Citrus Sinensis ID: 022898

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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
Protein Sequence
MDTRKRTKPETGINANGVFKKSKHESESGVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccHHHHHHHcccEEEEccccccccccEEEEEccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccHHEccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccEcccHHHHcccccccccccccccccccccccccccccccccccccccccEEEEEEHHHHHHHHHcccccccHHHHHHcccEEEEEcccccccccEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccEHHHHcccccccccccccccccHHHHHcccc
Coil and Loop (DISEMBL)
mdtrkrtkpetginangvfkkskhesesgvgskskpctkffstagcpfgeschflhyfpggyNAVAQMMnlpqavpapsrnmavpppasngptvvKSRMCNrlnsaegckfgdkchfahgewelgkpiaishddprafgavpgrmggryepppapgpaasfgasaTAKISVDASLAGaiigkggvnskQICRQtgaklsirdheadpnlrnielegSFEQIKQASAMVRELIVRIgpahaknpatagsaahplssnfktklcgnfakgsctfgdrchfahGAAELRKTAI
Flexible Loop (DISEMBL)
mdtrkrtkpetginangvfkkskhesesgvgskskpcTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKpiaishddpRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIigkggvnskqICRQTGaklsirdheadpnlrnIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI
Low Complexity Region (SEG)
MDTRKRTKPETGINANGVFKKSKHESESGVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEpppapgpaasfgasaTAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI
Disordered region (IsUnstruct)
************************************CTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMN****************************MCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISH************************************ISVDASLAGAIIGKGGVNSKQICRQTGAKL*******************FEQIKQASAMVRELIVRIGP******************NFKTKLCGNFAKGSCTFGDRCHFAHGA********
Disordered Region (DISOPRED)
*************************************TKFFSTAGCPFGESCHFLHYF************************************************************HGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTG****************IELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSA***L***FKTKLCGNFAKGSCTFGDRCHFAHGAA*L*****
Disordered Region (DISEMBL)
*********ETGINANGVFK**************KPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHA**********HPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI
Disordered Region (DISPRO)
*******************************SKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMA*******GPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAI*******************EPPPAP*******ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP******************NFKTKLCGNFAKGSCTFGDRCHFAHG*********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDTRKRTKPETGINANGVFKKSKHESESGVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI
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	290	2.2.26 [Sep-21-2011]
Q7F8R0	300	Zinc finger CCCH domain-c	yes	no	0.972	0.94	0.632	1e-90
Q69XQ3	295	Zinc finger CCCH domain-c	no	no	0.948	0.932	0.616	2e-89
Q7XPK1	309	Zinc finger CCCH domain-c	no	no	0.955	0.896	0.564	3e-80
Q9C7C3	248	Zinc finger CCCH domain-c	yes	no	0.803	0.939	0.523	2e-71
Q9FG30	240	Zinc finger CCCH domain-c	no	no	0.796	0.962	0.526	1e-70
Q9LT81	386	Zinc finger CCCH domain-c	no	no	0.665	0.5	0.271	5e-08
Q84UQ3	367	Zinc finger CCCH domain-c	no	no	0.324	0.256	0.355	7e-07
Q5PP65	252	Zinc finger CCCH domain-c	no	no	0.313	0.361	0.333	4e-05
Q9LQM3	384	Zinc finger CCCH domain-c	no	no	0.113	0.085	0.558	0.0007

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

 Score =  332 bits (852), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 188/297 (63%), Positives = 209/297 (70%), Gaps = 15/297 (5%)

Query: 4   RKRTKPETGINANGVFKKSKHESES---GVGSKSKPCTKFFSTAGCPFGESCHFLHYFPG 60
           RKR KP+    ANG   K   ESES   GVGSKSKPCTKFFST+GCPFGE CHFLH+FPG
Sbjct: 6   RKRGKPD---GANGAGGKRARESESFQTGVGSKSKPCTKFFSTSGCPFGEGCHFLHHFPG 62

Query: 61  GYNAVAQMMNL--PQAVPAPSRNMAVPPPASNGPTV--VKSRMCNRLNSAEGCKFGDKCH 116
           GY AVA+M NL  P   P P R M +     +GP    VK+R+CN+ N+AEGCK+GDKCH
Sbjct: 63  GYQAVAKMTNLGGPAIAPPPGR-MPMGNAVPDGPPTPTVKTRLCNKYNTAEGCKWGDKCH 121

Query: 117 FAHGEWELGKPIAISHDDPRAFGAVP-GRMGGRYEPPPAPGPAASFGASATAKISVDASL 175
           FAHGE ELGKP+ +    P   G  P G       P PA    ASFGASATAKISVDASL
Sbjct: 122 FAHGERELGKPMLMDSSMPPPMGPRPTGHFAPPPMPSPAMSTPASFGASATAKISVDASL 181

Query: 176 AGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI 235
           AG IIG+GGVN+KQI R TGAKL+IRDHE+D NL+NIELEG+F+QIK ASAMVRELIV I
Sbjct: 182 AGGIIGRGGVNTKQISRVTGAKLAIRDHESDTNLKNIELEGTFDQIKNASAMVRELIVSI 241

Query: 236 G---PAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTA 289
           G   P   K P           SNFKTKLC NF KGSCTFGDRCHFAHG  ELRK+A
Sbjct: 242 GGGAPPQGKKPVGGSHRGGGPGSNFKTKLCENFTKGSCTFGDRCHFAHGENELRKSA 298

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 =  328 bits (842), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 180/292 (61%), Positives = 209/292 (71%), Gaps = 17/292 (5%)

Query: 5   KRTKPETGINANGVFKKSKHESESGVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNA 64
           KR  PE G N      ++   S+ GVGSK KPCTKFFST+GCPFG SCHFLH FPGGY A
Sbjct: 7   KRAAPE-GTNGAAKRARASESSQVGVGSKLKPCTKFFSTSGCPFGSSCHFLHNFPGGYQA 65

Query: 65  VAQMMNLP-QAVPAPSRNMAVPPPASNGP--TVVKSRMCNRLNSAEGCKFGDKCHFAHGE 121
            A+M +    AV AP   M + P A NGP  + VK+RMCN+ N+AEGCK+G KCHFAHGE
Sbjct: 66  AAKMTSHGGTAVAAPPGRMPLGPGAPNGPPTSSVKTRMCNKYNTAEGCKWGSKCHFAHGE 125

Query: 122 WELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGP----AASFGASATAKISVDASLAG 177
            ELGKP+ + +  P   G++P      +E PP PGP     ++FGASATAKISVDASLAG
Sbjct: 126 RELGKPMLLDNSMPHPMGSMP------FEAPPMPGPDIVPPSTFGASATAKISVDASLAG 179

Query: 178 AIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI-- 235
            IIGKGG N+K I R TGAKL+IRD+E++PNL+NIELEG+F+QIK ASAMV ELIVRI  
Sbjct: 180 GIIGKGGTNTKHISRMTGAKLAIRDNESNPNLKNIELEGTFDQIKHASAMVTELIVRISG 239

Query: 236 GPAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRK 287
               AKNP     A  P  SNFKTKLC NF KGSCTFGDRCHFAHG +ELRK
Sbjct: 240 NAPPAKNPGRGSHAGGP-GSNFKTKLCENFNKGSCTFGDRCHFAHGESELRK 290

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 =  298 bits (763), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 175/310 (56%), Positives = 202/310 (65%), Gaps = 33/310 (10%)

Query: 4   RKRTKPET--GINANGVFKKSKHESESGVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGG 61
           RKR++P+T  G  A G   +     ++G+ SK KPCTKFFST GCPFGE CHF H+ PGG
Sbjct: 8   RKRSRPDTANGGAAGGKRSRETESFQTGLSSKLKPCTKFFSTIGCPFGEGCHFSHFVPGG 67

Query: 62  YNAVAQMMNLPQAVPAPSRNMAVPP-------PASNGPTVVKSRMCNRLNSAEGCKFGDK 114
           Y AVA+ +NL            +         PAS+G    K+RMC + N+AEGCKFGDK
Sbjct: 68  YQAVAKTLNLGNPAVPAPARAPMDHAAGGNSHPASSG----KTRMCTKYNTAEGCKFGDK 123

Query: 115 CHFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAA-------SFGASATA 167
           CHFAHGE ELGKP  +SH+      A+   MGGRY   P P P A       +FGASATA
Sbjct: 124 CHFAHGERELGKPAYMSHES-----AMAPPMGGRYGGRPEPPPPAAMGPPAGNFGASATA 178

Query: 168 KISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAM 227
           KISVDASLAG IIGKGGVN+KQICR TG KLSIRDHE+D NL+NIELEG+F+QIKQAS M
Sbjct: 179 KISVDASLAGGIIGKGGVNTKQICRVTGVKLSIRDHESDSNLKNIELEGNFDQIKQASNM 238

Query: 228 VRELIVRIGPA--------HAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFA 279
           V ELI  I P+         A   A AG       SN+KTKLC NF KG+CTFGDRCHFA
Sbjct: 239 VGELIATISPSTPAKKPAGSAAGAAPAGRGGPGGRSNYKTKLCENFVKGTCTFGDRCHFA 298

Query: 280 HGAAELRKTA 289
           HG  E RK A
Sbjct: 299 HGENEQRKGA 308

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 =  269 bits (687), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 159/304 (52%), Positives = 184/304 (60%), Gaps = 71/304 (23%)

Query: 1   MDTRKRTKPETG-INANGV-FKKSKHESES---GVGSKSKPCTKFFSTAGCPFGESCHFL 55
           MDTRKR +PE G  N+NG  +KKSK E ES   G+GSKSKPCTKFFST+GCPFGE+CHFL
Sbjct: 1   MDTRKRGRPEAGSFNSNGGGYKKSKQEMESYSTGLGSKSKPCTKFFSTSGCPFGENCHFL 60

Query: 56  HYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFGDKC 115
           HY PGGYNAV+QM N+   +P  SRNM                      S  G +F    
Sbjct: 61  HYVPGGYNAVSQMTNMGPPIPQVSRNMQ--------------------GSGNGGRF---- 96

Query: 116 HFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASL 175
                                          GR E  P  G  ++FG SATA+ SVDASL
Sbjct: 97  ------------------------------SGRGESGP--GHVSNFGDSATARFSVDASL 124

Query: 176 AGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI 235
           AGAIIGKGGV+SKQICRQTG KLSI+DHE DPNL+NI LEG+ EQI +ASAMV++LI R+
Sbjct: 125 AGAIIGKGGVSSKQICRQTGVKLSIQDHERDPNLKNIVLEGTLEQISEASAMVKDLIGRL 184

Query: 236 GPAHAKNPATAGSAA---------HPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELR 286
             A  K P                HP  SNFKTK+C  F+KG+CTFGDRCHFAHG AELR
Sbjct: 185 NSAAKKPPGGGLGGGGGMGSEGKPHP-GSNFKTKICERFSKGNCTFGDRCHFAHGEAELR 243

Query: 287 KTAI 290
           K+ I
Sbjct: 244 KSGI 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 =  266 bits (680), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 157/298 (52%), Positives = 183/298 (61%), Gaps = 67/298 (22%)

Query: 1   MDTRKRTKPETGI--NANGVFKKSKHESES---GVGSKSKPCTKFFSTAGCPFGESCHFL 55
           MD RKR +PE     N+NG FK+SK E ES   G+GSKSKPCTKFFST+GCPFG++CHFL
Sbjct: 1   MDARKRGRPEAAASHNSNGGFKRSKQEMESISTGLGSKSKPCTKFFSTSGCPFGDNCHFL 60

Query: 56  HYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFGDKC 115
           HY PGGYNA AQM NL   V   SRNM      S GP                       
Sbjct: 61  HYVPGGYNAAAQMTNLRPPVSQVSRNMQ----GSGGPG---------------------- 94

Query: 116 HFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASL 175
                                      GR  GR +  P  GP + FGAS T+KISVDASL
Sbjct: 95  ---------------------------GRFSGRGD--PGSGPVSIFGAS-TSKISVDASL 124

Query: 176 AGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI 235
           AGAIIGKGG++SKQICR+TGAKLSI+DHE DPNL+ IELEG+FEQI  AS MVRELI R+
Sbjct: 125 AGAIIGKGGIHSKQICRETGAKLSIKDHERDPNLKIIELEGTFEQINVASGMVRELIGRL 184

Query: 236 GPAHAKNPATAGSAA---HPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 290
           G    K P   G      HP  SN+KTK+C  ++KG+CT+GDRCHFAHG +ELR++ I
Sbjct: 185 GS--VKKPQGIGGPEGKPHP-GSNYKTKICDRYSKGNCTYGDRCHFAHGESELRRSGI 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 = 58.5 bits (140), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 92/236 (38%), Gaps = 43/236 (18%)

Query: 77  APSRNMAVPPPASNGPTVV--KSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDD 134
            PS N   PPP + G   +  K+RMC +   A  C+ G+ C+FAHG  +L +P       
Sbjct: 88  VPSLN---PPPVNKGTANIFYKTRMCAKF-RAGTCRNGELCNFAHGIEDLRQP------- 136

Query: 135 PRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQT 194
           P  +  + G       PPPA             +     SLA  +      + K I R  
Sbjct: 137 PSNWQEIVG-------PPPAGQDRERERERERERER--PSLAPVVNNNWEDDQKIILRMK 187

Query: 195 GAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVREL-IVRIGPAHAKNPATA------- 246
             +      E     R   +     + ++ S  +RE  ++ +G   A  P+         
Sbjct: 188 LCRKFCFGEECPYGDRCNFIHEDLSKFREDSGKLRESSVISVGATAADQPSDTASNLIEV 247

Query: 247 ---GSAAHPLSSN---------FKTKLCGNF-AKGSCTFGDRCHFAHGAAELRKTA 289
              GS   P   N         +KT+LC  F   G C FGD+CHFAHG AEL  + 
Sbjct: 248 NRQGSIPVPAPMNNGGVVKTVYWKTRLCMKFDITGQCPFGDKCHFAHGQAELHNSV 303

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 = 54.7 bits (130), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 38/107 (35%), Positives = 52/107 (48%), Gaps = 13/107 (12%)

Query: 33  KSKPCTKFFSTAGCPFGESCHFLHYFPGGYN---AVAQMMNLPQAVPAPSRNMAVPPPAS 89
           K + C KF++  GCP+G++C FLH          A++   ++       S N A    AS
Sbjct: 171 KGRHCKKFYTDEGCPYGDACTFLHDEQSKARESVAISLSPSVGGGGGGGSYNSAAAAAAS 230

Query: 90  ------NGP----TVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGK 126
                 NGP    +  K+R+CN+      C FG KCHFAHG  EL K
Sbjct: 231 ASAAAGNGPMQKPSNWKTRICNKWEMTGYCPFGSKCHFAHGAAELHK 277

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q5PP65|C3H28_ARATH Zinc finger CCCH domain-containing protein 28 OS=Arabidopsis thaliana GN=At2g35430 PE=2 SV=1

 Score = 48.9 bits (115), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 34/102 (33%), Positives = 46/102 (45%), Gaps = 11/102 (10%)

Query: 33  KSKPCTKFFSTAGCPF-GESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRN-----MAVPP 86
           K+K C KF     CP+   SCHF H             N  + V   SRN     +++ P
Sbjct: 73  KTKLCFKF-RAGTCPYSASSCHFAHSAEELRLPPPPPPNWQETVTEASRNRESFAVSLGP 131

Query: 87  PASNGPTV----VKSRMCNRLNSAEGCKFGDKCHFAHGEWEL 124
             +   T+     K+R+CN+  +   C FG  CHFAHG  EL
Sbjct: 132 RGNVAQTLKSPNWKTRICNKWQTTGYCPFGSHCHFAHGPSEL 173

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LQM3|C3H12_ARATH Zinc finger CCCH domain-containing protein 12 OS=Arabidopsis thaliana GN=At1g32360 PE=2 SV=1

 Score = 45.1 bits (105), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/34 (55%), Positives = 25/34 (73%), Gaps = 1/34 (2%)

Query: 255 SNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELRK 287
           SN+KT++C  +   G C FG +CHFAHGAAEL +
Sbjct: 259 SNWKTRICNKWEITGYCPFGAKCHFAHGAAELHR 292

Arabidopsis thaliana (taxid: 3702)

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	290
225441425	297	PREDICTED: zinc finger CCCH domain-conta	0.996	0.973	0.748	1e-121
255585533	295	conserved hypothetical protein [Ricinus	0.986	0.969	0.755	1e-119
255585535	295	conserved hypothetical protein [Ricinus	0.986	0.969	0.744	1e-115
449457299	305	PREDICTED: zinc finger CCCH domain-conta	0.989	0.940	0.704	1e-114
449437587	296	PREDICTED: zinc finger CCCH domain-conta	0.989	0.969	0.722	1e-113
363807948	295	uncharacterized protein LOC100803981 [Gl	0.989	0.972	0.724	1e-112
356504857	295	PREDICTED: zinc finger CCCH domain-conta	0.986	0.969	0.712	1e-109
356504859	295	PREDICTED: zinc finger CCCH domain-conta	0.986	0.969	0.712	1e-109
255634442	295	unknown [Glycine max]	0.986	0.969	0.709	1e-109
224139806	285	predicted protein [Populus trichocarpa]	0.965	0.982	0.693	1e-106

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

 Score =  442 bits (1136), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 223/298 (74%), Positives = 247/298 (82%), Gaps = 9/298 (3%)

Query: 1   MDTRKRTKPETGINANGVFKKSKHESES---GVGSKSKPCTKFFSTAGCPFGESCHFLHY 57
           MDTRKR +P   +NANG FKKSK E ES   G+GSKSKPCTKFFST+GCPFGESCHFLHY
Sbjct: 1   MDTRKRGRPGGALNANGGFKKSKQEVESLSTGIGSKSKPCTKFFSTSGCPFGESCHFLHY 60

Query: 58  FPGGYNAVAQMMNLPQAVPAPSRNMA-VPPPASNGPTV--VKSRMCNRLNSAEGCKFGDK 114
            PGGYNAVAQM N    +P  SRNMA  PPP  NG ++  VKS+MCN+ N+AEGCKFGDK
Sbjct: 61  VPGGYNAVAQMTNQAPILPPASRNMAGPPPPVPNGSSMPAVKSKMCNKFNTAEGCKFGDK 120

Query: 115 CHFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDAS 174
           CHFAHGEWELGKP+A  HDDPRA G++PGR+ GR EP P  GPAASFGASATAKISVDAS
Sbjct: 121 CHFAHGEWELGKPLAPYHDDPRAMGSIPGRLAGRIEPSPT-GPAASFGASATAKISVDAS 179

Query: 175 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR 234
           LAGAIIGKGGVNSKQICRQTGAKLSIR+H++DPNLRNIELEG+FEQIK+ASAMVRELIV 
Sbjct: 180 LAGAIIGKGGVNSKQICRQTGAKLSIREHDSDPNLRNIELEGTFEQIKEASAMVRELIVN 239

Query: 235 IG--PAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 290
           I   P HA+  A  G    P +SN+KTKLC NF KGSCTFG+RCHFAHGA ELRK+AI
Sbjct: 240 ISAMPGHARTTAMPGGGQAPPASNYKTKLCDNFTKGSCTFGERCHFAHGAGELRKSAI 297

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255585533|ref|XP_002533457.1| conserved hypothetical protein [Ricinus communis] gi|223526690|gb|EEF28926.1| conserved hypothetical protein [Ricinus communis]

 Score =  432 bits (1111), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 225/298 (75%), Positives = 241/298 (80%), Gaps = 12/298 (4%)

Query: 1   MDTRKRTKPETGINANGVFKKSKHESES---GVGSKSKPCTKFFSTAGCPFGESCHFLHY 57
           MDTRKR + +   NANG FKKSK E +S   GVGSKSKPCTKFFSTAGCPFGESCHFLHY
Sbjct: 2   MDTRKRGRND--FNANGGFKKSKREMDSLSTGVGSKSKPCTKFFSTAGCPFGESCHFLHY 59

Query: 58  FPGGYNAVAQMMNLPQAVPAPSRNMAVPPPA---SNGPTVVKSRMCNRLNSAEGCKFGDK 114
            PGGYNAVAQMMNL  AV +  RNM  P PA    + P+ VKSRMCN+ N+ EGCKFGDK
Sbjct: 60  VPGGYNAVAQMMNLGPAVTSVPRNMPAPSPAIPNGSAPSAVKSRMCNKYNTVEGCKFGDK 119

Query: 115 CHFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDAS 174
           C+FAHGEWELGK +A SHDDPRAFG   GRMGGR EPPP PGPAASFGASATAKISV+AS
Sbjct: 120 CNFAHGEWELGKSMAPSHDDPRAFGTFAGRMGGRMEPPP-PGPAASFGASATAKISVEAS 178

Query: 175 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR 234
           LAGAIIGKGGVNSKQICRQTGAKLSIR+HE DPNLRNIE EGSFEQIKQASAMV ELI  
Sbjct: 179 LAGAIIGKGGVNSKQICRQTGAKLSIREHETDPNLRNIEFEGSFEQIKQASAMVSELIAS 238

Query: 235 IGPAHAKNPAT--AGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 290
           I   +A   AT   G   HP  SNFKTKLC NF+KGSCTFG RCHFAHGAAELRK+ +
Sbjct: 239 ISSVNASAKATGLTGGHGHP-GSNFKTKLCENFSKGSCTFGQRCHFAHGAAELRKSGV 295

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255585535|ref|XP_002533458.1| conserved hypothetical protein [Ricinus communis] gi|223526691|gb|EEF28927.1| conserved hypothetical protein [Ricinus communis]

 Score =  420 bits (1079), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 222/298 (74%), Positives = 242/298 (81%), Gaps = 12/298 (4%)

Query: 1   MDTRKRTKPETGINANGVFKKSKHESES---GVGSKSKPCTKFFSTAGCPFGESCHFLHY 57
           MD RKR + +   N NG FKKS+ E +S   GVGSKSKPCTKFFSTAGCPFGESCHFLHY
Sbjct: 2   MDIRKRGRND--FNVNGGFKKSRKEMDSFSTGVGSKSKPCTKFFSTAGCPFGESCHFLHY 59

Query: 58  FPGGYNAVAQMMNLPQAVPAPSRNMAVPPPA---SNGPTVVKSRMCNRLNSAEGCKFGDK 114
            PGGYNAVAQMMNL  AV +  RNM  P PA    + P+ VKSR+CN+ N+AEGCKFGDK
Sbjct: 60  VPGGYNAVAQMMNLGPAVTSIPRNMPAPSPAIPNGSAPSAVKSRLCNKYNTAEGCKFGDK 119

Query: 115 CHFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDAS 174
           C+FAHGEWELGKP+  SHDDPRAFG +PGRMGGR EPPP PG AASFGASATAKISV+AS
Sbjct: 120 CNFAHGEWELGKPVVPSHDDPRAFGTIPGRMGGRMEPPP-PGSAASFGASATAKISVEAS 178

Query: 175 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR 234
           LAGAIIGKGGVNSKQICRQTGAKLSIR+HE DPN+RNIE EGSFEQIKQASAMV ELI  
Sbjct: 179 LAGAIIGKGGVNSKQICRQTGAKLSIREHETDPNVRNIEFEGSFEQIKQASAMVSELIAS 238

Query: 235 IGPAHAKNPATA--GSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 290
           I  A+A   AT   G   HP  SNFKTKLC NF+KGSCTFG RCHFAHGAAELRK+ +
Sbjct: 239 ISSANASAKATGLIGGHGHP-GSNFKTKLCENFSKGSCTFGQRCHFAHGAAELRKSGV 295

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449457299|ref|XP_004146386.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Cucumis sativus] gi|449480828|ref|XP_004156007.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Cucumis sativus]

 Score =  419 bits (1076), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 217/308 (70%), Positives = 241/308 (78%), Gaps = 21/308 (6%)

Query: 1   MDTRKRTKPETGINANGVFKKSKHESES--GVGSKSKPCTKFFSTAGCPFGESCHFLHYF 58
           MD RKR +PE   N+NG FKK K E ES   VGSKSKPCTKFFSTAGCPFGESCHFLHY 
Sbjct: 1   MDMRKRGRPEAAFNSNGSFKKHKQELESLSTVGSKSKPCTKFFSTAGCPFGESCHFLHYV 60

Query: 59  PGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNG----PTVVKSRMCNRLNSAEGCKFGDK 114
           PGGYN VAQMMNL      PSRN+A PP  +NG    P+ VK+RMCN+ N+AEGCKFGDK
Sbjct: 61  PGGYNVVAQMMNLAPVGAQPSRNIAAPPSVTNGGPSAPSQVKTRMCNKYNTAEGCKFGDK 120

Query: 115 CHFAHGEWELGKPIAISHDDPRAFGA---------VPGRMGGRYEPPPAPGPAASFGASA 165
           C+FAHGEWELG+P   SHD+PRA G          + GRMGGR + PP PGPAASFGASA
Sbjct: 121 CNFAHGEWELGRPNPPSHDNPRAMGGGGGGGGGVHMVGRMGGRMDLPP-PGPAASFGASA 179

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 225
           TAKIS+DASLAGAIIGKGG+NSKQICRQTGAKLSIRDHE+DPNLRNIELEG+FEQI +AS
Sbjct: 180 TAKISIDASLAGAIIGKGGINSKQICRQTGAKLSIRDHESDPNLRNIELEGTFEQINEAS 239

Query: 226 AMVRELIVRI---GPAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGA 282
           AMVRELI+ +   GP  A      G A  P  SN+KTKLC NFAKGSCTFG+RCHFAHGA
Sbjct: 240 AMVRELIITVSMAGPGKASGGMGGGPA--PTGSNYKTKLCDNFAKGSCTFGERCHFAHGA 297

Query: 283 AELRKTAI 290
           AELRK+ +
Sbjct: 298 AELRKSGV 305

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449437587|ref|XP_004136573.1| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Cucumis sativus]

 Score =  413 bits (1062), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 216/299 (72%), Positives = 241/299 (80%), Gaps = 12/299 (4%)

Query: 1   MDTRKRTKPETGINANGVFKKSKHESE---SGVGSKSKPCTKFFSTAGCPFGESCHFLHY 57
           MDTRKR + E G+ ANG  KK+K + E   +GV SKSKPCTKF+ST GCPFGE+CHFLHY
Sbjct: 1   MDTRKRGRAEVGLKANGGLKKNKQDMEYLSTGVASKSKPCTKFYSTTGCPFGEACHFLHY 60

Query: 58  FPGGYNAVAQMMNLPQAVPAPSRNM-AVPPPASNGPTV--VKSRMCNRLNSAEGCKFGDK 114
            PGGYNAVAQMMNLP A PAP RNM A PPP SNG     VKSRMCN+ NSAEGCKFGDK
Sbjct: 61  VPGGYNAVAQMMNLPPAPPAP-RNMGAPPPPMSNGSATQAVKSRMCNKYNSAEGCKFGDK 119

Query: 115 CHFAHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDAS 174
           CHFAH EWELGKP A SHDDPR+ G +P R+  R +  P PG AASFGAS+TAKISVDAS
Sbjct: 120 CHFAHAEWELGKPSAPSHDDPRSMGHIPNRLASRMDAGP-PGLAASFGASSTAKISVDAS 178

Query: 175 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR 234
           LAGAIIGKGG+NSKQICR+TGAKLSIRDHE+DPNLRNIELEGSF+QIK+ASAMV+ELIV 
Sbjct: 179 LAGAIIGKGGINSKQICRRTGAKLSIRDHESDPNLRNIELEGSFDQIKEASAMVQELIVT 238

Query: 235 I---GPAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 290
           +   GP  +      G  A P  +NFKTKLC NFAKGSCTFG+RCHFAHGAAELRK+ +
Sbjct: 239 VSMAGPPKSAT-GATGGTAGPAGNNFKTKLCDNFAKGSCTFGERCHFAHGAAELRKSGV 296

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807948|ref|NP_001242454.1| uncharacterized protein LOC100803981 [Glycine max] gi|255636900|gb|ACU18783.1| unknown [Glycine max]

 Score =  411 bits (1056), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 216/298 (72%), Positives = 236/298 (79%), Gaps = 11/298 (3%)

Query: 1   MDTRKRTKPETGINANGVFKKSKHESES---GVGSKSKPCTKFFSTAGCPFGESCHFLHY 57
           MDTRKR +PE G + NG FKKSK E ES   GVGSKSKPCTKFFSTAGCPFGE CHFLHY
Sbjct: 1   MDTRKRGRPEPGFSLNGGFKKSKQEMESLSTGVGSKSKPCTKFFSTAGCPFGEGCHFLHY 60

Query: 58  FPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNG--PTVVKSRMCNRLNSAEGCKFGDKC 115
            PGGYNAVA MMNL  A P  SRN+A PPP  NG  P  VK+R+CN+ N+AEGCKFGDKC
Sbjct: 61  VPGGYNAVAHMMNLTPAAPPASRNVAAPPPVPNGSAPPAVKTRICNKFNTAEGCKFGDKC 120

Query: 116 HFAHGEWELGKPIAISHDDPRAFGAV-PGRMGGRYEPPPAPGPAASFGASATAKISVDAS 174
           HFAHGEWELGK IA S DD R  G    GR+ GR EPPP  GPAASFGA+ATAKISV+AS
Sbjct: 121 HFAHGEWELGKHIAPSFDDHRTMGPTGVGRLAGRMEPPP--GPAASFGANATAKISVEAS 178

Query: 175 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR 234
           LAGAIIGKGGVNSKQICRQTGAKLSIR+HE+DPNLRNIELEGSF QIK+AS MV++L++ 
Sbjct: 179 LAGAIIGKGGVNSKQICRQTGAKLSIREHESDPNLRNIELEGSFVQIKEASNMVKDLLLT 238

Query: 235 IGPAHAKNPATAGSAAHPLS--SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 290
           +    A    T G    P S  SNFKTKLC NF KGSCTFGDRCHFAHGAAELRK+ +
Sbjct: 239 L-QMSAPPKTTPGVPGAPASHGSNFKTKLCENFTKGSCTFGDRCHFAHGAAELRKSGV 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 =  401 bits (1030), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 213/299 (71%), Positives = 237/299 (79%), Gaps = 13/299 (4%)

Query: 1   MDTRKRTKPETGINANGVFKKSKHESES---GVGSKSKPCTKFFSTAGCPFGESCHFLHY 57
           MD RKR +PE G + NG FKKSK E ES   GVGSKSKPCTKFFSTAGCPFGE CHFLHY
Sbjct: 1   MDIRKRGRPEPGFSLNGGFKKSKQEMESLSTGVGSKSKPCTKFFSTAGCPFGEGCHFLHY 60

Query: 58  FPGGYNAVAQMMNLPQAVPAP-SRNMAVPPPASNG--PTVVKSRMCNRLNSAEGCKFGDK 114
            PGGYNAVA MMNL  A P P +RN+A  P   NG  P+ VK+R+CN+ N+AEGCKFGDK
Sbjct: 61  VPGGYNAVAHMMNLTPAAPLPPTRNVAALPHVPNGSAPSAVKTRICNKFNTAEGCKFGDK 120

Query: 115 CHFAHGEWELGKPIAISHDDPRAFGAV-PGRMGGRYEPPPAPGPAASFGASATAKISVDA 173
           CHFAHGEWELGK IA S DD RA G    GR+ GR EPP   GPAASFGA++TAKISV+A
Sbjct: 121 CHFAHGEWELGKHIAPSFDDHRAMGPPGAGRLAGRMEPP---GPAASFGANSTAKISVEA 177

Query: 174 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIV 233
           SLAGAIIGKGGVNSKQICRQTGAKLSIR+HE+DPNLRNIELEGSFEQIK+AS MV++L++
Sbjct: 178 SLAGAIIGKGGVNSKQICRQTGAKLSIREHESDPNLRNIELEGSFEQIKEASNMVKDLLL 237

Query: 234 RIGPAHAKNPATAGSAAHPLS--SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 290
            +    A    T G    P S  SNFKTKLC NFAKGSCTFGDRCHFAHGA+ELRK+ +
Sbjct: 238 TL-QMSAPPKTTPGVPGAPASHGSNFKTKLCENFAKGSCTFGDRCHFAHGASELRKSGV 295

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  399 bits (1026), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 213/299 (71%), Positives = 237/299 (79%), Gaps = 13/299 (4%)

Query: 1   MDTRKRTKPETGINANGVFKKSKHESES---GVGSKSKPCTKFFSTAGCPFGESCHFLHY 57
           MD RKR + ETG + NG FK+SK E ES   GVGSKSKPCTKFFSTAGCPFGE CHFLHY
Sbjct: 1   MDIRKRGRHETGFSLNGGFKRSKQEMESLSTGVGSKSKPCTKFFSTAGCPFGEGCHFLHY 60

Query: 58  FPGGYNAVAQMMNL-PQAVPAPSRNMAVPPPASNG--PTVVKSRMCNRLNSAEGCKFGDK 114
            PGGYNAVA MMNL P A P PSRN+A  P   NG  P+ VK+R+CN+ N+AEGCKFGDK
Sbjct: 61  VPGGYNAVAHMMNLTPAAPPPPSRNVAALPHVPNGSAPSAVKTRICNKFNTAEGCKFGDK 120

