Citrus Sinensis ID: 022221

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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
Protein Sequence
MELGGGRKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGSGSGHSMKSNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKSVI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccEEccccccccccccHHccccEEEcccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHcccccccccccccccccccccHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccHHHccccccccccccHHHcccccccccccccEEEccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccEcccHHHHcccccccccccccccccccccccccccccccccccccccccccEEEEEEEHHHHHHHHcccccccHHHHHHcccEEEEEccccccccccEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHcccccccccccccccccHHHHHcccc
Coil and Loop (DISEMBL)
melgggrkrgrhdgasngnggfkkskqemenfptgigskskpctkffstsgcpfgegchflhyvpggFKAVSQMLnlggtpahppppprnsgappsfpdgssppavkSRLCnkynsaegckfgdkchfahgewelgrptvpsyedpramggpmhgrmggrlepppqslgaaasfgasATAKISIDAKLAGaiigkngvnsKQICRLtgaklsirdhevdpnlrnielegtFDQIKQASAMVRELIVNVgsgsghsmksnsssqsnnFKTKLCEnfakgsctfgdrchfahgsEELRKSVI
Flexible Loop (DISEMBL)
melgggrkrgrhdgasngnggfkkskQEMENFPtgigskskpcTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDAKLAGAiigkngvnskQICRLTgaklsirdhevdpnlrnielEGTFDQIKQASAMVRELIVNVGSGSGHSMKSNSSSQSNNFKTKLCENFAKGSCTFgdrchfahgseelrksvi
Low Complexity Region (SEG)
MELGGGRKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTpahppppprnsgappsfpDGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVPSYEDPramggpmhgrmggrLEPPPQSLgaaasfgasataKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVgsgsghsmksnsssqsnnFKTKLCENFAKGSCTFGDRCHFAHGSEELRKSVI
Disordered region (IsUnstruct)
******************************************CTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQML**********************************LCNKYNSAEGCKFGDKCHFAHGEWELG*****************************************ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNV*********************KLCENFAKGSCTFGDRCHFA***********
Disordered Region (DISOPRED)
******************************************CTKFFSTSGCPFGEGCHFLHY***************************************************************HFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDAKLA*******************A******************EGTFDQIKQASAMVRELIVNVGSGSGHSMKSNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEEL*****
Disordered Region (DISEMBL)
***********HDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGS****************FKTKLCENFAKGSCTFGDRCHFAHGS********
Disordered Region (DISPRO)
***************************************SKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQ********************************VKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVPSYEDPRAMGG*MHGRMGGRLEPPPQSLGAA*SFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGSG**************NFKTKLCENFAKGSCTFGDRCHFAHG*********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MELGGGRKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGSGSGHSMKSNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKSVI
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	300	2.2.26 [Sep-21-2011]
Q7F8R0	300	Zinc finger CCCH domain-c	yes	no	0.973	0.973	0.639	7e-96
Q7XPK1	309	Zinc finger CCCH domain-c	no	no	0.956	0.928	0.582	6e-84
Q69XQ3	295	Zinc finger CCCH domain-c	no	no	0.94	0.955	0.557	2e-82
Q9C7C3	248	Zinc finger CCCH domain-c	yes	no	0.77	0.931	0.491	5e-65
Q9FG30	240	Zinc finger CCCH domain-c	no	no	0.63	0.787	0.521	2e-45
Q9LT81	386	Zinc finger CCCH domain-c	no	no	0.313	0.243	0.314	2e-07
Q84UQ3	367	Zinc finger CCCH domain-c	no	no	0.33	0.269	0.336	6e-06

>sp|Q7F8R0|C3H14_ORYSJ Zinc finger CCCH domain-containing protein 14 OS=Oryza sativa subsp. japonica GN=Os02g0194200 PE=2 SV=1

 Score =  350 bits (898), Expect = 7e-96,   Method: Compositional matrix adjust.
 Identities = 195/305 (63%), Positives = 223/305 (73%), Gaps = 13/305 (4%)

Query: 1   MELGGGRKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHF 60
           ME+GG RKRG+ DGA NG GG  K  +E E+F TG+GSKSKPCTKFFSTSGCPFGEGCHF
Sbjct: 1   MEVGG-RKRGKPDGA-NGAGG--KRARESESFQTGVGSKSKPCTKFFSTSGCPFGEGCHF 56

Query: 61  LHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGC 120
           LH+ PGG++AV++M NLGG PA  PPP R      + PDG   P VK+RLCNKYN+AEGC
Sbjct: 57  LHHFPGGYQAVAKMTNLGG-PAIAPPPGRMPMGN-AVPDGPPTPTVKTRLCNKYNTAEGC 114

Query: 121 KFGDKCHFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATA 180
           K+GDKCHFAHGE ELG+P +     P  MG    G       P   ++   ASFGASATA
Sbjct: 115 KWGDKCHFAHGERELGKPMLMDSSMPPPMGPRPTGHFAPPPMPS-PAMSTPASFGASATA 173

Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAM 240
           KIS+DA LAG IIG+ GVN+KQI R+TGAKL+IRDHE D NL+NIELEGTFDQIK ASAM
Sbjct: 174 KISVDASLAGGIIGRGGVNTKQISRVTGAKLAIRDHESDTNLKNIELEGTFDQIKNASAM 233

Query: 241 VRELIVNVGSGSGHSMK------SNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEE 294
           VRELIV++G G+    K             +NFKTKLCENF KGSCTFGDRCHFAHG  E
Sbjct: 234 VRELIVSIGGGAPPQGKKPVGGSHRGGGPGSNFKTKLCENFTKGSCTFGDRCHFAHGENE 293

Query: 295 LRKSV 299
           LRKS 
Sbjct: 294 LRKSA 298

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q7XPK1|C3H31_ORYSJ Zinc finger CCCH domain-containing protein 31 OS=Oryza sativa subsp. japonica GN=Os04g0665700 PE=2 SV=1

 Score =  310 bits (795), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 180/309 (58%), Positives = 207/309 (66%), Gaps = 22/309 (7%)

Query: 4   GGGRKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHY 63
           G  RKR R D A+ G  G K+S+ E E+F TG+ SK KPCTKFFST GCPFGEGCHF H+
Sbjct: 5   GAARKRSRPDTANGGAAGGKRSR-ETESFQTGLSSKLKPCTKFFSTIGCPFGEGCHFSHF 63

Query: 64  VPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAV--KSRLCNKYNSAEGCK 121
           VPGG++AV++ LNLG      P       A      G+S PA   K+R+C KYN+AEGCK
Sbjct: 64  VPGGYQAVAKTLNLGNPAVPAPARAPMDHAA----GGNSHPASSGKTRMCTKYNTAEGCK 119

Query: 122 FGDKCHFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAA--SFGASAT 179
           FGDKCHFAHGE ELG+P   S+E   AM  PM GR GGR EPPP +       +FGASAT
Sbjct: 120 FGDKCHFAHGERELGKPAYMSHES--AMAPPMGGRYGGRPEPPPPAAMGPPAGNFGASAT 177

Query: 180 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASA 239
           AKIS+DA LAG IIGK GVN+KQICR+TG KLSIRDHE D NL+NIELEG FDQIKQAS 
Sbjct: 178 AKISVDASLAGGIIGKGGVNTKQICRVTGVKLSIRDHESDSNLKNIELEGNFDQIKQASN 237

Query: 240 MVRELIVNVGSGS-----------GHSMKSNSSSQSNNFKTKLCENFAKGSCTFGDRCHF 288
           MV ELI  +   +                       +N+KTKLCENF KG+CTFGDRCHF
Sbjct: 238 MVGELIATISPSTPAKKPAGSAAGAAPAGRGGPGGRSNYKTKLCENFVKGTCTFGDRCHF 297

Query: 289 AHGSEELRK 297
           AHG  E RK
Sbjct: 298 AHGENEQRK 306

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q69XQ3|C3H44_ORYSJ Zinc finger CCCH domain-containing protein 44 OS=Oryza sativa subsp. japonica GN=Os06g0618100 PE=2 SV=1

 Score =  305 bits (781), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 170/305 (55%), Positives = 203/305 (66%), Gaps = 23/305 (7%)

Query: 1   MELGGGRKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHF 60
           ME GGG++      A  G  G  K  +  E+   G+GSK KPCTKFFSTSGCPFG  CHF
Sbjct: 1   MEAGGGKR-----AAPEGTNGAAKRARASESSQVGVGSKLKPCTKFFSTSGCPFGSSCHF 55

Query: 61  LHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGC 120
           LH  PGG++A ++M + GGT    PP     G  P  P+G    +VK+R+CNKYN+AEGC
Sbjct: 56  LHNFPGGYQAAAKMTSHGGTAVAAPPGRMPLG--PGAPNGPPTSSVKTRMCNKYNTAEGC 113

Query: 121 KFGDKCHFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQ---SLGAAASFGAS 177
           K+G KCHFAHGE ELG+P +     P  MG           E PP     +   ++FGAS
Sbjct: 114 KWGSKCHFAHGERELGKPMLLDNSMPHPMGS-------MPFEAPPMPGPDIVPPSTFGAS 166

Query: 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQA 237
           ATAKIS+DA LAG IIGK G N+K I R+TGAKL+IRD+E +PNL+NIELEGTFDQIK A
Sbjct: 167 ATAKISVDASLAGGIIGKGGTNTKHISRMTGAKLAIRDNESNPNLKNIELEGTFDQIKHA 226

Query: 238 SAMVRELIVNVGSGSGHSMK-----SNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGS 292
           SAMV ELIV + SG+    K     S++    +NFKTKLCENF KGSCTFGDRCHFAHG 
Sbjct: 227 SAMVTELIVRI-SGNAPPAKNPGRGSHAGGPGSNFKTKLCENFNKGSCTFGDRCHFAHGE 285

Query: 293 EELRK 297
            ELRK
Sbjct: 286 SELRK 290

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9C7C3|C3H36_ARATH Zinc finger CCCH domain-containing protein 36 OS=Arabidopsis thaliana GN=At3g12130 PE=2 SV=1

 Score =  248 bits (632), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 151/307 (49%), Positives = 178/307 (57%), Gaps = 76/307 (24%)

Query: 7   RKRGRHD-GASNGNGG-FKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYV 64
           RKRGR + G+ N NGG +KKSKQEME++ TG+GSKSKPCTKFFSTSGCPFGE CHFLHYV
Sbjct: 4   RKRGRPEAGSFNSNGGGYKKSKQEMESYSTGLGSKSKPCTKFFSTSGCPFGENCHFLHYV 63

Query: 65  PGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGD 124
           PGG+ AVSQM N+G      PP P+ S                    N   S  G +F  
Sbjct: 64  PGGYNAVSQMTNMG------PPIPQVSR-------------------NMQGSGNGGRFSG 98

Query: 125 KCHFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISI 184
                                 R   GP H                 ++FG SATA+ S+
Sbjct: 99  ----------------------RGESGPGH----------------VSNFGDSATARFSV 120

Query: 185 DAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVREL 244
           DA LAGAIIGK GV+SKQICR TG KLSI+DHE DPNL+NI LEGT +QI +ASAMV++L
Sbjct: 121 DASLAGAIIGKGGVSSKQICRQTGVKLSIQDHERDPNLKNIVLEGTLEQISEASAMVKDL 180

Query: 245 IVNVGSGSGHSMKSNSSSQS-----------NNFKTKLCENFAKGSCTFGDRCHFAHGSE 293
           I  + S +                       +NFKTK+CE F+KG+CTFGDRCHFAHG  
Sbjct: 181 IGRLNSAAKKPPGGGLGGGGGMGSEGKPHPGSNFKTKICERFSKGNCTFGDRCHFAHGEA 240

Query: 294 ELRKSVI 300
           ELRKS I
Sbjct: 241 ELRKSGI 247

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FG30|C3H52_ARATH Zinc finger CCCH domain-containing protein 52 OS=Arabidopsis thaliana GN=At5g06770 PE=2 SV=1

 Score =  182 bits (463), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 108/207 (52%), Positives = 132/207 (63%), Gaps = 18/207 (8%)

Query: 107 KSRLCNKYNSAEGCKFGDKCHFAH---------GEWELGRPTVPSY-EDPRAMGGPMHGR 156
           KS+ C K+ S  GC FGD CHF H          +    RP V     + +  GGP  GR
Sbjct: 38  KSKPCTKFFSTSGCPFGDNCHFLHYVPGGYNAAAQMTNLRPPVSQVSRNMQGSGGP-GGR 96

Query: 157 MGGRLEPPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH 216
             GR +P     G  + FGAS T+KIS+DA LAGAIIGK G++SKQICR TGAKLSI+DH
Sbjct: 97  FSGRGDP---GSGPVSIFGAS-TSKISVDASLAGAIIGKGGIHSKQICRETGAKLSIKDH 152

Query: 217 EVDPNLRNIELEGTFDQIKQASAMVRELIVNVGSG---SGHSMKSNSSSQSNNFKTKLCE 273
           E DPNL+ IELEGTF+QI  AS MVRELI  +GS     G           +N+KTK+C+
Sbjct: 153 ERDPNLKIIELEGTFEQINVASGMVRELIGRLGSVKKPQGIGGPEGKPHPGSNYKTKICD 212

Query: 274 NFAKGSCTFGDRCHFAHGSEELRKSVI 300
            ++KG+CT+GDRCHFAHG  ELR+S I
Sbjct: 213 RYSKGNCTYGDRCHFAHGESELRRSGI 239

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LT81|C3H39_ARATH Zinc finger CCCH domain-containing protein 39 OS=Arabidopsis thaliana GN=At3g19360 PE=2 SV=1

 Score = 57.0 bits (136), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 39/124 (31%), Positives = 54/124 (43%), Gaps = 30/124 (24%)

Query: 36  IGSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKA------VSQMLNLGGTPAHPP---- 85
           I  + K C KF     CP+G+ C+F+H     F+        S ++++G T A  P    
Sbjct: 182 IILRMKLCRKFCFGEECPYGDRCNFIHEDLSKFREDSGKLRESSVISVGATAADQPSDTA 241

Query: 86  --------------PPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHG 131
                         P P N+G              K+RLC K++    C FGDKCHFAHG
Sbjct: 242 SNLIEVNRQGSIPVPAPMNNGG------VVKTVYWKTRLCMKFDITGQCPFGDKCHFAHG 295

Query: 132 EWEL 135
           + EL
Sbjct: 296 QAEL 299

Arabidopsis thaliana (taxid: 3702)

>sp|Q84UQ3|C3H56_ORYSJ Zinc finger CCCH domain-containing protein 56 OS=Oryza sativa subsp. japonica GN=Os08g0159800 PE=2 SV=1

 Score = 52.0 bits (123), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 36/107 (33%), Positives = 53/107 (49%), Gaps = 8/107 (7%)

Query: 39  KSKPCTKFFSTSGCPFGEGCHFLHYVPGGFK---AVS---QMLNLGGTPAHPPPPPRNSG 92
           K + C KF++  GCP+G+ C FLH      +   A+S    +   GG  ++       + 
Sbjct: 171 KGRHCKKFYTDEGCPYGDACTFLHDEQSKARESVAISLSPSVGGGGGGGSYNSAAAAAAS 230

Query: 93  APPSFPDG--SSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGR 137
           A  +  +G    P   K+R+CNK+     C FG KCHFAHG  EL +
Sbjct: 231 ASAAAGNGPMQKPSNWKTRICNKWEMTGYCPFGSKCHFAHGAAELHK 277

Oryza sativa subsp. japonica (taxid: 39947)

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	300
224057168	304	predicted protein [Populus trichocarpa]	0.986	0.973	0.763	1e-124
225435608	301	PREDICTED: zinc finger CCCH domain-conta	0.973	0.970	0.801	1e-124
224076054	315	predicted protein [Populus trichocarpa]	0.973	0.926	0.733	1e-122
356536568	297	PREDICTED: zinc finger CCCH domain-conta	0.966	0.976	0.776	1e-119
225450321	296	PREDICTED: zinc finger CCCH domain-conta	0.98	0.993	0.766	1e-118
358248424	297	uncharacterized protein LOC100818781 [Gl	0.966	0.976	0.762	1e-118
225441425	297	PREDICTED: zinc finger CCCH domain-conta	0.963	0.973	0.702	1e-114
356504859	295	PREDICTED: zinc finger CCCH domain-conta	0.96	0.976	0.681	1e-113
356504857	295	PREDICTED: zinc finger CCCH domain-conta	0.96	0.976	0.681	1e-111
255634442	295	unknown [Glycine max]	0.96	0.976	0.677	1e-111

>gi|224057168|ref|XP_002299153.1| predicted protein [Populus trichocarpa] gi|222846411|gb|EEE83958.1| predicted protein [Populus trichocarpa]

 Score =  449 bits (1156), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 232/304 (76%), Positives = 255/304 (83%), Gaps = 8/304 (2%)

Query: 1   MELGGG-RKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCH 59
           ME GGG RKR R+D A NGNGG KK++QEME+F TGIGSKSKPCTKFFSTSGCPFGEGCH
Sbjct: 1   MEFGGGHRKRTRNDAAFNGNGGHKKNRQEMESFSTGIGSKSKPCTKFFSTSGCPFGEGCH 60

Query: 60  FLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPP-SFPDGSSPPAVKSRLCNKYNSAE 118
           FLHYVPGGFKAVSQMLN+GG+PA  PP  RN G P  S+ D SSPP+VKSRLCNKYN+ E
Sbjct: 61  FLHYVPGGFKAVSQMLNVGGSPA-LPPASRNQGVPTLSYQDRSSPPSVKSRLCNKYNTVE 119

Query: 119 GCKFGDKCHFAHGEWELGRPT-VPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGAS 177
           GCKFGDKCHFAHGEWELG+ +  PSYEDPRAM GP+ GRM   +E P Q  GAAASFG+S
Sbjct: 120 GCKFGDKCHFAHGEWELGKASAAPSYEDPRAM-GPIPGRMSRHMEHPHQGHGAAASFGSS 178

Query: 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQA 237
           AT KISIDA LAGAIIGKNGVNSK ICR+TGAKLSIRDHE DP  R+IELEG+FDQI QA
Sbjct: 179 ATTKISIDASLAGAIIGKNGVNSKHICRVTGAKLSIRDHEADPKKRSIELEGSFDQISQA 238

Query: 238 SAMVRELIVNVGSGSGHSMKS---NSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEE 294
           S MVR+LI NVG  SG  +K+   +SS  SNNFKTK+CENF KGSCTFGDRCHFAHG+EE
Sbjct: 239 SDMVRQLISNVGQASGPPIKNQAMHSSGGSNNFKTKICENFNKGSCTFGDRCHFAHGAEE 298

Query: 295 LRKS 298
           LRKS
Sbjct: 299 LRKS 302

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225435608|ref|XP_002285629.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Vitis vinifera]

 Score =  449 bits (1155), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 242/302 (80%), Positives = 264/302 (87%), Gaps = 10/302 (3%)

Query: 1   MELGGGRKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHF 60
           MELGG RKRGR +G  NGNGGFKKSKQEME+F +GIGSKSKPCTKFFSTSGCPFGEGCHF
Sbjct: 1   MELGGARKRGRQEGTLNGNGGFKKSKQEMESFSSGIGSKSKPCTKFFSTSGCPFGEGCHF 60

Query: 61  LHYVPGGFKAVSQMLNLGG-TPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEG 119
           LHYVPGG KAVSQM+NLGG TP    PP RN   PPSFPDGSSPPAVK+RLCNKYNSAEG
Sbjct: 61  LHYVPGGIKAVSQMVNLGGNTPL--APPARNPAVPPSFPDGSSPPAVKTRLCNKYNSAEG 118

Query: 120 CKFGDKCHFAHGEWELGRPTVPSY-EDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASA 178
           CKFGDKCHFAHGEWELG+PT+PS+ ED R MG    GR+ GRLEPPP  L AAASFGASA
Sbjct: 119 CKFGDKCHFAHGEWELGKPTLPSHHEDHRGMGS---GRLAGRLEPPPPGLAAAASFGASA 175

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQAS 238
           TAKIS+DA LAGAIIGK+GVNSKQICRLTGAKLSI+DH+ DPNLRNIELEGTFDQIKQAS
Sbjct: 176 TAKISVDASLAGAIIGKSGVNSKQICRLTGAKLSIKDHDSDPNLRNIELEGTFDQIKQAS 235

Query: 239 AMVRELIVNVGSGSGHSMKS---NSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEEL 295
           AMVRELIVN+ S SG  M++    +S+ +NNFKTKLCENF KGSCTFG+RCHFAHG++EL
Sbjct: 236 AMVRELIVNISSASGPPMRNPAMQASAAANNFKTKLCENFTKGSCTFGERCHFAHGADEL 295

Query: 296 RK 297
           RK
Sbjct: 296 RK 297

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224076054|ref|XP_002304891.1| predicted protein [Populus trichocarpa] gi|222842323|gb|EEE79870.1| predicted protein [Populus trichocarpa]

 Score =  444 bits (1143), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 234/319 (73%), Positives = 252/319 (78%), Gaps = 27/319 (8%)

Query: 1   MELGGG-RKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCH 59
           ME GGG RKRGR D A NGNGG KK++QEME+F TGIGSKSKPCTKFFSTSGCPFGEGCH
Sbjct: 1   MEFGGGHRKRGRLDAAFNGNGGHKKTRQEMESFSTGIGSKSKPCTKFFSTSGCPFGEGCH 60

Query: 60  FLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPP-SFPDGSSPPAVKSRLCNKYNSAE 118
           FLHYVPGG+KAVSQML     PA  PP  RN GAPP SFPD SSPP+VKSRLCNKYN+ E
Sbjct: 61  FLHYVPGGYKAVSQML-----PA-LPPASRNQGAPPPSFPDRSSPPSVKSRLCNKYNTVE 114

Query: 119 GCKFGDKCHFAHGEWELGRPTVPSYEDPRAMG----------------GPMHGRMGGRLE 162
           GCKFGDKCHFAHGEWELG+ +  SY+DPRAMG                GPM GRM   +E
Sbjct: 115 GCKFGDKCHFAHGEWELGKASAASYDDPRAMGPMQGRAAAPYDDPRAMGPMQGRMSRHME 174

Query: 163 PPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNL 222
            P Q  GAAASFG+SAT KISIDA LAGAIIGKNGVNSK ICR TGAKLSIR+HE DP  
Sbjct: 175 HPHQGHGAAASFGSSATTKISIDASLAGAIIGKNGVNSKHICRATGAKLSIREHETDPKK 234

Query: 223 RNIELEGTFDQIKQASAMVRELIVNVGSGSGHSMKS---NSSSQSNNFKTKLCENFAKGS 279
           RNIELEG+FDQI QAS MVR+LI NVG  SG  MK+   +SS  SNNFKTK+CENF KGS
Sbjct: 235 RNIELEGSFDQISQASDMVRQLISNVGQASGPPMKNSSMHSSGGSNNFKTKICENFNKGS 294

Query: 280 CTFGDRCHFAHGSEELRKS 298
           CTFGDRCHFAHG+EELRKS
Sbjct: 295 CTFGDRCHFAHGAEELRKS 313

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356536568|ref|XP_003536809.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Glycine max]

 Score =  435 bits (1119), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 229/295 (77%), Positives = 255/295 (86%), Gaps = 5/295 (1%)

Query: 7   RKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPG 66
           RKRGRH+ A N NGG KKS+ EM++FPTG+GSKSKPCTKFFSTSGCPFGEGCHFLHYVPG
Sbjct: 3   RKRGRHEAAFNFNGGAKKSRPEMDSFPTGLGSKSKPCTKFFSTSGCPFGEGCHFLHYVPG 62

Query: 67  GFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKC 126
           GFKAVSQ++N+G  P  P    RN   PPSFPDGSSPP VK+RLCNK+N+AEGCKFGDKC
Sbjct: 63  GFKAVSQLINVGSNPVIPQVG-RNP-VPPSFPDGSSPPVVKTRLCNKFNTAEGCKFGDKC 120

Query: 127 HFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDA 186
           HFAHGEWELGRPT PSYEDPR MG     R+GGR+EPP  + GAAASFGASATAKISI+A
Sbjct: 121 HFAHGEWELGRPTAPSYEDPRVMGQMPSSRVGGRVEPPHPAHGAAASFGASATAKISINA 180

Query: 187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV 246
            LAGA+IGKNGVNSKQICR+TGAKLSIRDH+ DPNLRNIELEG+FDQIKQASAMV E+I+
Sbjct: 181 SLAGAVIGKNGVNSKQICRVTGAKLSIRDHDTDPNLRNIELEGSFDQIKQASAMVHEVIL 240

Query: 247 NVGSGSGHSMKSNSSSQS---NNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKS 298
           NV S SG  MKS +S  S   +NFKTKLCENFAKGSCTFG+RCHFAHG++ELRKS
Sbjct: 241 NVSSASGPPMKSFTSQNSAPASNFKTKLCENFAKGSCTFGERCHFAHGNDELRKS 295

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225450321|ref|XP_002273052.1| PREDICTED: zinc finger CCCH domain-containing protein 14 [Vitis vinifera] gi|147768909|emb|CAN75883.1| hypothetical protein VITISV_024456 [Vitis vinifera]

 Score =  430 bits (1106), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 230/300 (76%), Positives = 258/300 (86%), Gaps = 6/300 (2%)

Query: 1   MELGGGRKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHF 60
           ME+GG ++RGR DGA+ GNGGFKKSKQE E+F TGIGSKSKPCTKFFSTSGCPFGEGCHF
Sbjct: 1   MEVGG-KRRGRPDGAAFGNGGFKKSKQETESFSTGIGSKSKPCTKFFSTSGCPFGEGCHF 59

Query: 61  LHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGC 120
           LHYVPGG+ AV+QM NLGG PA PP   RN  APP+ PDG  PP VK+R+CNK+N+ EGC
Sbjct: 60  LHYVPGGYSAVTQMTNLGGNPAMPPIA-RNPMAPPTIPDG--PPTVKTRICNKFNTPEGC 116

Query: 121 KFGDKCHFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATA 180
           KFGDKCHFAHGE ELGRP VP++EDPRAMG PM GR+ GRLE PP  L AAASFGASATA
Sbjct: 117 KFGDKCHFAHGELELGRPIVPTHEDPRAMG-PMGGRLAGRLEAPPPGLAAAASFGASATA 175

Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAM 240
           KIS+DA LAGAIIGK GVNSKQICRLTG KLSI++HE DPN RNIELEGTFDQIKQASAM
Sbjct: 176 KISVDASLAGAIIGKGGVNSKQICRLTGVKLSIKEHESDPNQRNIELEGTFDQIKQASAM 235

Query: 241 VRELIVNVGSGSGHSMK-SNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKSV 299
           VRELI N+GS +GH+   + S++ +NNFKTK+C+NFAKGSCTFGDRCHFAHG+ ELRK V
Sbjct: 236 VRELIFNIGSAAGHAKNPTGSAASANNFKTKMCDNFAKGSCTFGDRCHFAHGANELRKPV 295

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248424|ref|NP_001240135.1| uncharacterized protein LOC100818781 [Glycine max] gi|255636715|gb|ACU18693.1| unknown [Glycine max]

 Score =  429 bits (1102), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 225/295 (76%), Positives = 254/295 (86%), Gaps = 5/295 (1%)

Query: 7   RKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPG 66
           RKRGR + A N NGG KKS+ E ++FPTG+GSKSKPCTKFFSTSGCPFGEGCHFLHYVPG
Sbjct: 3   RKRGRPEAAFNFNGGAKKSRPETDSFPTGLGSKSKPCTKFFSTSGCPFGEGCHFLHYVPG 62

Query: 67  GFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKC 126
           GFKAVSQ++N+G  P  P    RN   PPSFPDGSSPP VK+RLCNK+N+AEGCKFGDKC
Sbjct: 63  GFKAVSQLINVGSNPVTPQVG-RNP-VPPSFPDGSSPPVVKTRLCNKFNTAEGCKFGDKC 120

Query: 127 HFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDA 186
           HFAHGEWELGRPT PSYEDPR +G     R+GGR+EPP  + GAAASFGASATAKISI+A
Sbjct: 121 HFAHGEWELGRPTAPSYEDPRVLGQMPSSRVGGRVEPPHPAHGAAASFGASATAKISINA 180

Query: 187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV 246
            LAGA+IGKNGVNSKQICR+TGAKLSIRDH+ DPNLRNIELEG+FDQIKQASAMV E+I+
Sbjct: 181 SLAGAVIGKNGVNSKQICRVTGAKLSIRDHDTDPNLRNIELEGSFDQIKQASAMVHEVIL 240

Query: 247 NVGSGSGHSMK---SNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKS 298
           NV S SG  MK   S +S+ ++NFKTKLCENFAKGSCTFG+RCHFAHG++ELRKS
Sbjct: 241 NVSSASGPPMKSFTSQTSAPTSNFKTKLCENFAKGSCTFGERCHFAHGTDELRKS 295

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225441425|ref|XP_002279071.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like isoform 1 [Vitis vinifera]

 Score =  418 bits (1074), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 210/299 (70%), Positives = 242/299 (80%), Gaps = 10/299 (3%)

Query: 7   RKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPG 66
           RKRGR  GA N NGGFKKSKQE+E+  TGIGSKSKPCTKFFSTSGCPFGE CHFLHYVPG
Sbjct: 4   RKRGRPGGALNANGGFKKSKQEVESLSTGIGSKSKPCTKFFSTSGCPFGESCHFLHYVPG 63

Query: 67  GFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKC 126
           G+ AV+QM N    P  PP     +G PP  P+GSS PAVKS++CNK+N+AEGCKFGDKC
Sbjct: 64  GYNAVAQMTNQ--APILPPASRNMAGPPPPVPNGSSMPAVKSKMCNKFNTAEGCKFGDKC 121

Query: 127 HFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDA 186
           HFAHGEWELG+P  P ++DPRAMG  + GR+ GR+EP P   G AASFGASATAKIS+DA
Sbjct: 122 HFAHGEWELGKPLAPYHDDPRAMGS-IPGRLAGRIEPSPT--GPAASFGASATAKISVDA 178

Query: 187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV 246
            LAGAIIGK GVNSKQICR TGAKLSIR+H+ DPNLRNIELEGTF+QIK+ASAMVRELIV
Sbjct: 179 SLAGAIIGKGGVNSKQICRQTGAKLSIREHDSDPNLRNIELEGTFEQIKEASAMVRELIV 238

Query: 247 NVGSGSGHSMKS-----NSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKSVI 300
           N+ +  GH+  +       +  ++N+KTKLC+NF KGSCTFG+RCHFAHG+ ELRKS I
Sbjct: 239 NISAMPGHARTTAMPGGGQAPPASNYKTKLCDNFTKGSCTFGERCHFAHGAGELRKSAI 297

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356504859|ref|XP_003521212.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Glycine max]

 Score =  412 bits (1059), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 203/298 (68%), Positives = 242/298 (81%), Gaps = 10/298 (3%)

Query: 7   RKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPG 66
           RKRGRH+   + NGGFK+SKQEME+  TG+GSKSKPCTKFFST+GCPFGEGCHFLHYVPG
Sbjct: 4   RKRGRHETGFSLNGGFKRSKQEMESLSTGVGSKSKPCTKFFSTAGCPFGEGCHFLHYVPG 63

