 24/109 (22%), Gaps = 27/109 (24%)

Query: 157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQ 216
              + L       DV SE                 KF  LF                  +
Sbjct: 3   SGSSGLIACVANDDVFSESET------------RAKFESLFRTYD------KDTTFQYFK 44

Query: 217 VIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                    S     +  S    A  A    H+ +  G+ + +  A   
Sbjct: 45  ---------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL 84

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (117), Expect = 3e-08
 Identities = 14/65 (21%), Positives = 20/65 (30%), Gaps = 1/65 (1%)

Query: 297 EQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA 356
           E +  E  K    R +         G   V+     E +  I  LDG+   GR I     
Sbjct: 34  EDLRVECSKFGQIRKL-LLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

Query: 357 EDRQR 361
           +    
Sbjct: 93  DGTTD 97

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.6 bits (113), Expect = 8e-08
 Identities = 8/43 (18%), Positives = 13/43 (30%)

Query: 223 TDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
                G   V+    EEA+  ++        GR +T       
Sbjct: 53  DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGT 95

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.5 bits (110), Expect = 1e-07
 Identities = 12/80 (15%), Positives = 28/80 (35%), Gaps = 9/80 (11%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           + V   P    +  L   F+++G ++            +  +  +   S+ +   A+ + 
Sbjct: 7   VTVFGFPQASASYIL-LQFAQYGNILKHV------MSNTGNWMHIRYQSKLQARKAL-SK 58

Query: 342 DGQNLDGRA-IRVNVAEDRQ 360
           DG+       I V    D+ 
Sbjct: 59  DGRIFGESIMIGVKPCIDKN 78

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.2 bits (91), Expect = 4e-05
 Identities = 11/111 (9%), Positives = 23/111 (20%), Gaps = 35/111 (31%)

Query: 158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
           +D  + V   P    S  L    +                                    
Sbjct: 3   DDTWVTVFGFPQASASYILLQFAQYG---------------------------------N 29

Query: 218 IYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGR-LLTVNKAAPRGT 267
           I       +  +  +   +  +A KA+    R       ++ V     +  
Sbjct: 30  ILKHVMSNTGNWMHIRYQSKLQARKALSKDGR-IFGESIMIGVKPCIDKNV 79

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.9 bits (111), Expect = 1e-07
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 3/85 (3%)

Query: 284 VGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGF--VTMSSETELNDAIAAL 341
           + +  +E     +    S++G V +  +    +     G G   V  +S  +   A+  L
Sbjct: 19  LDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 78

Query: 342 DGQNLDGRAIRVNVA-EDRQRRSSF 365
            G+    R +       D   R  F
Sbjct: 79  TGRKFANRVVVTKYCDPDSYHRRDF 103

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 8/47 (17%), Positives = 17/47 (36%)

Query: 219 YNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPR 265
            +       G  FV  ++V + +KA++         R++      P 
Sbjct: 50  VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPD 96

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 2e-07
 Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 2/78 (2%)

Query: 281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
            +Y+   P +     +++   + G+V+N   +        +G  FV   S       +  
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKFV-E 65

Query: 341 LDGQNLDGRAIRVNVAED 358
             GQ      + +   +D
Sbjct: 66  TPGQKYKETDLLILFKDD 83

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 1e-04
 Identities = 13/105 (12%), Positives = 26/105 (24%), Gaps = 28/105 (26%)

Query: 158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQV 217
           ++  +++   P D   + +    E              +   Q                 
Sbjct: 5   KNRSVYIKGFPTDATLDDIKEWLE----------DKGQVLNIQMRRTLHK---------- 44

Query: 218 IYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
                    +G  FV   ++E A+K VE           L +   
Sbjct: 45  -------AFKGSIFVVFDSIESAKKFVET-PGQKYKETDLLILFK 81

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.3 bits (106), Expect = 3e-07
 Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 7/75 (9%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I +  LP +V N  +  + S++               + +G  FVT+ +  +   AI   
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYEL-------KYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 342 DGQNLDGRAIRVNVA 356
               L  R + V + 
Sbjct: 54  HQSRLRERELSVQLQ 68

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.1 bits (77), Expect = 0.003
 Identities = 19/101 (18%), Positives = 34/101 (33%), Gaps = 33/101 (32%)

Query: 162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR 221
           + +  LP DV ++++  L                                      +   
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSD---------------------------------YELKYC 27

Query: 222 ETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKA 262
             D+ +G  FVT+   E+AE A+  FH+  +  R L+V   
Sbjct: 28  FVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQ 68

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 6e-07
 Identities = 13/75 (17%), Positives = 27/75 (36%), Gaps = 7/75 (9%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           +  G L   V   +L  V  + G V    +  ++       + F    +  E   A   L
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYVTL 76

Query: 342 DGQNL-DGRAIRVNV 355
           +G+ + D    ++ +
Sbjct: 77  NGKEVVDDLGQKITL 91

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 13/107 (12%), Positives = 27/107 (25%), Gaps = 33/107 (30%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
              +   +  G L   V   +L  + EK G                     +        
Sbjct: 16  YATQSLVVANGGLGNGVSRNQLLPVLEKCGL-----------------VDALLMPPN--- 55

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDI-DGRLLTVN 260
                       + + F    T EE+++A    +  ++ D     + 
Sbjct: 56  ------------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT 90

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.4 bits (104), Expect = 1e-06
 Identities = 9/88 (10%), Positives = 25/88 (28%), Gaps = 8/88 (9%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
                ++V  L   V  A L +   + G +    ++  +          V   +     +
Sbjct: 13  SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKE 66

Query: 337 AIAALDGQ--NLDGRAIRVNVAEDRQRR 362
            +         + G+    N +  ++  
Sbjct: 67  CVTFAADVPVYIAGQQAFFNYSTSKRIT 94

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.4 bits (78), Expect = 0.004
 Identities = 9/113 (7%), Positives = 23/113 (20%), Gaps = 34/113 (30%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +      + V  L   V                  ++           ++ +        
Sbjct: 11  KVSVSPVVHVRGLCESVVEA---------------DLVEALEKFGTICYVMMMPFKR--- 52

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFH--RYDIDGRLLTVNKAAPR 265
                            V    ++ A++ V         I G+    N +  +
Sbjct: 53  --------------QALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK 91

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.9 bits (100), Expect = 3e-06
 Identities = 10/89 (11%), Positives = 31/89 (34%), Gaps = 8/89 (8%)

Query: 277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELND 336
            P   +++  LP EV    +  +            V +    + +   F+ +++E     
Sbjct: 6   APSRVLHIRKLPGEVTETEVIALGLPF------GKVTNILMLKGKNQAFLELATEEAAIT 59

Query: 337 AIAA--LDGQNLDGRAIRVNVAEDRQRRS 363
            +        +L  + I +  +  ++ ++
Sbjct: 60  MVNYYSAVTPHLRNQPIYIQYSNHKELKT 88

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.6 bits (94), Expect = 2e-05
 Identities = 12/113 (10%), Positives = 29/113 (25%), Gaps = 34/113 (30%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           +      L +  LP +V                  EV    L   +  ++ +        
Sbjct: 4   DGAPSRVLHIRKLPGEVTET---------------EVIALGLPFGKVTNILMLKGKN--- 45

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFH--RYDIDGRLLTVNKAAPR 265
                           F+ ++T E A   V  +      +  + + +  +  +
Sbjct: 46  --------------QAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK 84

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 42.5 bits (99), Expect = 3e-06
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 6/80 (7%)

Query: 278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDA 337
           P   +++ NLP E +   L  +F++       R+V +R         FV  ++E + N A
Sbjct: 7   PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFTTELQSNAA 61

Query: 338 IAALDGQNLD-GRAIRVNVA 356
             AL G  +    A+++  A
Sbjct: 62  KEALQGFKITPTHAMKITFA 81

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 36.4 bits (83), Expect = 5e-04
 Identities = 18/109 (16%), Positives = 33/109 (30%), Gaps = 32/109 (29%)

Query: 155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSL 214
           E P +  LF+ NLP + +   L+MLF +    +   +  +                    
Sbjct: 4   EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHD----------------- 46

Query: 215 LQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDID-GRLLTVNKA 262
                           FV  +T  ++  A E    + I     + +  A
Sbjct: 47  --------------IAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA 81

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.4 bits (99), Expect = 4e-06
 Identities = 11/84 (13%), Positives = 34/84 (40%), Gaps = 9/84 (10%)

Query: 282 IYVGNLP-WEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAA 340
           +++ +    +    +L Q+    G + N  ++            F+ M++  +   A+  
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN------EAFIEMATTEDAQAAVDY 64

Query: 341 --LDGQNLDGRAIRVNVAEDRQRR 362
                  + G+ +RV++++  +R 
Sbjct: 65  YTTTPALVFGKPVRVHLSQKYKRI 88

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.9 bits (100), Expect = 6e-06
 Identities = 13/82 (15%), Positives = 23/82 (28%), Gaps = 7/82 (8%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETE-LNDAIAA 340
            + G+L  +     L  +FS HG++     V           G +    + +        
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKD 67

Query: 341 LDGQNLDGRAIRVNVAEDRQRR 362
            +  NL  R   V         
Sbjct: 68  ANNGNLQLRNKEVTWEVLEGEV 89

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.2 bits (98), Expect = 7e-06
 Identities = 13/83 (15%), Positives = 22/83 (26%), Gaps = 6/83 (7%)

Query: 282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL 341
           I   NLP     A +++ FS  G +    +              V      E   A   L
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------ITAIVEFLEPLEARKAFRHL 66

Query: 342 DGQNLDGRAIRVNVAEDRQRRSS 364
                    + +  A      ++
Sbjct: 67  AYSKFHHVPLYLEWAPIGVFGAA 89

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.5 bits (83), Expect = 7e-04
 Identities = 16/99 (16%), Positives = 41/99 (41%), Gaps = 5/99 (5%)

Query: 264 PRGTQPERAPRVFEPGFRIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRG 322
           P G   ++  +  E G  I++ NLP     ++ + ++   +GK+ N   +  R   ++  
Sbjct: 3   PEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKN--YILMRMKSQAFI 60

Query: 323 FGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR 361
                  +   ++            GR ++V+++E  ++
Sbjct: 61  EMETREDAMAMVDH--CLKKALWFQGRCVKVDLSEKYKK 97

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	365
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	100.0
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.85
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.85
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.85
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.84
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.84
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.84
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.83
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.83
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.83
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.82
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.81
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.81
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.81
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.81
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.81
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.81
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.81
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.81
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.81
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.8
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.8
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.8
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.8
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.8
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.8
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.8
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.8
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.79
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.78
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.78
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.78
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.78
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.78
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.78
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.77
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.77
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.77
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.77
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.76
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.76
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.76
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.76
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.76
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.76
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.76
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.76
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.75
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.75
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.75
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.75
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.75
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.75
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.75
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.74
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.74
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.74
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.74
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.74
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.74
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.74
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.74
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.74
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.74
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.73
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.73
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.73
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.73
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.73
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.73
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.73
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.73
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.73
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.72
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.72
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.72
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.71
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.71
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.71
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.71
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.71
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.71
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.71
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.71
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.7
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.7
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.7
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.7
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.69
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.69
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.69
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.68
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.68
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.68
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.68
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.68
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.68
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.67
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.67
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.67
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.67
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.67
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.67
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.67
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.66
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.66
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.66
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.66
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.65
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.65
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.64
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.64
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.64
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.64
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.64
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.63
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.63
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.62
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.62
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.62
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.62
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.61
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.61
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.61
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.6
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.6
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.59
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.59
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.59
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.59
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.59
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.59
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.57
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.57
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.56
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.56
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.55
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.54
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.54
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.51
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.48
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.46
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.46
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.44
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.44
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.41
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.39
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.38
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.3
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.28
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.27
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.25
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.25
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.09
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.59
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.51
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.4
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.9
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.76
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	94.98
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	89.87
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	87.2

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.5e-32  Score=235.97  Aligned_cols=173  Identities=31%  Similarity=0.531  Sum_probs=154.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .|+|||||||+++|+++|+++|++||.|..+.                          ++.+..++.++|||||+|.+.+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~--------------------------~~~~~~~~~~~g~afv~f~~~~   59 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCV--------------------------VMRDPNTKRSRGFGFVTYATVE   59 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTCCEEEEEEEEESSHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEE--------------------------eeecccCCCccCceecccCCHH
Confidence            47999999999999999999999999998877                          7778889999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETG  318 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~  318 (365)
                      +|.+|+.. ++..++++.+.+....+......  .......++|||+|||+.+|+++|+++|+.||.|..+.|+.+..+|
T Consensus        60 ~a~~a~~~-~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~  136 (183)
T d1u1qa_          60 EVDAAMNA-RPHKVDGRVVEPKRAVSREDSQR--PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSG  136 (183)
T ss_dssp             HHHHHHHT-CSCEETTEECEEEECCCTTGGGS--TTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTC
T ss_pred             HHHHHHHh-cCCcccccchhhhhhhhcccccc--cccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccC
Confidence            99999987 77778889988887665543222  2233455699999999999999999999999999999999999999


Q ss_pred             CcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccccc
Q 017842          319 RSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQR  361 (365)
Q Consensus       319 ~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~~  361 (365)
                      .++|||||+|.+.++|.+||. +++..+.|++|+|.+|.++..
T Consensus       137 ~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k~e  178 (183)
T d1u1qa_         137 KKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQE  178 (183)
T ss_dssp             CEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCHHH
T ss_pred             ccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCccc
Confidence            999999999999999999998 799999999999999987654

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.85  E-value=2.5e-21  Score=147.21  Aligned_cols=83  Identities=24%  Similarity=0.446  Sum_probs=79.1

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ..+++|||+|||+.+++++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|+..|||..+.||+|+|+||
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 017842          357 EDR  359 (365)
Q Consensus       357 ~~~  359 (365)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            876

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=4e-21  Score=147.64  Aligned_cols=89  Identities=24%  Similarity=0.445  Sum_probs=82.8

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ..+++|||+|||+.+|+++|+++|+.||.|..|+|++++.++.++|||||+|.+.++|..|++.|||..+.||+|+|.||
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCCCC
Q 017842          357 EDRQRRSSF  365 (365)
Q Consensus       357 ~~~~~~~~~  365 (365)
                      ......+.|
T Consensus        85 ~~~~~grqy   93 (93)
T d1h2vz_          85 AGFKEGRQY   93 (93)
T ss_dssp             SCCCTTCC-
T ss_pred             CCCCCCCCC
Confidence            877665544

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.85  E-value=2.6e-21  Score=145.14  Aligned_cols=80  Identities=28%  Similarity=0.489  Sum_probs=77.4

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|+..|||..+.|++|+|+||++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999999999975

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=5.2e-21  Score=143.42  Aligned_cols=80  Identities=28%  Similarity=0.514  Sum_probs=77.2

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|+|+++..+|+++|||||+|.+.++|.+|++.|||..+.|++|+|.||+|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            35899999999999999999999999999999999999999999999999999999999999999999999999999975

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=5.1e-21  Score=147.04  Aligned_cols=83  Identities=37%  Similarity=0.563  Sum_probs=79.9

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+|+++|+++|+.||.|..|+|++++.+|.++|||||+|.+.++|.+|++.|||..|.||+|+|+||.+
T Consensus         9 ~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~   88 (93)
T d1x5ua1           9 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASA   88 (93)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTT
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            35999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q 017842          359 RQR  361 (365)
Q Consensus       359 ~~~  361 (365)
                      +.+
T Consensus        89 ~~~   91 (93)
T d1x5ua1          89 HNK   91 (93)
T ss_dssp             TSC
T ss_pred             CCC
Confidence            765

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=6.1e-21  Score=145.68  Aligned_cols=83  Identities=25%  Similarity=0.425  Sum_probs=79.4

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +.++|||+|||..+++++|+++|+.||.|..|+|++++.+|.++|||||+|.+.++|.+|++.|||..+.|++|+|.||+
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            44699999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q 017842          358 DRQ  360 (365)
Q Consensus       358 ~~~  360 (365)
                      ++.
T Consensus        87 p~~   89 (90)
T d2cq0a1          87 PST   89 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=2.6e-21  Score=147.49  Aligned_cols=83  Identities=34%  Similarity=0.524  Sum_probs=79.2

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|+..|||..++|++|+|.||++
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p   84 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP   84 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            45999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ccc
Q 017842          359 RQR  361 (365)
Q Consensus       359 ~~~  361 (365)
                      +..
T Consensus        85 ~~~   87 (89)
T d2cqba1          85 MRI   87 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.3e-20  Score=147.33  Aligned_cols=86  Identities=27%  Similarity=0.510  Sum_probs=81.9

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      +++++|||+|||+.+++++|+++|+.||.|..++++++..+|.++|||||+|.+.++|..||..|||..|.|++|+|+||
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccC
Q 017842          357 EDRQRR  362 (365)
Q Consensus       357 ~~~~~~  362 (365)
                      .++..+
T Consensus        96 ~~k~~~  101 (102)
T d2cpza1          96 RSKNDS  101 (102)
T ss_dssp             CCSCCC
T ss_pred             CCCCCC
Confidence            988754

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=7.1e-21  Score=142.03  Aligned_cols=77  Identities=27%  Similarity=0.487  Sum_probs=75.5

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +|||+|||+.+|+++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|+..|||..+.||+|+|.||+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999985

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=4.7e-21  Score=144.72  Aligned_cols=82  Identities=23%  Similarity=0.470  Sum_probs=79.4

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      +|||+|||+.+|+++|+++|+.||.|..|+|++|+.+|.++|||||+|.+.++|..|+..|||..|.|++|+|.||.+..
T Consensus         3 rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~   82 (85)
T d2u2fa_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA   82 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999877


Q ss_pred             cC
Q 017842          361 RR  362 (365)
Q Consensus       361 ~~  362 (365)
                      +.
T Consensus        83 ~~   84 (85)
T d2u2fa_          83 KN   84 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=1.9e-20  Score=145.53  Aligned_cols=84  Identities=29%  Similarity=0.428  Sum_probs=80.1

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||+|||+.+++++|+++|..||.|..|+|++++.+++++|||||+|.+.++|.+||+.|||..|.||+|+|.+|.
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34589999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 017842          358 DRQR  361 (365)
Q Consensus       358 ~~~~  361 (365)
                      .+..
T Consensus        87 ~~~~   90 (99)
T d1whwa_          87 IKKE   90 (99)
T ss_dssp             CCST
T ss_pred             CCCc
Confidence            8764

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=2.4e-20  Score=140.70  Aligned_cols=82  Identities=24%  Similarity=0.523  Sum_probs=76.3

Q ss_pred             EEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCC---CcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETG---RSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       282 lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~---~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      |||+|||+.+|+++|+++|+.||.|..|+|++++.++   +++|||||+|.+.++|.+|+..|||..++||+|+|.||+.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999999987664   5799999999999999999999999999999999999987


Q ss_pred             cccCC
Q 017842          359 RQRRS  363 (365)
Q Consensus       359 ~~~~~  363 (365)
                      ..+++
T Consensus        81 ~~kpa   85 (85)
T d2cpfa1          81 ATKPA   85 (85)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            76653

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.82  E-value=5.9e-20  Score=151.54  Aligned_cols=85  Identities=34%  Similarity=0.572  Sum_probs=80.5

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||+|||+.+++++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+||+.|||..|+||+|+|.||.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34589999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccccC
Q 017842          358 DRQRR  362 (365)
Q Consensus       358 ~~~~~  362 (365)
                      .+.++
T Consensus       121 ~~~~~  125 (139)
T d1u6fa1         121 SGHQR  125 (139)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76654