Query: 115 CHFAHGEWELGKPIAISHDDPRAFGAV-PGRMGGRYEPPPAPGPAASFGASATAKISVDA 173
           CHFAHGEWELGK IA S DD  A G    GR+ GR EPP   GPAASFGA++TAKISV+A
Sbjct: 121 CHFAHGEWELGKHIAPSFDDHHAMGPPGAGRLAGRMEPP---GPAASFGANSTAKISVEA 177

Query: 174 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIV 233
           SLAGAIIGKGGVNSKQICRQTGAKLSIR+HE+DPNLRNIELEGSFEQIK+AS MV++L++
Sbjct: 178 SLAGAIIGKGGVNSKQICRQTGAKLSIREHESDPNLRNIELEGSFEQIKEASNMVKDLLL 237

Query: 234 RIGPAHAKNPATAGSAAHPLS--SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 290
            +    A    T G    P S  SNFKTKLC NFAKGSCTFGDRCHFAHGA+ELRK+ +
Sbjct: 238 TL-QMSAPPKTTPGVPGAPASHGSNFKTKLCENFAKGSCTFGDRCHFAHGASELRKSGV 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 =  399 bits (1025), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 212/299 (70%), Positives = 236/299 (78%), Gaps = 13/299 (4%)

Query: 1   MDTRKRTKPETGINANGVFKKSKHESES---GVGSKSKPCTKFFSTAGCPFGESCHFLHY 57
           MD RKR +PE G + NG FKKSK E ES   GVGSKSKPCTKFFSTAGCPFGE CHFLHY
Sbjct: 1   MDIRKRGRPEPGFSLNGGFKKSKQEMESLSTGVGSKSKPCTKFFSTAGCPFGEGCHFLHY 60

Query: 58  FPGGYNAVAQMMNLPQAVPAP-SRNMAVPPPASNG--PTVVKSRMCNRLNSAEGCKFGDK 114
            PGGYNAVA MMNL  A P P +RN+A  P   NG  P+ VK+R+CN+ N+AEGCKFGDK
Sbjct: 61  VPGGYNAVAHMMNLTPAAPLPPTRNVAALPHVPNGSAPSAVKTRICNKFNTAEGCKFGDK 120

Query: 115 CHFAHGEWELGKPIAISHDDPRAFGAV-PGRMGGRYEPPPAPGPAASFGASATAKISVDA 173
           CHFAHGEWELGK IA S DD RA G    GR+ GR EPP   GPAASFGA++TAKISV+A
Sbjct: 121 CHFAHGEWELGKHIAPSFDDHRAMGPPGAGRLAGRMEPP---GPAASFGANSTAKISVEA 177

Query: 174 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIV 233
           SLAGAIIGKGGVNSKQICRQTGAKLSIR+HE+DPN RNIELEGSFEQIK+AS MV++L++
Sbjct: 178 SLAGAIIGKGGVNSKQICRQTGAKLSIREHESDPNFRNIELEGSFEQIKEASNMVKDLLL 237

Query: 234 RIGPAHAKNPATAGSAAHPLS--SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 290
            +    A    T G    P S  SNFKTKLC NFAKGSCTFGDRCHFAHGA+ELRK+ +
Sbjct: 238 TL-QMSAPPKTTPGVPGAPASHGSNFKTKLCENFAKGSCTFGDRCHFAHGASELRKSGV 295

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224139806|ref|XP_002323285.1| predicted protein [Populus trichocarpa] gi|222867915|gb|EEF05046.1| predicted protein [Populus trichocarpa]

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 204/294 (69%), Positives = 231/294 (78%), Gaps = 14/294 (4%)

Query: 1   MDTRKRTKPETGINANGVFKKSKHESES---GVGSKSKPCTKFFSTAGCPFGESCHFLHY 57
           MDTRKR +P+ G N  G FKKSK E +S   GVGSKSKPCTKFFSTAGCPFGESCHFLH+
Sbjct: 2   MDTRKRGRPDFGTNGYGGFKKSKQEMDSLSTGVGSKSKPCTKFFSTAGCPFGESCHFLHH 61

Query: 58  FPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFGDKCHF 117
            PGGY AVAQM+NL   V  P      P P S+ P+ VKSR+C + NSAEGCKFGDKCHF
Sbjct: 62  VPGGYKAVAQMVNLGPTVALP------PVPNSSAPSAVKSRLCKKYNSAEGCKFGDKCHF 115

Query: 118 AHGEWELGKPIAISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASA-TAKISVDASLA 176
           AHGEWELGK    SH+DP A G+VPGR+GGR EPPP PGPA SFG  A T +ISVDASLA
Sbjct: 116 AHGEWELGKAFVPSHNDPHAAGSVPGRLGGRVEPPP-PGPATSFGVFATTTRISVDASLA 174

Query: 177 GAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG 236
           G+IIGK GV+SKQICRQTG KLSI+DHE +PNL+NIELEGS EQI QAS MV EL VR+ 
Sbjct: 175 GSIIGKAGVHSKQICRQTGIKLSIKDHETNPNLKNIELEGSLEQIAQASKMVEEL-VRVT 233

Query: 237 PAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 290
            A+A   ++ G  A+P  SN+KTKLC NFAKGSCTFG RCHFAHGAAELRK+++
Sbjct: 234 SANAAAKSSGGH-ANP-GSNYKTKLCDNFAKGSCTFGQRCHFAHGAAELRKSSM 285

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	290
TAIR|locus:2170169	240	AT5G06770 [Arabidopsis thalian	0.651	0.787	0.509	2.3e-46
TAIR|locus:2099292	248	AT3G12130 [Arabidopsis thalian	0.658	0.770	0.518	6.2e-46
TAIR|locus:2028306	384	AT1G32360 [Arabidopsis thalian	0.144	0.109	0.5	3.8e-10
UNIPROTKB|P26651	326	ZFP36 "Tristetraprolin" [Homo	0.193	0.171	0.413	0.00013
TAIR|locus:2090669	386	AT3G19360 [Arabidopsis thalian	0.151	0.113	0.458	9.1e-07
RGD|620722	320	Zfp36 "zinc finger protein 36"	0.193	0.175	0.413	0.00036
UNIPROTKB|P47973	320	Zfp36 "Tristetraprolin" [Rattu	0.193	0.175	0.413	0.00036
WB|WBGene00009532	460	ccch-1 [Caenorhabditis elegans	0.334	0.210	0.291	2.3e-07
UNIPROTKB|Q6S9E0	325	ZFP36 "Tristetraprolin" [Ovis	0.175	0.156	0.415	0.00082
MGI|MGI:99180	319	Zfp36 "zinc finger protein 36"	0.193	0.175	0.413	0.00036

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

 Score = 486 (176.1 bits), Expect = 2.3e-46, P = 2.3e-46
 Identities = 106/208 (50%), Positives = 131/208 (62%)

Query:    96 KSRMCNRLNSAEGCKFGDKCHFAH---GEWE-------LGKPIAISHDDPRAFGAVPGRM 145
             KS+ C +  S  GC FGD CHF H   G +        L  P++    + +  G   GR 
Sbjct:    38 KSKPCTKFFSTSGCPFGDNCHFLHYVPGGYNAAAQMTNLRPPVSQVSRNMQGSGGPGGRF 97

Query:   146 GGRYEXXXXXXXXXXXXXXXTAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA 205
              GR +               T+KISVDASLAGAIIGKGG++SKQICR+TGAKLSI+DHE 
Sbjct:    98 SGRGDPGSGPVSIFGAS---TSKISVDASLAGAIIGKGGIHSKQICRETGAKLSIKDHER 154

Query:   206 DPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAA---HPLSSNFKTKLC 262
             DPNL+ IELEG+FEQI  AS MVRELI R+G    K P   G      HP  SN+KTK+C
Sbjct:   155 DPNLKIIELEGTFEQINVASGMVRELIGRLGSV--KKPQGIGGPEGKPHP-GSNYKTKIC 211

Query:   263 GNFAKGSCTFGDRCHFAHGAAELRKTAI 290
               ++KG+CT+GDRCHFAHG +ELR++ I
Sbjct:   212 DRYSKGNCTYGDRCHFAHGESELRRSGI 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 = 482 (174.7 bits), Expect = 6.2e-46, P = 6.2e-46
 Identities = 111/214 (51%), Positives = 131/214 (61%)

Query:    96 KSRMCNRLNSAEGCKFGDKCHFAH---GEWE-------LGKPIAISHDDPRAFGAVPGRM 145
             KS+ C +  S  GC FG+ CHF H   G +        +G PI     + +  G   GR 
Sbjct:    38 KSKPCTKFFSTSGCPFGENCHFLHYVPGGYNAVSQMTNMGPPIPQVSRNMQGSGN-GGRF 96

Query:   146 GGRYEXXXXXXXXXXXXXXXTAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA 205
              GR E               TA+ SVDASLAGAIIGKGGV+SKQICRQTG KLSI+DHE 
Sbjct:    97 SGRGESGPGHVSNFGDSA--TARFSVDASLAGAIIGKGGVSSKQICRQTGVKLSIQDHER 154

Query:   206 DPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATA-------GSAA--HPLSSN 256
             DPNL+NI LEG+ EQI +ASAMV++LI R+  A  K P          GS    HP  SN
Sbjct:   155 DPNLKNIVLEGTLEQISEASAMVKDLIGRLNSAAKKPPGGGLGGGGGMGSEGKPHP-GSN 213

Query:   257 FKTKLCGNFAKGSCTFGDRCHFAHGAAELRKTAI 290
             FKTK+C  F+KG+CTFGDRCHFAHG AELRK+ I
Sbjct:   214 FKTKICERFSKGNCTFGDRCHFAHGEAELRKSGI 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

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

 Score = 110 (43.8 bits), Expect = 3.8e-10, Sum P(2) = 3.8e-10
 Identities = 22/44 (50%), Positives = 29/44 (65%)

Query:   246 AGSAAHPLS-SNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELRK 287
             +GS    L  SN+KT++C  +   G C FG +CHFAHGAAEL +
Sbjct:   249 SGSGIQILKPSNWKTRICNKWEITGYCPFGAKCHFAHGAAELHR 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|P26651 ZFP36 "Tristetraprolin" [Homo sapiens (taxid:9606)]

 Score = 118 (46.6 bits), Expect = 0.00013, P = 0.00013
 Identities = 24/58 (41%), Positives = 36/58 (62%)

Query:   231 LIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAELRK 287
             L  R+GP  + +P T+ +A     S +KT+LC  F++ G C +G +C FAHG  ELR+
Sbjct:    79 LAPRLGPELSPSP-TSPTATSTTPSRYKTELCRTFSESGRCRYGAKCQFAHGLGELRQ 135

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IEA

GO:0007243 "intracellular protein kinase cascade" evidence=IEA

GO:0035925 "mRNA 3'-UTR AU-rich region binding" evidence=IEA

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=IEA

GO:0050728 "negative regulation of inflammatory response" evidence=IEA

GO:0050779 "RNA destabilization" evidence=IEA

GO:0017091 "AU-rich element binding" evidence=IMP;IDA

GO:0006402 "mRNA catabolic process" evidence=IDA

GO:0060213 "positive regulation of nuclear-transcribed mRNA poly(A) tail shortening" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0019957 "C-C chemokine binding" evidence=IPI

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0019901 "protein kinase binding" evidence=IPI

GO:0006950 "response to stress" evidence=IDA

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0071889 "14-3-3 protein binding" evidence=IDA

GO:0032680 "regulation of tumor necrosis factor production" evidence=IDA

GO:0070935 "3'-UTR-mediated mRNA stabilization" evidence=IDA

GO:1900153 "positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=ISS

GO:0035278 "negative regulation of translation involved in gene silencing by miRNA" evidence=ISS

GO:0003727 "single-stranded RNA binding" evidence=TAS

GO:0003729 "mRNA binding" evidence=IDA

GO:0005829 "cytosol" evidence=IDA;TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

 Score = 112 (44.5 bits), Expect = 9.1e-07, Sum P(2) = 9.1e-07
 Identities = 22/48 (45%), Positives = 30/48 (62%)

Query:    81 NMAVPPPASNGPTVV----KSRMCNRLNSAEGCKFGDKCHFAHGEWEL 124
             ++ VP P +NG  V     K+R+C + +    C FGDKCHFAHG+ EL
Sbjct:   252 SIPVPAPMNNGGVVKTVYWKTRLCMKFDITGQCPFGDKCHFAHGQAEL 299

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

RGD|620722 Zfp36 "zinc finger protein 36" [Rattus norvegicus (taxid:10116)]

 Score = 114 (45.2 bits), Expect = 0.00036, P = 0.00036
 Identities = 24/58 (41%), Positives = 36/58 (62%)

Query:   231 LIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAELRK 287
             L  R GP  + +P T+ +A    SS +KT+LC  +++ G C +G +C FAHG  ELR+
Sbjct:    72 LAPRPGPELSPSP-TSPTATPTTSSRYKTELCRTYSESGRCRYGAKCQFAHGPGELRQ 128

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA;ISO

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

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IEA;ISO

GO:0003677 "DNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA;ISO;ISS;IDA

GO:0005737 "cytoplasm" evidence=ISO;ISS;IDA

GO:0005829 "cytosol" evidence=IEA;ISO

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0006402 "mRNA catabolic process" evidence=ISO;ISS

GO:0006950 "response to stress" evidence=IEA;ISO;ISS

GO:0007243 "intracellular protein kinase cascade" evidence=IEA;ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA;ISO;ISS

GO:0017091 "AU-rich element binding" evidence=ISO;ISS

GO:0019901 "protein kinase binding" evidence=IEA;ISO

GO:0019957 "C-C chemokine binding" evidence=IEA;ISO

GO:0032680 "regulation of tumor necrosis factor production" evidence=IEA;ISO;ISS

GO:0035925 "mRNA 3'-UTR AU-rich region binding" evidence=IEA;ISO

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

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=IEA;ISO

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

GO:0050728 "negative regulation of inflammatory response" evidence=IEA;ISO

GO:0050779 "RNA destabilization" evidence=IEA;ISO

GO:0060213 "positive regulation of nuclear-transcribed mRNA poly(A) tail shortening" evidence=IEA;ISO;ISS

GO:0070935 "3'-UTR-mediated mRNA stabilization" evidence=IEA;ISO;ISS

GO:0071889 "14-3-3 protein binding" evidence=IEA;ISO;ISS

UNIPROTKB|P47973 Zfp36 "Tristetraprolin" [Rattus norvegicus (taxid:10116)]

 Score = 114 (45.2 bits), Expect = 0.00036, P = 0.00036
 Identities = 24/58 (41%), Positives = 36/58 (62%)

Query:   231 LIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAELRK 287
             L  R GP  + +P T+ +A    SS +KT+LC  +++ G C +G +C FAHG  ELR+
Sbjct:    72 LAPRPGPELSPSP-TSPTATPTTSSRYKTELCRTYSESGRCRYGAKCQFAHGPGELRQ 128

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0007243 "intracellular protein kinase cascade" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

GO:0019957 "C-C chemokine binding" evidence=IEA

GO:0035925 "mRNA 3'-UTR AU-rich region binding" evidence=IEA

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=IEA

GO:0050728 "negative regulation of inflammatory response" evidence=IEA

GO:0050779 "RNA destabilization" evidence=IEA

WB|WBGene00009532 ccch-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 112 (44.5 bits), Expect = 2.3e-07, Sum P(2) = 2.3e-07
 Identities = 30/103 (29%), Positives = 46/103 (44%)

Query:    28 SGVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMM--NLPQAVPAPSRNMAVP 85
             S  GS     ++F +  G P G      H    G N V+     + PQ  P  + N   P
Sbjct:   133 SFAGSSLFGASEFGNPLGAP-GTPIGSQHQMSIGQNLVSASSPYSTPQLTPMATPNGQAP 191

Query:    86 PPASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPI 128
             PP +  P + K+ +C        C +G++C +AHGE E  +P+
Sbjct:   192 PPKN--PKLYKTELCRSWMDHGRCNYGERCQYAHGELEK-RPV 231

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016529 "sarcoplasmic reticulum" evidence=IDA

UNIPROTKB|Q6S9E0 ZFP36 "Tristetraprolin" [Ovis aries (taxid:9940)]

 Score = 111 (44.1 bits), Expect = 0.00082, P = 0.00082
 Identities = 22/53 (41%), Positives = 32/53 (60%)

Query:   237 PAHAKNPATAGSAAHPL-SSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAELRK 287
             P+   +P+     A P  SS +KT+LC  F++ G C +G +C FAHG  ELR+
Sbjct:    81 PSSELSPSPTSPTATPTTSSRYKTELCRTFSESGRCRYGAKCQFAHGLGELRQ 133

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0006402 "mRNA catabolic process" evidence=ISS

GO:0006950 "response to stress" evidence=ISS

GO:0010494 "cytoplasmic stress granule" evidence=ISS

GO:0017091 "AU-rich element binding" evidence=ISS

GO:0032680 "regulation of tumor necrosis factor production" evidence=ISS

GO:0060213 "positive regulation of nuclear-transcribed mRNA poly(A) tail shortening" evidence=ISS

GO:0070935 "3'-UTR-mediated mRNA stabilization" evidence=ISS

GO:0071889 "14-3-3 protein binding" evidence=ISS

MGI|MGI:99180 Zfp36 "zinc finger protein 36" [Mus musculus (taxid:10090)]

 Score = 114 (45.2 bits), Expect = 0.00036, P = 0.00036
 Identities = 24/58 (41%), Positives = 36/58 (62%)

Query:   231 LIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAELRK 287
             L  R GP  + +P T+ +A    SS +KT+LC  +++ G C +G +C FAHG  ELR+
Sbjct:    71 LAPRPGPELSPSP-TSPTATPTTSSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQ 127

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO;IMP

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

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IDA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO;IDA

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=ISO;IDA

GO:0005829 "cytosol" evidence=ISO;IDA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IGI

GO:0006402 "mRNA catabolic process" evidence=ISO

GO:0006950 "response to stress" evidence=ISO

GO:0007243 "intracellular protein kinase cascade" evidence=IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=ISO

GO:0017091 "AU-rich element binding" evidence=ISO;IDA

GO:0019901 "protein kinase binding" evidence=ISO

GO:0019957 "C-C chemokine binding" evidence=ISO

GO:0032680 "regulation of tumor necrosis factor production" evidence=ISO

GO:0035925 "mRNA 3'-UTR AU-rich region binding" evidence=IDA

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

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=IMP

GO:0046872 "metal ion binding" evidence=IEA

GO:0050728 "negative regulation of inflammatory response" evidence=IMP

GO:0050779 "RNA destabilization" evidence=IMP

GO:0060213 "positive regulation of nuclear-transcribed mRNA poly(A) tail shortening" evidence=ISO

GO:0070935 "3'-UTR-mediated mRNA stabilization" evidence=ISO

GO:0071889 "14-3-3 protein binding" evidence=ISO

---

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	0.6329	0.9724	0.94	yes	no
Q9C7C3	C3H36_ARATH	No assigned EC number	0.5230	0.8034	0.9395	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	290
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	8e-15
pfam00013	59	pfam00013, KH_1, KH domain	2e-12
smart00322	68	smart00322, KH, K homology RNA-binding domain	2e-12
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	4e-09
pfam13014	42	pfam13014, KH_3, KH domain	3e-08
smart00356	27	smart00356, ZnF_C3H1, zinc finger	9e-07
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	8e-06
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	3e-04
PRK13764	602	PRK13764, PRK13764, ATPase; Provisional	3e-04
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	0.001
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.002

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

 Score = 67.2 bits (165), Expect = 8e-15
 Identities = 23/63 (36%), Positives = 38/63 (60%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 225
           T ++ V +SL G IIGKGG   K+I  +TGAK+ I D  +    R + + G+ E +++A 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60

Query: 226 AMV 228
            ++
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|215657 pfam00013, KH_1, KH domain

 Score = 60.7 bits (148), Expect = 2e-12
 Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 4/63 (6%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 225
           T +I +     G IIGKGG N K+I  +TG K+ I D   D     + + G+ EQ+++A 
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDRDDT----VTISGTPEQVEKAK 56

Query: 226 AMV 228
            ++
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|197652 smart00322, KH, K homology RNA-binding domain

 Score = 61.2 bits (149), Expect = 2e-12
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIK 222
              T ++ + A   G IIGKGG   K+I  +TG K+ I         R +E+ G  E ++
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGP--GSEERVVEITGPPENVE 58

Query: 223 QASAMVRELI 232
           +A+ ++ E++
Sbjct: 59  KAAELILEIL 68

Length = 68

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

 Score = 51.7 bits (125), Expect = 4e-09
 Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEGSFEQIKQA 224
           T ++ V +S AG+IIGKGG   K+I  +TGAK+ +          R + + G    +++A
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 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|221895 pfam13014, KH_3, KH domain

 Score = 48.7 bits (117), Expect = 3e-08
 Identities = 19/42 (45%), Positives = 24/42 (57%)

Query: 175 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG 216
           L GAIIGKGG   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|214632 smart00356, ZnF_C3H1, zinc finger

 Score = 44.2 bits (105), Expect = 9e-07
 Identities = 14/26 (53%), Positives = 17/26 (65%)

Query: 256 NFKTKLCGNFAKGSCTFGDRCHFAHG 281
            +KT+LC  F +G C  GDRC FAH 
Sbjct: 1   KYKTELCKFFKRGYCPRGDRCKFAHP 26

Length = 27

>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: 257 FKTKLCGNFAK-GSCTFGDRCHFAHG 281
           +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 = 42.1 bits (100), Expect = 8e-06
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 225
           T ++ +   L   IIGK G N ++I  +TG K+   D  +  +   I + G  E +++A 
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSD--TITITGPKENVEKAK 58

Query: 226 AMVR 229
             + 
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|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

 Score = 37.9 bits (89), Expect = 3e-04
 Identities = 11/34 (32%), Positives = 17/34 (50%)

Query: 169 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202
           + +       +IG GG   K+I  +TG K+ I D
Sbjct: 6   MKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED 39

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. Length = 61

>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional

 Score = 41.7 bits (99), Expect = 3e-04
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 7/81 (8%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE-GSFEQIKQA 224
            A + V       +IGKGG   K+I ++ G  + +R  + +P     E E  + E+ K  
Sbjct: 482 KAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEPGEEAEEGEEVTVEETK-- 539

Query: 225 SAMVRELIVRIGPAHAKNPAT 245
               + +I+ +GP +A     
Sbjct: 540 ----KHVILIVGPDYAGKTVD 556

Length = 602

>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 40.0 bits (95), Expect = 0.001
 Identities = 12/34 (35%), Positives = 18/34 (52%)

Query: 169 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202
           I +       +IG GG   ++I  +TGAK+ I D
Sbjct: 558 IKIPPDKIRDVIGPGGKTIREITEETGAKIDIED 591

Length = 693

>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 39.4 bits (93), Expect = 0.002
 Identities = 12/35 (34%), Positives = 19/35 (54%)

Query: 168 KISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202
            I ++      +IG GG   ++I  +TGAK+ I D
Sbjct: 554 TIKINPDKIRDVIGPGGKVIREITEETGAKIDIED 588

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) [Transcription, Degradation of RNA]. Length = 684

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	290
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.74
KOG1677	332	consensus CCCH-type Zn-finger protein [General fun	99.6
KOG1677	332	consensus CCCH-type Zn-finger protein [General fun	99.43
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.29
COG5063	351	CTH1 CCCH-type Zn-finger protein [General function	99.19
COG5063	351	CTH1 CCCH-type Zn-finger protein [General function	99.13
KOG1676	600	consensus K-homology type RNA binding proteins [RN	99.1
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.08
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.02
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	98.98
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	98.97
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.94
KOG1676	600	consensus K-homology type RNA binding proteins [RN	98.92
PF00642	27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	98.8
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	98.72
KOG1040	325	consensus Polyadenylation factor I complex, subuni	98.66
PF00642	27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	98.64
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	98.62
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.6
KOG1595	528	consensus CCCH-type Zn-finger protein [General fun	98.57
PF13014	43	KH_3: KH domain	98.55
smart00322	69	KH K homology RNA-binding domain.	98.51
KOG1595	528	consensus CCCH-type Zn-finger protein [General fun	98.37
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.35
smart00356	27	ZnF_C3H1 zinc finger.	98.27
smart00356	27	ZnF_C3H1 zinc finger.	98.22
KOG2333	614	consensus Uncharacterized conserved protein [Gener	98.11
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.04
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.02
PRK13763	180	putative RNA-processing protein; Provisional	97.96
KOG1492	377	consensus C3H1-type Zn-finger protein [General fun	97.91
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	97.76
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	97.74
PRK13763	180	putative RNA-processing protein; Provisional	97.57
KOG1040	325	consensus Polyadenylation factor I complex, subuni	97.45
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	97.44
COG5084	285	YTH1 Cleavage and polyadenylation specificity fact	97.42
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.2
KOG1763	343	consensus Uncharacterized conserved protein, conta	97.18
COG5252	299	Uncharacterized conserved protein, contains CCCH-t	97.06
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	96.96
KOG2494	331	consensus C3H1-type Zn-finger protein [Transcripti	96.9
PF14608	19	zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	96.72
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	96.64
KOG0119	554	consensus Splicing factor 1/branch point binding p	96.55
KOG4791	667	consensus Uncharacterized conserved protein [Funct	96.52
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.22
KOG2185	486	consensus Predicted RNA-processing protein, contai	96.14
KOG2185	486	consensus Predicted RNA-processing protein, contai	96.11
PF14608	19	zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	96.07
KOG2494	331	consensus C3H1-type Zn-finger protein [Transcripti	96.01
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	95.93
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	95.74
KOG2113	394	consensus Predicted RNA binding protein, contains	95.37
COG5152	259	Uncharacterized conserved protein, contains RING a	95.29
KOG2333	614	consensus Uncharacterized conserved protein [Gener	95.18
COG1094	194	Predicted RNA-binding protein (contains KH domains	94.73
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	94.48
KOG1492	377	consensus C3H1-type Zn-finger protein [General fun	94.44
COG5152	259	Uncharacterized conserved protein, contains RING a	94.06
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	93.62
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	93.22
KOG1763	343	consensus Uncharacterized conserved protein, conta	93.08
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	92.95
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	92.45
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	92.32
COG5176	269	MSL5 Splicing factor (branch point binding protein	92.25
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	92.05
COG5084	285	YTH1 Cleavage and polyadenylation specificity fact	91.12
COG5252	299	Uncharacterized conserved protein, contains CCCH-t	91.05
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	89.62
PRK08406	140	transcription elongation factor NusA-like protein;	89.32
KOG2814	345	consensus Transcription coactivator complex, P50 c	89.08
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	88.34
PRK00468	75	hypothetical protein; Provisional	87.7
COG1837	76	Predicted RNA-binding protein (contains KH domain)	87.5
PRK01064	78	hypothetical protein; Provisional	87.39
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	87.38
PRK02821	77	hypothetical protein; Provisional	87.37
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	86.96
PRK12704	520	phosphodiesterase; Provisional	86.73
PRK00106	535	hypothetical protein; Provisional	86.21
PRK08406	140	transcription elongation factor NusA-like protein;	85.8
PF10650	23	zf-C3H1: Putative zinc-finger domain; InterPro: IP	84.76
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	83.99
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	82.74
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	82.04
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	81.7
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	81.51
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	81.4
COG1094	194	Predicted RNA-binding protein (contains KH domains	81.13

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

Probab=99.74  E-value=2.1e-18  Score=154.11  Aligned_cols=164  Identities=21%  Similarity=0.194  Sum_probs=127.9

Q ss_pred             eEecccCCCchhhhhhccCCCCCCCCCCCCCC---CCCCCCCCCcccccccccccccccCCCCCcccccccccccCCCcc
Q 022898           53 HFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAV---PPPASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIA  129 (290)
Q Consensus        53 ~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~---~s~~~~~~~~~ktr~C~~~~~~g~C~~G~~C~f~H~~~el~~~~~  129 (290)
                      .|+..|+|+|+++++|+++|++|.++|+++++   +|.+.+++|++.+|+|.+.++.....   ..+-...+        
T Consensus        39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~---av~efI~d--------  107 (402)
T KOG2191|consen   39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALN---AVHEFIAD--------  107 (402)
T ss_pred             eEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHH---HHHHHHHH--------
Confidence            88999999999999999999999999999998   78999999999999999988876444   11211212        


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc-CCC--C
Q 022898          130 ISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEA--D  206 (290)
Q Consensus       130 ~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~s~~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~-~~~--~  206 (290)
                          +++..+..........++..       -....++++.||++.+|+||||+|.+||.|+++++++|+|++ .+.  .
T Consensus       108 ----Kire~p~~~~k~v~~~~pqt-------~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~s  176 (402)
T KOG2191|consen  108 ----KIREKPQAVAKPVDILQPQT-------PDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGIS  176 (402)
T ss_pred             ----HHHHhHHhhcCCccccCCCC-------ccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCcc
Confidence                12222222222222222211       123577999999999999999999999999999999999984 333  3


Q ss_pred             CCcceeEEcCCHHHHHHHHHHHHHHHHhcCCC
Q 022898          207 PNLRNIELEGSFEQIKQASAMVRELIVRIGPA  238 (290)
Q Consensus       207 ~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~  238 (290)
                      ..+|+++++|++++..+|..+|.++|.|++..
T Consensus       177 Lqervvt~sge~e~~~~A~~~IL~Ki~eDpqs  208 (402)
T KOG2191|consen  177 LQERVVTVSGEPEQNMKAVSLILQKIQEDPQS  208 (402)
T ss_pred             ceeEEEEecCCHHHHHHHHHHHHHHhhcCCcc
Confidence            34899999999999999999999999988765

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

Probab=99.60  E-value=1.1e-15  Score=142.11  Aligned_cols=76  Identities=29%  Similarity=0.625  Sum_probs=59.6

Q ss_pred             ccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCCC-CC
Q 022898           35 KPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKF-GD  113 (290)
Q Consensus        35 ~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~~-G~  113 (290)
                      ..|.+|...+.|.++..|+|.|..-          .....+..       .......+..+||.+|..|...|.|+| |+
T Consensus        87 ~~~~~~~~~~~~~~~s~~~~~~p~~----------~~~~~~~~-------~~~~~~~p~~~kt~lc~~~~~~g~c~y~ge  149 (332)
T KOG1677|consen   87 GDCSAYLRTGVCGYGSSCRYNHPDL----------RLRPRPVR-------RSRGERKPERYKTPLCRSFRKSGTCKYRGE  149 (332)
T ss_pred             cccccccccCCCCCCCCCCccCccc----------ccccCCcc-------ccccccCcccccCCcceeeecCccccccCc
Confidence            7999999999999999999999740          11110000       012335678999999999999999999 99


Q ss_pred             cccccccccccCCC
Q 022898          114 KCHFAHGEWELGKP  127 (290)
Q Consensus       114 ~C~f~H~~~el~~~  127 (290)
                      +|+|+|+.++++.+
T Consensus       150 ~crfah~~~e~r~~  163 (332)
T KOG1677|consen  150 QCRFAHGLEELRLP  163 (332)
T ss_pred             hhhhcCCccccccc
Confidence            99999999888765

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

Probab=99.43  E-value=7.3e-14  Score=129.99  Aligned_cols=81  Identities=27%  Similarity=0.587  Sum_probs=66.1

Q ss_pred             CCCccccccccccccCCCCCC-CCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCccccccccccccc
Q 022898           28 SGVGSKSKPCTKFFSTAGCPF-GESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSA  106 (290)
Q Consensus        28 ~~~~~Kt~lC~~~~~~g~C~~-G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~  106 (290)
                      ....|||.+|.+|..+|+|+| |++|+|+|++          .+++...         .......++.|||++|.+|..+
T Consensus       126 ~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~----------~e~r~~~---------~~~~~~~~~~~kt~lC~~f~~t  186 (332)
T KOG1677|consen  126 KPERYKTPLCRSFRKSGTCKYRGEQCRFAHGL----------EELRLPS---------SENQVGNPPKYKTKLCPKFQKT  186 (332)
T ss_pred             CcccccCCcceeeecCccccccCchhhhcCCc----------ccccccc---------cchhhcCCCCCCCcCCCccccC
Confidence            367899999999999999999 9999999986          2332110         0012346899999999999999


Q ss_pred             ccCCCCCcccccccccccCCC
Q 022898          107 EGCKFGDKCHFAHGEWELGKP  127 (290)
Q Consensus       107 g~C~~G~~C~f~H~~~el~~~  127 (290)
                      |.|+||.+|+|+|+..++...
T Consensus       187 G~C~yG~rC~F~H~~~~~~~~  207 (332)
T KOG1677|consen  187 GLCKYGSRCRFIHGEPEDRAS  207 (332)
T ss_pred             CCCCCCCcCeecCCCcccccc
Confidence            999999999999999877764

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.29  E-value=6.3e-12  Score=89.31  Aligned_cols=63  Identities=32%  Similarity=0.502  Sum_probs=58.2