Query: 67  GFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKC 126
           G+ AV+ M+NL  TPA PPPP RN  A P  P+GS+P AVK+R+CNK+N+AEGCKFGDKC
Sbjct: 64  GYNAVAHMMNL--TPAAPPPPSRNVAALPHVPNGSAPSAVKTRICNKFNTAEGCKFGDKC 121

Query: 127 HFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDA 186
           HFAHGEWELG+   PS++D  AMG P  GR+ GR+EPP    G AASFGA++TAKIS++A
Sbjct: 122 HFAHGEWELGKHIAPSFDDHHAMGPPGAGRLAGRMEPP----GPAASFGANSTAKISVEA 177

Query: 187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV 246
            LAGAIIGK GVNSKQICR TGAKLSIR+HE DPNLRNIELEG+F+QIK+AS MV++L++
Sbjct: 178 SLAGAIIGKGGVNSKQICRQTGAKLSIREHESDPNLRNIELEGSFEQIKEASNMVKDLLL 237

Query: 247 NVGSG----SGHSMKSNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKSVI 300
            +       +   +    +S  +NFKTKLCENFAKGSCTFGDRCHFAHG+ ELRKS +
Sbjct: 238 TLQMSAPPKTTPGVPGAPASHGSNFKTKLCENFAKGSCTFGDRCHFAHGASELRKSGV 295

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356504857|ref|XP_003521211.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Glycine max]

 Score =  407 bits (1046), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 203/298 (68%), Positives = 241/298 (80%), Gaps = 10/298 (3%)

Query: 7   RKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPG 66
           RKRGR +   + NGGFKKSKQEME+  TG+GSKSKPCTKFFST+GCPFGEGCHFLHYVPG
Sbjct: 4   RKRGRPEPGFSLNGGFKKSKQEMESLSTGVGSKSKPCTKFFSTAGCPFGEGCHFLHYVPG 63

Query: 67  GFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKC 126
           G+ AV+ M+NL  TPA P PP RN  A P  P+GS+P AVK+R+CNK+N+AEGCKFGDKC
Sbjct: 64  GYNAVAHMMNL--TPAAPLPPTRNVAALPHVPNGSAPSAVKTRICNKFNTAEGCKFGDKC 121

Query: 127 HFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDA 186
           HFAHGEWELG+   PS++D RAMG P  GR+ GR+EPP    G AASFGA++TAKIS++A
Sbjct: 122 HFAHGEWELGKHIAPSFDDHRAMGPPGAGRLAGRMEPP----GPAASFGANSTAKISVEA 177

Query: 187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV 246
            LAGAIIGK GVNSKQICR TGAKLSIR+HE DPNLRNIELEG+F+QIK+AS MV++L++
Sbjct: 178 SLAGAIIGKGGVNSKQICRQTGAKLSIREHESDPNLRNIELEGSFEQIKEASNMVKDLLL 237

Query: 247 NVGSG----SGHSMKSNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKSVI 300
            +       +   +    +S  +NFKTKLCENFAKGSCTFGDRCHFAHG+ ELRKS +
Sbjct: 238 TLQMSAPPKTTPGVPGAPASHGSNFKTKLCENFAKGSCTFGDRCHFAHGASELRKSGV 295

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255634442|gb|ACU17586.1| unknown [Glycine max]

 Score =  405 bits (1042), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 202/298 (67%), Positives = 240/298 (80%), Gaps = 10/298 (3%)

Query: 7   RKRGRHDGASNGNGGFKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPG 66
           RKRGR +   + NGGFKKSKQEME+  TG+GSKSKPCTKFFST+GCPFGEGCHFLHYVPG
Sbjct: 4   RKRGRPEPGFSLNGGFKKSKQEMESLSTGVGSKSKPCTKFFSTAGCPFGEGCHFLHYVPG 63

Query: 67  GFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKC 126
           G+ AV+ M+NL  TPA P PP RN  A P  P+GS+P AVK+R+CNK+N+AEGCKFGDKC
Sbjct: 64  GYNAVAHMMNL--TPAAPLPPTRNVAALPHVPNGSAPSAVKTRICNKFNTAEGCKFGDKC 121

Query: 127 HFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDA 186
           HFAHGEWELG+   PS++D RAMG P  GR+ GR+EPP    G AASFGA++TAKIS++A
Sbjct: 122 HFAHGEWELGKHIAPSFDDHRAMGPPGAGRLAGRMEPP----GPAASFGANSTAKISVEA 177

Query: 187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV 246
            LAGAIIGK GVNSKQICR TGAKLSIR+HE DPN RNIELEG+F+QIK+AS MV++L++
Sbjct: 178 SLAGAIIGKGGVNSKQICRQTGAKLSIREHESDPNFRNIELEGSFEQIKEASNMVKDLLL 237

Query: 247 NVGSG----SGHSMKSNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKSVI 300
            +       +   +    +S  +NFKTKLCENFAKGSCTFGDRCHFAHG+ ELRKS +
Sbjct: 238 TLQMSAPPKTTPGVPGAPASHGSNFKTKLCENFAKGSCTFGDRCHFAHGASELRKSGV 295

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	300
TAIR|locus:2170169	240	AT5G06770 [Arabidopsis thalian	0.4	0.5	0.601	1.6e-63
TAIR|locus:2099292	248	AT3G12130 [Arabidopsis thalian	0.646	0.782	0.433	4.4e-36
UNIPROTKB|G3V2D5	176	ZFP36L1 "Zinc finger protein 3	0.1	0.170	0.516	3.7e-08
TAIR|locus:2028306	384	AT1G32360 [Arabidopsis thalian	0.116	0.091	0.542	4e-08
UNIPROTKB|G3V2P5	207	ZFP36L1 "Zinc finger protein 3	0.1	0.144	0.516	9e-08
TAIR|locus:2090669	386	AT3G19360 [Arabidopsis thalian	0.11	0.085	0.588	1.9e-07
UNIPROTKB|Q7ZXW9	363	zfp36l2-A "Zinc finger protein	0.106	0.088	0.484	5e-07
UNIPROTKB|A7MB98	338	ZFP36L1 "Uncharacterized prote	0.1	0.088	0.516	5.5e-07
UNIPROTKB|E2R2W0	338	ZFP36L1 "Uncharacterized prote	0.1	0.088	0.516	5.5e-07
UNIPROTKB|Q07352	338	ZFP36L1 "Zinc finger protein 3	0.1	0.088	0.516	5.5e-07

TAIR|locus:2170169 AT5G06770 [Arabidopsis thaliana (taxid:3702)]

 Score = 364 (133.2 bits), Expect = 1.6e-63, Sum P(2) = 1.6e-63
 Identities = 74/123 (60%), Positives = 89/123 (72%)

Query:   181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAM 240
             KIS+DA LAGAIIGK G++SKQICR TGAKLSI+DHE DPNL+ IELEGTF+QI  AS M
Sbjct:   117 KISVDASLAGAIIGKGGIHSKQICRETGAKLSIKDHERDPNLKIIELEGTFEQINVASGM 176

Query:   241 VRELIV---NVXXXXXXXXXXXXXXXXXXFKTKLCENFAKGSCTFGDRCHFAHGSEELRK 297
             VRELI    +V                  +KTK+C+ ++KG+CT+GDRCHFAHG  ELR+
Sbjct:   177 VRELIGRLGSVKKPQGIGGPEGKPHPGSNYKTKICDRYSKGNCTYGDRCHFAHGESELRR 236

Query:   298 SVI 300
             S I
Sbjct:   237 SGI 239

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

TAIR|locus:2099292 AT3G12130 [Arabidopsis thaliana (taxid:3702)]

 Score = 389 (142.0 bits), Expect = 4.4e-36, P = 4.4e-36
 Identities = 91/210 (43%), Positives = 111/210 (52%)

Query:   107 KSRLCNKYNSAEGCKFGDKCHFAH---GEWE-LGRPTVPSYEDPXXXXXXXXXXXXXXLE 162
             KS+ C K+ S  GC FG+ CHF H   G +  + + T      P                
Sbjct:    38 KSKPCTKFFSTSGCPFGENCHFLHYVPGGYNAVSQMTNMGPPIPQVSRNMQGSGNGGRFS 97

Query:   163 PPPQS-LXXXXXXXXXXXXKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPN 221
                +S              + S+DA LAGAIIGK GV+SKQICR TG KLSI+DHE DPN
Sbjct:    98 GRGESGPGHVSNFGDSATARFSVDASLAGAIIGKGGVSSKQICRQTGVKLSIQDHERDPN 157

Query:   222 LRNIELEGTFDQIKQASAMVRELIVNVXXXXXX-----------XXXXXXXXXXXXFKTK 270
             L+NI LEGT +QI +ASAMV++LI  +                             FKTK
Sbjct:   158 LKNIVLEGTLEQISEASAMVKDLIGRLNSAAKKPPGGGLGGGGGMGSEGKPHPGSNFKTK 217

Query:   271 LCENFAKGSCTFGDRCHFAHGSEELRKSVI 300
             +CE F+KG+CTFGDRCHFAHG  ELRKS I
Sbjct:   218 ICERFSKGNCTFGDRCHFAHGEAELRKSGI 247

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

UNIPROTKB|G3V2D5 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" [Homo sapiens (taxid:9606)]

 Score = 90 (36.7 bits), Expect = 3.7e-08, Sum P(2) = 3.7e-08
 Identities = 16/31 (51%), Positives = 20/31 (64%)

Query:   267 FKTKLCENFAK-GSCTFGDRCHFAHGSEELR 296
             +KT+LC  F   G C +G RCHF H +EE R
Sbjct:   131 YKTELCRTFHTIGFCPYGPRCHFIHNAEERR 161

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=IEA

GO:0001570 "vasculogenesis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0033077 "T cell differentiation in thymus" evidence=IEA

TAIR|locus:2028306 AT1G32360 [Arabidopsis thaliana (taxid:3702)]

 Score = 101 (40.6 bits), Expect = 4.0e-08, Sum P(2) = 4.0e-08
 Identities = 19/35 (54%), Positives = 22/35 (62%)

Query:   103 PPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGR 137
             P   K+R+CNK+     C FG KCHFAHG  EL R
Sbjct:   258 PSNWKTRICNKWEITGYCPFGAKCHFAHGAAELHR 292

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA;TAS

UNIPROTKB|G3V2P5 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" [Homo sapiens (taxid:9606)]

 Score = 90 (36.7 bits), Expect = 9.0e-08, Sum P(2) = 9.0e-08
 Identities = 16/31 (51%), Positives = 20/31 (64%)

Query:   267 FKTKLCENFAK-GSCTFGDRCHFAHGSEELR 296
             +KT+LC  F   G C +G RCHF H +EE R
Sbjct:   159 YKTELCRTFHTIGFCPYGPRCHFIHNAEERR 189

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2090669 AT3G19360 [Arabidopsis thaliana (taxid:3702)]

 Score = 110 (43.8 bits), Expect = 1.9e-07, Sum P(2) = 1.9e-07
 Identities = 20/34 (58%), Positives = 23/34 (67%)

Query:   267 FKTKLCENF-AKGSCTFGDRCHFAHGSEELRKSV 299
             +KT+LC  F   G C FGD+CHFAHG  EL  SV
Sbjct:   270 WKTRLCMKFDITGQCPFGDKCHFAHGQAELHNSV 303

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA;TAS

GO:0043687 "post-translational protein modification" evidence=RCA

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

UNIPROTKB|Q7ZXW9 zfp36l2-A "Zinc finger protein 36, C3H1 type-like 2-A" [Xenopus laevis (taxid:8355)]

 Score = 92 (37.4 bits), Expect = 5.0e-07, Sum P(2) = 5.0e-07
 Identities = 16/33 (48%), Positives = 22/33 (66%)

Query:   267 FKTKLCENFAK-GSCTFGDRCHFAHGSEELRKS 298
             +KT+LC  F   G C +G RCHF H +EE R++
Sbjct:   170 YKTELCRTFHTIGFCPYGPRCHFIHNAEERRQA 202

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0043488 "regulation of mRNA stability" evidence=ISS

GO:0048793 "pronephros development" evidence=ISS

UNIPROTKB|A7MB98 ZFP36L1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 90 (36.7 bits), Expect = 5.5e-07, Sum P(2) = 5.5e-07
 Identities = 16/31 (51%), Positives = 20/31 (64%)

Query:   267 FKTKLCENFAK-GSCTFGDRCHFAHGSEELR 296
             +KT+LC  F   G C +G RCHF H +EE R
Sbjct:   153 YKTELCRTFHTIGFCPYGPRCHFIHNAEERR 183

GO:0043488 "regulation of mRNA stability" evidence=IEA

GO:0033077 "T cell differentiation in thymus" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0001570 "vasculogenesis" evidence=IEA

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|E2R2W0 ZFP36L1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 90 (36.7 bits), Expect = 5.5e-07, Sum P(2) = 5.5e-07
 Identities = 16/31 (51%), Positives = 20/31 (64%)

Query:   267 FKTKLCENFAK-GSCTFGDRCHFAHGSEELR 296
             +KT+LC  F   G C +G RCHF H +EE R
Sbjct:   153 YKTELCRTFHTIGFCPYGPRCHFIHNAEERR 183

GO:0043488 "regulation of mRNA stability" evidence=IEA

GO:0033077 "T cell differentiation in thymus" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0001570 "vasculogenesis" evidence=IEA

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q07352 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" [Homo sapiens (taxid:9606)]

 Score = 90 (36.7 bits), Expect = 5.5e-07, Sum P(2) = 5.5e-07
 Identities = 16/31 (51%), Positives = 20/31 (64%)

Query:   267 FKTKLCENFAK-GSCTFGDRCHFAHGSEELR 296
             +KT+LC  F   G C +G RCHF H +EE R
Sbjct:   153 YKTELCRTFHTIGFCPYGPRCHFIHNAEERR 183

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=IEA

GO:0001570 "vasculogenesis" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0033077 "T cell differentiation in thymus" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003729 "mRNA binding" evidence=IDA

GO:0043488 "regulation of mRNA stability" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=NAS

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0006355 "regulation of transcription, DNA-dependent" evidence=NAS

---

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)
Q7F8R0	C3H14_ORYSJ	No assigned EC number	0.6393	0.9733	0.9733	yes	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	300
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	9e-14
smart00322	68	smart00322, KH, K homology RNA-binding domain	1e-12
pfam00013	59	pfam00013, KH_1, KH domain	5e-12
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	8e-08
smart00356	27	smart00356, ZnF_C3H1, zinc finger	7e-07
pfam13014	42	pfam13014, KH_3, KH domain	1e-06
pfam00642	27	pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H t	2e-06
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	2e-04
TIGR03665	172	TIGR03665, arCOG04150, arCOG04150 universal archae	3e-04
pfam00642	27	pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H t	7e-04
COG5063	351	COG5063, CTH1, CCCH-type Zn-finger protein [Genera	0.002
PRK13763	180	PRK13763, PRK13763, putative RNA-processing protei	0.004

>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 64.5 bits (158), Expect = 9e-14
 Identities = 20/63 (31%), Positives = 34/63 (53%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQAS 238
           T ++ + + L G IIGK G   K+I   TGAK+ I D       R + + GT + +++A 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60

Query: 239 AMV 241
            ++
Sbjct: 61  ELI 63

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension. Length = 64

>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIK 235
              T ++ I A   G IIGK G   K+I   TG K+ I         R +E+ G  + ++
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGP--GSEERVVEITGPPENVE 58

Query: 236 QASAMVRELI 245
           +A+ ++ E++
Sbjct: 59  KAAELILEIL 68

Length = 68

>gnl|CDD|215657 pfam00013, KH_1, KH domain

 Score = 59.9 bits (146), Expect = 5e-12
 Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQAS 238
           T +I I     G IIGK G N K+I   TG K+ I D   D     + + GT +Q+++A 
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDRDDT----VTISGTPEQVEKAK 56

Query: 239 AMV 241
            ++
Sbjct: 57  ELI 59

KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Length = 59

>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 48.2 bits (116), Expect = 8e-08
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 3/61 (4%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNL--RNIELEGTFDQIKQ 236
           T ++ + +  AG+IIGK G   K+I   TGAK+ +    V P    R + + G    +++
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSK-SVLPGSTERVVTISGKPSAVQK 59

Query: 237 A 237
           A
Sbjct: 60  A 60

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 65

>gnl|CDD|214632 smart00356, ZnF_C3H1, zinc finger

 Score = 44.5 bits (106), Expect = 7e-07
 Identities = 14/26 (53%), Positives = 18/26 (69%)

Query: 266 NFKTKLCENFAKGSCTFGDRCHFAHG 291
            +KT+LC+ F +G C  GDRC FAH 
Sbjct: 1   KYKTELCKFFKRGYCPRGDRCKFAHP 26

Length = 27

>gnl|CDD|221895 pfam13014, KH_3, KH domain

 Score = 44.1 bits (105), Expect = 1e-06
 Identities = 18/42 (42%), Positives = 22/42 (52%)

Query: 188 LAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG 229
           L GAIIGK G   K+I   TGAK+ I   E     R + + G
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42

KH motifs bind RNA in vitro. This RNA-binding domain is required for the efficient anchoring of ASH1-mRNA to the distal tip of the daughter cell. ASH1 is a specific repressor of transcription that localizes asymmetrically to the daughter cell nucleus. RNA localisation is a widespread mechanism for achieving localised protein synthesis. Length = 42

>gnl|CDD|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and similar)

 Score = 42.9 bits (102), Expect = 2e-06
 Identities = 15/26 (57%), Positives = 21/26 (80%), Gaps = 1/26 (3%)

Query: 267 FKTKLCENFAK-GSCTFGDRCHFAHG 291
           +KT+LC  F++ G+C +GDRC FAHG
Sbjct: 1   YKTELCRFFSRTGTCKYGDRCKFAHG 26

Length = 27

>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 2/64 (3%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQAS 238
           T ++ I  KL   IIGK G N ++I   TG K+   D     +   I + G  + +++A 
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSD--TITITGPKENVEKAK 58

Query: 239 AMVR 242
             + 
Sbjct: 59  EEIL 62

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 62

>gnl|CDD|211858 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain protein

 Score = 40.6 bits (96), Expect = 3e-04
 Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 11/66 (16%)

Query: 190 GAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG 249
           G IIG+ G   + I  LTG  +S+    V        + G  +Q++    + RE I  + 
Sbjct: 101 GRIIGEGGKTRRIIEELTGVSISVYGKTV-------GIIGDPEQVQ----IAREAIEMLI 149

Query: 250 SGSGHS 255
            G+ H 
Sbjct: 150 EGAPHG 155

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA. Length = 172

>gnl|CDD|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and similar)

 Score = 36.0 bits (84), Expect = 7e-04
 Identities = 12/26 (46%), Positives = 18/26 (69%)

Query: 107 KSRLCNKYNSAEGCKFGDKCHFAHGE 132
           K+ LC  ++    CK+GD+C FAHG+
Sbjct: 2   KTELCRFFSRTGTCKYGDRCKFAHGQ 27

Length = 27

>gnl|CDD|227395 COG5063, CTH1, CCCH-type Zn-finger protein [General function prediction only]

 Score = 38.9 bits (90), Expect = 0.002
 Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 2/48 (4%)

Query: 250 SGSGHSM-KSNSSSQSNNFKTKLCENFAK-GSCTFGDRCHFAHGSEEL 295
           +  GH + +  S  +  NF+T+ C N+ K G C +G RC F HG +  
Sbjct: 254 ACRGHGLNELKSKKKKQNFRTEPCINWEKSGYCPYGLRCCFKHGDDSD 301

Length = 351

>gnl|CDD|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional

 Score = 37.2 bits (87), Expect = 0.004
 Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 11/66 (16%)

Query: 190 GAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG 249
           G IIG+ G   + I  LTG  +S+    V        + G  +Q++ A   +  LI    
Sbjct: 107 GRIIGEGGKTRRIIEELTGVDISVYGKTV-------AIIGDPEQVEIAREAIEMLI---- 155

Query: 250 SGSGHS 255
            G+ H 
Sbjct: 156 EGAPHG 161

Length = 180

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	300
KOG1677	332	consensus CCCH-type Zn-finger protein [General fun	99.62
KOG1677	332	consensus CCCH-type Zn-finger protein [General fun	99.6
COG5063	351	CTH1 CCCH-type Zn-finger protein [General function	99.06
COG5063	351	CTH1 CCCH-type Zn-finger protein [General function	98.97
KOG1595	528	consensus CCCH-type Zn-finger protein [General fun	98.91
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	98.86
PF00642	27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	98.83
PF00642	27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	98.81
KOG1676	600	consensus K-homology type RNA binding proteins [RN	98.66
KOG1595	528	consensus CCCH-type Zn-finger protein [General fun	98.64
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	98.54
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	98.54
smart00356	27	ZnF_C3H1 zinc finger.	98.46
KOG1040	325	consensus Polyadenylation factor I complex, subuni	98.45
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	98.45
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	98.45
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.44
KOG2333	614	consensus Uncharacterized conserved protein [Gener	98.33
smart00356	27	ZnF_C3H1 zinc finger.	98.31
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.31
KOG2494	331	consensus C3H1-type Zn-finger protein [Transcripti	98.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	97.89
PF13014	43	KH_3: KH domain	97.88
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	97.85
KOG2494	331	consensus C3H1-type Zn-finger protein [Transcripti	97.77
KOG1492	377	consensus C3H1-type Zn-finger protein [General fun	97.77
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	97.74
smart00322	69	KH K homology RNA-binding domain.	97.72
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	97.67
KOG1763	343	consensus Uncharacterized conserved protein, conta	97.66
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.51
KOG1040	325	consensus Polyadenylation factor I complex, subuni	97.44
COG5252	299	Uncharacterized conserved protein, contains CCCH-t	97.26
COG5084	285	YTH1 Cleavage and polyadenylation specificity fact	97.17
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.16
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	97.14
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	96.95
KOG4791	667	consensus Uncharacterized conserved protein [Funct	96.94
PRK13763	180	putative RNA-processing protein; Provisional	96.94
PF14608	19	zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	96.81
KOG2185	486	consensus Predicted RNA-processing protein, contai	96.77
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	96.67
PRK13763	180	putative RNA-processing protein; Provisional	96.2
PF14608	19	zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	96.16
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	96.16
COG5152	259	Uncharacterized conserved protein, contains RING a	96.12
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	96.1
KOG2185	486	consensus Predicted RNA-processing protein, contai	95.85
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.76
KOG2333	614	consensus Uncharacterized conserved protein [Gener	95.37
KOG1492	377	consensus C3H1-type Zn-finger protein [General fun	95.31
COG5084	285	YTH1 Cleavage and polyadenylation specificity fact	95.29
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	95.2
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	95.19
COG5152	259	Uncharacterized conserved protein, contains RING a	95.17
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.16
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	93.48
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	92.98
KOG0119	554	consensus Splicing factor 1/branch point binding p	92.64
KOG1763	343	consensus Uncharacterized conserved protein, conta	91.93
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	91.48
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	91.17
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	90.78
KOG2113	394	consensus Predicted RNA binding protein, contains	90.56
COG1094	194	Predicted RNA-binding protein (contains KH domains	90.52
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	89.78
COG5252	299	Uncharacterized conserved protein, contains CCCH-t	89.37
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	87.21
KOG4791	667	consensus Uncharacterized conserved protein [Funct	86.3
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	84.42
PF10650	23	zf-C3H1: Putative zinc-finger domain; InterPro: IP	83.94
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	82.59
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	81.98
PRK00106	535	hypothetical protein; Provisional	81.4
PRK12704	520	phosphodiesterase; Provisional	80.67
COG5176	269	MSL5 Splicing factor (branch point binding protein	80.65

>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]

Probab=99.62  E-value=4.3e-16  Score=145.08  Aligned_cols=75  Identities=27%  Similarity=0.567  Sum_probs=58.2

Q ss_pred             ccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccccCcCC
Q 022221           41 KPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGC  120 (300)
Q Consensus        41 ~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~~~~C  120 (300)
                      ..|..|...+.|.++..|+|.|........+..                      .......+..|||.+|.+|.+.+.|
T Consensus        87 ~~~~~~~~~~~~~~~s~~~~~~p~~~~~~~~~~----------------------~~~~~~~p~~~kt~lc~~~~~~g~c  144 (332)
T KOG1677|consen   87 GDCSAYLRTGVCGYGSSCRYNHPDLRLRPRPVR----------------------RSRGERKPERYKTPLCRSFRKSGTC  144 (332)
T ss_pred             cccccccccCCCCCCCCCCccCcccccccCCcc----------------------ccccccCcccccCCcceeeecCccc
Confidence            789999999999999999999975332111100                      0112234578999999999999999


Q ss_pred             CC-CCCCccCCCccccCC
Q 022221          121 KF-GDKCHFAHGEWELGR  137 (300)
Q Consensus       121 ~~-g~~C~f~H~~~~~~~  137 (300)
                      +| |++|+|+|+.++++.
T Consensus       145 ~y~ge~crfah~~~e~r~  162 (332)
T KOG1677|consen  145 KYRGEQCRFAHGLEELRL  162 (332)
T ss_pred             cccCchhhhcCCcccccc
Confidence            99 999999999988884

>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]

Probab=99.60  E-value=4.1e-15  Score=138.48  Aligned_cols=81  Identities=31%  Similarity=0.577  Sum_probs=67.3

Q ss_pred             CCCccccccccccccccccCC-CCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccc
Q 022221           34 TGIGSKSKPCTKFFSTSGCPF-GEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCN  112 (300)
Q Consensus        34 ~~~~~Kt~lC~~y~~~g~C~~-G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~  112 (300)
                      ....|||.+|+.|..+|.|+| |++|+|+|.+.++....                        .......+.+|||++|.
T Consensus       126 ~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~~------------------------~~~~~~~~~~~kt~lC~  181 (332)
T KOG1677|consen  126 KPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLPS------------------------SENQVGNPPKYKTKLCP  181 (332)
T ss_pred             CcccccCCcceeeecCccccccCchhhhcCCcccccccc------------------------cchhhcCCCCCCCcCCC
Confidence            345799999999999999999 99999999987653111                        12344567899999999


Q ss_pred             ccccCcCCCCCCCCccCCCccccCCC
Q 022221          113 KYNSAEGCKFGDKCHFAHGEWELGRP  138 (300)
Q Consensus       113 ~~~~~~~C~~g~~C~f~H~~~~~~~~  138 (300)
                      +|++.|.|+||.+|+|+|+..++...
T Consensus       182 ~f~~tG~C~yG~rC~F~H~~~~~~~~  207 (332)
T KOG1677|consen  182 KFQKTGLCKYGSRCRFIHGEPEDRAS  207 (332)
T ss_pred             ccccCCCCCCCCcCeecCCCcccccc
Confidence            99999999999999999999877754

>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]

Probab=99.06  E-value=1.9e-10  Score=101.98  Aligned_cols=74  Identities=22%  Similarity=0.458  Sum_probs=60.6

Q ss_pred             CCCCcccc--ccccccccccccCC---CCCCCCC---CCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 022221           33 PTGIGSKS--KPCTKFFSTSGCPF---GEGCHFL---HYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPP  104 (300)
Q Consensus        33 ~~~~~~Kt--~lC~~y~~~g~C~~---G~~C~F~---H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  104 (300)
                      +....||+  .||.-|-..|.|++   |+.|.|+   |+..++..                              ...-.
T Consensus       221 ~n~~L~kt~~~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~l~~------------------------------k~k~~  270 (351)
T COG5063         221 QNKPLYKTNPELCESFTRKGTCPYWISGVKCQFACRGHGLNELKS------------------------------KKKKQ  270 (351)
T ss_pred             ccchhhcCCHHHhhccCcCCCCccccccccccccccccccccccc------------------------------ccccc
Confidence            34456899  99999999999999   9999999   98654311                              11235


Q ss_pred             ccccccccccccCcCCCCCCCCccCCCccccC
Q 022221          105 AVKSRLCNKYNSAEGCKFGDKCHFAHGEWELG  136 (300)
Q Consensus       105 ~~kt~~C~~~~~~~~C~~g~~C~f~H~~~~~~  136 (300)
                      +|||+.|.+|.+-|+|+||.+|-|+|+.+++-
T Consensus       271 ~frTePcinwe~sGyc~yg~Rc~F~hgd~~~i  302 (351)
T COG5063         271 NFRTEPCINWEKSGYCPYGLRCCFKHGDDSDI  302 (351)
T ss_pred             ccccCCccchhhcccCccccccccccCChhhc
Confidence            89999999999999999999999999986554

>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]

Probab=98.97  E-value=7.2e-10  Score=98.36  Aligned_cols=32  Identities=41%  Similarity=0.906  Sum_probs=29.0

Q ss_pred             CCcccccccccc-cccccCCCCCcCCCCcchhc
Q 022221          265 NNFKTKLCENFA-KGSCTFGDRCHFAHGSEELR  296 (300)
Q Consensus       265 ~~ykt~~C~~~~-~G~C~~G~~C~faH~~~el~  296 (300)
                      ..|+|+.|.+|. -|.|+||-+|-|+||++++.
T Consensus       270 ~~frTePcinwe~sGyc~yg~Rc~F~hgd~~~i  302 (351)
T COG5063         270 QNFRTEPCINWEKSGYCPYGLRCCFKHGDDSDI  302 (351)
T ss_pred             cccccCCccchhhcccCccccccccccCChhhc
Confidence            569999999999 79999999999999998864

>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]

Probab=98.91  E-value=1.1e-09  Score=104.42  Aligned_cols=31  Identities=35%  Similarity=0.756  Sum_probs=28.5

Q ss_pred             CCcccccccccccccccCCCCCcCCCCcchhccc
Q 022221          265 NNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKS  298 (300)
Q Consensus       265 ~~ykt~~C~~~~~G~C~~G~~C~faH~~~el~~~  298 (300)
                      ..|||++|++-  |.|++ -.|.|||..+|||..
T Consensus       267 a~YRT~~CkDg--~~C~R-rvCfFAH~~eqLR~l  297 (528)
T KOG1595|consen  267 ARYRTRKCKDG--GYCPR-RVCFFAHSPEQLRPL  297 (528)
T ss_pred             HHhccccccCC--CCCcc-ceEeeecChHHhccc
Confidence            56999999997  99999 999999999999864

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=98.86  E-value=2.6e-09  Score=75.57  Aligned_cols=64  Identities=27%  Similarity=0.432  Sum_probs=57.6

Q ss_pred             ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCC-CCCccceeecCcHHHHHHHhhcce
Q 022221          179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV-DPNLRNIELEGTFDQIKQASAMVR  242 (300)
Q Consensus       179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~-~~~~~~~~i~G~~~qi~~A~~~I~  242 (300)
                      +.++.||...+|.|||++|.+|+.|++.|+++|.+.+... ...++.++|.|+++++..|..+|.
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence            3678999999999999999999999999999999976554 677899999999999999988763

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran

>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.83  E-value=6e-10  Score=64.67  Aligned_cols=26  Identities=62%  Similarity=1.385  Sum_probs=21.2

Q ss_pred             cccccccccc-cccccCCCCCcCCCCc
Q 022221          267 FKTKLCENFA-KGSCTFGDRCHFAHGS  292 (300)
Q Consensus       267 ykt~~C~~~~-~G~C~~G~~C~faH~~  292 (300)
                      ||+++|.+|+ +|.|+||++|+|+|++
T Consensus         1 ~k~~~C~~f~~~g~C~~G~~C~f~H~~   27 (27)
T PF00642_consen    1 YKTKLCRFFMRTGTCPFGDKCRFAHGE   27 (27)
T ss_dssp             TTSSB-HHHHHTS--TTGGGSSSBSSG
T ss_pred             CccccChhhccCCccCCCCCcCccCCC
Confidence            6899999999 6999999999999974

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....