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=4e-20  Score=142.22  Aligned_cols=84  Identities=27%  Similarity=0.519  Sum_probs=78.0

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHh-CCCccCCeeEEEEE
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRE-TGRSRGFGFVTMSSETELNDAIAAL-DGQNLDGRAIRVNV  355 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~-~~~~kG~afV~F~s~~~a~~Al~~l-~~~~l~gr~l~V~~  355 (365)
                      ..++|||+|||+.+++++|+++|+.||.|..|+|+++.. +|+++|||||+|.+.++|.+||..| ||..+.||+|+|.|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            345899999999999999999999999999999998854 7899999999999999999999998 89999999999999


Q ss_pred             cccccc
Q 017842          356 AEDRQR  361 (365)
Q Consensus       356 a~~~~~  361 (365)
                      |+.+.+
T Consensus        87 A~~~~~   92 (94)
T d2cpha1          87 ADSEVT   92 (94)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            987754

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=5.9e-20  Score=140.05  Aligned_cols=82  Identities=28%  Similarity=0.499  Sum_probs=76.4

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||+|||+.+|+++|+++|+.||.|..|+|++|+.+|+++|||||+|.+.++|.+||.  ++..|+||.|.|.+|.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~--~~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh--cCCccCCEEeEEEeCC
Confidence            34589999999999999999999999999999999999999999999999999999999998  4558999999999998


Q ss_pred             cccc
Q 017842          358 DRQR  361 (365)
Q Consensus       358 ~~~~  361 (365)
                      ++..
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            8764

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=3.7e-20  Score=144.84  Aligned_cols=83  Identities=36%  Similarity=0.592  Sum_probs=77.1

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+||+.+++ .|.||+|+|.+|..
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~   88 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYL   88 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTT
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCC
Confidence            35899999999999999999999999999999999999999999999999999999999997765 79999999999986


Q ss_pred             cccC
Q 017842          359 RQRR  362 (365)
Q Consensus       359 ~~~~  362 (365)
                      +.++
T Consensus        89 ~~~p   92 (103)
T d2cqda1          89 GAKP   92 (103)
T ss_dssp             TCCC
T ss_pred             CCCC
Confidence            6554

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=3e-20  Score=141.72  Aligned_cols=85  Identities=44%  Similarity=0.731  Sum_probs=80.7

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      .+|||+|||+.+++++|+++|+.||.|..+.++++..+|.++|||||+|.+.++|.+|+..|||..|+|++|+|.+|.++
T Consensus         6 ~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~   85 (90)
T d1x5sa1           6 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS   85 (90)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECC
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            48999999999999999999999999999999999899999999999999999999999999999999999999999988


Q ss_pred             ccCCC
Q 017842          360 QRRSS  364 (365)
Q Consensus       360 ~~~~~  364 (365)
                      ...+|
T Consensus        86 ~~~rs   90 (90)
T d1x5sa1          86 SDNRS   90 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76553

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=5.8e-20  Score=138.31  Aligned_cols=78  Identities=31%  Similarity=0.580  Sum_probs=74.8

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      ++|||+|||+.+++++|+++|+.||.|..|+|++|+.+|+++|||||+|.+.++|.+||. ++++.|.||+|+|..|.+
T Consensus         7 ~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~s   84 (84)
T d1l3ka1           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (84)
T ss_dssp             GEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeeeC
Confidence            489999999999999999999999999999999999999999999999999999999998 799999999999998853

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=6e-20  Score=138.55  Aligned_cols=78  Identities=37%  Similarity=0.675  Sum_probs=74.2

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eeEEEEEc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDG--RAIRVNVA  356 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g--r~l~V~~a  356 (365)
                      .++|||+|||+.+|+++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|++.|||..+.|  ++|+|.||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            3589999999999999999999999999999999999999999999999999999999999999999988  56999986

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=6e-20  Score=137.91  Aligned_cols=76  Identities=36%  Similarity=0.587  Sum_probs=73.5

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      +.++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..|||..|+||+|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4569999999999999999999999999999999999999999999999999999999999999999999999987

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=1e-20  Score=140.02  Aligned_cols=76  Identities=33%  Similarity=0.639  Sum_probs=73.7

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      |+|||+|||+.+|+++|+++|+.||.|..++|++|+.+|+++|||||+|.+.++|.+||. ++++.++||+|+|.+|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            589999999999999999999999999999999999999999999999999999999998 7999999999999986

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.81  E-value=3e-20  Score=138.91  Aligned_cols=79  Identities=14%  Similarity=0.312  Sum_probs=69.8

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      ++|||+|||+.+|+++|+++|+.||.|..+.++++..+|+++|||||+|.+.++|.+|++.|||..+.|++|+|+||+|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            5999999999999999999999999999998888888899999999999999999999999999999999999999986

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.81  E-value=9.5e-20  Score=137.41  Aligned_cols=78  Identities=32%  Similarity=0.615  Sum_probs=74.8

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eeEEEEEc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDG--RAIRVNVA  356 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g--r~l~V~~a  356 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|++.|||..+.|  ++|+|+||
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            3589999999999999999999999999999999999999999999999999999999999999999976  89999997

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=8.3e-20  Score=141.38  Aligned_cols=87  Identities=26%  Similarity=0.525  Sum_probs=80.1

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC------CCccCCe
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD------GQNLDGR  349 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~------~~~l~gr  349 (365)
                      ...+++|||+|||+.+|+++|+++|+.||.|..+++..+..++.++|||||+|.+.++|.+||+.|+      |..+.||
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3345699999999999999999999999999999999999999999999999999999999999987      5678999


Q ss_pred             eEEEEEccccccC
Q 017842          350 AIRVNVAEDRQRR  362 (365)
Q Consensus       350 ~l~V~~a~~~~~~  362 (365)
                      +|+|.||.+|.+.
T Consensus        85 ~l~v~~a~~k~~a   97 (98)
T d1x4ha1          85 QLKVDLAVTRDEA   97 (98)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEEEEECCCCCcC
Confidence            9999999988764

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=3.2e-20  Score=139.42  Aligned_cols=81  Identities=33%  Similarity=0.589  Sum_probs=76.4

Q ss_pred             EEEeCCCCcCcHHHHHHHHhccCCeEEE-EEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccc
Q 017842          282 IYVGNLPWEVDNARLEQVFSEHGKVVNA-RVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       282 lfV~nLp~~~tee~L~~~F~~~G~V~~v-~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      |||+|||+.+++++|+++|+.||.|..+ +|++++.+|+++|||||+|.+.++|.+|+..|+|..+.||+|+|+||.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998764 789999999999999999999999999999999999999999999999876


Q ss_pred             cC
Q 017842          361 RR  362 (365)
Q Consensus       361 ~~  362 (365)
                      .+
T Consensus        81 ~k   82 (83)
T d1x5ta1          81 SK   82 (83)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=2e-19  Score=137.97  Aligned_cols=83  Identities=31%  Similarity=0.615  Sum_probs=77.2

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||+|||+.+++++|+++|+.||.|..|+++++.  +.++|||||+|.+.++|.+|+..|||..|.||+|+|.||+
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            44589999999999999999999999999999999885  3479999999999999999999999999999999999999


Q ss_pred             ccccC
Q 017842          358 DRQRR  362 (365)
Q Consensus       358 ~~~~~  362 (365)
                      +|.+.
T Consensus        88 ~r~~t   92 (93)
T d2cq3a1          88 ARVMT   92 (93)
T ss_dssp             SSCCC
T ss_pred             cCCCC
Confidence            98764

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=7.7e-20  Score=135.65  Aligned_cols=77  Identities=31%  Similarity=0.579  Sum_probs=74.0

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      +|||+|||+.+++++|+++|+.||.|..|+|.+++ +|+++|||||+|.+.++|.+|+..|||..+.||+|+|++|.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            79999999999999999999999999999999885 789999999999999999999999999999999999999864

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=5.1e-20  Score=143.94  Aligned_cols=83  Identities=33%  Similarity=0.577  Sum_probs=79.0

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..+.|++|+.++.++|||||+|.+.++|.+||+ ++|..|.||.|.|.+|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            3589999999999999999999999999999999999999999999999999999999997 899999999999999998


Q ss_pred             cccC
Q 017842          359 RQRR  362 (365)
Q Consensus       359 ~~~~  362 (365)
                      +..+
T Consensus        99 ke~~  102 (103)
T d1x4ba1          99 REES  102 (103)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8764

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=9.1e-20  Score=141.99  Aligned_cols=88  Identities=25%  Similarity=0.394  Sum_probs=80.5

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCe--------EEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKV--------VNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDG  348 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V--------~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g  348 (365)
                      ...++|||+|||+.+|+++|+++|+.||.|        ..+.+.+++.+|+++|||||+|.+.++|.+|+..|||..|.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            345699999999999999999999999987        466778888899999999999999999999999999999999


Q ss_pred             eeEEEEEccccccCCC
Q 017842          349 RAIRVNVAEDRQRRSS  364 (365)
Q Consensus       349 r~l~V~~a~~~~~~~~  364 (365)
                      |+|+|++|++++.++|
T Consensus        86 r~i~V~~a~~~~p~~s  101 (101)
T d2cpea1          86 SKLKVSLARKKPPMNS  101 (101)
T ss_dssp             EECEEECSSCCCCSTT
T ss_pred             EEEEEEEcCCCCCCCC
Confidence            9999999999887654

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=2.6e-20  Score=146.01  Aligned_cols=81  Identities=40%  Similarity=0.785  Sum_probs=77.9

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      ++|||+|||+.+++++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+|+..|||..|.|++|+|.||.++
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             c
Q 017842          360 Q  360 (365)
Q Consensus       360 ~  360 (365)
                      .
T Consensus        89 ~   89 (104)
T d1p1ta_          89 K   89 (104)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=2e-19  Score=137.11  Aligned_cols=83  Identities=24%  Similarity=0.460  Sum_probs=76.1

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +.++|||+|||..+++++|+++|+.||.|..|+|+++..++  +|||||+|.+.++|..|+..|||..|.|+.|+|.||+
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            34599999999999999999999999999999999886544  8999999999999999999999999999999999998


Q ss_pred             ccccC
Q 017842          358 DRQRR  362 (365)
Q Consensus       358 ~~~~~  362 (365)
                      ++..+
T Consensus        85 ~~~~~   89 (90)
T d2cqia1          85 TPSSQ   89 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            76543

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=3.2e-20  Score=144.63  Aligned_cols=80  Identities=30%  Similarity=0.464  Sum_probs=76.6

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      ++|||+|||+.+++++|+++|+.||.|..|+|+++..+|+++|||||+|.+.++|.+|+. |||..|.|++|+|.+|.++
T Consensus        19 ~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~~   97 (101)
T d2cq4a1          19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAE   97 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCCC
Confidence            589999999999999999999999999999999999999999999999999999999996 9999999999999998765


Q ss_pred             c
Q 017842          360 Q  360 (365)
Q Consensus       360 ~  360 (365)
                      .
T Consensus        98 ~   98 (101)
T d2cq4a1          98 K   98 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=9.2e-20  Score=134.16  Aligned_cols=75  Identities=32%  Similarity=0.681  Sum_probs=72.1

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      +|||+|||+.+++++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+||. +++..|.||+|+|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            59999999999999999999999999999999999999999999999999999999998 8999999999999765

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.79  E-value=7e-20  Score=138.48  Aligned_cols=81  Identities=20%  Similarity=0.333  Sum_probs=71.5

Q ss_pred             CceEEEeCCCCcCc-HHHHHHHHhccCCeEEEEEEee-CCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          279 GFRIYVGNLPWEVD-NARLEQVFSEHGKVVNARVVYD-RETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       279 ~~~lfV~nLp~~~t-ee~L~~~F~~~G~V~~v~i~~d-~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      +++|||+|||+.++ ++.|+++|+.||.|..|+|+++ ..+++++|||||+|.+.++|.+|++ |||..|+||+|+|++|
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEEC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEc
Confidence            45999999999986 4569999999999999998764 5689999999999999999999997 9999999999999999


Q ss_pred             cccc
Q 017842          357 EDRQ  360 (365)
Q Consensus       357 ~~~~  360 (365)
                      +++|
T Consensus        83 ~~kP   86 (86)
T d2ghpa3          83 DKKP   86 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9875

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.78  E-value=2.9e-19  Score=133.69  Aligned_cols=80  Identities=24%  Similarity=0.496  Sum_probs=75.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      +++|||+|||+++++++|+++|++||.|..++                          +++++.+++++|||||+|.+.+
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~--------------------------i~~~~~~g~~~g~afV~f~~~~   55 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCR--------------------------IMRDYKTGYSYGYAFVDFTSEM   55 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCEETTTTEECSEEEEEESSHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceee--------------------------eeeecccCCccccceEEECCHH
Confidence            57899999999999999999999999999887                          7788889999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      +|.+|+..|||..+.|+.|+|.++.|
T Consensus        56 ~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          56 DSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            99999999999999999999999875

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=6.6e-20  Score=143.09  Aligned_cols=88  Identities=24%  Similarity=0.406  Sum_probs=82.4

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ..+.++|||+|||..+++++|+++|+.||.|..+.+..+..+|+++|||||+|.+.++|.+|+..|||..|.|++|+|+|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34567999999999999999999999999999999998888899999999999999999999999999999999999999


Q ss_pred             ccccccCC
Q 017842          356 AEDRQRRS  363 (365)
Q Consensus       356 a~~~~~~~  363 (365)
                      |+++..++
T Consensus        95 ak~k~~rs  102 (102)
T d2cpxa1          95 GKNKKQRS  102 (102)
T ss_dssp             CCCCSCCC
T ss_pred             CCCcccCC
Confidence            99887653

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=4.5e-19  Score=135.98  Aligned_cols=83  Identities=31%  Similarity=0.499  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||||||+++++++|+++|++||.|..++                          +++++.+++++|||||+|.+.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~--------------------------~~~d~~tg~~kg~afV~f~~~   61 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTH--------------------------MPKDRVTGQHQGYGFVEFLSE   61 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCBCSSSCSBCSCEEEEESSH
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccc--------------------------eeecccccccccceEEEECCH
Confidence            467999999999999999999999999998887                          778888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ++|.+|+..|||..|+|+.|+|.++.++.
T Consensus        62 ~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~   90 (93)
T d1x5ua1          62 EDADYAIKIMDMIKLYGKPIRVNKASAHN   90 (93)
T ss_dssp             HHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             HHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            99999999999999999999999998765

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2e-19  Score=136.78  Aligned_cols=84  Identities=30%  Similarity=0.485  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||||||+++++++|+++|++||+|..+.                          ++++..+++++|||||.|.+.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~d~~~~~~kg~afV~f~~~   57 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQ--------------------------IPLDYETEKHRGFAFVEFELA   57 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEE--------------------------CCCCSSSCCCSSEEEECCSSH
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecc--------------------------cccccccccccceeEEEECCH
Confidence            468999999999999999999999999998887                          778888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|.+|+..|||..|+|+.|+|.++.++..
T Consensus        58 ~~A~~ai~~l~~~~i~g~~l~v~~a~p~~~   87 (89)
T d2cqba1          58 EDAAAAIDNMNESELFGRTIRVNLAKPMRI   87 (89)
T ss_dssp             HHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             HHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            999999999999999999999999986543

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=7.7e-20  Score=134.51  Aligned_cols=75  Identities=24%  Similarity=0.457  Sum_probs=72.0

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      +|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||. ++++.++|+.|.|.+|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999998 6888999999999876

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=5e-19  Score=131.44  Aligned_cols=76  Identities=25%  Similarity=0.512  Sum_probs=73.3

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ++|||+|||+.+|+++|+++|+.||.|..+.+..++.++.++|||||+|.+.++|.+|+. |+|..|+||+|+|++|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            489999999999999999999999999999999999999999999999999999999997 8999999999999987

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.2e-19  Score=136.53  Aligned_cols=80  Identities=30%  Similarity=0.537  Sum_probs=75.0

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      .+|||+|||+.+++++|+++|+.||.|..++|+++.  +.++|||||+|.+.++|.+|+..|||..++|++|+|.+|+++
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            489999999999999999999999999999999885  447899999999999999999999999999999999999977


Q ss_pred             cc
Q 017842          360 QR  361 (365)
Q Consensus       360 ~~  361 (365)
                      ..
T Consensus        87 ~~   88 (89)
T d1cvja2          87 KE   88 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=9.3e-19  Score=134.18  Aligned_cols=83  Identities=24%  Similarity=0.405  Sum_probs=77.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..+||||+|||+++++++|+++|++||.|.++.                          ++.++.+++++|||||+|.+.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~kg~afV~f~~~   59 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKII--------------------------MGLDKMKKTACGFCFVEYYSR   59 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTCCEEEEEEEEESSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceec--------------------------cccccccccccceEEEEECCH
Confidence            567999999999999999999999999999987                          788888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ++|..|+..|||..++|+.|+|.++....
T Consensus        60 ~~A~~Ai~~l~g~~~~gr~i~V~~a~~~~   88 (93)
T d1h2vz_          60 ADAENAMRYINGTRLDDRIIRTDWDAGFK   88 (93)
T ss_dssp             HHHHHHHHHTTTSEETTEECEEEEESCCC
T ss_pred             HHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            99999999999999999999999986543

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=9e-19  Score=130.96  Aligned_cols=80  Identities=28%  Similarity=0.520  Sum_probs=75.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||+|||+++++++|+++|++||.|..++                          ++++..+++++|||||+|.+.+
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~--------------------------i~~~~~~~~~~g~afv~f~~~~   55 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCK--------------------------LVRDKITGQSLGYGFVNYIDPK   55 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------EEECTTTCCEEEEEEEEESSHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCccccc--------------------------ceeeccCCCceeeEEEEECCHH
Confidence            35799999999999999999999999999887                          7778889999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      +|.+|+..|||..|+|+.|+|.++.|
T Consensus        56 ~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          56 DAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            99999999999999999999999875

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.77  E-value=6.8e-19  Score=133.55  Aligned_cols=83  Identities=22%  Similarity=0.300  Sum_probs=77.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      .+.++|||+|||+++++++|+++|+.||.|..++                          +++++.+|+++|||||+|.+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~--------------------------i~~d~~tg~~~g~afV~f~~   58 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIH--------------------------LNLDRRTGFSKGYALVEYET   58 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTSSEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccccc--------------------------ccccccccccccceeEEECC
Confidence            3567999999999999999999999999999887                          78888899999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      .++|.+|+..|||..++|+.|+|.++.++
T Consensus        59 ~~~A~~A~~~lng~~l~g~~l~V~~a~~k   87 (88)
T d1rk8a_          59 HKQALAAKEALNGAEIMGQTIQVDWCFVK   87 (88)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             HHHHHHHHHHcCCCEECCEEEEEEEecCC
Confidence            99999999999999999999999998765

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=6e-19  Score=132.65  Aligned_cols=79  Identities=39%  Similarity=0.639  Sum_probs=74.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||||||+++++++|+++|++||.|..++                          ++++..+|+++|||||+|.+.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~d~~tg~~kG~afV~f~~~   58 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV--------------------------VMRDPNTKRSRGFGFVTYATV   58 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTCCEEEEEEEEESSH
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhcccccee--------------------------ecccccCCCcccEEEEEEcCH
Confidence            457999999999999999999999999999887                          788899999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      ++|.+|+.. ++..|+||.|+|.+|.
T Consensus        59 ~~a~~ai~~-~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          59 EEVDAAMNA-RPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             HHHHHHHHT-CSCEETTEECEEEECC
T ss_pred             HHHHHHHHh-CCCEECCEEEEEEeee
Confidence            999999986 9999999999999875