Q ss_pred             eEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCC-CCCcceeEEcCCHHHHHHHHHHH
Q 022898          166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA-DPNLRNIELEGSFEQIKQASAMV  228 (290)
Q Consensus       166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~-~~~~r~v~i~G~~~~i~~A~~~I  228 (290)
                      +.+|.||.+.+|.|||++|.+|+.|++.||+.|.|.+... +..+|.|+|.|+++++..|..||
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence            4689999999999999999999999999999999976654 67789999999999999999987

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

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

Probab=99.19  E-value=1.6e-11  Score=109.17  Aligned_cols=74  Identities=23%  Similarity=0.487  Sum_probs=61.5

Q ss_pred             CCcccc--ccccccccCCCCCC---CCCceEe---cccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCccccccc
Q 022898           29 GVGSKS--KPCTKFFSTAGCPF---GESCHFL---HYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMC  100 (290)
Q Consensus        29 ~~~~Kt--~lC~~~~~~g~C~~---G~~C~F~---H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C  100 (290)
                      ...|||  .||.-|...|+|+|   |++|+|+   |++-+          +               .....-.+|+|+.|
T Consensus       223 ~~L~kt~~~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~----------l---------------~~k~k~~~frTePc  277 (351)
T COG5063         223 KPLYKTNPELCESFTRKGTCPYWISGVKCQFACRGHGLNE----------L---------------KSKKKKQNFRTEPC  277 (351)
T ss_pred             chhhcCCHHHhhccCcCCCCcccccccccccccccccccc----------c---------------cccccccccccCCc
Confidence            778999  99999999999999   9999999   98711          1               01124578999999


Q ss_pred             ccccccccCCCCCcccccccccccCCC
Q 022898          101 NRLNSAEGCKFGDKCHFAHGEWELGKP  127 (290)
Q Consensus       101 ~~~~~~g~C~~G~~C~f~H~~~el~~~  127 (290)
                      ..|...|+|+||.+|-|+|+.+++..+
T Consensus       278 inwe~sGyc~yg~Rc~F~hgd~~~ie~  304 (351)
T COG5063         278 INWEKSGYCPYGLRCCFKHGDDSDIEM  304 (351)
T ss_pred             cchhhcccCccccccccccCChhhccc
Confidence            999999999999999999988655543

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

Probab=99.13  E-value=9.2e-11  Score=104.38  Aligned_cols=93  Identities=17%  Similarity=0.357  Sum_probs=55.5

Q ss_pred             CCccccccccccccCCCCCCCCCceEecccCCCchhhhhhc---cCCCCCC--CCCCCCCCC-------CCCCCCCCccc
Q 022898           29 GVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMM---NLPQAVP--APSRNMAVP-------PPASNGPTVVK   96 (290)
Q Consensus        29 ~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~---~~g~~~~--~~~~~~~~~-------s~~~~~~~~~k   96 (290)
                      ..+|||+-|.-|.+-+.|+++.+|-|.|.---..+...++.   +++....  ...++..+.       ......-+.++
T Consensus       148 ~~K~kt~slev~in~~~vp~s~~~~~~slP~t~~~~q~l~~rkpks~~~~~s~t~~kes~a~P~~~~~~~~~e~n~~L~k  227 (351)
T COG5063         148 HPKYKTESLEVFINPGYVPYSKRCCFISLPLTDINLQPLSQRKPKSGKNCTSYTLGKESDAHPHDELIYQKQEQNKPLYK  227 (351)
T ss_pred             CccccccceeEEecCCccccccccccccccccccCcchhhccCcccCcCccccccccccccCchhhhhhhhhhccchhhc
Confidence            67788888888888788888888888874211111111111   1110000  111111110       01223456677


Q ss_pred             c--cccccccccccCCC---CCccccc---ccc
Q 022898           97 S--RMCNRLNSAEGCKF---GDKCHFA---HGE  121 (290)
Q Consensus        97 t--r~C~~~~~~g~C~~---G~~C~f~---H~~  121 (290)
                      +  .+|.-|-..|.|+|   |.+|.|+   |+.
T Consensus       228 t~~~lc~~ft~kg~~p~~~sG~~~q~a~~~HGl  260 (351)
T COG5063         228 TNPELCESFTRKGTCPYWISGVKCQFACRGHGL  260 (351)
T ss_pred             CCHHHhhccCcCCCCcccccccccccccccccc
Confidence            7  89999999999999   9999999   864

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

Probab=99.10  E-value=2.2e-10  Score=110.29  Aligned_cols=78  Identities=33%  Similarity=0.536  Sum_probs=71.8

Q ss_pred             CCCceEEEEecccccceeeCCCCCchhhHHHhhCCceee-ccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCCC
Q 022898          162 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAH  239 (290)
Q Consensus       162 ~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v-~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~p  239 (290)
                      +.+.+.+|.||...||+||||+|++||.|+..||++|++ .+.++.+.+|.+.|.|+.++|.+|..+|.++|.+.+...
T Consensus       227 g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~  305 (600)
T KOG1676|consen  227 GGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGA  305 (600)
T ss_pred             cccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccC
Confidence            346689999999999999999999999999999999999 566677889999999999999999999999999988863

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

Probab=99.08  E-value=5.9e-10  Score=97.82  Aligned_cols=75  Identities=31%  Similarity=0.493  Sum_probs=70.3

Q ss_pred             CCCCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898          161 FGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  235 (290)
Q Consensus       161 ~~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~  235 (290)
                      .++..+.+|.||.++.|.||||||..|++|++++||+|.|.....+..+|+++|+|+.+||+.|+.++.+.+.+.
T Consensus       311 GGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~  385 (390)
T KOG2192|consen  311 GGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY  385 (390)
T ss_pred             CCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence            356899999999999999999999999999999999999998888889999999999999999999999988753

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.02  E-value=7.1e-10  Score=77.79  Aligned_cols=61  Identities=28%  Similarity=0.460  Sum_probs=55.4

Q ss_pred             eEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHH
Q 022898          166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMV  228 (290)
Q Consensus       166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I  228 (290)
                      +..+.||.++++.|||++|++|+.|++.+|+.|.+.+..  ..++.|+|+|+.+++..|..+|
T Consensus         1 ~~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i   61 (62)
T cd02394           1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEI   61 (62)
T ss_pred             CeEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHh
Confidence            357899999999999999999999999999999997655  5678899999999999999876

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.

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

Probab=98.98  E-value=1.7e-09  Score=75.95  Aligned_cols=62  Identities=35%  Similarity=0.597  Sum_probs=57.4

Q ss_pred             EEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHH
Q 022898          167 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMV  228 (290)
Q Consensus       167 ~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I  228 (290)
                      .++.||...++.|||++|++|+.|++.||+.|.|.....+..++.|.|.|+.+++..|..+|
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            67999999999999999999999999999999998766667889999999999999998876

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=98.97  E-value=2.8e-10  Score=79.31  Aligned_cols=60  Identities=43%  Similarity=0.635  Sum_probs=54.9

Q ss_pred             eEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHH
Q 022898          166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMV  228 (290)
Q Consensus       166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I  228 (290)
                      |.+|.||.+.++.|||++|++|+.|++.||+.|.+.+.  + ....+.|.|+.++++.|..+|
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 556999999999999999876

; 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=98.94  E-value=2.3e-09  Score=75.19  Aligned_cols=57  Identities=26%  Similarity=0.421  Sum_probs=52.1

Q ss_pred             eEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCC-HHHHHHHHHHH
Q 022898          166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGS-FEQIKQASAMV  228 (290)
Q Consensus       166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~-~~~i~~A~~~I  228 (290)
                      ...+.||.+.++.|||++|++|++|++.||+.|.|.+      ++.|.|.|+ .+.++.|..+|
T Consensus         3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCHHHHHHHHHHh
Confidence            5679999999999999999999999999999999976      257999998 99999999887

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.

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

Probab=98.92  E-value=2.8e-10  Score=109.56  Aligned_cols=153  Identities=20%  Similarity=0.235  Sum_probs=104.7

Q ss_pred             CCCchhhhhhccCCCCCCCCCCCCCCCC-CCCCCCCcccccccccccccccCCCCCcccccccccccCCCcccCCCCCCC
Q 022898           59 PGGYNAVAQMMNLPQAVPAPSRNMAVPP-PASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPRA  137 (290)
Q Consensus        59 ~~~~~~~~~~~~~g~~~~~~~~~~~~~s-~~~~~~~~~ktr~C~~~~~~g~C~~G~~C~f~H~~~el~~~~~~~~~~~~~  137 (290)
                      ++....+.+|++.|++|.-++.++++-- ---+-.+.+.+|.-.+.+....|-   .|  ++...||...+..       
T Consensus       236 VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie---~A--a~lI~eii~~~~~-------  303 (600)
T KOG1676|consen  236 VPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIE---HA--AELINEIIAEAEA-------  303 (600)
T ss_pred             ccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHH---HH--HHHHHHHHHHHhc-------
Confidence            4667778899999999988888777521 000111255667777777776665   33  3333333332111       


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCcCCCCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC--CCCCCcceeEEc
Q 022898          138 FGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH--EADPNLRNIELE  215 (290)
Q Consensus       138 ~~p~~~~~~~~~~~~~~p~~~~s~~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~--~~~~~~r~v~i~  215 (290)
                       ...++  .++..    |      +.-....|.||++++|+||||||++||+|+.+|||++++...  ..+..+|.|.|.
T Consensus       304 -~~~~~--~~~G~----P------~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~Ir  370 (600)
T KOG1676|consen  304 -GAGGG--MGGGA----P------GLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIR  370 (600)
T ss_pred             -cCCCC--cCCCC----c------cceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEe
Confidence             00011  11110    0      011278899999999999999999999999999999999543  456679999999


Q ss_pred             CCHHHHHHHHHHHHHHHHhcC
Q 022898          216 GSFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       216 G~~~~i~~A~~~I~~~i~~~~  236 (290)
                      |+..+|+.|..||..++-...
T Consensus       371 G~~~QIdhAk~LIr~kvg~~~  391 (600)
T KOG1676|consen  371 GDKRQIDHAKQLIRDKVGDIA  391 (600)
T ss_pred             cCcccchHHHHHHHHHhcccC
Confidence            999999999999999997643

>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=98.80  E-value=6e-10  Score=65.07  Aligned_cols=26  Identities=46%  Similarity=0.991  Sum_probs=21.9

Q ss_pred             cccccccccccCCCCCCCCCceEecc
Q 022898           32 SKSKPCTKFFSTAGCPFGESCHFLHY   57 (290)
Q Consensus        32 ~Kt~lC~~~~~~g~C~~G~~C~F~H~   57 (290)
                      |||++|++|+.+|.|+||++|+|+|+
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            79999999999999999999999996

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 ....

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

Probab=98.72  E-value=3.5e-08  Score=95.61  Aligned_cols=73  Identities=27%  Similarity=0.447  Sum_probs=68.0

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeec-cCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR-DHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~-~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~  236 (290)
                      ..+.+|.||.+.+|.||||+|..|++|++.|||+|+|. +..+...+|.|+|+|.+++|..|+..|...|.+..
T Consensus       137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~  210 (485)
T KOG2190|consen  137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENP  210 (485)
T ss_pred             ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcC
Confidence            46899999999999999999999999999999999995 44788889999999999999999999999999964

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

Probab=98.66  E-value=1.7e-08  Score=92.80  Aligned_cols=56  Identities=27%  Similarity=0.689  Sum_probs=50.0

Q ss_pred             ccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCC
Q 022898           31 GSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCK  110 (290)
Q Consensus        31 ~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~  110 (290)
                      ..++.+|++|++ |.|..||.|.|+|..                                  ...+-+.|.+|...|.|.
T Consensus        74 ~~~~~vcK~~l~-glC~kgD~C~Flhe~----------------------------------~~~k~rec~ff~~~g~c~  118 (325)
T KOG1040|consen   74 SRGKVVCKHWLR-GLCKKGDQCEFLHEY----------------------------------DLTKMRECKFFSLFGECT  118 (325)
T ss_pred             cCCceeehhhhh-hhhhccCcCcchhhh----------------------------------hhcccccccccccccccc
Confidence            678999999995 699999999999964                                  556677899999999999


Q ss_pred             CCCcccccccc
Q 022898          111 FGDKCHFAHGE  121 (290)
Q Consensus       111 ~G~~C~f~H~~  121 (290)
                      .+.+|.|.|+.
T Consensus       119 ~~~~c~y~h~d  129 (325)
T KOG1040|consen  119 NGKDCPYLHGD  129 (325)
T ss_pred             cccCCcccCCC
Confidence            99999999966

>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=98.64  E-value=3.1e-09  Score=62.01  Aligned_cols=26  Identities=62%  Similarity=1.364  Sum_probs=21.1

Q ss_pred             cccccCCCCC-CCCCCCCCCCcCCCCh
Q 022898          257 FKTKLCGNFA-KGSCTFGDRCHFAHGA  282 (290)
Q Consensus       257 ~k~~~C~~~~-~g~C~~g~~C~f~Hg~  282 (290)
                      ||+++|.+|. .|.|++|++|.|+|++
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            6889999999 6999999999999985

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 ....

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

Probab=98.62  E-value=8e-08  Score=86.81  Aligned_cols=74  Identities=23%  Similarity=0.362  Sum_probs=67.8

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC---CCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~---~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ...++|+||+-.+|.||||||.+|.+++.++|++|+++.+   -++..+|++.|+|+.+.+....+.|.++|.|...
T Consensus        38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~  114 (402)
T KOG2191|consen   38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQ  114 (402)
T ss_pred             ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHH
Confidence            4779999999999999999999999999999999999755   3888899999999999999999999999987544

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

Probab=98.60  E-value=9.2e-08  Score=88.90  Aligned_cols=75  Identities=27%  Similarity=0.276  Sum_probs=69.1

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC-CCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH-EADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA  238 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~-~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~  238 (290)
                      ..++++.||...||+|||+.|.+||+|...+||.|+|... -+|..+|.|.|+|.+++..+|+..|..+|.|....
T Consensus       410 ~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEenf~  485 (584)
T KOG2193|consen  410 QEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFF  485 (584)
T ss_pred             hhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccC
Confidence            6788999999999999999999999999999999999655 47778999999999999999999999999887665

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

Probab=98.57  E-value=3.3e-08  Score=94.62  Aligned_cols=77  Identities=25%  Similarity=0.473  Sum_probs=64.9

Q ss_pred             ccccCCCCCCCccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccc
Q 022898           20 KKSKHESESGVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRM   99 (290)
Q Consensus        20 ~~~~~~~~~~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~   99 (290)
                      .|.|..+..+..|.-..|+.|.+ |.|..||.|.|+|++.+-|                           ..|..|+|+.
T Consensus       222 EkARRRDPRkyhYs~tpCPefrk-G~C~rGD~CEyaHgvfEcw---------------------------LHPa~YRT~~  273 (528)
T KOG1595|consen  222 EKARRRDPRKYHYSSTPCPEFRK-GSCERGDSCEYAHGVFECW---------------------------LHPARYRTRK  273 (528)
T ss_pred             cccccCCcccccccCccCccccc-CCCCCCCccccccceehhh---------------------------cCHHHhcccc
Confidence            34555788899999999999986 7999999999999985533                           4678999999


Q ss_pred             cccccccccCCCCCcccccccccccCCCc
Q 022898          100 CNRLNSAEGCKFGDKCHFAHGEWELGKPI  128 (290)
Q Consensus       100 C~~~~~~g~C~~G~~C~f~H~~~el~~~~  128 (290)
                      |+-   .++|+- .-|.|||..++||...
T Consensus       274 CkD---g~~C~R-rvCfFAH~~eqLR~l~  298 (528)
T KOG1595|consen  274 CKD---GGYCPR-RVCFFAHSPEQLRPLP  298 (528)
T ss_pred             ccC---CCCCcc-ceEeeecChHHhcccC
Confidence            974   489996 9999999999997653

>PF13014 KH_3: KH domain

Probab=98.55  E-value=1.1e-07  Score=61.76  Aligned_cols=42  Identities=43%  Similarity=0.692  Sum_probs=37.5

Q ss_pred             ccceeeCCCCCchhhHHHhhCCceeecc-CCCCCCcceeEEcC
Q 022898          175 LAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEG  216 (290)
Q Consensus       175 ~vg~iIGkgG~~Ik~i~~~sga~i~v~~-~~~~~~~r~v~i~G  216 (290)
                      ++|+|||++|++|++|+++|+++|+|.+ ..++..++.|+|+|
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            4789999999999999999999999977 56677789999987

>smart00322 KH K homology RNA-binding domain

Probab=98.51  E-value=5.1e-07  Score=63.22  Aligned_cols=66  Identities=32%  Similarity=0.562  Sum_probs=58.1

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHH
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI  232 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i  232 (290)
                      .+.++.||...++.+||++|.+|+.|++.+++.|.+.....  ....+.|.|..+++..|..+|...+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHh
Confidence            46789999999999999999999999999999999964332  5678999999999999999887764

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

Probab=98.37  E-value=2.3e-07  Score=88.85  Aligned_cols=31  Identities=32%  Similarity=0.715  Sum_probs=28.0

Q ss_pred             cccccccCCCCCCCCCCCCCCCcCCCChhhhccc
Q 022898          255 SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKT  288 (290)
Q Consensus       255 ~~~k~~~C~~~~~g~C~~g~~C~f~Hg~~el~~~  288 (290)
                      ..|||++|+.=  |+|+. --|.|||..+|||..
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            57999999985  89998 889999999999975

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

Probab=98.35  E-value=4.9e-07  Score=84.18  Aligned_cols=71  Identities=27%  Similarity=0.424  Sum_probs=66.1

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceee-ccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHh
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRNIELEGSFEQIKQASAMVRELIVR  234 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v-~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~  234 (290)
                      .-..++.||..++|+|||+.|++|++|..+|.++|.| +....+..++.++|.+++|....|..+|.++|..
T Consensus       198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqk  269 (584)
T KOG2193|consen  198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQK  269 (584)
T ss_pred             CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHH
Confidence            5678999999999999999999999999999999999 5667888899999999999999999999999864

>smart00356 ZnF_C3H1 zinc finger

Probab=98.27  E-value=4.4e-07  Score=52.64  Aligned_cols=26  Identities=35%  Similarity=0.851  Sum_probs=23.4

Q ss_pred             ccccccccccccCCCCCCCCCceEecc
Q 022898           31 GSKSKPCTKFFSTAGCPFGESCHFLHY   57 (290)
Q Consensus        31 ~~Kt~lC~~~~~~g~C~~G~~C~F~H~   57 (290)
                      .+|+.+|++| .+|.|++|++|.|+|+
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            3689999999 6789999999999996

>smart00356 ZnF_C3H1 zinc finger

Probab=98.22  E-value=7.7e-07  Score=51.59  Aligned_cols=26  Identities=54%  Similarity=1.212  Sum_probs=23.7

Q ss_pred             cccccCCCCCCCCCCCCCCCcCCCCh
Q 022898          257 FKTKLCGNFAKGSCTFGDRCHFAHGA  282 (290)
Q Consensus       257 ~k~~~C~~~~~g~C~~g~~C~f~Hg~  282 (290)
                      +|+.+|.+|.+|.|.+|++|.|+|..
T Consensus         2 ~k~~~C~~~~~g~C~~g~~C~~~H~~   27 (27)
T smart00356        2 YKTELCKFFKRGYCPYGDRCKFAHPL   27 (27)
T ss_pred             CCCCcCcCccCCCCCCCCCcCCCCcC
Confidence            57889999999999999999999973

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

Probab=98.11  E-value=5.9e-07  Score=85.22  Aligned_cols=61  Identities=25%  Similarity=0.644  Sum_probs=45.5

Q ss_pred             ccccccccccC--CCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCC
Q 022898           33 KSKPCTKFFST--AGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCK  110 (290)
Q Consensus        33 Kt~lC~~~~~~--g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~  110 (290)
                      +-.||+....+  ..|+|||+|+|.|++ +-|-                         ..+++... --|.+|.+.|.|+
T Consensus        75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi-~ayL-------------------------atK~~Dig-~~Cp~f~s~G~Cp  127 (614)
T KOG2333|consen   75 QNRLCPSLIQGDISKCSFGDNCRFVHDI-EAYL-------------------------ATKAPDIG-PSCPVFESLGFCP  127 (614)
T ss_pred             hhccChHhhcCCCccCcccccccccccH-HHHH-------------------------hccCcccC-CccceeeccccCC
Confidence            46899999988  689999999999986 1111                         01122222 2499999999999


Q ss_pred             CCCccccccc
Q 022898          111 FGDKCHFAHG  120 (290)
Q Consensus       111 ~G~~C~f~H~  120 (290)
                      ||.+|||+-.
T Consensus       128 ~G~~CRFl~a  137 (614)
T KOG2333|consen  128 YGFKCRFLGA  137 (614)
T ss_pred             ccceeehhhc
Confidence            9999999743

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.04  E-value=4.5e-06  Score=70.66  Aligned_cols=61  Identities=25%  Similarity=0.421  Sum_probs=53.5

Q ss_pred             EEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEE---cCCHHHHHHHHHHHHHHHHh
Q 022898          169 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIEL---EGSFEQIKQASAMVRELIVR  234 (290)
Q Consensus       169 i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i---~G~~~~i~~A~~~I~~~i~~  234 (290)
                      +.||.+.+++|||++|++|+.|++.+|++|+|.+.     ...|.|   +++++++..|..+|..+...
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~i~kA~~~I~~i~~g   65 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAVMKAREVVKAIGRG   65 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence            57899999999999999999999999999999753     245666   88999999999999987653

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=98.02  E-value=1.6e-05  Score=63.31  Aligned_cols=63  Identities=27%  Similarity=0.380  Sum_probs=49.1

Q ss_pred             cccceeeCCCCCchhhHHHhhCCceeeccCCCCC-----------------CcceeEEcC-C--HHHHHHHHHHHHHHHH
Q 022898          174 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADP-----------------NLRNIELEG-S--FEQIKQASAMVRELIV  233 (290)
Q Consensus       174 ~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~-----------------~~r~v~i~G-~--~~~i~~A~~~I~~~i~  233 (290)
                      .++|.|||.+|.+|++|++.||++|.|.......                 ..--|.|++ +  .+.++.|..+|..++.
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            5778999999999999999999999997542110                 113466666 5  6999999999999988


Q ss_pred             hcC
Q 022898          234 RIG  236 (290)
Q Consensus       234 ~~~  236 (290)
                      ...
T Consensus        95 ~~~   97 (120)
T cd02395          95 PAI   97 (120)
T ss_pred             cCC
Confidence            443

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.

>PRK13763 putative RNA-processing protein; Provisional

Probab=97.96  E-value=1.3e-05  Score=68.46  Aligned_cols=64  Identities=22%  Similarity=0.309  Sum_probs=56.4

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEE----cCCHHHHHHHHHHHHHHHH
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIEL----EGSFEQIKQASAMVRELIV  233 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i----~G~~~~i~~A~~~I~~~i~  233 (290)
                      ....+.||.+.++.|||++|.+|+.|++.+|++|+|.+.     ...|.|    +++++++.+|..+|..++.
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i~kA~~~I~ai~~   70 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAVLKARDIVKAIGR   70 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence            357899999999999999999999999999999999753     245666    5899999999999998876

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

Probab=97.91  E-value=3e-06  Score=73.06  Aligned_cols=72  Identities=22%  Similarity=0.495  Sum_probs=52.9

Q ss_pred             CCCCCccccccCCCCCCCccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCC
Q 022898           13 INANGVFKKSKHESESGVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGP   92 (290)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~   92 (290)
                      ++..-.-||+|+-.|-+-.....-|+||..+|.|-.|..|+|.|.                                   
T Consensus       185 nnksyllkkkrflkevgnspsavycryynangicgkgaacrfvhe-----------------------------------  229 (377)
T KOG1492|consen  185 NNKSYLLKKKRFLKEVGNSPSAVYCRYYNANGICGKGAACRFVHE-----------------------------------  229 (377)
T ss_pred             cChhHHHHHHHHHHHhCCCCceeEEEEecCCCcccCCceeeeecc-----------------------------------
Confidence            333334456665555555556778999999999999999999995                                   


Q ss_pred             CcccccccccccccccCCCCCcccccccc
Q 022898           93 TVVKSRMCNRLNSAEGCKFGDKCHFAHGE  121 (290)
Q Consensus        93 ~~~ktr~C~~~~~~g~C~~G~~C~f~H~~  121 (290)
                      +..|| +|.+|.. |.|...++|...|..
T Consensus       230 ptrkt-icpkfln-grcnkaedcnlshel  256 (377)
T KOG1492|consen  230 PTRKT-ICPKFLN-GRCNKAEDCNLSHEL  256 (377)
T ss_pred             ccccc-cChHHhc-CccCchhcCCccccc
Confidence            33343 7998865 689999999999944

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=97.76  E-value=3.7e-05  Score=65.07  Aligned_cols=55  Identities=29%  Similarity=0.469  Sum_probs=49.7

Q ss_pred             cccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898          174 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  235 (290)
Q Consensus       174 ~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~  235 (290)
                      ..+|.|||++|.+++.|+..||+.|+|.+       +.|.|.|++++++.|..+|..++...
T Consensus        98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665        98 RIKGRIIGEGGKTRRIIEELTGVSISVYG-------KTVGIIGDPEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             HHHhhhcCCCcHHHHHHHHHHCCeEEEcC-------CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence            36889999999999999999999999974       57999999999999999999988544

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.

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

Probab=97.74  E-value=0.00012  Score=71.25  Aligned_cols=74  Identities=22%  Similarity=0.253  Sum_probs=67.0

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC---------CHHHHHHHHHHHHHHHHh
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG---------SFEQIKQASAMVRELIVR  234 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G---------~~~~i~~A~~~I~~~i~~  234 (290)
                      ..+.|+..+...+|.||||.|..|++|+..+.++|.|.+...+..+|+|+|+|         ..+++.+|..+|...+.+
T Consensus        42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~  121 (485)
T KOG2190|consen   42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEE  121 (485)
T ss_pred             cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcccc
Confidence            44579999999999999999999999999999999999999999999999999         999999999999887664


Q ss_pred             cCC
Q 022898          235 IGP  237 (290)
Q Consensus       235 ~~~  237 (290)
                      .+.
T Consensus       122 d~~  124 (485)
T KOG2190|consen  122 DDE  124 (485)
T ss_pred             ccc
Confidence            333

>PRK13763 putative RNA-processing protein; Provisional

Probab=97.57  E-value=9.6e-05  Score=63.02  Aligned_cols=55  Identities=29%  Similarity=0.475  Sum_probs=48.7

Q ss_pred             cccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898          174 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  235 (290)
Q Consensus       174 ~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~  235 (290)
                      ...|.|||++|.+++.|++.||++|+|.+       +.+.|.|+++++..|...|..++...
T Consensus       104 r~~griIG~~G~~~k~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        104 RIKGRIIGEGGKTRRIIEELTGVDISVYG-------KTVAIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             HHhhheeCCCcHHHHHHHHHHCcEEEEcC-------CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence            36789999999999999999999999974       24889999999999999999988443

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

Probab=97.45  E-value=7.9e-05  Score=68.77  Aligned_cols=53  Identities=25%  Similarity=0.494  Sum_probs=44.8

Q ss_pred             cccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCCC
Q 022898           32 SKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKF  111 (290)
Q Consensus        32 ~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~~  111 (290)
                      .|+..|.+|...|.|..+.+|.|.|+.                                  +.++-+.|. |+..|.|.-
T Consensus       103 ~k~rec~ff~~~g~c~~~~~c~y~h~d----------------------------------pqt~~k~c~-~~~~g~c~~  147 (325)
T KOG1040|consen  103 TKMRECKFFSLFGECTNGKDCPYLHGD----------------------------------PQTAIKKCK-WYKEGFCRG  147 (325)
T ss_pred             cccccccccccccccccccCCcccCCC----------------------------------hhhhhhccc-hhhhccCCC
Confidence            356689999999999999999999974                                  344556785 778899999


Q ss_pred             CCcccccc
Q 022898          112 GDKCHFAH  119 (290)
Q Consensus       112 G~~C~f~H  119 (290)
                      |..|++.|
T Consensus       148 g~~c~~~h  155 (325)
T KOG1040|consen  148 GPSCKKRH  155 (325)
T ss_pred             cchhhhhh
Confidence            99999999

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

Probab=97.44  E-value=0.00011  Score=65.16  Aligned_cols=72  Identities=22%  Similarity=0.363  Sum_probs=63.9

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC-CCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH-EADPNLRNIELEGSFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~-~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~  236 (290)
                      -.++++|.++++|.|||+.|+.||++++.+.|+++|... -+...+|++.|.|.+..|-.....|...+.+.+
T Consensus       123 ce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~p  195 (390)
T KOG2192|consen  123 CELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESP  195 (390)
T ss_pred             hhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCC
Confidence            357899999999999999999999999999999999654 577889999999999999888888888887653

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

Probab=97.42  E-value=0.0002  Score=64.82  Aligned_cols=58  Identities=28%  Similarity=0.541  Sum_probs=46.1

Q ss_pred             ccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCC
Q 022898           31 GSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCK  110 (290)
Q Consensus        31 ~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~  110 (290)
                      .+....|++|.. |.|+-++.|.|+|+...                               -.. ..-.|..|...|.|.
T Consensus       101 ~~s~V~c~~~~~-g~c~s~~~c~~lh~~d~-------------------------------~~s-~~~~c~~Fs~~G~cs  147 (285)
T COG5084         101 LSSSVVCKFFLR-GLCKSGFSCEFLHEYDL-------------------------------RSS-QGPPCRSFSLKGSCS  147 (285)
T ss_pred             ccCCcccchhcc-ccCcCCCccccccCCCc-------------------------------ccc-cCCCcccccccceec
Confidence            578899998885 69999999999997511                               010 234699999999999


Q ss_pred             CCCcccccccc
Q 022898          111 FGDKCHFAHGE  121 (290)
Q Consensus       111 ~G~~C~f~H~~  121 (290)
                      .|..|.|.|..
T Consensus       148 ~g~~c~~~h~d  158 (285)
T COG5084         148 SGPSCGYSHID  158 (285)
T ss_pred             cCCCCCccccC
Confidence            99999999954

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.20  E-value=0.00063  Score=68.88  Aligned_cols=65  Identities=23%  Similarity=0.306  Sum_probs=56.8

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHh
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVR  234 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~  234 (290)
                      -....+.||.+.++.|||.||.+|+.|++.||+.|.|.+      +..|.|.+ +.++++.|..+|..++..
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 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            456789999999999999999999999999999999976      24566666 789999999999998884

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.