>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.81  E-value=7.6e-10  Score=64.25  Aligned_cols=26  Identities=46%  Similarity=0.975  Sum_probs=21.6

Q ss_pred             cccccccccccccccCCCCCCCCCCC
Q 022221           38 SKSKPCTKFFSTSGCPFGEGCHFLHY   63 (300)
Q Consensus        38 ~Kt~lC~~y~~~g~C~~G~~C~F~H~   63 (300)
                      ||+++|++|++.|.|++|++|+|+|+
T Consensus         1 ~k~~~C~~f~~~g~C~~G~~C~f~H~   26 (27)
T PF00642_consen    1 YKTKLCRFFMRTGTCPFGDKCRFAHG   26 (27)
T ss_dssp             TTSSB-HHHHHTS--TTGGGSSSBSS
T ss_pred             CccccChhhccCCccCCCCCcCccCC
Confidence            69999998999999999999999996

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]

Probab=98.66  E-value=1.1e-08  Score=98.46  Aligned_cols=78  Identities=33%  Similarity=0.516  Sum_probs=70.3

Q ss_pred             cccCcceEEEeCccccceeccCCCccccchhcccCCeeEec-cCCCCCCccceeecCcHHHHHHHhhcceeeEeccCCC
Q 022221          174 FGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIR-DHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGSG  251 (300)
Q Consensus       174 ~g~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~-~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~~~  251 (300)
                      .+++.+.+|.||...||+||||+|++||.|+..||++|++. |+++.+.+|.+.|+|+.++|.+|..+|.+++...+..
T Consensus       226 ~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~  304 (600)
T KOG1676|consen  226 GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG  304 (600)
T ss_pred             ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence            34466899999999999999999999999999999999994 5666788999999999999999999999999877764

>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]

Probab=98.64  E-value=1.3e-08  Score=97.19  Aligned_cols=67  Identities=27%  Similarity=0.538  Sum_probs=56.8

Q ss_pred             CccccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccc
Q 022221           36 IGSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYN  115 (300)
Q Consensus        36 ~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~  115 (300)
                      .-|.-+.|..|. .|.|..||.|.|+|++.|-|                                .+|..|||++|+   
T Consensus       232 yhYs~tpCPefr-kG~C~rGD~CEyaHgvfEcw--------------------------------LHPa~YRT~~Ck---  275 (528)
T KOG1595|consen  232 YHYSSTPCPEFR-KGSCERGDSCEYAHGVFECW--------------------------------LHPARYRTRKCK---  275 (528)
T ss_pred             ccccCccCcccc-cCCCCCCCccccccceehhh--------------------------------cCHHHhcccccc---
Confidence            459999999995 59999999999999998764                                245689999995   


Q ss_pred             cCcCCCCCCCCccCCCccccCCCC
Q 022221          116 SAEGCKFGDKCHFAHGEWELGRPT  139 (300)
Q Consensus       116 ~~~~C~~g~~C~f~H~~~~~~~~~  139 (300)
                      .+++|+. .-|.|||.+++||...
T Consensus       276 Dg~~C~R-rvCfFAH~~eqLR~l~  298 (528)
T KOG1595|consen  276 DGGYCPR-RVCFFAHSPEQLRPLP  298 (528)
T ss_pred             CCCCCcc-ceEeeecChHHhcccC
Confidence            5678999 9999999999998543

>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]

Probab=98.54  E-value=4.1e-08  Score=85.95  Aligned_cols=72  Identities=33%  Similarity=0.460  Sum_probs=66.7

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEecc
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNV  248 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~  248 (300)
                      .+++++.||..+-|.||||+|..|++|.+.+|+.|.|......+.+++++|.|+.+|+++|++++++.+.+.
T Consensus       314 itTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~  385 (390)
T KOG2192|consen  314 ITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY  385 (390)
T ss_pred             eeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence            778999999999999999999999999999999999988777888999999999999999999998876543

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=98.54  E-value=9.2e-08  Score=66.82  Aligned_cols=60  Identities=28%  Similarity=0.454  Sum_probs=53.8

Q ss_pred             eEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcc
Q 022221          180 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMV  241 (300)
Q Consensus       180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I  241 (300)
                      ..+.||..+.+.|||++|.+|+.|++.++++|.+.+..  .....++|.|..+++..|..+|
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i   61 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEI   61 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHh
Confidence            57899999999999999999999999999999997654  5568899999999999888765

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>smart00356 ZnF_C3H1 zinc finger

Probab=98.46  E-value=9.7e-08  Score=55.22  Aligned_cols=26  Identities=54%  Similarity=1.230  Sum_probs=24.0

Q ss_pred             cccccccccccccccCCCCCcCCCCc
Q 022221          267 FKTKLCENFAKGSCTFGDRCHFAHGS  292 (300)
Q Consensus       267 ykt~~C~~~~~G~C~~G~~C~faH~~  292 (300)
                      +|+.+|.+|++|.|++|++|+|+|..
T Consensus         2 ~k~~~C~~~~~g~C~~g~~C~~~H~~   27 (27)
T smart00356        2 YKTELCKFFKRGYCPYGDRCKFAHPL   27 (27)
T ss_pred             CCCCcCcCccCCCCCCCCCcCCCCcC
Confidence            68889999999999999999999973

>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]

Probab=98.45  E-value=8.7e-08  Score=87.95  Aligned_cols=56  Identities=29%  Similarity=0.612  Sum_probs=46.9

Q ss_pred             ccccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccccc
Q 022221           37 GSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNS  116 (300)
Q Consensus        37 ~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~  116 (300)
                      ..++++| +|+..|.|+.||.|.|+|.. ++                                      .|-+.|.||..
T Consensus        74 ~~~~~vc-K~~l~glC~kgD~C~Flhe~-~~--------------------------------------~k~rec~ff~~  113 (325)
T KOG1040|consen   74 SRGKVVC-KHWLRGLCKKGDQCEFLHEY-DL--------------------------------------TKMRECKFFSL  113 (325)
T ss_pred             cCCceee-hhhhhhhhhccCcCcchhhh-hh--------------------------------------ccccccccccc
Confidence            5789999 55577999999999999976 22                                      12345999999


Q ss_pred             CcCCCCCCCCccCCCc
Q 022221          117 AEGCKFGDKCHFAHGE  132 (300)
Q Consensus       117 ~~~C~~g~~C~f~H~~  132 (300)
                      .|.|..+..|-|.|+.
T Consensus       114 ~g~c~~~~~c~y~h~d  129 (325)
T KOG1040|consen  114 FGECTNGKDCPYLHGD  129 (325)
T ss_pred             ccccccccCCcccCCC
Confidence            9999999999999987

>cd00105 KH-I K homology RNA-binding domain, type I

Probab=98.45  E-value=2.4e-07  Score=64.85  Aligned_cols=62  Identities=31%  Similarity=0.516  Sum_probs=56.0

Q ss_pred             eEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcc
Q 022221          180 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMV  241 (300)
Q Consensus       180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I  241 (300)
                      .++.||..+++.|||++|.+|+.|++.|++.|.+.....+.....+.+.|..+++..|..+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence            57899999999999999999999999999999997765566788999999999999988765

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=98.45  E-value=5e-08  Score=67.71  Aligned_cols=60  Identities=37%  Similarity=0.599  Sum_probs=53.5

Q ss_pred             ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcc
Q 022221          179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMV  241 (300)
Q Consensus       179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I  241 (300)
                      |.++.||..+++.|||++|.+|++|+..|++.|.+.+.  + ....+.|.|++++++.|..+|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--~-~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--D-ERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHHHHHHHHhhC
Confidence            57899999999999999999999999999999999765  3 456899999999999998764

; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

Probab=98.44  E-value=1.7e-07  Score=65.34  Aligned_cols=57  Identities=23%  Similarity=0.380  Sum_probs=50.6

Q ss_pred             ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCc-HHHHHHHhhcc
Q 022221          179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGT-FDQIKQASAMV  241 (300)
Q Consensus       179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~-~~qi~~A~~~I  241 (300)
                      ...+.||+.++|.|||++|++|++|+..|+++|.|.+.      ..+.|.|. .+.++.|..+|
T Consensus         3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~------g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDD------GTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCCC------CEEEEEeCCHHHHHHHHHHh
Confidence            46789999999999999999999999999999999762      46999997 88888888766

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]

Probab=98.33  E-value=1.2e-07  Score=89.51  Aligned_cols=61  Identities=26%  Similarity=0.666  Sum_probs=45.8

Q ss_pred             ccccccccccc--cccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccccc
Q 022221           39 KSKPCTKFFST--SGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNS  116 (300)
Q Consensus        39 Kt~lC~~y~~~--g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~  116 (300)
                      +-+||.....+  ..|.|||+|+|.|++.....+..        +++                        ..-|+.|..
T Consensus        75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~--------~Di------------------------g~~Cp~f~s  122 (614)
T KOG2333|consen   75 QNRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKA--------PDI------------------------GPSCPVFES  122 (614)
T ss_pred             hhccChHhhcCCCccCcccccccccccHHHHHhccC--------ccc------------------------CCccceeec
Confidence            57799999877  68999999999999854321111        000                        013999999


Q ss_pred             CcCCCCCCCCccCCC
Q 022221          117 AEGCKFGDKCHFAHG  131 (300)
Q Consensus       117 ~~~C~~g~~C~f~H~  131 (300)
                      .|.|+||.+|||+-.
T Consensus       123 ~G~Cp~G~~CRFl~a  137 (614)
T KOG2333|consen  123 LGFCPYGFKCRFLGA  137 (614)
T ss_pred             cccCCccceeehhhc
Confidence            999999999999754

>smart00356 ZnF_C3H1 zinc finger

Probab=98.31  E-value=3.9e-07  Score=52.64  Aligned_cols=26  Identities=35%  Similarity=0.839  Sum_probs=23.2

Q ss_pred             ccccccccccccccccCCCCCCCCCCC
Q 022221           37 GSKSKPCTKFFSTSGCPFGEGCHFLHY   63 (300)
Q Consensus        37 ~~Kt~lC~~y~~~g~C~~G~~C~F~H~   63 (300)
                      .+|+.+|++| .+|.|.+|++|+|+|+
T Consensus         1 ~~k~~~C~~~-~~g~C~~g~~C~~~H~   26 (27)
T smart00356        1 KYKTELCKFF-KRGYCPYGDRCKFAHP   26 (27)
T ss_pred             CCCCCcCcCc-cCCCCCCCCCcCCCCc
Confidence            3688999777 8899999999999996

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.31  E-value=6.3e-07  Score=83.13  Aligned_cols=76  Identities=26%  Similarity=0.291  Sum_probs=67.7

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEecc-CCCCCCccceeecCcHHHHHHHhhcceeeEeccCCCC
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD-HEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGSGS  252 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~-~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~~~~  252 (300)
                      ...+.+.||..++|+|||+.|.+||+|.+.+|+.|+|.. ..++..++++.|+|.+++..+|+..|...|.+.+.+.
T Consensus       410 ~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEenf~~  486 (584)
T KOG2193|consen  410 QEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFL  486 (584)
T ss_pred             hhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccCC
Confidence            567889999999999999999999999999999999965 4467788999999999999999999999888766543

>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]

Probab=98.00  E-value=3.4e-06  Score=76.27  Aligned_cols=67  Identities=19%  Similarity=0.407  Sum_probs=47.4

Q ss_pred             CCCCccccccccccccccccCCCCC-CCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccc
Q 022221           33 PTGIGSKSKPCTKFFSTSGCPFGEG-CHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLC  111 (300)
Q Consensus        33 ~~~~~~Kt~lC~~y~~~g~C~~G~~-C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C  111 (300)
                      ..+-|...++|+.|. -++|..||+ |||+|.....  .|                                ++-+-..|
T Consensus        30 kd~~wl~~eVCReF~-rn~C~R~d~~CkfaHP~~~~--~V--------------------------------~~g~v~aC   74 (331)
T KOG2494|consen   30 KDTKWLTLEVCREFL-RNTCSRGDRECKFAHPPKNC--QV--------------------------------SNGRVIAC   74 (331)
T ss_pred             cccchhHHHHHHHHH-hccccCCCccccccCCCCCC--Cc--------------------------------cCCeEEEE
Confidence            445577788998885 599999999 9999964321  00                                01122359


Q ss_pred             cccccCcCCCCCCCCccCCCccccC
Q 022221          112 NKYNSAEGCKFGDKCHFAHGEWELG  136 (300)
Q Consensus       112 ~~~~~~~~C~~g~~C~f~H~~~~~~  136 (300)
                      .-|++++ |.. ++|+|+|...+++
T Consensus        75 ~Ds~kgr-CsR-~nCkylHpp~hlk   97 (331)
T KOG2494|consen   75 FDSQKGR-CSR-ENCKYLHPPQHLK   97 (331)
T ss_pred             eccccCc-cCc-ccceecCCChhhh
Confidence            8898888 964 5599999976554

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]

Probab=97.89  E-value=6.5e-06  Score=79.72  Aligned_cols=74  Identities=27%  Similarity=0.425  Sum_probs=64.1

Q ss_pred             cCcceEEEeCccccceeccCCCccccchhcccCCeeEec-cCCC-CCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221          176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIR-DHEV-DPNLRNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       176 ~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~-~~~~-~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      ..++.++.||+..+|+||||+|+.|++++..+++++.+. +... ...++.+.|+|++.+++.|..+|.++|.+..
T Consensus       137 ~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~  212 (600)
T KOG1676|consen  137 VETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREED  212 (600)
T ss_pred             cceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcc
Confidence            357888999999999999999999999999999999984 3332 2367999999999999999999999998533

>PF13014 KH_3: KH domain

Probab=97.88  E-value=8.4e-06  Score=52.56  Aligned_cols=42  Identities=40%  Similarity=0.590  Sum_probs=35.6

Q ss_pred             ccceeccCCCccccchhcccCCeeEecc-CCCCCCccceeecC
Q 022221          188 LAGAIIGKNGVNSKQICRLTGAKLSIRD-HEVDPNLRNIELEG  229 (300)
Q Consensus       188 ~~G~iiG~gG~~ik~i~~~Sga~i~i~~-~~~~~~~~~~~i~G  229 (300)
                      .+|+|||++|.+|++|++.|+++|.+.+ ...+...+.++|.|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            3689999999999999999999999976 44556678888765

>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=97.85  E-value=1.1e-05  Score=78.31  Aligned_cols=72  Identities=24%  Similarity=0.376  Sum_probs=64.5

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEecc-CCCCCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD-HEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~-~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      .+..+.||..++|.||||+|+.|++|++.|+++|.|.+ ..+..+++.+.|.|.++++.+|...|..+|.+..
T Consensus       138 v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~  210 (485)
T KOG2190|consen  138 VTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENP  210 (485)
T ss_pred             eEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcC
Confidence            46889999999999999999999999999999999954 5677888999999999999999999888876543

>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]

Probab=97.77  E-value=1e-05  Score=73.24  Aligned_cols=27  Identities=26%  Similarity=0.691  Sum_probs=23.5

Q ss_pred             ccccccccccccCCCCCcCCCCcchhcc
Q 022221          270 KLCENFAKGSCTFGDRCHFAHGSEELRK  297 (300)
Q Consensus       270 ~~C~~~~~G~C~~G~~C~faH~~~el~~  297 (300)
                      -.|.+|++|.|.+ ++|+|.|+..+|+-
T Consensus        72 ~aC~Ds~kgrCsR-~nCkylHpp~hlkd   98 (331)
T KOG2494|consen   72 IACFDSQKGRCSR-ENCKYLHPPQHLKD   98 (331)
T ss_pred             EEEeccccCccCc-ccceecCCChhhhh
Confidence            3699999999999 68999999888763

>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]

Probab=97.77  E-value=2.9e-05  Score=66.75  Aligned_cols=60  Identities=20%  Similarity=0.492  Sum_probs=47.4

Q ss_pred             ccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccccCc
Q 022221           39 KSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAE  118 (300)
Q Consensus        39 Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~~~  118 (300)
                      ...-|++|...|.|..|..|+|.|....                                         ..+|+.|+.+.
T Consensus       205 savycryynangicgkgaacrfvheptr-----------------------------------------kticpkflngr  243 (377)
T KOG1492|consen  205 SAVYCRYYNANGICGKGAACRFVHEPTR-----------------------------------------KTICPKFLNGR  243 (377)
T ss_pred             ceeEEEEecCCCcccCCceeeeeccccc-----------------------------------------cccChHHhcCc
Confidence            4457988888999999999999996532                                         24699998887


Q ss_pred             CCCCCCCCccCCCccccCCCCC
Q 022221          119 GCKFGDKCHFAHGEWELGRPTV  140 (300)
Q Consensus       119 ~C~~g~~C~f~H~~~~~~~~~~  140 (300)
                       |..-++|...|..+..|.+.-
T Consensus       244 -cnkaedcnlsheldprripac  264 (377)
T KOG1492|consen  244 -CNKAEDCNLSHELDPRRIPAC  264 (377)
T ss_pred             -cCchhcCCcccccCccccchh
Confidence             999999999997766665433

>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=97.74  E-value=2.2e-05  Score=71.08  Aligned_cols=73  Identities=26%  Similarity=0.316  Sum_probs=62.2

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCC---CCCccceeecCcHHHHHHHhhcceeeEeccCC
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV---DPNLRNIELEGTFDQIKQASAMVRELIVNVGS  250 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~---~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~~  250 (300)
                      ..+++.+|+..+|.||||+|.+||.+..+++++|+|....+   ...++.+++.|.+++..+|..+|-..+.+.+.
T Consensus       132 kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq  207 (402)
T KOG2191|consen  132 KQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ  207 (402)
T ss_pred             ceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence            45889999999999999999999999999999999984332   34469999999999999999988777766553

>smart00322 KH K homology RNA-binding domain

Probab=97.72  E-value=2.8e-05  Score=54.20  Aligned_cols=65  Identities=31%  Similarity=0.489  Sum_probs=54.8

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceee
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVREL  244 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~  244 (300)
                      .+..+.||...++.+||++|.+|+.|...+++++.+.....  ....+.|.|...++..|..+|...
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~   67 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEI   67 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHH
Confidence            35788999999999999999999999999999999865332  567899999999998888776543

>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=97.67  E-value=2.2e-05  Score=71.02  Aligned_cols=71  Identities=24%  Similarity=0.361  Sum_probs=61.8

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEecc-CC--CCCCccceeecCcHHHHHHHhhcceeeEecc
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD-HE--VDPNLRNIELEGTFDQIKQASAMVRELIVNV  248 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~-~~--~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~  248 (300)
                      ..+++.||...+|.||||||+.|.+++..++++|++.. .+  +..++|++-|.|+-+.+......|.+.|.+.
T Consensus        39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~  112 (402)
T KOG2191|consen   39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREK  112 (402)
T ss_pred             eEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHh
Confidence            56889999999999999999999999999999999953 33  6778899999999999988888877776553

>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]

Probab=97.66  E-value=1.1e-05  Score=71.79  Aligned_cols=34  Identities=35%  Similarity=0.837  Sum_probs=29.5

Q ss_pred             ccCCCCCccccccccccccccccCCCCCCCCCCCC
Q 022221           30 ENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYV   64 (300)
Q Consensus        30 ~~~~~~~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~   64 (300)
                      ...+.++..|+.+| -||..|.|..|+.|+|+|++
T Consensus        82 qkv~~gvDPKSvvC-afFk~g~C~KG~kCKFsHdl  115 (343)
T KOG1763|consen   82 QKVPKGVDPKSVVC-AFFKQGTCTKGDKCKFSHDL  115 (343)
T ss_pred             cccccCCCchHHHH-HHHhccCCCCCCcccccchH
Confidence            34567888999999 66689999999999999976

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.51  E-value=3e-05  Score=72.27  Aligned_cols=71  Identities=25%  Similarity=0.417  Sum_probs=60.8

Q ss_pred             ceEEEeCccccceeccCCCccccchhcccCCeeEe-ccCCCCCCc-cceeecCcHHHHHHHhhcceeeEeccC
Q 022221          179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPNL-RNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i-~~~~~~~~~-~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      ...++||...+|.||||||.++.++++.|++.+.| ++..++.++ .++.|+|.+.+.++|+..|.+++.++-
T Consensus       494 ethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~qvk  566 (584)
T KOG2193|consen  494 ETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVNQVK  566 (584)
T ss_pred             eeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHHHHH
Confidence            34578999999999999999999999999999999 566666654 688999999999999998888875543

>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]

Probab=97.44  E-value=0.0001  Score=67.90  Aligned_cols=54  Identities=28%  Similarity=0.557  Sum_probs=42.6

Q ss_pred             ccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccccCc
Q 022221           39 KSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAE  118 (300)
Q Consensus        39 Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~~~  118 (300)
                      |.+.|.+|...|.|..++.|.|.|..++.                                       +.+.|++| +.|
T Consensus       104 k~rec~ff~~~g~c~~~~~c~y~h~dpqt---------------------------------------~~k~c~~~-~~g  143 (325)
T KOG1040|consen  104 KMRECKFFSLFGECTNGKDCPYLHGDPQT---------------------------------------AIKKCKWY-KEG  143 (325)
T ss_pred             ccccccccccccccccccCCcccCCChhh---------------------------------------hhhccchh-hhc
Confidence            56679888899999999999999987422                                       24569666 455


Q ss_pred             CCCCCCCCccCCCc
Q 022221          119 GCKFGDKCHFAHGE  132 (300)
Q Consensus       119 ~C~~g~~C~f~H~~  132 (300)
                      +|+-|+.|++.|-.
T Consensus       144 ~c~~g~~c~~~h~~  157 (325)
T KOG1040|consen  144 FCRGGPSCKKRHER  157 (325)
T ss_pred             cCCCcchhhhhhhc
Confidence            69999999998844

>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]

Probab=97.26  E-value=5.5e-05  Score=65.39  Aligned_cols=36  Identities=25%  Similarity=0.567  Sum_probs=29.5

Q ss_pred             ccCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 022221           30 ENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPG   66 (300)
Q Consensus        30 ~~~~~~~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~   66 (300)
                      .....++..|+.+|..| ..+.|..|+.|+|+|+..+
T Consensus        75 q~iragvdpK~~vcalF-~~~~c~kg~~ckF~h~~ee  110 (299)
T COG5252          75 QVIRAGVDPKTVVCALF-LNKTCAKGDACKFAHGKEE  110 (299)
T ss_pred             hhhccccCchhHHHHHh-ccCccccCchhhhhcchHH
Confidence            33567788999999555 6799999999999998643

>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

Probab=97.17  E-value=0.00078  Score=60.84  Aligned_cols=58  Identities=29%  Similarity=0.555  Sum_probs=43.4

Q ss_pred             ccccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccccc
Q 022221           37 GSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNS  116 (300)
Q Consensus        37 ~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~  116 (300)
                      .+...+| +++..|.|+.++.|.|+|+.+-..                                    . -.-.|++|-.
T Consensus       101 ~~s~V~c-~~~~~g~c~s~~~c~~lh~~d~~~------------------------------------s-~~~~c~~Fs~  142 (285)
T COG5084         101 LSSSVVC-KFFLRGLCKSGFSCEFLHEYDLRS------------------------------------S-QGPPCRSFSL  142 (285)
T ss_pred             ccCCccc-chhccccCcCCCccccccCCCccc------------------------------------c-cCCCcccccc
Confidence            4777889 555779999999999999764210                                    0 0223999977


Q ss_pred             CcCCCCCCCCccCCCc
Q 022221          117 AEGCKFGDKCHFAHGE  132 (300)
Q Consensus       117 ~~~C~~g~~C~f~H~~  132 (300)
                      .|.|..|..|.|.|.+
T Consensus       143 ~G~cs~g~~c~~~h~d  158 (285)
T COG5084         143 KGSCSSGPSCGYSHID  158 (285)
T ss_pred             cceeccCCCCCccccC
Confidence            7779999999999976

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=97.16  E-value=0.00033  Score=65.72  Aligned_cols=85  Identities=22%  Similarity=0.279  Sum_probs=62.3

Q ss_pred             CCCcCCCCCCCCCccccccCcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHH
Q 022221          158 GGRLEPPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQA  237 (300)
Q Consensus       158 ~g~~~p~p~~~~~~~~~g~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A  237 (300)
                      +++|.-+.-.+.++++.+...++.+.|-..++|+|||++|++|+.||..++++|+|...+..   ..++|.|.-+...+|
T Consensus        27 g~~w~g~~~~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e---~kv~ifg~~~m~~ka  103 (629)
T KOG0336|consen   27 GNYWAGHRDSRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLE---VKVTIFGINHMRKKA  103 (629)
T ss_pred             CCCccCCCCCCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCce---eEEEEechHHHHHHH
Confidence            34444444444455666667788899999999999999999999999999999999875533   345577766666666


Q ss_pred             hhcceeeE
Q 022221          238 SAMVRELI  245 (300)
Q Consensus       238 ~~~I~~~l  245 (300)
                      ...|...+
T Consensus       104 ka~id~~~  111 (629)
T KOG0336|consen  104 KASIDRGQ  111 (629)
T ss_pred             HhhHhhhh
Confidence            65555444

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=97.14  E-value=0.00015  Score=61.30  Aligned_cols=60  Identities=25%  Similarity=0.381  Sum_probs=51.8

Q ss_pred             EEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceee---cCcHHHHHHHhhcceeeEe
Q 022221          182 ISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIEL---EGTFDQIKQASAMVRELIV  246 (300)
Q Consensus       182 ~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i---~G~~~qi~~A~~~I~~~l~  246 (300)
                      +.||...+|+|||++|++|+.|+..++++|.|.+..     ..+.|   .+++.++.+|..+|..+..
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~-----g~V~I~~~t~d~~~i~kA~~~I~~i~~   64 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSET-----GEVKIEEEDEDPLAVMKAREVVKAIGR   64 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCC-----ceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence            578999999999999999999999999999997632     34666   7899999999999987654

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH)

Probab=96.95  E-value=0.00049  Score=54.58  Aligned_cols=62  Identities=27%  Similarity=0.387  Sum_probs=47.6

Q ss_pred             cccceeccCCCccccchhcccCCeeEeccCCCCC-----------------CccceeecC-c--HHHHHHHhhcceeeEe
Q 022221          187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDP-----------------NLRNIELEG-T--FDQIKQASAMVRELIV  246 (300)
Q Consensus       187 ~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~-----------------~~~~~~i~G-~--~~qi~~A~~~I~~~l~  246 (300)
                      ..+|.|||.+|.+++.|+..|+++|.|++..+..                 ..-.+.|++ +  .+.+++|..+|..++.
T Consensus        15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~   94 (120)
T cd02395          15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK   94 (120)
T ss_pred             CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence            4678999999999999999999999997642110                 114566666 4  5788999999998887


Q ss_pred             cc
Q 022221          247 NV  248 (300)
Q Consensus       247 ~~  248 (300)
                      ..
T Consensus        95 ~~   96 (120)
T cd02395          95 PA   96 (120)
T ss_pred             cC
Confidence            43

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>KOG4791 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.94  E-value=0.00034  Score=66.25  Aligned_cols=23  Identities=39%  Similarity=0.804  Sum_probs=19.9

Q ss_pred             cccccccccccCCCCCCCCCCCCC
Q 022221           42 PCTKFFSTSGCPFGEGCHFLHYVP   65 (300)
Q Consensus        42 lC~~y~~~g~C~~G~~C~F~H~~~   65 (300)
                      .| +|+....|+++|.|.|.|...
T Consensus         5 dc-yff~ys~cKk~d~c~~rh~E~   27 (667)
T KOG4791|consen    5 DC-YFFFYSTCKKGDSCPFRHCEA   27 (667)
T ss_pred             cc-hhhhhhhhhccCcCcchhhHH
Confidence            48 777889999999999999753

>PRK13763 putative RNA-processing protein; Provisional

Probab=96.94  E-value=0.00042  Score=58.99  Aligned_cols=63  Identities=24%  Similarity=0.310  Sum_probs=54.5

Q ss_pred             ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceee----cCcHHHHHHHhhcceeeEe
Q 022221          179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIEL----EGTFDQIKQASAMVRELIV  246 (300)
Q Consensus       179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i----~G~~~qi~~A~~~I~~~l~  246 (300)
                      ...+.||+..+|.|||++|.+|+.|+..++++|.|.+..     ..+.|    .+++.++.+|..+|..+..
T Consensus         4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~-----g~V~I~~~~~~d~~~i~kA~~~I~ai~~   70 (180)
T PRK13763          4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSET-----GEVIIEPTDGEDPLAVLKARDIVKAIGR   70 (180)
T ss_pred             eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCC-----CeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence            467899999999999999999999999999999997642     45566    4799999999999987765

>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type

Probab=96.81  E-value=0.00082  Score=35.40  Aligned_cols=19  Identities=42%  Similarity=0.852  Sum_probs=16.4

Q ss_pred             cccccccccccCCCCCcCCCC
Q 022221          271 LCENFAKGSCTFGDRCHFAHG  291 (300)
Q Consensus       271 ~C~~~~~G~C~~G~~C~faH~  291 (300)
                      .|+||..  |+++++|.|.|+
T Consensus         1 ~Ck~~~~--C~~~~~C~f~HP   19 (19)
T PF14608_consen    1 PCKFGPN--CTNGDNCPFSHP   19 (19)
T ss_pred             CCcCcCC--CCCCCcCccCCc
Confidence            4888864  999999999996

>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]

Probab=96.77  E-value=0.00048  Score=64.08  Aligned_cols=24  Identities=46%  Similarity=1.182  Sum_probs=21.8

Q ss_pred             ccccccccccccCCCCCcCCCCcc
Q 022221          270 KLCENFAKGSCTFGDRCHFAHGSE  293 (300)
Q Consensus       270 ~~C~~~~~G~C~~G~~C~faH~~~  293 (300)
                      ..|.||+.|.|+|+++|||.||..
T Consensus       141 kpC~ffLeg~CRF~enCRfSHG~~  164 (486)
T KOG2185|consen  141 KPCKFFLEGRCRFGENCRFSHGLD  164 (486)
T ss_pred             ccchHhhccccccCcccccccCcc
Confidence            469999999999999999999853

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=96.67  E-value=0.00051  Score=58.05  Aligned_cols=52  Identities=29%  Similarity=0.526  Sum_probs=47.9

Q ss_pred             cccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeE
Q 022221          187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELI  245 (300)
Q Consensus       187 ~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l  245 (300)
                      ...|.|||++|.+++.|+..|+++|.|.+       +.+.|+|++++++.|...|..++
T Consensus        98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~~i~~li  149 (172)
T TIGR03665        98 RIKGRIIGEGGKTRRIIEELTGVSISVYG-------KTVGIIGDPEQVQIAREAIEMLI  149 (172)
T ss_pred             HHHhhhcCCCcHHHHHHHHHHCCeEEEcC-------CEEEEECCHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999975       56899999999999999998887