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=2.9e-19  Score=131.30  Aligned_cols=75  Identities=29%  Similarity=0.570  Sum_probs=72.7

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      +|||+|||+.+|+++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|++ |||+.|+||+|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999997 9999999999999986

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=1.5e-18  Score=134.51  Aligned_cols=86  Identities=29%  Similarity=0.395  Sum_probs=79.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|.+||.|..++                          ++.+..+++++|||||+|.+.
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~--------------------------i~~d~~tg~~~g~afV~f~~~   60 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELH--------------------------YPIDSLTKKPKGFAFVTFMFP   60 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCCCTTTCCCCSEEEEEESSH
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeee--------------------------ecccccccccCcceEEEECCH
Confidence            456899999999999999999999999998887                          777888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      ++|.+|+..|||..|+|+.|+|.++.++....
T Consensus        61 ~~a~~A~~~l~g~~~~gr~i~V~~a~~~~~~~   92 (99)
T d1whwa_          61 EHAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS   92 (99)
T ss_dssp             HHHHHHHHHTTTEESSSCEEEEEECCCCSTTC
T ss_pred             HHHHHHHHHcCCCEECCEEEEEEECCCCCccC
Confidence            99999999999999999999999998765443

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2e-18  Score=134.62  Aligned_cols=85  Identities=28%  Similarity=0.487  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ++.++|||+|||+++++++|+++|+.||.|..+.                          ++.+..+++++|||||+|.+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~--------------------------~~~~~~~g~~kG~afV~f~~   69 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAK--------------------------VFIDKQTNLSKCFGFVSYDN   69 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEE--------------------------EEECSSSCSEEEEEEEECSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccc--------------------------eeeecccCCCccceEEEeCC
Confidence            3567899999999999999999999999998887                          78888899999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      .++|..|+..|||..|+|+.|+|.++.++..
T Consensus        70 ~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~~  100 (102)
T d2cpza1          70 PVSAQAAIQSMNGFQIGMKRLKVQLKRSKND  100 (102)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEECCCCSCC
T ss_pred             HHHHHHHHHHhCCCEECCEEEEEEEeCCCCC
Confidence            9999999999999999999999999987654

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.1e-18  Score=130.85  Aligned_cols=78  Identities=31%  Similarity=0.515  Sum_probs=73.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +.+.++|||+|||+++|+++|+++|++||.|..+.                          ++++..+++++|||||+|.
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~~~~g~afV~f~   59 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVS--------------------------IVYDQQSRRSRGFAFVYFE   59 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEE--------------------------EEECSSSSSEEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCcccc--------------------------ccccccccccccceEEEEC
Confidence            44578999999999999999999999999999887                          7788889999999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEE
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTV  259 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V  259 (365)
                      +.++|.+|+..|||..|+|+.|+|
T Consensus        60 ~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          60 NVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             SHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CHHHHHHHHHHcCCCEECCEEeEC
Confidence            999999999999999999999987

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=9.7e-19  Score=134.85  Aligned_cols=77  Identities=21%  Similarity=0.519  Sum_probs=72.5

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||..+++++|+++|+.||.|..|+|+++      +|||||+|.+.++|.+|+..|||..|.|++|+|.|+++
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            458999999999999999999999999999999865      89999999999999999999999999999999999987


Q ss_pred             ccc
Q 017842          359 RQR  361 (365)
Q Consensus       359 ~~~  361 (365)
                      ++.
T Consensus        92 ~p~   94 (96)
T d1x4ga1          92 SPD   94 (96)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            653

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.2e-18  Score=138.56  Aligned_cols=79  Identities=22%  Similarity=0.347  Sum_probs=73.2

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      .+++|||+|||+.+++++|+++|+.||.|..|++..+   +.++|||||+|.+.++|..|++.|||..|.||.|+|.|+.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3459999999999999999999999999999999854   5679999999999999999999999999999999999987


Q ss_pred             cc
Q 017842          358 DR  359 (365)
Q Consensus       358 ~~  359 (365)
                      ..
T Consensus        83 ~~   84 (114)
T d2f9da1          83 AN   84 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.1e-18  Score=132.88  Aligned_cols=83  Identities=27%  Similarity=0.433  Sum_probs=77.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +..+|||+|||.++++++|+.+|++||.|..++                          +..+..++.++|||||.|.+.
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~--------------------------i~~d~~t~~~rg~afV~f~~~   60 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIY--------------------------LAKDKTTGQSKGFAFISFHRR   60 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEE--------------------------EEECSSSCSEEEEEEEEESSH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccccc--------------------------ccccccccccccceeEEECCH
Confidence            457899999999999999999999999998887                          778888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ++|.+|+..|||..|+|+.|+|.++.|+.
T Consensus        61 ~~A~~Ai~~l~g~~~~g~~i~v~~akp~~   89 (90)
T d2cq0a1          61 EDAARAIAGVSGFGYDHLILNVEWAKPST   89 (90)
T ss_dssp             HHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             HHHHHHHHHhCCCEECCEEEEEEeeeCCC
Confidence            99999999999999999999999998753

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.2e-18  Score=129.80  Aligned_cols=77  Identities=27%  Similarity=0.387  Sum_probs=73.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      +|||||||+++++++|+++|++||.|..++                          +++++.+++++|||||+|.+.++|
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~--------------------------i~~d~~tg~~~g~aFV~f~~~~~a   55 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIR--------------------------VCRDMITRRSLGYAYVNFQQPADA   55 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTCCEEEEEEEEESSHHHH
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEE--------------------------EEecccccCCCCceEEEECCHHHH
Confidence            699999999999999999999999999887                          888889999999999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEeecC
Q 017842          241 EKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      .+|+..|||..++|+.|+|.++.
T Consensus        56 ~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1          56 ERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             HHHHTTSTTCEETTEECEEEECC
T ss_pred             HHHHHHcCCCEECCEEEEEEEeC
Confidence            99999999999999999999874

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.9e-18  Score=131.56  Aligned_cols=84  Identities=37%  Similarity=0.700  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||||||+++++++|+++|+.||.|..+.                          ++.+..++.++|||||+|.+.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~--------------------------~~~~~~~~~~~g~afV~f~~~   57 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVV--------------------------VVKDRETQRSRGFGFVTFENI   57 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEE--------------------------ECCCSSSCSCCSEEEEECSSH
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhcccccccee--------------------------eccccccccccceEEEEECCH
Confidence            467899999999999999999999999998876                          677778899999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|.+|+..|||..|+|+.|+|.++.++..
T Consensus        58 ~~a~~Ai~~l~~~~~~g~~l~V~~a~~~~~   87 (90)
T d1x5sa1          58 DDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   87 (90)
T ss_dssp             HHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             HHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            999999999999999999999999876543

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.76  E-value=9.6e-19  Score=130.54  Aligned_cols=80  Identities=20%  Similarity=0.387  Sum_probs=68.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      ++||||+|||+++|+++|+++|++||.|..+.                          ++.+...|.++|||||+|.+.+
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~--------------------------~~~~~~~~~~~g~afV~f~~~e   54 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSI--------------------------RLPSLRFNTSRRFAYIDVTSKE   54 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEE--------------------------ECC-------CCEEEEECSSHH
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeee--------------------------eecccccccccceeEEEECCHH
Confidence            36999999999999999999999999997765                          5666778899999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      +|.+|+..|||..++|++|+|.++.|
T Consensus        55 ~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1          55 DARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHHHHHhCCCEECCEEEEEEEccC
Confidence            99999999999999999999999876

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=3.7e-18  Score=129.94  Aligned_cols=83  Identities=24%  Similarity=0.366  Sum_probs=74.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      .+.++|||||||.++++++|+++|+.||.|..+.                          ++++..+  .+|||||+|.+
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~d~~~--~~~~afV~f~~   57 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCK--------------------------MITEHTS--NDPYCFVEFYE   57 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEE--------------------------EECCCCS--SCCEEEEEESS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeee--------------------------eecccCc--cceeeEEEECC
Confidence            3578999999999999999999999999998877                          5555544  37999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      .++|.+|+..|||..|.|+.|+|.++.++..
T Consensus        58 ~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~   88 (90)
T d2cqia1          58 HRDAAAALAAMNGRKILGKEVKVNWATTPSS   88 (90)
T ss_dssp             HHHHHHHHHHHTTEEETTEEEEEEECCCTTC
T ss_pred             HHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            9999999999999999999999999986543

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.3e-18  Score=131.00  Aligned_cols=81  Identities=20%  Similarity=0.430  Sum_probs=76.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      .+|||||||+++++++|+++|++||+|..++                          +++++.+|.++|||||+|.+.++
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~--------------------------i~~d~~tg~~rg~aFV~f~~~~~   55 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFN--------------------------LVKDSATGLSKGYAFCEYVDINV   55 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEE--------------------------EECCCSSSCCCCEEEEEESSSHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEE--------------------------eeccccccccceeEEEEECCHHH
Confidence            4799999999999999999999999999887                          78888999999999999999999


Q ss_pred             HHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      |..|+..|||..|+|+.|+|.++.+..
T Consensus        56 A~~a~~~l~~~~l~g~~l~V~~A~~~~   82 (85)
T d2u2fa_          56 TDQAIAGLNGMQLGDKKLLVQRASVGA   82 (85)
T ss_dssp             HHHHHHTSSSCCCSSSCCEEEECCCCC
T ss_pred             HHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            999999999999999999999997654

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.75  E-value=6.5e-18  Score=139.09  Aligned_cols=87  Identities=32%  Similarity=0.535  Sum_probs=80.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||||||+++++++|+++|+.||.|..++                          ++.+..+++++|||||+|.+
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~d~~t~~~rg~afV~f~~   93 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVK--------------------------IVCDRETRQSRGYGFVKFQS   93 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEE--------------------------EEEETTTTEEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccc--------------------------cccccccccccceeeEEECC
Confidence            3467899999999999999999999999999887                          78888899999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQP  269 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~  269 (365)
                      .++|.+|+..|||..|+||.|+|.++.++..++
T Consensus        94 ~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~~~p  126 (139)
T d1u6fa1          94 GSSAQQAIAGLNGFNILNKRLKVALAASGHQRP  126 (139)
T ss_dssp             HHHHHHHHHHTTTEECSSCEEEEEESSCCCCCC
T ss_pred             HHHHHHHHHHhCCCEECCEEEEEEEcCCCCCCC
Confidence            999999999999999999999999998766543

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.5e-18  Score=132.25  Aligned_cols=80  Identities=29%  Similarity=0.503  Sum_probs=73.4

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      +.++|||+|||+.+++++|+++|+.||.|..+.+.++   +.++|||||+|.+.++|.+||+.|||..|.|++|+|+||+
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            4458999999999999999999999999999988654   4578999999999999999999999999999999999998


Q ss_pred             ccc
Q 017842          358 DRQ  360 (365)
Q Consensus       358 ~~~  360 (365)
                      +..
T Consensus        90 ~~r   92 (95)
T d1x4aa1          90 SGR   92 (95)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.75  E-value=3.5e-18  Score=128.66  Aligned_cols=79  Identities=30%  Similarity=0.538  Sum_probs=73.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|++||.|..++                          +++++.+++++|||||+|.+.
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~--------------------------~~~d~~~g~~~g~afV~f~~~   58 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN--------------------------ILRDKLTGRPRGVAFVRYNKR   58 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEE--------------------------EEECTTTCCEEEEEEEEESSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeee--------------------------eecccccccCceeEEEEECCH
Confidence            467899999999999999999999999999887                          788888999999999999999


Q ss_pred             HHHHHHHHHHccCcccC--eeEEEeec
Q 017842          238 EEAEKAVEMFHRYDIDG--RLLTVNKA  262 (365)
Q Consensus       238 e~a~~Al~~lng~~~~g--r~l~V~~a  262 (365)
                      ++|.+|++.|||..+.|  ++|+|.+|
T Consensus        59 ~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          59 EEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             HHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            99999999999999977  88999875

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=3.4e-18  Score=128.76  Aligned_cols=77  Identities=16%  Similarity=0.272  Sum_probs=72.4

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      ++|||+|||+.+|+++|+++|+.||.|..|+|.++. +|+++|||||+|.+.++|.+||+ ++|..+.||.|+|.+.++
T Consensus         7 rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~d   83 (85)
T d1zh5a2           7 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   83 (85)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGGG
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcCC
Confidence            489999999999999999999999999999998874 78999999999999999999997 899999999999998653

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=3.9e-18  Score=128.66  Aligned_cols=79  Identities=29%  Similarity=0.402  Sum_probs=72.4

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..+++.+      ++|||||+|.+.++|..|+..|||..|.|++|+|+||++
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            35899999999999999999999999998887753      489999999999999999999999999999999999998


Q ss_pred             cccCC
Q 017842          359 RQRRS  363 (365)
Q Consensus       359 ~~~~~  363 (365)
                      +.+.+
T Consensus        82 ~~~~s   86 (86)
T d2cpda1          82 VDKDS   86 (86)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87753

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=5.9e-18  Score=128.76  Aligned_cols=82  Identities=28%  Similarity=0.447  Sum_probs=74.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++|+++|+++|++||.|..++                          +++++.+|+++|||||.|.+.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~d~~tg~srG~aFV~f~~~   60 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQ--------------------------VKKDLKTGHSKGFGFVRFTEY   60 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEE--------------------------EEECSSSCSEEEEEEEEESSH
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceee--------------------------eccCCCCcccCCEEEEEECCH
Confidence            467899999999999999999999999999988                          888888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|.+|+..  +..|+|+.|.|.++.++..
T Consensus        61 ~~a~~al~~--~~~l~Gr~i~v~~a~~k~~   88 (90)
T d2cqga1          61 ETQVKVMSQ--RHMIDGRWCDCKLPNSKQS   88 (90)
T ss_dssp             HHHHHHHHS--CEEETTEEEEEECCCTTCC
T ss_pred             HHHHHHHhc--CCccCCEEeEEEeCCCCCC
Confidence            999999984  4578999999999887654

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1.1e-18  Score=129.92  Aligned_cols=78  Identities=27%  Similarity=0.494  Sum_probs=71.6

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCC-ccCCeeEEEEEccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQ-NLDGRAIRVNVAED  358 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~-~l~gr~l~V~~a~~  358 (365)
                      ++|||+|||+.+|+++|+++|+.||.|..+++.+.      +|||||+|.+.++|.+|++.|||. .+.|++|+|.||.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            37999999999999999999999999988877754      799999999999999999999996 69999999999998


Q ss_pred             cccCC
Q 017842          359 RQRRS  363 (365)
Q Consensus       359 ~~~~~  363 (365)
                      +..++
T Consensus        76 k~~rs   80 (80)
T d2cqha1          76 KKLRS   80 (80)
T ss_dssp             CCCCC
T ss_pred             cCcCC
Confidence            87754

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=6.8e-18  Score=129.54  Aligned_cols=83  Identities=28%  Similarity=0.481  Sum_probs=75.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecC-CCCCccceEEEEeCC
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR-ETDRSRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~g~afV~f~~  236 (365)
                      ..++|||+|||+++++++|+.+|+.||.|..++                          ++.+. .+|+++|||||.|.+
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~--------------------------i~~~~~~~g~~rg~afV~f~~   60 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVR--------------------------LPKKMTGTGAHRGFGFVDFIT   60 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCCCCSSSCSSCSEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEE--------------------------EEeccccCCCcccEEEEEECC
Confidence            567899999999999999999999999998887                          55543 478999999999999


Q ss_pred             HHHHHHHHHHH-ccCcccCeeEEEeecCCCC
Q 017842          237 VEEAEKAVEMF-HRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       237 ~e~a~~Al~~l-ng~~~~gr~l~V~~a~~~~  266 (365)
                      .++|.+|+..| ||..|.|+.|+|.++....
T Consensus        61 ~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~~   91 (94)
T d2cpha1          61 KQDAKKAFNALCHSTHLYGRRLVLEWADSEV   91 (94)
T ss_dssp             HHHHHHHHHHHHTCCBSSSCBCEEEECCCCC
T ss_pred             HHHHHHHHHHccCCcEECCEEEEEEEcCCCC
Confidence            99999999988 8999999999999998654

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.3e-18  Score=133.09  Aligned_cols=84  Identities=26%  Similarity=0.588  Sum_probs=74.8

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeC-CCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDR-ETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~-~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      .+.++|||+|||+.+++++|+++|+.|| |..++++++. .+++++|||||+|.+.++|.+|+. ||+..|.||+|+|.|
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            4567999999999999999999999998 7888877765 468899999999999999987776 999999999999999


Q ss_pred             ccccccC
Q 017842          356 AEDRQRR  362 (365)
Q Consensus       356 a~~~~~~  362 (365)
                      |.++...
T Consensus        91 a~~~~~~   97 (104)
T d1wi8a_          91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9977653

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.74  E-value=3.8e-18  Score=127.89  Aligned_cols=78  Identities=26%  Similarity=0.431  Sum_probs=71.0

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc-CCeeEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL-DGRAIRVN  354 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l-~gr~l~V~  354 (365)
                      .+|+++|||+|||..+++++|+.+|+.||.|..|++++++     +|||||+|.+.++|..|+..|||..+ +|++|+|.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            4556799999999999999999999999999999998552     78999999999999999999999988 57999999


Q ss_pred             Eccc
Q 017842          355 VAED  358 (365)
Q Consensus       355 ~a~~  358 (365)
                      ||+.
T Consensus        80 ~akk   83 (83)
T d2b0ga1          80 FAKK   83 (83)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            9973

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.5e-18  Score=128.08  Aligned_cols=78  Identities=31%  Similarity=0.501  Sum_probs=72.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      +++|||||||+++++++|+++|++||.|..++                          +++++.+++++|||||+|.+.+
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~--------------------------i~~d~~~g~~kg~afV~f~~~~   59 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSR--------------------------ILVDQVTGVSRGVGFIRFDKRI   59 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTCCEEEEEEEEESSHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccc--------------------------cccccccccCCCeeEEEEcCHH
Confidence            57899999999999999999999999999988                          7888889999999999999999


Q ss_pred             HHHHHHHHHccCcccC--eeEEEeec
Q 017842          239 EAEKAVEMFHRYDIDG--RLLTVNKA  262 (365)
Q Consensus       239 ~a~~Al~~lng~~~~g--r~l~V~~a  262 (365)
                      +|.+|+..|||..+.|  ++|+|.+|
T Consensus        60 ~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          60 EAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             HHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            9999999999999998  55888875

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1.1e-18  Score=136.15  Aligned_cols=82  Identities=34%  Similarity=0.588  Sum_probs=75.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||||||+++++++|+++|.+||.|..+.                          +.++..++.++|||||+|.+.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~--------------------------i~~d~~~~~~kg~aFV~f~~~~   73 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCV--------------------------VMRDPASKRSRGFGFVTFSSMA   73 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEE--------------------------EECCTTTSSCCSEEEEECSSHH
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCccccee--------------------------ecccccCCCccCeEEEEECCHH
Confidence            47899999999999999999999999999988                          7788889999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      +|.+|+.+ +|..|+|+.|.|.++.++..
T Consensus        74 ~a~~al~~-~~~~l~G~~i~V~~a~~ke~  101 (103)
T d1x4ba1          74 EVDAAMAA-RPHSIDGRVVEPKRAVAREE  101 (103)
T ss_dssp             HHHHHHTS-CSEEETTEEEEEECCSSCCC
T ss_pred             HHHHHHHh-CCCeECCEEEEEEECcccCC
Confidence            99999975 99999999999999887653

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2.4e-18  Score=133.87  Aligned_cols=81  Identities=27%  Similarity=0.497  Sum_probs=75.1