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

Probab=97.18  E-value=0.00012  Score=65.56  Aligned_cols=32  Identities=34%  Similarity=0.654  Sum_probs=26.9

Q ss_pred             CCCCCccccccccccccCCCCCCCCCceEeccc
Q 022898           26 SESGVGSKSKPCTKFFSTAGCPFGESCHFLHYF   58 (290)
Q Consensus        26 ~~~~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~   58 (290)
                      .+..+-.|+.+|.+|. .|.|..|++|+|+|++
T Consensus        84 v~~gvDPKSvvCafFk-~g~C~KG~kCKFsHdl  115 (343)
T KOG1763|consen   84 VPKGVDPKSVVCAFFK-QGTCTKGDKCKFSHDL  115 (343)
T ss_pred             cccCCCchHHHHHHHh-ccCCCCCCcccccchH
Confidence            3347788999997665 5799999999999997

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

Probab=97.06  E-value=0.00013  Score=63.44  Aligned_cols=82  Identities=23%  Similarity=0.478  Sum_probs=48.8

Q ss_pred             CCccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCC----CCCCCCCCCCCCCCCCccccccccccc
Q 022898           29 GVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPA----PSRNMAVPPPASNGPTVVKSRMCNRLN  104 (290)
Q Consensus        29 ~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~----~~~~~~~~s~~~~~~~~~ktr~C~~~~  104 (290)
                      .+-.|+..|.-|. .+.|..|+.|+|+|+.-          +.+.+...    .-++....-+-...|--...++|.+|.
T Consensus        80 gvdpK~~vcalF~-~~~c~kg~~ckF~h~~e----------e~r~~eK~DLYsDvRd~~ed~pl~krP~intd~VCkffi  148 (299)
T COG5252          80 GVDPKTVVCALFL-NKTCAKGDACKFAHGKE----------EARKTEKPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFI  148 (299)
T ss_pred             ccCchhHHHHHhc-cCccccCchhhhhcchH----------HHhhhcccchhhhhhhhhccCCcccCCCCChhHHHHHHH
Confidence            6778999998777 57999999999999851          11111000    000000000111223344567898763


Q ss_pred             ------ccc---cCCCC-Ccccccccc
Q 022898          105 ------SAE---GCKFG-DKCHFAHGE  121 (290)
Q Consensus       105 ------~~g---~C~~G-~~C~f~H~~  121 (290)
                            ..|   .|++| .+|-|.|.-
T Consensus       149 eA~e~GkYgw~W~CPng~~~C~y~H~L  175 (299)
T COG5252         149 EAMESGKYGWGWTCPNGNMRCSYIHKL  175 (299)
T ss_pred             HHHhcCCccceeeCCCCCceeeeeecc
Confidence                  222   79996 799999954

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

Probab=96.96  E-value=0.0014  Score=61.93  Aligned_cols=72  Identities=21%  Similarity=0.316  Sum_probs=55.5

Q ss_pred             cCCCCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHh
Q 022898          160 SFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR  234 (290)
Q Consensus       160 s~~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~  234 (290)
                      ..+.....-+.|-+.+||.|||+||++|+.||..++++|+|..-+...   .|.|-|.-..-.+|...|...+..
T Consensus        42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~---kv~ifg~~~m~~kaka~id~~~~k  113 (629)
T KOG0336|consen   42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEV---KVTIFGINHMRKKAKASIDRGQDK  113 (629)
T ss_pred             cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCcee---EEEEechHHHHHHHHhhHhhhhhh
Confidence            444577788899999999999999999999999999999997655443   455667666666666666555543

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

Probab=96.90  E-value=0.0004  Score=63.28  Aligned_cols=64  Identities=19%  Similarity=0.390  Sum_probs=42.0

Q ss_pred             CccccccccccccCCCCCCCCC-ceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCccccccccccccccc
Q 022898           30 VGSKSKPCTKFFSTAGCPFGES-CHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEG  108 (290)
Q Consensus        30 ~~~Kt~lC~~~~~~g~C~~G~~-C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~  108 (290)
                      .+..-..|+.|+++ .|..||. |+|+|..  ..-.   +                        .+-+---| +-.+.|.
T Consensus        33 ~wl~~eVCReF~rn-~C~R~d~~CkfaHP~--~~~~---V------------------------~~g~v~aC-~Ds~kgr   81 (331)
T KOG2494|consen   33 KWLTLEVCREFLRN-TCSRGDRECKFAHPP--KNCQ---V------------------------SNGRVIAC-FDSQKGR   81 (331)
T ss_pred             chhHHHHHHHHHhc-cccCCCccccccCCC--CCCC---c------------------------cCCeEEEE-eccccCc
Confidence            44456899999975 9999999 9999953  1000   0                        00011136 4456778


Q ss_pred             CCCCCcccccccccccC
Q 022898          109 CKFGDKCHFAHGEWELG  125 (290)
Q Consensus       109 C~~G~~C~f~H~~~el~  125 (290)
                      |. .++|+|+|.-.+++
T Consensus        82 Cs-R~nCkylHpp~hlk   97 (331)
T KOG2494|consen   82 CS-RENCKYLHPPQHLK   97 (331)
T ss_pred             cC-cccceecCCChhhh
Confidence            98 57799999765543

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

Probab=96.72  E-value=0.0012  Score=35.04  Aligned_cols=19  Identities=42%  Similarity=0.812  Sum_probs=16.4

Q ss_pred             cCCCCCCCCCCCCCCCcCCCC
Q 022898          261 LCGNFAKGSCTFGDRCHFAHG  281 (290)
Q Consensus       261 ~C~~~~~g~C~~g~~C~f~Hg  281 (290)
                      +|+||..  |+++++|.|.|+
T Consensus         1 ~Ck~~~~--C~~~~~C~f~HP   19 (19)
T PF14608_consen    1 PCKFGPN--CTNGDNCPFSHP   19 (19)
T ss_pred             CCcCcCC--CCCCCcCccCCc
Confidence            4888774  999999999995

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=96.64  E-value=0.0024  Score=65.18  Aligned_cols=66  Identities=23%  Similarity=0.388  Sum_probs=54.1

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEc-CCHHHHHHHHHHHHHHHHhc
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE-GSFEQIKQASAMVRELIVRI  235 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~-G~~~~i~~A~~~I~~~i~~~  235 (290)
                      -....+.||.+.++.|||+||.+|+.|.++||+.|.|.+.      ..|.|. .+.+.++.|..+|..+....
T Consensus       550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd------G~V~i~~~~~~~~~~a~~~I~~~~~~~  616 (684)
T TIGR03591       550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD------GTVKIAASDGEAAEAAIKMIEGITAEP  616 (684)
T ss_pred             CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC------eEEEEEECcHHHHHHHHHHHHhhhccc
Confidence            3456799999999999999999999999999999999752      233443 46788999999998886643

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).

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

Probab=96.55  E-value=0.0053  Score=58.88  Aligned_cols=74  Identities=31%  Similarity=0.443  Sum_probs=56.5

Q ss_pred             CceEEEEecc------cccceeeCCCCCchhhHHHhhCCceeeccCC---------CC--------CCcceeEEcCCHHH
Q 022898          164 SATAKISVDA------SLAGAIIGKGGVNSKQICRQTGAKLSIRDHE---------AD--------PNLRNIELEGSFEQ  220 (290)
Q Consensus       164 ~~t~~i~VP~------~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~---------~~--------~~~r~v~i~G~~~~  220 (290)
                      ..+.+|.||.      .+||+|||..|.+.|.+..+|||+|.|....         .+        ..........+.|.
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek  216 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK  216 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence            3456666654      6899999999999999999999999996521         10        11244556668999


Q ss_pred             HHHHHHHHHHHHHhcCC
Q 022898          221 IKQASAMVRELIVRIGP  237 (290)
Q Consensus       221 i~~A~~~I~~~i~~~~~  237 (290)
                      |++|+.+|.++|.+.-.
T Consensus       217 i~~Ai~vienli~~av~  233 (554)
T KOG0119|consen  217 IKKAIAVIENLIQSAVS  233 (554)
T ss_pred             HHHHHHHHHHHHHhhcc
Confidence            99999999999987433

>KOG4791 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.52  E-value=0.0014  Score=62.34  Aligned_cols=22  Identities=14%  Similarity=-0.245  Sum_probs=20.1

Q ss_pred             cCCCCCCCCCCCCCCCcCCCCh
Q 022898          261 LCGNFAKGSCTFGDRCHFAHGA  282 (290)
Q Consensus       261 ~C~~~~~g~C~~g~~C~f~Hg~  282 (290)
                      .|.+|..+.|.-+|.|.|.|.-
T Consensus       120 P~l~~~K~~e~~~D~~s~Lh~P  141 (667)
T KOG4791|consen  120 PQLRSVKKVESSEDVPSPLHPP  141 (667)
T ss_pred             hHHHHhhhhhhhccccccCCCC
Confidence            5999999999999999999974

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

Probab=96.22  E-value=0.0072  Score=42.08  Aligned_cols=37  Identities=32%  Similarity=0.515  Sum_probs=33.9

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceee
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI  200 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v  200 (290)
                      .....+.|+.+.++.+|||+|.+|+.++..++..|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3678999999999999999999999999999988776

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.

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

Probab=96.14  E-value=0.0019  Score=60.35  Aligned_cols=26  Identities=42%  Similarity=1.028  Sum_probs=22.9

Q ss_pred             ccccCCCCCCCCCCCCCCCcCCCChh
Q 022898          258 KTKLCGNFAKGSCTFGDRCHFAHGAA  283 (290)
Q Consensus       258 k~~~C~~~~~g~C~~g~~C~f~Hg~~  283 (290)
                      ...+|+||..|.|+|+.+|+|.||..
T Consensus       139 sMkpC~ffLeg~CRF~enCRfSHG~~  164 (486)
T KOG2185|consen  139 SMKPCKFFLEGRCRFGENCRFSHGLD  164 (486)
T ss_pred             hhccchHhhccccccCcccccccCcc
Confidence            34569999999999999999999963

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

Probab=96.11  E-value=0.002  Score=60.27  Aligned_cols=25  Identities=44%  Similarity=1.015  Sum_probs=22.1

Q ss_pred             ccccccccccCCCCCCCCCceEeccc
Q 022898           33 KSKPCTKFFSTAGCPFGESCHFLHYF   58 (290)
Q Consensus        33 Kt~lC~~~~~~g~C~~G~~C~F~H~~   58 (290)
                      -+++|+||+. |.|+|+++|+|.|++
T Consensus       139 sMkpC~ffLe-g~CRF~enCRfSHG~  163 (486)
T KOG2185|consen  139 SMKPCKFFLE-GRCRFGENCRFSHGL  163 (486)
T ss_pred             hhccchHhhc-cccccCcccccccCc
Confidence            3689999884 699999999999996

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

Probab=96.07  E-value=0.0032  Score=33.39  Aligned_cols=19  Identities=37%  Similarity=0.775  Sum_probs=15.5

Q ss_pred             cccccccCCCCCCCCCceEecc
Q 022898           36 PCTKFFSTAGCPFGESCHFLHY   57 (290)
Q Consensus        36 lC~~~~~~g~C~~G~~C~F~H~   57 (290)
                      +|++|.   .|+++++|.|.|.
T Consensus         1 ~Ck~~~---~C~~~~~C~f~HP   19 (19)
T PF14608_consen    1 PCKFGP---NCTNGDNCPFSHP   19 (19)
T ss_pred             CCcCcC---CCCCCCcCccCCc
Confidence            587554   4999999999994

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

Probab=96.01  E-value=0.0034  Score=57.35  Aligned_cols=26  Identities=27%  Similarity=0.703  Sum_probs=22.4

Q ss_pred             cCCCCCCCCCCCCCCCcCCCChhhhcc
Q 022898          261 LCGNFAKGSCTFGDRCHFAHGAAELRK  287 (290)
Q Consensus       261 ~C~~~~~g~C~~g~~C~f~Hg~~el~~  287 (290)
                      -|-.+.+|.|.. ++|+|+|+-.+|+.
T Consensus        73 aC~Ds~kgrCsR-~nCkylHpp~hlkd   98 (331)
T KOG2494|consen   73 ACFDSQKGRCSR-ENCKYLHPPQHLKD   98 (331)
T ss_pred             EEeccccCccCc-ccceecCCChhhhh
Confidence            499999999995 57999999988864

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=95.93  E-value=0.0084  Score=62.26  Aligned_cols=69  Identities=19%  Similarity=0.374  Sum_probs=57.5

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCc-eeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHhcCCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAK-LSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGPA  238 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~-i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~~~~~  238 (290)
                      -....+.||.+.++.|||.||.+|+.|.+++|+. |.|.+.      -.|.|.+ +.+.++.|..+|.+++.....+
T Consensus       684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd------g~V~I~a~d~~~i~~A~~~I~~l~~~~~vG  754 (891)
T PLN00207        684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD------GTVKITAKDLSSLEKSKAIISSLTMVPTVG  754 (891)
T ss_pred             CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC------eeEEEEeCCHHHHHHHHHHHHHHhcCcCCC
Confidence            4567899999999999999999999999999999 888762      3445555 8899999999999998765443

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

Probab=95.74  E-value=0.014  Score=58.32  Aligned_cols=69  Identities=23%  Similarity=0.392  Sum_probs=58.2

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHhcCCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGPA  238 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~~~~~  238 (290)
                      -.-..+.|+.+.+.-+||+||.+|+.|.+.+|++|+|.+.      ..|.|.+ +.+.+..|...|.++..+.+.+
T Consensus       551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd------Gtv~i~~s~~~~~~~ak~~I~~i~~e~evg  620 (692)
T COG1185         551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD------GTVKIAASDGESAKKAKERIEAITREVEVG  620 (692)
T ss_pred             CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC------CcEEEEecchHHHHHHHHHHHHHHhhcccc
Confidence            4557789999999999999999999999999999999732      2455555 4588999999999999888775

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

Probab=95.37  E-value=0.032  Score=50.76  Aligned_cols=67  Identities=16%  Similarity=0.305  Sum_probs=57.4

Q ss_pred             CCCCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHH
Q 022898          161 FGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRE  230 (290)
Q Consensus       161 ~~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~  230 (290)
                      ++...+..+.||...|+.|+|++|..||.++..|...|.....+   .+-+|.++|-.+.+++|...|..
T Consensus        22 ~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~edv~~aRrei~s   88 (394)
T KOG2113|consen   22 IGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHEDVRRARREIPS   88 (394)
T ss_pred             CCCccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCchhHHHHhhcCcc
Confidence            34577889999999999999999999999999999999875443   34789999999999999877755

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

Probab=95.29  E-value=0.0077  Score=51.30  Aligned_cols=28  Identities=32%  Similarity=0.772  Sum_probs=24.8

Q ss_pred             ccccccccccccCCCCCCCCCceEeccc
Q 022898           31 GSKSKPCTKFFSTAGCPFGESCHFLHYF   58 (290)
Q Consensus        31 ~~Kt~lC~~~~~~g~C~~G~~C~F~H~~   58 (290)
                      -|.-..|+-|..+|.|-|||.|+|+|..
T Consensus       138 D~qpdVCKdyk~TGYCGYGDsCKflH~R  165 (259)
T COG5152         138 DTQPDVCKDYKETGYCGYGDSCKFLHDR  165 (259)
T ss_pred             ecCcccccchhhcccccCCchhhhhhhh
Confidence            3556799999999999999999999974

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

Probab=95.18  E-value=0.011  Score=56.97  Aligned_cols=25  Identities=40%  Similarity=1.030  Sum_probs=20.9

Q ss_pred             ccccccccccc--ccCCCCCccccccc
Q 022898           96 KSRMCNRLNSA--EGCKFGDKCHFAHG  120 (290)
Q Consensus        96 ktr~C~~~~~~--g~C~~G~~C~f~H~  120 (290)
                      +-++|.-.-+.  ..|.||++|+|.|.
T Consensus        75 ~n~LCPsli~g~~~~C~f~d~Crf~HD  101 (614)
T KOG2333|consen   75 QNRLCPSLIQGDISKCSFGDNCRFVHD  101 (614)
T ss_pred             hhccChHhhcCCCccCccccccccccc
Confidence            56789877666  69999999999994

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

Probab=94.73  E-value=0.073  Score=45.52  Aligned_cols=55  Identities=31%  Similarity=0.466  Sum_probs=48.2

Q ss_pred             cceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          176 AGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       176 vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      .|-|||++|.+-+.|.+.|++.|.|.+       ..|.|-|.+++++.|...|..++.-...
T Consensus       113 kgRIIG~~GkTr~~IE~lt~~~I~V~g-------~tVaiiG~~~~v~iAr~AVemli~G~~h  167 (194)
T COG1094         113 KGRIIGREGKTRRAIEELTGVYISVYG-------KTVAIIGGFEQVEIAREAVEMLINGAPH  167 (194)
T ss_pred             hceeeCCCchHHHHHHHHhCCeEEEeC-------cEEEEecChhhhHHHHHHHHHHHcCCCc
Confidence            356999999999999999999999976       3699999999999999999888765543

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

Probab=94.48  E-value=0.017  Score=56.22  Aligned_cols=74  Identities=24%  Similarity=0.422  Sum_probs=65.7

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      .......+|...++.|+|++|..|.+|+..++|+|.+..+..+...+.+.|.+.......|..++.+.+.+.+.
T Consensus       139 pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edee  212 (608)
T KOG2279|consen  139 PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEE  212 (608)
T ss_pred             cccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhH
Confidence            56677889999999999999999999999999999999887777789999999998888999999888875543

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

Probab=94.44  E-value=0.029  Score=48.76  Aligned_cols=52  Identities=21%  Similarity=0.557  Sum_probs=38.5

Q ss_pred             ccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCCCC
Q 022898           33 KSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFG  112 (290)
Q Consensus        33 Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~~G  112 (290)
                      +..+|++|+ +|.|...+.|...|.+.+                                 . .-..|++|. .|.|. .
T Consensus       232 rkticpkfl-ngrcnkaedcnlsheldp---------------------------------r-ripacryfl-lgkcn-n  274 (377)
T KOG1492|consen  232 RKTICPKFL-NGRCNKAEDCNLSHELDP---------------------------------R-RIPACRYFL-LGKCN-N  274 (377)
T ss_pred             ccccChHHh-cCccCchhcCCcccccCc---------------------------------c-ccchhhhhh-hccCC-C
Confidence            456899999 579999999999998721                                 1 112487664 57887 5


Q ss_pred             Ccccccccc
Q 022898          113 DKCHFAHGE  121 (290)
Q Consensus       113 ~~C~f~H~~  121 (290)
                      ..|+|.|..
T Consensus       275 pncryvhih  283 (377)
T KOG1492|consen  275 PNCRYVHIH  283 (377)
T ss_pred             CCceEEEEe
Confidence            799999954

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

Probab=94.06  E-value=0.022  Score=48.62  Aligned_cols=31  Identities=26%  Similarity=0.860  Sum_probs=25.9

Q ss_pred             cccccccCCCCC-CCCCCCCCCCcCCCChhhh
Q 022898          255 SNFKTKLCGNFA-KGSCTFGDRCHFAHGAAEL  285 (290)
Q Consensus       255 ~~~k~~~C~~~~-~g~C~~g~~C~f~Hg~~el  285 (290)
                      -.|....|..|. +|+|-||+.|.|.|.-++.
T Consensus       137 iD~qpdVCKdyk~TGYCGYGDsCKflH~R~D~  168 (259)
T COG5152         137 IDTQPDVCKDYKETGYCGYGDSCKFLHDRSDF  168 (259)
T ss_pred             eecCcccccchhhcccccCCchhhhhhhhhhh
Confidence            345566799998 9999999999999987654

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

Probab=93.62  E-value=0.073  Score=51.93  Aligned_cols=74  Identities=26%  Similarity=0.395  Sum_probs=61.9

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA  238 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~  238 (290)
                      .....+.|+...|..|||++|++|+.+...++++|.+.+.+.+ .++.-.++|-+.++..|...+.+++.+.+..
T Consensus        67 ~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-~e~~~~~~~~p~~v~~a~a~~~~~~~~~~pv  140 (608)
T KOG2279|consen   67 DIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-DERVLLISGFPVQVCKAKAAIHQILTENTPV  140 (608)
T ss_pred             heeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-cccchhhccCCCCCChHHHHHHHHHhcCCcc
Confidence            5678899999999999999999999999999999999754333 3456666778888889999999998877665

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=93.22  E-value=0.087  Score=54.05  Aligned_cols=66  Identities=21%  Similarity=0.363  Sum_probs=53.4

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHhcC
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~~~  236 (290)
                      ....+.|+.+.++.+||.||.+|+.|.+++|+.|.+.+.      -.+.|.+ +.+.++.|..+|..+.....
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~------G~v~i~~~~~~~~~~a~~~I~~~~~~~~  620 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD------GTVKIAATDGEAAEAAKERIEGITAEPE  620 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC------ceEEEEcccHHHHHHHHHHHHHhcccCc
Confidence            445778899999999999999999999999999888542      2345555 78899999999998886533

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

Probab=93.08  E-value=0.027  Score=50.83  Aligned_cols=36  Identities=39%  Similarity=0.751  Sum_probs=31.2

Q ss_pred             CCcccccccCCCCCCCCCCCCCCCcCCCChhhhccc
Q 022898          253 LSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKT  288 (290)
Q Consensus       253 ~~~~~k~~~C~~~~~g~C~~g~~C~f~Hg~~el~~~  288 (290)
                      .....|+.+|-+|..|.|.-|+.|.|+|+...-|+.
T Consensus        86 ~gvDPKSvvCafFk~g~C~KG~kCKFsHdl~~~~k~  121 (343)
T KOG1763|consen   86 KGVDPKSVVCAFFKQGTCTKGDKCKFSHDLAVERKK  121 (343)
T ss_pred             cCCCchHHHHHHHhccCCCCCCcccccchHHHhhhc
Confidence            335679999999999999999999999999877653

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=92.95  E-value=0.22  Score=44.19  Aligned_cols=67  Identities=15%  Similarity=0.227  Sum_probs=53.7

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHhcC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~~~  236 (290)
                      ..-..+.||.++++.+||++|..|+.|.+.+++.|.|..+      -.|.|.+ +.+.+..|..+|...-.++.
T Consensus       144 ~~G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N------G~VwI~~~~~~~~~~a~~~I~~~e~~~~  211 (235)
T PRK04163        144 EGGTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN------GRIWIKGPDEEDEEIAIEAIKKIEREAH  211 (235)
T ss_pred             CCCEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC------cEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence            3457799999999999999999999999999999999653      3455555 66688888888877655543

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

Probab=92.45  E-value=0.088  Score=46.75  Aligned_cols=29  Identities=31%  Similarity=0.913  Sum_probs=26.2

Q ss_pred             CcccccccCCCCCCCCCCCCCCCcCCCCh
Q 022898          254 SSNFKTKLCGNFAKGSCTFGDRCHFAHGA  282 (290)
Q Consensus       254 ~~~~k~~~C~~~~~g~C~~g~~C~f~Hg~  282 (290)
                      ...++...|..|..+.|.+|..|.|.|-.
T Consensus       147 vT~~rea~C~~~e~~~C~rG~~CnFmH~k  175 (260)
T KOG2202|consen  147 VTDFREAICGQFERTECSRGGACNFMHVK  175 (260)
T ss_pred             cCchhhhhhcccccccCCCCCcCcchhhh
Confidence            37789999999998899999999999954

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

Probab=92.32  E-value=0.16  Score=47.51  Aligned_cols=28  Identities=21%  Similarity=0.267  Sum_probs=23.4

Q ss_pred             cccccccCCCCCCCCCCCCCCCcCCCCh
Q 022898          255 SNFKTKLCGNFAKGSCTFGDRCHFAHGA  282 (290)
Q Consensus       255 ~~~k~~~C~~~~~g~C~~g~~C~f~Hg~  282 (290)
                      ..-++++|.+-..|.|.+|..|.++|+.
T Consensus        89 ~~s~~~~~~~~~~~~~~~g~~~~~~~~~  116 (344)
T KOG1039|consen   89 EPSSTQENPYSNHGQCRFGNGDVTLNGN  116 (344)
T ss_pred             cccccccCccccccccccCCcccccccc
Confidence            4446788999889999999999999963

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

Probab=92.25  E-value=0.2  Score=43.16  Aligned_cols=40  Identities=33%  Similarity=0.473  Sum_probs=33.2

Q ss_pred             CceEEEEecc------cccceeeCCCCCchhhHHHhhCCceeeccC
Q 022898          164 SATAKISVDA------SLAGAIIGKGGVNSKQICRQTGAKLSIRDH  203 (290)
Q Consensus       164 ~~t~~i~VP~------~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~  203 (290)
                      ..+-++.||-      .+||+|||..|++.+++...|+|+|-|...
T Consensus       147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            4455566653      689999999999999999999999999654

>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]

Probab=92.05  E-value=0.056  Score=56.92  Aligned_cols=75  Identities=17%  Similarity=0.177  Sum_probs=62.2

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc-CCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA  238 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~-~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~  238 (290)
                      .....+.+|.-.+.-|||+||+||..++..+|+.|.|.. .+.+..+|.+.+.|.++.++.|-.+|.-.+...+..
T Consensus      1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpdv~ 1414 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPDVS 1414 (2131)
T ss_pred             ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeecCCcC
Confidence            455567778777888999999999999999999999977 455567999999999999999988887766655544

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

Probab=91.12  E-value=0.16  Score=46.23  Aligned_cols=55  Identities=27%  Similarity=0.619  Sum_probs=41.8

Q ss_pred             cccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCccccccccccc--ccccCCC
Q 022898           34 SKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLN--SAEGCKF  111 (290)
Q Consensus        34 t~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~--~~g~C~~  111 (290)
                      +-.|++|..-|.|..|..|.+.|.+|.                                  ...-.|..|-  +.+.|++
T Consensus       134 ~~~c~~Fs~~G~cs~g~~c~~~h~dp~----------------------------------~~~~~~~~~~~~~~~f~p~  179 (285)
T COG5084         134 GPPCRSFSLKGSCSSGPSCGYSHIDPD----------------------------------SFAGNCDQYSGATYGFCPL  179 (285)
T ss_pred             CCCcccccccceeccCCCCCccccCcc----------------------------------cccccccccCcccccccCC
Confidence            678999977899999999999997622                                  1222343322  3789999


Q ss_pred             CCccccccccc
Q 022898          112 GDKCHFAHGEW  122 (290)
Q Consensus       112 G~~C~f~H~~~  122 (290)
                      |..|+|-|...
T Consensus       180 g~~c~~~H~~~  190 (285)
T COG5084         180 GASCKFSHTLK  190 (285)
T ss_pred             CCccccccccc
Confidence            99999999764

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

Probab=91.05  E-value=0.051  Score=47.59  Aligned_cols=34  Identities=47%  Similarity=0.835  Sum_probs=30.5

Q ss_pred             cccccccCCCCCCCCCCCCCCCcCCCChhhhccc
Q 022898          255 SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKT  288 (290)
Q Consensus       255 ~~~k~~~C~~~~~g~C~~g~~C~f~Hg~~el~~~  288 (290)
                      ...|+..|-.|..+.|-.|+.|.|+|+.+|.|+.
T Consensus        81 vdpK~~vcalF~~~~c~kg~~ckF~h~~ee~r~~  114 (299)
T COG5252          81 VDPKTVVCALFLNKTCAKGDACKFAHGKEEARKT  114 (299)
T ss_pred             cCchhHHHHHhccCccccCchhhhhcchHHHhhh
Confidence            4558999999999999999999999999998864

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

Probab=89.62  E-value=0.1  Score=47.31  Aligned_cols=35  Identities=31%  Similarity=0.686  Sum_probs=27.9

Q ss_pred             CccccccccccccCCCCCCCCCceEecccCCCchhh
Q 022898           30 VGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAV   65 (290)
Q Consensus        30 ~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~   65 (290)
                      .-|---+|+-|-.+|.|-||+.|.|+|.. .+|.++
T Consensus       182 ~d~qpDicKdykeTgycg~gdSckFlh~r-~DyK~G  216 (313)
T KOG1813|consen  182 IDYQPDICKDYKETGYCGYGDSCKFLHDR-SDYKAG  216 (313)
T ss_pred             eecCchhhhhhHhhCcccccchhhhhhhh-hhcccc
Confidence            33556799999999999999999999985 444433

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=89.32  E-value=0.39  Score=39.23  Aligned_cols=37  Identities=27%  Similarity=0.400  Sum_probs=33.5

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeec
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR  201 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~  201 (290)
                      ..+.+.|+...+|+.||++|++|+.|++..|-+|.|-
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv   68 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV   68 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence            5677888999999999999999999999999998883

>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]

Probab=89.08  E-value=0.63  Score=42.95  Aligned_cols=71  Identities=21%  Similarity=0.180  Sum_probs=56.9

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~  236 (290)
                      .+..+.|++...+.|||+.|.+-+.|.+++++.|.+..+..+. ..++.+.+..++|.+|...|.-+|.+..
T Consensus        57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~-~~i~i~~~~~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNK-EEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCc-ceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            4556889999999999999999999999999999996543332 2344445588999999999988887665

>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]

Probab=88.34  E-value=0.52  Score=42.12  Aligned_cols=39  Identities=33%  Similarity=0.524  Sum_probs=34.0

Q ss_pred             CceEEEEeccc------ccceeeCCCCCchhhHHHhhCCceeecc
Q 022898          164 SATAKISVDAS------LAGAIIGKGGVNSKQICRQTGAKLSIRD  202 (290)
Q Consensus       164 ~~t~~i~VP~~------~vg~iIGkgG~~Ik~i~~~sga~i~v~~  202 (290)
                      ..+.+|.||-.      +||-|||..|.++++++++|+++|-|..
T Consensus        91 k~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG  135 (259)
T KOG1588|consen   91 KLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG  135 (259)
T ss_pred             eEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence            56677888764      8999999999999999999999999953

>PRK00468 hypothetical protein; Provisional

Probab=87.70  E-value=0.57  Score=34.03  Aligned_cols=30  Identities=30%  Similarity=0.353  Sum_probs=26.3

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHh
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQ  193 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~  193 (290)
                      ....++.+..+-+|-||||+|.+|+.|+.-
T Consensus        29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         29 SVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             eEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            456778899999999999999999999874

>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]

Probab=87.50  E-value=0.59  Score=34.02  Aligned_cols=30  Identities=27%  Similarity=0.365  Sum_probs=26.6

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHh
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQ  193 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~  193 (290)
                      ....++.|..+-+|-||||+|.+|+.|+..
T Consensus        29 ~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          29 TVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             eEEEEEEECcccccceecCCChhHHHHHHH
Confidence            456888999999999999999999999863

>PRK01064 hypothetical protein; Provisional

Probab=87.39  E-value=0.71  Score=33.80  Aligned_cols=30  Identities=30%  Similarity=0.348  Sum_probs=26.4

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHh
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQ  193 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~  193 (290)
                      ....++.|..+-.|.+|||+|.+|+.|+.-
T Consensus        29 ~~~~~l~v~~~D~g~vIGk~G~~i~air~l   58 (78)
T PRK01064         29 TIIYELTVAKPDIGKIIGKEGRTIKAIRTL   58 (78)
T ss_pred             EEEEEEEECcccceEEECCCCccHHHHHHH
Confidence            456778889999999999999999999874

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

Probab=87.38  E-value=0.18  Score=45.76  Aligned_cols=33  Identities=24%  Similarity=0.841  Sum_probs=27.7

Q ss_pred             CCcccccccCCCCC-CCCCCCCCCCcCCCChhhh
Q 022898          253 LSSNFKTKLCGNFA-KGSCTFGDRCHFAHGAAEL  285 (290)
Q Consensus       253 ~~~~~k~~~C~~~~-~g~C~~g~~C~f~Hg~~el  285 (290)
                      ....|...+|..|. +|+|-||+.|.|.|--...
T Consensus       180 ~~~d~qpDicKdykeTgycg~gdSckFlh~r~Dy  213 (313)
T KOG1813|consen  180 ERIDYQPDICKDYKETGYCGYGDSCKFLHDRSDY  213 (313)
T ss_pred             ceeecCchhhhhhHhhCcccccchhhhhhhhhhc
Confidence            44677788999998 9999999999999976543

>PRK02821 hypothetical protein; Provisional

Probab=87.37  E-value=0.59  Score=34.12  Aligned_cols=33  Identities=24%  Similarity=0.422  Sum_probs=28.0

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGA  196 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga  196 (290)
                      .....+.|.++-+|-||||+|.+|+.|+.--.+
T Consensus        30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             cEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            456788899999999999999999999975443

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=86.96  E-value=1.7  Score=43.04  Aligned_cols=54  Identities=26%  Similarity=0.487  Sum_probs=40.3

Q ss_pred             CceEEEEeccccc-ceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHH
Q 022898          164 SATAKISVDASLA-GAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQ  223 (290)
Q Consensus       164 ~~t~~i~VP~~~v-g~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~  223 (290)
                      .....|.+|++-+ |-|||+.|.||+.+...||+-|-|.+.     ...|.|++ ++.|++
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~-fdp~rr  257 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSG-FDPVRR  257 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC-----CCeEEecC-CchHHH
Confidence            4455688899555 889999999999999999999999763     22455555 555533

>PRK12704 phosphodiesterase; Provisional

Probab=86.73  E-value=1.9  Score=42.80  Aligned_cols=64  Identities=27%  Similarity=0.446  Sum_probs=45.0

Q ss_pred             CceEEEEeccccc-ceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHH--HHHHHHHHHHH
Q 022898          164 SATAKISVDASLA-GAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIK--QASAMVRELIV  233 (290)
Q Consensus       164 ~~t~~i~VP~~~v-g~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~--~A~~~I~~~i~  233 (290)
                      .....|.+|++-+ |-|||+.|.||+-+...||+-|-|.+.     .-.|.|++ ++.++  .|...+...+.
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~-~~~~rre~a~~~l~~l~~  275 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSG-FDPIRREIARLALEKLVQ  275 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC-----CCeEEEec-CChhhHHHHHHHHHHHHh
Confidence            3445678898555 889999999999999999999999763     23455666 33443  55555544443

>PRK00106 hypothetical protein; Provisional

Probab=86.21  E-value=2.2  Score=42.46  Aligned_cols=54  Identities=26%  Similarity=0.456  Sum_probs=40.4

Q ss_pred             CceEEEEeccccc-ceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHH
Q 022898          164 SATAKISVDASLA-GAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQ  223 (290)
Q Consensus       164 ~~t~~i~VP~~~v-g~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~  223 (290)
                      .....|.+|++-+ |-|||+-|.||+-+...||+-|-|.+.     ...|.|++ |+.|++
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt-----p~~v~lS~-fdpvRR  278 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT-----PEVVVLSG-FDPIRR  278 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC-----CCeEEEeC-CChHHH
Confidence            4455688899555 889999999999999999999999753     23455665 444443

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=85.80  E-value=0.59  Score=38.13  Aligned_cols=38  Identities=24%  Similarity=0.281  Sum_probs=33.4

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeec
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR  201 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~  201 (290)
                      .....+.|+.+..+.+|||+|.||+.++..++-.+.|.
T Consensus        98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            34567889999999999999999999999999888764

>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=84.76  E-value=0.52  Score=26.11  Aligned_cols=22  Identities=23%  Similarity=0.628  Sum_probs=17.9

Q ss_pred             ccccccccCCCCCCCCCceEecc
Q 022898           35 KPCTKFFSTAGCPFGESCHFLHY   57 (290)
Q Consensus        35 ~lC~~~~~~g~C~~G~~C~F~H~   57 (290)
                      .||.|-+.+|.|. -+.|.|.|.
T Consensus         1 ~lC~yEl~Gg~Cn-d~~C~~QHf   22 (23)
T PF10650_consen    1 PLCPYELTGGVCN-DPDCEFQHF   22 (23)
T ss_pred             CCCccccCCCeeC-CCCCCcccc
Confidence            3899888888995 469999994

>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A

Probab=83.99  E-value=1  Score=32.14  Aligned_cols=35  Identities=34%  Similarity=0.537  Sum_probs=27.1

Q ss_pred             EEEEecccc-----cceeeCCCCCchhhHHHhh-CCceeec
Q 022898          167 AKISVDASL-----AGAIIGKGGVNSKQICRQT-GAKLSIR  201 (290)
Q Consensus       167 ~~i~VP~~~-----vg~iIGkgG~~Ik~i~~~s-ga~i~v~  201 (290)
                      ..+.|-...     +|+.||++|..|+.|.+.. |.+|.|-
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV   45 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV   45 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence            455555555     8999999999999999999 8888873

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=82.74  E-value=1.1  Score=36.52  Aligned_cols=36  Identities=31%  Similarity=0.441  Sum_probs=32.2

Q ss_pred             eEEEEecccccceeeCCCCCchhhHHHhhCCceeec
Q 022898          166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR  201 (290)
Q Consensus       166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~  201 (290)
                      ..-+.|....+|+.||++|++|+.+++..|-+|.|-
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV   69 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI   69 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence            566778889999999999999999999999888883

This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=82.04  E-value=0.89  Score=42.19  Aligned_cols=25  Identities=32%  Similarity=0.860  Sum_probs=21.9

Q ss_pred             cccCCCCCCCCCCCCCCCcCCCChh
Q 022898          259 TKLCGNFAKGSCTFGDRCHFAHGAA  283 (290)
Q Consensus       259 ~~~C~~~~~g~C~~g~~C~f~Hg~~  283 (290)
                      ..+|.+|..|+|+.|+.|.|.|-.-
T Consensus       161 p~Icsf~v~geckRG~ec~yrhEkp  185 (377)
T KOG0153|consen  161 PHICSFFVKGECKRGAECPYRHEKP  185 (377)
T ss_pred             CccccceeeccccccccccccccCC
Confidence            3479999999999999999999653

>cd02409 KH-II KH-II (K homology RNA-binding domain, type II)

Probab=81.70  E-value=2.3  Score=29.06  Aligned_cols=33  Identities=27%  Similarity=0.336  Sum_probs=25.6

Q ss_pred             eEEEEecccccceeeCCCCCchhhHHHhhCCce
Q 022898          166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKL  198 (290)
Q Consensus       166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i  198 (290)
                      ...+.+.....+.+||+.|.+++.++..++..+
T Consensus        26 ~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          26 EIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            444555555689999999999999999887554

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. 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. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.