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

>PRK13763 putative RNA-processing protein; Provisional

Probab=96.20  E-value=0.0014  Score=55.77  Aligned_cols=52  Identities=29%  Similarity=0.518  Sum_probs=46.8

Q ss_pred             cccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeE
Q 022221          187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELI  245 (300)
Q Consensus       187 ~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l  245 (300)
                      ...|.|||++|.+++.|+..|+++|.|.+.       .+.|.|++.++..|...|..++
T Consensus       104 r~~griIG~~G~~~k~ie~~t~~~i~i~~~-------~v~i~G~~~~~~~A~~~I~~li  155 (180)
T PRK13763        104 RIKGRIIGEGGKTRRIIEELTGVDISVYGK-------TVAIIGDPEQVEIAREAIEMLI  155 (180)
T ss_pred             HHhhheeCCCcHHHHHHHHHHCcEEEEcCC-------EEEEEeCHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999752       3889999999999999998877

>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type

Probab=96.16  E-value=0.0036  Score=32.91  Aligned_cols=19  Identities=37%  Similarity=0.810  Sum_probs=15.6

Q ss_pred             cccccccCcCCCCCCCCccCCC
Q 022221          110 LCNKYNSAEGCKFGDKCHFAHG  131 (300)
Q Consensus       110 ~C~~~~~~~~C~~g~~C~f~H~  131 (300)
                      .|++|..   |++++.|.|.|.
T Consensus         1 ~Ck~~~~---C~~~~~C~f~HP   19 (19)
T PF14608_consen    1 PCKFGPN---CTNGDNCPFSHP   19 (19)
T ss_pred             CCcCcCC---CCCCCcCccCCc
Confidence            3887643   999999999995

>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=96.16  E-value=0.0097  Score=58.13  Aligned_cols=71  Identities=25%  Similarity=0.392  Sum_probs=61.5

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCC--CCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV--DPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~--~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      ..+.++.||..++|.|||++|.+|.+|++.|++.|.|...+.  ...+..++|.+...+...++..+...+..
T Consensus       337 ~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~  409 (485)
T KOG2190|consen  337 TVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSA  409 (485)
T ss_pred             eeeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhccccccc
Confidence            467889999999999999999999999999999999976554  56789999999999998888888665533

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]

Probab=96.12  E-value=0.0019  Score=54.69  Aligned_cols=30  Identities=30%  Similarity=0.762  Sum_probs=26.3

Q ss_pred             CccccccccccccccccCCCCCCCCCCCCC
Q 022221           36 IGSKSKPCTKFFSTSGCPFGEGCHFLHYVP   65 (300)
Q Consensus        36 ~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~   65 (300)
                      +.|...+|.-|-.+|.|-|||.|+|+|...
T Consensus       137 iD~qpdVCKdyk~TGYCGYGDsCKflH~R~  166 (259)
T COG5152         137 IDTQPDVCKDYKETGYCGYGDSCKFLHDRS  166 (259)
T ss_pred             eecCcccccchhhcccccCCchhhhhhhhh
Confidence            356777999999999999999999999763

>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]

Probab=96.10  E-value=0.0012  Score=58.33  Aligned_cols=70  Identities=24%  Similarity=0.357  Sum_probs=57.2

Q ss_pred             ceEEEeCccccceeccCCCccccchhcccCCeeEecc-CCCCCCccceeecCcHHHHHHHhhcceeeEecc
Q 022221          179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD-HEVDPNLRNIELEGTFDQIKQASAMVRELIVNV  248 (300)
Q Consensus       179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~-~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~  248 (300)
                      .+++.|-++++|.|||++|++||+++..+.++++|.. --+.++++++.+.|.+..+......|.++|++.
T Consensus       124 e~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~  194 (390)
T KOG2192|consen  124 ELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISES  194 (390)
T ss_pred             hhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcC
Confidence            3567788999999999999999999999999999964 445678899999998887766666666665543

>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]

Probab=95.85  E-value=0.0034  Score=58.54  Aligned_cols=26  Identities=50%  Similarity=1.083  Sum_probs=21.7

Q ss_pred             cccccccccccccccCCCCCCCCCCCC
Q 022221           38 SKSKPCTKFFSTSGCPFGEGCHFLHYV   64 (300)
Q Consensus        38 ~Kt~lC~~y~~~g~C~~G~~C~F~H~~   64 (300)
                      .-.++| .||..|.|+|+++|+|.|+.
T Consensus       138 ~sMkpC-~ffLeg~CRF~enCRfSHG~  163 (486)
T KOG2185|consen  138 ESMKPC-KFFLEGRCRFGENCRFSHGL  163 (486)
T ss_pred             hhhccc-hHhhccccccCcccccccCc
Confidence            356789 55578999999999999975

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.76  E-value=0.0045  Score=54.58  Aligned_cols=29  Identities=28%  Similarity=0.626  Sum_probs=25.1

Q ss_pred             cccccccccccCCCCCCCCCCCCCCCCcc
Q 022221           42 PCTKFFSTSGCPFGEGCHFLHYVPGGFKA   70 (300)
Q Consensus        42 lC~~y~~~g~C~~G~~C~F~H~~~~~~~~   70 (300)
                      -|..|+++|.|++|+.|.=.|..|+..++
T Consensus        17 ~c~fy~k~gacR~gdrcsR~h~kpt~s~t   45 (260)
T KOG2202|consen   17 NCSFYFKIGACRHGDRCSRLHEKPTFSQT   45 (260)
T ss_pred             ccchHHhhcccccccHHHHhhcccccchH
Confidence            39999999999999999999988776543

>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]

Probab=95.37  E-value=0.0067  Score=58.09  Aligned_cols=27  Identities=37%  Similarity=0.837  Sum_probs=21.3

Q ss_pred             ccccccccccC--cCCCCCCCCccCCCcc
Q 022221          107 KSRLCNKYNSA--EGCKFGDKCHFAHGEW  133 (300)
Q Consensus       107 kt~~C~~~~~~--~~C~~g~~C~f~H~~~  133 (300)
                      +..+|+---.+  ..|.||++|+|.|..+
T Consensus        75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi~  103 (614)
T KOG2333|consen   75 QNRLCPSLIQGDISKCSFGDNCRFVHDIE  103 (614)
T ss_pred             hhccChHhhcCCCccCcccccccccccHH
Confidence            45689876555  4599999999999863

>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]

Probab=95.31  E-value=0.009  Score=51.61  Aligned_cols=29  Identities=24%  Similarity=0.591  Sum_probs=23.6

Q ss_pred             cccccccccccccccCCCCCCCCCCCCCCC
Q 022221           38 SKSKPCTKFFSTSGCPFGEGCHFLHYVPGG   67 (300)
Q Consensus        38 ~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~   67 (300)
                      .+..+|.+|+ .|+|...+.|...|.+...
T Consensus       231 trkticpkfl-ngrcnkaedcnlsheldpr  259 (377)
T KOG1492|consen  231 TRKTICPKFL-NGRCNKAEDCNLSHELDPR  259 (377)
T ss_pred             cccccChHHh-cCccCchhcCCcccccCcc
Confidence            3556899995 5999999999999987543

>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

Probab=95.29  E-value=0.035  Score=50.30  Aligned_cols=30  Identities=27%  Similarity=0.381  Sum_probs=24.4

Q ss_pred             cccccccccccCcCCCCCCCCccCCCccccC
Q 022221          106 VKSRLCNKYNSAEGCKFGDKCHFAHGEWELG  136 (300)
Q Consensus       106 ~kt~~C~~~~~~~~C~~g~~C~f~H~~~~~~  136 (300)
                      +....|++|..+. |+-++.|-|+|..+-+.
T Consensus       102 ~s~V~c~~~~~g~-c~s~~~c~~lh~~d~~~  131 (285)
T COG5084         102 SSSVVCKFFLRGL-CKSGFSCEFLHEYDLRS  131 (285)
T ss_pred             cCCcccchhcccc-CcCCCccccccCCCccc
Confidence            3455799998887 99999999999875554

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=95.20  E-value=0.012  Score=59.78  Aligned_cols=65  Identities=25%  Similarity=0.316  Sum_probs=54.8

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEec
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIVN  247 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~~  247 (300)
                      .....+.||++.++.|||.||.+|+.|+..||++|.|.+.      ..+.|.+ +.+..++|..+|..++..
T Consensus       577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~------G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD------GTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC------cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            4456789999999999999999999999999999999763      4566666 667888999998888763

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.19  E-value=0.018  Score=53.72  Aligned_cols=25  Identities=36%  Similarity=0.935  Sum_probs=22.0

Q ss_pred             ccccccccCcCCCCCCCCccCCCccc
Q 022221          109 RLCNKYNSAEGCKFGDKCHFAHGEWE  134 (300)
Q Consensus       109 ~~C~~~~~~~~C~~g~~C~f~H~~~~  134 (300)
                      .+|+||+++- |+||+.|+|.|....
T Consensus         9 tic~~~~~g~-c~~g~~cr~~h~~~~   33 (344)
T KOG1039|consen    9 TICKYYQKGN-CKFGDLCRLSHSLPD   33 (344)
T ss_pred             hhhhhccccc-ccccceeeeeccCch
Confidence            6799998886 999999999998753

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]

Probab=95.17  E-value=0.0076  Score=51.09  Aligned_cols=29  Identities=28%  Similarity=0.935  Sum_probs=24.6

Q ss_pred             cccccccccc-cccccCCCCCcCCCCcchh
Q 022221          267 FKTKLCENFA-KGSCTFGDRCHFAHGSEEL  295 (300)
Q Consensus       267 ykt~~C~~~~-~G~C~~G~~C~faH~~~el  295 (300)
                      |-.-.|..|. +|.|-|||.|+|.|..++.
T Consensus       139 ~qpdVCKdyk~TGYCGYGDsCKflH~R~D~  168 (259)
T COG5152         139 TQPDVCKDYKETGYCGYGDSCKFLHDRSDF  168 (259)
T ss_pred             cCcccccchhhcccccCCchhhhhhhhhhh
Confidence            4445699998 9999999999999988754

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.16  E-value=0.0055  Score=54.04  Aligned_cols=31  Identities=29%  Similarity=0.791  Sum_probs=26.8

Q ss_pred             CCCCCcccccccccccccccCCCCCcCCCCc
Q 022221          262 SQSNNFKTKLCENFAKGSCTFGDRCHFAHGS  292 (300)
Q Consensus       262 ~~~~~ykt~~C~~~~~G~C~~G~~C~faH~~  292 (300)
                      .+...++...|..|..+.|.+|..|-|+|-.
T Consensus       145 ~pvT~~rea~C~~~e~~~C~rG~~CnFmH~k  175 (260)
T KOG2202|consen  145 SPVTDFREAICGQFERTECSRGGACNFMHVK  175 (260)
T ss_pred             cCcCchhhhhhcccccccCCCCCcCcchhhh
Confidence            3456788899999998899999999999954

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=93.48  E-value=0.042  Score=56.24  Aligned_cols=63  Identities=22%  Similarity=0.357  Sum_probs=50.0

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEe
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIV  246 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~  246 (300)
                      ....+.||++.++.|||+||++|+.|...||++|.|.+.      ..+.|.+ +...++.|...|..+..
T Consensus       551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd------G~V~i~~~~~~~~~~a~~~I~~~~~  614 (684)
T TIGR03591       551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD------GTVKIAASDGEAAEAAIKMIEGITA  614 (684)
T ss_pred             eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC------eEEEEEECcHHHHHHHHHHHHhhhc
Confidence            356689999999999999999999999999999999763      3445554 55677788777766643

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=92.98  E-value=0.029  Score=50.52  Aligned_cols=30  Identities=30%  Similarity=0.716  Sum_probs=26.4

Q ss_pred             CccccccccccccccccCCCCCCCCCCCCC
Q 022221           36 IGSKSKPCTKFFSTSGCPFGEGCHFLHYVP   65 (300)
Q Consensus        36 ~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~   65 (300)
                      +.|--.+|.-|-.+|.|.|||.|+|.|+..
T Consensus       182 ~d~qpDicKdykeTgycg~gdSckFlh~r~  211 (313)
T KOG1813|consen  182 IDYQPDICKDYKETGYCGYGDSCKFLHDRS  211 (313)
T ss_pred             eecCchhhhhhHhhCcccccchhhhhhhhh
Confidence            357777999999999999999999999764

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=92.64  E-value=0.056  Score=51.95  Aligned_cols=70  Identities=33%  Similarity=0.438  Sum_probs=50.6

Q ss_pred             cceEEEeC------ccccceeccCCCccccchhcccCCeeEeccCC---------CCCC------c-cceeecC-cHHHH
Q 022221          178 ATAKISID------AKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE---------VDPN------L-RNIELEG-TFDQI  234 (300)
Q Consensus       178 ~t~~~~iP------~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~---------~~~~------~-~~~~i~G-~~~qi  234 (300)
                      ...++.||      -..+|+|||..|.+.|.|..+|+++|.|+...         .+..      + =.+-|+. +.+.+
T Consensus       138 ~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki  217 (554)
T KOG0119|consen  138 LHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKI  217 (554)
T ss_pred             cccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHH
Confidence            34556664      46789999999999999999999999997511         1011      1 1234444 67788


Q ss_pred             HHHhhcceeeEec
Q 022221          235 KQASAMVRELIVN  247 (300)
Q Consensus       235 ~~A~~~I~~~l~~  247 (300)
                      ++|..+|+.+|..
T Consensus       218 ~~Ai~vienli~~  230 (554)
T KOG0119|consen  218 KKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999988864

>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]

Probab=91.93  E-value=0.042  Score=49.42  Aligned_cols=35  Identities=37%  Similarity=0.758  Sum_probs=30.0

Q ss_pred             CCCCcccccccccccccccCCCCCcCCCCcchhcc
Q 022221          263 QSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRK  297 (300)
Q Consensus       263 ~~~~ykt~~C~~~~~G~C~~G~~C~faH~~~el~~  297 (300)
                      ...-+|+-+|-||..|.|.-|+.|.|+|...+-|.
T Consensus        86 ~gvDPKSvvCafFk~g~C~KG~kCKFsHdl~~~~k  120 (343)
T KOG1763|consen   86 KGVDPKSVVCAFFKQGTCTKGDKCKFSHDLAVERK  120 (343)
T ss_pred             cCCCchHHHHHHHhccCCCCCCcccccchHHHhhh
Confidence            33567889999999999999999999999876654

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=91.48  E-value=0.056  Score=48.75  Aligned_cols=30  Identities=27%  Similarity=0.967  Sum_probs=24.9

Q ss_pred             CCcccccccccc-cccccCCCCCcCCCCcch
Q 022221          265 NNFKTKLCENFA-KGSCTFGDRCHFAHGSEE  294 (300)
Q Consensus       265 ~~ykt~~C~~~~-~G~C~~G~~C~faH~~~e  294 (300)
                      .-|-.-+|..|. ||.|-||+.|+|.|-...
T Consensus       182 ~d~qpDicKdykeTgycg~gdSckFlh~r~D  212 (313)
T KOG1813|consen  182 IDYQPDICKDYKETGYCGYGDSCKFLHDRSD  212 (313)
T ss_pred             eecCchhhhhhHhhCcccccchhhhhhhhhh
Confidence            334556799998 999999999999997664

>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH)

Probab=91.17  E-value=0.12  Score=35.70  Aligned_cols=36  Identities=31%  Similarity=0.519  Sum_probs=32.0

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEe
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI  213 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i  213 (300)
                      ....+.++....|.+||++|.+|+.++..++.+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            567889999999999999999999999999877665

NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=90.78  E-value=0.085  Score=54.96  Aligned_cols=64  Identities=17%  Similarity=0.386  Sum_probs=51.3

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCe-eEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEe
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAK-LSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIV  246 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~-i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~  246 (300)
                      .....+.||+..++.|||.||.+|+.|...++++ |.|.+.      ..+.|.+ +.+.++.|..+|..+..
T Consensus       684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd------g~V~I~a~d~~~i~~A~~~I~~l~~  749 (891)
T PLN00207        684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD------GTVKITAKDLSSLEKSKAIISSLTM  749 (891)
T ss_pred             CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC------eeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            3456789999999999999999999999999999 888763      3456665 66778888777666653

>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]

Probab=90.56  E-value=0.66  Score=42.33  Aligned_cols=65  Identities=12%  Similarity=0.264  Sum_probs=54.6

Q ss_pred             cCcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhccee
Q 022221          176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRE  243 (300)
Q Consensus       176 ~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~  243 (300)
                      .+.++.+.+|...++.|.|++|..||.++..|..+|+--..+   .+.+|.++|-.+.++.|...|..
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~edv~~aRrei~s   88 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHEDVRRARREIPS   88 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCchhHHHHhhcCcc
Confidence            567888999999999999999999999999999888764332   34788999999999988877754

>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]

Probab=90.52  E-value=0.11  Score=44.32  Aligned_cols=52  Identities=33%  Similarity=0.554  Sum_probs=45.6

Q ss_pred             ccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEe
Q 022221          188 LAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV  246 (300)
Q Consensus       188 ~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~  246 (300)
                      ..|.|||++|.+-+.|...|++.|.|.+..       +.|.|.+.+++.|...|..++.
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~t-------VaiiG~~~~v~iAr~AVemli~  163 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVYGKT-------VAIIGGFEQVEIAREAVEMLIN  163 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEeCcE-------EEEecChhhhHHHHHHHHHHHc
Confidence            458899999999999999999999997754       8999999999988888877764

>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=89.78  E-value=0.12  Score=48.26  Aligned_cols=24  Identities=33%  Similarity=0.996  Sum_probs=21.9

Q ss_pred             ccccccccccccCCCCCCCCCCCCC
Q 022221           41 KPCTKFFSTSGCPFGEGCHFLHYVP   65 (300)
Q Consensus        41 ~lC~~y~~~g~C~~G~~C~F~H~~~   65 (300)
                      .+| +|+.-|.|+||+.|+|.|..+
T Consensus         9 tic-~~~~~g~c~~g~~cr~~h~~~   32 (344)
T KOG1039|consen    9 TIC-KYYQKGNCKFGDLCRLSHSLP   32 (344)
T ss_pred             hhh-hhcccccccccceeeeeccCc
Confidence            789 777889999999999999987

>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]

Probab=89.37  E-value=0.085  Score=46.04  Aligned_cols=34  Identities=47%  Similarity=0.849  Sum_probs=30.2

Q ss_pred             CCcccccccccccccccCCCCCcCCCCcchhccc
Q 022221          265 NNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKS  298 (300)
Q Consensus       265 ~~ykt~~C~~~~~G~C~~G~~C~faH~~~el~~~  298 (300)
                      ...|+..|-.|..+.|.-|+.|.|+|+.+|.|..
T Consensus        81 vdpK~~vcalF~~~~c~kg~~ckF~h~~ee~r~~  114 (299)
T COG5252          81 VDPKTVVCALFLNKTCAKGDACKFAHGKEEARKT  114 (299)
T ss_pred             cCchhHHHHHhccCccccCchhhhhcchHHHhhh
Confidence            4478899999999999999999999999887753

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=87.21  E-value=0.48  Score=42.03  Aligned_cols=60  Identities=17%  Similarity=0.264  Sum_probs=48.8

Q ss_pred             ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceee
Q 022221          179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVREL  244 (300)
Q Consensus       179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~  244 (300)
                      -..+.||+.+++.+||++|..++.|...+++.|.+...      ..++|.+ +.+....|..+|..+
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N------G~VwI~~~~~~~~~~a~~~I~~~  206 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN------GRIWIKGPDEEDEEIAIEAIKKI  206 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC------cEEEEeeCCHHHHHHHHHHHHHH
Confidence            47789999999999999999999999999999999664      3677777 444667777766654

>KOG4791 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.30  E-value=0.66  Score=44.61  Aligned_cols=81  Identities=15%  Similarity=0.114  Sum_probs=42.7

Q ss_pred             ccccccccccccc-cCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccccC
Q 022221           39 KSKPCTKFFSTSG-CPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSA  117 (300)
Q Consensus        39 Kt~lC~~y~~~g~-C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~~  117 (300)
                      ..++| +|...+. |.. ++|-|-|..|.+...+..   .+..++-.-.++.....++++       ..-...|-+|+++
T Consensus        60 ~e~~C-Ywe~~p~gC~k-~~CgfRH~~pPLkg~l~~---~p~~pe~ev~~~~~SAq~~sV-------~~~p~P~l~~~K~  127 (667)
T KOG4791|consen   60 SEIPC-YWENQPTGCQK-LNCGFRHNRPPLKGVLPT---VPESPEEEVKASQLSAQQNSV-------QSNPSPQLRSVKK  127 (667)
T ss_pred             Ccccc-eeecCCCccCC-CccccccCCCchhhhccC---CCCCcccccccccccCCCccc-------ccCCchHHHHhhh
Confidence            34679 7766655 876 589999966544222211   111111000011111111122       2223458777766


Q ss_pred             cCCCCCCCCccCCCc
Q 022221          118 EGCKFGDKCHFAHGE  132 (300)
Q Consensus       118 ~~C~~g~~C~f~H~~  132 (300)
                      - |--+|.|.|+|..
T Consensus       128 ~-e~~~D~~s~Lh~P  141 (667)
T KOG4791|consen  128 V-ESSEDVPSPLHPP  141 (667)
T ss_pred             h-hhhccccccCCCC
Confidence            4 9999999999976

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

Probab=84.42  E-value=0.7  Score=46.57  Aligned_cols=66  Identities=24%  Similarity=0.374  Sum_probs=51.1

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcH-HHHHHHhhcceeeEeccC
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTF-DQIKQASAMVRELIVNVG  249 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~-~qi~~A~~~I~~~l~~~~  249 (300)
                      ....+.|++..+..+||++|..|+.|...++++|.|.+..      .+.|.++. ..+..|...|..+..+.+
T Consensus       552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~IdieddG------tv~i~~s~~~~~~~ak~~I~~i~~e~e  618 (692)
T COG1185         552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDG------TVKIAASDGESAKKAKERIEAITREVE  618 (692)
T ss_pred             ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCCC------cEEEEecchHHHHHHHHHHHHHHhhcc
Confidence            3566889999999999999999999999999999997432      35555543 567778777777665444

>PF10650 zf-C3H1: Putative zinc-finger domain; InterPro: IPR019607 This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger

Probab=83.94  E-value=0.69  Score=25.44  Aligned_cols=20  Identities=35%  Similarity=0.747  Sum_probs=16.7

Q ss_pred             ccccccccc-cccCCCCCcCCC
Q 022221          270 KLCENFAKG-SCTFGDRCHFAH  290 (300)
Q Consensus       270 ~~C~~~~~G-~C~~G~~C~faH  290 (300)
                      .+|.|-++| .|.- +.|.|.|
T Consensus         1 ~lC~yEl~Gg~Cnd-~~C~~QH   21 (23)
T PF10650_consen    1 PLCPYELTGGVCND-PDCEFQH   21 (23)
T ss_pred             CCCccccCCCeeCC-CCCCccc
Confidence            379998876 9987 6999998

>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]

Probab=82.59  E-value=0.73  Score=45.10  Aligned_cols=71  Identities=23%  Similarity=0.427  Sum_probs=57.3

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      ...+...+|+..++.|+||+|..+..++..++++|-++....+...+...|.+...-...|+.++.+.+.+
T Consensus       139 pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~e  209 (608)
T KOG2279|consen  139 PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSE  209 (608)
T ss_pred             cccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccc
Confidence            34556788999999999999999999999999999998877666677777777766666777777666544

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=81.98  E-value=0.82  Score=45.31  Aligned_cols=64  Identities=27%  Similarity=0.431  Sum_probs=44.3

Q ss_pred             CcceEEEeCc-cccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeE
Q 022221          177 SATAKISIDA-KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELI  245 (300)
Q Consensus       177 ~~t~~~~iP~-~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l  245 (300)
                      .+...+.+|+ .+-|.||||.|.||+.+...||+-+.|++.+     ..+.+++ +|--.+-|...+..++
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~fdp~rreia~~~l~~li  268 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPVRREIARMALEKLI  268 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC-----CeEEecCCchHHHHHHHHHHHHHH
Confidence            3445578885 7789999999999999999999999998865     3444554 3322234444444443

>PRK00106 hypothetical protein; Provisional

Probab=81.40  E-value=0.96  Score=44.89  Aligned_cols=65  Identities=25%  Similarity=0.375  Sum_probs=45.1

Q ss_pred             CcceEEEeCc-cccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEe
Q 022221          177 SATAKISIDA-KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIV  246 (300)
Q Consensus       177 ~~t~~~~iP~-~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~  246 (300)
                      .+...+.+|+ .+-|.||||.|.||+.+...||+-+.|++.+     ..+.+++ +|--.+-|...+..++.
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~v~lS~fdpvRReiAr~~le~Li~  290 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP-----EVVVLSGFDPIRREIARMTLESLIK  290 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC-----CeEEEeCCChHHHHHHHHHHHHHHH
Confidence            3445578885 7889999999999999999999999998765     3445555 33333344444444443

>PRK12704 phosphodiesterase; Provisional

Probab=80.67  E-value=1  Score=44.67  Aligned_cols=65  Identities=25%  Similarity=0.405  Sum_probs=45.5

Q ss_pred             CcceEEEeCc-cccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEe
Q 022221          177 SATAKISIDA-KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIV  246 (300)
Q Consensus       177 ~~t~~~~iP~-~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~  246 (300)
                      .+...+.+|+ .+-|.||||.|.||+.+...||+-+.|++.+     ..+.+++ ++--.+.|...+..++.
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~~~~~rre~a~~~l~~l~~  275 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPIRREIARLALEKLVQ  275 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC-----CeEEEecCChhhHHHHHHHHHHHHh
Confidence            3445578885 7889999999999999999999999998864     3445555 33333344444444433

>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]

Probab=80.65  E-value=0.72  Score=39.72  Aligned_cols=32  Identities=34%  Similarity=0.599  Sum_probs=28.8

Q ss_pred             ccccceeccCCCccccchhcccCCeeEeccCC
Q 022221          186 AKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE  217 (300)
Q Consensus       186 ~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~  217 (300)
                      ...+|+|||..|.++++++..|+++|-|+...
T Consensus       162 ~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g  193 (269)
T COG5176         162 SNFVGLLIGPRGSTLKQLERISRAKIAIRGSG  193 (269)
T ss_pred             cceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence            56789999999999999999999999997543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	300
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	8e-22
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	4e-20
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-18
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-17
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	1e-16
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	1e-16
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	6e-16
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-14
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	9e-14
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-13
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	3e-13
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	5e-08
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	1e-06
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	3e-06
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	3e-04
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	3e-13
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	8e-12
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	4e-10
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	9e-12
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-10
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-11
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	1e-10
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-11
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	4e-11
1we8_A	104	Tudor and KH domain containing protein; structural	3e-11
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	4e-11
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	9e-10
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	5e-10
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	1e-09
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	1e-09
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	4e-08
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	5e-04
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	5e-08
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	6e-08
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	2e-07
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	3e-07
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	1e-06
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	4e-04
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	4e-06
1tua_A	191	Hypothetical protein APE0754; structural genomics,	8e-06
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-05
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	3e-04
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	3e-04
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	6e-04
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	8e-04

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 86.2 bits (214), Expect = 8e-22
 Identities = 25/74 (33%), Positives = 39/74 (52%)

Query: 172 ASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTF 231
            + G   T +++I   LAG+IIGK G   KQI   +GA + I +       R I + GT 
Sbjct: 1   GAMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 60

Query: 232 DQIKQASAMVRELI 245
           DQI+ A  +++  +
Sbjct: 61  DQIQNAQYLLQNSV 74

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89

 Score = 82.0 bits (203), Expect = 4e-20
 Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 164 PPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLR 223
              S G     G   T +++I   LAG+IIGK G   KQI   +GA + I +       R
Sbjct: 2   SHMSYGDLG--GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDR 59

Query: 224 NIELEGTFDQIKQASAMVRELI 245
            I + GT DQI+ A  +++  +
Sbjct: 60  IITITGTQDQIQNAQYLLQNSV 81

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 77.1 bits (190), Expect = 4e-18
 Identities = 14/96 (14%), Positives = 35/96 (36%)

Query: 169 GAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELE 228
             A          + +     G +IG++G   K+I    G ++  +  +     +   + 
Sbjct: 2   AMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM 61

Query: 229 GTFDQIKQASAMVRELIVNVGSGSGHSMKSNSSSQS 264
           G  D+ + A+ ++ +L+ ++ SG             
Sbjct: 62  GPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPG 97

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 75.7 bits (186), Expect = 1e-17
 Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 172 ASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH---EVDPNLRNIELE 228
            +         SI     G +IG+ G N K I + TGA + I        DPN +   + 
Sbjct: 1   GAMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR 60

Query: 229 GTFDQIKQASAMVRELI 245
           G+  QI  A  ++ E I
Sbjct: 61  GSPQQIDHAKQLIEEKI 77

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 72.4 bits (178), Expect = 1e-16
 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 169 GAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPN-LRNIE 226
             A         +I I A  AG +IGK G   KQ+    G K+ + +D   + N  + + 
Sbjct: 5   DNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLR 64

Query: 227 LEGTFDQIKQASAMVRELI 245
           + G   +++QA  MV +++
Sbjct: 65  IIGDPYKVQQACEMVMDIL 83

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82

 Score = 72.3 bits (178), Expect = 1e-16
 Identities = 18/79 (22%), Positives = 38/79 (48%)

Query: 175 GASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQI 234
           G+  T +++I   L G IIG+ G N  +I +++GA++ I +     + R + + G+   I
Sbjct: 3   GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASI 62

Query: 235 KQASAMVRELIVNVGSGSG 253
             A  ++   + +      
Sbjct: 63  SLAQYLINARLSSEKGMGC 81

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 70.4 bits (173), Expect = 6e-16
 Identities = 15/71 (21%), Positives = 34/71 (47%)

Query: 175 GASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQI 234
             + + +++I   L G IIG+ G    +I +++GA++ I +       R + + G+   I
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASI 61

Query: 235 KQASAMVRELI 245
             A  ++   +
Sbjct: 62  SLAQYLINVRL 72

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 67.5 bits (165), Expect = 1e-14
 Identities = 17/79 (21%), Positives = 35/79 (44%)

Query: 175 GASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQI 234
            +  T +  +   + G IIG+ G    +I + +G K+ I         R+  L GT + +
Sbjct: 12  RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESV 71

Query: 235 KQASAMVRELIVNVGSGSG 253
           + A  ++ +++    SG  
Sbjct: 72  QSAKRLLDQIVEKGRSGPS 90

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94

 Score = 64.7 bits (158), Expect = 9e-14
 Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 2/87 (2%)

Query: 169 GAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNL--RNIE 226
                   +A  +I I A  AG +IGK G   KQ+    G K+ +           + + 
Sbjct: 6   SGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLR 65

Query: 227 LEGTFDQIKQASAMVRELIVNVGSGSG 253
           + G   +++QA  MV ELI + GSG  
Sbjct: 66  ITGDPYKVQQAKEMVLELIRDQGSGPS 92