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||+|||+.+++++|+++|+.||.|..+++..+ .++.++|||||+|.+.++|.+|+..|||..|.||++.|.+++
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            3469999999999999999999999999999999888 478999999999999999999999999999999999998876


Q ss_pred             cc
Q 017842          358 DR  359 (365)
Q Consensus       358 ~~  359 (365)
                      +-
T Consensus        96 Pl   97 (101)
T d1x5oa1          96 PL   97 (101)
T ss_dssp             CB
T ss_pred             Cc
Confidence            53

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2.4e-18  Score=132.65  Aligned_cols=84  Identities=23%  Similarity=0.287  Sum_probs=75.3

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCC-eEEEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCC--ccCCeeEEEE
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGK-VVNARVVYDRE-TGRSRGFGFVTMSSETELNDAIAALDGQ--NLDGRAIRVN  354 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~-V~~v~i~~d~~-~~~~kG~afV~F~s~~~a~~Al~~l~~~--~l~gr~l~V~  354 (365)
                      +|+|||+|||..+++++|+++|+.||. |..|+++++.. +++++|||||+|.+..+|..|++.|++.  .++|+.|+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999995 99999998854 6889999999999999999999988654  5589999999


Q ss_pred             EccccccC
Q 017842          355 VAEDRQRR  362 (365)
Q Consensus       355 ~a~~~~~~  362 (365)
                      ||+++..+
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99987654

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=3.4e-18  Score=125.63  Aligned_cols=75  Identities=31%  Similarity=0.575  Sum_probs=70.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      +|||||||+++++++|+++|++||.|..+.                          +..+..+++++|||||+|.+.++|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~--------------------------i~~d~~t~~~kg~afV~f~~~~~a   54 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCT--------------------------LKLDPITGRSRGFGFVLFKESESV   54 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCCBTTTTBCCSEEEEEESSHHHH
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccc--------------------------cccCCCCCCcCceEEEEECCHHHH
Confidence            599999999999999999999999999888                          778888999999999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEeec
Q 017842          241 EKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      .+|+.+ ++..|+|+.|+|.+|
T Consensus        55 ~~Al~~-~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_          55 DKVMDQ-KEHKLNGKVIDPKRA   75 (75)
T ss_dssp             HHHHHT-CCCCBTTBCCEECCC
T ss_pred             HHHHhc-CCCEECCCEEEeeEC
Confidence            999984 999999999999764

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2.9e-18  Score=134.16  Aligned_cols=81  Identities=33%  Similarity=0.626  Sum_probs=76.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||+|||+++++++|+++|++||.|..++                          ++.++.+|+++|||||+|.+.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~--------------------------i~~~~~tg~~~g~afV~f~~~~   61 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFR--------------------------LVYDRETGKPKGYGFCEYQDQE   61 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEE--------------------------EEEETTTTEEEEEEEEECSCHH
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccc--------------------------cccccceeccCCceEEEECCHH
Confidence            57899999999999999999999999999887                          7788889999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      +|.+|+..|||..|+|+.|+|.++.+.
T Consensus        62 ~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_          62 TALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             HHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             HHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            999999999999999999999998754

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.74  E-value=3.2e-19  Score=136.21  Aligned_cols=80  Identities=30%  Similarity=0.449  Sum_probs=74.2

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||+|||+.+++++|+++|+.||.|..++|..+ .+|+++|||||+|.+.++|.+||+ |||..+.||+|+|.+|+
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecC
Confidence            4569999999999999999999999999999988755 579999999999999999999997 99999999999999998


Q ss_pred             cc
Q 017842          358 DR  359 (365)
Q Consensus       358 ~~  359 (365)
                      .|
T Consensus        90 ~k   91 (91)
T d1fjeb1          90 GR   91 (91)
T ss_dssp             CS
T ss_pred             CC
Confidence            75

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=8.5e-18  Score=131.21  Aligned_cols=82  Identities=43%  Similarity=0.581  Sum_probs=75.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||||||+.+++++|+++|+.||.|..++                          ++++..+++++|||||+|.+.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~d~~tg~~kg~afV~f~~~   62 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAV--------------------------VITDRQTGKSRGYGFVTMADR   62 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEE--------------------------ESCCSSSCCCCSEEEEEESSH
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhccccccee--------------------------ccccccccccCCeEEEEECCH
Confidence            356899999999999999999999999999887                          778888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ++|.+|++.+|+ .|+||.|+|.++....
T Consensus        63 ~~A~~Ai~~~~~-~l~Gr~l~V~~a~~~~   90 (103)
T d2cqda1          63 AAAERACKDPNP-IIDGRKANVNLAYLGA   90 (103)
T ss_dssp             HHHHHHHTCSSC-EETTEECEEEESTTTC
T ss_pred             HHHHHHHHHCCC-cCCCEEEEEEEcCCCC
Confidence            999999999776 6999999999987654

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=5.8e-18  Score=125.55  Aligned_cols=77  Identities=31%  Similarity=0.537  Sum_probs=71.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||||||+++|+++|+++|++||.|..+.                          +..+..++.++|||||+|.+.+
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~--------------------------~~~~~~~~~~~g~afV~f~~~e   55 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE--------------------------IMTDRGSGKKRGFAFVTFDDHD   55 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEE--------------------------EEECTTTCCEEEEEEEEESSHH
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccc--------------------------cccCCCCcccccEEEEEEcCHH
Confidence            47999999999999999999999999999887                          7788889999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeec
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      ++.+|+. ++|..|+||.|+|..|
T Consensus        56 ~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          56 SVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             HHHHHHH-CSCCEETTEECEEEEC
T ss_pred             HHHHHHH-hCCCEECCEEEEEEEC
Confidence            9999997 5999999999999876

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=3.5e-18  Score=128.93  Aligned_cols=77  Identities=30%  Similarity=0.526  Sum_probs=71.9

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||+|||..+++++|+++|+.||.|..|++.++      +|||||+|.+.++|.+|+..|||..|.|++|+|+||.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3458999999999999999999999999999999855      7899999999999999999999999999999999998


Q ss_pred             ccc
Q 017842          358 DRQ  360 (365)
Q Consensus       358 ~~~  360 (365)
                      ...
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            764

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=8.6e-18  Score=130.57  Aligned_cols=94  Identities=23%  Similarity=0.387  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+++|..||.|..+.+.                  ......+..+..+++++|||||+|.+
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~------------------~~~~~~~~~d~~~~~~~g~afV~f~~   67 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRT------------------GQPMIHIYLDKETGKPKGDATVSYED   67 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSS------------------CCBSEECCBCTTTCSBCSEEEEEBSS
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeec------------------ccceeEEeeccccccccceeeEEecC
Confidence            357899999999999999999999999988543211                  01112256677889999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      .++|.+|+..|||..|+||.|+|.++.++.+.
T Consensus        68 ~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          68 PPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM   99 (101)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEECSSCCCCS
T ss_pred             HHHHHHHHHHhCCCEECCEEEEEEEcCCCCCC
Confidence            99999999999999999999999999876543

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=4.1e-18  Score=127.63  Aligned_cols=80  Identities=23%  Similarity=0.461  Sum_probs=73.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHHccCCeEEE-EEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          162 LFVGNLPYDVDSEKLAMLFEKAGTVEIA-EVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       162 vfVgnLp~~~t~~~L~~~F~~~G~i~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      |||+|||+++++++|+++|++||.|..+ +                          ++++..+++++|||||+|.+.++|
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~--------------------------i~~~~~~g~~~g~afV~f~~~~~a   54 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPK--------------------------IMRDPDTGNSKGYAFINFASFDAS   54 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCE--------------------------ECCCTTTCSCCSEEEEEBSSHHHH
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEE--------------------------EEeeccccccCceEEEEECCHHHH
Confidence            7999999999999999999999998543 3                          677888999999999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          241 EKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      .+|+..|+|..++|+.|+|.++.++..
T Consensus        55 ~~Ai~~~~g~~~~gr~l~v~~a~~k~~   81 (83)
T d1x5ta1          55 DAAIEAMNGQYLCNRPITVSYAFKKDS   81 (83)
T ss_dssp             HHHHHTTTTCEETTEECEEEESCCCCC
T ss_pred             HHHHHhCCCcEECCEEEEEEEecCCCc
Confidence            999999999999999999999887643

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=8.9e-18  Score=127.22  Aligned_cols=80  Identities=25%  Similarity=0.473  Sum_probs=71.6

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc-CCeeEEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL-DGRAIRVN  354 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l-~gr~l~V~  354 (365)
                      .+|.++|||+|||+.+++++|+++|+.||.|..+++..+    +++|||||+|.+.++|.+|+..|||..+ .||+|+|+
T Consensus         7 ~pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~   82 (88)
T d2adca2           7 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS   82 (88)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEE
Confidence            355679999999999999999999999999988877643    4588999999999999999999999988 58999999


Q ss_pred             Ecccc
Q 017842          355 VAEDR  359 (365)
Q Consensus       355 ~a~~~  359 (365)
                      |++++
T Consensus        83 ~sk~~   87 (88)
T d2adca2          83 FSKST   87 (88)
T ss_dssp             ECSSC
T ss_pred             eCCCC
Confidence            99864

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=1.8e-18  Score=127.71  Aligned_cols=76  Identities=32%  Similarity=0.529  Sum_probs=71.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      ++|||||||+++++++|+++|++||.|..++                          +++++.+++++|||||+|.+.++
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~--------------------------i~~d~~tg~~kG~aFV~f~~~~~   54 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECL--------------------------VMRDPLTKRSRGFGFVTFMDQAG   54 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEE--------------------------EECCCCSSSCSSEEEECCCCTTH
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceee--------------------------eecccCCCCccceEEEEECCHHH
Confidence            4799999999999999999999999998887                          78888999999999999999999


Q ss_pred             HHHHHHHHccCcccCeeEEEeec
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      |.+|+.+ |+..++||.|+|..|
T Consensus        55 a~~al~~-~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          55 VDKVLAQ-SRHELDSKTIDPKVA   76 (77)
T ss_dssp             HHHHHHT-TTCCCSSCCCEEEEC
T ss_pred             HHHHHHc-CCCEECCeEEEEEEC
Confidence            9999985 999999999999875

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=1.4e-17  Score=128.53  Aligned_cols=84  Identities=29%  Similarity=0.519  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||||||+++++++|+++|++||.|..+.                          ++.+..+++++|||||+|.+
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~--------------------------~~~~~~~~~~~g~afV~F~~   59 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVR--------------------------VVLHPDTEHSKGCAFAQFMT   59 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------CCBCSSSCCBCSEEEEEESS
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeee--------------------------eccccccccccceEEEEEcC
Confidence            3578999999999999999999999999998877                          67777889999999999999


Q ss_pred             HHHHHHHHHHHc------cCcccCeeEEEeecCCCC
Q 017842          237 VEEAEKAVEMFH------RYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       237 ~e~a~~Al~~ln------g~~~~gr~l~V~~a~~~~  266 (365)
                      .++|.+|+..||      |..++||.|+|.++.++.
T Consensus        60 ~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          60 QEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD   95 (98)
T ss_dssp             HHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCC
T ss_pred             HHHHHHHHHHcccccccCCcEECCEEEEEEECCCCC
Confidence            999999999886      677899999999988754

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=8.1e-18  Score=124.52  Aligned_cols=76  Identities=32%  Similarity=0.501  Sum_probs=70.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      +|||+|||+++++++|+++|++||.|..++                          +..+. +++++|||||+|.+.++|
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~--------------------------i~~~~-~g~~~g~afV~f~~~~~A   54 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAA--------------------------VHYDR-SGRSLGTADVHFERKADA   54 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEE--------------------------ESCSS-CCCSCCEEEEEESCHHHH
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEE--------------------------EEEee-ccccceeEEEEECCHHHH
Confidence            699999999999999999999999999887                          55554 788999999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEeecC
Q 017842          241 EKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      .+|+..|||..++|+.|+|.++.
T Consensus        55 ~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_          55 LKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             HHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHhCCCEECCEEEEEEEee
Confidence            99999999999999999999875

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=3.9e-18  Score=132.61  Aligned_cols=79  Identities=19%  Similarity=0.357  Sum_probs=73.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||||||+++++++|+++|+.||.|..++                          ++++..+|+++|||||+|.+.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~--------------------------i~~d~~tg~~kG~afV~F~~~e   71 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVR--------------------------IISDRNSRRSKGIAYVEFCEIQ   71 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEE--------------------------ECCSCCSSSCCCCEEEEESCGG
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEE--------------------------eeecCCCccccceEEEEECCHH
Confidence            47999999999999999999999999999887                          7888889999999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      +|.+|+. |||..|+|+.|+|.++.+
T Consensus        72 ~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          72 SVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             GHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             HHHHHHH-HCCCEECCEEEEEEECCC
Confidence            9999996 799999999999998753

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=4.6e-18  Score=128.25  Aligned_cols=79  Identities=19%  Similarity=0.276  Sum_probs=71.6

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ..++|||+|||+.+++++|+++|+.||.|....++.+..+++++|||||+|.+.++|.+|+..|||..|.||+|+|.+|
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4468999999999999999999999999877544455578999999999999999999999999999999999999985

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=8.3e-18  Score=132.90  Aligned_cols=77  Identities=17%  Similarity=0.092  Sum_probs=71.1

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.||.|..|.|.      ..+|||||+|.+.++|.+|+..|||..|.||+|+|.||..
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            4589999999999999999999999999999884      3489999999999999999999999999999999999986


Q ss_pred             ccc
Q 017842          359 RQR  361 (365)
Q Consensus       359 ~~~  361 (365)
                      ...
T Consensus        84 ~~~   86 (111)
T d1whxa_          84 GVF   86 (111)
T ss_dssp             TTT
T ss_pred             Ccc
Confidence            654

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=3.2e-17  Score=125.43  Aligned_cols=81  Identities=33%  Similarity=0.602  Sum_probs=73.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|+.||.|..+.                          ++.+.  +.++|||||+|.+.
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~--------------------------~~~~~--~~~kg~afV~f~~~   61 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE--------------------------IIFNE--RGSKGFGFVTFENS   61 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEE--------------------------EECCT--TTTCCEEEEEESCH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcceeeecc--------------------------ccccc--cCCcceeEEEECCH
Confidence            467899999999999999999999999998887                          55553  34689999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ++|.+|+..|||..|+|+.|+|.++.++.
T Consensus        62 ~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~   90 (93)
T d2cq3a1          62 ADADRAREKLHGTVVEGRKIEVNNATARV   90 (93)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEEECCSSC
T ss_pred             HHHHHHHHHcCCCEECCEEEEEEecCcCC
Confidence            99999999999999999999999998764

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.72  E-value=7.7e-18  Score=129.73  Aligned_cols=82  Identities=17%  Similarity=0.424  Sum_probs=73.4

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .+.++|||+|||+.+++++|+++|+.||.|..++.     +++++|||||+|.+.++|.+|+..|||..|.||+|+|.||
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34569999999999999999999999998766542     5788999999999999999999999999999999999999


Q ss_pred             cccccCC
Q 017842          357 EDRQRRS  363 (365)
Q Consensus       357 ~~~~~~~  363 (365)
                      .++...+
T Consensus        89 ~~k~~~r   95 (96)
T d1fjca_          89 GEKGGTR   95 (96)
T ss_dssp             SSSCCCC
T ss_pred             CCCCCCC
Confidence            9887543

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=1.6e-17  Score=124.97  Aligned_cols=78  Identities=29%  Similarity=0.502  Sum_probs=69.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCC---CccceEEEEeCCHH
Q 017842          162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETD---RSRGFGFVTMSTVE  238 (365)
Q Consensus       162 vfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~g~afV~f~~~e  238 (365)
                      |||+|||+++++++|+.+|++||.|..+.                          ++.+..++   +++|||||+|.+.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~--------------------------i~~~~~~~~~~~~kG~afV~f~~~~   54 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCT--------------------------ISKKKNKAGVLLSMGFGFVEYKKPE   54 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------EEEEECTTCCEEEEEEEEEEESSHH
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccc--------------------------eecccccccccccceEEEEEECCHH
Confidence            79999999999999999999999999988                          44444443   57899999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      +|.+|+..|||..++|+.|+|.++...
T Consensus        55 ~A~~A~~~~~~~~~~g~~i~V~~a~~~   81 (85)
T d2cpfa1          55 QAQKALKQLQGHTVDGHKLEVRISERA   81 (85)
T ss_dssp             HHHHHHHHSTTCEETTEECEEECSSCS
T ss_pred             HHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            999999999999999999999998543

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=6.4e-18  Score=128.88  Aligned_cols=80  Identities=23%  Similarity=0.468  Sum_probs=72.2

Q ss_pred             CCceEEEeCCCCcCcHHHHHH----HHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          278 PGFRIYVGNLPWEVDNARLEQ----VFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~----~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      |+++|||+|||+.+++++|++    +|+.||.|..|++.+   ++.++|||||+|.+.++|.+|+..|||..+.|++|+|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            456999999999999998864    689999999998864   4678999999999999999999999999999999999


Q ss_pred             EEccccc
Q 017842          354 NVAEDRQ  360 (365)
Q Consensus       354 ~~a~~~~  360 (365)
                      .||+.+.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9998765

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=8.5e-18  Score=124.73  Aligned_cols=74  Identities=24%  Similarity=0.420  Sum_probs=68.7

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      +++|||+||+  +|+++|+++|+.||.|..|++.++      +|||||+|.+.++|..|+..|||..+.|++|+|.||++
T Consensus         5 ~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   76 (79)
T d2bz2a1           5 GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             CCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCS
T ss_pred             CCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            4599999996  899999999999999999999744      78999999999999999999999999999999999987


Q ss_pred             cc
Q 017842          359 RQ  360 (365)
Q Consensus       359 ~~  360 (365)
                      ++
T Consensus        77 ~P   78 (79)
T d2bz2a1          77 QP   78 (79)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.71  E-value=1.6e-17  Score=121.98  Aligned_cols=74  Identities=16%  Similarity=0.199  Sum_probs=68.6

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ++|||+|||+.+++++|+++|+.||.|..|++++++.+  ++|||||+|.+.++|.+|+. +|++.|+|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            48999999999999999999999999999999998653  46899999999999999997 8999999999999875

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.71  E-value=6e-18  Score=127.66  Aligned_cols=82  Identities=21%  Similarity=0.325  Sum_probs=69.1

Q ss_pred             CCCeEEEcCCCCCCC-HHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          158 EDAKLFVGNLPYDVD-SEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t-~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ..++|||+|||++++ ++.|+++|++||.|..++|                         ...+..+++++|||||+|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i-------------------------~~~~~~~~~~kg~afV~f~~   57 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINI-------------------------PAGQKEHSFNNCCAFMVFEN   57 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEEC-------------------------CSCCC---CCCEEEEEEESS
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceee-------------------------ecccCCccccceeeeEEECC
Confidence            468999999999986 5569999999999999873                         22345688999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      .++|.+|++ +||..|+|+.|+|.++.++
T Consensus        58 ~~~a~~Al~-~n~~~~~gr~l~V~~a~~k   85 (86)
T d2ghpa3          58 KDSAERALQ-MNRSLLGNREISVSLADKK   85 (86)
T ss_dssp             HHHHHHHGG-GTTEEETTEEEEEEECCCC
T ss_pred             HHHHHHHHh-cCCCEECCEEEEEEEcCCC
Confidence            999999996 7999999999999998764

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=3.4e-17  Score=127.96  Aligned_cols=83  Identities=20%  Similarity=0.219  Sum_probs=76.1

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ...+|||+|||+.+|+++|+++|..+|.|..+.++.+..+++++|||||+|.+.++|.+|+. +|+..|.||.|+|.++.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECC
Confidence            34489999999999999999999999999887777777889999999999999999999997 99999999999999998