>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]

Probab=81.51  E-value=1  Score=38.72  Aligned_cols=59  Identities=31%  Similarity=0.469  Sum_probs=50.7

Q ss_pred             ccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCC
Q 022898          173 ASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA  238 (290)
Q Consensus       173 ~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~  238 (290)
                      ...+|-|+||+|.+-..|...|.++|.+.+       ..|.|-|.++.++.|...|..+|.-++++
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~niriAR~avcsLIlGsppg  235 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQNIRIARDAVCSLILGSPPG  235 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchhhHHHHHhhHhhhccCCch
Confidence            455678999999999999999999999865       36899999999999999999988766553

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

Probab=81.40  E-value=0.67  Score=43.41  Aligned_cols=24  Identities=29%  Similarity=0.851  Sum_probs=21.5

Q ss_pred             ccccccccCCCCCCCCCceEecccC
Q 022898           35 KPCTKFFSTAGCPFGESCHFLHYFP   59 (290)
Q Consensus        35 ~lC~~~~~~g~C~~G~~C~F~H~~~   59 (290)
                      .+|+||. .|.|+||+.|+|.|.++
T Consensus         9 tic~~~~-~g~c~~g~~cr~~h~~~   32 (344)
T KOG1039|consen    9 TICKYYQ-KGNCKFGDLCRLSHSLP   32 (344)
T ss_pred             hhhhhcc-cccccccceeeeeccCc
Confidence            7998777 57999999999999987

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

Probab=81.13  E-value=3.3  Score=35.53  Aligned_cols=63  Identities=22%  Similarity=0.351  Sum_probs=49.1

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEc-----CCHHHHHHHHHHHHHH
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE-----GSFEQIKQASAMVREL  231 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~-----G~~~~i~~A~~~I~~~  231 (290)
                      ..+..+.||.+.++++||+.|..-+.|.+.++.++.|...     ...|.|.     .+|-.+..|...|..+
T Consensus         7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp~~~~ka~d~VkAI   74 (194)
T COG1094           7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDPLALLKARDVVKAI   74 (194)
T ss_pred             cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCChHHHHHHHHHHHHH
Confidence            4566799999999999999999999999999999999643     2233332     3677777887777655

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	290
1j4w_A	174	Complex Of The Kh3 And Kh4 Domains Of Fbp With A Si		2e-04
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		3e-04
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		3e-04
2hh2_A	107	Solution Structure Of The Fourth Kh Domain Of Ksrp		6e-04

>pdb|1J4W|A Chain A, Complex Of The Kh3 And Kh4 Domains Of Fbp With A Single_stranded 29mer Dna Oligonucleotide From The Fuse Element Of The C-Myc Oncogene Length = 174

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 176 AGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELI 232
            G IIGKGG   K I +Q+GA++ ++ +    ADPN++   + G+ +QI  A  ++ E I
Sbjct: 115 TGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

>pdb|1ZZI|A Chain A, Crystal Structure Analysis Of The Third Kh Domain Of Hnrnp K In Complex With Ssdna Length = 82

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/64 (34%), Positives = 38/64 (59%)
Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 225
           T ++++   LAG+IIGKGG   KQI  ++GA + I +       R I + G+ +QI+ A 
Sbjct: 8   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 67
Query: 226 AMVR 229
            +++
Sbjct: 68  YLLQ 71

>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A Single_stranded 10mer Dna Oligonucleotide Length = 89

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/64 (34%), Positives = 38/64 (59%)
Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 225
           T ++++   LAG+IIGKGG   KQI  ++GA + I +       R I + G+ +QI+ A 
Sbjct: 15  TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 74
Query: 226 AMVR 229
            +++
Sbjct: 75  YLLQ 78

>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp Length = 107

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 170 SVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASA 226
           S+     G +IG+GG N K I +QTGA + I        DPN +   + GS +QI  A  
Sbjct: 12  SIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQ 71
Query: 227 MVRELI 232
           ++ E I
Sbjct: 72  LIEEKI 77

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	290
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	6e-23
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-21
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	2e-21
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-20
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-19
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	2e-17
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	3e-17
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	6e-17
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	1e-16
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	4e-15
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	8e-15
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	5e-13
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-14
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	7e-12
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-14
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-13
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	4e-12
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-13
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-12
1we8_A	104	Tudor and KH domain containing protein; structural	3e-13
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	9e-13
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-12
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	1e-12
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	1e-07
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	6e-06
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	9e-06
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	3e-11
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	5e-11
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	2e-10
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	4e-09
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	6e-09
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	2e-08
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-07
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	5e-07
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	5e-05
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	9e-07
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	9e-06
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	1e-05
1tua_A	191	Hypothetical protein APE0754; structural genomics,	3e-05
1tua_A	191	Hypothetical protein APE0754; structural genomics,	3e-04
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	2e-04
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	3e-04
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	5e-04
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	5e-04
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	7e-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 = 88.9 bits (221), Expect = 6e-23
 Identities = 23/74 (31%), Positives = 41/74 (55%)

Query: 159 ASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSF 218
            + G   T ++++   LAG+IIGKGG   KQI  ++GA + I +       R I + G+ 
Sbjct: 1   GAMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 60

Query: 219 EQIKQASAMVRELI 232
           +QI+ A  +++  +
Sbjct: 61  DQIQNAQYLLQNSV 74

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

 Score = 85.7 bits (212), Expect = 2e-21
 Identities = 27/95 (28%), Positives = 38/95 (40%), Gaps = 3/95 (3%)

Query: 159 ASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELE 215
            +         S+     G +IG+GG N K I +QTGA + I        DPN +   + 
Sbjct: 1   GAMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR 60

Query: 216 GSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAA 250
           GS +QI  A  ++ E I          P   G A 
Sbjct: 61  GSPQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAG 95

>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 = 85.1 bits (211), Expect = 2e-21
 Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 4/81 (4%)

Query: 156 GPAASFGASA----TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRN 211
           G   S+G       T ++++   LAG+IIGKGG   KQI  ++GA + I +       R 
Sbjct: 1   GSHMSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRI 60

Query: 212 IELEGSFEQIKQASAMVRELI 232
           I + G+ +QI+ A  +++  +
Sbjct: 61  ITITGTQDQIQNAQYLLQNSV 81

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

 Score = 82.1 bits (203), Expect = 4e-20
 Identities = 14/95 (14%), Positives = 33/95 (34%)

Query: 156 GPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE 215
             A          + V     G +IG+ G   K+I    G ++  +  +     +   + 
Sbjct: 2   AMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM 61

Query: 216 GSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAA 250
           G  ++ + A+ ++ +L+  +       P   G   
Sbjct: 62  GPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPP 96

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

 Score = 79.7 bits (197), Expect = 2e-19
 Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 7/88 (7%)

Query: 147 GRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEAD 206
           G++      G           +I + A  AG +IGKGG   KQ+  + G K+ +    + 
Sbjct: 1   GQFHDNANGGQN-----GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ 55

Query: 207 PNL--RNIELEGSFEQIKQASAMVRELI 232
                + + + G   +++QA  MV +++
Sbjct: 56  NTNVDKPLRIIGDPYKVQQACEMVMDIL 83

>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 = 74.8 bits (184), Expect = 2e-17
 Identities = 17/80 (21%), Positives = 35/80 (43%)

Query: 153 PAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNI 212
                     +  T +  V   + G IIG+GG    +I +++G K+ I         R+ 
Sbjct: 3   SGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSC 62

Query: 213 ELEGSFEQIKQASAMVRELI 232
            L G+ E ++ A  ++ +++
Sbjct: 63  MLTGTPESVQSAKRLLDQIV 82

>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 = 73.9 bits (182), Expect = 3e-17
 Identities = 18/71 (25%), Positives = 37/71 (52%)

Query: 162 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQI 221
           G+  T ++++  +L G IIG+ G N  +I + +GA++ I +     + R + + GS   I
Sbjct: 3   GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASI 62

Query: 222 KQASAMVRELI 232
             A  ++   +
Sbjct: 63  SLAQYLINARL 73

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

 Score = 73.1 bits (180), Expect = 6e-17
 Identities = 15/71 (21%), Positives = 33/71 (46%)

Query: 162 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQI 221
             + + ++++   L G IIG+ G    +I + +GA++ I +       R + + GS   I
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASI 61

Query: 222 KQASAMVRELI 232
             A  ++   +
Sbjct: 62  SLAQYLINVRL 72

>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 = 72.8 bits (179), Expect = 1e-16
 Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 152 PPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNL-- 209
                       +A  +I + AS AG +IGKGG   KQ+  + G K+ +           
Sbjct: 2   SSGSSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGAD 61

Query: 210 RNIELEGSFEQIKQASAMVRELI 232
           + + + G   +++QA  MV ELI
Sbjct: 62  KPLRITGDPYKVQQAKEMVLELI 84

>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 = 68.5 bits (168), Expect = 4e-15
 Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNL--RNIELEGSFEQIK 222
             +I+V  +L GAI+GKGG    +    TGA++ I +  E  P    R + + GS    +
Sbjct: 4   LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 223 QASAMVRELIVRIGPAHAKNP 243
            A  ++ + +       A NP
Sbjct: 64  AAQYLISQRVTYEQGVRASNP 84

>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 = 69.9 bits (171), Expect = 8e-15
 Identities = 27/104 (25%), Positives = 41/104 (39%), Gaps = 3/104 (2%)

Query: 132 HDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQIC 191
                     PG  G               G        V     G IIGKGG   K I 
Sbjct: 71  RSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSIS 130

Query: 192 RQTGAKLSIRDHE---ADPNLRNIELEGSFEQIKQASAMVRELI 232
           +Q+GA++ ++ +    ADPN++   + G+ +QI  A  ++ E I
Sbjct: 131 QQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 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 = 64.9 bits (158), Expect = 5e-13
 Identities = 15/93 (16%), Positives = 36/93 (38%)

Query: 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQ 223
           S    + +     G +IG+ G   K+I    G ++  +  +     R  ++ G  ++ + 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 224 ASAMVRELIVRIGPAHAKNPATAGSAAHPLSSN 256
           A+ ++ +L+  +   +   P   G        N
Sbjct: 62  AAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGN 94

>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 = 69.4 bits (170), Expect = 1e-14
 Identities = 14/97 (14%), Positives = 35/97 (36%)

Query: 136 RAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTG 195
           +A   V   +  R +                  + V     G +IG+ G   K+I    G
Sbjct: 62  QACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAG 121

Query: 196 AKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI 232
            ++  +  +     +   + G  ++ + A+ ++ +L+
Sbjct: 122 VRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL 158

>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 = 7e-12
 Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNL--RNIELEGSFEQIKQ 223
             +I + A  AG +IGKGG   KQ+  + G K+ +    +      + + + G   +++Q
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 62

Query: 224 ASAMVRELIVRIGPAHAKNPATAGSAAH 251
           A  MV +++         +    GS   
Sbjct: 63  ACEMVMDILRERDQGGFGDRNEYGSRIG 90

>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 = 66.9 bits (164), Expect = 1e-14
 Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 3/70 (4%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNL--RNIELEGSFEQIK 222
             +++V  +L GAI+GKGG    +    TGA++ I +  E  P    R + + GS    +
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 223 QASAMVRELI 232
            A  ++ + +
Sbjct: 64  AAQYLISQRV 73

>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 = 66.0 bits (161), Expect = 2e-13
 Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 2/89 (2%)

Query: 146 GGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI--RDH 203
                    P    +   +   KI V  S AG IIGKGG   K I  Q+GA + +  +  
Sbjct: 85  KTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD 144

Query: 204 EADPNLRNIELEGSFEQIKQASAMVRELI 232
             +   R + + G  EQ ++A  ++ + I
Sbjct: 145 GINLQNRVVTVSGEPEQNRKAVELIIQKI 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 = 62.6 bits (152), Expect = 4e-12
 Identities = 22/101 (21%), Positives = 43/101 (42%), Gaps = 3/101 (2%)

Query: 162 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNL--RNIELEGSF 218
           G+    K+ + +  AG+IIGKGG    Q+ ++TGA + + +  +  P    R   ++G+ 
Sbjct: 3   GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI 62

Query: 219 EQIKQASAMVRELIVRIGPAHAKNPATAGSAAHPLSSNFKT 259
           E +      + E I  +    AK    +        +  + 
Sbjct: 63  EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRA 103

>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 = 65.6 bits (160), Expect = 2e-13
 Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 2/99 (2%)

Query: 136 RAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTG 195
           +AF  +  ++             A+     T ++ V AS  G++IGKGG   K+I   TG
Sbjct: 61  KAFAMIIDKLE-EDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTG 119

Query: 196 AKLSI-RDHEADPNLRNIELEGSFEQIKQASAMVRELIV 233
           A++ +  D   +   R I + G  + I +    +  +++
Sbjct: 120 AQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVML 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 = 61.3 bits (149), Expect = 7e-12
 Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 225
           T ++ +     G+IIGK G + K++  ++GA+++I +       R I L G    I +A 
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP--ERIITLAGPTNAIFKAF 63

Query: 226 AMVRELIVRIGPAHAKNPATAGSAAHPL 253
           AM+ + +     +   N   A      L
Sbjct: 64  AMIIDKLEEDISSSMTNSTAASRPPVTL 91

>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 = 63.7 bits (155), Expect = 3e-13
 Identities = 24/103 (23%), Positives = 45/103 (43%), Gaps = 7/103 (6%)

Query: 154 APGPAASFGASA--TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNL-- 209
           + G +     +     ++SV     G IIG+GG   + IC+ +GAK++         L  
Sbjct: 2   SSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLS 61

Query: 210 RNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAAHP 252
           R I++ G+ +++  A  ++ E +             A SA+ P
Sbjct: 62  RLIKISGTQKEVAAAKHLILEKVSE---DEELRKRIAHSASGP 101

>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 = 64.0 bits (156), Expect = 9e-13
 Identities = 24/108 (22%), Positives = 46/108 (42%), Gaps = 8/108 (7%)

Query: 136 RAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTG 195
           +A G + G++  + E    P             I V AS AG +IGKGG    ++   T 
Sbjct: 62  KAQGRIYGKL--KEENFFGPKE----EVKLETHIRVPASAAGRVIGKGGKTVNELQNLTA 115

Query: 196 AKLSIRDHEADPNL--RNIELEGSFEQIKQASAMVRELIVRIGPAHAK 241
           A++ +   +         +++ G F   + A   +R+++ ++   H K
Sbjct: 116 AEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQQHQK 163

>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 = 63.6 bits (155), Expect = 1e-12
 Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 1/81 (1%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRNIELEGSFEQIKQA 224
             ++ + A   GAIIGK G + KQ+ R   A + I      D  +R + + G  E   +A
Sbjct: 4   MVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKA 63

Query: 225 SAMVRELIVRIGPAHAKNPAT 245
              +   +        K    
Sbjct: 64  QGRIYGKLKEENFFGPKEEVK 84

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

 Score = 61.1 bits (148), Expect = 1e-12
 Identities = 16/91 (17%), Positives = 27/91 (29%), Gaps = 25/91 (27%)

Query: 33  KSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGP 92
           K++ C  +  +  C +G  C F H                                    
Sbjct: 11  KTELCRTYSESGRCRYGAKCQFAH----------------------GLGELRQANRHPKY 48

Query: 93  TVVKSRMCNRLNSAEGCKFGDKCHFAHGEWE 123
              K+ +C++      C +G +CHF H   E
Sbjct: 49  ---KTELCHKFKLQGRCPYGSRCHFIHNPTE 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 = 47.6 bits (113), Expect = 1e-07
 Identities = 14/29 (48%), Positives = 21/29 (72%), Gaps = 1/29 (3%)

Query: 254 SSNFKTKLCGNFAK-GSCTFGDRCHFAHG 281
           SS +KT+LC  +++ G C +G +C FAHG
Sbjct: 7   SSRYKTELCRTYSESGRCRYGAKCQFAHG 35

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

 Score = 42.6 bits (100), Expect = 6e-06
 Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 1/35 (2%)

Query: 251 HPLSSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAE 284
                 +KT+LC  F   G C +G RCHF H   E
Sbjct: 42  ANRHPKYKTELCHKFKLQGRCPYGSRCHFIHNPTE 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 = 42.2 bits (99), Expect = 9e-06
 Identities = 12/41 (29%), Positives = 19/41 (46%)

Query: 96  KSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPR 136
           K+ +C   + +  C++G KC FAHG  EL +          
Sbjct: 11  KTELCRTYSESGRCRYGAKCQFAHGLGELRQANRHPKYKTE 51

>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 = 57.3 bits (139), Expect = 3e-11
 Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 2/67 (2%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 225
           T ++ +     G+IIGK G + K++  ++GA+++I +       R I L G    I +A 
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPE--RIITLAGPTNAIFKAF 63

Query: 226 AMVRELI 232
           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 = 57.4 bits (139), Expect = 5e-11
 Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIK 222
             A+A +++       +IGK G   + +  +T  K+ I   +   N   I++ G+ E I+
Sbjct: 15  TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQ--IKITGTKEGIE 72

Query: 223 QASAMVRELI 232
           +A   V  + 
Sbjct: 73  KARHEVLLIS 82

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

 Score = 55.1 bits (133), Expect = 2e-10
 Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 225
             +I++D      +IGK G N  +I  Q    + I       N   I +EG  + ++QA 
Sbjct: 6   YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSN--LIRIEGDPQGVQQAK 63

Query: 226 AMVRELI 232
             + EL 
Sbjct: 64  RELLELA 70

>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 = 51.5 bits (123), Expect = 4e-09
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 156 GPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE 215
           G + S G   T ++ V   + G ++G  G   K+I ++T   +     + +P      + 
Sbjct: 1   GSSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEP---VFAVT 57

Query: 216 GSFEQIKQASAMVRELI 232
           G  E + +A   +   I
Sbjct: 58  GMPENVDRAREEIEAHI 74

>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 = 51.7 bits (124), Expect = 6e-09
 Identities = 13/70 (18%), Positives = 25/70 (35%), Gaps = 1/70 (1%)

Query: 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNL-RNIELEGSFEQIK 222
           S    ++VD      IIG+ G    QI  +    +   D +        I + G  +  +
Sbjct: 16  SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTE 75

Query: 223 QASAMVRELI 232
            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 = 50.6 bits (121), Expect = 2e-08
 Identities = 12/70 (17%), Positives = 28/70 (40%), Gaps = 2/70 (2%)

Query: 163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIK 222
              T ++ V   L   +IG+ G   +++  +    + +   E   +   I + G    + 
Sbjct: 15  VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSD--IIAITGLAANLD 72

Query: 223 QASAMVRELI 232
           +A A + E +
Sbjct: 73  RAKAGLLERV 82

>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 = 47.1 bits (112), Expect = 2e-07
 Identities = 11/67 (16%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 225
           +  + +D  +   IIG  G   ++I  +    +        P+   + + G  E +++A 
Sbjct: 18  SEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPENVEEAI 76

Query: 226 AMVRELI 232
             +  L 
Sbjct: 77  DHILNLE 83

>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 = 47.3 bits (112), Expect = 5e-07
 Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 6/89 (6%)

Query: 150 EPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGA-KLSIRDHE---- 204
           E   A   A SF   A   I V  +L G +IGK G   ++I  ++G  ++ I        
Sbjct: 52  EDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV 111

Query: 205 -ADPNLRNIELEGSFEQIKQASAMVRELI 232
             +  +      G+ + I  A+ ++   +
Sbjct: 112 PQEEGMVPFVFVGTKDSIANATVLLDYHL 140

>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 = 41.5 bits (97), Expect = 5e-05
 Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 5/74 (6%)

Query: 163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQI 221
           +    +  V   L G  IG  G N +Q  +  G    +   + D +     + G   + +
Sbjct: 2   SRFHEQFIVREDLMGLAIGTHGANIQQARKVPG----VTAIDLDEDTCTFHIYGEDQDAV 57

Query: 222 KQASAMVRELIVRI 235
           K+A + +      I
Sbjct: 58  KKARSFLEFAEDVI 71

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

 Score = 44.5 bits (105), Expect = 9e-07
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 260 KLCGNFAKGSCTFGDRCHFAHGAAELRK 287
            +C  +  G+C  G+ C FAHG AEL +
Sbjct: 21  SICDRYMNGTCPEGNSCKFAHGNAELHE 48

>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 = 44.7 bits (105), Expect = 9e-06
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 7/56 (12%)

Query: 177 GAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI 232
           G IIG+ G   + I   +GA +S+         + + + G+  QI+ A   + +L 
Sbjct: 141 GRIIGRKGRTRQIIEEMSGASVSVYG-------KTVAIIGNPIQIEIAKTAIEKLA 189

>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 = 42.5 bits (100), Expect = 1e-05
 Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 4/83 (4%)

Query: 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQA 224
           A  ++S+ A L  ++IG  G   + I  + G  + I           + + G    +++A
Sbjct: 17  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECG-GVHIHFPVEGSGSDTVVIRGPSSDVEKA 75

Query: 225 SAMVRELIVRIGPAHAKNPATAG 247
              +  L         K+  ++G
Sbjct: 76  KKQLLHL---AEEKQTKSGPSSG 95

>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 = 42.7 bits (100), Expect = 3e-05
 Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 7/56 (12%)

Query: 177 GAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI 232
           G IIG+GG   + I   T   +++ +         + + G +E+   A   +  L 
Sbjct: 110 GRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGDYERAMAAKQAIEMLA 158

>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 = 39.6 bits (92), Expect = 3e-04
 Identities = 14/79 (17%), Positives = 30/79 (37%)

Query: 162 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQI 221
                  + V     GA+IG  G    +I R+TG  +++    +   +           +
Sbjct: 1   AMKPRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNL 60

Query: 222 KQASAMVRELIVRIGPAHA 240
            +A+ +V+ + +   P  A
Sbjct: 61  MKAAEVVKAISLGFPPEKA 79

>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 = 38.7 bits (90), Expect = 2e-04
 Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 8/76 (10%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQA- 224
            + ++  + L   IIGK G N  +I +Q   K+ I   E +     I LEG  E +  A 
Sbjct: 28  VSSVAAPSWLHRFIIGKKGQNLAKITQQMP-KVHIEFTEGE---DKITLEGPTEDVSVAQ 83

Query: 225 ---SAMVRELIVRIGP 237
                MV++LI R GP
Sbjct: 84  EQIEGMVKDLINRSGP 99

>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 = 38.1 bits (88), Expect = 3e-04
 Identities = 10/40 (25%), Positives = 16/40 (40%)

Query: 247 GSAAHPLSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELR 286
           GS+        K +LC  +  G C   + C + HG    +
Sbjct: 1   GSSGSSGELPKKRELCKFYITGFCARAENCPYMHGDFPCK 40

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

 Score = 37.2 bits (86), Expect = 5e-04
 Identities = 12/29 (41%), Positives = 17/29 (58%)

Query: 252 PLSSNFKTKLCGNFAKGSCTFGDRCHFAH 280
             SS  KT +C ++ +G C  GD+C F H
Sbjct: 3   SGSSGEKTVVCKHWLRGLCKKGDQCEFLH 31

>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 Length = 131

 Score = 38.3 bits (89), Expect = 5e-04
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 17/85 (20%)

Query: 175 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-----------------S 217
             G +IG  G   K I ++  AK+ IR   +    +    +G                 +
Sbjct: 23  FVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANT 82

Query: 218 FEQIKQASAMVRELIVRIGPAHAKN 242
            E +K+A   +R ++ +        
Sbjct: 83  MENVKKAVEQIRNILKQGIETPEDQ 107

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

 Score = 39.9 bits (92), Expect = 7e-04
 Identities = 12/76 (15%), Positives = 26/76 (34%), Gaps = 7/76 (9%)

Query: 164 SATAKISVDASLAGAIIGKGGV--NSKQICRQTGAKLSIRDHE-----ADPNLRNIELEG 216
             T  +  ++     +    G   N   I  +T   + + D        DP  + + + G
Sbjct: 29  RVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITG 88

Query: 217 SFEQIKQASAMVRELI 232
            F  + +A  ++R   
Sbjct: 89  YFGDVDRARMLMRRNC 104

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	290
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	99.66
1m9o_A	77	Tristetraproline; Cys3His type zinc finger, metal	99.55
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.45
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.44
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.42
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.41
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.4
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.36
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.35
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.35
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.34
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.34
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.34
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.3
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.29
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	99.26
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	99.21
1we8_A	104	Tudor and KH domain containing protein; structural	99.2
2rhk_C	72	Cleavage and polyadenylation specificity factor su	99.14
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.14
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.07
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.05
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.04
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.03
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	98.99
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	98.98
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	98.98
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	98.97
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	98.96
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	98.95
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	98.94
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	98.94
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	98.92
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	98.91
2cqe_A	98	KIAA1064 protein; CCCH zinc-finger, structural gen	98.84
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	98.81
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	98.76
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	98.75
2d9m_A	69	Zinc finger CCCH-type domain containing protein 7A	98.69
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.68
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	98.65
2rhk_C	72	Cleavage and polyadenylation specificity factor su	98.58
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	98.54
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	98.52
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	98.51
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.47
2e5s_A	98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	98.33
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.3
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	98.27
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.25
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	98.18
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	97.86
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	97.81
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	97.78
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.76
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	97.75
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	97.72
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	97.67
1tua_A	191	Hypothetical protein APE0754; structural genomics,	97.66
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	97.44
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	97.32
3u9g_A	229	Zinc finger CCCH-type antiviral protein 1; zinc fi	97.27
1tua_A	191	Hypothetical protein APE0754; structural genomics,	97.23
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.11
2fc6_A	50	Nuclear, target of EGR1, member 1; structure genom	96.54
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.51
2fc6_A	50	Nuclear, target of EGR1, member 1; structure genom	94.94
3u9g_A	229	Zinc finger CCCH-type antiviral protein 1; zinc fi	94.79
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	93.68
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	92.15
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	91.39
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	90.53
3v33_A	223	Ribonuclease ZC3H12A; rossmann-like sandwich fold,	82.86
3v33_A	223	Ribonuclease ZC3H12A; rossmann-like sandwich fold,	82.75
2lhn_A	80	Nuclear polyadenylated RNA-binding protein NAB2; n	82.39

>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=1.8e-17  Score=120.89  Aligned_cols=70  Identities=29%  Similarity=0.677  Sum_probs=29.0

Q ss_pred             CCccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCccccccccccccccc
Q 022898           29 GVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEG  108 (290)
Q Consensus        29 ~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~  108 (290)
                      +..|||+||++|+.+|.|+||++|+|+|++.+          +...               ...+.+++++|..|...|.
T Consensus         7 ~~~~kt~~C~~f~~~G~C~~G~~C~f~H~~~e----------~~~~---------------~~~~~~k~~~C~~f~~~G~   61 (77)
T 1m9o_A            7 SSRYKTELCRTYSESGRCRYGAKCQFAHGLGE----------LRQA---------------NRHPKYKTELCHKFKLQGR   61 (77)
T ss_dssp             SSCCCSCCCSGGGGTSCCTTTTTCSSCSSSCC----------GGGT---------------C------------------
T ss_pred             CCCccchhCHHhhhCCCcCCCCCccCCCCChh----------hccc---------------cccccccCCcccchhhCcC
Confidence            67899999999988899999999999998621          1100               1236788999999999999


Q ss_pred             CCCCCcccccccccc
Q 022898          109 CKFGDKCHFAHGEWE  123 (290)
Q Consensus       109 C~~G~~C~f~H~~~e  123 (290)
                      |+||.+|+|+|...|
T Consensus        62 C~~G~~C~f~H~~~e   76 (77)
T 1m9o_A           62 CPYGSRCHFIHNPTE   76 (77)
T ss_dssp             ---------------
T ss_pred             CCCcCcCCCCCCCCC
Confidence            999999999997644

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

Probab=99.55  E-value=1.5e-15  Score=110.56  Aligned_cols=35  Identities=34%  Similarity=0.795  Sum_probs=30.7

Q ss_pred             CCcccccccccccccccCCCCCcccccccccccCC
Q 022898           92 PTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGK  126 (290)
Q Consensus        92 ~~~~ktr~C~~~~~~g~C~~G~~C~f~H~~~el~~  126 (290)
                      .+.+|+++|.+|...|.|+||++|+|+|...+++.
T Consensus         7 ~~~~kt~~C~~f~~~G~C~~G~~C~f~H~~~e~~~   41 (77)
T 1m9o_A            7 SSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQ   41 (77)
T ss_dssp             SSCCCSCCCSGGGGTSCCTTTTTCSSCSSSCCGGG
T ss_pred             CCCccchhCHHhhhCCCcCCCCCccCCCCChhhcc
Confidence            46889999999988999999999999998766654

>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=99.45  E-value=9.3e-14  Score=102.33  Aligned_cols=76  Identities=30%  Similarity=0.498  Sum_probs=69.6

Q ss_pred             CCCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          162 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       162 ~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ++..+.+|.||.+.+|.|||++|++|++|++.||++|+|.+..++..++.|+|+|++++++.|..+|.+++.+...
T Consensus         4 g~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~g   79 (82)
T 1zzk_A            4 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYSG   79 (82)
T ss_dssp             CCCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhccC
Confidence            4567899999999999999999999999999999999998766677789999999999999999999999987644

>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=99.44  E-value=2.4e-13  Score=102.26  Aligned_cols=76  Identities=22%  Similarity=0.379  Sum_probs=69.9

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAH  239 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~p  239 (290)
                      ..+.+|.||.+.+|.|||++|.+|++|++.||++|+|.+...+..++.|+|+|++++++.|..+|.+++.+....|
T Consensus        14 ~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~~~p   89 (92)
T 1x4n_A           14 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGRSGP   89 (92)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTCCS
T ss_pred             CEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcccCC
Confidence            5789999999999999999999999999999999999876666678999999999999999999999999877653

>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=99.42  E-value=1.1e-13  Score=101.87  Aligned_cols=75  Identities=24%  Similarity=0.427  Sum_probs=67.0

Q ss_pred             CCCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898          162 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       162 ~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~  236 (290)
                      +...+.+|.||.+.+|.|||++|++|+.|++.||++|+|.+..++..++.|+|+|++++++.|..+|.+++.+..
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   77 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSEK   77 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC---
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhhh
Confidence            346789999999999999999999999999999999999876667779999999999999999999999987763

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

Probab=99.41  E-value=2.6e-13  Score=104.64  Aligned_cols=78  Identities=14%  Similarity=0.330  Sum_probs=67.0

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCCCCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAK  241 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~p~~  241 (290)
                      ..+.+|.||.+.++.||||+|++|++|+++|+++|+|.+...+..+|.|+|+|++++++.|+.+|.+++.+.+..|+.
T Consensus        10 ~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~~g~~g   87 (106)
T 2hh3_A           10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSGPPG   87 (106)
T ss_dssp             --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC-----
T ss_pred             CeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhccccCCCC
Confidence            357899999999999999999999999999999999986665667899999999999999999999999998887543