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 63.8 bits (156), Expect = 1e-13
 Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPNL--RNIELEGTFDQIK 235
             ++++   L GAI+GK G    +   LTGA++ I +  E  P    R + + G+    +
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 236 QASAMVRELI 245
            A  ++ + +
Sbjct: 64  AAQYLISQRV 73

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77

 Score = 63.0 bits (153), Expect = 3e-13
 Identities = 20/96 (20%), Positives = 30/96 (31%), Gaps = 30/96 (31%)

Query: 39  KSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFP 98
           K++ C  +  +  C +G  C F H               G                    
Sbjct: 11  KTELCRTYSESGRCRYGAKCQFAH---------------GLGELRQANRH---------- 45

Query: 99  DGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWE 134
                P  K+ LC+K+     C +G +CHF H   E
Sbjct: 46  -----PKYKTELCHKFKLQGRCPYGSRCHFIHNPTE 76

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77

 Score = 48.4 bits (115), Expect = 5e-08
 Identities = 16/36 (44%), Positives = 25/36 (69%), Gaps = 1/36 (2%)

Query: 262 SQSNNFKTKLCENFAK-GSCTFGDRCHFAHGSEELR 296
           + S+ +KT+LC  +++ G C +G +C FAHG  ELR
Sbjct: 5   TTSSRYKTELCRTYSESGRCRYGAKCQFAHGLGELR 40

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77

 Score = 44.6 bits (105), Expect = 1e-06
 Identities = 14/50 (28%), Positives = 22/50 (44%)

Query: 98  PDGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVPSYEDPR 147
              ++    K+ LC  Y+ +  C++G KC FAHG  EL +          
Sbjct: 2   SHMTTSSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQANRHPKYKTE 51

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77

 Score = 43.4 bits (102), Expect = 3e-06
 Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 262 SQSNNFKTKLCENFAK-GSCTFGDRCHFAHGSEE 294
           ++   +KT+LC  F   G C +G RCHF H   E
Sbjct: 43  NRHPKYKTELCHKFKLQGRCPYGSRCHFIHNPTE 76

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 13/41 (31%), Positives = 18/41 (43%)

Query: 22 FKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLH 62
          F     E+         K++ C KF     CP+G  CHF+H
Sbjct: 32 FAHGLGELRQANRHPKYKTELCHKFKLQGRCPYGSRCHFIH 72

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 63.5 bits (155), Expect = 3e-13
 Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPNL--RNIELEGTFDQIK 235
             +I++   L GAI+GK G    +   LTGA++ I +  E  P    R + + G+    +
Sbjct: 4   LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 236 QASAMVRELI 245
            A  ++ + +
Sbjct: 64  AAQYLISQRV 73

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score = 61.3 bits (149), Expect = 8e-12
 Identities = 18/86 (20%), Positives = 37/86 (43%), Gaps = 1/86 (1%)

Query: 162 EPPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDP 220
           +       + A+     T ++ + A   G++IGK G   K+I   TGA++ +  D   + 
Sbjct: 73  DISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNS 132

Query: 221 NLRNIELEGTFDQIKQASAMVRELIV 246
             R I + G    I +    +  +++
Sbjct: 133 TERAITIAGIPQSIIECVKQICVVML 158

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score = 56.7 bits (137), Expect = 4e-10
 Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 2/85 (2%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQAS 238
           T ++ +  K  G+IIGK G + K++   +GA+++I +       R I L G  + I +A 
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP--ERIITLAGPTNAIFKAF 63

Query: 239 AMVRELIVNVGSGSGHSMKSNSSSQ 263
           AM+ + +    S S  +  + S   
Sbjct: 64  AMIIDKLEEDISSSMTNSTAASRPP 88

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score = 61.3 bits (149), Expect = 9e-12
 Identities = 13/77 (16%), Positives = 34/77 (44%)

Query: 175 GASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQI 234
                  + +     G +IG++G   K+I    G ++  +  +     +   + G  D+ 
Sbjct: 88  RIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRC 147

Query: 235 KQASAMVRELIVNVGSG 251
           + A+ ++ +L+ ++ SG
Sbjct: 148 EHAARIINDLLQSLRSG 164

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score = 57.5 bits (139), Expect = 2e-10
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 2/92 (2%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPNL-RNIELEGTFDQIKQ 236
             +I I A  AG +IGK G   KQ+    G K+ + +D   + N+ + + + G   +++Q
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 62

Query: 237 ASAMVRELIVNVGSGSGHSMKSNSSSQSNNFK 268
           A  MV +++     G         S       
Sbjct: 63  ACEMVMDILRERDQGGFGDRNEYGSRIGGGID 94

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score = 60.7 bits (147), Expect = 2e-11
 Identities = 27/99 (27%), Positives = 40/99 (40%), Gaps = 3/99 (3%)

Query: 150 GGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGA 209
           G P     GGR     Q        G        +     G IIGK G   K I + +GA
Sbjct: 76  GNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGA 135

Query: 210 KLSIRDHE---VDPNLRNIELEGTFDQIKQASAMVRELI 245
           ++ ++ +     DPN++   + GT  QI  A  ++ E I
Sbjct: 136 RIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score = 58.3 bits (141), Expect = 1e-10
 Identities = 17/90 (18%), Positives = 38/90 (42%)

Query: 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQ 236
           S    + I     G +IG+NG   K+I    G ++  +  +     R  ++ G  D+ + 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 237 ASAMVRELIVNVGSGSGHSMKSNSSSQSNN 266
           A+ ++ +L+ +V +G+          +   
Sbjct: 62  AAEIITDLLRSVQAGNPGGPGPGGRGRGRG 91

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 60.2 bits (146), Expect = 2e-11
 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 175 GASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNL--RNIELEGTFD 232
                  I + A  AG +IGK G    ++  LT A++ +   +         +++ G F 
Sbjct: 82  EVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFY 141

Query: 233 QIKQASAMVRELI 245
             + A   +R+++
Sbjct: 142 ASQMAQRKIRDIL 154

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 59.4 bits (144), Expect = 4e-11
 Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV-DPNLRNIELEGTFDQIKQA 237
             ++ I A+  GAIIGK G + KQ+ R   A + I   E  D  +R + + G  +   +A
Sbjct: 4   MVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKA 63

Query: 238 SAMVRELIVNVGSGSG 253
              +   +        
Sbjct: 64  QGRIYGKLKEENFFGP 79

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 58.3 bits (141), Expect = 3e-11
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 170 AAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNL--RNIEL 227
              +       ++S+  +  G IIG+ G   + IC+ +GAK++         L  R I++
Sbjct: 7   GILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKI 66

Query: 228 EGTFDQIKQASAMVRELI 245
            GT  ++  A  ++ E +
Sbjct: 67  SGTQKEVAAAKHLILEKV 84

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score = 59.9 bits (145), Expect = 4e-11
 Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 2/94 (2%)

Query: 154 HGRMGGRLEPPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI 213
              +               +   +   KI +    AG IIGK G   K I   +GA + +
Sbjct: 80  PQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQL 139

Query: 214 RDHEVDPNL--RNIELEGTFDQIKQASAMVRELI 245
                  NL  R + + G  +Q ++A  ++ + I
Sbjct: 140 SQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKI 173

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score = 56.0 bits (135), Expect = 9e-10
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 175 GASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPNL--RNIELEGTF 231
           G+    K+ I +  AG+IIGK G    Q+ + TGA + + +  +  P    R   ++GT 
Sbjct: 3   GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI 62

Query: 232 DQIKQASAMVRELI 245
           + +      + E I
Sbjct: 63  EALNAVHGFIAEKI 76

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 54.2 bits (131), Expect = 5e-10
 Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 2/67 (2%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQAS 238
           T ++ +  K  G+IIGK G + K++   +GA+++I +       R I L G  + I +A 
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPE--RIITLAGPTNAIFKAF 63

Query: 239 AMVRELI 245
           AM+ + +
Sbjct: 64  AMIIDKL 70

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 53.6 bits (129), Expect = 1e-09
 Identities = 24/94 (25%), Positives = 41/94 (43%), Gaps = 9/94 (9%)

Query: 169 GAAASFG-------ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPN 221
           G++ S G         A+A ++I  +    +IGKNG   + +   T  K+ I   +   N
Sbjct: 1   GSSGSSGDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSN 60

Query: 222 LRNIELEGTFDQIKQASAMVRELIVNVGSGSGHS 255
              I++ GT + I++A   V  +       SG S
Sbjct: 61  Q--IKITGTKEGIEKARHEVLLISAEQDKRSGPS 92

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 52.7 bits (127), Expect = 1e-09
 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQAS 238
             +I+ID K    +IGK+G N  +I       + I       N   I +EG    ++QA 
Sbjct: 6   YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSN--LIRIEGDPQGVQQAK 63

Query: 239 AMVRELI 245
             + EL 
Sbjct: 64  RELLELA 70

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69

 Score = 48.8 bits (116), Expect = 4e-08
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 7/47 (14%)

Query: 258 SNSSSQSNNFKT-------KLCENFAKGSCTFGDRCHFAHGSEELRK 297
           S+ SS    ++         +C+ +  G+C  G+ C FAHG+ EL +
Sbjct: 2   SSGSSGQYCWQHRFPTGYFSICDRYMNGTCPEGNSCKFAHGNAELHE 48

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69

 Score = 37.2 bits (86), Expect = 5e-04
 Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 1/33 (3%)

Query: 103 PPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWEL 135
            P     +C++Y +   C  G+ C FAHG  EL
Sbjct: 15  FPTGYFSICDRYMNG-TCPEGNSCKFAHGNAEL 46

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 49.0 bits (117), Expect = 5e-08
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQAS 238
           +  + +D ++   IIG  G   ++I       +        P+   + + G  + +++A 
Sbjct: 18  SEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPENVEEAI 76

Query: 239 AMVRELIVNVGSGSGHS 255
             +  L     + SG S
Sbjct: 77  DHILNLEEEYLADSGPS 93

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 48.4 bits (115), Expect = 6e-08
 Identities = 17/86 (19%), Positives = 37/86 (43%), Gaps = 4/86 (4%)

Query: 169 GAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELE 228
           G++ S G   T ++ +  ++ G ++G  G   K+I + T   +     + +P      + 
Sbjct: 1   GSSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEP---VFAVT 57

Query: 229 GTFDQIKQASAMVRELI-VNVGSGSG 253
           G  + + +A   +   I +  G  SG
Sbjct: 58  GMPENVDRAREEIEAHITLRSGPSSG 83

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 47.1 bits (112), Expect = 2e-07
 Identities = 12/70 (17%), Positives = 24/70 (34%), Gaps = 1/70 (1%)

Query: 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPNLRNIELEGTFDQIK 235
           S    +++D K    IIG+ G    QI       +      + +     I + G     +
Sbjct: 16  SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTE 75

Query: 236 QASAMVRELI 245
            A   +  ++
Sbjct: 76  AARDAILRIV 85

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 46.7 bits (111), Expect = 3e-07
 Identities = 11/70 (15%), Positives = 28/70 (40%), Gaps = 2/70 (2%)

Query: 176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIK 235
              T ++ +   L   +IG+ G   +++       + +   E+  +   I + G    + 
Sbjct: 15  VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSD--IIAITGLAANLD 72

Query: 236 QASAMVRELI 245
           +A A + E +
Sbjct: 73  RAKAGLLERV 82

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 46.2 bits (109), Expect = 1e-06
 Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 6/92 (6%)

Query: 163 PPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGA-KLSIRDHEV--- 218
               ++  A SF   A   I +   L G +IGKNG   ++I   +G  ++ I        
Sbjct: 52  EDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV 111

Query: 219 --DPNLRNIELEGTFDQIKQASAMVRELIVNV 248
             +  +      GT D I  A+ ++   +  +
Sbjct: 112 PQEEGMVPFVFVGTKDSIANATVLLDYHLNYL 143

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 13/67 (19%), Positives = 29/67 (43%), Gaps = 5/67 (7%)

Query: 176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQI 234
           +    +  +   L G  IG +G N +Q  ++ G    +   ++D +     + G   D +
Sbjct: 2   SRFHEQFIVREDLMGLAIGTHGANIQQARKVPG----VTAIDLDEDTCTFHIYGEDQDAV 57

Query: 235 KQASAMV 241
           K+A + +
Sbjct: 58  KKARSFL 64

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219

 Score = 45.9 bits (108), Expect = 4e-06
 Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 11/66 (16%)

Query: 190 GAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG 249
           G IIG+ G   + I  ++GA +S+         + + + G   QI+ A   + +L     
Sbjct: 141 GRIIGRKGRTRQIIEEMSGASVSVYG-------KTVAIIGNPIQIEIAKTAIEKLA---- 189

Query: 250 SGSGHS 255
            GS H 
Sbjct: 190 RGSPHG 195

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Length = 191

 Score = 44.6 bits (105), Expect = 8e-06
 Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 11/66 (16%)

Query: 190 GAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG 249
           G IIG+ G   + I  +T   +++ +         + + G +++   A   +  L     
Sbjct: 110 GRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGDYERAMAAKQAIEMLA---- 158

Query: 250 SGSGHS 255
            G  HS
Sbjct: 159 EGRMHS 164

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQA 237
           A  ++SI AKL  ++IG  G   + I    G  + I           + + G    +++A
Sbjct: 17  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECG-GVHIHFPVEGSGSDTVVIRGPSSDVEKA 75

Query: 238 SAMVRELIVNVGSGSGHS 255
              +  L     + SG S
Sbjct: 76  KKQLLHLAEEKQTKSGPS 93

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 77

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 13/30 (43%), Positives = 20/30 (66%)

Query: 261 SSQSNNFKTKLCENFAKGSCTFGDRCHFAH 290
           SS S+  KT +C+++ +G C  GD+C F H
Sbjct: 2   SSGSSGEKTVVCKHWLRGLCKKGDQCEFLH 31

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score = 40.7 bits (94), Expect = 3e-04
 Identities = 19/119 (15%), Positives = 39/119 (32%), Gaps = 7/119 (5%)

Query: 163 PPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGV--NSKQICRLTGAKLSIRDHEV-- 218
           P P ++          T  +  +++    +   NG   N   I   T   + + D  V  
Sbjct: 15  PLPSNIPMIEINPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGG 74

Query: 219 ---DPNLRNIELEGTFDQIKQASAMVRELIVNVGSGSGHSMKSNSSSQSNNFKTKLCEN 274
              DP  + + + G F  + +A  ++R         +   MK        + +    +N
Sbjct: 75  TTPDPFAQQVTITGYFGDVDRARMLMRRNCHFTVFMALSKMKMPLHELQAHVRQNPIQN 133

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1 Length = 98

 Score = 37.8 bits (87), Expect = 6e-04
 Identities = 11/39 (28%), Positives = 18/39 (46%)

Query: 258 SNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELR 296
           S+ SS     K +LC+ +  G C   + C + HG    +
Sbjct: 2   SSGSSGELPKKRELCKFYITGFCARAENCPYMHGDFPCK 40

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 102

 Score = 37.2 bits (86), Expect = 8e-04
 Identities = 23/98 (23%), Positives = 41/98 (41%), Gaps = 9/98 (9%)

Query: 164 PPQSLGAAASF-----GASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV 218
            P+ LG A +       +   + ++  + L   IIGK G N  +I +    K+ I   E 
Sbjct: 8   EPEKLGQALTEVYAKANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMP-KVHI---EF 63

Query: 219 DPNLRNIELEGTFDQIKQASAMVRELIVNVGSGSGHSM 256
                 I LEG  + +  A   +  ++ ++ + SG S 
Sbjct: 64  TEGEDKITLEGPTEDVSVAQEQIEGMVKDLINRSGPSS 101

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	300
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	99.72
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	99.66
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	99.38
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	99.31
2rhk_C	72	Cleavage and polyadenylation specificity factor su	99.26
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	99.06
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	99.01
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	98.99
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	98.98
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	98.98
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	98.98
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	98.97
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	98.96
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	98.94
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	98.94
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	98.91
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	98.89
2rhk_C	72	Cleavage and polyadenylation specificity factor su	98.88
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	98.86
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	98.85
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	98.83
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	98.79
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	98.78
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	98.77
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	98.75
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	98.75
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	98.64
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	98.63
1we8_A	104	Tudor and KH domain containing protein; structural	98.62
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	98.48
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	98.47
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	98.4
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	98.39
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	98.37
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.34
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	98.34
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	98.31
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	98.3
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	98.29
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	98.27
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	98.26
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	98.25
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	98.24
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	98.24
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	98.19
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	98.06
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	98.03
2cpq_A	91	FragIle X mental retardation syndrome related prot	97.97
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	97.96
3u9g_A	229	Zinc finger CCCH-type antiviral protein 1; zinc fi	97.87
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	97.8
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	97.6
2fc6_A	50	Nuclear, target of EGR1, member 1; structure genom	97.23
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	97.12
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	97.1
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	97.09
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.01
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	96.47
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	96.37
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	96.31
3u9g_A	229	Zinc finger CCCH-type antiviral protein 1; zinc fi	96.3
2fc6_A	50	Nuclear, target of EGR1, member 1; structure genom	96.26
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	96.11
1tua_A	191	Hypothetical protein APE0754; structural genomics,	96.01
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	95.97
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	95.79
1tua_A	191	Hypothetical protein APE0754; structural genomics,	95.57
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	93.64
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	93.64
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	91.63
2lhn_A	80	Nuclear polyadenylated RNA-binding protein NAB2; n	88.03
2lhn_A	80	Nuclear polyadenylated RNA-binding protein NAB2; n	84.55
3v33_A	223	Ribonuclease ZC3H12A; rossmann-like sandwich fold,	82.31
3v33_A	223	Ribonuclease ZC3H12A; rossmann-like sandwich fold,	81.99

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A

Probab=99.72  E-value=1.7e-18  Score=126.11  Aligned_cols=71  Identities=30%  Similarity=0.667  Sum_probs=30.5

Q ss_pred             CCCccccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q 022221           34 TGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNK  113 (300)
Q Consensus        34 ~~~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~  113 (300)
                      ....|||+||++|+.+|.|++|++|+|+|+..+++..                              ...+.+||++|++
T Consensus         6 ~~~~~kt~~C~~f~~~G~C~~G~~C~f~H~~~e~~~~------------------------------~~~~~~k~~~C~~   55 (77)
T 1m9o_A            6 TSSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQA------------------------------NRHPKYKTELCHK   55 (77)
T ss_dssp             CSSCCCSCCCSGGGGTSCCTTTTTCSSCSSSCCGGGT------------------------------C------------
T ss_pred             CCCCccchhCHHhhhCCCcCCCCCccCCCCChhhccc------------------------------cccccccCCcccc
Confidence            3467999999888789999999999999998765311                              0124678999998


Q ss_pred             cccCcCCCCCCCCccCCCccc
Q 022221          114 YNSAEGCKFGDKCHFAHGEWE  134 (300)
Q Consensus       114 ~~~~~~C~~g~~C~f~H~~~~  134 (300)
                      |...|.|++|++|+|+|+..|
T Consensus        56 f~~~G~C~~G~~C~f~H~~~e   76 (77)
T 1m9o_A           56 FKLQGRCPYGSRCHFIHNPTE   76 (77)
T ss_dssp             ---------------------
T ss_pred             hhhCcCCCCcCcCCCCCCCCC
Confidence            888888999999999998765

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A

Probab=99.66  E-value=2.4e-17  Score=120.01  Aligned_cols=34  Identities=41%  Similarity=0.897  Sum_probs=30.1

Q ss_pred             CCccccccccccccCcCCCCCCCCccCCCccccC
Q 022221          103 PPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELG  136 (300)
Q Consensus       103 ~~~~kt~~C~~~~~~~~C~~g~~C~f~H~~~~~~  136 (300)
                      ..+|||++|++|+..|.|++|++|+|+|+..+++
T Consensus         7 ~~~~kt~~C~~f~~~G~C~~G~~C~f~H~~~e~~   40 (77)
T 1m9o_A            7 SSRYKTELCRTYSESGRCRYGAKCQFAHGLGELR   40 (77)
T ss_dssp             SSCCCSCCCSGGGGTSCCTTTTTCSSCSSSCCGG
T ss_pred             CCCccchhCHHhhhCCCcCCCCCccCCCCChhhc
Confidence            4589999999998778899999999999987665

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.38  E-value=4e-13  Score=97.37  Aligned_cols=66  Identities=26%  Similarity=0.442  Sum_probs=51.6

Q ss_pred             CCCCccccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccc
Q 022221           33 PTGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCN  112 (300)
Q Consensus        33 ~~~~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~  112 (300)
                      +....+|+++|++| ..|.|++|++|+|+|+....                                       ++.+|+
T Consensus         3 p~~~~~k~~~C~~f-l~G~C~~G~~C~fsH~~~~~---------------------------------------~~~~C~   42 (77)
T 2d9n_A            3 SGSSGEKTVVCKHW-LRGLCKKGDQCEFLHEYDMT---------------------------------------KMPECY   42 (77)
T ss_dssp             CCCSCCTTSBCHHH-HTTCCSCTTSSSSBCSCCTT---------------------------------------TSCBCH
T ss_pred             CCCCCCcceeCHhH-ccCcCCCCCCCCCccccccC---------------------------------------cCCCCc
Confidence            34567899999655 55999999999999986321                                       245799


Q ss_pred             ccccCcCCCCCCCCccCCCccccCCCC
Q 022221          113 KYNSAEGCKFGDKCHFAHGEWELGRPT  139 (300)
Q Consensus       113 ~~~~~~~C~~g~~C~f~H~~~~~~~~~  139 (300)
                      +|++.|.|. |++|+|+|...+.....
T Consensus        43 ~f~~~G~C~-~~~C~f~H~~~~~~~~~   68 (77)
T 2d9n_A           43 FYSKFGECS-NKECPFLHIDPESKIKD   68 (77)
T ss_dssp             HHHHTCCCC-CSSCSSBCCCTTSSCSS
T ss_pred             ccCCCCccC-CCCeeccCCCccccCCC
Confidence            999966799 99999999986655443

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1

Probab=99.31  E-value=8.6e-13  Score=99.91  Aligned_cols=53  Identities=28%  Similarity=0.627  Sum_probs=45.3

Q ss_pred             CCccccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q 022221           35 GIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKY  114 (300)
Q Consensus        35 ~~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~  114 (300)
                      .+.+|+.+|++| ..|.|++|++|+|+|+.                                            .+|++|
T Consensus         8 ~~~~k~~lC~~f-~~G~C~~G~~C~f~H~~--------------------------------------------~~C~~f   42 (98)
T 2cqe_A            8 ELPKKRELCKFY-ITGFCARAENCPYMHGD--------------------------------------------FPCKLY   42 (98)
T ss_dssp             CCSCCCSBCTTT-TTTCCSCSTTCSSBSSS--------------------------------------------SBCSHH
T ss_pred             CCCCCCccCccc-ccCcCCCCCCCCCCCCC--------------------------------------------CcCcCc
Confidence            356899999655 68999999999999972                                            259999


Q ss_pred             ccCcCCCCCCCCccCCCc
Q 022221          115 NSAEGCKFGDKCHFAHGE  132 (300)
Q Consensus       115 ~~~~~C~~g~~C~f~H~~  132 (300)
                      +..|.|++|++|+|+|..
T Consensus        43 ~~~G~C~~G~~C~f~H~~   60 (98)
T 2cqe_A           43 HTTGNCINGDDCMFSHDP   60 (98)
T ss_dssp             HHTSCCSSCTTCSSBCCC
T ss_pred             ccCCcCCCCCCCcccCCC
Confidence            877779999999999975

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}

Probab=99.26  E-value=1.3e-12  Score=93.26  Aligned_cols=61  Identities=28%  Similarity=0.466  Sum_probs=48.0

Q ss_pred             CCCccccccccccccccccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q 022221           34 TGIGSKSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNK  113 (300)
Q Consensus        34 ~~~~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~  113 (300)
                      .+.+.|+++|++| ..|.|++|++|+|+|+....                                       ++.+|++
T Consensus        10 ~~~~~k~~vCk~f-l~G~C~~G~~C~fsH~~~~~---------------------------------------~~~~C~~   49 (72)
T 2rhk_C           10 HMSGEKTVVCKHW-LRGLCKKGDQCEFLHEYDMT---------------------------------------KMSECYF   49 (72)
T ss_dssp             SSSCCCCSBCHHH-HTTCCCCGGGSSSBCSCCTT---------------------------------------SCCBCHH
T ss_pred             cCCCCcCeeCHHH-hcCCCCCCCCCCCccccccc---------------------------------------cCCcccc
Confidence            4567899999655 55999999999999986311                                       3457999


Q ss_pred             cccCcCCCCCCCCccCCCcccc
Q 022221          114 YNSAEGCKFGDKCHFAHGEWEL  135 (300)
Q Consensus       114 ~~~~~~C~~g~~C~f~H~~~~~  135 (300)
                      |++.|.|.+ ++|.|.|...+.
T Consensus        50 f~~~G~C~~-~~C~y~H~~p~~   70 (72)
T 2rhk_C           50 YSKFGECSN-KECPFLHIDPES   70 (72)
T ss_dssp             HHHHSCCSB-TTCCSBCCCCC-
T ss_pred             cCCCCCCCC-CCeeccCCCccc
Confidence            999566999 999999987543

>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 1.50A {Homo sapiens} PDB: 3d2s_A

Probab=99.06  E-value=4e-11  Score=85.13  Aligned_cols=64  Identities=22%  Similarity=0.511  Sum_probs=49.5

Q ss_pred             cccccccccccccccCCCC-CCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccccc
Q 022221           38 SKSKPCTKFFSTSGCPFGE-GCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNS  116 (300)
Q Consensus        38 ~Kt~lC~~y~~~g~C~~G~-~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~~  116 (300)
                      .|..+|+.| ..|.|..|+ .|+|+|...+.+..                                ....++.+|.+|++
T Consensus         4 ~k~~vC~~f-~~G~C~rg~~~C~f~H~~~~~~~~--------------------------------~~~~~~~vC~~flk   50 (70)
T 3d2q_A            4 DRLEVCREY-QRGNCNRGENDCRFAHPADSTMID--------------------------------TNDNTVTVCMDYIK   50 (70)
T ss_dssp             CEEEBCHHH-HTTCCSSCTTTCSSBCCCTTSCCB--------------------------------TTTTEEEBCHHHHT
T ss_pred             ccchhCHHH-hcCCCCCCCCCCCCccCccccccc--------------------------------ccCCcceeccccCc
Confidence            467899666 789999999 59999987543210                                12446788999998


Q ss_pred             CcCCCCCCCCccCCCccccC
Q 022221          117 AEGCKFGDKCHFAHGEWELG  136 (300)
Q Consensus       117 ~~~C~~g~~C~f~H~~~~~~  136 (300)
                      +. |..+ .|+|+|...+|+
T Consensus        51 G~-C~r~-~C~y~H~~~~L~   68 (70)
T 3d2q_A           51 GR-CSRE-KCKYFHPPAHLQ   68 (70)
T ss_dssp             TC-CCCT-TCCSBCCCHHHH
T ss_pred             CC-CCCC-CcCeeCCHHHHh
Confidence            65 9999 999999987775

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.01  E-value=5.8e-11  Score=82.52  Aligned_cols=30  Identities=37%  Similarity=0.967  Sum_probs=28.5

Q ss_pred             ccccccccccccccCCCCCcCCCCcchhcc
Q 022221          268 KTKLCENFAKGSCTFGDRCHFAHGSEELRK  297 (300)
Q Consensus       268 kt~~C~~~~~G~C~~G~~C~faH~~~el~~  297 (300)
                      |++||.+|++|.|+||++|+||||++|||.
T Consensus        19 k~~LC~~~~~G~C~~G~~C~FAHG~~ELr~   48 (69)
T 2d9m_A           19 YFSICDRYMNGTCPEGNSCKFAHGNAELHE   48 (69)
T ss_dssp             CCSBCHHHHHSCCSSCSSCSSBSSHHHHHH
T ss_pred             CcccCcccCcCCCCCCCccCCcCCHHHHhh
Confidence            669999999999999999999999999986

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.99  E-value=2.6e-10  Score=82.45  Aligned_cols=28  Identities=32%  Similarity=0.688  Sum_probs=24.3

Q ss_pred             CccccccccccccCcCCCCCCCCccCCCc
Q 022221          104 PAVKSRLCNKYNSAEGCKFGDKCHFAHGE  132 (300)
Q Consensus       104 ~~~kt~~C~~~~~~~~C~~g~~C~f~H~~  132 (300)
                      ..+|+.+|+||+.+ .|++|+.|.|+|..
T Consensus         6 ~~~k~~~C~~fl~G-~C~~G~~C~fsH~~   33 (77)
T 2d9n_A            6 SGEKTVVCKHWLRG-LCKKGDQCEFLHEY   33 (77)
T ss_dssp             SCCTTSBCHHHHTT-CCSCTTSSSSBCSC
T ss_pred             CCCcceeCHhHccC-cCCCCCCCCCcccc
Confidence            46788999999984 59999999999965

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1

Probab=98.98  E-value=4.5e-10  Score=84.92  Aligned_cols=26  Identities=31%  Similarity=0.691  Sum_probs=22.5

Q ss_pred             ccccccccccccCcCCCCCCCCccCCC
Q 022221          105 AVKSRLCNKYNSAEGCKFGDKCHFAHG  131 (300)
Q Consensus       105 ~~kt~~C~~~~~~~~C~~g~~C~f~H~  131 (300)
                      .+|+.+|++|+ .|.|++|++|+|+|.
T Consensus        10 ~~k~~lC~~f~-~G~C~~G~~C~f~H~   35 (98)
T 2cqe_A           10 PKKRELCKFYI-TGFCARAENCPYMHG   35 (98)
T ss_dssp             SCCCSBCTTTT-TTCCSCSTTCSSBSS
T ss_pred             CCCCccCcccc-cCcCCCCCCCCCCCC
Confidence            46889999996 556999999999995

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=98.98  E-value=1.3e-10  Score=87.02  Aligned_cols=73  Identities=21%  Similarity=0.319  Sum_probs=66.1

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      ..+..+.||..++|.|||++|.+|+.|++.|+++|.|.+......++.+.|.|+++++++|..+|..++.+..
T Consensus        14 ~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~   86 (92)
T 1x4n_A           14 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGR   86 (92)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             CEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            5678899999999999999999999999999999999876555678999999999999999999999887655

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1

Probab=98.98  E-value=7.7e-11  Score=86.36  Aligned_cols=74  Identities=24%  Similarity=0.461  Sum_probs=65.1

Q ss_pred             ccCcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEecc
Q 022221          175 GASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNV  248 (300)
Q Consensus       175 g~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~  248 (300)
                      +...+..+.||..++|.|||++|++|++|++.|+++|.|.+..+...++.+.|.|++++++.|..+|..++.+.
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            34567899999999999999999999999999999999987555667899999999999999999999887654

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=98.97  E-value=9.8e-11  Score=85.80  Aligned_cols=72  Identities=33%  Similarity=0.454  Sum_probs=65.0

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEecc
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNV  248 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~  248 (300)
                      ..+..+.||+.++|.|||++|++|++|++.|+++|.|.+..++..++.+.|+|+++++++|..+|..++.+.
T Consensus         6 ~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            6 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            567889999999999999999999999999999999987655667899999999999999999998887654

