Citrus Sinensis ID: 021032

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------32
Protein Sequence
MRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVTS
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHHHccccccccEEEEEEEEEcccEEEEEccccccHHHHHHHHcccEEEEccccccccccccccEEEEcccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccccccccccHHHHHHHHHccEEEEcccccccccEEEEEEccHHHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHHHHccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHcccEEEEccccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccEEEEEEEccHcccEEEcccccHHHHHHHHcccEEEEEccccccccEEEEEEccHHHHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
MRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCllgrgghivSEMRRATgasirvfpkdqaprcgsphdEIVQVIGNYHSVQDALFHITSRLREtifpmkrpgpnnghsylppfpemppppfrprhnpaspgsypspvgpfhsmdrgmgpsqpfdhqaafshgmdpmvppnsdripfpygserpghgptfdrppsprswtpqgvgggdprgfdassgftprnrpvesgnhaailTSTTIEVVIPQLYMAHVygennsnlshirqisganvvvndpkpgategvVMVSGTSDQMRAAQSLIHAFILCGVTS
Flexible Loop (DISEMBL)
mrhspaqdaVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVTS
Low Complexity Region (SEG)
MRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLppfpemppppfrprhnpaspGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVTS
Disordered region (IsUnstruct)
***********RVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKD***RCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIF************************************************************************************************************************************HAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN********GVVMV*******RAAQSLIHAFILCGV**
Disordered Region (DISOPRED)
***SPAQDAVMRVHS**************ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET****************PPFPEMPPPPFRP*H*************************************************************************TPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQI*****************VVMVSGTSDQMRAAQSLIHAFILCG***
Disordered Region (DISEMBL)
*********VMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVTS
Disordered Region (DISPRO)
***SPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFP*******************PP****PRH****************SMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTP*******PRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC****
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVTS
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	318	2.2.26 [Sep-21-2011]
P58223	606	KH domain-containing prot	no	no	0.289	0.151	0.339	2e-09
O19048	356	Poly(rC)-binding protein	yes	no	0.770	0.688	0.244	2e-08
P60335	356	Poly(rC)-binding protein	yes	no	0.770	0.688	0.244	2e-08
Q15365	356	Poly(rC)-binding protein	yes	no	0.770	0.688	0.244	2e-08
Q5E9A3	356	Poly(rC)-binding protein	yes	no	0.770	0.688	0.244	2e-08
Q15366	365	Poly(rC)-binding protein	no	no	0.710	0.619	0.234	9e-07
Q61990	362	Poly(rC)-binding protein	no	no	0.720	0.632	0.239	9e-07
O19049	463	Heterogeneous nuclear rib	no	no	0.185	0.127	0.296	8e-05
P61980	463	Heterogeneous nuclear rib	no	no	0.185	0.127	0.296	8e-05
P61979	463	Heterogeneous nuclear rib	no	no	0.185	0.127	0.296	8e-05

>sp|P58223|Y4837_ARATH KH domain-containing protein At4g18375 OS=Arabidopsis thaliana GN=At4g18375 PE=2 SV=1

 Score = 63.9 bits (154), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 57/103 (55%), Gaps = 11/103 (10%)

Query: 3   HSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIR 62
            S A +AV+ +   I +   E  + V  +LLV S+ IGC++G+ G +++E+R+ T A+I 
Sbjct: 373 KSMAVEAVLLLQEYIND---EDAENVKMQLLVSSKVIGCVIGKSGSVINEIRKRTNANIC 429

Query: 63  VFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIF 105
           +             D++V+V G   SV+DAL  I  RLRE + 
Sbjct: 430 ISK--------GKKDDLVEVSGEVSSVRDALIQIVLRLREDVL 464

Arabidopsis thaliana (taxid: 3702)

>sp|O19048|PCBP1_RABIT Poly(rC)-binding protein 1 OS=Oryctolagus cuniculus GN=PCBP1 PE=2 SV=1

 Score = 60.1 bits (144), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 70/286 (24%), Positives = 116/286 (40%), Gaps = 41/286 (14%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
           V  RL+V + Q G L+G+GG  + E+R +TGA ++V   D  P   +  +  + + G   
Sbjct: 98  VTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQV-AGDMLP---NSTERAITIAGVPQ 153

Query: 88  SVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVG 147
           SV + +  I   + ET+         +    +   P  P P   P              G
Sbjct: 154 SVTECVKQICLVMLETL-------SQSPQGRVMTIPYQPMPASSPVICAGGQDRCSDAAG 206

Query: 148 PFHSMDRGMGPSQPFD-HQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRS 206
             H+     GP  P D +     H + P+     D       + +  H            
Sbjct: 207 YPHATHDLEGP--PLDAYSIQGQHTISPL-----DLAKLNQVARQQSHFAMMH------- 252

Query: 207 WTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAI--LTSTTIEVVIPQLYMAHVYGENN 264
                 GG    G D+SS       P   G  A++   T TT E+ IP   +  + G   
Sbjct: 253 ------GGTGFAGIDSSS-------PEVKGYWASLDASTQTTHELTIPNNLIGCIIGRQG 299