Q ss_pred             cccc
Q 017842          358 DRQR  361 (365)
Q Consensus       358 ~~~~  361 (365)
                      .+.-
T Consensus        93 ~~~~   96 (104)
T d1wg5a_          93 RAEV   96 (104)
T ss_dssp             TTTS
T ss_pred             HHHh
Confidence            7653

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=6.1e-18  Score=128.46  Aligned_cols=75  Identities=17%  Similarity=0.301  Sum_probs=69.4

Q ss_pred             ceEEEeCCCCcCcHHHH---HHHHhccCCeEEEEEEeeCCCCCc---ceEEEEEecCHHHHHHHHHHhCCCccCCeeEEE
Q 017842          280 FRIYVGNLPWEVDNARL---EQVFSEHGKVVNARVVYDRETGRS---RGFGFVTMSSETELNDAIAALDGQNLDGRAIRV  353 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L---~~~F~~~G~V~~v~i~~d~~~~~~---kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V  353 (365)
                      ++|||+|||+.+++++|   +++|+.||.|..|.|++++.++.+   +|||||+|.+.++|.+|++.|||..+.||.|+|
T Consensus         9 n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkv   88 (89)
T d2cpia1           9 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA   88 (89)
T ss_dssp             SCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEEE
Confidence            48999999999999999   678999999999999999776544   599999999999999999999999999999998


Q ss_pred             E
Q 017842          354 N  354 (365)
Q Consensus       354 ~  354 (365)
                      +
T Consensus        89 S   89 (89)
T d2cpia1          89 S   89 (89)
T ss_dssp             E
T ss_pred             C
Confidence            5

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=2.9e-18  Score=124.93  Aligned_cols=71  Identities=23%  Similarity=0.509  Sum_probs=68.9

Q ss_pred             EEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEE
Q 017842          282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR  352 (365)
Q Consensus       282 lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~  352 (365)
                      |||+|||+.+|+++|+++|+.||.|..+++.+++.++.++|||||+|.+.++|.+|+..|||..+.||.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999999999999999999999999999999999999999874

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=1.1e-17  Score=122.69  Aligned_cols=75  Identities=36%  Similarity=0.663  Sum_probs=69.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      +|||||||+++|+++|+++|+.||.|..+.                          ++.+..++.++|||||+|.+.++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~--------------------------~~~~~~~~~~~~~afV~F~~~~~a   54 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAM--------------------------LMFDKTTNRHRGFGFVTFESEDIV   54 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEEC--------------------------CBCCTTCTTSCCEEEEECSCHHHH
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceee--------------------------eeeeccccccCceeEEEECCHHHH
Confidence            599999999999999999999999998876                          677778899999999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEeec
Q 017842          241 EKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      .+|++ +||..|+||.|+|.+|
T Consensus        55 ~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          55 EKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             HHHHH-CSSCCBTTBCCEEEEC
T ss_pred             HHHHh-cCCCEECCeEEEEEEC
Confidence            99997 7999999999999875

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=6.6e-18  Score=123.96  Aligned_cols=75  Identities=31%  Similarity=0.448  Sum_probs=69.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      +|||||||+++|+++|+++|++||.|..++                          +..++.+++++|||||+|.+.++|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~--------------------------i~~d~~t~~~rG~~FV~f~~~~~a   54 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIE--------------------------LPMDNKTNKRRGFCFITFKEEEPV   54 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEE--------------------------CCCCTTTCCTTCCEEEEESSSHHH
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCccccc--------------------------ccccccccccccEEEEEECCHHHH
Confidence            599999999999999999999999999887                          778888999999999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEeec
Q 017842          241 EKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      .+|+.. ++..++|+.|.|..|
T Consensus        55 ~~al~~-~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1          55 KKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             HHHTTC-SSCCBTTBCCEEECC
T ss_pred             HHHHhh-CCCEECCEEeEEEEC
Confidence            999986 888899999999864

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=2e-17  Score=127.79  Aligned_cols=76  Identities=32%  Similarity=0.599  Sum_probs=69.1

Q ss_pred             CCCceEEEeCCC-CcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEE
Q 017842          277 EPGFRIYVGNLP-WEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNV  355 (365)
Q Consensus       277 ~~~~~lfV~nLp-~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~  355 (365)
                      ...++|||+||| +.+++++|+++|+.||.|..|+|.        +|||||+|.+.++|.+||..|||..|.|++|+|.|
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            334589999996 678899999999999999999983        79999999999999999999999999999999999


Q ss_pred             ccccc
Q 017842          356 AEDRQ  360 (365)
Q Consensus       356 a~~~~  360 (365)
                      |.++.
T Consensus        85 a~~~~   89 (98)
T d1wf2a_          85 AAEPK   89 (98)
T ss_dssp             TTSCC
T ss_pred             CCCCC
Confidence            98654

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=3.4e-17  Score=130.04  Aligned_cols=105  Identities=21%  Similarity=0.362  Sum_probs=85.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +...++|||||||+++++++|+++|++||.|..|+                          +.   .++.++|||||+|.
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~--------------------------~~---~~~~~kG~afV~f~   54 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIR--------------------------VG---NTPETRGTAYVVYE   54 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEE--------------------------EE---CSTTTTTEEEEEES
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeec--------------------------cc---ccCCcCCeEEEEEC
Confidence            44578999999999999999999999999999877                          33   24567899999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCCCCCCCCCcCCCCceEEEeCCCCcCcHHHHHHHHhccCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQPERAPRVFEPGFRIYVGNLPWEVDNARLEQVFSEHGK  305 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~  305 (365)
                      +.++|..|+..|||..|.|+.|+|.++.......                .......++.+..+.+.||.
T Consensus        55 ~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~~~~----------------~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          55 DIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQ----------------KMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEECCHHHHTT----------------TSCHHHHHHHHHHHHHHHCC
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEEcCCCchhh----------------hhHHHHHHHHHHHHHHHhCC
Confidence            9999999999999999999999999876432211                12223456778888888763

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=2.1e-17  Score=130.16  Aligned_cols=77  Identities=22%  Similarity=0.423  Sum_probs=70.7

Q ss_pred             CceEEEeCCCC-cCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          279 GFRIYVGNLPW-EVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       279 ~~~lfV~nLp~-~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      .++|||+|||+ .+++++|+++|+.||.|..|+|++++     +|||||+|.+.++|.+|+..|||..|.|+.|+|.|++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            35999999965 59999999999999999999998774     7999999999999999999999999999999999997


Q ss_pred             ccc
Q 017842          358 DRQ  360 (365)
Q Consensus       358 ~~~  360 (365)
                      .+.
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1.9e-17  Score=128.98  Aligned_cols=83  Identities=17%  Similarity=0.267  Sum_probs=74.4

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ..+.+|||+|||+.+|+++|+++|..|| |..|+++++. ++.++|||||+|.+.++|.+|+. ||+..|+||.|+|.++
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3456999999999999999999999997 5678888875 58899999999999999999997 8999999999999999


Q ss_pred             cccccC
Q 017842          357 EDRQRR  362 (365)
Q Consensus       357 ~~~~~~  362 (365)
                      ..+...
T Consensus        90 ~~~~~~   95 (102)
T d1weza_          90 STAGTS   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            877654

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=7.7e-17  Score=124.25  Aligned_cols=79  Identities=27%  Similarity=0.410  Sum_probs=72.1

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCC--eeEEEE
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDG--RAIRVN  354 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~g--r~l~V~  354 (365)
                      .|.++|||+|||+.+++++|+++|+.||.|..|++.++      +|||||+|.+.++|.+|++.|||..|.|  ++|+|.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            45679999999999999999999999999999999754      7899999999999999999999999976  589999


Q ss_pred             Ecccccc
Q 017842          355 VAEDRQR  361 (365)
Q Consensus       355 ~a~~~~~  361 (365)
                      ||++.+.
T Consensus        89 ~ak~~~~   95 (97)
T d1whya_          89 FAKSGPS   95 (97)
T ss_dssp             ECCCCCC
T ss_pred             eCCCCCC
Confidence            9987654

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=2.4e-17  Score=125.14  Aligned_cols=80  Identities=28%  Similarity=0.472  Sum_probs=71.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      ..+|||+|||+++++++|+++|+.||.|..++                          ++.+.  +.++|||||+|.+.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~--------------------------i~~~~--~~~kg~afV~f~~~~   59 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCK--------------------------VVCDE--NGSKGYGFVHFETQE   59 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEE--------------------------ECCBT--TBCCSCEEEEESCHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEE--------------------------EEeec--CCCcceeEEEECCHH
Confidence            45899999999999999999999999998887                          45443  346899999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      +|.+|+..|||..|+|+.|+|.++.++.
T Consensus        60 ~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2          60 AAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             HHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             HHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            9999999999999999999999998664

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.6e-17  Score=129.30  Aligned_cols=84  Identities=23%  Similarity=0.366  Sum_probs=76.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +.++|||+|||.++++++|+++|..||.|..+.                          +..+..+|+++|||||+|.+.
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~--------------------------~~~~~~~g~~~g~~fV~f~~~   70 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPP--------------------------IQFRMMTGRMRGQAFITFPNK   70 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSC--------------------------CEEEEECSSSCSEEEEECSSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEE--------------------------eecccccccccccceEEeccH
Confidence            578999999999999999999999999987665                          566667889999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|.+|+..|||..|.|+.|+|.++.++..
T Consensus        71 ~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~~  100 (102)
T d2cpxa1          71 EIAWQALHLVNGYKLYGKILVIEFGKNKKQ  100 (102)
T ss_dssp             HHHHHHHHHSTTCBCSSCBCEEEECCCCSC
T ss_pred             HHHHHHHHHhCCCEECCEEEEEEeCCCccc
Confidence            999999999999999999999999987654

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=2.4e-17  Score=124.77  Aligned_cols=76  Identities=18%  Similarity=0.303  Sum_probs=67.2

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      .++|||+|||+.+++++|+++|+.|| +..+.+      ++.+|||||+|.+.++|.+|+..|||..|.||+|+|+|+++
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            45899999999999999999999999 333333      34589999999999999999999999999999999999987


Q ss_pred             ccc
Q 017842          359 RQR  361 (365)
Q Consensus       359 ~~~  361 (365)
                      +..
T Consensus        78 ~~~   80 (88)
T d1wg1a_          78 DAL   80 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=5.4e-17  Score=126.11  Aligned_cols=80  Identities=24%  Similarity=0.443  Sum_probs=71.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|+.||.|..+.                          +..+ .+++++|||||+|.+.
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~--------------------------~~~~-~~~~~~g~afV~f~~~   69 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTR--------------------------ILRD-SSGTSRGVGFARMEST   69 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEE--------------------------EEEC-SSSCEEEEEEEEESCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccccccee--------------------------eecc-cccccccceeEEeCCH
Confidence            357899999999999999999999999998776                          4444 4788999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      ++|.+|+..|||..|.|+++.|.++.|
T Consensus        70 ~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          70 EKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             HHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             HHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            999999999999999999999977654

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.3e-17  Score=126.30  Aligned_cols=78  Identities=19%  Similarity=0.364  Sum_probs=70.1

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      ..++|||+|||+.+|+++|+++|+.||.|..|++.     +.++|||||+|.+.++|.+|+.  +++.|.|++|+|.+|.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            34599999999999999999999999999999875     3458999999999999999986  8889999999999998


Q ss_pred             ccccC
Q 017842          358 DRQRR  362 (365)
Q Consensus       358 ~~~~~  362 (365)
                      ++...
T Consensus        77 ~k~~~   81 (88)
T d1wf0a_          77 PKHNS   81 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77654

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.9e-17  Score=131.17  Aligned_cols=84  Identities=25%  Similarity=0.453  Sum_probs=75.8

Q ss_pred             cCCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          275 VFEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ....+++|||+|||+.+|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|+. |||..|+||.|.|.
T Consensus        14 ~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~   92 (112)
T d1wela1          14 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   92 (112)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEE
Confidence            34456799999999999999999999999999887777777889999999999999999999997 99999999999999


Q ss_pred             Ecccc
Q 017842          355 VAEDR  359 (365)
Q Consensus       355 ~a~~~  359 (365)
                      .+..+
T Consensus        93 ~~~~~   97 (112)
T d1wela1          93 PITKK   97 (112)
T ss_dssp             EECHH
T ss_pred             EcChH
Confidence            88654

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.1e-17  Score=126.44  Aligned_cols=72  Identities=22%  Similarity=0.282  Sum_probs=67.0

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcccc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDR  359 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~  359 (365)
                      +|||+|||+.+++++|+++|+.||.|..++|.+       +|||||+|.+.++|.+||..|||..|.|+.|+|.++..+
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            799999999999999999999999999999864       389999999999999999999999999999998887644

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.7e-17  Score=129.39  Aligned_cols=81  Identities=20%  Similarity=0.247  Sum_probs=72.7

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ...++|||+|||+.+|+++|+++|..||.|..+.++....+|+++|||||+|.+.++|.+||. |||..|.||.|+|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            344589999999999999999999999998876555565789999999999999999999997 9999999999999987


Q ss_pred             cc
Q 017842          357 ED  358 (365)
Q Consensus       357 ~~  358 (365)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            64

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=6.9e-17  Score=127.04  Aligned_cols=79  Identities=25%  Similarity=0.354  Sum_probs=71.9

Q ss_pred             CCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc--CCeeEEEEE
Q 017842          278 PGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL--DGRAIRVNV  355 (365)
Q Consensus       278 ~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l--~gr~l~V~~  355 (365)
                      +..+|||+|||+.+|+++|+++|+.||.|..|.|.+++    .+|||||+|.+.++|..|+..|||..|  .|++|+|.|
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            34589999999999999999999999999999998774    489999999999999999999999988  578999999


Q ss_pred             ccccc
Q 017842          356 AEDRQ  360 (365)
Q Consensus       356 a~~~~  360 (365)
                      ++.+.
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            87654

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=7.9e-17  Score=124.42  Aligned_cols=79  Identities=23%  Similarity=0.308  Sum_probs=72.0

Q ss_pred             CCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          277 EPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       277 ~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ...++|||+|||+.+++++|+++|+.||.|..|.|.+       +|||||+|.+.++|.+||+.|||..|.|+.|+|.|+
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            3456899999999999999999999999999999863       589999999999999999999999999999999999


Q ss_pred             cccccC
Q 017842          357 EDRQRR  362 (365)
Q Consensus       357 ~~~~~~  362 (365)
                      +.++.+
T Consensus        86 ~~~~~~   91 (98)
T d1wg4a_          86 RVYPER   91 (98)
T ss_dssp             EEECCC
T ss_pred             ecCCCC
Confidence            876543

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.67  E-value=1e-17  Score=127.72  Aligned_cols=83  Identities=25%  Similarity=0.392  Sum_probs=72.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          155 EPPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       155 ~~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      .+...++|||+|||+++++++|+++|+.||.|..+.                          ++ +..+|+++|||||.|
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~--------------------------v~-~~~~g~~kg~afv~F   61 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA--------------------------VV-DVRTGTNRKFGYVDF   61 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCC--------------------------CC-EEEEETTTTEEEEEE
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEee--------------------------ee-ecCCCCccEEeEEee
Confidence            344577999999999999999999999999987665                          33 335788999999999


Q ss_pred             CCHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          235 STVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       235 ~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      .+.++|.+|++ |||..++|+.|+|.++..+
T Consensus        62 ~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~k   91 (91)
T d1fjeb1          62 ESAEDLEKALE-LTGLKVFGNEIKLEKPKGR   91 (91)
T ss_dssp             SSHHHHHHHHH-GGGEEETTEEEEEECCCCS
T ss_pred             CCHHHHHHHHh-cCCcEECCEEEEEEecCCC
Confidence            99999999996 7999999999999998753

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.5e-16  Score=120.37  Aligned_cols=79  Identities=16%  Similarity=0.233  Sum_probs=71.3

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHh--CCCccCCeeEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL--DGQNLDGRAIRV  353 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l--~~~~l~gr~l~V  353 (365)
                      .+|.++|||+|||+.+++++|+++|+.||.|..+++.++      +|||||+|.+.++|.+|+..+  ++..++||+|+|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            456679999999999999999999999999999998754      689999999999999999865  677999999999


Q ss_pred             EEccccc
Q 017842          354 NVAEDRQ  360 (365)
Q Consensus       354 ~~a~~~~  360 (365)
                      .|++.+.
T Consensus        79 ~~sk~~~   85 (88)
T d2cq1a1          79 QYSNHKE   85 (88)
T ss_dssp             EECSCSS
T ss_pred             EECCCCC
Confidence            9998664

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=1.1e-16  Score=117.32  Aligned_cols=72  Identities=22%  Similarity=0.367  Sum_probs=64.8

Q ss_pred             EEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEccccc
Q 017842          282 IYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAEDRQ  360 (365)
Q Consensus       282 lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~~~~  360 (365)
                      |||+|||+.+++++|+++|+.|| +..+++      ++++|||||+|.+.++|.+|+..|||..+.||+|+|+|+....
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999998 555544      4568999999999999999999999999999999999997543

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.67  E-value=4.8e-17  Score=125.18  Aligned_cols=80  Identities=23%  Similarity=0.470  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++++++|+++|.+||.|..+.                               .+++++|||||+|.+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-------------------------------~~~~~~~~afV~f~~   62 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-------------------------------QDGKSKGIAYIEFKS   62 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-------------------------------ETTEEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-------------------------------ecCccccEEEEEeCC
Confidence            3467999999999999999999999999875433                               367889999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      .++|.+|+..|||..|+|+.|+|.++.++..
T Consensus        63 ~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          63 EADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             HHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             HHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            9999999999999999999999999988764

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1e-16  Score=120.51  Aligned_cols=77  Identities=18%  Similarity=0.224  Sum_probs=69.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||+|||+++|+++|+.+|+.||+|..++                          +..+ .+++++|||||+|.+.+
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~--------------------------l~~~-~~~~~kG~afV~f~~~e   58 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ--------------------------MRRT-LHKAFKGSIFVVFDSIE   58 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEE--------------------------EEEC-TTCCEEEEEEEEESCHH
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccce--------------------------eeee-ccCCcceEEEEEEcCHH
Confidence            67999999999999999999999999998887                          4444 47889999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      +|.+|+++ +|..|.|+.|.|.+..
T Consensus        59 ~a~~al~~-~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2          59 SAKKFVET-PGQKYKETDLLILFKD   82 (85)
T ss_dssp             HHHHHHTC-CCCEETTEECEEEEGG
T ss_pred             HHHHHHHH-CCCEECCEEEEEEEcC
Confidence            99999975 9999999999998753

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.9e-16  Score=121.80  Aligned_cols=77  Identities=19%  Similarity=0.391  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      +..++|||+|||.++++++|+.+|++||.|..++                          ++      +.+|||||.|.+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~--------------------------i~------~~kg~afV~f~~   63 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIR--------------------------VF------PEKGYSFVRFST   63 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEE--------------------------EE------TTTTEEEEEESS
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEE--------------------------EE------ecceEEEEEECC
Confidence            3467999999999999999999999999999887                          33      348999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      .++|.+|+..|||..|+|+.|+|.++.+.
T Consensus        64 ~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          64 HESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             HHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            99999999999999999999999998654

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=2.2e-16  Score=118.82  Aligned_cols=76  Identities=25%  Similarity=0.360  Sum_probs=69.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||+|||+++++++|+++|+.||.|..+.+                                ++++|||||.|.+.+
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~--------------------------------~~~rg~afV~f~~~~   55 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV--------------------------------KKIRDYAFVHFSNRE   55 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE--------------------------------EECSSEEEEEESSHH
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEE--------------------------------ccccEEEEEEeCCHH
Confidence            479999999999999999999999999877652                                246899999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      +|..|+..|||..|+|+.|+|.++.|+.
T Consensus        56 ~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1          56 DAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             HHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             HHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            9999999999999999999999988664