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=98.96  E-value=9.3e-11  Score=90.05  Aligned_cols=75  Identities=17%  Similarity=0.361  Sum_probs=65.0

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEeccCCC
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGSG  251 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~~~  251 (300)
                      ..+..+.||+.+++.|||++|++|++|++.|+++|+|.+......++.++|+|+++++++|..+|.+++.+.+..
T Consensus        10 ~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~~g   84 (106)
T 2hh3_A           10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSG   84 (106)
T ss_dssp             --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC--
T ss_pred             CeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhccccC
Confidence            457899999999999999999999999999999999976555566789999999999999999999998776643

>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.94  E-value=1.5e-10  Score=87.45  Aligned_cols=65  Identities=25%  Similarity=0.515  Sum_probs=49.7

Q ss_pred             ccccccccccccccccCCCC-CCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccc
Q 022221           37 GSKSKPCTKFFSTSGCPFGE-GCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYN  115 (300)
Q Consensus        37 ~~Kt~lC~~y~~~g~C~~G~-~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~  115 (300)
                      ..|..+|++| ..|.|..|| .|+|+|+....+..                                ....+..+|.+|+
T Consensus        17 ~~k~~VCr~F-lrG~C~rgd~~C~FsH~~~~~~~~--------------------------------~~~~~~~vC~~fl   63 (98)
T 2e5s_A           17 TDKLEVCREF-QRGNCARGETDCRFAHPADSTMID--------------------------------TSDNTVTVCMDYI   63 (98)
T ss_dssp             SSEEEBCSHH-HHTCCSSHHHHCSSBCCSSCCSCC--------------------------------TTTCEEEBCHHHH
T ss_pred             hhhhhhhHHH-hcCcCCCCCCCCCCcCCchhcccc--------------------------------ccCCccccchhhc
Confidence            3588899666 459999999 79999987543210                                1234677899999


Q ss_pred             cCcCCCCCCCCccCCCccccC
Q 022221          116 SAEGCKFGDKCHFAHGEWELG  136 (300)
Q Consensus       116 ~~~~C~~g~~C~f~H~~~~~~  136 (300)
                      ++. |.++ .|+|.|...+|.
T Consensus        64 kG~-C~r~-~C~y~H~~~~l~   82 (98)
T 2e5s_A           64 KGR-CMRE-KCKYFHPPAHLQ   82 (98)
T ss_dssp             HTC-CCCT-TCCSBCCCHHHH
T ss_pred             cCC-CCCC-CcCccCChHHHH
Confidence            976 9999 999999987665

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=98.94  E-value=9.3e-11  Score=84.64  Aligned_cols=70  Identities=21%  Similarity=0.433  Sum_probs=63.2

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEe
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV  246 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~  246 (300)
                      ..+..+.||..++|.|||++|.+|+.|++.||++|.|.+..+...++.+.|.|++++++.|..+|..++.
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~   73 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLS   73 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHHHHHHHHHHHHHHH
Confidence            3567899999999999999999999999999999999876666778999999999999999999987764

>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 1.50A {Homo sapiens} PDB: 3d2s_A

Probab=98.91  E-value=3.8e-10  Score=80.03  Aligned_cols=30  Identities=23%  Similarity=0.682  Sum_probs=27.3

Q ss_pred             cccccccccccccccCCCCCcCCCCcchhcc
Q 022221          267 FKTKLCENFAKGSCTFGDRCHFAHGSEELRK  297 (300)
Q Consensus       267 ykt~~C~~~~~G~C~~G~~C~faH~~~el~~  297 (300)
                      .++.+|.+|++|.|.+| +|+|.|...+|+.
T Consensus        40 ~~~~vC~~flkG~C~r~-~C~y~H~~~~L~~   69 (70)
T 3d2q_A           40 NTVTVCMDYIKGRCSRE-KCKYFHPPAHLQA   69 (70)
T ss_dssp             TEEEBCHHHHTTCCCCT-TCCSBCCCHHHHC
T ss_pred             CcceeccccCcCCCCCC-CcCeeCCHHHHhc
Confidence            46678999999999999 9999999999974

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=98.89  E-value=6.5e-10  Score=85.56  Aligned_cols=71  Identities=31%  Similarity=0.416  Sum_probs=63.3

Q ss_pred             ceEEEeCccccceeccCCCccccchhcccCCeeEeccCC---CCCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221          179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE---VDPNLRNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~---~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      +.++.||..++|.|||++|++|++|++.|+++|+|.+..   .+..++.+.|.|+++++++|..+|.+++.+..
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~   81 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhccc
Confidence            689999999999999999999999999999999997642   23467999999999999999999999987644

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}

Probab=98.88  E-value=5.5e-10  Score=79.57  Aligned_cols=28  Identities=32%  Similarity=0.688  Sum_probs=23.6

Q ss_pred             CccccccccccccCcCCCCCCCCccCCCc
Q 022221          104 PAVKSRLCNKYNSAEGCKFGDKCHFAHGE  132 (300)
Q Consensus       104 ~~~kt~~C~~~~~~~~C~~g~~C~f~H~~  132 (300)
                      ...++.+|+||+.+ .|++|+.|.|+|..
T Consensus        12 ~~~k~~vCk~fl~G-~C~~G~~C~fsH~~   39 (72)
T 2rhk_C           12 SGEKTVVCKHWLRG-LCKKGDQCEFLHEY   39 (72)
T ss_dssp             SCCCCSBCHHHHTT-CCCCGGGSSSBCSC
T ss_pred             CCCcCeeCHHHhcC-CCCCCCCCCCcccc
Confidence            35578899999995 59999999999964

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A

Probab=98.86  E-value=2.1e-10  Score=85.32  Aligned_cols=72  Identities=33%  Similarity=0.454  Sum_probs=65.0

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEecc
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNV  248 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~  248 (300)
                      ..+.++.||..++|.|||++|.+|++|++.|+++|+|.+..++..++.+.|+|+++++++|..+|.+++.+.
T Consensus        13 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           13 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            457889999999999999999999999999999999987656677899999999999999999998887654

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=98.85  E-value=4.9e-10  Score=80.76  Aligned_cols=69  Identities=22%  Similarity=0.399  Sum_probs=60.6

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCC---CCCCccceeecCcHHHHHHHhhcceeeEe
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE---VDPNLRNIELEGTFDQIKQASAMVRELIV  246 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~---~~~~~~~~~i~G~~~qi~~A~~~I~~~l~  246 (300)
                      .+..+.||...+|.|||++|.+|+.|++.|+++|.|.+..   +...++.+.|.|+++++..|..+|..++.
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~   74 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVT   74 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHh
Confidence            4678999999999999999999999999999999997532   34567999999999999999999987764

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1

Probab=98.83  E-value=1.1e-09  Score=82.28  Aligned_cols=73  Identities=32%  Similarity=0.413  Sum_probs=64.7

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCC--CCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV--DPNLRNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~--~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      ..+.++.||+.++|.|||++|.+|++|++.|+++|.|.+...  ...++.+.|.|++++++.|..+|..++.+.+
T Consensus        14 ~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   88 (94)
T 1x4m_A           14 NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQG   88 (94)
T ss_dssp             CEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCCS
T ss_pred             cEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhccC
Confidence            567889999999999999999999999999999999976432  3467999999999999999999999987654

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.79  E-value=1e-09  Score=80.38  Aligned_cols=69  Identities=14%  Similarity=0.272  Sum_probs=60.1

Q ss_pred             cCcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       176 ~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      ...+..+.||..++|+|||++|++|++|++.|+++|+|....   .++.+.|+|+++++++|..+|.+.+..
T Consensus         8 ~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~---~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            8 GQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD---KEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS---SCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC---CCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            356788999999999999999999999999999999996432   246799999999999999999986543

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*

Probab=98.78  E-value=5.7e-10  Score=79.85  Aligned_cols=67  Identities=30%  Similarity=0.427  Sum_probs=59.9

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEe
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV  246 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~  246 (300)
                      .+.++.||+..+|.|||++|.+|+.|++.||++|.|.+.  +..++.+.|.|+++++..|..+|.+.+.
T Consensus         5 ~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l~   71 (73)
T 2axy_A            5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLE   71 (73)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC--CCCcEEEEEEeCHHHHHHHHHHHHHHHh
Confidence            467889999999999999999999999999999999764  3567899999999999999999877654

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=98.77  E-value=8.5e-10  Score=81.67  Aligned_cols=70  Identities=23%  Similarity=0.394  Sum_probs=61.9

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCC---CCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE---VDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~---~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      .+..+.||..++|.|||++|.+|+.|+..||++|.|.+..   +...++.+.|.|+++++..|..+|..++.+
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~   75 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            4678999999999999999999999999999999997542   345679999999999999999999888754

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=98.75  E-value=1.8e-09  Score=79.58  Aligned_cols=69  Identities=26%  Similarity=0.364  Sum_probs=60.1

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCC--CCCccceeecCcHHHHHHHhhcceeeE
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV--DPNLRNIELEGTFDQIKQASAMVRELI  245 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~--~~~~~~~~i~G~~~qi~~A~~~I~~~l  245 (300)
                      .....+.||+..+|.|||++|++|+.|++.|+++|.|.+...  ...++.+.|.|+++++..|..+|..++
T Consensus        13 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~   83 (85)
T 2opv_A           13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDIL   83 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHh
Confidence            356789999999999999999999999999999999976432  456788999999999999999987664

>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.75  E-value=2.8e-09  Score=80.39  Aligned_cols=30  Identities=23%  Similarity=0.659  Sum_probs=26.5

Q ss_pred             cccccccccccccccCCCCCcCCCCcchhcc
Q 022221          267 FKTKLCENFAKGSCTFGDRCHFAHGSEELRK  297 (300)
Q Consensus       267 ykt~~C~~~~~G~C~~G~~C~faH~~~el~~  297 (300)
                      .++.+|.+|++|.|.++ +|+|.|...+|+.
T Consensus        54 ~~~~vC~~flkG~C~r~-~C~y~H~~~~l~~   83 (98)
T 2e5s_A           54 NTVTVCMDYIKGRCMRE-KCKYFHPPAHLQA   83 (98)
T ss_dssp             CEEEBCHHHHHTCCCCT-TCCSBCCCHHHHH
T ss_pred             CccccchhhccCCCCCC-CcCccCChHHHHH
Confidence            45568999999999999 9999999988864

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.64  E-value=3.5e-09  Score=73.52  Aligned_cols=33  Identities=36%  Similarity=0.796  Sum_probs=28.1

Q ss_pred             CccccccccccccCcCCCCCCCCccCCCccccCC
Q 022221          104 PAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGR  137 (300)
Q Consensus       104 ~~~kt~~C~~~~~~~~C~~g~~C~f~H~~~~~~~  137 (300)
                      +..|++||.+|.++ .|+||++|.|||+++||+.
T Consensus        16 P~~k~~LC~~~~~G-~C~~G~~C~FAHG~~ELr~   48 (69)
T 2d9m_A           16 PTGYFSICDRYMNG-TCPEGNSCKFAHGNAELHE   48 (69)
T ss_dssp             CCSCCSBCHHHHHS-CCSSCSSCSSBSSHHHHHH
T ss_pred             CCCCcccCcccCcC-CCCCCCccCCcCCHHHHhh
Confidence            34467999999655 6999999999999999985

>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 2.70A {Homo sapiens}

Probab=98.63  E-value=1.5e-08  Score=74.04  Aligned_cols=64  Identities=19%  Similarity=0.305  Sum_probs=47.7

Q ss_pred             CccccccccccccccccCCCC-CCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q 022221           36 IGSKSKPCTKFFSTSGCPFGE-GCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKY  114 (300)
Q Consensus        36 ~~~Kt~lC~~y~~~g~C~~G~-~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~  114 (300)
                      -+.|..+|+.|.+ |.|..|| .|+|+|......  +                                ...+...|.+|
T Consensus         5 ~~~~~~VCr~Flr-G~C~r~d~~C~f~H~~~~~~--~--------------------------------~~~~~~vC~df   49 (83)
T 3d2n_A            5 KWLTLEVCREFQR-GTCSRPDTECKFAHPSKSCQ--V--------------------------------ENGRVIACFDS   49 (83)
T ss_dssp             GGGEEEBCTTGGG-TCCCSCTTTCSSBCCCTTCC--E--------------------------------ETTEEECCHHH
T ss_pred             ccccchhcHHHhc-CCCCCCCCCCCCcCCCcccc--c--------------------------------cCCceeehhHh
Confidence            4678889966654 9999997 999999864320  0                                01234569999


Q ss_pred             ccCcCCCCCCCCccCCCccccC
Q 022221          115 NSAEGCKFGDKCHFAHGEWELG  136 (300)
Q Consensus       115 ~~~~~C~~g~~C~f~H~~~~~~  136 (300)
                      +++. |..+ .|+|.|....|.
T Consensus        50 lkG~-C~r~-~C~y~H~~~~l~   69 (83)
T 3d2n_A           50 LKGR-CSRE-NCKYLHPPPHLK   69 (83)
T ss_dssp             HTTC-CCCS-SCSSCCCCHHHH
T ss_pred             hhcc-ccCC-CcceeCChHHHH
Confidence            9876 9998 999999876554

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=98.62  E-value=4.6e-09  Score=80.36  Aligned_cols=70  Identities=24%  Similarity=0.448  Sum_probs=61.2

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCC--CCccceeecCcHHHHHHHhhcceeeEec
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVD--PNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~--~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      .+..+.||..++|.|||++|.+|++|++.|+++|.|.+....  ..++.+.|.|+++++++|..+|..++.+
T Consensus        15 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T 1we8_A           15 VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             EEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            467899999999999999999999999999999999764322  3578999999999999999999888744

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=98.48  E-value=3.3e-08  Score=70.17  Aligned_cols=66  Identities=27%  Similarity=0.335  Sum_probs=57.4

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceee
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVREL  244 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~  244 (300)
                      ..+..+.||+.+++.|||++|.+|+.|++.|+++|.+.+..  ...+.+.|.|..+.++.|..+|..+
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g--~~~~~V~I~G~~~~v~~A~~~I~~i   69 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS--EKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC--SSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC--CcccEEEEEcCHHHHHHHHHHHHHH
Confidence            35688999999999999999999999999999999996643  2457899999999999999888654

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.47  E-value=4e-08  Score=74.09  Aligned_cols=71  Identities=18%  Similarity=0.264  Sum_probs=61.4

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCC-CCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE-VDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~-~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      ..+..+.||+.+++.|||++|.+|+.|+..|+++|.|.+.. +....+.+.|.|..+++..|..+|..++.+
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999999996543 223568899999999999999999877654

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.40  E-value=4.3e-08  Score=73.49  Aligned_cols=71  Identities=24%  Similarity=0.297  Sum_probs=61.2

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      ..+..+.||...+|.|||++|.+|+.|+..|+++|.|.+..  .....+.|.|.++++.+|..+|..++.+..
T Consensus        16 ~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~--~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~   86 (94)
T 2cte_A           16 QASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD--DPSNQIKITGTKEGIEKARHEVLLISAEQD   86 (94)
T ss_dssp             CEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT--SSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC--CCCCeEEEEECHHHHHHHHHHHHHHhhccc
Confidence            45788999999999999999999999999999999996532  234689999999999999999988876544

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}

Probab=98.39  E-value=1.6e-07  Score=69.29  Aligned_cols=64  Identities=19%  Similarity=0.320  Sum_probs=46.7

Q ss_pred             CccccccccccccccccCCCC-CCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q 022221           36 IGSKSKPCTKFFSTSGCPFGE-GCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKY  114 (300)
Q Consensus        36 ~~~Kt~lC~~y~~~g~C~~G~-~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~  114 (300)
                      -+-+..+|+.|. .|.|..|| .|+|+|......  +                                ..-+...|..|
T Consensus        13 ~~~~~~VCrdFl-rG~C~r~d~~CrfsH~~~~~~--v--------------------------------~~~~~~vC~df   57 (89)
T 2rpp_A           13 KWLTLEVCRQFQ-RGTCSRSDEECKFAHPPKSCQ--V--------------------------------ENGRVIACFDS   57 (89)
T ss_dssp             SSSEECBCHHHH-HTCCCCCTTTSSSBCCCSSSC--C--------------------------------BTTBEEBCHHH
T ss_pred             CcchhhhchHHh-cCCCCCCCCCCCCcCCCcccc--c--------------------------------cCCceeeehhh
Confidence            345778997775 59999998 999999764310  0                                01134569999


Q ss_pred             ccCcCCCCCCCCccCCCccccC
Q 022221          115 NSAEGCKFGDKCHFAHGEWELG  136 (300)
Q Consensus       115 ~~~~~C~~g~~C~f~H~~~~~~  136 (300)
                      +++. |..+ .|+|.|....|.
T Consensus        58 lkG~-C~r~-~Cky~H~~~hl~   77 (89)
T 2rpp_A           58 LKGR-CSRE-NCKYLHPPTHLK   77 (89)
T ss_dssp             HHTC-CCCT-TCCSBCCCHHHH
T ss_pred             hhCc-CCCC-CcceecCHHHHH
Confidence            9876 9998 999999876544

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1

Probab=98.37  E-value=3.9e-08  Score=81.93  Aligned_cols=73  Identities=22%  Similarity=0.367  Sum_probs=64.6

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      +.+.++.||..++|.|||++|.+|+.|+..|+++|.|.+......++.+.|.|+++++.+|..+|.+++.+..
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~   74 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQ   74 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            4568899999999999999999999999999999999765555667899999999999999999988886654

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.34  E-value=1.1e-07  Score=71.43  Aligned_cols=73  Identities=14%  Similarity=0.242  Sum_probs=62.5

Q ss_pred             cCcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221          176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       176 ~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      ...+..+.||+.+++.|||++|.+|+.|+..|+++|.+.+.. +.+.+.+.|.|.+++++.|..+|..++.+..
T Consensus        15 ~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g-~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~   87 (95)
T 2ctm_A           15 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPENVEEAIDHILNLEEEYL   87 (95)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-CSCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC-CCCCcEEEEEcCHHHHHHHHHHHHHHHHHHH
Confidence            356789999999999999999999999999999999996532 2345789999999999999999988776544

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=98.34  E-value=7.2e-08  Score=79.35  Aligned_cols=70  Identities=16%  Similarity=0.339  Sum_probs=62.3

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      .+..+.||..++|.|||++|.+|+.|+..|+++|.|.+......++.+.|.|+++++..|..+|..++.+
T Consensus        91 ~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~  160 (164)
T 2jvz_A           91 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQS  160 (164)
T ss_dssp             SSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEEcCHHHHHHHHHHHHHHHhh
Confidence            3578899999999999999999999999999999997765555679999999999999999999887654

>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 2.70A {Homo sapiens}

Probab=98.31  E-value=2.1e-07  Score=67.89  Aligned_cols=28  Identities=25%  Similarity=0.583  Sum_probs=24.4

Q ss_pred             cccccccccccccCCCCCcCCCCcchhcc
Q 022221          269 TKLCENFAKGSCTFGDRCHFAHGSEELRK  297 (300)
Q Consensus       269 t~~C~~~~~G~C~~G~~C~faH~~~el~~  297 (300)
                      ...|.+|++|.|..+ +|+|.|....|..
T Consensus        43 ~~vC~dflkG~C~r~-~C~y~H~~~~l~~   70 (83)
T 3d2n_A           43 VIACFDSLKGRCSRE-NCKYLHPPPHLKT   70 (83)
T ss_dssp             EECCHHHHTTCCCCS-SCSSCCCCHHHHH
T ss_pred             eeehhHhhhccccCC-CcceeCChHHHHH
Confidence            347999999999998 9999999887754

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=98.30  E-value=1.8e-07  Score=76.90  Aligned_cols=72  Identities=25%  Similarity=0.328  Sum_probs=62.3

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCC--CCCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE--VDPNLRNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~--~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      .+.++.||+..+|.|||++|.+|+.|+..|+++|.+.+..  ....++.+.|.|+++++..|..+|..++.+..
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~   75 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERD   75 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhcc
Confidence            4678999999999999999999999999999999996432  34557899999999999999999988876544

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1

Probab=98.29  E-value=1.4e-07  Score=78.57  Aligned_cols=68  Identities=28%  Similarity=0.468  Sum_probs=59.1

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCC---CCCCccceeecCcHHHHHHHhhcceee
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE---VDPNLRNIELEGTFDQIKQASAMVREL  244 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~---~~~~~~~~~i~G~~~qi~~A~~~I~~~  244 (300)
                      ..+..+.||..++|.|||++|.+|++|++.|+++|.|.+..   .+..++.+.|.|+++++..|..+|.++
T Consensus       103 ~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~  173 (174)
T 1j4w_A          103 LQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEK  173 (174)
T ss_dssp             -CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHh
Confidence            35788999999999999999999999999999999996542   235679999999999999999988764

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=98.27  E-value=1.2e-07  Score=79.24  Aligned_cols=71  Identities=25%  Similarity=0.389  Sum_probs=61.8

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCC--CCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE--VDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~--~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      ..+..+.||..++|.|||++|.+|++|++.|+++|.|.+..  ++..++.+.|.|+++++..|..+|.+++.+
T Consensus       103 ~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  175 (178)
T 2anr_A          103 ANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQE  175 (178)
T ss_dssp             GGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEEEEEEESSHHHHHHHHHHHHHHHHS
T ss_pred             ceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Confidence            46788999999999999999999999999999999996543  345678999999999999999999887754

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=98.26  E-value=1.6e-07  Score=77.24  Aligned_cols=71  Identities=25%  Similarity=0.358  Sum_probs=63.3

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccC-CCCCCccceeecCcHHHHHHHhhcceeeEecc
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH-EVDPNLRNIELEGTFDQIKQASAMVRELIVNV  248 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~-~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~  248 (300)
                      .+.++.||...+|+|||++|.+|+.|+..|+++|.+.+. .++..++.+.|.|+++++..|..+|.+.+...
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~   74 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEE   74 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            367899999999999999999999999999999999764 45677899999999999999999998877654

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=98.25  E-value=9.5e-08  Score=78.42  Aligned_cols=69  Identities=23%  Similarity=0.379  Sum_probs=60.8

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEecc-CCCCCCccceeecCcHHHHHHHhhcceeeEe
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD-HEVDPNLRNIELEGTFDQIKQASAMVRELIV  246 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~-~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~  246 (300)
                      .+..+.||..++|.|||++|.+|++|++.|+++|.|.+ ..+...++.+.|.|+++++..|..+|.+++.
T Consensus        89 ~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~  158 (160)
T 2jzx_A           89 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVML  158 (160)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Confidence            57889999999999999999999999999999999964 3345678999999999999999998876653

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.24  E-value=1.6e-07  Score=71.67  Aligned_cols=68  Identities=16%  Similarity=0.255  Sum_probs=59.0

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      .+..+.||+.+++.|||++|.+|+.|+..|+++|.|.+...  ....+.|.|.+++++.|..+|..++.+
T Consensus        17 ~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~--~~~~V~I~G~~e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL--QSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT--TCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCC--CcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            56889999999999999999999999999999999976432  235899999999999999998877644

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=98.24  E-value=1.5e-07  Score=77.49  Aligned_cols=72  Identities=25%  Similarity=0.403  Sum_probs=61.6

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCC-CCCCc-cceeecCcHHHHHHHhhcceeeEeccC
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE-VDPNL-RNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~-~~~~~-~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      .+..+.||..++|.|||++|.+|+.|+..|+++|.+.+.. ++.+. +.+.|.|+++++..|..+|..++.+..
T Consensus        85 ~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~  158 (163)
T 3krm_A           85 LETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVK  158 (163)
T ss_dssp             EEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEEEEEECHHHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHHHH
Confidence            4568999999999999999999999999999999996532 33333 489999999999999999998887655

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=98.19  E-value=2.2e-07  Score=77.62  Aligned_cols=73  Identities=25%  Similarity=0.361  Sum_probs=63.1

Q ss_pred             cCcceEEEeCccccceeccCCCccccchhcccCCeeEeccCC---CCCCccceeecCcHHHHHHHhhcceeeEecc
Q 022221          176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE---VDPNLRNIELEGTFDQIKQASAMVRELIVNV  248 (300)
Q Consensus       176 ~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~---~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~  248 (300)
                      +..+.++.||...+|.|||++|.+|+.|++.|+++|.|.+..   +...++.+.|.|+++++.+|..+|.+.+.+.
T Consensus         4 ~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~   79 (178)
T 2anr_A            4 SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREM   79 (178)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCC
T ss_pred             CCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            346788999999999999999999999999999999996532   3456789999999999999999988877554

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=98.06  E-value=4.7e-07  Score=73.18  Aligned_cols=68  Identities=25%  Similarity=0.388  Sum_probs=56.3

Q ss_pred             eEEEeCccccceeccCCCccccchhcccCC-eeEeccCC-CC-C-Cc--cceeecCcHHHHHHHhhcceeeEec
Q 022221          180 AKISIDAKLAGAIIGKNGVNSKQICRLTGA-KLSIRDHE-VD-P-NL--RNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga-~i~i~~~~-~~-~-~~--~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      ..+.||...+|.+|||+|.+|+.+++.||+ +|.|.+.. .. + .+  ..++|+|++++++.|..+|.+.+.+
T Consensus        69 ~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A           69 DVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             EEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred             EEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            788999999999999999999999999997 89995432 11 1 12  3588999999999999999877654

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}

Probab=98.03  E-value=1.9e-06  Score=63.56  Aligned_cols=28  Identities=25%  Similarity=0.587  Sum_probs=24.2

Q ss_pred             cccccccccccccCCCCCcCCCCcchhcc
Q 022221          269 TKLCENFAKGSCTFGDRCHFAHGSEELRK  297 (300)
Q Consensus       269 t~~C~~~~~G~C~~G~~C~faH~~~el~~  297 (300)
                      ...|.+|++|.|..+ +|+|.|....|+.
T Consensus        51 ~~vC~dflkG~C~r~-~Cky~H~~~hl~~   78 (89)
T 2rpp_A           51 VIACFDSLKGRCSRE-NCKYLHPPTHLKT   78 (89)
T ss_dssp             EEBCHHHHHTCCCCT-TCCSBCCCHHHHH
T ss_pred             eeeehhhhhCcCCCC-CcceecCHHHHHH
Confidence            346999999999998 9999999887754

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=97.97  E-value=3.5e-06  Score=62.23  Aligned_cols=71  Identities=18%  Similarity=0.340  Sum_probs=59.8

Q ss_pred             cccCcceEEEeCccccceeccCCCccccchhcccCCe-eEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEeccC
Q 022221          174 FGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAK-LSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       174 ~g~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~-i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~~~~  249 (300)
                      ..++....+.||+.+++.+||++|.+|+.|+..||++ |.|.+.     +..+.|.| +.+++++|..+|..+-..+.
T Consensus        11 ~~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~ed-----dG~V~I~g~~~ea~~~A~~~I~~ie~~~~   83 (91)
T 2cpq_A           11 LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED-----TGTFRIYGESADAVKKARGFLEFVEDFIQ   83 (91)
T ss_dssp             SSCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHSCCCCCCC
T ss_pred             ccCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEcC-----CCEEEEEECCHHHHHHHHHHHHhhheEEe
Confidence            3446678899999999999999999999999999998 999642     26788998 88999999999987765444

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=97.96  E-value=7.6e-07  Score=72.96  Aligned_cols=68  Identities=29%  Similarity=0.426  Sum_probs=59.8

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      .+.++.||...+|.|||++|.+|+.|++.|+++|.+.+.  ...++.+.|.|.++++..|..+|.+.+.+
T Consensus         5 ~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   72 (160)
T 2jzx_A            5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (160)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            357889999999999999999999999999999999764  34578999999999999999988777654

>3u9g_A Zinc finger CCCH-type antiviral protein 1; zinc finger protein; 1.80A {Rattus norvegicus}

Probab=97.87  E-value=8.1e-06  Score=69.55  Aligned_cols=21  Identities=33%  Similarity=1.001  Sum_probs=18.8

Q ss_pred             cccccccccccCCCCCcCCCCc
Q 022221          271 LCENFAKGSCTFGDRCHFAHGS  292 (300)
Q Consensus       271 ~C~~~~~G~C~~G~~C~faH~~  292 (300)
                      +|++|.+|+|+| .+|+-+|..
T Consensus       177 IC~~Fl~G~C~f-~~CkRsH~~  197 (229)
T 3u9g_A          177 ICEHFTRGNCSY-LNCLRSHNL  197 (229)
T ss_dssp             SCHHHHTTCCCC-SSCSSCCCT
T ss_pred             ccchhhcCCcCC-CCccCccCc
Confidence            599999999999 799999975

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=97.80  E-value=3.9e-06  Score=62.77  Aligned_cols=72  Identities=19%  Similarity=0.276  Sum_probs=61.9

Q ss_pred             cCcceEEEeCccccceeccCCCccccchhccc-CCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221          176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLT-GAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       176 ~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~S-ga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      ...+..+.||+.+.+.|||++|.+|+.|+..+ +++|.+.+..  .....+.|.|....+++|..+|..++.+.+
T Consensus        15 ~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g--~~~~~V~I~G~~~~v~~A~~~I~~iv~e~e   87 (95)
T 2ctj_A           15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG--SGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   87 (95)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT--TTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             hcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC--CCcceEEEEcCHHHHHHHHHHHHHHHhhhh
Confidence            35678899999999999999999999999999 9999996533  345689999999999999999998876544

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=97.60  E-value=1.3e-05  Score=60.68  Aligned_cols=67  Identities=19%  Similarity=0.327  Sum_probs=57.3

Q ss_pred             cceEEEeCccccceeccCCCccccchhcc-cCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRL-TGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~-Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      .+..+.||+.+.+.|||++|.+|+.|+.. +++.|.+.+     ....++|.|..+++.+|...|..++.+..
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-----~~~~ItI~G~~~~V~~a~~~I~~~v~el~   94 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTEDVSVAQEQIEGMVKDLI   94 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-----CCCEEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            57889999999999999999999999995 688888755     24689999999999999999887775533

>2fc6_A Nuclear, target of EGR1, member 1; structure genomics, ZF-CCCH domain, member 1(nuclear), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.66.1.1

Probab=97.23  E-value=0.00014  Score=46.59  Aligned_cols=29  Identities=24%  Similarity=0.544  Sum_probs=26.6

Q ss_pred             ccccccccccccccccCCCCCCCCCCCCC
Q 022221           37 GSKSKPCTKFFSTSGCPFGEGCHFLHYVP   65 (300)
Q Consensus        37 ~~Kt~lC~~y~~~g~C~~G~~C~F~H~~~   65 (300)
                      ..++.+|.+|..-|.|++|..|.|.|++.
T Consensus        17 ~~~~~iC~~FSayGwCp~G~~Cp~SHDiD   45 (50)
T 2fc6_A           17 PHPTSICDNFSAYGWCPLGPQCPQSHDIS   45 (50)
T ss_dssp             CCCSCBCSHHHHTCCCTTGGGCSSBCCCC
T ss_pred             ccccchhhhccccccCCCCCCCCccccCC
Confidence            36899999999999999999999999873

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=97.12  E-value=0.00012  Score=57.80  Aligned_cols=70  Identities=23%  Similarity=0.381  Sum_probs=54.4