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

Probab=99.40  E-value=1.3e-13  Score=100.08  Aligned_cols=71  Identities=21%  Similarity=0.409  Sum_probs=66.3

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHh
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR  234 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~  234 (290)
                      ..+.+|.||.+.+|.|||++|++|+.|++.||++|+|.+..++..++.|.|+|++++++.|..+|.+++.+
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   74 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSS   74 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            56789999999999999999999999999999999998776777899999999999999999999998864

>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=99.36  E-value=3.2e-13  Score=97.23  Aligned_cols=69  Identities=28%  Similarity=0.413  Sum_probs=63.8

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHh
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR  234 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~  234 (290)
                      ..+.+|.||.+.+|.|||++|++|++|++.||++|+|.+.  +..+|.++|.|+++++..|..+|.+.+.+
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC--CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            4678999999999999999999999999999999999765  45689999999999999999999999876

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

Probab=99.35  E-value=1e-12  Score=101.60  Aligned_cols=74  Identities=32%  Similarity=0.443  Sum_probs=65.7

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCC---CCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE---ADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~---~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ..+.+|.||.+.++.|||++|++|++|++.|||+|+|.+..   .+..++.|+|+|+.++++.|+.+|.+++.+...
T Consensus         6 g~~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~~   82 (107)
T 2hh2_A            6 GGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLC   82 (107)
T ss_dssp             -CCEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCCC
T ss_pred             CCeEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhcccc
Confidence            34789999999999999999999999999999999997652   345679999999999999999999999987653

>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=99.35  E-value=3.5e-13  Score=100.76  Aligned_cols=75  Identities=29%  Similarity=0.476  Sum_probs=68.7

Q ss_pred             CCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       163 ~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      +..+.+|.||.+.+|.|||++|++|++|++.||++|+|.+..++..++.|+|+|++++++.|+.+|.+++.+...
T Consensus        12 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~~g   86 (89)
T 1j5k_A           12 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYSG   86 (89)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHC-
T ss_pred             CeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHHhhhc
Confidence            467899999999999999999999999999999999998766677889999999999999999999999987643

>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=99.34  E-value=7.8e-13  Score=95.80  Aligned_cols=70  Identities=24%  Similarity=0.395  Sum_probs=62.6

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC---CCCCCcceeEEcCCHHHHHHHHHHHHHHHHh
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELIVR  234 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~---~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~  234 (290)
                      .+.+|.||.+.+|.|||++|++|+.|++.||++|+|.+.   .++..++.|.|+|++++++.|..+|.+++.+
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999754   2455689999999999999999999988753

>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=99.34  E-value=1.2e-12  Score=96.56  Aligned_cols=72  Identities=17%  Similarity=0.245  Sum_probs=64.0

Q ss_pred             CCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       163 ~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ...+..|.||.+.+|+||||+|++|++|+++||++|+|...+   .++.++|+|++++++.|..+|.+.+.....
T Consensus         8 ~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~---~~~~v~ItG~~e~v~~A~~~I~~~i~~r~~   79 (83)
T 2dgr_A            8 GQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD---KEPVFAVTGMPENVDRAREEIEAHITLRSG   79 (83)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS---SCCEEEEEECTTTHHHHHHHHHHHHHSCCS
T ss_pred             CceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC---CCCeEEEEcCHHHHHHHHHHHHHHHhcccC
Confidence            467899999999999999999999999999999999997533   257899999999999999999998766554

>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=99.34  E-value=9.5e-13  Score=99.41  Aligned_cols=76  Identities=32%  Similarity=0.444  Sum_probs=68.3

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCC--CCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA--DPNLRNIELEGSFEQIKQASAMVRELIVRIGPAH  239 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~--~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~p  239 (290)
                      ..+.+|.||.+.+|.||||+|++|+.|++.||++|+|.+...  ...+|.|.|+|++++++.|+.+|.+++.+.+..|
T Consensus        14 ~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~   91 (94)
T 1x4m_A           14 NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQGSGP   91 (94)
T ss_dssp             CEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCCSSCS
T ss_pred             cEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhccCCCC
Confidence            678999999999999999999999999999999999976533  3468999999999999999999999998877653

>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=99.30  E-value=1.6e-12  Score=96.69  Aligned_cols=74  Identities=24%  Similarity=0.366  Sum_probs=66.1

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCC---CCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE---ADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~---~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ..+.+|.||.+.+|.|||++|.+|+.|++.||++|+|.+..   ++..++.|+|+|+++++..|..+|.+++.+.+.
T Consensus         2 k~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~   78 (87)
T 1ec6_A            2 KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQG   78 (87)
T ss_dssp             CSEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccc
Confidence            35789999999999999999999999999999999997642   456689999999999999999999999887544

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

Probab=99.29  E-value=4.2e-12  Score=94.03  Aligned_cols=71  Identities=25%  Similarity=0.408  Sum_probs=63.5

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCC--CCCcceeEEcCCHHHHHHHHHHHHHHHHh
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA--DPNLRNIELEGSFEQIKQASAMVRELIVR  234 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~--~~~~r~v~i~G~~~~i~~A~~~I~~~i~~  234 (290)
                      ..+..|.||.+.+|.|||++|++|+.|++.||++|.|.+...  ...+|.|.|+|++++++.|..+|.+++.+
T Consensus        13 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            567899999999999999999999999999999999976432  45689999999999999999999988753

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

Probab=99.26  E-value=3.3e-12  Score=92.83  Aligned_cols=62  Identities=26%  Similarity=0.542  Sum_probs=50.3

Q ss_pred             CCccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCccccccccccccccc
Q 022898           29 GVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEG  108 (290)
Q Consensus        29 ~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~  108 (290)
                      ...+|+.+|++|++ |.|.+|++|.|+|++.                                  ..++.+|.+|.+.|.
T Consensus         5 ~~~~k~~~C~~fl~-G~C~~G~~C~fsH~~~----------------------------------~~~~~~C~~f~~~G~   49 (77)
T 2d9n_A            5 SSGEKTVVCKHWLR-GLCKKGDQCEFLHEYD----------------------------------MTKMPECYFYSKFGE   49 (77)
T ss_dssp             CSCCTTSBCHHHHT-TCCSCTTSSSSBCSCC----------------------------------TTTSCBCHHHHHTCC
T ss_pred             CCCCcceeCHhHcc-CcCCCCCCCCCccccc----------------------------------cCcCCCCcccCCCCc
Confidence            45679999999997 8999999999999861                                  124558998888799


Q ss_pred             CCCCCcccccccccccCC
Q 022898          109 CKFGDKCHFAHGEWELGK  126 (290)
Q Consensus       109 C~~G~~C~f~H~~~el~~  126 (290)
                      |. |++|+|+|...+...
T Consensus        50 C~-~~~C~f~H~~~~~~~   66 (77)
T 2d9n_A           50 CS-NKECPFLHIDPESKI   66 (77)
T ss_dssp             CC-CSSCSSBCCCTTSSC
T ss_pred             cC-CCCeeccCCCccccC
Confidence            99 999999997744433

>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=99.21  E-value=4.6e-12  Score=96.20  Aligned_cols=53  Identities=26%  Similarity=0.613  Sum_probs=46.7

Q ss_pred             CCccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCccccccccccccccc
Q 022898           29 GVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEG  108 (290)
Q Consensus        29 ~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~  108 (290)
                      .+.+|+.+|++|. .|.|.+|++|.|+|+                                       +.+|.+|.+.|.
T Consensus         8 ~~~~k~~lC~~f~-~G~C~~G~~C~f~H~---------------------------------------~~~C~~f~~~G~   47 (98)
T 2cqe_A            8 ELPKKRELCKFYI-TGFCARAENCPYMHG---------------------------------------DFPCKLYHTTGN   47 (98)
T ss_dssp             CCSCCCSBCTTTT-TTCCSCSTTCSSBSS---------------------------------------SSBCSHHHHTSC
T ss_pred             CCCCCCccCcccc-cCcCCCCCCCCCCCC---------------------------------------CCcCcCcccCCc
Confidence            4668999999986 689999999999994                                       357999988999


Q ss_pred             CCCCCcccccccc
Q 022898          109 CKFGDKCHFAHGE  121 (290)
Q Consensus       109 C~~G~~C~f~H~~  121 (290)
                      |+||++|+|+|..
T Consensus        48 C~~G~~C~f~H~~   60 (98)
T 2cqe_A           48 CINGDDCMFSHDP   60 (98)
T ss_dssp             CSSCTTCSSBCCC
T ss_pred             CCCCCCCcccCCC
Confidence            9999999999953

>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=99.20  E-value=1.4e-11  Score=94.61  Aligned_cols=73  Identities=25%  Similarity=0.436  Sum_probs=64.4

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCC--CCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEAD--PNLRNIELEGSFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~--~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~  236 (290)
                      ..+.+|.||.+.+|.|||++|.+|+.|++.||++|+|.+....  ..++.|+|.|+.++++.|..+|.+++.+.+
T Consensus        14 p~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T 1we8_A           14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             EEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhCh
Confidence            3578999999999999999999999999999999999765432  358999999999999999999999987543

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

Probab=99.14  E-value=1e-11  Score=88.96  Aligned_cols=57  Identities=26%  Similarity=0.593  Sum_probs=48.0

Q ss_pred             CCccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCccccccccccccccc
Q 022898           29 GVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEG  108 (290)
Q Consensus        29 ~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~  108 (290)
                      ....|+.+|++|++ |.|.+|++|.|+|++                                  ...++.+|.+|.+.|.
T Consensus        11 ~~~~k~~vCk~fl~-G~C~~G~~C~fsH~~----------------------------------~~~~~~~C~~f~~~G~   55 (72)
T 2rhk_C           11 MSGEKTVVCKHWLR-GLCKKGDQCEFLHEY----------------------------------DMTKMSECYFYSKFGE   55 (72)
T ss_dssp             SSCCCCSBCHHHHT-TCCCCGGGSSSBCSC----------------------------------CTTSCCBCHHHHHHSC
T ss_pred             CCCCcCeeCHHHhc-CCCCCCCCCCCcccc----------------------------------ccccCCcccccCCCCC
Confidence            56779999999997 799999999999975                                  1124568998887799


Q ss_pred             CCCCCcccccccc
Q 022898          109 CKFGDKCHFAHGE  121 (290)
Q Consensus       109 C~~G~~C~f~H~~  121 (290)
                      |.+ ++|.|.|..
T Consensus        56 C~~-~~C~y~H~~   67 (72)
T 2rhk_C           56 CSN-KECPFLHID   67 (72)
T ss_dssp             CSB-TTCCSBCCC
T ss_pred             CCC-CCeeccCCC
Confidence            999 999999965

>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=99.14  E-value=6.4e-11  Score=89.79  Aligned_cols=74  Identities=18%  Similarity=0.278  Sum_probs=65.5

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCC-CCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE-ADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~-~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ..+..|.||.++++.|||++|++|+.|++.||++|+|.+.. +...++.|+|+|+.+++..|..+|..++.+.+.
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~e~   90 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGELEQ   90 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHHHHh
Confidence            57899999999999999999999999999999999997643 334678999999999999999999999876543

>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=99.07  E-value=1.6e-10  Score=87.03  Aligned_cols=72  Identities=21%  Similarity=0.278  Sum_probs=63.9

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ..+..|.||.+.++.|||+||.+|+.|+++||++|+|.+.+  ...+.|+|+|+++++..|..+|..++.+...
T Consensus        16 ~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~--~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~~   87 (94)
T 2cte_A           16 QASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD--DPSNQIKITGTKEGIEKARHEVLLISAEQDK   87 (94)
T ss_dssp             CEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT--SSCCEEEEEECHHHHHHHHHHHHHHHHHHHT
T ss_pred             ceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC--CCCCeEEEEECHHHHHHHHHHHHHHhhcccc
Confidence            56899999999999999999999999999999999997532  2346899999999999999999999887554

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

Probab=99.05  E-value=1.4e-10  Score=82.88  Aligned_cols=66  Identities=26%  Similarity=0.341  Sum_probs=59.3

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHH
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVREL  231 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~  231 (290)
                      ..+..|.||.++++.|||++|.+|+.|++.||++|.|.+..  ...+.|+|.|+.++++.|..+|.++
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            46789999999999999999999999999999999997643  2568999999999999999999875

>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=99.04  E-value=3.8e-10  Score=85.17  Aligned_cols=74  Identities=15%  Similarity=0.237  Sum_probs=65.8

Q ss_pred             CCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       163 ~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ...+..|.||.+.++.|||++|.+|+.|++.||++|+|.+.. +.+.+.|+|+|.+++++.|..+|..++.+.+.
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~~~   88 (95)
T 2ctm_A           15 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPENVEEAIDHILNLEEEYLA   88 (95)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-CSCTTEEEEESCHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC-CCCCcEEEEEcCHHHHHHHHHHHHHHHHHHHH
Confidence            367899999999999999999999999999999999997542 23467899999999999999999999987765

>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=99.03  E-value=1.4e-10  Score=95.86  Aligned_cols=73  Identities=15%  Similarity=0.357  Sum_probs=66.4

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      .+.+|.||.+.+|.|||++|.+|+.|++.||++|.|.+...+..++.|+|+|+++++..|..+|.+++.+.+.
T Consensus        91 ~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~  163 (164)
T 2jvz_A           91 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRS  163 (164)
T ss_dssp             SSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEESCHHHHHHHHHHHHHHHHHHHC
T ss_pred             ceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEEcCHHHHHHHHHHHHHHHhhhhC
Confidence            4578999999999999999999999999999999998766666689999999999999999999999987654

>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=98.99  E-value=2e-10  Score=95.99  Aligned_cols=74  Identities=16%  Similarity=0.371  Sum_probs=67.0

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      +.+.+|.||.+.+|.|||++|++|++|++.||++|+|.+.+.+..+|.|.|+|+++++..|..+|.+++.+.+.
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~   75 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQA   75 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC-
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhccc
Confidence            35789999999999999999999999999999999997655566789999999999999999999999988754

>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=98.98  E-value=3.9e-10  Score=93.17  Aligned_cols=73  Identities=25%  Similarity=0.302  Sum_probs=66.9

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC-CCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH-EADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~-~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      .+.+|.||.+.+|.|||++|++|+.|++.||++|+|.+. .++..+|.|+|+|+++++..|..+|.+.+.+...
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~   76 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENF   76 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTS
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccc
Confidence            478999999999999999999999999999999999765 4677899999999999999999999999988743

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

Probab=98.98  E-value=5e-11  Score=83.31  Aligned_cols=30  Identities=40%  Similarity=0.951  Sum_probs=28.4

Q ss_pred             ccccCCCCCCCCCCCCCCCcCCCChhhhcc
Q 022898          258 KTKLCGNFAKGSCTFGDRCHFAHGAAELRK  287 (290)
Q Consensus       258 k~~~C~~~~~g~C~~g~~C~f~Hg~~el~~  287 (290)
                      +++||.+|.+|.|+||++|.||||++|||.
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            669999998899999999999999999996

>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=98.97  E-value=2.8e-10  Score=95.40  Aligned_cols=73  Identities=32%  Similarity=0.398  Sum_probs=65.1

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCC--CCCCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE--ADPNLRNIELEGSFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~--~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~  236 (290)
                      ..+.+|.||.+.+|.|||++|.+|++|++.||++|+|.+..  ++..++.|+|+|+++++..|..+|.+++.+.+
T Consensus       103 ~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          103 ANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDP  177 (178)
T ss_dssp             GGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEEEEEEESSHHHHHHHHHHHHHHHHSCC
T ss_pred             ceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhCC
Confidence            57889999999999999999999999999999999997643  34567999999999999999999999998754

>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=98.96  E-value=3.7e-10  Score=86.64  Aligned_cols=70  Identities=17%  Similarity=0.251  Sum_probs=62.6

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~  236 (290)
                      .+..|.||.+.++.|||+||.+|+.|++.||++|+|.+...  ..+.|+|+|+.++++.|..+|..++.+.+
T Consensus        17 ~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~--~~~~V~I~G~~e~v~~A~~~I~~i~~e~e   86 (104)
T 2ctk_A           17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL--QSDIIAITGLAANLDRAKAGLLERVKELQ   86 (104)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT--TCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCC--CcceEEEEcCHHHHHHHHHHHHHHHhhHH
Confidence            67899999999999999999999999999999999976433  34689999999999999999999987654

>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=98.95  E-value=3.6e-10  Score=93.05  Aligned_cols=71  Identities=27%  Similarity=0.431  Sum_probs=64.7

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc-CCCCCCcceeEEcCCHHHHHHHHHHHHHHHHh
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEGSFEQIKQASAMVRELIVR  234 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~-~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~  234 (290)
                      ..+.++.||.+.+|.|||++|.+|++|++.||++|+|.+ ..++..++.|+|+|+++++..|..+|.+.+.+
T Consensus        88 ~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A           88 PVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             SEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            468999999999999999999999999999999999965 34566789999999999999999999999876

>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=98.94  E-value=7.5e-10  Score=91.34  Aligned_cols=73  Identities=25%  Similarity=0.378  Sum_probs=65.0

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCC--CCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE--ADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~--~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      .+.+|.||.+.+|.|||++|++|+.|++.||++|+|.+..  ++..+|.+.|+|+++++..|..+|.+++.+.+.
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~   76 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQ   76 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhccC
Confidence            4689999999999999999999999999999999996432  345679999999999999999999999987654

>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=98.94  E-value=7.1e-10  Score=91.57  Aligned_cols=74  Identities=26%  Similarity=0.428  Sum_probs=64.6

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCC-CCCC-cceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE-ADPN-LRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~-~~~~-~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ..+.+|.||.+.+|.|||++|.+|+.|++.||++|.|.+.. ++.. .+.|.|+|+++++..|..+|.+++.+...
T Consensus        84 ~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~  159 (163)
T 3krm_A           84 KLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQ  159 (163)
T ss_dssp             CEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEEEEEECHHHHHHHHHHHHHHHHHHTC
T ss_pred             ceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHHHHH
Confidence            45779999999999999999999999999999999996542 3333 45899999999999999999999988654

>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=98.92  E-value=7e-10  Score=92.67  Aligned_cols=69  Identities=33%  Similarity=0.550  Sum_probs=61.3

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCC---CCCCcceeEEcCCHHHHHHHHHHHHHHH
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE---ADPNLRNIELEGSFEQIKQASAMVRELI  232 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~---~~~~~r~v~i~G~~~~i~~A~~~I~~~i  232 (290)
                      ..+.+|.||.+.+|.|||++|.+|++|++.||++|+|.+..   .+..++.|+|.|+++++..|..+|.++|
T Consensus       103 ~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          103 LQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             -CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            46889999999999999999999999999999999996542   3456899999999999999999998864

>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=98.91  E-value=6.6e-10  Score=93.12  Aligned_cols=75  Identities=24%  Similarity=0.398  Sum_probs=66.7

Q ss_pred             CCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCC---CCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE---ADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       163 ~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~---~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ...+.+|.||.+.+|.|||++|++|+.|++.||++|+|.+..   ++..+|.+.|+|+.+++..|..+|.+.+.+...
T Consensus         4 ~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~~   81 (178)
T 2anr_A            4 SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQ   81 (178)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhccCC
Confidence            357899999999999999999999999999999999996542   456789999999999999999999999876543

>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=98.84  E-value=1.9e-09  Score=81.74  Aligned_cols=27  Identities=19%  Similarity=0.439  Sum_probs=23.9

Q ss_pred             CCcccccccccccccccCCCCCcccccc
Q 022898           92 PTVVKSRMCNRLNSAEGCKFGDKCHFAH  119 (290)
Q Consensus        92 ~~~~ktr~C~~~~~~g~C~~G~~C~f~H  119 (290)
                      ...+|+.+|.+| ..|.|.+|++|+|+|
T Consensus         8 ~~~~k~~lC~~f-~~G~C~~G~~C~f~H   34 (98)
T 2cqe_A            8 ELPKKRELCKFY-ITGFCARAENCPYMH   34 (98)
T ss_dssp             CCSCCCSBCTTT-TTTCCSCSTTCSSBS
T ss_pred             CCCCCCccCccc-ccCcCCCCCCCCCCC
Confidence            455799999988 579999999999999

>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=98.81  E-value=1.8e-09  Score=88.77  Aligned_cols=69  Identities=28%  Similarity=0.387  Sum_probs=63.3

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  235 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~  235 (290)
                      .+.+|.||.+.+|.|||++|++|++|++.||++|+|.+.  +..+|.+.|+|+.+++..|..+|.+.+.+.
T Consensus         5 ~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   73 (160)
T 2jzx_A            5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEED   73 (160)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHHHHHHHHHHHHHHHHhh
Confidence            578999999999999999999999999999999999764  356899999999999999999999998775

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

Probab=98.76  E-value=2.6e-09  Score=77.41  Aligned_cols=28  Identities=32%  Similarity=0.618  Sum_probs=24.3

Q ss_pred             CCcccccccccccccccCCCCCccccccc
Q 022898           92 PTVVKSRMCNRLNSAEGCKFGDKCHFAHG  120 (290)
Q Consensus        92 ~~~~ktr~C~~~~~~g~C~~G~~C~f~H~  120 (290)
                      ...+|+.+|.+|.+ |.|.+|+.|.|+|.
T Consensus         5 ~~~~k~~~C~~fl~-G~C~~G~~C~fsH~   32 (77)
T 2d9n_A            5 SSGEKTVVCKHWLR-GLCKKGDQCEFLHE   32 (77)
T ss_dssp             CSCCTTSBCHHHHT-TCCSCTTSSSSBCS
T ss_pred             CCCCcceeCHhHcc-CcCCCCCCCCCccc
Confidence            35678899998877 89999999999994

>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=98.75  E-value=4.2e-09  Score=85.43  Aligned_cols=70  Identities=21%  Similarity=0.359  Sum_probs=59.0

Q ss_pred             eEEEEecccccceeeCCCCCchhhHHHhhCC-ceeeccC-CCC--CCc--ceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898          166 TAKISVDASLAGAIIGKGGVNSKQICRQTGA-KLSIRDH-EAD--PNL--RNIELEGSFEQIKQASAMVRELIVRI  235 (290)
Q Consensus       166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga-~i~v~~~-~~~--~~~--r~v~i~G~~~~i~~A~~~I~~~i~~~  235 (290)
                      ...+.||.+.+|.+|||+|.+|+.+++.||+ +|+|.+. +..  ..+  +.|+|+|++++++.|..+|.+.+.+.
T Consensus        68 e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~l  143 (144)
T 2qnd_A           68 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNYL  143 (144)
T ss_dssp             EEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHHHTC
T ss_pred             eEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            3789999999999999999999999999997 8999543 221  122  45899999999999999999998753

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

Probab=98.69  E-value=2.2e-09  Score=74.96  Aligned_cols=36  Identities=31%  Similarity=0.500  Sum_probs=31.6

Q ss_pred             CCCcccccccccccccccCCCCCcccccccccccCCC
Q 022898           91 GPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKP  127 (290)
Q Consensus        91 ~~~~~ktr~C~~~~~~g~C~~G~~C~f~H~~~el~~~  127 (290)
                      .+|..+++||..| ..|.|+||++|+|||+++||+..
T Consensus        14 R~P~~k~~LC~~~-~~G~C~~G~~C~FAHG~~ELr~~   49 (69)
T 2d9m_A           14 RFPTGYFSICDRY-MNGTCPEGNSCKFAHGNAELHEW   49 (69)
T ss_dssp             CCCCSCCSBCHHH-HHSCCSSCSSCSSBSSHHHHHHH
T ss_pred             cCCCCCcccCccc-CcCCCCCCCccCCcCCHHHHhhH
Confidence            4556688999999 77899999999999999999974

>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=98.68  E-value=2e-08  Score=75.68  Aligned_cols=74  Identities=16%  Similarity=0.261  Sum_probs=65.7

Q ss_pred             CCCceEEEEecccccceeeCCCCCchhhHHHhh-CCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          162 GASATAKISVDASLAGAIIGKGGVNSKQICRQT-GAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       162 ~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~s-ga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ....+..|.||.++.+.|||++|.+|+.|.+++ |++|.+.+..  ...+.|+|.|..++++.|..+|..++.+.+.
T Consensus        14 ~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g--~~~~~V~I~G~~~~v~~A~~~I~~iv~e~e~   88 (95)
T 2ctj_A           14 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG--SGSDTVVIRGPSSDVEKAKKQLLHLAEEKQT   88 (95)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT--TTCCEEEEESCHHHHHHHHHHHHHHHHHHSC
T ss_pred             hhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC--CCcceEEEEcCHHHHHHHHHHHHHHHhhhhh
Confidence            346789999999999999999999999999999 9999996533  3466899999999999999999999988765

>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=98.65  E-value=5.3e-09  Score=74.35  Aligned_cols=64  Identities=20%  Similarity=0.409  Sum_probs=47.6

Q ss_pred             cccccccccccCCCCCCCC-CceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCC
Q 022898           32 SKSKPCTKFFSTAGCPFGE-SCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCK  110 (290)
Q Consensus        32 ~Kt~lC~~~~~~g~C~~G~-~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~  110 (290)
                      .|..+|++|. .|.|..|+ .|.|+|+....+                           ......++.+|..|.+ |.|.
T Consensus         4 ~k~~vC~~f~-~G~C~rg~~~C~f~H~~~~~~---------------------------~~~~~~~~~vC~~flk-G~C~   54 (70)
T 3d2q_A            4 DRLEVCREYQ-RGNCNRGENDCRFAHPADSTM---------------------------IDTNDNTVTVCMDYIK-GRCS   54 (70)
T ss_dssp             CEEEBCHHHH-TTCCSSCTTTCSSBCCCTTSC---------------------------CBTTTTEEEBCHHHHT-TCCC
T ss_pred             ccchhCHHHh-cCCCCCCCCCCCCccCccccc---------------------------ccccCCcceeccccCc-CCCC
Confidence            3678999996 57999999 599999751100                           0123456778987766 8999


Q ss_pred             CCCcccccccccccC
Q 022898          111 FGDKCHFAHGEWELG  125 (290)
Q Consensus       111 ~G~~C~f~H~~~el~  125 (290)
                      .+ .|+|+|...+|+
T Consensus        55 r~-~C~y~H~~~~L~   68 (70)
T 3d2q_A           55 RE-KCKYFHPPAHLQ   68 (70)
T ss_dssp             CT-TCCSBCCCHHHH
T ss_pred             CC-CcCeeCCHHHHh
Confidence            99 999999877664

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

Probab=98.58  E-value=8.6e-09  Score=73.59  Aligned_cols=27  Identities=33%  Similarity=0.636  Sum_probs=23.3

Q ss_pred             CcccccccccccccccCCCCCccccccc
Q 022898           93 TVVKSRMCNRLNSAEGCKFGDKCHFAHG  120 (290)
Q Consensus        93 ~~~ktr~C~~~~~~g~C~~G~~C~f~H~  120 (290)
                      ...++.+|.+|.+ |.|.+|+.|.|+|.
T Consensus        12 ~~~k~~vCk~fl~-G~C~~G~~C~fsH~   38 (72)
T 2rhk_C           12 SGEKTVVCKHWLR-GLCKKGDQCEFLHE   38 (72)
T ss_dssp             SCCCCSBCHHHHT-TCCCCGGGSSSBCS
T ss_pred             CCCcCeeCHHHhc-CCCCCCCCCCCccc
Confidence            4567889998877 89999999999993

>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=98.54  E-value=1e-07  Score=72.61  Aligned_cols=68  Identities=22%  Similarity=0.334  Sum_probs=60.4

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHh-hCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQ-TGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~-sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      .+..|.||..+.+.|||++|++|+.|++. +++.|.+.+     .++.|+|.|..+.|..|...|...+.+...
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-----~~~~ItI~G~~~~V~~a~~~I~~~v~el~~   95 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTEDVSVAQEQIEGMVKDLIN   95 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-----CCCEEEEECCHHHHHHHHHHHHHHHHHHHh
Confidence            67899999999999999999999999996 688898875     346899999999999999999998876543

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

Probab=98.52  E-value=5.1e-09  Score=79.25  Aligned_cols=65  Identities=23%  Similarity=0.417  Sum_probs=48.1

Q ss_pred             cccccccccccCCCCCCCC-CceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCC
Q 022898           32 SKSKPCTKFFSTAGCPFGE-SCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCK  110 (290)
Q Consensus        32 ~Kt~lC~~~~~~g~C~~G~-~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~  110 (290)
                      .|..+|++|++ |.|..|+ .|+|+|......                           ......+..+|..|.+ |.|.
T Consensus        18 ~k~~VCr~Flr-G~C~rgd~~C~FsH~~~~~~---------------------------~~~~~~~~~vC~~flk-G~C~   68 (98)
T 2e5s_A           18 DKLEVCREFQR-GNCARGETDCRFAHPADSTM---------------------------IDTSDNTVTVCMDYIK-GRCM   68 (98)
T ss_dssp             SEEEBCSHHHH-TCCSSHHHHCSSBCCSSCCS---------------------------CCTTTCEEEBCHHHHH-TCCC
T ss_pred             hhhhhhHHHhc-CcCCCCCCCCCCcCCchhcc---------------------------ccccCCccccchhhcc-CCCC
Confidence            47789999997 7999999 799999751100                           0123456678976655 8999


Q ss_pred             CCCcccccccccccCC
Q 022898          111 FGDKCHFAHGEWELGK  126 (290)
Q Consensus       111 ~G~~C~f~H~~~el~~  126 (290)
                      ++ .|+|.|...+|+.
T Consensus        69 r~-~C~y~H~~~~l~~   83 (98)
T 2e5s_A           69 RE-KCKYFHPPAHLQA   83 (98)
T ss_dssp             CT-TCCSBCCCHHHHH
T ss_pred             CC-CcCccCChHHHHH
Confidence            99 9999998766644

>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=98.51  E-value=2.8e-08  Score=70.57  Aligned_cols=30  Identities=27%  Similarity=0.691  Sum_probs=27.1

Q ss_pred             cccccCCCCCCCCCCCCCCCcCCCChhhhcc
Q 022898          257 FKTKLCGNFAKGSCTFGDRCHFAHGAAELRK  287 (290)
Q Consensus       257 ~k~~~C~~~~~g~C~~g~~C~f~Hg~~el~~  287 (290)
                      .++.+|.+|..|.|..| +|+|.|...+|+.
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            35668999999999999 9999999999985

>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=98.47  E-value=7.2e-08  Score=71.64  Aligned_cols=69  Identities=20%  Similarity=0.297  Sum_probs=58.8

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCc-eeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHhcCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAK-LSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~-i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      .....|.||.+.++.|||++|.+|+.|++.||++ |.|.+     ....|.|.| +.++++.|..+|...-.....
T Consensus        14 ~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e-----ddG~V~I~g~~~ea~~~A~~~I~~ie~~~~v   84 (91)
T 2cpq_A           14 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-----DTGTFRIYGESADAVKKARGFLEFVEDFIQV   84 (91)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHSCCCCCCCC
T ss_pred             ceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc-----CCCEEEEEECCHHHHHHHHHHHHhhheEEec
Confidence            5778899999999999999999999999999998 99964     236789999 899999999988665444443

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

Probab=98.33  E-value=1.7e-07  Score=70.78  Aligned_cols=30  Identities=27%  Similarity=0.668  Sum_probs=26.3

Q ss_pred             cccccCCCCCCCCCCCCCCCcCCCChhhhcc
Q 022898          257 FKTKLCGNFAKGSCTFGDRCHFAHGAAELRK  287 (290)
Q Consensus       257 ~k~~~C~~~~~g~C~~g~~C~f~Hg~~el~~  287 (290)
                      .++.+|.+|..|.|.++ +|+|.|...+|+.
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            35567999999999999 9999999998864

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.30  E-value=1.1e-06  Score=68.55  Aligned_cols=72  Identities=18%  Similarity=0.174  Sum_probs=55.6

Q ss_pred             CceEEEEeccc-------ccceeeCCCCCchhhHHHhhCCceeeccCCC-----------CCCcceeEEcCCHHHHHHHH
Q 022898          164 SATAKISVDAS-------LAGAIIGKGGVNSKQICRQTGAKLSIRDHEA-----------DPNLRNIELEGSFEQIKQAS  225 (290)
Q Consensus       164 ~~t~~i~VP~~-------~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~-----------~~~~r~v~i~G~~~~i~~A~  225 (290)
                      ..+.+|.||.+       +++.|||++|.+|+.|+++||++|.|.....           +....+.....+.++++.|.
T Consensus        11 ~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~   90 (119)
T 2yqr_A           11 YVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAK   90 (119)
T ss_dssp             CEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHH
T ss_pred             EEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHH
Confidence            35677888775       6778999999999999999999999963321           11224444456899999999


Q ss_pred             HHHHHHHHhc
Q 022898          226 AMVRELIVRI  235 (290)
Q Consensus       226 ~~I~~~i~~~  235 (290)
                      .+|.+++...
T Consensus        91 ~~Ie~Ll~~v  100 (119)
T 2yqr_A           91 KLCENLLQTV  100 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHhhch
Confidence            9999998754