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=2.5e-16  Score=119.08  Aligned_cols=78  Identities=29%  Similarity=0.447  Sum_probs=68.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ++.++|||+|||+++++++|+.+|+.||.|..+.+                          .    .++++|||||+|.+
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~--------------------------~----~~~~~~~afV~f~~   57 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFK--------------------------F----FQKDRKMALIQMGS   57 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEE--------------------------E----CSSSTTCEEEEESS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEE--------------------------e----eecccceeEEEECC
Confidence            46789999999999999999999999999876542                          1    34568999999999


Q ss_pred             HHHHHHHHHHHccCcc-cCeeEEEeecCC
Q 017842          237 VEEAEKAVEMFHRYDI-DGRLLTVNKAAP  264 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~-~gr~l~V~~a~~  264 (365)
                      .++|.+|+..|+|..+ +|+.|+|.++++
T Consensus        58 ~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2          58 VEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             HHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             HHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            9999999999999988 689999999875

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=1e-16  Score=123.96  Aligned_cols=80  Identities=19%  Similarity=0.291  Sum_probs=71.3

Q ss_pred             cCCCCceEEEeCCCCc-CcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHH--HhCCCccCCeeE
Q 017842          275 VFEPGFRIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIA--ALDGQNLDGRAI  351 (365)
Q Consensus       275 ~~~~~~~lfV~nLp~~-~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~--~l~~~~l~gr~l  351 (365)
                      ...++++|||+|||.. +|+++|.++|+.||.|..|++.++      +|||||+|.+.++|.+|+.  .+++..+.||+|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEE
Confidence            3455679999999985 899999999999999999999754      7899999999999999997  578889999999


Q ss_pred             EEEEccccc
Q 017842          352 RVNVAEDRQ  360 (365)
Q Consensus       352 ~V~~a~~~~  360 (365)
                      +|+||+.++
T Consensus        88 ~V~~s~~~~   96 (99)
T d1x4fa1          88 KVDLSEKYK   96 (99)
T ss_dssp             EEEEECSCS
T ss_pred             EEEEcCCcc
Confidence            999998664

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=2.8e-16  Score=120.54  Aligned_cols=79  Identities=29%  Similarity=0.459  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|+.||.|..+.+                          .   .....+|||||.|.+.
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~--------------------------~---~~~~~~g~afV~f~~~   63 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL--------------------------K---NRRGGPPFAFVEFEDP   63 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEE--------------------------C---CSSSSSCCEEEEESCH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEe--------------------------c---ccccccceEEEEECCH
Confidence            4678999999999999999999999999977652                          1   2345789999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      ++|.+|+..|||..|.|+.|+|.++.+.
T Consensus        64 e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          64 RDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             HHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            9999999999999999999999998754

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=5.5e-17  Score=118.01  Aligned_cols=71  Identities=21%  Similarity=0.460  Sum_probs=67.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHHH
Q 017842          162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAE  241 (365)
Q Consensus       162 vfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~  241 (365)
                      |||+|||+++++++|+++|++||.|..++                          +.++..++.++|||||+|.+.++|.
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~--------------------------~~~~~~~~~~~g~afV~f~~~~~A~   54 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTK--------------------------AILDKTTNKCKGYGFVDFDSPSAAQ   54 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEE--------------------------EECCSSSCSCCSEEEEEESCHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccc--------------------------cccccccccccceeEEEECCHHHHH
Confidence            79999999999999999999999998877                          7778889999999999999999999


Q ss_pred             HHHHHHccCcccCeeEE
Q 017842          242 KAVEMFHRYDIDGRLLT  258 (365)
Q Consensus       242 ~Al~~lng~~~~gr~l~  258 (365)
                      +|+..|||..|+|+.|+
T Consensus        55 ~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1          55 KAVTALKASGVQAQMAK   71 (72)
T ss_dssp             HHHHHHHHHTCCEESCC
T ss_pred             HHHHHhCCCEECCEECc
Confidence            99999999999999875

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.6e-16  Score=122.81  Aligned_cols=84  Identities=20%  Similarity=0.420  Sum_probs=70.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +.++|||+|||+++++++|+++|+.|| +..+.+                         +.....+++++|||||+|.+.
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~-------------------------~~~~~~~g~~~g~afV~f~~~   67 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRL-------------------------PREPSNPERLKGFGYAEFEDL   67 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEEC-------------------------CBCSSCTTSBCSCEEEEESSH
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-ccccee-------------------------eeeeccCCCcceeeeEEECCH
Confidence            458999999999999999999999999 555542                         233345788999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      ++|++|+. ||+..|+||.|+|.++.++...
T Consensus        68 e~a~~~~~-~~~~~~~gr~l~V~~a~~~~~~   97 (104)
T d1wi8a_          68 DSLLSALS-LNEESLGNKRIRVDVADQAQDK   97 (104)
T ss_dssp             HHHHHHHG-GGTCEETTEECEEEECCCCCCC
T ss_pred             HHHHHHHH-cCCCEECCEEEEEEECCCCCCC
Confidence            99987775 7999999999999998876543

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=2.2e-16  Score=118.92  Aligned_cols=76  Identities=34%  Similarity=0.536  Sum_probs=69.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .++|||+|||.++++++|+.+|++||.|..+++                          .      +.+|||||+|.+.+
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~--------------------------~------~~k~~afV~f~~~~   55 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI--------------------------H------KDKGFGFIRLETRT   55 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEE--------------------------E------TTTTEEEEECSSSH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeee--------------------------e------cccceEEEEECCHH
Confidence            468999999999999999999999999998873                          2      35799999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      +|.+|+..|||..|+|+.|+|.++.+..
T Consensus        56 ~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1          56 LAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             HHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             HHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            9999999999999999999999988764

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.64  E-value=6e-16  Score=115.65  Aligned_cols=77  Identities=22%  Similarity=0.376  Sum_probs=67.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      .++.++|||+|||.++++++|+++|+.||.|..++                          ++.     ..+|||||+|.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~--------------------------~~~-----~~~g~afV~f~   53 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVR--------------------------LVP-----NRHDIAFVEFT   53 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEE--------------------------ECT-----TTCSCEEEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEee--------------------------eec-----ccceeEEEecC
Confidence            45678999999999999999999999999998877                          322     24789999999


Q ss_pred             CHHHHHHHHHHHccCcc-cCeeEEEeecC
Q 017842          236 TVEEAEKAVEMFHRYDI-DGRLLTVNKAA  263 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~-~gr~l~V~~a~  263 (365)
                      +.++|..|+..|+|..| +|+.|+|.+++
T Consensus        54 ~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          54 TELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             SHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            99999999999999888 57899999875

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=4.2e-16  Score=122.91  Aligned_cols=77  Identities=16%  Similarity=0.096  Sum_probs=69.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|+.||.|..+.|                                .+.+|||||.|.+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l--------------------------------~~~kg~afV~f~~~   56 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL--------------------------------PEGGITAIVEFLEP   56 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC--------------------------------CSSSSCEEEEESCH
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEe--------------------------------eccCceEEEEEcCH
Confidence            3579999999999999999999999999988762                                24689999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ++|.+|+..|||..|.|+.|+|.++....
T Consensus        57 ~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_          57 LEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             HHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             HHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            99999999999999999999999886543

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=5.1e-16  Score=121.13  Aligned_cols=84  Identities=24%  Similarity=0.318  Sum_probs=73.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...+|||+|||+++|+++|+++|..+|.+....                          ++.+..+++++|||||+|.++
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v--------------------------~~~~~~~~~~kG~afV~F~~~   67 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGM--------------------------TLPVDFQGRSTGEAFVQFASQ   67 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEE--------------------------ECCBCSSSCBCSEEEEEESSH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEE--------------------------EEEeCCCCCcceEEEEEeCCH
Confidence            456899999999999999999999999887654                          555666889999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      ++|.+|+. +|+..|+||.|+|.++.+....
T Consensus        68 e~a~~a~~-~~~~~i~gR~i~V~~~~~~~~~   97 (104)
T d1wg5a_          68 EIAEKALK-KHKERIGHRYIEIFKSSRAEVR   97 (104)
T ss_dssp             HHHHHHHT-TTTCCSSSSCCEEEEECTTTSC
T ss_pred             HHHHHHHh-hCCCEEcceEEEEEECCHHHhc
Confidence            99999997 6999999999999988776543

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=1.5e-16  Score=118.20  Aligned_cols=76  Identities=24%  Similarity=0.434  Sum_probs=66.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      .+|||||||+++++++|+.+|++||.|..+.                          +.      ..+|||||+|.+.++
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~--------------------------~~------~~rg~aFV~f~~~~~   49 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQ--------------------------VL------LKSGYAFVDYPDQNW   49 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSC--------------------------EE------EETTEEEECCSCHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeE--------------------------Ee------cccceEEEEECCHHH
Confidence            3799999999999999999999999875543                          22      357999999999999


Q ss_pred             HHHHHHHHccC-cccCeeEEEeecCCCCC
Q 017842          240 AEKAVEMFHRY-DIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       240 a~~Al~~lng~-~~~gr~l~V~~a~~~~~  267 (365)
                      |.+|+..|||. .++|+.|+|.++.++..
T Consensus        50 A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1          50 AIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             HHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             HHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            99999999996 59999999999987654

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=9.9e-16  Score=119.45  Aligned_cols=79  Identities=11%  Similarity=0.096  Sum_probs=70.6

Q ss_pred             CCCCceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHh--CCCccCCeeEEE
Q 017842          276 FEPGFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL--DGQNLDGRAIRV  353 (365)
Q Consensus       276 ~~~~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l--~~~~l~gr~l~V  353 (365)
                      ..+..+|||+|||..+++++|.++|+.||.|..|++.++      +|+|||+|.+.++|..|+..|  ++..++|++|+|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            345669999999999999999999999999999999754      789999999999999999977  556789999999


Q ss_pred             EEccccc
Q 017842          354 NVAEDRQ  360 (365)
Q Consensus       354 ~~a~~~~  360 (365)
                      .|++.+.
T Consensus        86 ~~s~~~~   92 (104)
T d1wexa_          86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEcCCCc
Confidence            9997643

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=1.3e-16  Score=120.90  Aligned_cols=77  Identities=19%  Similarity=0.287  Sum_probs=67.3

Q ss_pred             CCCeEEEcCCCCCCCHHHH---HHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCC---ccceEE
Q 017842          158 EDAKLFVGNLPYDVDSEKL---AMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDR---SRGFGF  231 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L---~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~g~af  231 (365)
                      ..++|||+|||+++++++|   +++|++||.|..+.                          +..++.++.   .+||||
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~--------------------------i~~~~~~~~~~~~~g~aF   60 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVV--------------------------INNSTSYAGSQGPSASAY   60 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEE--------------------------EECCSSCCSSSCCCEEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEE--------------------------EeeccCcCCCCCcceEEE
Confidence            3568999999999999999   67899999999987                          555555544   459999


Q ss_pred             EEeCCHHHHHHHHHHHccCcccCeeEEEe
Q 017842          232 VTMSTVEEAEKAVEMFHRYDIDGRLLTVN  260 (365)
Q Consensus       232 V~f~~~e~a~~Al~~lng~~~~gr~l~V~  260 (365)
                      |+|.+.++|.+|+..|||..|+|+.|+|.
T Consensus        61 V~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          61 VTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             EEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             EecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            99999999999999999999999999984

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=1.9e-16  Score=119.25  Aligned_cols=79  Identities=18%  Similarity=0.212  Sum_probs=69.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...+|||+|||+++++++|+++|..||.+....                          ++....+++++|+|||+|.+.
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~--------------------------~~~~~~~g~~~G~afV~f~~~   61 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSV--------------------------CLKYNEKGMPTGEAMVAFESR   61 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTC--------------------------EEEECSSSCEEEEEEEEESCH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEE--------------------------EEEeCCCCCcceEEEEEEcCc
Confidence            356799999999999999999999999875422                          344556899999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeec
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      ++|.+|+..|||..++||.|+|.++
T Consensus        62 e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          62 DEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             HHHHHHHHHTTTCEETTEECEEEES
T ss_pred             HHHHHHHHHcCCCEECCEEEEEEEC
Confidence            9999999999999999999999864

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=2.8e-16  Score=119.56  Aligned_cols=80  Identities=18%  Similarity=0.336  Sum_probs=69.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHH----HHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEE
Q 017842          158 EDAKLFVGNLPYDVDSEKLA----MLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVT  233 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~----~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~  233 (365)
                      +.+||||||||+++++++|+    .+|++||.|..+++                          .   .+++++|||||+
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~--------------------------~---~~~~~~g~afV~   52 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV--------------------------S---RSLKMRGQAFVI   52 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEEC--------------------------C---HHHHHTTCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEE--------------------------e---eeccCCCceEEE
Confidence            46899999999999998886    46899999987662                          1   245679999999


Q ss_pred             eCCHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          234 MSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       234 f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      |.+.++|.+|+..+||..++|+.|+|.++.++.
T Consensus        53 F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~~~   85 (91)
T d1nu4a_          53 FKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS   85 (91)
T ss_dssp             ESSHHHHHHHHHHHTTCEETTEECEEEECSSCC
T ss_pred             ECCHHHHHHHHHHhCCCEECCEEEEEEEeCCCc
Confidence            999999999999999999999999999987653

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=7.5e-16  Score=118.34  Aligned_cols=83  Identities=23%  Similarity=0.298  Sum_probs=71.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCC-eEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecC-CCCCccceEEEEeCCH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGT-VEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR-ETDRSRGFGFVTMSTV  237 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~-i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~g~afV~f~~~  237 (365)
                      ++|||||||.++++++|+++|+.||+ |..++                          ++.+. .+++++|||||+|.+.
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~--------------------------~~~~~~~~~~~rg~aFV~F~~~   55 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVI--------------------------VYASAADKMKNRGFAFVEYESH   55 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEE--------------------------CCSSSCTTTTTCCEEEEEESSH
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEE--------------------------EeeeccccccCCCeEEEEEcCH
Confidence            57999999999999999999999996 77766                          44443 4788999999999999


Q ss_pred             HHHHHHHHHHcc--CcccCeeEEEeecCCCCCC
Q 017842          238 EEAEKAVEMFHR--YDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       238 e~a~~Al~~lng--~~~~gr~l~V~~a~~~~~~  268 (365)
                      ++|..|++.|++  ..+.|+.|+|.++.++...
T Consensus        56 ~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~~~   88 (96)
T d2disa1          56 RAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDV   88 (96)
T ss_dssp             HHHHHHHTTTTTCCSCBTTBCCEEEESCSSCST
T ss_pred             HHHHHHHHHHcCCCeEECCEEEEEEEcCCCCCC
Confidence            999999998864  5568999999999876543

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.62  E-value=6e-16  Score=113.33  Aligned_cols=74  Identities=16%  Similarity=0.241  Sum_probs=65.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEE  239 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~  239 (365)
                      +||||+|||+++++++|+++|+.||.|..++                          +..+..  ..++||||+|.+.++
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~--------------------------~~~~~~--~~~~~afV~F~~~~~   52 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVD--------------------------VADSLK--KNFRFARIEFARYDG   52 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTT--SSSEEEEEEESSHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEE--------------------------EEeecc--ccceEEEEEEcchHH
Confidence            4899999999999999999999999999887                          455443  346899999999999


Q ss_pred             HHHHHHHHccCcccCeeEEEeec
Q 017842          240 AEKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       240 a~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      |.+|+. +||..|+|+.|.|..+
T Consensus        53 a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2          53 ALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             HHHHHT-TTTCEETTEECEEEEC
T ss_pred             hHHHHH-hcCcEECCEEEEEEEC
Confidence            999996 5999999999999865

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=7e-16  Score=116.83  Aligned_cols=79  Identities=15%  Similarity=0.214  Sum_probs=70.1

Q ss_pred             CCCceEEEeCCCCc-CcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHh--CCCccCCeeEEE
Q 017842          277 EPGFRIYVGNLPWE-VDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAAL--DGQNLDGRAIRV  353 (365)
Q Consensus       277 ~~~~~lfV~nLp~~-~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l--~~~~l~gr~l~V  353 (365)
                      ++..+|||+|||.. +|+++|+++|+.||.|..|++.++      +++|||+|.+.++|..|+..|  ++..+.||+|+|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            44569999999986 899999999999999999999865      679999999999999999966  677899999999


Q ss_pred             EEcccccc
Q 017842          354 NVAEDRQR  361 (365)
Q Consensus       354 ~~a~~~~~  361 (365)
                      +||++.++
T Consensus        80 ~~s~~~~~   87 (89)
T d1x4da1          80 HLSQKYKR   87 (89)
T ss_dssp             EEECCCTT
T ss_pred             EECCCccc
Confidence            99986543

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=8.7e-16  Score=113.64  Aligned_cols=76  Identities=24%  Similarity=0.288  Sum_probs=67.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      |...++|||+||+  +|+++|+++|++||.|..+.+                          .      +.+|||||+|.
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~--------------------------~------~~~~~afV~f~   47 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSM--------------------------D------PPRNCAFVTYE   47 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEE--------------------------E------TTTTEEEEECS
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeee--------------------------c------cCCCEEEEEEc
Confidence            4467899999986  899999999999999988763                          2      45789999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      +.++|.+|+..|||..++|+.|+|.++.++
T Consensus        48 ~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1          48 KMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             SHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             ccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            999999999999999999999999999754

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=1.4e-15  Score=119.38  Aligned_cols=78  Identities=21%  Similarity=0.373  Sum_probs=68.6

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          159 DAKLFVGNLPY-DVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       159 ~~tvfVgnLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      +++|||+|||+ .+++++|+++|+.||.|..+.                          ++.+     .+|||||+|.+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~--------------------------i~~~-----~kg~afV~f~~~   50 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVK--------------------------ILFN-----KKENALVQMADG   50 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEE--------------------------ECCT-----TSCCEEEEESCH
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEE--------------------------EEec-----ccceEEEEECCH
Confidence            47999999965 589999999999999999987                          3333     378999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|.+|+..|||..|.|+.|+|.++.....
T Consensus        51 ~~A~~ai~~lng~~l~g~~l~v~~s~~~~~   80 (109)
T d2adca1          51 NQAQLAMSHLNGHKLHGKPIRITLSKHQNV   80 (109)
T ss_dssp             HHHHHHHHHHTTCBCSSSBCEEECCSCCCC
T ss_pred             HHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999999999875543

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=8.2e-16  Score=112.61  Aligned_cols=71  Identities=27%  Similarity=0.430  Sum_probs=63.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHHH
Q 017842          162 LFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAE  241 (365)
Q Consensus       162 vfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~  241 (365)
                      |||+|||+++++++|+++|++|| +..+.                                .++++|||||.|.+.++|.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~--------------------------------~~~~~g~afv~f~~~~~A~   47 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCF--------------------------------VDKYKGTAFVTLLNGEQAE   47 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEE--------------------------------EETTTTEEEEEESSHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-cccee--------------------------------ecccceeEEEEECCHHHHH
Confidence            79999999999999999999999 33332                                2467899999999999999


Q ss_pred             HHHHHHccCcccCeeEEEeecCCC
Q 017842          242 KAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       242 ~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      +|+..|||..++|+.|+|.++...
T Consensus        48 ~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1          48 AAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             HHHHHHTTEESSSCEEEEEECCST
T ss_pred             HHHHHhCCccCCCCEEEEEEeCCC
Confidence            999999999999999999998654