Q ss_pred             cceEEEeCcc------ccceeccCCCccccchhcccCCeeEeccCCC----------------CCCccceeecC-cHHHH
Q 022221          178 ATAKISIDAK------LAGAIIGKNGVNSKQICRLTGAKLSIRDHEV----------------DPNLRNIELEG-TFDQI  234 (300)
Q Consensus       178 ~t~~~~iP~~------~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~----------------~~~~~~~~i~G-~~~qi  234 (300)
                      .+.++.||..      .+|.|||.+|.+|+.|+..||++|.|....+                ....-.+.|++ +.+.+
T Consensus         7 ~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~~   86 (131)
T 1k1g_A            7 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENV   86 (131)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHH
T ss_pred             EEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHHH
Confidence            4577888877      8899999999999999999999999965221                01123455666 67889


Q ss_pred             HHHhhcceeeEec
Q 022221          235 KQASAMVRELIVN  247 (300)
Q Consensus       235 ~~A~~~I~~~l~~  247 (300)
                      ++|..+|..++..
T Consensus        87 ~~A~~~I~~ll~~   99 (131)
T 1k1g_A           87 KKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhc
Confidence            9999999998854

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=97.10  E-value=0.00017  Score=66.57  Aligned_cols=70  Identities=19%  Similarity=0.346  Sum_probs=59.3

Q ss_pred             ccCcceEEEeCccccceeccCCC--ccccchhcccCCeeEeccCC-----CCCCccceeecCcHHHHHHHhhcceee
Q 022221          175 GASATAKISIDAKLAGAIIGKNG--VNSKQICRLTGAKLSIRDHE-----VDPNLRNIELEGTFDQIKQASAMVREL  244 (300)
Q Consensus       175 g~~~t~~~~iP~~~~G~iiG~gG--~~ik~i~~~Sga~i~i~~~~-----~~~~~~~~~i~G~~~qi~~A~~~I~~~  244 (300)
                      ....|.++.||......|||++|  ++|+.|.+.|+++|++-+..     .......++|+|..+.+++|...|..+
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l  103 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRN  103 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHS
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhc
Confidence            34678899999999999999999  99999999999999995543     123456899999999999999888653

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.09  E-value=9e-05  Score=57.55  Aligned_cols=71  Identities=17%  Similarity=0.202  Sum_probs=52.2

Q ss_pred             cceEEEeCcc-------ccceeccCCCccccchhcccCCeeEeccCCC---------CC-Cccceeec-CcHHHHHHHhh
Q 022221          178 ATAKISIDAK-------LAGAIIGKNGVNSKQICRLTGAKLSIRDHEV---------DP-NLRNIELE-GTFDQIKQASA  239 (300)
Q Consensus       178 ~t~~~~iP~~-------~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~---------~~-~~~~~~i~-G~~~qi~~A~~  239 (300)
                      .+.++.||..       .+|.|||.+|.+|+.|+..||++|.|....+         .. ..-.+.|. .+++.+++|..
T Consensus        12 ~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~~   91 (119)
T 2yqr_A           12 VQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKK   91 (119)
T ss_dssp             EEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHHH
T ss_pred             EEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHHH
Confidence            3456777644       6678999999999999999999999964321         01 12245555 47889999999


Q ss_pred             cceeeEecc
Q 022221          240 MVRELIVNV  248 (300)
Q Consensus       240 ~I~~~l~~~  248 (300)
                      +|.+++...
T Consensus        92 ~Ie~Ll~~v  100 (119)
T 2yqr_A           92 LCENLLQTV  100 (119)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHhhch
Confidence            999887543

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.01  E-value=0.00032  Score=55.06  Aligned_cols=66  Identities=12%  Similarity=0.206  Sum_probs=57.9

Q ss_pred             ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeE
Q 022221          179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELI  245 (300)
Q Consensus       179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l  245 (300)
                      ...+.+.+.++++|||++|+.|+.|+..|.+.|+|..-++ ++...+.|.|++...+.+..+|..+.
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s-~g~tEVtIfG~~~~Q~rak~MI~sLA  122 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP-ERRAEIWIFGPPPFRRDVDRMLTDLA  122 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT-TSCEEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC-CCcEEEEEECCHHHHHHHHHHHHHHH
Confidence            4778999999999999999999999999999999976654 46788999999999988888887654

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=96.47  E-value=0.00044  Score=59.44  Aligned_cols=63  Identities=19%  Similarity=0.229  Sum_probs=52.3

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeec-----CcHHHHHHHhhcceeeE
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELE-----GTFDQIKQASAMVRELI  245 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~-----G~~~qi~~A~~~I~~~l  245 (300)
                      ....+.||+..+|.|||++|..|+.|+..++++|.|...+     ..+.|.     |++.++++|.++|..+.
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~~-----g~V~I~~~~~t~d~~~i~kA~~~I~~i~  101 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSET-----GEVWITSTKETEDPLAVWKARDIVLAIG  101 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTTT-----CEEEEEECTTCCSHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcCC-----CEEEEecCCCCCCHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999999999996322     334444     45799999999998765

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=96.37  E-value=0.00034  Score=60.16  Aligned_cols=53  Identities=26%  Similarity=0.459  Sum_probs=47.9

Q ss_pred             cccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEe
Q 022221          187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV  246 (300)
Q Consensus       187 ~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~  246 (300)
                      ..+|.|||++|.+++.|+..|+++|.|.+       +.+.|.|++++++.|..+|..++.
T Consensus       138 r~~GriIGk~G~tik~ie~~Tg~~I~v~~-------~~v~i~G~~~~i~~A~~~i~~li~  190 (219)
T 2e3u_A          138 RVRGRIIGRKGRTRQIIEEMSGASVSVYG-------KTVAIIGNPIQIEIAKTAIEKLAR  190 (219)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHCCEEEEET-------TEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             hhhheeECCCchHHHHHHHHhCceEEECC-------eEEEEEeCHHHHHHHHHHHHHHHc
Confidence            46899999999999999999999999964       458999999999999999988873

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=96.31  E-value=0.00054  Score=54.57  Aligned_cols=70  Identities=26%  Similarity=0.370  Sum_probs=49.6

Q ss_pred             ceEEEeCccc------cceeccCCCccccchhcccCCeeEeccCCCC-----------------CCc-cceeecC-cHH-
Q 022221          179 TAKISIDAKL------AGAIIGKNGVNSKQICRLTGAKLSIRDHEVD-----------------PNL-RNIELEG-TFD-  232 (300)
Q Consensus       179 t~~~~iP~~~------~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~-----------------~~~-~~~~i~G-~~~-  232 (300)
                      +.++.||...      +|.|||.+|.+++.|+..||++|.|+...+.                 ..+ =-+.|++ ++. 
T Consensus         3 ~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~   82 (140)
T 2bl5_A            3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQN   82 (140)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCH
T ss_pred             eeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCchh
Confidence            3566776443      7899999999999999999999999753321                 001 1344555 332 


Q ss_pred             ----HHHHHhhcceeeEecc
Q 022221          233 ----QIKQASAMVRELIVNV  248 (300)
Q Consensus       233 ----qi~~A~~~I~~~l~~~  248 (300)
                          .+++|..+|..++...
T Consensus        83 ~~~~~l~~A~~~I~~lL~p~  102 (140)
T 2bl5_A           83 RAELKLKRAVEEVKKLLVPA  102 (140)
T ss_dssp             HHHHHHHHHHHHHHHHSSCC
T ss_pred             hHHHHHHHHHHHHHHHCCCC
Confidence                6788999999888643

>3u9g_A Zinc finger CCCH-type antiviral protein 1; zinc finger protein; 1.80A {Rattus norvegicus}

Probab=96.30  E-value=0.0019  Score=54.99  Aligned_cols=43  Identities=21%  Similarity=0.664  Sum_probs=37.4

Q ss_pred             cccccccccc----cccCCCCCCCCCCCCCCCCcchhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccc
Q 022221           40 SKPCTKFFST----SGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYN  115 (300)
Q Consensus        40 t~lC~~y~~~----g~C~~G~~C~F~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~C~~~~  115 (300)
                      -++|..| ++    |.|.+++.|...|                                               +|.+|+
T Consensus       151 PeiC~~Y-kG~g~~g~C~~~~~C~kLH-----------------------------------------------IC~~Fl  182 (229)
T 3u9g_A          151 PEICKSY-KGEGRKQTCGQPQPCERLH-----------------------------------------------ICEHFT  182 (229)
T ss_dssp             CCBCTTC-CCSSSCCSCSSSSCCCSBC-----------------------------------------------SCHHHH
T ss_pred             chHHHHh-CCCCCCCcCCCCCCCccee-----------------------------------------------ccchhh
Confidence            5689777 64    6899999999999                                               499998


Q ss_pred             cCcCCCCCCCCccCCCc
Q 022221          116 SAEGCKFGDKCHFAHGE  132 (300)
Q Consensus       116 ~~~~C~~g~~C~f~H~~  132 (300)
                      .+. |+| ..|+-.|.-
T Consensus       183 ~G~-C~f-~~CkRsH~~  197 (229)
T 3u9g_A          183 RGN-CSY-LNCLRSHNL  197 (229)
T ss_dssp             TTC-CCC-SSCSSCCCT
T ss_pred             cCC-cCC-CCccCccCc
Confidence            887 999 899999975

>2fc6_A Nuclear, target of EGR1, member 1; structure genomics, ZF-CCCH domain, member 1(nuclear), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.66.1.1

Probab=96.26  E-value=0.0017  Score=41.59  Aligned_cols=28  Identities=32%  Similarity=0.780  Sum_probs=25.3

Q ss_pred             Ccccccccccc-cccccCCCCCcCCCCcc
Q 022221          266 NFKTKLCENFA-KGSCTFGDRCHFAHGSE  293 (300)
Q Consensus       266 ~ykt~~C~~~~-~G~C~~G~~C~faH~~~  293 (300)
                      ..++.+|..|. -|.|++|..|.|.|..+
T Consensus        17 ~~~~~iC~~FSayGwCp~G~~Cp~SHDiD   45 (50)
T 2fc6_A           17 PHPTSICDNFSAYGWCPLGPQCPQSHDIS   45 (50)
T ss_dssp             CCCSCBCSHHHHTCCCTTGGGCSSBCCCC
T ss_pred             ccccchhhhccccccCCCCCCCCccccCC
Confidence            47899999998 79999999999999765

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=96.11  E-value=0.0014  Score=64.72  Aligned_cols=62  Identities=18%  Similarity=0.287  Sum_probs=51.4

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeE
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELI  245 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l  245 (300)
                      ....+.||+..++.|||+||++|+.|+..||++|.|.+.      ..+.|.+ +.+..++|..+|..++
T Consensus       567 ~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d~------G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          567 VVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDE------ETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS------SEEEEEESSHHHHHHHHHHTTC--
T ss_pred             eEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcCC------cEEEEEeCCHHHHHHHHHHHHHHh
Confidence            356789999999999999999999999999999999752      4677776 4577899999887764

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=96.01  E-value=0.0013  Score=55.23  Aligned_cols=62  Identities=19%  Similarity=0.304  Sum_probs=52.6

Q ss_pred             eEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeec-----CcHHHHHHHhhcceeeEe
Q 022221          180 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELE-----GTFDQIKQASAMVRELIV  246 (300)
Q Consensus       180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~-----G~~~qi~~A~~~I~~~l~  246 (300)
                      ..+.||+..+|+|||++|+.++.|+..+++++.++..     ++.++|.     |++..+.+|.++|..+..
T Consensus         6 ~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~~-----~~~V~i~t~~~t~dp~~i~KA~dlI~ai~r   72 (191)
T 1tua_A            6 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE-----NSMVIVEPEAEGIPPVNLMKAAEVVKAISL   72 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT-----TTEEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEcC-----CCeEEEEeCCCCCCHHHHHHHHHHHHHHHc
Confidence            6899999999999999999999999999999999653     3445555     899999999999966543

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=95.97  E-value=0.0025  Score=58.85  Aligned_cols=69  Identities=17%  Similarity=0.273  Sum_probs=54.5

Q ss_pred             CcceEEEeCccccceeccCCCccc--cchhcccCCeeEeccCC--CC--CCccceeecCcHHHHHHHhhcceeeE
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNS--KQICRLTGAKLSIRDHE--VD--PNLRNIELEGTFDQIKQASAMVRELI  245 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~i--k~i~~~Sga~i~i~~~~--~~--~~~~~~~i~G~~~qi~~A~~~I~~~l  245 (300)
                      +.+..+.|++.....|||++|.++  +.|++.||++|.+-+..  .+  .....++|+|..+++..|...|.++|
T Consensus       185 ~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lL  259 (376)
T 3n89_A          185 NFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLL  259 (376)
T ss_dssp             CEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTS
T ss_pred             ceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhC
Confidence            456788999999999999999655  99999999999985432  11  23468999999999999998887664

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=95.79  E-value=0.0036  Score=50.14  Aligned_cols=60  Identities=22%  Similarity=0.294  Sum_probs=43.1

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhh
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASA  239 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~  239 (300)
                      +.+.++.||...+|++||++|++|+.+++.++  |.+.....+ ....+...+++..+..+..
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~~~-~~~~i~~~~~p~~v~~~~~   62 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLDED-TCTFHIYGEDQDAVKKARS   62 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEETT-TTEEEEEESSHHHHHHHHH
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccCCC-chheeeccCCHHHHHHHHH
Confidence            34688999999999999999999999999999  554322112 2234444457888877743

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=95.57  E-value=0.001  Score=55.83  Aligned_cols=53  Identities=19%  Similarity=0.427  Sum_probs=47.5

Q ss_pred             cccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEe
Q 022221          187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIV  246 (300)
Q Consensus       187 ~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~  246 (300)
                      .+.|.|||++|.+++.|+..|++.|.|.+.       .+.|.|++++++.|...|..++.
T Consensus       107 r~~GrIIGk~G~tik~iE~~Tg~~I~v~~~-------~v~i~G~~~~i~~Ar~~i~~li~  159 (191)
T 1tua_A          107 RIKGRIIGEGGRARRTIEEMTDTYINVGEY-------EVAIIGDYERAMAAKQAIEMLAE  159 (191)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHTCEEEECSS-------EEEEEEEHHHHHHHHHHHHHHHT
T ss_pred             HHhhheeCCCccHHHHHHHHHCceEEEcCC-------EEEEEeChHHHHHHHHHHHHHHc
Confidence            467999999999999999999999999753       68999999999999988888874

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=93.64  E-value=0.011  Score=51.35  Aligned_cols=22  Identities=41%  Similarity=0.970  Sum_probs=20.8

Q ss_pred             ccccccccccccCCCCCcCCCC
Q 022221          270 KLCENFAKGSCTFGDRCHFAHG  291 (300)
Q Consensus       270 ~~C~~~~~G~C~~G~~C~faH~  291 (300)
                      .+|.||.+|.|++|+.|.|.|.
T Consensus        71 ~~C~ffakG~C~~G~~C~y~H~   92 (240)
T 3u1l_A           71 FFCLFFAKGMCCLGPKCEYLHH   92 (240)
T ss_dssp             SBCHHHHTTCCSCGGGCSSBBS
T ss_pred             eEcCccccCCCCCCCCCCccCC
Confidence            4899999999999999999996

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=93.64  E-value=0.02  Score=57.22  Aligned_cols=65  Identities=23%  Similarity=0.331  Sum_probs=10.1

Q ss_pred             ceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEeccC
Q 022221          179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~~~~  249 (300)
                      ...+.||+..++.|||+||.+|+.|+..||++|.|.+.      ..+.|.+ +...+++|...|..++....
T Consensus       571 ~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~dd------G~v~I~~~~~~~~~~A~~~i~~i~~~~~  636 (726)
T 4aid_A          571 IETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDD------GVVKVSASDGAKIKAAIDWIKSITDEAE  636 (726)
T ss_dssp             -------------------------------------------------CCSCHHHHHHHHHC---------
T ss_pred             EEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEECC------ceEEEEeCCHHHHHHHHHHHHHHhhhhc
Confidence            46688999999999999999999999999999999653      2445555 56778888888888875433

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=91.63  E-value=0.04  Score=47.78  Aligned_cols=27  Identities=30%  Similarity=0.654  Sum_probs=21.9

Q ss_pred             cccccccccccccCCCCCCCCCCCCCCC
Q 022221           40 SKPCTKFFSTSGCPFGEGCHFLHYVPGG   67 (300)
Q Consensus        40 t~lC~~y~~~g~C~~G~~C~F~H~~~~~   67 (300)
                      ..+|.+| .-|.|+.|+.|.|.|.+|..
T Consensus        70 ~~~C~ff-akG~C~~G~~C~y~H~lPt~   96 (240)
T 3u1l_A           70 LFFCLFF-AKGMCCLGPKCEYLHHIPDE   96 (240)
T ss_dssp             CSBCHHH-HTTCCSCGGGCSSBBSCCCH
T ss_pred             CeEcCcc-ccCCCCCCCCCCccCCCCCc
Confidence            3489555 55999999999999998753

>2lhn_A Nuclear polyadenylated RNA-binding protein NAB2; nuclear protein; NMR {Saccharomyces cerevisiae S288C}

Probab=88.03  E-value=0.091  Score=37.44  Aligned_cols=21  Identities=29%  Similarity=0.651  Sum_probs=15.3

Q ss_pred             cccccccccccccCCCCCCCCCCCC
Q 022221           40 SKPCTKFFSTSGCPFGEGCHFLHYV   64 (300)
Q Consensus        40 t~lC~~y~~~g~C~~G~~C~F~H~~   64 (300)
                      .++| +|.  -.|+. +.|.|.|..
T Consensus         9 ~e~C-Kf~--~~Ctn-~~C~f~Hp~   29 (80)
T 2lhn_A            9 LEQC-KFG--THCTN-KRCKYRHAR   29 (80)
Confidence            4568 553  47888 899999954

>2lhn_A Nuclear polyadenylated RNA-binding protein NAB2; nuclear protein; NMR {Saccharomyces cerevisiae S288C}

Probab=84.55  E-value=0.2  Score=35.64  Aligned_cols=19  Identities=32%  Similarity=0.427  Sum_probs=14.3

Q ss_pred             cccccccCcCCCCCCCCccCCCc
Q 022221          110 LCNKYNSAEGCKFGDKCHFAHGE  132 (300)
Q Consensus       110 ~C~~~~~~~~C~~g~~C~f~H~~  132 (300)
                      +|+|+.   .|.+ ..|.|.|.+
T Consensus        54 ~Crf~~---~C~n-~~C~F~Hp~   72 (80)
T 2lhn_A           54 DCRFGV---NCKN-IYCLFRHPP   72 (80)
Confidence            487753   3888 789999965

>3v33_A Ribonuclease ZC3H12A; rossmann-like sandwich fold, RNAse, cytoplastic, hydrolase; 2.00A {Homo sapiens}

Probab=82.31  E-value=0.26  Score=41.98  Aligned_cols=28  Identities=25%  Similarity=0.602  Sum_probs=0.0

Q ss_pred             CcccccccccccccccCCCCCcCCCCcchh
Q 022221          266 NFKTKLCENFAKGSCTFGDRCHFAHGSEEL  295 (300)
Q Consensus       266 ~ykt~~C~~~~~G~C~~G~~C~faH~~~el  295 (300)
                      ..+.++|+|-.  .|-||.+|+|.|++.--
T Consensus       189 ~~~~~~~~~~~--~~~~~~~~~~~~~~~~~  216 (223)
T 3v33_A          189 EHRKQPCPYGR--KCTYGIKCRFFHPERPS  216 (223)
T ss_dssp             ------------------------------
T ss_pred             ccCCCCCCCCc--ccccCCcceecCCccCC
Confidence            34678899953  89999999999998643

>3v33_A Ribonuclease ZC3H12A; rossmann-like sandwich fold, RNAse, cytoplastic, hydrolase; 2.00A {Homo sapiens}

Probab=81.99  E-value=0.27  Score=41.86  Aligned_cols=24  Identities=29%  Similarity=0.928  Sum_probs=0.0

Q ss_pred             cccccccccccccccCCCCCCCCCCCC
Q 022221           38 SKSKPCTKFFSTSGCPFGEGCHFLHYV   64 (300)
Q Consensus        38 ~Kt~lC~~y~~~g~C~~G~~C~F~H~~   64 (300)
                      .|..+| -|  +.+|+||.+|+|.|..
T Consensus       190 ~~~~~~-~~--~~~~~~~~~~~~~~~~  213 (223)
T 3v33_A          190 HRKQPC-PY--GRKCTYGIKCRFFHPE  213 (223)
T ss_dssp             ---------------------------
T ss_pred             cCCCCC-CC--CcccccCCcceecCCc
Confidence            467789 66  5799999999999964

---

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	300
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-16
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	6e-15
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	1e-14
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	2e-14
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-14
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-14
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	4e-14
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	4e-14
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	7e-13
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	8e-13
d1m9oa_	40	g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475	9e-13
d1m9oa_	40	g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475	3e-09
d1m9oa_	40	g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475	4e-04
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-12
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	3e-12
d1rgoa1	36	g.66.1.1 (A:151-186) Butyrate response factor 2 (T	4e-12
d1rgoa1	36	g.66.1.1 (A:151-186) Butyrate response factor 2 (T	9e-09
d1rgoa1	36	g.66.1.1 (A:151-186) Butyrate response factor 2 (T	3e-04
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	9e-12
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	7e-11
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	3e-10
d1rgoa2	34	g.66.1.1 (A:187-220) Butyrate response factor 2 (T	5e-10
d1rgoa2	34	g.66.1.1 (A:187-220) Butyrate response factor 2 (T	3e-09
d1rgoa2	34	g.66.1.1 (A:187-220) Butyrate response factor 2 (T	8e-05
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	2e-07
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	2e-07
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	3e-07
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	9e-06
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	2e-05
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	6e-05
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	1e-04
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	0.001

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 70.6 bits (173), Expect = 2e-16
 Identities = 15/70 (21%), Positives = 33/70 (47%)

Query: 176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIK 235
           +  T +  +   + G IIG+ G    +I + +G K+ I         R+  L GT + ++
Sbjct: 6   SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQ 65

Query: 236 QASAMVRELI 245
            A  ++ +++
Sbjct: 66  SAKRLLDQIV 75

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.4 bits (162), Expect = 6e-15
 Identities = 25/71 (35%), Positives = 38/71 (53%)

Query: 175 GASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQI 234
           G   T +++I   LAG+IIGK G   KQI   +GA + I +       R I + GT DQI
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQI 60

Query: 235 KQASAMVRELI 245
           + A  +++  +
Sbjct: 61  QNAQYLLQNSV 71

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.2 bits (159), Expect = 1e-14
 Identities = 17/68 (25%), Positives = 35/68 (51%)

Query: 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQA 237
            T +++I   L G IIG+ G N  +I +++GA++ I +     + R + + G+   I  A
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLA 61

Query: 238 SAMVRELI 245
             ++   +
Sbjct: 62  QYLINARL 69

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.3 bits (159), Expect = 2e-14
 Identities = 16/72 (22%), Positives = 34/72 (47%)

Query: 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQ 236
           S    + I     G +IG+NG   K+I    G ++  +  +     R  ++ G  D+ + 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 237 ASAMVRELIVNV 248
           A+ ++ +L+ +V
Sbjct: 62  AAEIITDLLRSV 73

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.3 bits (159), Expect = 2e-14
 Identities = 12/70 (17%), Positives = 24/70 (34%), Gaps = 1/70 (1%)

Query: 177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPNLRNIELEGTFDQIK 235
           S    +++D K    IIG+ G    QI       +      + +     I + G     +
Sbjct: 9   SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTE 68

Query: 236 QASAMVRELI 245
            A   +  ++
Sbjct: 69  AARDAILRIV 78

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.7 bits (158), Expect = 3e-14
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 172 ASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTF 231
           A     A+A ++I  +    +IGKNG   + +   T  K+ I   +       I++ GT 
Sbjct: 4   ARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPS--NQIKITGTK 61

Query: 232 DQIKQASAMVRELI 245
           + I++A   V  + 
Sbjct: 62  EGIEKARHEVLLIS 75

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.1 bits (156), Expect = 4e-14
 Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPNL--RNIELEGTFDQIK 235
             ++++   L GAI+GK G    +   LTGA++ I +  E  P    R + + G+    +
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 236 QASAMVRELI 245
            A  ++ + +
Sbjct: 64  AAQYLISQRV 73

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.0 bits (156), Expect = 4e-14
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQAS 238
           T ++ +  K  G+IIGK G + K++   +GA+++I +   +   R I L G  + I +A 
Sbjct: 5   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAF 62

Query: 239 AMVRELI 245
           AM+ + +
Sbjct: 63  AMIIDKL 69

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (147), Expect = 7e-13
 Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQA 237
              +I+ID K    +IGK+G N  +I       + I           I +EG    ++QA
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKS--NLIRIEGDPQGVQQA 62

Query: 238 SAMVRELI 245
              + EL 
Sbjct: 63  KRELLELA 70

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.6 bits (147), Expect = 8e-13
 Identities = 10/68 (14%), Positives = 26/68 (38%), Gaps = 1/68 (1%)

Query: 178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQA 237
            +  + +D ++   IIG  G   ++I       +        P+   + + G  + +++A
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-PQSGAPDPNCVTVTGLPENVEEA 68

Query: 238 SAMVRELI 245
              +  L 
Sbjct: 69  IDHILNLE 76

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]} Length = 40

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Tristetraproline (ttp, tis11, nup475)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.4 bits (144), Expect = 9e-13
 Identities = 16/37 (43%), Positives = 24/37 (64%), Gaps = 1/37 (2%)

Query: 262 SQSNNFKTKLCENF-AKGSCTFGDRCHFAHGSEELRK 297
           + S+ +KT+LC  +   G C +G +C FAHG  ELR+
Sbjct: 2   TTSSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQ 38

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]} Length = 40

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Tristetraproline (ttp, tis11, nup475)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.4 bits (118), Expect = 3e-09
 Identities = 14/38 (36%), Positives = 22/38 (57%)

Query: 101 SSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRP 138
           ++    K+ LC  Y+ +  C++G KC FAHG  EL + 
Sbjct: 2   TTSSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQA 39

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]} Length = 40

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Tristetraproline (ttp, tis11, nup475)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.1 bits (81), Expect = 4e-04
 Identities = 7/24 (29%), Positives = 12/24 (50%)

Query: 39 KSKPCTKFFSTSGCPFGEGCHFLH 62
          K++ C  +  +  C +G  C F H
Sbjct: 8  KTELCRTYSESGRCRYGAKCQFAH 31

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.1 bits (143), Expect = 2e-12
 Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 3/68 (4%)

Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI---RDHEVDPNLRNIELEGTFDQIKQA 237
              +     G IIGK G   K I + +GA++ +        DPN++   + GT  QI  A
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYA 63

Query: 238 SAMVRELI 245
             ++ E I
Sbjct: 64  RQLIEEKI 71

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.2 bits (143), Expect = 3e-12
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNL--RNIELEGTFDQ 233
            +A  +I I A  AG +IGK G   KQ+    G K+ +           + + + G   +
Sbjct: 6   GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYK 65

Query: 234 IKQASAMVRELIVNVG 249
           ++QA  MV ELI + G
Sbjct: 66  VQQAKEMVLELIRDQG 81

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 36

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (140), Expect = 4e-12
 Identities = 17/34 (50%), Positives = 23/34 (67%), Gaps = 1/34 (2%)

Query: 264 SNNFKTKLCENFA-KGSCTFGDRCHFAHGSEELR 296
           S  +KT+LC  F   G+C +G++C FAHG  ELR
Sbjct: 1   STRYKTELCRPFEESGTCKYGEKCQFAHGFHELR 34

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 36

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (115), Expect = 9e-09
 Identities = 14/29 (48%), Positives = 19/29 (65%)

Query: 107 KSRLCNKYNSAEGCKFGDKCHFAHGEWEL 135
           K+ LC  +  +  CK+G+KC FAHG  EL
Sbjct: 5   KTELCRPFEESGTCKYGEKCQFAHGFHEL 33

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 36

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.5 bits (82), Expect = 3e-04
 Identities = 9/24 (37%), Positives = 13/24 (54%)

Query: 39 KSKPCTKFFSTSGCPFGEGCHFLH 62
          K++ C  F  +  C +GE C F H
Sbjct: 5  KTELCRPFEESGTCKYGEKCQFAH 28

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.3 bits (141), Expect = 9e-12
 Identities = 11/67 (16%), Positives = 27/67 (40%), Gaps = 2/67 (2%)

Query: 179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQAS 238
           T ++ +   L   +IG+ G   +++       + +   E+      I + G    + +A 
Sbjct: 11  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQS--DIIAITGLAANLDRAK 68

Query: 239 AMVRELI 245
           A + E +
Sbjct: 69  AGLLERV 75

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.1 bits (135), Expect = 7e-11
 Identities = 20/98 (20%), Positives = 38/98 (38%), Gaps = 2/98 (2%)

Query: 169 GAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH--EVDPNLRNIE 226
               +       ++S+  +  G IIG+ G   + IC+ +GAK++            R I+
Sbjct: 6   SGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIK 65

Query: 227 LEGTFDQIKQASAMVRELIVNVGSGSGHSMKSNSSSQS 264
           + GT  ++  A  ++ E +            S S   S
Sbjct: 66  ISGTQKEVAAAKHLILEKVSEDEELRKRIAHSASGPSS 103

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.7 bits (129), Expect = 3e-10
 Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 3/69 (4%)

Query: 178 ATAKISIDAKLAGAIIGKNGVNSKQIC-RLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQ 236
           A  ++SI AKL  ++IG  G   + I     G    I           + + G    +++
Sbjct: 10  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVH--IHFPVEGSGSDTVVIRGPSSDVEK 67

Query: 237 ASAMVRELI 245
           A   +  L 
Sbjct: 68  AKKQLLHLA 76

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 34

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (124), Expect = 5e-10
 Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 1/34 (2%)

Query: 262 SQSNNFKTKLCENFAK-GSCTFGDRCHFAHGSEE 294
           ++   +KT+LC  F   G C +G RCHF H ++E
Sbjct: 1   TRHPKYKTELCRTFHTIGFCPYGPRCHFIHNADE 34

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 34

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (118), Expect = 3e-09
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 101 SSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWE 134
           +  P  K+ LC  +++   C +G +CHF H   E
Sbjct: 1   TRHPKYKTELCRTFHTIGFCPYGPRCHFIHNADE 34

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 34

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (86), Expect = 8e-05
 Identities = 10/24 (41%), Positives = 15/24 (62%)

Query: 39 KSKPCTKFFSTSGCPFGEGCHFLH 62
          K++ C  F +   CP+G  CHF+H
Sbjct: 7  KTELCRTFHTIGFCPYGPRCHFIH 30

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 46.2 bits (110), Expect = 2e-07
 Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 7/59 (11%)

Query: 190 GAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNV 248
           G IIG+ G   + I  +T   +++ ++EV        + G +++   A   +  L    
Sbjct: 25  GRIIGEGGRARRTIEEMTDTYINVGEYEV-------AIIGDYERAMAAKQAIEMLAEGR 76

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 45.5 bits (108), Expect = 2e-07
 Identities = 11/63 (17%), Positives = 26/63 (41%)

Query: 182 ISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMV 241
           + +  +  GA+IG  G    +I R TG  +++        +           + +A+ +V
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVV 66