>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=98.27  E-value=2.6e-07  Score=67.62  Aligned_cols=64  Identities=17%  Similarity=0.265  Sum_probs=45.7

Q ss_pred             CccccccccccccCCCCCCCC-CceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCccccccccccccccc
Q 022898           30 VGSKSKPCTKFFSTAGCPFGE-SCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEG  108 (290)
Q Consensus        30 ~~~Kt~lC~~~~~~g~C~~G~-~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~  108 (290)
                      .+.|...|++|.+ |.|..|| .|+|+|.... +                            .-..-+..+|..|. .|.
T Consensus         5 ~~~~~~VCr~Flr-G~C~r~d~~C~f~H~~~~-~----------------------------~~~~~~~~vC~dfl-kG~   53 (83)
T 3d2n_A            5 KWLTLEVCREFQR-GTCSRPDTECKFAHPSKS-C----------------------------QVENGRVIACFDSL-KGR   53 (83)
T ss_dssp             GGGEEEBCTTGGG-TCCCSCTTTCSSBCCCTT-C----------------------------CEETTEEECCHHHH-TTC
T ss_pred             ccccchhcHHHhc-CCCCCCCCCCCCcCCCcc-c----------------------------cccCCceeehhHhh-hcc
Confidence            3567789999997 7999997 9999997511 0                            00122345787774 579


Q ss_pred             CCCCCcccccccccccC
Q 022898          109 CKFGDKCHFAHGEWELG  125 (290)
Q Consensus       109 C~~G~~C~f~H~~~el~  125 (290)
                      |..+ .|+|.|....|.
T Consensus        54 C~r~-~C~y~H~~~~l~   69 (83)
T 3d2n_A           54 CSRE-NCKYLHPPPHLK   69 (83)
T ss_dssp             CCCS-SCSSCCCCHHHH
T ss_pred             ccCC-CcceeCChHHHH
Confidence            9988 999999765443

>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=98.25  E-value=1.3e-06  Score=69.38  Aligned_cols=74  Identities=20%  Similarity=0.367  Sum_probs=58.4

Q ss_pred             CCCceEEEEeccc------ccceeeCCCCCchhhHHHhhCCceeeccCCC----------------CCCcceeEEcC-CH
Q 022898          162 GASATAKISVDAS------LAGAIIGKGGVNSKQICRQTGAKLSIRDHEA----------------DPNLRNIELEG-SF  218 (290)
Q Consensus       162 ~~~~t~~i~VP~~------~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~----------------~~~~r~v~i~G-~~  218 (290)
                      ....+.+|.||.+      ++|.|||.+|.+|+.|+++||++|.|.....                ....--|.|++ +.
T Consensus         4 ~~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~   83 (131)
T 1k1g_A            4 ATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTM   83 (131)
T ss_dssp             -CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSH
T ss_pred             CceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCH
Confidence            3467889999998      8899999999999999999999999965211                01123455555 79


Q ss_pred             HHHHHHHHHHHHHHHhc
Q 022898          219 EQIKQASAMVRELIVRI  235 (290)
Q Consensus       219 ~~i~~A~~~I~~~i~~~  235 (290)
                      +.++.|..+|..++...
T Consensus        84 e~~~~A~~~I~~ll~~~  100 (131)
T 1k1g_A           84 ENVKKAVEQIRNILKQG  100 (131)
T ss_dssp             HHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHhcc
Confidence            99999999999998763

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

Probab=98.18  E-value=1.7e-06  Score=80.16  Aligned_cols=69  Identities=17%  Similarity=0.359  Sum_probs=60.9

Q ss_pred             CCceEEEEecccccceeeCCCC--CchhhHHHhhCCceeeccCC-----CCCCcceeEEcCCHHHHHHHHHHHHHH
Q 022898          163 ASATAKISVDASLAGAIIGKGG--VNSKQICRQTGAKLSIRDHE-----ADPNLRNIELEGSFEQIKQASAMVREL  231 (290)
Q Consensus       163 ~~~t~~i~VP~~~vg~iIGkgG--~~Ik~i~~~sga~i~v~~~~-----~~~~~r~v~i~G~~~~i~~A~~~I~~~  231 (290)
                      ...|..+.||......||||+|  ++|++|+++||++|++.+.+     .......|+|+|.++.|+.|...|.+.
T Consensus        28 ~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l  103 (376)
T 3n89_A           28 TRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRN  103 (376)
T ss_dssp             TEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHS
T ss_pred             CEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhc
Confidence            3788999999999999999999  99999999999999997654     123457899999999999999999874

>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=97.86  E-value=3.9e-06  Score=62.05  Aligned_cols=62  Identities=18%  Similarity=0.308  Sum_probs=44.0

Q ss_pred             ccccccccccccCCCCCCCC-CceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccC
Q 022898           31 GSKSKPCTKFFSTAGCPFGE-SCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGC  109 (290)
Q Consensus        31 ~~Kt~lC~~~~~~g~C~~G~-~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C  109 (290)
                      +.+...|+.|.+ |.|..|+ .|+|+|.... .                            .-..-+..+|..| ..|.|
T Consensus        14 ~~~~~VCrdFlr-G~C~r~d~~CrfsH~~~~-~----------------------------~v~~~~~~vC~df-lkG~C   62 (89)
T 2rpp_A           14 WLTLEVCRQFQR-GTCSRSDEECKFAHPPKS-C----------------------------QVENGRVIACFDS-LKGRC   62 (89)
T ss_dssp             SSEECBCHHHHH-TCCCCCTTTSSSBCCCSS-S----------------------------CCBTTBEEBCHHH-HHTCC
T ss_pred             cchhhhchHHhc-CCCCCCCCCCCCcCCCcc-c----------------------------cccCCceeeehhh-hhCcC
Confidence            446779999997 7999998 9999997411 0                            0011234578766 56899


Q ss_pred             CCCCccccccccccc
Q 022898          110 KFGDKCHFAHGEWEL  124 (290)
Q Consensus       110 ~~G~~C~f~H~~~el  124 (290)
                      ..+ .|+|.|....|
T Consensus        63 ~r~-~Cky~H~~~hl   76 (89)
T 2rpp_A           63 SRE-NCKYLHPPTHL   76 (89)
T ss_dssp             CCT-TCCSBCCCHHH
T ss_pred             CCC-CcceecCHHHH
Confidence            977 99999976444

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

Probab=97.81  E-value=3.8e-06  Score=72.52  Aligned_cols=64  Identities=17%  Similarity=0.228  Sum_probs=54.8

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-----CHHHHHHHHHHHHHHHH
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-----SFEQIKQASAMVRELIV  233 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-----~~~~i~~A~~~I~~~i~  233 (290)
                      ....+.||.+.++.|||++|.+|+.|++.+|++|+|...     .+.|.|.+     +++++++|..+|..++.
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~-----~g~V~I~~~~~t~d~~~i~kA~~~I~~i~r  102 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE-----TGEVWITSTKETEDPLAVWKARDIVLAIGR  102 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT-----TCEEEEEECTTCCSHHHHHHHHHHHHHHHT
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC-----CCEEEEecCCCCCCHHHHHHHHHHHHHHhc
Confidence            457899999999999999999999999999999999632     34556655     47999999999999873

>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=97.78  E-value=8.7e-06  Score=59.45  Aligned_cols=27  Identities=26%  Similarity=0.597  Sum_probs=23.7

Q ss_pred             ccCCCCCCCCCCCCCCCcCCCChhhhcc
Q 022898          260 KLCGNFAKGSCTFGDRCHFAHGAAELRK  287 (290)
Q Consensus       260 ~~C~~~~~g~C~~g~~C~f~Hg~~el~~  287 (290)
                      ..|.+|..|.|..+ .|+|.|...+|..
T Consensus        44 ~vC~dflkG~C~r~-~C~y~H~~~~l~~   70 (83)
T 3d2n_A           44 IACFDSLKGRCSRE-NCKYLHPPPHLKT   70 (83)
T ss_dssp             ECCHHHHTTCCCCS-SCSSCCCCHHHHH
T ss_pred             eehhHhhhccccCC-CcceeCChHHHHH
Confidence            36999999999998 9999999887753

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.76  E-value=4.6e-05  Score=60.08  Aligned_cols=69  Identities=13%  Similarity=0.174  Sum_probs=61.7

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHH
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIV  233 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~  233 (290)
                      .....+.|.+..+++|||++|+.|+.|...|.+.|+|..-+++ +.-.|+|.|++.....+..+|..+..
T Consensus        55 ~dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s~-g~tEVtIfG~~~~Q~rak~MI~sLA~  123 (140)
T 3v69_A           55 EDPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGPE-RRAEIWIFGPPPFRRDVDRMLTDLAH  123 (140)
T ss_dssp             SSCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCTT-SCEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCCC-CcEEEEEECCHHHHHHHHHHHHHHHH
Confidence            5668999999999999999999999999999999999776553 67889999999999999999987653

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

Probab=97.75  E-value=2.3e-05  Score=72.58  Aligned_cols=70  Identities=16%  Similarity=0.270  Sum_probs=57.9

Q ss_pred             CceEEEEecccccceeeCCCCCc--hhhHHHhhCCceeeccCCC--C--CCcceeEEcCCHHHHHHHHHHHHHHHH
Q 022898          164 SATAKISVDASLAGAIIGKGGVN--SKQICRQTGAKLSIRDHEA--D--PNLRNIELEGSFEQIKQASAMVRELIV  233 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~--Ik~i~~~sga~i~v~~~~~--~--~~~r~v~i~G~~~~i~~A~~~I~~~i~  233 (290)
                      ..+..|.|+......|||++|.+  |+.|+++||++|.+.+.+.  +  .....|+|+|+.++|..|...|.+.|.
T Consensus       185 ~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lLP  260 (376)
T 3n89_A          185 NFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLLP  260 (376)
T ss_dssp             CEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTSE
T ss_pred             ceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhCC
Confidence            57889999999999999999965  4999999999999965422  1  235789999999999999999999863

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

Probab=97.72  E-value=1.2e-05  Score=69.45  Aligned_cols=55  Identities=25%  Similarity=0.375  Sum_probs=50.0

Q ss_pred             ccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898          175 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       175 ~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~  236 (290)
                      .+|.|||++|.+|+.|++.||+.|.|.+       +.++|.|++++++.|..+|.+++....
T Consensus       139 ~~GriIGk~G~tik~ie~~Tg~~I~v~~-------~~v~i~G~~~~i~~A~~~i~~li~g~~  193 (219)
T 2e3u_A          139 VRGRIIGRKGRTRQIIEEMSGASVSVYG-------KTVAIIGNPIQIEIAKTAIEKLARGSP  193 (219)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEEET-------TEEEEEECHHHHHHHHHHHHHHHTTCC
T ss_pred             hhheeECCCchHHHHHHHHhCceEEECC-------eEEEEEeCHHHHHHHHHHHHHHHcCCC
Confidence            6888999999999999999999999964       569999999999999999999995543

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=97.67  E-value=2.6e-05  Score=62.47  Aligned_cols=71  Identities=25%  Similarity=0.374  Sum_probs=52.4

Q ss_pred             ceEEEEecccc------cceeeCCCCCchhhHHHhhCCceeeccCCCCC-----------------C-cceeEEcC-CHH
Q 022898          165 ATAKISVDASL------AGAIIGKGGVNSKQICRQTGAKLSIRDHEADP-----------------N-LRNIELEG-SFE  219 (290)
Q Consensus       165 ~t~~i~VP~~~------vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~-----------------~-~r~v~i~G-~~~  219 (290)
                      .+.+|.||...      +|.|||.+|.++|.|++.||++|.|......-                 . .--|.|++ +++
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            35678888655      88999999999999999999999997533110                 0 11445665 443


Q ss_pred             -----HHHHHHHHHHHHHHhc
Q 022898          220 -----QIKQASAMVRELIVRI  235 (290)
Q Consensus       220 -----~i~~A~~~I~~~i~~~  235 (290)
                           .++.|..+|..++...
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p~  102 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVPA  102 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCC
T ss_pred             hhHHHHHHHHHHHHHHHCCCC
Confidence                 7899999999988643

>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=97.66  E-value=3.2e-05  Score=65.25  Aligned_cols=66  Identities=20%  Similarity=0.294  Sum_probs=57.7

Q ss_pred             eEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEc-----CCHHHHHHHHHHHHHHHHhcC
Q 022898          166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE-----GSFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~-----G~~~~i~~A~~~I~~~i~~~~  236 (290)
                      ...+.||...+|+|||++|+.++.|++.++++|++..     .++.++|.     |++.++.+|..+|..+....+
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~-----~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf~   75 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFP   75 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET-----TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCC
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc-----CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCC
Confidence            4789999999999999999999999999999999964     35566666     999999999999988776544

>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=97.44  E-value=5.4e-05  Score=61.05  Aligned_cols=61  Identities=21%  Similarity=0.270  Sum_probs=45.9

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHH
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAM  227 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~  227 (290)
                      ..+.++.||.+.+|++||++|++|+.|++.+|  |.+-....+ ..+.+...++++.+..|..+
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~~~-~~~~i~~~~~p~~v~~~~~~   63 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLDED-TCTFHIYGEDQDAVKKARSF   63 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEETT-TTEEEEEESSHHHHHHHHHH
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccCCC-chheeeccCCHHHHHHHHHh
Confidence            45789999999999999999999999999999  655322222 23445555679999888654

>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=97.32  E-value=0.00012  Score=54.09  Aligned_cols=27  Identities=26%  Similarity=0.600  Sum_probs=23.5

Q ss_pred             ccCCCCCCCCCCCCCCCcCCCChhhhcc
Q 022898          260 KLCGNFAKGSCTFGDRCHFAHGAAELRK  287 (290)
Q Consensus       260 ~~C~~~~~g~C~~g~~C~f~Hg~~el~~  287 (290)
                      ..|.+|..|.|..+ .|+|.|....|..
T Consensus        52 ~vC~dflkG~C~r~-~Cky~H~~~hl~~   78 (89)
T 2rpp_A           52 IACFDSLKGRCSRE-NCKYLHPPTHLKT   78 (89)
T ss_dssp             EBCHHHHHTCCCCT-TCCSBCCCHHHHH
T ss_pred             eeehhhhhCcCCCC-CcceecCHHHHHH
Confidence            35999999999998 9999999887753

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

Probab=97.27  E-value=0.00012  Score=62.51  Aligned_cols=21  Identities=29%  Similarity=0.945  Sum_probs=19.3

Q ss_pred             cCCCCCCCCCCCCCCCcCCCCh
Q 022898          261 LCGNFAKGSCTFGDRCHFAHGA  282 (290)
Q Consensus       261 ~C~~~~~g~C~~g~~C~f~Hg~  282 (290)
                      +|.+|..|+|+| ..|+-.|..
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            499999999999 899999986

>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=97.23  E-value=7.8e-05  Score=62.83  Aligned_cols=54  Identities=22%  Similarity=0.421  Sum_probs=48.9

Q ss_pred             cccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHh
Q 022898          174 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR  234 (290)
Q Consensus       174 ~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~  234 (290)
                      ..+|-|||++|.+|+.|++.||+.|.|.+       +.+.|.|++++++.|...|..++..
T Consensus       107 r~~GrIIGk~G~tik~iE~~Tg~~I~v~~-------~~v~i~G~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          107 RIKGRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGDYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHTCEEEECS-------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HHhhheeCCCccHHHHHHHHHCceEEEcC-------CEEEEEeChHHHHHHHHHHHHHHcC
Confidence            35788999999999999999999999975       3799999999999999999999853

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.11  E-value=0.00011  Score=72.68  Aligned_cols=62  Identities=21%  Similarity=0.333  Sum_probs=51.8

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHH
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELI  232 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i  232 (290)
                      ....+.||.+.++.|||+||.+|+.|++.||+.|.|.+      +..|.|.+ +.+.++.|..+|..++
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 VVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD------EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS------SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             eEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC------CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999999999999974      24667766 5788999999887654

>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=96.54  E-value=0.001  Score=42.90  Aligned_cols=28  Identities=25%  Similarity=0.549  Sum_probs=26.2

Q ss_pred             ccccccccccccCCCCCCCCCceEeccc
Q 022898           31 GSKSKPCTKFFSTAGCPFGESCHFLHYF   58 (290)
Q Consensus        31 ~~Kt~lC~~~~~~g~C~~G~~C~F~H~~   58 (290)
                      ..++.+|..|...|-|++|.+|.|.|++
T Consensus        17 ~~~~~iC~~FSayGwCp~G~~Cp~SHDi   44 (50)
T 2fc6_A           17 PHPTSICDNFSAYGWCPLGPQCPQSHDI   44 (50)
T ss_dssp             CCCSCBCSHHHHTCCCTTGGGCSSBCCC
T ss_pred             ccccchhhhccccccCCCCCCCCccccC
Confidence            4689999999999999999999999986

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=96.51  E-value=0.0006  Score=68.21  Aligned_cols=67  Identities=22%  Similarity=0.345  Sum_probs=10.9

Q ss_pred             eEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHhcCCC
Q 022898          166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGPA  238 (290)
Q Consensus       166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~~~~~  238 (290)
                      ...+.||.+.++.|||+||.+|+.|.+.||++|.|.+.      ..|.|.+ +.+.++.|..+|..++.+...+
T Consensus       571 ~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~dd------G~v~I~~~~~~~~~~A~~~i~~i~~~~~vG  638 (726)
T 4aid_A          571 IETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDD------GVVKVSASDGAKIKAAIDWIKSITDEAEVG  638 (726)
T ss_dssp             -------------------------------------------------CCSCHHHHHHHHHC-----------
T ss_pred             EEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEECC------ceEEEEeCCHHHHHHHHHHHHHHhhhhcCC
Confidence            46789999999999999999999999999999999642      2344444 6889999999999888766554

>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=94.94  E-value=0.007  Score=38.96  Aligned_cols=28  Identities=18%  Similarity=0.513  Sum_probs=25.2

Q ss_pred             cccccccccccccccCCCCCcccccccc
Q 022898           94 VVKSRMCNRLNSAEGCKFGDKCHFAHGE  121 (290)
Q Consensus        94 ~~ktr~C~~~~~~g~C~~G~~C~f~H~~  121 (290)
                      ..++.+|..|-..|+|++|.+|.+.|..
T Consensus        17 ~~~~~iC~~FSayGwCp~G~~Cp~SHDi   44 (50)
T 2fc6_A           17 PHPTSICDNFSAYGWCPLGPQCPQSHDI   44 (50)
T ss_dssp             CCCSCBCSHHHHTCCCTTGGGCSSBCCC
T ss_pred             ccccchhhhccccccCCCCCCCCccccC
Confidence            3578899999999999999999999954

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

Probab=94.79  E-value=0.012  Score=50.31  Aligned_cols=45  Identities=20%  Similarity=0.569  Sum_probs=37.3

Q ss_pred             cccccccccccC----CCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccc
Q 022898           32 SKSKPCTKFFST----AGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAE  107 (290)
Q Consensus        32 ~Kt~lC~~~~~~----g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g  107 (290)
                      .=-.+|.+| ++    |.|.++++|...|                                          +|.+|. .|
T Consensus       149 lLPeiC~~Y-kG~g~~g~C~~~~~C~kLH------------------------------------------IC~~Fl-~G  184 (229)
T 3u9g_A          149 FLPEICKSY-KGEGRKQTCGQPQPCERLH------------------------------------------ICEHFT-RG  184 (229)
T ss_dssp             GSCCBCTTC-CCSSSCCSCSSSSCCCSBC------------------------------------------SCHHHH-TT
T ss_pred             cCchHHHHh-CCCCCCCcCCCCCCCccee------------------------------------------ccchhh-cC
Confidence            345799999 75    6899999999999                                          697775 56


Q ss_pred             cCCCCCcccccccc
Q 022898          108 GCKFGDKCHFAHGE  121 (290)
Q Consensus       108 ~C~~G~~C~f~H~~  121 (290)
                      .|+| ..|+-.|.-
T Consensus       185 ~C~f-~~CkRsH~~  197 (229)
T 3u9g_A          185 NCSY-LNCLRSHNL  197 (229)
T ss_dssp             CCCC-SSCSSCCCT
T ss_pred             CcCC-CCccCccCc
Confidence            8999 899999953

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=93.68  E-value=0.0087  Score=52.09  Aligned_cols=22  Identities=41%  Similarity=0.946  Sum_probs=20.8

Q ss_pred             ccCCCCCCCCCCCCCCCcCCCC
Q 022898          260 KLCGNFAKGSCTFGDRCHFAHG  281 (290)
Q Consensus       260 ~~C~~~~~g~C~~g~~C~f~Hg  281 (290)
                      .+|.||..|.|..|+.|.|.|.
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            4799999999999999999996

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=92.15  E-value=0.026  Score=49.03  Aligned_cols=26  Identities=31%  Similarity=0.636  Sum_probs=22.6

Q ss_pred             cccccccccCCCCCCCCCceEecccCC
Q 022898           34 SKPCTKFFSTAGCPFGESCHFLHYFPG   60 (290)
Q Consensus        34 t~lC~~~~~~g~C~~G~~C~F~H~~~~   60 (290)
                      ...|.||.+ |.|++|+.|.|.|.+|.
T Consensus        70 ~~~C~ffak-G~C~~G~~C~y~H~lPt   95 (240)
T 3u1l_A           70 LFFCLFFAK-GMCCLGPKCEYLHHIPD   95 (240)
T ss_dssp             CSBCHHHHT-TCCSCGGGCSSBBSCCC
T ss_pred             CeEcCcccc-CCCCCCCCCCccCCCCC
Confidence            359999987 79999999999998854

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=91.39  E-value=0.036  Score=55.54  Aligned_cols=67  Identities=22%  Similarity=0.372  Sum_probs=0.0

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHhcCC
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ....+.||.+.++.|||+||.+|+.|.+.+|+.|.|.+      ...+.|.+ +.+.++.|..+|..++.+...
T Consensus       560 ~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~------dg~v~I~~~~~~~~~~a~~~i~~i~~~~~v  627 (723)
T 3cdi_A          560 RIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED------DGTVKIAATDGEKAKHAIRRIEEITAEIEV  627 (723)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             eEEEEEECHHHhcccccccceeeeeeehhhCceEEecC------CccEEEecCCHHHHHHHHHHHHHHhhhhhc
Confidence            34668899999999999999999999999999998864      22344444 556677777777766654443

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=90.53  E-value=0.025  Score=56.96  Aligned_cols=60  Identities=22%  Similarity=0.279  Sum_probs=19.0

Q ss_pred             EEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHH
Q 022898          167 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELI  232 (290)
Q Consensus       167 ~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i  232 (290)
                      ..+.||.+.++.+||++|.+|+.|.+.+|+.|.|.+      +..+.|+. +.+.++.|..+|..+.
T Consensus       600 ~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          600 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CCC------------------CTTCCCCCSCC--------------CCCBSSHHHHCC---------
T ss_pred             EEEEEChHHeehcccccceeeehhhHhhCCEEEecC------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            457899999999999999999999999999999874      23444544 5666666766666654

>3v33_A Ribonuclease ZC3H12A; rossmann-like sandwich fold, RNAse, cytoplastic, hydrolase; 2.00A {Homo sapiens}

Probab=82.86  E-value=0.47  Score=40.50  Aligned_cols=29  Identities=24%  Similarity=0.530  Sum_probs=0.0

Q ss_pred             cccccccCCCCCCCCCCCCCCCcCCCChhhh
Q 022898          255 SNFKTKLCGNFAKGSCTFGDRCHFAHGAAEL  285 (290)
Q Consensus       255 ~~~k~~~C~~~~~g~C~~g~~C~f~Hg~~el  285 (290)
                      ..-+.++|+|-.  .|-||.+|+|.|.|+--
T Consensus       188 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~  216 (223)
T 3v33_A          188 LEHRKQPCPYGR--KCTYGIKCRFFHPERPS  216 (223)
T ss_dssp             -------------------------------
T ss_pred             cccCCCCCCCCc--ccccCCcceecCCccCC
Confidence            334678899954  79999999999998643

>3v33_A Ribonuclease ZC3H12A; rossmann-like sandwich fold, RNAse, cytoplastic, hydrolase; 2.00A {Homo sapiens}

Probab=82.75  E-value=0.45  Score=40.64  Aligned_cols=24  Identities=29%  Similarity=0.822  Sum_probs=0.0

Q ss_pred             cccccccccccCCCCCCCCCceEeccc
Q 022898           32 SKSKPCTKFFSTAGCPFGESCHFLHYF   58 (290)
Q Consensus        32 ~Kt~lC~~~~~~g~C~~G~~C~F~H~~   58 (290)
                      .+..+|+|   +..|.||.+|+|.|..
T Consensus       190 ~~~~~~~~---~~~~~~~~~~~~~~~~  213 (223)
T 3v33_A          190 HRKQPCPY---GRKCTYGIKCRFFHPE  213 (223)
T ss_dssp             ---------------------------
T ss_pred             cCCCCCCC---CcccccCCcceecCCc
Confidence            36789985   3489999999999975

>2lhn_A Nuclear polyadenylated RNA-binding protein NAB2; nuclear protein; NMR {Saccharomyces cerevisiae S288C}

Probab=82.39  E-value=0.29  Score=34.94  Aligned_cols=21  Identities=19%  Similarity=0.374  Sum_probs=15.9

Q ss_pred             cccccccccCCCCCCCCCceEeccc
Q 022898           34 SKPCTKFFSTAGCPFGESCHFLHYF   58 (290)
Q Consensus        34 t~lC~~~~~~g~C~~G~~C~F~H~~   58 (290)
                      ..+|+|+.   .|.. ..|.|.|..
T Consensus         9 ~e~CKf~~---~Ctn-~~C~f~Hp~   29 (80)
T 2lhn_A            9 LEQCKFGT---HCTN-KRCKYRHAR   29 (80)
Confidence            36787665   6888 899999953

---

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	290
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-17
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	6e-16
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	8e-16
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-15
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-15
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	4e-15
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	4e-15
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	8e-15
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-13
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	3e-13
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	3e-13
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	4e-13
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	1e-12
d1m9oa_	40	g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475	5e-12
d1m9oa_	40	g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475	2e-08
d1m9oa_	40	g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475	2e-04
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	8e-12
d1rgoa1	36	g.66.1.1 (A:151-186) Butyrate response factor 2 (T	9e-12
d1rgoa1	36	g.66.1.1 (A:151-186) Butyrate response factor 2 (T	5e-08
d1rgoa1	36	g.66.1.1 (A:151-186) Butyrate response factor 2 (T	1e-04
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	5e-11
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	3e-09
d1rgoa2	34	g.66.1.1 (A:187-220) Butyrate response factor 2 (T	5e-09
d1rgoa2	34	g.66.1.1 (A:187-220) Butyrate response factor 2 (T	2e-07
d1rgoa2	34	g.66.1.1 (A:187-220) Butyrate response factor 2 (T	4e-05
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	4e-08
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	2e-07
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	5e-06
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	1e-05
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	5e-05
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	2e-04
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	3e-04
d2bl5a1	134	d.51.1.1 (A:1-134) Quaking protein A (Xqua) {Afric	0.003
d1k1ga_	122	d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo s	0.004

>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 = 73.7 bits (181), Expect = 1e-17
 Identities = 17/70 (24%), Positives = 35/70 (50%)

Query: 163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIK 222
           +  T +  V   + G IIG+GG    +I +++G K+ I         R+  L G+ E ++
Sbjct: 6   SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQ 65

Query: 223 QASAMVRELI 232
            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 = 69.1 bits (169), Expect = 6e-16
 Identities = 23/71 (32%), Positives = 40/71 (56%)

Query: 162 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQI 221
           G   T ++++   LAG+IIGKGG   KQI  ++GA + I +       R I + G+ +QI
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQI 60

Query: 222 KQASAMVRELI 232
           + 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 = 68.7 bits (168), Expect = 8e-16
 Identities = 17/68 (25%), Positives = 35/68 (51%)

Query: 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQA 224
            T ++++  +L G IIG+ G N  +I + +GA++ I +     + R + + GS   I  A
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLA 61

Query: 225 SAMVRELI 232
             ++   +
Sbjct: 62  QYLINARL 69

>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 = 67.5 bits (165), Expect = 2e-15
 Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 2/67 (2%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 225
           T ++ +     G+IIGK G + K++  ++GA+  I   E +   R I L G    I +A 
Sbjct: 5   TIRLLMHGKEVGSIIGKKGESVKKMREESGAR--INISEGNCPERIITLAGPTNAIFKAF 62

Query: 226 AMVRELI 232
           AM+ + +
Sbjct: 63  AMIIDKL 69

>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 = 67.6 bits (165), Expect = 2e-15
 Identities = 12/70 (17%), Positives = 25/70 (35%), Gaps = 1/70 (1%)

Query: 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRNIELEGSFEQIK 222
           S    ++VD      IIG+ G    QI  +    +      + +     I + G  +  +
Sbjct: 9   SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTE 68

Query: 223 QASAMVRELI 232
            A   +  ++
Sbjct: 69  AARDAILRIV 78

>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 = 66.8 bits (163), Expect = 4e-15
 Identities = 12/69 (17%), Positives = 31/69 (44%)

Query: 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQ 223
           S    + +     G +IG+ G   K+I    G ++  +  +     R  ++ G  ++ + 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 224 ASAMVRELI 232
           A+ ++ +L+
Sbjct: 62  AAEIITDLL 70

>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 = 66.7 bits (163), Expect = 4e-15
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 159 ASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSF 218
           A     A+A +++       +IGK G   + +  +T  K+ I   +       I++ G+ 
Sbjct: 4   ARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPS--NQIKITGTK 61

Query: 219 EQIKQASAMVRELI 232
           E 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 = 66.0 bits (161), Expect = 8e-15
 Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI---RDHEADPNLRNIELEGSFEQIK 222
             +++V  +L GAI+GKGG    +    TGA++ I    +       R + + GS    +
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 223 QASAMVRELI 232
            A  ++ + +
Sbjct: 64  AAQYLISQRV 73

>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 = 62.1 bits (151), Expect = 3e-13
 Identities = 11/68 (16%), Positives = 26/68 (38%), Gaps = 1/68 (1%)

Query: 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQA 224
            +  + +D  +   IIG  G   ++I  +    +        P+   + + G  E +++A
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-PQSGAPDPNCVTVTGLPENVEEA 68

Query: 225 SAMVRELI 232
              +  L 
Sbjct: 69  IDHILNLE 76

>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 = 61.5 bits (149), Expect = 3e-13
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 168 KISVDASLAGAIIGKGGVNSKQICRQTGAKLSI---RDHEADPNLRNIELEGSFEQIKQA 224
              V     G IIGKGG   K I +Q+GA++ +       ADPN++   + G+ +QI  A
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYA 63

Query: 225 SAMVRELI 232
             ++ 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 = 61.5 bits (149), Expect = 3e-13
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNL--RNIELEGSFEQ 220
            +A  +I + AS AG +IGKGG   KQ+  + G K+ +           + + + G   +
Sbjct: 6   GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYK 65

Query: 221 IKQASAMVRELI 232
           ++QA  MV ELI
Sbjct: 66  VQQAKEMVLELI 77

>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 = 61.3 bits (149), Expect = 4e-13
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQA 224
              +I++D      +IGK G N  +I  Q    + I           I +EG  + ++QA
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKS--NLIRIEGDPQGVQQA 62

Query: 225 SAMVRELI 232
              + EL 
Sbjct: 63  KRELLELA 70

>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 = 60.2 bits (146), Expect = 1e-12
 Identities = 12/67 (17%), Positives = 27/67 (40%), Gaps = 2/67 (2%)

Query: 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 225
           T ++ V   L   +IG+ G   +++  +    + +   E       I + G    + +A 
Sbjct: 11  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQS--DIIAITGLAANLDRAK 68

Query: 226 AMVRELI 232
           A + E +
Sbjct: 69  AGLLERV 75

>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 = 57.5 bits (139), Expect = 5e-12
 Identities = 17/35 (48%), Positives = 23/35 (65%), Gaps = 1/35 (2%)

Query: 254 SSNFKTKLCGNF-AKGSCTFGDRCHFAHGAAELRK 287
           SS +KT+LC  +   G C +G +C FAHG  ELR+
Sbjct: 4   SSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQ 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 = 47.4 bits (113), Expect = 2e-08
 Identities = 12/32 (37%), Positives = 19/32 (59%)

Query: 96  KSRMCNRLNSAEGCKFGDKCHFAHGEWELGKP 127
           K+ +C   + +  C++G KC FAHG  EL + 
Sbjct: 8   KTELCRTYSESGRCRYGAKCQFAHGLGELRQA 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 = 36.3 bits (84), Expect = 2e-04
 Identities = 7/24 (29%), Positives = 12/24 (50%)

Query: 33 KSKPCTKFFSTAGCPFGESCHFLH 56
          K++ C  +  +  C +G  C F H
Sbjct: 8  KTELCRTYSESGRCRYGAKCQFAH 31

>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 = 58.4 bits (141), Expect = 8e-12
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 2/83 (2%)

Query: 152 PPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH--EADPNL 209
                   +       ++SV     G IIG+GG   + IC+ +GAK++            
Sbjct: 2   SSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLS 61