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=6.1e-16  Score=116.92  Aligned_cols=78  Identities=23%  Similarity=0.351  Sum_probs=68.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|++||.|..+++                               ...++|||||+|.+.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~-------------------------------~~~~~gfafV~f~~~   52 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-------------------------------PKPFRAFAFVTFADD   52 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEEC-------------------------------CSSCCSCCEEECSCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEE-------------------------------eeccCceEEEEECCH
Confidence            4689999999999999999999999999987652                               335689999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      ++|++|+.  ++..|+|+.|+|.++.++...
T Consensus        53 ~~a~~a~~--~~~~i~g~~l~v~~a~~k~~~   81 (88)
T d1wf0a_          53 QIAQSLCG--EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             HHHHHTTT--CEEEETTEEEEEECCCCCCCC
T ss_pred             HHHHHHHh--CCCEECCEEeEEEeCCCCCCC
Confidence            99999985  888999999999999876543

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.5e-15  Score=114.65  Aligned_cols=76  Identities=28%  Similarity=0.472  Sum_probs=66.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|.+||. ..+.                                .++.+|||||+|.+.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~--------------------------------~~~~kg~afV~f~~~   50 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCY--------------------------------VDRNKRTAFVTLLNG   50 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEE--------------------------------EEGGGTEEEECCSCH
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcCc-eeee--------------------------------eeccCCceEEEECCH
Confidence            3578999999999999999999999992 2222                                235789999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ++|.+|+..|||..|+|+.|+|.++.+..
T Consensus        51 ~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_          51 EQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             HHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             HHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            99999999999999999999999986554

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.3e-15  Score=117.43  Aligned_cols=75  Identities=29%  Similarity=0.430  Sum_probs=67.1

Q ss_pred             CCCeEEEcCCC-CCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          158 EDAKLFVGNLP-YDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       158 ~~~tvfVgnLp-~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...+|||+||| ..+++.+|+.+|++||.|..+.                          +        .+|||||+|.+
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~--------------------------i--------~rg~aFV~f~~   59 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS--------------------------V--------HKGFAFVQYVN   59 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEE--------------------------E--------ETEEEEEEESS
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEE--------------------------E--------eCCeEEEEECC
Confidence            35689999996 5788999999999999998876                          2        37999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      .++|.+|+..|||..|.|+.|+|.++.++.
T Consensus        60 ~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          60 ERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             HHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             HHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            999999999999999999999999987643

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=6.1e-16  Score=120.43  Aligned_cols=79  Identities=18%  Similarity=0.288  Sum_probs=69.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...+|||+|||+++++++|.++|..||.|..+.                          ++....+|+++|||||+|.+.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~--------------------------~~~~~~~g~~~G~afV~F~s~   60 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAV--------------------------HVLVDNNGQGLGQALVQFKNE   60 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTE--------------------------EECCCTTSSCSSCEEEECSSH
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEE--------------------------EEEeCCCCCcCccEEEEECCH
Confidence            456899999999999999999999999876532                          444556889999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      ++|.+|+. +||..|+||.|.|.++.
T Consensus        61 ~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1          61 DDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             HHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             HHHHHHHh-cCCCeECCcEEEEEECC
Confidence            99999997 69999999999998764

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=4.5e-16  Score=117.38  Aligned_cols=73  Identities=21%  Similarity=0.196  Sum_probs=65.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      +|||||||+++++++|+++|++||.|..+.+                          .       ..|||||+|.+.++|
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i--------------------------~-------~~g~afV~f~~~~~a   48 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADV--------------------------Y-------RDGTGVVEFVRKEDM   48 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEE--------------------------C-------TTSEEEEEESSHHHH
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhcccccccc--------------------------c-------ccceeeEEeCCHHHH
Confidence            6999999999999999999999999988763                          2       248999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEeecCCCC
Q 017842          241 EKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      .+|+..|||..|.|+.|+|.++....
T Consensus        49 ~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1          49 TYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             HHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             HHHHHHhCCCEECCcEeEEeEEecCc
Confidence            99999999999999999998775443

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=1.2e-15  Score=117.69  Aligned_cols=77  Identities=21%  Similarity=0.211  Sum_probs=69.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+++|++||.|..+.+                          .       .+|||||+|.+.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i--------------------------~-------~~g~afV~f~~~   60 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADV--------------------------Q-------KDGMGMVEYLRK   60 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEE--------------------------E-------TTTEEEEEESSH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccc--------------------------c-------ccceEEEEECCH
Confidence            4678999999999999999999999999988763                          2       358999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      ++|.+|++.|||..|+|+.|+|.++..+..
T Consensus        61 ~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~   90 (98)
T d1wg4a_          61 EDMEYALRKLDDTKFRSHEGETSYIRVYPE   90 (98)
T ss_dssp             HHHHHHHHHHSSEEEECTTSCEEEEEEECC
T ss_pred             HHHHHHHHHhCCCEeCCeEEEEEEEecCCC
Confidence            999999999999999999999998865543

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=4.1e-15  Score=112.27  Aligned_cols=79  Identities=15%  Similarity=0.214  Sum_probs=69.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      .++.++|||||||+++++++|+++|++||.|..+++                          .      +.+|||||+|.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~--------------------------~------~~~~~afV~f~   52 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM--------------------------L------KGKNQAFLELA   52 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEE--------------------------E------TTTTEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccc--------------------------c------ccceEEEEEeC
Confidence            457899999999999999999999999999988763                          2      45789999999


Q ss_pred             CHHHHHHHHHHH--ccCcccCeeEEEeecCCCC
Q 017842          236 TVEEAEKAVEMF--HRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       236 ~~e~a~~Al~~l--ng~~~~gr~l~V~~a~~~~  266 (365)
                      +.++|.+|+..+  ++..+.|++|+|.++..+.
T Consensus        53 ~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~~   85 (88)
T d2cq1a1          53 TEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   85 (88)
T ss_dssp             SHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             CHHHHHHHHHHHccCCCccCCCEEEEEECCCCC
Confidence            999999999876  4678999999999987654

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.7e-15  Score=117.69  Aligned_cols=83  Identities=17%  Similarity=0.240  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +....+|||+|||+++|+++|+++|..||.+ .+.                          ++++ ..+..+|||||+|.
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~--------------------------~~~~-~~g~~~G~afVeF~   63 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVH--------------------------IEIG-PDGRVTGEADVEFA   63 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEE--------------------------EEES-SSSCEEEEEEEECS
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eee--------------------------eEEe-cCCcceEEEEEEEC
Confidence            3456799999999999999999999999855 443                          4444 45789999999999


Q ss_pred             CHHHHHHHHHHHccCcccCeeEEEeecCCCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~  267 (365)
                      +.++|++|+. +|+..|+||.|+|.++.+...
T Consensus        64 ~~~~a~~Al~-~~~~~i~gR~I~V~~s~~~~~   94 (102)
T d1weza_          64 THEDAVAAMA-KDKANMQHRYVELFLNSTAGT   94 (102)
T ss_dssp             SSHHHHHHHT-TSSCCSSSSCCEEEEECCCCC
T ss_pred             CHHHHHHHHH-cCCCEECCEEEEEEEcCCCCC
Confidence            9999999997 599999999999998876653

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=7.4e-15  Score=112.89  Aligned_cols=78  Identities=21%  Similarity=0.430  Sum_probs=69.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ..+.++|||+|||+++++++|+++|++||.|..+++                          .      +.++||||+|.
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~--------------------------~------~~~~~afV~f~   61 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH--------------------------V------KGDSFAYIQYE   61 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEE--------------------------C------SSSCCEEEEES
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEee--------------------------e------ccccEEEeccC
Confidence            346789999999999999999999999999988763                          2      35789999999


Q ss_pred             CHHHHHHHHHHHccCcccC--eeEEEeecCCC
Q 017842          236 TVEEAEKAVEMFHRYDIDG--RLLTVNKAAPR  265 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~~g--r~l~V~~a~~~  265 (365)
                      +.++|.+|+..|||..|.|  ++|+|.++.+.
T Consensus        62 ~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          62 SLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             SHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            9999999999999999976  58999998754

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=3.1e-15  Score=117.37  Aligned_cols=81  Identities=19%  Similarity=0.152  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      .+-.+|||+|||+.+|+++|+++|++||.|..+.                          +..+    +.+|||||+|.+
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~--------------------------i~~~----~~~g~aFV~f~~   54 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKII--------------------------TFTK----NNQFQALLQYAD   54 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEE--------------------------EEEE----TTEEEEEEEESC
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEE--------------------------EEee----CCCCeEEEEECC
Confidence            3556899999999999999999999999998887                          3333    358999999999


Q ss_pred             HHHHHHHHHHHccCcc--cCeeEEEeecCCCCC
Q 017842          237 VEEAEKAVEMFHRYDI--DGRLLTVNKAAPRGT  267 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~--~gr~l~V~~a~~~~~  267 (365)
                      .++|.+|+..|||..|  .|++|+|.++.+...
T Consensus        55 ~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~~   87 (108)
T d2adba1          55 PVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL   87 (108)
T ss_dssp             HHHHHHHHHHHHSCCSSTTCCCCEEEECSSCSC
T ss_pred             HHHHHHHHHHHCCCEeccCCcEEEEEecCCccc
Confidence            9999999999999988  578999998876544

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1.2e-15  Score=120.52  Aligned_cols=81  Identities=19%  Similarity=0.329  Sum_probs=70.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCC
Q 017842          157 PEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMST  236 (365)
Q Consensus       157 ~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~  236 (365)
                      ...++|||+|||+++|+++|+++|+.||.+..+.                          ++.+..+|.++|||||+|.+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~--------------------------~~~~~~~g~~~G~afVeF~~   69 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSI--------------------------YIAYGPNGKATGEGFVEFRN   69 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTC--------------------------EEEECTTSSEEEEEEEEBSS
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccce--------------------------eeecCcccceeeEEEEEECC
Confidence            3567999999999999999999999999875433                          45566789999999999999


Q ss_pred             HHHHHHHHHHHccCcccCeeEEEeecCC
Q 017842          237 VEEAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       237 ~e~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      .++|.+|+. +||..|+||.|.|..+..
T Consensus        70 ~e~a~~al~-~~~~~i~gR~i~V~~~~~   96 (112)
T d1wela1          70 EADYKAALC-RHKQYMGNRFIQVHPITK   96 (112)
T ss_dssp             SHHHHHHHT-SCSBCSTTSCBEEEEECH
T ss_pred             HHHHHHHHH-cCCCcCCCEEEEEEEcCh
Confidence            999999997 699999999999987643

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=8.2e-17  Score=122.32  Aligned_cols=84  Identities=18%  Similarity=0.391  Sum_probs=69.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      .|+|||||||+++++++|+++|++||.+..+.+..                     ...+.+..+++++|||||+|.+.+
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~---------------------~~~~~~~~~~~~kg~afV~f~~~e   59 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAP---------------------GNPVLAVQINQDKNFAFLEFRSVD   59 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSS---------------------SCSEEECCEETTTTEEEEEESSCT
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEec---------------------cceeeecccCCCceEEEEEeCCHH
Confidence            37899999999999999999999999876544210                     113445567889999999999999


Q ss_pred             HHHHHHHHHccCcccCeeEEEeecCC
Q 017842          239 EAEKAVEMFHRYDIDGRLLTVNKAAP  264 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~l~V~~a~~  264 (365)
                      +|.+|+. |||..+.|+.|+|.++..
T Consensus        60 ~a~~a~~-l~g~~~~Gr~l~V~r~k~   84 (90)
T d1u2fa_          60 ETTQAMA-FDGIIFQGQSLKIRRPHD   84 (90)
T ss_dssp             TTTTGGG-GSSCCSSSSCCCCBCTTC
T ss_pred             HHHHHHh-hCCcEECCEEEEECCCCC
Confidence            9999986 799999999999986543

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.56  E-value=1.6e-15  Score=118.17  Aligned_cols=79  Identities=15%  Similarity=0.066  Sum_probs=70.0

Q ss_pred             CCceEEEeCCCCcCc-----HHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEE
Q 017842          278 PGFRIYVGNLPWEVD-----NARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIR  352 (365)
Q Consensus       278 ~~~~lfV~nLp~~~t-----ee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~  352 (365)
                      ..++|||+||+..+.     +++|+.+|+.||.|..+++.+      ++|||||+|.+.++|.+|+..|||..|+|++|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            346999999998763     367999999999999999974      378999999999999999999999999999999


Q ss_pred             EEEccccccC
Q 017842          353 VNVAEDRQRR  362 (365)
Q Consensus       353 V~~a~~~~~~  362 (365)
                      |.||+.+...
T Consensus        78 v~~a~~~~~~   87 (104)
T d1weya_          78 LYFAQTLHIG   87 (104)
T ss_dssp             EECCCCSSCC
T ss_pred             EeecccCCCC
Confidence            9999877653

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=7.9e-15  Score=113.15  Aligned_cols=78  Identities=21%  Similarity=0.271  Sum_probs=67.6

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEe
Q 017842          156 PPEDAKLFVGNLPYD-VDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTM  234 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f  234 (365)
                      +...++|||+|||.+ +|+++|..+|+.||.|..+.+                          .      +++|||||+|
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~--------------------------~------~~k~~afV~f   62 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL--------------------------M------RMKSQAFIEM   62 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEE--------------------------E------TTTTEEEEEC
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEE--------------------------e------ecCCcEEEEe
Confidence            345789999999986 899999999999999988873                          2      4579999999


Q ss_pred             CCHHHHHHHHH--HHccCcccCeeEEEeecCCC
Q 017842          235 STVEEAEKAVE--MFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       235 ~~~e~a~~Al~--~lng~~~~gr~l~V~~a~~~  265 (365)
                      .+.++|.+|+.  .+++..|+|+.|+|.++..+
T Consensus        63 ~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~   95 (99)
T d1x4fa1          63 ETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY   95 (99)
T ss_dssp             SSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             cchHHHHHHHHHHhcCCceECCEEEEEEEcCCc
Confidence            99999999997  45788999999999988644

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=9.6e-17  Score=121.93  Aligned_cols=78  Identities=22%  Similarity=0.492  Sum_probs=69.0

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEE-----eeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEE
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVV-----YDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVN  354 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~-----~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~  354 (365)
                      ++|||+|||+.+|+++|+++|+.||.|..+.+.     .+..+++++|||||+|.+.++|.+|+. |||..+.||+|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            389999999999999999999999987766553     455678899999999999999999996 99999999999998


Q ss_pred             Eccc
Q 017842          355 VAED  358 (365)
Q Consensus       355 ~a~~  358 (365)
                      .+++
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6654

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.54  E-value=4.8e-14  Score=109.67  Aligned_cols=80  Identities=18%  Similarity=0.177  Sum_probs=69.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          156 PPEDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ..+.++|||+|||.++++++|+++|+.||.|..+.+                          .      +.+|+|||+|.
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~--------------------------~------~~k~~AfV~f~   59 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM--------------------------M------PFKRQALVEFE   59 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEE--------------------------E------TTTTEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEE--------------------------E------ecceeEEEEeC
Confidence            346889999999999999999999999999988763                          2      46899999999


Q ss_pred             CHHHHHHHHHHHc--cCcccCeeEEEeecCCCCC
Q 017842          236 TVEEAEKAVEMFH--RYDIDGRLLTVNKAAPRGT  267 (365)
Q Consensus       236 ~~e~a~~Al~~ln--g~~~~gr~l~V~~a~~~~~  267 (365)
                      +.++|..|+..++  +..+.|+.|+|.++..+..
T Consensus        60 ~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~~   93 (104)
T d1wexa_          60 NIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRI   93 (104)
T ss_dssp             SHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSC
T ss_pred             CHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCcc
Confidence            9999999999874  5678999999999976543

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.6e-15  Score=118.15  Aligned_cols=75  Identities=15%  Similarity=0.187  Sum_probs=70.9

Q ss_pred             eEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          281 RIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       281 ~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      .++|++++..++++.|+++|++||.|..|+|+++ .+++++|||||+|.+.++|.+|+..|||+.++||+|+|.|+
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            5888889999999999999999999999999877 57999999999999999999999999999999999999985

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.48  E-value=5.5e-14  Score=106.15  Aligned_cols=77  Identities=17%  Similarity=0.200  Sum_probs=67.0

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          157 PEDAKLFVGNLPYD-VDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       157 ~~~~tvfVgnLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      ...++|||+|||.. +|+++|.++|+.||.|..+.+                          .      +.+++|||.|.
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i--------------------------~------~~k~~afV~f~   53 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI--------------------------L------NKINEAFIEMA   53 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEE--------------------------C------SSSSCEEEEES
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEe--------------------------e------ccceEEEEEEc
Confidence            35789999999986 789999999999999998873                          2      35679999999


Q ss_pred             CHHHHHHHHHHH--ccCcccCeeEEEeecCCC
Q 017842          236 TVEEAEKAVEMF--HRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       236 ~~e~a~~Al~~l--ng~~~~gr~l~V~~a~~~  265 (365)
                      +.++|..|+..|  ++..+.|++|+|.++...
T Consensus        54 ~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~   85 (89)
T d1x4da1          54 TTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   85 (89)
T ss_dssp             SHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             chhhHHHHHHHHhhCCCccCCceEEEEECCCc
Confidence            999999999976  567899999999998743

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=8.1e-14  Score=118.95  Aligned_cols=81  Identities=30%  Similarity=0.524  Sum_probs=74.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ..++|||+|||+++++++|+.+|+.||.|..+.                          ++.+..++.++|||||.|.+.
T Consensus        96 ~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~--------------------------i~~~~~~~~~~g~~fV~f~~~  149 (183)
T d1u1qa_          96 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE--------------------------IMTDRGSGKKRGFAFVTFDDH  149 (183)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEE--------------------------EEECTTTCCEEEEEEEEESCH
T ss_pred             ccceeEEccCCCcCCHHHHhhhhccCCceeeee--------------------------eecccccCccceeEEEEECCH
Confidence            467999999999999999999999999998887                          777888999999999999999


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecCCC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAAPR  265 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~~~  265 (365)
                      ++|.+|+.+ ++..++|+.|.|.++.++
T Consensus       150 e~A~~Al~~-~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         150 DSVDKIVIQ-KYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             HHHHHHHTS-SCEEETTEEEEEEECCCH
T ss_pred             HHHHHHHHh-CCCeECCEEEEEEecCCc
Confidence            999999985 888999999999988764

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=1.3e-13  Score=106.25  Aligned_cols=80  Identities=19%  Similarity=0.277  Sum_probs=69.2

Q ss_pred             CCceEEEeCC--CCcC---------cHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 017842          278 PGFRIYVGNL--PWEV---------DNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL  346 (365)
Q Consensus       278 ~~~~lfV~nL--p~~~---------tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l  346 (365)
                      ...+|+|+||  |..+         ..++|++.|++||.|..|.+..+    .++|||||+|.+.++|.+|+..|||..+
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            3459999999  5433         23689999999999999988754    4689999999999999999999999999


Q ss_pred             CCeeEEEEEcccccc
Q 017842          347 DGRAIRVNVAEDRQR  361 (365)
Q Consensus       347 ~gr~l~V~~a~~~~~  361 (365)
                      +||+|+|.|+.++.+
T Consensus        83 ~gr~i~v~~~~g~~~   97 (99)
T d2dita1          83 GGRQITAQAWDGTTD   97 (99)
T ss_dssp             TTEECEEEECCSCCC
T ss_pred             CCEEEEEEEeCCcCC
Confidence            999999999987765

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=1e-13  Score=107.21  Aligned_cols=64  Identities=20%  Similarity=0.257  Sum_probs=58.1