Query: 242 REL 244
           + +
Sbjct: 67  KAI 69

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 45.5 bits (108), Expect = 3e-07
 Identities = 9/64 (14%), Positives = 23/64 (35%), Gaps = 6/64 (9%)

Query: 182 ISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMV 241
           ++I+      +IGK G   K +      ++ +  +        I + G   ++  A   +
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQN------GLIWVNGDRRKVSIAEEAI 58

Query: 242 RELI 245
             + 
Sbjct: 59  YLIE 62

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (96), Expect = 9e-06
 Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 5/73 (6%)

Query: 174 FGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFD 232
             A+   +  +   L G  IG +G N +Q  ++ G      D     +     + G + D
Sbjct: 4   LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGESAD 59

Query: 233 QIKQASAMVRELI 245
            +K+A   +  + 
Sbjct: 60  AVKKARGFLEFVE 72

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.2 bits (94), Expect = 2e-05
 Identities = 19/93 (20%), Positives = 38/93 (40%), Gaps = 11/93 (11%)

Query: 164 PPQSLGAA-----ASFGASATAKISIDAKLAGAIIGKNGVNSKQIC-RLTGAKLSIRDHE 217
            P+ LG A     A   +   + ++  + L   IIGK G N  +I  ++    +   + E
Sbjct: 2   EPEKLGQALTEVYAKANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGE 61

Query: 218 VDPNLRNIELEGTFDQIKQASAMVRELIVNVGS 250
                  I LEG  + +  A   +  ++ ++ +
Sbjct: 62  -----DKITLEGPTEDVSVAQEQIEGMVKDLIN 89

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 37.7 bits (88), Expect = 6e-05
 Identities = 12/40 (30%), Positives = 17/40 (42%)

Query: 176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD 215
           A     + I     G +IG       QI   TGA+++I D
Sbjct: 1   APRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED 40

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 37.4 bits (87), Expect = 1e-04
 Identities = 9/65 (13%), Positives = 21/65 (32%), Gaps = 7/65 (10%)

Query: 182 ISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTF-DQIKQASAM 240
           I I       +IGKN    + +   +G  + + ++        I          +     
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGR------IWATCPSRFSEEILIEA 58

Query: 241 VRELI 245
           +R++ 
Sbjct: 59  IRKIE 63

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 6/34 (17%), Positives = 12/34 (35%)

Query: 182 ISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD 215
           + I       +IG+     K +   T  K+ +  
Sbjct: 5   VEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR 38

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	300
d1m9oa_	40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	99.48
d1rgoa1	36	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.48
d1m9oa_	40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	99.37
d1rgoa1	36	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.33
d1rgoa2	34	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.29
d1rgoa2	34	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.26
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.09
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.09
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.04
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	98.94
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	98.92
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	98.9
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	98.85
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	98.81
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	98.74
d2cpqa1	78	Fragile X mental retardation syndrome related prot	98.6
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.57
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.51
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.46
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.45
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.36
d2cqea2	29	Zinc finger CCCH domain-containing protein C19orf7	98.34
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.29
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.24
d2cqea2	29	Zinc finger CCCH domain-containing protein C19orf7	98.18
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.16
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.89
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	97.76
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	97.62
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	97.61
d2cqea1	56	Zinc finger CCCH domain-containing protein C19orf7	97.13
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	97.09
d2cqea1	56	Zinc finger CCCH domain-containing protein C19orf7	96.97
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	96.05
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	91.63
d2fc6a1	37	Target of EGR1 protein 1, TOE1 {Human (Homo sapien	89.93
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	88.51
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	87.27

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Tristetraproline (ttp, tis11, nup475)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.48  E-value=8e-15  Score=90.35  Aligned_cols=35  Identities=46%  Similarity=1.109  Sum_probs=32.9

Q ss_pred             CCCcccccccccc-cccccCCCCCcCCCCcchhccc
Q 022221          264 SNNFKTKLCENFA-KGSCTFGDRCHFAHGSEELRKS  298 (300)
Q Consensus       264 ~~~ykt~~C~~~~-~G~C~~G~~C~faH~~~el~~~  298 (300)
                      +++|||+||.+|. .|.|+||++|+|||+++|||.+
T Consensus         4 ~~~yKT~lC~~~~~~g~C~~G~~C~FAHg~~ELr~~   39 (40)
T d1m9oa_           4 SSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQA   39 (40)
T ss_dssp             SSCCCSCCCSGGGGTSCCTTTTTCSSCSSSCCGGGT
T ss_pred             CCccccccChhhhcCCcCCCCCCCCCCCCHHHhcCC
Confidence            4789999999998 7999999999999999999986

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=2.2e-15  Score=90.68  Aligned_cols=33  Identities=48%  Similarity=1.174  Sum_probs=31.4

Q ss_pred             CCcccccccccc-cccccCCCCCcCCCCcchhcc
Q 022221          265 NNFKTKLCENFA-KGSCTFGDRCHFAHGSEELRK  297 (300)
Q Consensus       265 ~~ykt~~C~~~~-~G~C~~G~~C~faH~~~el~~  297 (300)
                      ++|||+||.+|. .|.|+||++|+|||+++|||.
T Consensus         2 ~kyKT~lC~~~~~~g~C~~G~~C~FAHg~~ELr~   35 (36)
T d1rgoa1           2 TRYKTELCRPFEESGTCKYGEKCQFAHGFHELRS   35 (36)
T ss_dssp             TTTTSSBCHHHHHHSCCTTGGGCSSBSSGGGCCC
T ss_pred             CCcchhhCcchhcCCcCCCCCcCCCcCCHHHccC
Confidence            689999999998 799999999999999999995

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Tristetraproline (ttp, tis11, nup475)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.37  E-value=1e-13  Score=85.26  Aligned_cols=36  Identities=39%  Similarity=0.864  Sum_probs=33.4

Q ss_pred             CCccccccccccccCcCCCCCCCCccCCCccccCCC
Q 022221          103 PPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRP  138 (300)
Q Consensus       103 ~~~~kt~~C~~~~~~~~C~~g~~C~f~H~~~~~~~~  138 (300)
                      +.+|||++|++|...|.|+||++|.|||+++||+.+
T Consensus         4 ~~~yKT~lC~~~~~~g~C~~G~~C~FAHg~~ELr~~   39 (40)
T d1m9oa_           4 SSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQA   39 (40)
T ss_dssp             SSCCCSCCCSGGGGTSCCTTTTTCSSCSSSCCGGGT
T ss_pred             CCccccccChhhhcCCcCCCCCCCCCCCCHHHhcCC
Confidence            468999999999998899999999999999999864

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=8.8e-14  Score=83.52  Aligned_cols=34  Identities=41%  Similarity=0.909  Sum_probs=31.7

Q ss_pred             CccccccccccccCcCCCCCCCCccCCCccccCC
Q 022221          104 PAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGR  137 (300)
Q Consensus       104 ~~~kt~~C~~~~~~~~C~~g~~C~f~H~~~~~~~  137 (300)
                      .+|||+||++|...|.|+||++|.|||+++|||.
T Consensus         2 ~kyKT~lC~~~~~~g~C~~G~~C~FAHg~~ELr~   35 (36)
T d1rgoa1           2 TRYKTELCRPFEESGTCKYGEKCQFAHGFHELRS   35 (36)
T ss_dssp             TTTTSSBCHHHHHHSCCTTGGGCSSBSSGGGCCC
T ss_pred             CCcchhhCcchhcCCcCCCCCcCCCcCCHHHccC
Confidence            4899999999998888999999999999999985

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=1.4e-13  Score=81.26  Aligned_cols=30  Identities=47%  Similarity=1.121  Sum_probs=28.3

Q ss_pred             CCcccccccccc-cccccCCCCCcCCCCcch
Q 022221          265 NNFKTKLCENFA-KGSCTFGDRCHFAHGSEE  294 (300)
Q Consensus       265 ~~ykt~~C~~~~-~G~C~~G~~C~faH~~~e  294 (300)
                      .+|||+||.+|. .|.|+||++|+|||+++|
T Consensus         4 pkyKT~lC~~f~~~g~C~yG~~C~FaHg~~E   34 (34)
T d1rgoa2           4 PKYKTELCRTFHTIGFCPYGPRCHFIHNADE   34 (34)
T ss_dssp             TTTTCSBCHHHHHHSCCTTGGGCSSBCCSCC
T ss_pred             CCccchhccccCCCCcCCCCCcccCcCCCCC
Confidence            479999999998 799999999999999987

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Butyrate response factor 2 (Tis11D)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=3.3e-13  Score=79.67  Aligned_cols=32  Identities=34%  Similarity=0.834  Sum_probs=29.5

Q ss_pred             CCccccccccccccCcCCCCCCCCccCCCccc
Q 022221          103 PPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWE  134 (300)
Q Consensus       103 ~~~~kt~~C~~~~~~~~C~~g~~C~f~H~~~~  134 (300)
                      .++|||+||++|...|.|+||++|.|||+++|
T Consensus         3 hpkyKT~lC~~f~~~g~C~yG~~C~FaHg~~E   34 (34)
T d1rgoa2           3 HPKYKTELCRTFHTIGFCPYGPRCHFIHNADE   34 (34)
T ss_dssp             CTTTTCSBCHHHHHHSCCTTGGGCSSBCCSCC
T ss_pred             CCCccchhccccCCCCcCCCCCcccCcCCCCC
Confidence            46899999999999899999999999999875

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.09  E-value=6.3e-12  Score=87.69  Aligned_cols=68  Identities=25%  Similarity=0.473  Sum_probs=62.2

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeE
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELI  245 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l  245 (300)
                      +|.++.||...+|.|||++|.+|++|++.|+++|.|.+...+..++.+.|.|++++++.|..+|...+
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            47889999999999999999999999999999999987766777899999999999999999987654

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.09  E-value=6.3e-12  Score=88.87  Aligned_cols=72  Identities=33%  Similarity=0.454  Sum_probs=64.9

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEecc
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNV  248 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~  248 (300)
                      ..+.++.||..++|.|||++|.+|++|++.|+++|.+.+......++.+.|.|+++++..|..+|.+.+.++
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            357899999999999999999999999999999999987766777899999999999999999998876543

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.04  E-value=7.9e-12  Score=88.14  Aligned_cols=71  Identities=21%  Similarity=0.366  Sum_probs=64.2

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      +..+++.||..++|.|||++|.+|++|++.|+++|+|.....+..++.+.|.|+++++++|..+|.+++.+
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   72 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            35688999999999999999999999999999999998776677789999999999999999999877654

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.94  E-value=7.8e-11  Score=82.21  Aligned_cols=66  Identities=29%  Similarity=0.501  Sum_probs=57.4

Q ss_pred             ceEEEeCccccceeccCCCccccchhcccCCeeEeccC---CCCCCccceeecCcHHHHHHHhhcceee
Q 022221          179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH---EVDPNLRNIELEGTFDQIKQASAMVREL  244 (300)
Q Consensus       179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~---~~~~~~~~~~i~G~~~qi~~A~~~I~~~  244 (300)
                      ..++.||...+|.|||++|.+|++|+..|+++|.|...   .....++.+.|+|+++++++|..+|.+.
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~   70 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEK   70 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHH
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhh
Confidence            35789999999999999999999999999999999542   2345678999999999999999998764

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.92  E-value=9.2e-11  Score=82.50  Aligned_cols=67  Identities=22%  Similarity=0.401  Sum_probs=59.1

Q ss_pred             ceEEEeCccccceeccCCCccccchhcccCCeeEeccC---CCCCCccceeecCcHHHHHHHhhcceeeE
Q 022221          179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH---EVDPNLRNIELEGTFDQIKQASAMVRELI  245 (300)
Q Consensus       179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~---~~~~~~~~~~i~G~~~qi~~A~~~I~~~l  245 (300)
                      .+++.||...+|.|||++|.+|++|++.|+++|.|.+.   .++.+++.+.|+|++++++.|..+|.+.+
T Consensus         4 ~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           4 LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            46899999999999999999999999999999999542   24456799999999999999999987654

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.90  E-value=1e-10  Score=83.31  Aligned_cols=71  Identities=21%  Similarity=0.348  Sum_probs=64.9

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      ..+.++.||..++|.|||++|.+|+.|+..|+++|.|.+...+..++.+.|.|+++++..|..+|..++.+
T Consensus         7 ~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   77 (79)
T d1x4na1           7 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEK   77 (79)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            46788999999999999999999999999999999998777777889999999999999999999877654

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.85  E-value=2.1e-10  Score=82.07  Aligned_cols=72  Identities=31%  Similarity=0.396  Sum_probs=62.8

Q ss_pred             cCcceEEEeCccccceeccCCCccccchhcccCCeeEeccCC--CCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE--VDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       176 ~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~--~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      +..+.++.||...+|.|||++|.+|++|++.|+++|.|.+..  +...++.+.|.|+++++.+|..+|.+++.+
T Consensus         6 ~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           6 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             ccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            357889999999999999999999999999999999996532  345678999999999999999999887643

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.81  E-value=1.9e-10  Score=80.19  Aligned_cols=66  Identities=30%  Similarity=0.443  Sum_probs=58.9

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeE
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELI  245 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l  245 (300)
                      .+.++.||...+|+|||++|.+|++|+..|+++|.+.+.  ...++.+.|.|+++++.+|..+|.+.+
T Consensus         4 vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l   69 (71)
T d2axya1           4 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKL   69 (71)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC--CCCcceEEEEECHHHHHHHHHHHHHHh
Confidence            467899999999999999999999999999999999653  345789999999999999999887655

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.74  E-value=8e-10  Score=82.75  Aligned_cols=71  Identities=24%  Similarity=0.433  Sum_probs=62.1

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCC--CCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHE--VDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~--~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      ..+.++.||..++|.|||++|.+|++|+..|+++|.|.+..  ....++.+.|+|+++++.+|..+|.+++.+
T Consensus        14 ~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T d1we8a_          14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             EEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhC
Confidence            45678999999999999999999999999999999996533  344568999999999999999999888854

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.60  E-value=6.2e-09  Score=73.51  Aligned_cols=67  Identities=19%  Similarity=0.280  Sum_probs=57.6

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEec
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIVN  247 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~~  247 (300)
                      ..+.++.||..++|.|||++|.+|+.|++.||+++.+.+.    ....+.|.| +++++.+|..+|+.+...
T Consensus         7 ~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~----~~g~v~I~g~~~eav~~A~~~Ie~~~~~   74 (78)
T d2cpqa1           7 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGESADAVKKARGFLEFVEDF   74 (78)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----TTTEEEEEESSHHHHHHHHHHHSCCCCC
T ss_pred             CceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC----CCceEEEEECCHHHHHHHHHHHHHhhee
Confidence            4578899999999999999999999999999999988653    235688888 799999999999876544

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.57  E-value=5.1e-09  Score=75.14  Aligned_cols=72  Identities=18%  Similarity=0.267  Sum_probs=62.1

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEecc-CCCCCCccceeecCcHHHHHHHhhcceeeEecc
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD-HEVDPNLRNIELEGTFDQIKQASAMVRELIVNV  248 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~-~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~  248 (300)
                      +.++.+.||..+++.|||++|.+|+.|+..|+++|.+.+ ...+.+.+.+.|.|+++++.+|..+|..++.+.
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            346789999999999999999999999999999999954 344566789999999999999999988776543

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.51  E-value=1e-08  Score=72.95  Aligned_cols=70  Identities=14%  Similarity=0.279  Sum_probs=59.6

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      ..+..+.||..+.+.|||++|.+|++|+..|+++|.+.+.. +.+...++|.|+++++.+|..+|.+++.+
T Consensus         9 ~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-~~~~~~v~I~G~~~~V~~A~~~I~~i~~e   78 (81)
T d2ctma1           9 MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPENVEEAIDHILNLEEE   78 (81)
T ss_dssp             CCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-CSCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCcc-CCCCCEEEEeCCHHHHHHHHHHHHHHHHH
Confidence            45688999999999999999999999999999999996543 23346799999999999999998776543

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.46  E-value=1.5e-08  Score=72.15  Aligned_cols=70  Identities=26%  Similarity=0.320  Sum_probs=60.8

Q ss_pred             cCcceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          176 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       176 ~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      ...+..+.||..+.+.|||++|.+|+.|++.||++|.+...  +.....+.|.|+++++..|...|.+++.+
T Consensus         8 ~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~--~~~~~~v~I~G~~~~v~~A~~~I~~iv~e   77 (81)
T d2ctea1           8 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP--DDPSNQIKITGTKEGIEKARHEVLLISAE   77 (81)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT--TSSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC--CCCCCEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            34678999999999999999999999999999999999543  33457899999999999999999887654

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.45  E-value=2e-08  Score=69.62  Aligned_cols=65  Identities=28%  Similarity=0.349  Sum_probs=57.1

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceee
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVREL  244 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~  244 (300)
                      .++++.||..+.+.|||++|.+|++|++.|+++|.+.+.  +.....+.|.|++++++.|..+|.++
T Consensus         5 ~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~--~~~~~~v~I~G~~~~v~~A~~~I~~i   69 (71)
T d1viga_           5 DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD--SEKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             EEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC--CSSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             EEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC--CCCCCEEEEECCHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999999543  34457899999999999999988765

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.36  E-value=3.8e-08  Score=70.08  Aligned_cols=71  Identities=20%  Similarity=0.272  Sum_probs=59.4

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcc-cCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEeccC
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRL-TGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVG  249 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~-Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~~~  249 (300)
                      ..+..+.||..++|.|||++|++|++|+.. +++.|.+.+  .+...+.++|.|+++++.+|..+|..++.+.+
T Consensus         9 ~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~--~~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~~   80 (82)
T d2ctja1           9 IAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV--EGSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   80 (82)
T ss_dssp             SCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCC--TTTTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             cEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeC--CCCCCceEEEeCCHHHHHHHHHHHHHHHhhhh
Confidence            457889999999999999999999999876 588877744  23456889999999999999999988775543

>d2cqea2 g.66.1.1 (A:429-457) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.34  E-value=9.4e-08  Score=51.85  Aligned_cols=26  Identities=31%  Similarity=0.807  Sum_probs=23.9

Q ss_pred             cccccccccccccccCCCCCcCCCCc
Q 022221          267 FKTKLCENFAKGSCTFGDRCHFAHGS  292 (300)
Q Consensus       267 ykt~~C~~~~~G~C~~G~~C~faH~~  292 (300)
                      -|.++|.||.+|.|-.|++|.|+|.+
T Consensus         4 kkkelCKfYvqGyCtrgenC~ymH~e   29 (29)
T d2cqea2           4 KKRELCKFYITGFCARAENCPYMHGD   29 (29)
T ss_dssp             CCCSBCTTTTTTCCSCSTTCSSBSSS
T ss_pred             hhhhhhhhheeeeecCCcCcccccCC
Confidence            47789999999999999999999975

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.29  E-value=5.1e-08  Score=69.66  Aligned_cols=62  Identities=15%  Similarity=0.173  Sum_probs=55.2

Q ss_pred             eEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          180 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      ..+.||+.++|.|||++|++|+.|+..|+++|.|.+.      ..+.|.|++++++.|..+|..++.+
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~~------g~v~I~G~~e~v~~A~~~I~~i~~e   64 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQN------GLIWVNGDRRKVSIAEEAIYLIEQE   64 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECTT------SEEEEESCHHHHHHHHHHHHHHHHC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECCC------CEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            4678999999999999999999999999999999542      4689999999999999999777654

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=5.9e-08  Score=70.45  Aligned_cols=68  Identities=15%  Similarity=0.230  Sum_probs=59.4

Q ss_pred             cceEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          178 ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       178 ~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      .+..+.||..+.+.|||++|.+|++|+..++++|.+.+.  +.....+.|.|+.++++.|...|..++.+
T Consensus        10 vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~--~~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1          10 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP--ELQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT--TTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC--CCCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            468899999999999999999999999999999999543  34456899999999999999999877654

>d2cqea2 g.66.1.1 (A:429-457) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.18  E-value=4e-07  Score=49.33  Aligned_cols=25  Identities=36%  Similarity=0.774  Sum_probs=22.3

Q ss_pred             cccccccccccccccCCCCCCCCCCC
Q 022221           38 SKSKPCTKFFSTSGCPFGEGCHFLHY   63 (300)
Q Consensus        38 ~Kt~lC~~y~~~g~C~~G~~C~F~H~   63 (300)
                      .|.+|| +|+.+|.|..|++|.|.|+
T Consensus         4 kkkelC-KfYvqGyCtrgenC~ymH~   28 (29)
T d2cqea2           4 KKRELC-KFYITGFCARAENCPYMHG   28 (29)
T ss_dssp             CCCSBC-TTTTTTCCSCSTTCSSBSS
T ss_pred             hhhhhh-hhheeeeecCCcCcccccC
Confidence            578899 7778899999999999996

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.16  E-value=8.4e-08  Score=68.37  Aligned_cols=65  Identities=17%  Similarity=0.223  Sum_probs=50.9

Q ss_pred             eEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceee
Q 022221          180 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVREL  244 (300)
Q Consensus       180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~  244 (300)
                      ..+.||++.+|+|||++|++|+.|+..|+++|+|.+....-........+.+.++++|.++|..+
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g~v~i~~~~~~~~~~a~~~a~~iI~aI   69 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAI   69 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTTEEEEEESSTTSCHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCCeEEEecCCccccHHHHHHHHHHHHHH
Confidence            56899999999999999999999999999999996433111223334457788888888888765

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.89  E-value=1.1e-06  Score=63.46  Aligned_cols=67  Identities=19%  Similarity=0.323  Sum_probs=57.3

Q ss_pred             cCcceEEEeCccccceeccCCCccccchhcc-cCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          176 ASATAKISIDAKLAGAIIGKNGVNSKQICRL-TGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       176 ~~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~-Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      ...+..+.||....+.|||++|.+|+.|+.. ++++|.+.+.     ...+.|.|++++++.|..+|..++.+
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~-----~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG-----EDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS-----SCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC-----CceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            3568899999999999999999999999988 5788888542     35799999999999999998877654

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=97.76  E-value=4.1e-07  Score=62.32  Aligned_cols=61  Identities=15%  Similarity=0.089  Sum_probs=44.2

Q ss_pred             eEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCc-HHHHHHHhhcceeeEe
Q 022221          180 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGT-FDQIKQASAMVRELIV  246 (300)
Q Consensus       180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~-~~qi~~A~~~I~~~l~  246 (300)
                      ..+.||+.++|.|||++|++|+.|+..|+++|.|.+.      ..+.|.|. .+.++.|..+|..+..
T Consensus         3 ~vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~------g~v~I~g~~~~~v~~A~~~I~~i~~   64 (69)
T d2je6i3           3 IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN------GRIWATCPSRFSEEILIEAIRKIEN   64 (69)
T ss_dssp             CEEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT------SEEEC-----CTTCCTHHHHTTTTT
T ss_pred             EEEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC------CEEEEEeCCHHHHHHHHHHHHHHHH
Confidence            4578999999999999999999999999999999542      35788884 5677778777765543

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.62  E-value=1.4e-05  Score=56.70  Aligned_cols=61  Identities=18%  Similarity=0.132  Sum_probs=51.9

Q ss_pred             eEEEeCccccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecC-cHHHHHHHhhcceeeEe
Q 022221          180 AKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEG-TFDQIKQASAMVRELIV  246 (300)
Q Consensus       180 ~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G-~~~qi~~A~~~I~~~l~  246 (300)
                      ..+.||+.+++.|||++|++|+.|+..|+++|.|.+.      ..++|.| +.+.+..|..+|..+..
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~------G~V~I~g~~~~~~~~A~~~I~~I~~   64 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN------GRIHLECPNEDLEAIAVMAIKIIDE   64 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETT------TEEEEECSCHHHHHHHHHHHHHHHH
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCC------cEEEEEeCCHHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999999999653      3689999 56778888888876644

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=97.61  E-value=4.8e-06  Score=53.77  Aligned_cols=37  Identities=30%  Similarity=0.402  Sum_probs=10.9

Q ss_pred             ceEEEeCccccceeccCCCccccchhcccCCeeEecc
Q 022221          179 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD  215 (300)
Q Consensus       179 t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~  215 (300)
                      ...+.||+..+|.|||+||.+|+.|+..|+++|.|.+
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d   40 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED   40 (54)
T ss_dssp             CC---------------------CHHHHSCCCC----
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC
Confidence            3568899999999999999999999999999999965

>d2cqea1 g.66.1.1 (A:458-513) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.13  E-value=5.7e-05  Score=47.88  Aligned_cols=22  Identities=36%  Similarity=0.925  Sum_probs=20.5

Q ss_pred             cccccccCcCCCCCCCCccCCC
Q 022221          110 LCNKYNSAEGCKFGDKCHFAHG  131 (300)
Q Consensus       110 ~C~~~~~~~~C~~g~~C~f~H~  131 (300)
                      +|+||.++..|..|+.|+|.|.
T Consensus         2 PCK~yHtg~kCy~gd~C~FSH~   23 (56)
T d2cqea1           2 PCKLYHTTGNCINGDDCMFSHD   23 (56)
T ss_dssp             BCSHHHHTSCCSSCTTCSSBCC
T ss_pred             CcceeecCCcccCCCcccccCC
Confidence            4999999999999999999995

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.09  E-value=1.7e-05  Score=58.21  Aligned_cols=54  Identities=19%  Similarity=0.422  Sum_probs=46.6

Q ss_pred             cccceeccCCCccccchhcccCCeeEeccCCCCCCccceeecCcHHHHHHHhhcceeeEec
Q 022221          187 KLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVN  247 (300)
Q Consensus       187 ~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~~~~~~~~~i~G~~~qi~~A~~~I~~~l~~  247 (300)
                      .+.|.|||++|.+|+.|+..||+.|.|.+.       .+.+.|+++++..|..+|..++..
T Consensus        22 R~~GrIIG~gGktik~Ie~~Tg~~I~I~d~-------~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          22 RIKGRIIGEGGRARRTIEEMTDTYINVGEY-------EVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHTCEEEECSS-------EEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HHhcceeCCCcHHHHHHHHHHCCeEEEeCC-------eEEEEECchhHHHHHHHHHHHHcC
Confidence            357889999999999999999999999653       367789999999999999888753

>d2cqea1 g.66.1.1 (A:458-513) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.97  E-value=0.0001  Score=46.73  Aligned_cols=22  Identities=36%  Similarity=0.914  Sum_probs=19.4

Q ss_pred             cccccccccccCCCCCCCCCCC
Q 022221           42 PCTKFFSTSGCPFGEGCHFLHY   63 (300)
Q Consensus        42 lC~~y~~~g~C~~G~~C~F~H~   63 (300)
                      +|++|..+..|..||+|+|+|.
T Consensus         2 PCK~yHtg~kCy~gd~C~FSH~   23 (56)
T d2cqea1           2 PCKLYHTTGNCINGDDCMFSHD   23 (56)
T ss_dssp             BCSHHHHTSCCSSCTTCSSBCC
T ss_pred             CcceeecCCcccCCCcccccCC
Confidence            5977777889999999999995

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.05  E-value=0.00091  Score=50.18  Aligned_cols=69  Identities=25%  Similarity=0.395  Sum_probs=49.2

Q ss_pred             ceEEEeCcc------ccceeccCCCccccchhcccCCeeEeccCCC---------CC------Cc-cceeecC-cHHHHH
Q 022221          179 TAKISIDAK------LAGAIIGKNGVNSKQICRLTGAKLSIRDHEV---------DP------NL-RNIELEG-TFDQIK  235 (300)
Q Consensus       179 t~~~~iP~~------~~G~iiG~gG~~ik~i~~~Sga~i~i~~~~~---------~~------~~-~~~~i~G-~~~qi~  235 (300)
                      +.++.||..      .+|.|||.+|.+++.|+..|+++|.|+.-.+         +.      .+ =-+.|++ ++..+.
T Consensus         4 ~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~~   83 (122)
T d1k1ga_           4 SDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVK   83 (122)
T ss_dssp             EEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHHH
T ss_pred             eEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhHH
Confidence            456777654      3789999999999999999999999964221         00      11 1333444 667788


Q ss_pred             HHhhcceeeEec
Q 022221          236 QASAMVRELIVN  247 (300)
Q Consensus       236 ~A~~~I~~~l~~  247 (300)
                      .|..+|..++..
T Consensus        84 ~A~~~i~~ll~~   95 (122)
T d1k1ga_          84 KAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHh
Confidence            998888888853

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=91.63  E-value=0.013  Score=44.26  Aligned_cols=36  Identities=31%  Similarity=0.584  Sum_probs=30.5

Q ss_pred             eEEEeCc------cccceeccCCCccccchhcccCCeeEecc
Q 022221          180 AKISIDA------KLAGAIIGKNGVNSKQICRLTGAKLSIRD  215 (300)
Q Consensus       180 ~~~~iP~------~~~G~iiG~gG~~ik~i~~~Sga~i~i~~  215 (300)
                      .++.||.      ..+|.|||.+|.+++.|+..||++|.|+.
T Consensus         4 eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrG   45 (134)
T d2bl5a1           4 EKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRG   45 (134)
T ss_dssp             EEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEES
T ss_pred             eEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEe
Confidence            4566663      46688999999999999999999999965

>d2fc6a1 g.66.1.1 (A:8-44) Target of EGR1 protein 1, TOE1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Target of EGR1 protein 1, TOE1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.93  E-value=0.041  Score=30.95  Aligned_cols=28  Identities=25%  Similarity=0.559  Sum_probs=25.0

Q ss_pred             ccccccccccccccccCCCCCCCCCCCC
Q 022221           37 GSKSKPCTKFFSTSGCPFGEGCHFLHYV   64 (300)
Q Consensus        37 ~~Kt~lC~~y~~~g~C~~G~~C~F~H~~   64 (300)
                      ..++-+|.+|..-|-|+.|..|.-.|++
T Consensus        10 ~~~~~iC~~FsAyGWCP~G~qCp~SHdi   37 (37)
T d2fc6a1          10 PHPTSICDNFSAYGWCPLGPQCPQSHDI   37 (37)
T ss_dssp             CCCSCBCSHHHHTCCCTTGGGCSSBCCC
T ss_pred             CCccchhhhhhhccccCCCCCCcccCcC
Confidence            3578899999999999999999999974

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=88.51  E-value=0.061  Score=35.34  Aligned_cols=39  Identities=31%  Similarity=0.490  Sum_probs=35.1

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEecc
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRD  215 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~  215 (300)
                      .....+.+|.......|||+|.|++-....||.+|.|..
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            446778999999999999999999999999999999954

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=87.27  E-value=0.066  Score=35.30  Aligned_cols=40  Identities=28%  Similarity=0.444  Sum_probs=35.8

Q ss_pred             CcceEEEeCccccceeccCCCccccchhcccCCeeEeccC
Q 022221          177 SATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH  216 (300)
Q Consensus       177 ~~t~~~~iP~~~~G~iiG~gG~~ik~i~~~Sga~i~i~~~  216 (300)
                      .....+.+|.......|||+|.|++-....+|.+|.|.+.
T Consensus        26 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~   65 (68)
T d1hh2p3          26 NKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI   65 (68)
T ss_dssp             TTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             CCEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEc
Confidence            4467789999999999999999999999999999999664