Query: 210 RNIELEGSFEQIKQASAMVRELI 232
           R I++ G+ +++  A  ++ E +
Sbjct: 62  RLIKISGTQKEVAAAKHLILEKV 84

>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 = 56.3 bits (136), Expect = 9e-12
 Identities = 17/34 (50%), Positives = 24/34 (70%), Gaps = 1/34 (2%)

Query: 254 SSNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELR 286
           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 = 45.9 bits (109), Expect = 5e-08
 Identities = 13/29 (44%), Positives = 18/29 (62%)

Query: 96  KSRMCNRLNSAEGCKFGDKCHFAHGEWEL 124
           K+ +C     +  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 = 36.2 bits (84), Expect = 1e-04
 Identities = 9/24 (37%), Positives = 13/24 (54%)

Query: 33 KSKPCTKFFSTAGCPFGESCHFLH 56
          K++ C  F  +  C +GE C F H
Sbjct: 5  KTELCRPFEESGTCKYGEKCQFAH 28

>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 = 55.6 bits (134), Expect = 5e-11
 Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 1/68 (1%)

Query: 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQA 224
           A  ++S+ A L  ++IG  G   + I  + G  + I           + + G    +++A
Sbjct: 10  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECG-GVHIHFPVEGSGSDTVVIRGPSSDVEKA 68

Query: 225 SAMVRELI 232
              +  L 
Sbjct: 69  KKQLLHLA 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 = 50.9 bits (122), Expect = 3e-09
 Identities = 14/72 (19%), Positives = 30/72 (41%)

Query: 169 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMV 228
           + V     GA+IG  G    +I R+TG  +++    +   +           + +A+ +V
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVV 66

Query: 229 RELIVRIGPAHA 240
           + + +   P  A
Sbjct: 67  KAISLGFPPEKA 78

>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 = 48.5 bits (116), Expect = 5e-09
 Identities = 17/35 (48%), Positives = 20/35 (57%), Gaps = 4/35 (11%)

Query: 251 HPLSSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAE 284
           HP    +KT+LC  F   G C +G RCHF H A E
Sbjct: 3   HP---KYKTELCRTFHTIGFCPYGPRCHFIHNADE 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 = 44.7 bits (106), Expect = 2e-07
 Identities = 9/28 (32%), Positives = 15/28 (53%)

Query: 96  KSRMCNRLNSAEGCKFGDKCHFAHGEWE 123
           K+ +C   ++   C +G +CHF H   E
Sbjct: 7   KTELCRTFHTIGFCPYGPRCHFIHNADE 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 = 37.7 bits (88), Expect = 4e-05
 Identities = 10/24 (41%), Positives = 15/24 (62%)

Query: 33 KSKPCTKFFSTAGCPFGESCHFLH 56
          K++ C  F +   CP+G  CHF+H
Sbjct: 7  KTELCRTFHTIGFCPYGPRCHFIH 30

>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 = 47.4 bits (113), Expect = 4e-08
 Identities = 8/64 (12%), Positives = 25/64 (39%), Gaps = 6/64 (9%)

Query: 169 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMV 228
           ++++ +    +IGK G   K +  +   ++ +  +        I + G   ++  A   +
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQN------GLIWVNGDRRKVSIAEEAI 58

Query: 229 RELI 232
             + 
Sbjct: 59  YLIE 62

>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 = 46.6 bits (111), Expect = 2e-07
 Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 9/65 (13%)

Query: 177 GAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG 236
           G IIG+GG   + I   T   +++ ++E       + + G +E+   A   +  L    G
Sbjct: 25  GRIIGEGGRARRTIEEMTDTYINVGEYE-------VAIIGDYERAMAAKQAIEMLAE--G 75

Query: 237 PAHAK 241
             H+ 
Sbjct: 76  RMHST 80

>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 = 40.8 bits (96), Expect = 5e-06
 Identities = 11/40 (27%), Positives = 17/40 (42%)

Query: 163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202
           A     + +     G +IG       QI   TGA+++I D
Sbjct: 1   APRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED 40

>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 = 40.6 bits (95), Expect = 1e-05
 Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 5/73 (6%)

Query: 161 FGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFE 219
             A+   +  V   L G  IG  G N +Q  +  G      D     +     + G S +
Sbjct: 4   LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGESAD 59

Query: 220 QIKQASAMVRELI 232
            +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 = 39.1 bits (91), Expect = 5e-05
 Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 6/69 (8%)

Query: 165 ATAKISVDASLAGAIIGKGGVNSKQICRQ-TGAKLSIRDHEADPNLRNIELEGSFEQIKQ 223
             + ++  + L   IIGK G N  +I +Q     +   + E       I LEG  E +  
Sbjct: 21  TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGE-----DKITLEGPTEDVSV 75

Query: 224 ASAMVRELI 232
           A   +  ++
Sbjct: 76  AQEQIEGMV 84

>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 = 37.0 bits (86), Expect = 2e-04
 Identities = 7/65 (10%), Positives = 21/65 (32%), Gaps = 7/65 (10%)

Query: 169 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSF-EQIKQASAM 227
           I +       +IGK     + +  ++G  + + ++        I          +     
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN------GRIWATCPSRFSEEILIEA 58

Query: 228 VRELI 232
           +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 = 37.0 bits (86), Expect = 3e-04
 Identities = 5/34 (14%), Positives = 14/34 (41%)

Query: 169 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202
           + +  +    +IG+     K +  +T  K+ +  
Sbjct: 5   VEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR 38

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 134

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]

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 18/89 (20%), Positives = 35/89 (39%), Gaps = 24/89 (26%)

Query: 175 LAGAIIGKGGVNSKQICRQTGAKLSIR--------------------DHEADPNLRNIEL 214
             G I+G  G+ +KQ+  +TG K+ +R                    +H  +     I +
Sbjct: 18  FVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITV 77

Query: 215 EGS----FEQIKQASAMVRELIVRIGPAH 239
           E +      ++K+A   V++L+V      
Sbjct: 78  EDAQNRAELKLKRAVEEVKKLLVPAAEGE 106

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 122

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]

 Score = 34.4 bits (79), Expect = 0.004
 Identities = 15/85 (17%), Positives = 28/85 (32%), Gaps = 17/85 (20%)

Query: 175 LAGAIIGKGGVNSKQICRQTGAKLSIR----------DHEADPNLRNIELE-------GS 217
             G +IG  G   K I ++  AK+ IR            +    L   +          +
Sbjct: 19  FVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANT 78

Query: 218 FEQIKQASAMVRELIVRIGPAHAKN 242
            E +K+A   +R ++ +        
Sbjct: 79  MENVKKAVEQIRNILKQGIETPEDQ 103

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	290
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.49
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.47
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.46
d1m9oa_	40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	99.45
d1rgoa1	36	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.43
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.38
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.37
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.37
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.36
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.32
d1m9oa_	40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	99.28
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.25
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.22
d1rgoa2	34	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.22
d1rgoa1	36	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.2
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.14
d1rgoa2	34	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.14
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.08
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.03
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.03
d2cpqa1	78	Fragile X mental retardation syndrome related prot	98.99
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.95
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.94
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.77
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.7
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.47
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.42
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.16
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.05
d2cqea2	29	Zinc finger CCCH domain-containing protein C19orf7	98.01
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.66
d2cqea2	29	Zinc finger CCCH domain-containing protein C19orf7	97.47
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	96.81
d2cqea1	56	Zinc finger CCCH domain-containing protein C19orf7	96.35
d2cqea1	56	Zinc finger CCCH domain-containing protein C19orf7	95.28
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.75
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	93.37
d2fc6a1	37	Target of EGR1 protein 1, TOE1 {Human (Homo sapien	89.1
d2fc6a1	37	Target of EGR1 protein 1, TOE1 {Human (Homo sapien	85.8

>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=99.49  E-value=1.2e-14  Score=103.61  Aligned_cols=73  Identities=30%  Similarity=0.494  Sum_probs=68.2

Q ss_pred             CCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898          163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  235 (290)
Q Consensus       163 ~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~  235 (290)
                      +..|.+|.||.+.+|.|||++|++|+.|++.||+.|+|.+...+..+|.+.|+|++++++.|+.+|.+.+.+.
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            4568899999999999999999999999999999999988777788999999999999999999999999874

>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=99.47  E-value=1.4e-14  Score=101.90  Aligned_cols=68  Identities=25%  Similarity=0.456  Sum_probs=64.3

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHH
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI  232 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i  232 (290)
                      .|.+|.||.+.+|+|||++|.+|++|++.||++|+|.+...+..+|.++|+|++++++.|..+|.+.|
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            57899999999999999999999999999999999988777888999999999999999999999876

>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=99.46  E-value=1.5e-14  Score=102.78  Aligned_cols=72  Identities=17%  Similarity=0.385  Sum_probs=67.1

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  235 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~  235 (290)
                      +...+|.||.+.+|+|||++|++|++|++.||++|+|.....+..+|.++|+|+++++..|..+|.+++.+.
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            357899999999999999999999999999999999988777778899999999999999999999999864

>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=99.45  E-value=1.3e-14  Score=89.92  Aligned_cols=35  Identities=49%  Similarity=1.124  Sum_probs=32.8

Q ss_pred             CcccccccCCCCC-CCCCCCCCCCcCCCChhhhccc
Q 022898          254 SSNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELRKT  288 (290)
Q Consensus       254 ~~~~k~~~C~~~~-~g~C~~g~~C~f~Hg~~el~~~  288 (290)
                      +..|||+||.+|. .|.|+||++|.||||++|||+.
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 7999999999999999999985

>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=99.43  E-value=3.5e-15  Score=90.35  Aligned_cols=34  Identities=50%  Similarity=1.151  Sum_probs=31.7

Q ss_pred             CcccccccCCCCC-CCCCCCCCCCcCCCChhhhcc
Q 022898          254 SSNFKTKLCGNFA-KGSCTFGDRCHFAHGAAELRK  287 (290)
Q Consensus       254 ~~~~k~~~C~~~~-~g~C~~g~~C~f~Hg~~el~~  287 (290)
                      ++.|||+||.+|. .|.|+||++|.||||++|||.
T Consensus         1 ~~kyKT~lC~~~~~~g~C~~G~~C~FAHg~~ELr~   35 (36)
T d1rgoa1           1 STRYKTELCRPFEESGTCKYGEKCQFAHGFHELRS   35 (36)
T ss_dssp             CTTTTSSBCHHHHHHSCCTTGGGCSSBSSGGGCCC
T ss_pred             CCCcchhhCcchhcCCcCCCCCcCCCcCCHHHccC
Confidence            3689999999998 799999999999999999995

>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=99.38  E-value=1.4e-13  Score=96.83  Aligned_cols=67  Identities=34%  Similarity=0.585  Sum_probs=59.6

Q ss_pred             eEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC---CCCCCcceeEEcCCHHHHHHHHHHHHHHH
Q 022898          166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELI  232 (290)
Q Consensus       166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~---~~~~~~r~v~i~G~~~~i~~A~~~I~~~i  232 (290)
                      +..|.||++.+|.|||++|++|++|++.||++|+|...   ..+..+|.|+|+|++++++.|..+|.+++
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            46899999999999999999999999999999999543   33456899999999999999999998864

>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=99.37  E-value=1.9e-13  Score=98.17  Aligned_cols=72  Identities=24%  Similarity=0.406  Sum_probs=67.8

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  235 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~  235 (290)
                      ..+..|.||.+.+|.|||++|.+|+.|++.||++|.|.+...+..++.++|+|++++|+.|..+|.++|.+.
T Consensus         7 ~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           7 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             cEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            567899999999999999999999999999999999988778888999999999999999999999999864

>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=99.37  E-value=2.5e-13  Score=96.35  Aligned_cols=68  Identities=25%  Similarity=0.415  Sum_probs=61.1

Q ss_pred             ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC---CCCCCcceeEEcCCHHHHHHHHHHHHHHH
Q 022898          165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELI  232 (290)
Q Consensus       165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~---~~~~~~r~v~i~G~~~~i~~A~~~I~~~i  232 (290)
                      ...++.||.+.+|.|||++|++|++|++.||++|+|.+.   .++..+|.|+|+|++++++.|..+|.+.|
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            457899999999999999999999999999999999643   34556899999999999999999998875

>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=99.36  E-value=1.5e-13  Score=96.78  Aligned_cols=69  Identities=28%  Similarity=0.413  Sum_probs=62.9

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHh
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR  234 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~  234 (290)
                      ..+.+|.||+..+|.|||++|++|++|++.||++|+|.+.  +..+|.++|+|+++++..|..+|.+.+.|
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC--CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            4578999999999999999999999999999999999753  44579999999999999999999998864

>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=99.32  E-value=4.8e-13  Score=96.49  Aligned_cols=71  Identities=32%  Similarity=0.463  Sum_probs=64.3

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC--CCCCCcceeEEcCCHHHHHHHHHHHHHHHHh
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH--EADPNLRNIELEGSFEQIKQASAMVRELIVR  234 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~--~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~  234 (290)
                      ..+.+|.||...+|.|||++|.+|++|++.||++|+|.+.  .....+|.|+|+|++++|..|..+|.+.|.+
T Consensus         7 ~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           7 NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             cEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            6789999999999999999999999999999999999654  3445689999999999999999999998865

>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=99.28  E-value=7.1e-13  Score=81.95  Aligned_cols=36  Identities=33%  Similarity=0.776  Sum_probs=34.3

Q ss_pred             CCcccccccccccccccCCCCCcccccccccccCCC
Q 022898           92 PTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKP  127 (290)
Q Consensus        92 ~~~~ktr~C~~~~~~g~C~~G~~C~f~H~~~el~~~  127 (290)
                      ...|||++|..|...|.|+||++|+|||+++|||.+
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            578999999999999999999999999999999986

>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=99.25  E-value=4.9e-12  Score=95.39  Aligned_cols=74  Identities=24%  Similarity=0.412  Sum_probs=65.3

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCC--CCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE--ADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~--~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ..+.+|.||...+|.|||++|.+|++|++.||+.|+|.+..  .+..+|.|+|+|++++|..|..+|.+++.+.+.
T Consensus        14 ~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~   89 (104)
T d1we8a_          14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEE   89 (104)
T ss_dssp             EEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhCcHH
Confidence            46688999999999999999999999999999999996543  344579999999999999999999999976543

>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=99.22  E-value=7.4e-12  Score=90.70  Aligned_cols=73  Identities=18%  Similarity=0.282  Sum_probs=65.8

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc-CCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~-~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~  236 (290)
                      +.+..|.||..+++.|||++|++|+.|++.||++|.+.+ ...+..++.|.|+|+.++|..|..+|.+.+.+.+
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~e   82 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGELE   82 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHHhHh
Confidence            467899999999999999999999999999999999954 3556678899999999999999999999988754

>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=99.22  E-value=5e-13  Score=79.44  Aligned_cols=30  Identities=33%  Similarity=0.795  Sum_probs=28.2

Q ss_pred             CCccccccccccccCCCCCCCCCceEeccc
Q 022898           29 GVGSKSKPCTKFFSTAGCPFGESCHFLHYF   58 (290)
Q Consensus        29 ~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~   58 (290)
                      .++|||+||++|..+|.|+||++|+|||+.
T Consensus         3 hpkyKT~lC~~f~~~g~C~yG~~C~FaHg~   32 (34)
T d1rgoa2           3 HPKYKTELCRTFHTIGFCPYGPRCHFIHNA   32 (34)
T ss_dssp             CTTTTCSBCHHHHHHSCCTTGGGCSSBCCS
T ss_pred             CCCccchhccccCCCCcCCCCCcccCcCCC
Confidence            578999999999999999999999999985

>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=99.20  E-value=1.4e-12  Score=78.65  Aligned_cols=34  Identities=41%  Similarity=0.877  Sum_probs=32.1

Q ss_pred             CcccccccccccccccCCCCCcccccccccccCC
Q 022898           93 TVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGK  126 (290)
Q Consensus        93 ~~~ktr~C~~~~~~g~C~~G~~C~f~H~~~el~~  126 (290)
                      ..|||++|..|...|.|+||++|+|||+++|||.
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            4799999999999999999999999999999986

>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=99.14  E-value=3.7e-11  Score=86.30  Aligned_cols=73  Identities=22%  Similarity=0.284  Sum_probs=64.7

Q ss_pred             CCCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898          162 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       162 ~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~  236 (290)
                      ....+..|.||..+++.|||++|.+|++|++.||++|.+...  +...+.|+|+|+.++|..|..+|.+++.+.+
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~--~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~~   79 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP--DDPSNQIKITGTKEGIEKARHEVLLISAEQD   79 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT--TSSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC--CCCCCEEEEEeCHHHHHHHHHHHHHHHHHHh
Confidence            346789999999999999999999999999999999999643  3456789999999999999999999988753

>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=99.14  E-value=3.7e-12  Score=75.60  Aligned_cols=32  Identities=28%  Similarity=0.695  Sum_probs=29.8

Q ss_pred             CCcccccccccccccccCCCCCcccccccccc
Q 022898           92 PTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWE  123 (290)
Q Consensus        92 ~~~~ktr~C~~~~~~g~C~~G~~C~f~H~~~e  123 (290)
                      .+.|||++|..|...|.|+||++|+|||+++|
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            47899999999999999999999999999865

>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=99.08  E-value=9.8e-11  Score=84.04  Aligned_cols=71  Identities=17%  Similarity=0.280  Sum_probs=62.3

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  235 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~  235 (290)
                      ..+..+.||..+++.|||++|++|++|++.||+.|.+...+. .+.+.|+|+|++++|..|..+|.+++.+.
T Consensus         9 ~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~-~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           9 MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA-PDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             CCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC-SCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC-CCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            567899999999999999999999999999999999965432 23568999999999999999999988763

>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=99.03  E-value=1.1e-10  Score=83.91  Aligned_cols=72  Identities=17%  Similarity=0.267  Sum_probs=62.7

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHh-hCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQ-TGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~-sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ..+..|.||..+++.|||++|++|++|++. +++.|.+..  .+...+.|+|+|+++++..|..+|.+.+.+.+.
T Consensus         9 ~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~--~~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~~~   81 (82)
T d2ctja1           9 IAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV--EGSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQT   81 (82)
T ss_dssp             SCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCC--TTTTCCEEEEESCHHHHHHHHHHHHHHHHHHSC
T ss_pred             cEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeC--CCCCCceEEEeCCHHHHHHHHHHHHHHHhhhhc
Confidence            467899999999999999999999999977 588888754  344568999999999999999999999987654

>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=99.03  E-value=9.8e-11  Score=81.92  Aligned_cols=67  Identities=25%  Similarity=0.333  Sum_probs=59.4

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHH
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI  232 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i  232 (290)
                      ..+..|.||..+.+.|||++|++|+.|++.||++|++.+.  +...+.|.|+|++++++.|..+|.+++
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~--~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD--SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC--CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC--CCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            4578899999999999999999999999999999999643  345678999999999999999998753

>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=98.99  E-value=3e-11  Score=86.12  Aligned_cols=68  Identities=22%  Similarity=0.253  Sum_probs=58.0

Q ss_pred             CCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHh
Q 022898          163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVR  234 (290)
Q Consensus       163 ~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~  234 (290)
                      ...+..|.||.+++|.|||++|++|+.|++.||++|.+.+.    ..+.|.|.| ++++++.|..||..+..+
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~----~~g~v~I~g~~~eav~~A~~~Ie~~~~~   74 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGESADAVKKARGFLEFVEDF   74 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----TTTEEEEEESSHHHHHHHHHHHSCCCCC
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC----CCceEEEEECCHHHHHHHHHHHHHhhee
Confidence            35688999999999999999999999999999999998642    345788888 799999999999654433

>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=98.95  E-value=2.7e-10  Score=82.18  Aligned_cols=65  Identities=12%  Similarity=0.153  Sum_probs=58.7

Q ss_pred             EEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          167 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       167 ~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ..+.||++.++.|||++|++|+.|+++||+.|+|.+      ...|.|.|++++++.|..+|...+.+...
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~------~g~v~I~G~~e~v~~A~~~I~~i~~ea~~   67 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ------NGLIWVNGDRRKVSIAEEAIYLIEQEAHT   67 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT------TSEEEEESCHHHHHHHHHHHHHHHHCSCC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC------CCEEEEEeCHHHHHHHHHHHHHHHHhccc
Confidence            468999999999999999999999999999999964      24799999999999999999888877654

>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=98.94  E-value=3.3e-10  Score=83.04  Aligned_cols=71  Identities=15%  Similarity=0.240  Sum_probs=62.7

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~  236 (290)
                      ..+..|.||..+++.|||++|.+|++|++.+|+.|.+...  +.....|+|+|+.++|+.|..+|.+++.+.+
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~--~~~~~~v~I~G~~~~V~~A~~~I~~~v~e~~   79 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP--ELQSDIIAITGLAANLDRAKAGLLERVKELQ   79 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT--TTTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC--CCCcceEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            3578999999999999999999999999999999999653  4446789999999999999999999887543

>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=98.77  E-value=6.9e-10  Score=79.83  Aligned_cols=67  Identities=18%  Similarity=0.242  Sum_probs=53.5

Q ss_pred             EEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHH
Q 022898          167 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIV  233 (290)
Q Consensus       167 ~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~  233 (290)
                      +.+.||.+.+|+|||++|++|+.|++.||++|+|.+.......+...+.+.+.++++|..+|.++..
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g~v~i~~~~~~~~~~a~~~a~~iI~aI~r   71 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAISL   71 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTTEEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCCeEEEecCCccccHHHHHHHHHHHHHHhC
Confidence            5789999999999999999999999999999999643222223334456788899999999887643

>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=98.70  E-value=1.3e-08  Score=74.13  Aligned_cols=67  Identities=22%  Similarity=0.352  Sum_probs=60.1

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHh-hCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQ-TGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI  235 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~-sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~  235 (290)
                      ..+..|.||..+.+.|||++|++|+.|++. +++.|.+.+     ....|+|+|++++|+.|..+|.+.+.+.
T Consensus        20 ~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~-----~~~~v~i~G~~~~ve~Ak~~I~~iv~el   87 (90)
T d2ctfa1          20 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC-----CCceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            578999999999999999999999999998 589998864     2467999999999999999999998764

>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=98.47  E-value=2.5e-09  Score=74.10  Aligned_cols=64  Identities=13%  Similarity=0.084  Sum_probs=48.3

Q ss_pred             EEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHhcC
Q 022898          167 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIG  236 (290)
Q Consensus       167 ~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~~~  236 (290)
                      ..+.||++.+|.|||++|++|+.|++.||+.|.|.+.      ..|.|.| +.+.++.|..+|.....++.
T Consensus         3 ~vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~------g~v~I~g~~~~~v~~A~~~I~~i~~ea~   67 (69)
T d2je6i3           3 IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN------GRIWATCPSRFSEEILIEAIRKIENESH   67 (69)
T ss_dssp             CEEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT------SEEEC-----CTTCCTHHHHTTTTTTTT
T ss_pred             EEEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC------CEEEEEeCCHHHHHHHHHHHHHHHHhhc
Confidence            4688999999999999999999999999999999542      3688888 47789999999977665543

>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=98.42  E-value=1.4e-07  Score=67.76  Aligned_cols=65  Identities=14%  Similarity=0.105  Sum_probs=57.1

Q ss_pred             EEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHhcCC
Q 022898          167 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       167 ~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ..+.||.+.++.|||++|++|+.|++.||+.|.|.++      -.|.|.| +.+.+..|..+|..+..+...
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~------G~V~I~g~~~~~~~~A~~~I~~I~~ea~v   68 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN------GRIHLECPNEDLEAIAVMAIKIIDEEAYT   68 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETT------TEEEEECSCHHHHHHHHHHHHHHHHCSCC
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCC------cEEEEEeCCHHHHHHHHHHHHHHHHhchh
Confidence            4688999999999999999999999999999999653      2688999 588999999999998877654

>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=98.16  E-value=1.5e-07  Score=61.40  Aligned_cols=37  Identities=27%  Similarity=0.421  Sum_probs=10.9

Q ss_pred             eEEEEecccccceeeCCCCCchhhHHHhhCCceeecc
Q 022898          166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD  202 (290)
Q Consensus       166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~  202 (290)
                      ..+|.||.+.+|.|||+||.+|++|+++||++|+|.+
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            3578899999999999999999999999999999964

>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=98.05  E-value=7e-07  Score=66.12  Aligned_cols=56  Identities=21%  Similarity=0.363  Sum_probs=48.8

Q ss_pred             ccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898          175 LAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP  237 (290)
Q Consensus       175 ~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~  237 (290)
                      ..|.|||++|.+|+.|++.||+.|.|.+.       .+.|.|++++++.|..+|..++...+.
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d~-------~v~iig~~e~i~~A~~~Ie~li~~~e~   78 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGEY-------EVAIIGDYERAMAAKQAIEMLAEGRMH   78 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECSS-------EEEEEEEHHHHHHHHHHHHHHHTTCCH
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeCC-------eEEEEECchhHHHHHHHHHHHHcCCCc
Confidence            36779999999999999999999999642       467789999999999999999976554

>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=98.01  E-value=1.6e-06  Score=47.35  Aligned_cols=26  Identities=31%  Similarity=0.768  Sum_probs=23.9

Q ss_pred             cccccCCCCCCCCCCCCCCCcCCCCh
Q 022898          257 FKTKLCGNFAKGSCTFGDRCHFAHGA  282 (290)
Q Consensus       257 ~k~~~C~~~~~g~C~~g~~C~f~Hg~  282 (290)
                      .|.+||.||.+|.|..|++|.|.|.+
T Consensus         4 kkkelCKfYvqGyCtrgenC~ymH~e   29 (29)
T d2cqea2           4 KKRELCKFYITGFCARAENCPYMHGD   29 (29)
T ss_dssp             CCCSBCTTTTTTCCSCSTTCSSBSSS
T ss_pred             hhhhhhhhheeeeecCCcCcccccCC
Confidence            47789999999999999999999975

>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=97.66  E-value=3.4e-05  Score=58.52  Aligned_cols=72  Identities=24%  Similarity=0.374  Sum_probs=55.1

Q ss_pred             ceEEEEecccc------cceeeCCCCCchhhHHHhhCCceeeccCCC-----------------CCCcceeEEcCCHHHH
Q 022898          165 ATAKISVDASL------AGAIIGKGGVNSKQICRQTGAKLSIRDHEA-----------------DPNLRNIELEGSFEQI  221 (290)
Q Consensus       165 ~t~~i~VP~~~------vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~-----------------~~~~r~v~i~G~~~~i  221 (290)
                      .+.+|.||.+.      ||.|||.+|.++++|+++||++|.|.....                 +....+.....+++.+
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~   82 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENV   82 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHH
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhH
Confidence            45778888765      889999999999999999999999953211                 1112444455578899


Q ss_pred             HHHHHHHHHHHHhcC
Q 022898          222 KQASAMVRELIVRIG  236 (290)
Q Consensus       222 ~~A~~~I~~~i~~~~  236 (290)
                      +.|..+|..+|...-
T Consensus        83 ~~A~~~i~~ll~~~~   97 (122)
T d1k1ga_          83 KKAVEQIRNILKQGI   97 (122)
T ss_dssp             HHHHHHHHHHHTTTT
T ss_pred             HHHHHHHHHHHHhcC
Confidence            999999999997543

>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=97.47  E-value=2e-05  Score=42.87  Aligned_cols=24  Identities=25%  Similarity=0.653  Sum_probs=21.4

Q ss_pred             ccccccccccCCCCCCCCCceEecc
Q 022898           33 KSKPCTKFFSTAGCPFGESCHFLHY   57 (290)
Q Consensus        33 Kt~lC~~~~~~g~C~~G~~C~F~H~   57 (290)
                      |..+|++|.+ |.|..|++|.|.|.
T Consensus         5 kkelCKfYvq-GyCtrgenC~ymH~   28 (29)
T d2cqea2           5 KRELCKFYIT-GFCARAENCPYMHG   28 (29)
T ss_dssp             CCSBCTTTTT-TCCSCSTTCSSBSS
T ss_pred             hhhhhhhhee-eeecCCcCcccccC
Confidence            6789998885 69999999999995

>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=96.81  E-value=0.00035  Score=53.49  Aligned_cols=70  Identities=24%  Similarity=0.370  Sum_probs=48.5

Q ss_pred             eEEEEecc------cccceeeCCCCCchhhHHHhhCCceeeccCCCC-----------------C-CcceeEEcC-CH--
Q 022898          166 TAKISVDA------SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEAD-----------------P-NLRNIELEG-SF--  218 (290)
Q Consensus       166 t~~i~VP~------~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~-----------------~-~~r~v~i~G-~~--  218 (290)
                      +.+|.||.      .++|.|||.+|.+++.|+++||++|.|......                 . ..==|.|++ ++  
T Consensus         3 ~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~~   82 (134)
T d2bl5a1           3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQN   82 (134)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCH
T ss_pred             ceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcHH
Confidence            45677775      467889999999999999999999999643210                 0 111234444 33  


Q ss_pred             ---HHHHHHHHHHHHHHHhc
Q 022898          219 ---EQIKQASAMVRELIVRI  235 (290)
Q Consensus       219 ---~~i~~A~~~I~~~i~~~  235 (290)
                         ..+..|..+|..++...
T Consensus        83 ~a~~kl~~A~~~I~~lL~p~  102 (134)
T d2bl5a1          83 RAELKLKRAVEEVKKLLVPA  102 (134)
T ss_dssp             HHHHHHHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHHHHHHHHHcCCC
Confidence               24788889998888543

>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=96.35  E-value=0.00037  Score=44.35  Aligned_cols=22  Identities=36%  Similarity=0.922  Sum_probs=20.5

Q ss_pred             cccccccCCCCCCCCCceEecc
Q 022898           36 PCTKFFSTAGCPFGESCHFLHY   57 (290)
Q Consensus        36 lC~~~~~~g~C~~G~~C~F~H~   57 (290)
                      +|++|..+..|--|++|+|.|.
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            6999998899999999999995

>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=95.28  E-value=0.0023  Score=40.55  Aligned_cols=21  Identities=33%  Similarity=0.841  Sum_probs=20.0

Q ss_pred             ccccccccccCCCCCcccccc
Q 022898           99 MCNRLNSAEGCKFGDKCHFAH  119 (290)
Q Consensus        99 ~C~~~~~~g~C~~G~~C~f~H  119 (290)
                      +|.+|.++..|-.|+.|+|.|
T Consensus         2 PCK~yHtg~kCy~gd~C~FSH   22 (56)
T d2cqea1           2 PCKLYHTTGNCINGDDCMFSH   22 (56)
T ss_dssp             BCSHHHHTSCCSSCTTCSSBC
T ss_pred             CcceeecCCcccCCCcccccC
Confidence            599999999999999999999

>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=94.75  E-value=0.005  Score=41.04  Aligned_cols=39  Identities=31%  Similarity=0.434  Sum_probs=35.9

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD  202 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~  202 (290)
                      .....+.||.+.....|||+|.|++-..+.||..|.|..
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            567889999999999999999999999999999999943

>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=93.37  E-value=0.012  Score=39.24  Aligned_cols=39  Identities=31%  Similarity=0.493  Sum_probs=36.0

Q ss_pred             CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc
Q 022898          164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD  202 (290)
Q Consensus       164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~  202 (290)
                      .....+.||.+..+..|||+|.||+-..+.+|..|.|..
T Consensus        26 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          26 NKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             TTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CCEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            457889999999999999999999999999999999954

>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=89.10  E-value=0.056  Score=30.65  Aligned_cols=26  Identities=19%  Similarity=0.609  Sum_probs=23.1

Q ss_pred             ccccccccccccccCCCCCccccccc
Q 022898           95 VKSRMCNRLNSAEGCKFGDKCHFAHG  120 (290)
Q Consensus        95 ~ktr~C~~~~~~g~C~~G~~C~f~H~  120 (290)
                      -.+.+|..|-..|+|+.|.+|...|.
T Consensus        11 ~~~~iC~~FsAyGWCP~G~qCp~SHd   36 (37)
T d2fc6a1          11 HPTSICDNFSAYGWCPLGPQCPQSHD   36 (37)
T ss_dssp             CCSCBCSHHHHTCCCTTGGGCSSBCC
T ss_pred             CccchhhhhhhccccCCCCCCcccCc
Confidence            35679999999999999999999984

>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=85.80  E-value=0.072  Score=30.17  Aligned_cols=26  Identities=27%  Similarity=0.599  Sum_probs=23.9

Q ss_pred             cccccccccccCCCCCCCCCceEecc
Q 022898           32 SKSKPCTKFFSTAGCPFGESCHFLHY   57 (290)
Q Consensus        32 ~Kt~lC~~~~~~g~C~~G~~C~F~H~   57 (290)
                      ..|.+|..|.--|=|+.|.+|.-.|+
T Consensus        11 ~~~~iC~~FsAyGWCP~G~qCp~SHd   36 (37)
T d2fc6a1          11 HPTSICDNFSAYGWCPLGPQCPQSHD   36 (37)
T ss_dssp             CCSCBCSHHHHTCCCTTGGGCSSBCC
T ss_pred             CccchhhhhhhccccCCCCCCcccCc
Confidence            47889999999999999999999996