Q ss_pred             CCCceEEEeC--CCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCcc
Q 017842          277 EPGFRIYVGN--LPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNL  346 (365)
Q Consensus       277 ~~~~~lfV~n--Lp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l  346 (365)
                      .|..+|+|+|  ||..+|+++|+++|+.||.|..|++.++      +|||||+|.+.++|.+|+..|||..+
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            4456899955  9999999999999999999999998754      78999999999999999999999977

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=7.7e-14  Score=110.15  Aligned_cols=73  Identities=19%  Similarity=0.191  Sum_probs=64.5

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCH-HHHHHHHHHhCCCccCCeeEEEEEccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSE-TELNDAIAALDGQNLDGRAIRVNVAED  358 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~-~~a~~Al~~l~~~~l~gr~l~V~~a~~  358 (365)
                      ..+||||||+.+|+++|+.+|+.||.|.+|+|+++      +|||||.|.+. ++|..|+..|++..+.++.+.|.++..
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            35699999999999999999999999999999854      89999999985 789999999999999888777777653

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=1.6e-13  Score=106.54  Aligned_cols=79  Identities=16%  Similarity=0.080  Sum_probs=68.6

Q ss_pred             CCCeEEEcCCCCCC-C----HHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEE
Q 017842          158 EDAKLFVGNLPYDV-D----SEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFV  232 (365)
Q Consensus       158 ~~~tvfVgnLp~~~-t----~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV  232 (365)
                      ...+|||+||+.++ +    .++|+.+|+.||.|..+++                          .      ++++||||
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~--------------------------~------k~~~~afV   51 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQY--------------------------F------KSFKRVRI   51 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEE--------------------------E------TTTTEEEE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEE--------------------------e------cCCCEEEE
Confidence            46789999999987 3    3679999999999988763                          2      56889999


Q ss_pred             EeCCHHHHHHHHHHHccCcccCeeEEEeecCCCCCC
Q 017842          233 TMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRGTQ  268 (365)
Q Consensus       233 ~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~~~  268 (365)
                      .|.+.++|.+|+..|||..|.|+.|+|.++.+....
T Consensus        52 ~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~~   87 (104)
T d1weya_          52 NFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIG   87 (104)
T ss_dssp             ECSSTTHHHHHHHTSTTSEETTEECEEECCCCSSCC
T ss_pred             EECCHHHHHHHHHHhcccccCCCEeEEeecccCCCC
Confidence            999999999999999999999999999999766543

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=3.4e-13  Score=104.78  Aligned_cols=81  Identities=19%  Similarity=0.215  Sum_probs=69.9

Q ss_pred             CCceEEEeCC--CCcC--------cHHHHHHHHhccCCeEEEEEEeeCCC--CCcceEEEEEecCHHHHHHHHHHhCCCc
Q 017842          278 PGFRIYVGNL--PWEV--------DNARLEQVFSEHGKVVNARVVYDRET--GRSRGFGFVTMSSETELNDAIAALDGQN  345 (365)
Q Consensus       278 ~~~~lfV~nL--p~~~--------tee~L~~~F~~~G~V~~v~i~~d~~~--~~~kG~afV~F~s~~~a~~Al~~l~~~~  345 (365)
                      |+.+|+|+||  |..+        ..++|++.|++||.|..|.|+++..+  ....|++||+|.+.++|.+|+..|||+.
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4568999999  4333        34789999999999999999887654  3457999999999999999999999999


Q ss_pred             cCCeeEEEEEccc
Q 017842          346 LDGRAIRVNVAED  358 (365)
Q Consensus       346 l~gr~l~V~~a~~  358 (365)
                      ++||+|.+.|+..
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999874

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.38  E-value=4.8e-13  Score=98.91  Aligned_cols=73  Identities=16%  Similarity=0.226  Sum_probs=63.6

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCe-eEEEEEccc
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGR-AIRVNVAED  358 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr-~l~V~~a~~  358 (365)
                      +.|+|+|+|+..+++.| ++|+.||.|..+++.+      .+|||||+|.+..+|.+||. +||..|+|+ .|.|..+.+
T Consensus         5 ~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           5 TWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             cEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            47999999999997655 5799999999998753      47999999999999999997 999999998 467999877


Q ss_pred             cc
Q 017842          359 RQ  360 (365)
Q Consensus       359 ~~  360 (365)
                      +.
T Consensus        77 k~   78 (81)
T d1wwha1          77 KN   78 (81)
T ss_dssp             HH
T ss_pred             hh
Confidence            64

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=1.7e-13  Score=106.41  Aligned_cols=75  Identities=24%  Similarity=0.179  Sum_probs=68.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHH
Q 017842          161 KLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEA  240 (365)
Q Consensus       161 tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a  240 (365)
                      .++|++++.+++++.|+++|++||.|..++                          |..+ .+++++|||||+|.+.++|
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~--------------------------I~~~-~~~~~~G~~fV~f~~~~~A   81 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMN--------------------------VCDN-LGDHLVGNVYVKFRREEDA   81 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEE--------------------------ECCS-SSSSSEEEEEEEESCHHHH
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEE--------------------------eecC-CCCCEeeEEEEEEechhHH
Confidence            477888888999999999999999999987                          5444 5889999999999999999


Q ss_pred             HHHHHHHccCcccCeeEEEeec
Q 017842          241 EKAVEMFHRYDIDGRLLTVNKA  262 (365)
Q Consensus       241 ~~Al~~lng~~~~gr~l~V~~a  262 (365)
                      .+|+..|||..|+||.|.|.++
T Consensus        82 ~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          82 EKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHTTCEETTEECCEEEC
T ss_pred             HHHHHHHCCCEECCEEEEEEEC
Confidence            9999999999999999999864

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.28  E-value=2.1e-12  Score=101.68  Aligned_cols=73  Identities=19%  Similarity=0.212  Sum_probs=62.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH-
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV-  237 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~-  237 (365)
                      -..+||||||+.+|+++|+.+|++||+|..|.|                          +      +.+|||||.|.+. 
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i--------------------------~------~~kg~gfV~F~~~~   58 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDF--------------------------V------RGAKEGIILFKEKA   58 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEEC--------------------------C------TTCSEEEEEESSCH
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEE--------------------------e------cCCceEEEEecCcH
Confidence            345799999999999999999999999998873                          2      4589999999985 


Q ss_pred             HHHHHHHHHHccCcccCeeEEEeecC
Q 017842          238 EEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       238 e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      ++|..|+..+|+..+.++.+.|.+..
T Consensus        59 ~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          59 KEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             HHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             HHHHHHHHHhcCCceecCceEEEEee
Confidence            68889999999998888887776654

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.27  E-value=2.2e-12  Score=95.28  Aligned_cols=73  Identities=15%  Similarity=0.145  Sum_probs=61.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHH
Q 017842          159 DAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVE  238 (365)
Q Consensus       159 ~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e  238 (365)
                      ++.|+|+++|++++++.| .+|++||.|..++                                .++.+|||||.|.+++
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~--------------------------------~~~~~~~~fV~f~~~~   50 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHV--------------------------------MSNTGNWMHIRYQSKL   50 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEE--------------------------------ECSSSSEEEEEESSHH
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEE--------------------------------ecCCCCEEEEEEcccH
Confidence            468999999999987655 5899999998766                                2366899999999999


Q ss_pred             HHHHHHHHHccCcccCee-EEEeecCCC
Q 017842          239 EAEKAVEMFHRYDIDGRL-LTVNKAAPR  265 (365)
Q Consensus       239 ~a~~Al~~lng~~~~gr~-l~V~~a~~~  265 (365)
                      +|.+|+. +||..|+|+. |.|..+..+
T Consensus        51 ~A~~Al~-~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1          51 QARKALS-KDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             HHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             HHHHHHh-cCCCeECCcEEEEEEeCCCh
Confidence            9999997 6999999985 678876543

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=9.1e-12  Score=95.58  Aligned_cols=81  Identities=19%  Similarity=0.244  Sum_probs=67.9

Q ss_pred             CCCCCeEEEcCC--CCCC---------CHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCC
Q 017842          156 PPEDAKLFVGNL--PYDV---------DSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETD  224 (365)
Q Consensus       156 ~~~~~tvfVgnL--p~~~---------t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (365)
                      ....++|+|.||  |.++         ..++|+..|++||.|..+.+                          .    .+
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~--------------------------~----~~   54 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL--------------------------F----DR   54 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE--------------------------E----TT
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEec--------------------------c----CC
Confidence            346889999999  6543         23678899999999988763                          2    33


Q ss_pred             CccceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecCCCC
Q 017842          225 RSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAAPRG  266 (365)
Q Consensus       225 ~~~g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~~~~  266 (365)
                      ..+|+|||.|.+.++|.+|+..|||..|+||.|+|.++.++.
T Consensus        55 ~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          55 HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCC
T ss_pred             CCccEEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCCcC
Confidence            567999999999999999999999999999999999987654

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=1.1e-11  Score=95.56  Aligned_cols=69  Identities=22%  Similarity=0.300  Sum_probs=58.0

Q ss_pred             CCCeEEEc--CCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeC
Q 017842          158 EDAKLFVG--NLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMS  235 (365)
Q Consensus       158 ~~~tvfVg--nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~  235 (365)
                      +.+++||+  |||.++|+++|+.+|++||.|..+++                          .      +.+|||||.|.
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~--------------------------~------~~k~~aFV~f~   64 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM--------------------------P------PNKPYSFARYR   64 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEEC--------------------------C------TTCSCEEEEES
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEee--------------------------c------cCccEEEEEEC
Confidence            56788885  59999999999999999999988762                          1      45789999999


Q ss_pred             CHHHHHHHHHHHccCcc-cCeeEE
Q 017842          236 TVEEAEKAVEMFHRYDI-DGRLLT  258 (365)
Q Consensus       236 ~~e~a~~Al~~lng~~~-~gr~l~  258 (365)
                      +.++|.+|+..|||..+ .|+.+.
T Consensus        65 ~~e~A~~A~~~lng~~i~~~~~~~   88 (101)
T d2cq2a1          65 TTEESKRAYVTLNGKEVVDDLGQK   88 (101)
T ss_dssp             SHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CHHHHHHHHHHhCCCCCCCCCCcE
Confidence            99999999999999877 443333

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.09  E-value=5.6e-11  Score=91.87  Aligned_cols=81  Identities=19%  Similarity=0.165  Sum_probs=66.6

Q ss_pred             CCCCeEEEcCC--CCCC--------CHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecC--CCC
Q 017842          157 PEDAKLFVGNL--PYDV--------DSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNR--ETD  224 (365)
Q Consensus       157 ~~~~tvfVgnL--p~~~--------t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~  224 (365)
                      ++.+.|.|.|+  |.++        ..++|+..|++||.|..+.                          |.++.  ...
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~--------------------------I~~~~~~~~~   55 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE--------------------------IPRPVDGVEV   55 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEE--------------------------CCCCTTSSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEE--------------------------EeecCCCCcc
Confidence            35789999999  5554        2357899999999999987                          33332  234


Q ss_pred             CccceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          225 RSRGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       225 ~~~g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      ...|++||.|.+.++|.+|+..|||..++||.|.|.++.
T Consensus        56 ~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~   94 (104)
T d1o0pa_          56 PGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD   94 (104)
T ss_dssp             TTCCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEEC
T ss_pred             CCceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcC
Confidence            567999999999999999999999999999999998865

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.59  E-value=0.00015  Score=52.98  Aligned_cols=78  Identities=9%  Similarity=0.083  Sum_probs=63.8

Q ss_pred             ceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCc--ceEEEEEecCHHHHHHHHHHhCCCccCC-----eeEE
Q 017842          280 FRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRS--RGFGFVTMSSETELNDAIAALDGQNLDG-----RAIR  352 (365)
Q Consensus       280 ~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~--kG~afV~F~s~~~a~~Al~~l~~~~l~g-----r~l~  352 (365)
                      ++|.|++||..+|++++++.+...|.+..........+.++  -..|||.|.+.+++....+..+|+.+.+     .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            47999999999999999999999999998888776555333  2358999999999999999999998832     2556


Q ss_pred             EEEcc
Q 017842          353 VNVAE  357 (365)
Q Consensus       353 V~~a~  357 (365)
                      |.||-
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66664

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.51  E-value=9.6e-05  Score=53.38  Aligned_cols=54  Identities=22%  Similarity=0.372  Sum_probs=48.9

Q ss_pred             HHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEc
Q 017842          294 ARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVA  356 (365)
Q Consensus       294 e~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a  356 (365)
                      ..|.+.|..||.|.-||++.+        -.+|+|.+-++|..|+. ++|..++|+.|.|+.-
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            468888999999999999955        58999999999999999 9999999999999853

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.40  E-value=0.0002  Score=49.08  Aligned_cols=62  Identities=21%  Similarity=0.301  Sum_probs=53.8

Q ss_pred             HHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCCccCCeeEEEEEcc
Q 017842          293 NARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALDGQNLDGRAIRVNVAE  357 (365)
Q Consensus       293 ee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~~~~l~gr~l~V~~a~  357 (365)
                      .+.|...|.+||.|..+.|.....   +.-.|-|...+.++|.-|+..|+..++++++|.|+|+.
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~~d---g~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPHTD---YQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSCCS---TTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHHhheeEEEEEEEeccC---CcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            456778899999999999875532   34479999999999999999999999999999999975

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.90  E-value=0.0016  Score=47.41  Aligned_cols=69  Identities=13%  Similarity=0.147  Sum_probs=52.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCC-CCccceEEEEeCCHH
Q 017842          160 AKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRET-DRSRGFGFVTMSTVE  238 (365)
Q Consensus       160 ~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~g~afV~f~~~e  238 (365)
                      ++|-|++||+++|++++.+.+...|.+......                         ..+... ...-.-|||.|.+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~-------------------------~Gk~s~~~~~~SRAYi~F~~~~   56 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFF-------------------------SNDTSLYPHMYARAYINFKNQE   56 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEE-------------------------ESCCSSTTCCCEEEEEEESSSH
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEe-------------------------CCCcCCCCCcceEEEEEeCCHH
Confidence            478999999999999999999988877654321                         111111 123356999999999


Q ss_pred             HHHHHHHHHccCccc
Q 017842          239 EAEKAVEMFHRYDID  253 (365)
Q Consensus       239 ~a~~Al~~lng~~~~  253 (365)
                      ++......++|..|.
T Consensus        57 ~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_          57 DIILFRDRFDGYVFL   71 (91)
T ss_dssp             HHHHHHHHHTTCEEE
T ss_pred             HHHHHHHHcCCcEEE
Confidence            999999999998873

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.76  E-value=0.0021  Score=46.21  Aligned_cols=73  Identities=18%  Similarity=0.304  Sum_probs=57.0

Q ss_pred             CCCCCeEEEcCCCCCCCH---------HHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCc
Q 017842          156 PPEDAKLFVGNLPYDVDS---------EKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRS  226 (365)
Q Consensus       156 ~~~~~tvfVgnLp~~~t~---------~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  226 (365)
                      -+++.||.|.=..++..+         .+|.+.|..||+|.-+|+                          +        
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRF--------------------------v--------   57 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRI--------------------------N--------   57 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEE--------------------------E--------
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEE--------------------------e--------
Confidence            346778888655544433         468888999999877763                          2        


Q ss_pred             cceEEEEeCCHHHHHHHHHHHccCcccCeeEEEeecC
Q 017842          227 RGFGFVTMSTVEEAEKAVEMFHRYDIDGRLLTVNKAA  263 (365)
Q Consensus       227 ~g~afV~f~~~e~a~~Al~~lng~~~~gr~l~V~~a~  263 (365)
                      .+..+|+|.+-..|.+|+.+ +|..+.|+.|.|....
T Consensus        58 ~d~mwVTF~dG~SAL~al~l-~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          58 QGQMLVTFADSHSALSVLDV-DGMKVKGRAVKISGPS   93 (95)
T ss_dssp             TTEEEEECSCSHHHHHHHHG-GGSEETTEEEEEECCC
T ss_pred             CCeEEEEECCcHHHHHHhcc-CCeEEcceEEEEecCC
Confidence            44689999999999999987 9999999999997543

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.98  E-value=0.074  Score=36.00  Aligned_cols=60  Identities=27%  Similarity=0.345  Sum_probs=49.0

Q ss_pred             HHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCHHHHHHHHHHHccCcccC
Q 017842          175 KLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTVEEAEKAVEMFHRYDIDG  254 (365)
Q Consensus       175 ~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~e~a~~Al~~lng~~~~g  254 (365)
                      .|.+.|.++|.|.++.+..                             .....-.|-|...+..+|..|+..|+...|++
T Consensus        12 ~L~~~f~~h~~V~sv~l~~-----------------------------~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~   62 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSP-----------------------------HTDYQLKAVVQMENLQDAIGAVNSLHRYKIGS   62 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECS-----------------------------CCSTTCCEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHHHhheeEEEEEEEe-----------------------------ccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCC
Confidence            4556789999998876431                             22345679999999999999999999999999


Q ss_pred             eeEEEeecC
Q 017842          255 RLLTVNKAA  263 (365)
Q Consensus       255 r~l~V~~a~  263 (365)
                      +.|.|.++.
T Consensus        63 KRI~Vs~~~   71 (73)
T d2dgxa1          63 KKILVSLAT   71 (73)
T ss_dssp             EEEEEEECC
T ss_pred             eEEEEEEec
Confidence            999998764

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.87  E-value=0.74  Score=33.01  Aligned_cols=56  Identities=21%  Similarity=0.278  Sum_probs=46.2

Q ss_pred             CceEEEeCCCCcCcHHHHHHHHhccCCeEEEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 017842          279 GFRIYVGNLPWEVDNARLEQVFSEHGKVVNARVVYDRETGRSRGFGFVTMSSETELNDAIAALD  342 (365)
Q Consensus       279 ~~~lfV~nLp~~~tee~L~~~F~~~G~V~~v~i~~d~~~~~~kG~afV~F~s~~~a~~Al~~l~  342 (365)
                      ..-||.-..|..+...+|.++|+.||.|.--.| .+.       -|||...+.++|..++..++
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-ddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cCc-------eEEEEecCHHHHHHHHHHhc
Confidence            347999999999999999999999998755444 332       69999999999999888654

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.20  E-value=0.98  Score=32.35  Aligned_cols=57  Identities=23%  Similarity=0.337  Sum_probs=46.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHccCCeEEEEEeeeeccCCCcccceeeeeeeeeeeeEEecCCCCCccceEEEEeCCH
Q 017842          158 EDAKLFVGNLPYDVDSEKLAMLFEKAGTVEIAEVKFHFLFGNQGFHMWVCAVFYVSLLQVIYNRETDRSRGFGFVTMSTV  237 (365)
Q Consensus       158 ~~~tvfVgnLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~afV~f~~~  237 (365)
                      ...-||.-..|......+|.++|+.||.|..--                           +       +-.-|||...+.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~Vsw---------------------------I-------ddTSa~V~L~~~   59 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISW---------------------------I-------DDTSAFVSLSQP   59 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEE---------------------------E-------ETTEEEEECSCH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEEE---------------------------e-------cCceEEEEecCH
Confidence            455799999999999999999999999885432                           1       122699999999


Q ss_pred             HHHHHHHHHHc
Q 017842          238 EEAEKAVEMFH  248 (365)
Q Consensus       238 e~a~~Al~~ln  248 (365)
                      ++|..++..++
T Consensus        60 e~~~~v~~~~~   70 (100)
T d1whva_          60 EQVQIAVNTSK   70 (100)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhc
Confidence            99998887654