Query: 265 SNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHA 310
           +N++ IRQ+SGA + + +P  G++   V ++G++  +  AQ LI+A
Sbjct: 300 ANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA 345

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Oryctolagus cuniculus (taxid: 9986)

>sp|P60335|PCBP1_MOUSE Poly(rC)-binding protein 1 OS=Mus musculus GN=Pcbp1 PE=1 SV=1

 Score = 60.1 bits (144), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 70/286 (24%), Positives = 116/286 (40%), Gaps = 41/286 (14%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
           V  RL+V + Q G L+G+GG  + E+R +TGA ++V   D  P   +  +  + + G   
Sbjct: 98  VTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQV-AGDMLP---NSTERAITIAGVPQ 153

Query: 88  SVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVG 147
           SV + +  I   + ET+         +    +   P  P P   P              G
Sbjct: 154 SVTECVKQICLVMLETL-------SQSPQGRVMTIPYQPMPASSPVICAGGQDRCSDAAG 206

Query: 148 PFHSMDRGMGPSQPFD-HQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRS 206
             H+     GP  P D +     H + P+     D       + +  H            
Sbjct: 207 YPHATHDLEGP--PLDAYSIQGQHTISPL-----DLAKLNQVARQQSHFAMMH------- 252

Query: 207 WTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAI--LTSTTIEVVIPQLYMAHVYGENN 264
                 GG    G D+SS       P   G  A++   T TT E+ IP   +  + G   
Sbjct: 253 ------GGTGFAGIDSSS-------PEVKGYWASLDASTQTTHELTIPNNLIGCIIGRQG 299

Query: 265 SNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHA 310
           +N++ IRQ+SGA + + +P  G++   V ++G++  +  AQ LI+A
Sbjct: 300 ANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA 345

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Mus musculus (taxid: 10090)

>sp|Q15365|PCBP1_HUMAN Poly(rC)-binding protein 1 OS=Homo sapiens GN=PCBP1 PE=1 SV=2

 Score = 60.1 bits (144), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 70/286 (24%), Positives = 116/286 (40%), Gaps = 41/286 (14%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
           V  RL+V + Q G L+G+GG  + E+R +TGA ++V   D  P   +  +  + + G   
Sbjct: 98  VTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQV-AGDMLP---NSTERAITIAGVPQ 153

Query: 88  SVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVG 147
           SV + +  I   + ET+         +    +   P  P P   P              G
Sbjct: 154 SVTECVKQICLVMLETL-------SQSPQGRVMTIPYQPMPASSPVICAGGQDRCSDAAG 206

Query: 148 PFHSMDRGMGPSQPFD-HQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRS 206
             H+     GP  P D +     H + P+     D       + +  H            
Sbjct: 207 YPHATHDLEGP--PLDAYSIQGQHTISPL-----DLAKLNQVARQQSHFAMMH------- 252

Query: 207 WTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAI--LTSTTIEVVIPQLYMAHVYGENN 264
                 GG    G D+SS       P   G  A++   T TT E+ IP   +  + G   
Sbjct: 253 ------GGTGFAGIDSSS-------PEVKGYWASLDASTQTTHELTIPNNLIGCIIGRQG 299

Query: 265 SNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHA 310
           +N++ IRQ+SGA + + +P  G++   V ++G++  +  AQ LI+A
Sbjct: 300 ANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA 345

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Homo sapiens (taxid: 9606)

>sp|Q5E9A3|PCBP1_BOVIN Poly(rC)-binding protein 1 OS=Bos taurus GN=PCBP1 PE=2 SV=1

 Score = 60.1 bits (144), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 70/286 (24%), Positives = 116/286 (40%), Gaps = 41/286 (14%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
           V  RL+V + Q G L+G+GG  + E+R +TGA ++V   D  P   +  +  + + G   
Sbjct: 98  VTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQV-AGDMLP---NSTERAITIAGVPQ 153

Query: 88  SVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVG 147
           SV + +  I   + ET+         +    +   P  P P   P              G
Sbjct: 154 SVTECVKQICLVMLETL-------SQSPQGRVMTIPYQPMPASSPVICAGGQDRCSDAAG 206

Query: 148 PFHSMDRGMGPSQPFD-HQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRS 206
             H+     GP  P D +     H + P+     D       + +  H            
Sbjct: 207 YPHATHDLEGP--PLDAYSIQGQHTISPL-----DLAKLNQVARQQSHFAMMH------- 252

Query: 207 WTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAI--LTSTTIEVVIPQLYMAHVYGENN 264
                 GG    G D+SS       P   G  A++   T TT E+ IP   +  + G   
Sbjct: 253 ------GGTGFAGIDSSS-------PEVKGYWASLDASTQTTHELTIPNNLIGCIIGRQG 299

Query: 265 SNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHA 310
           +N++ IRQ+SGA + + +P  G++   V ++G++  +  AQ LI+A
Sbjct: 300 ANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA 345

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Bos taurus (taxid: 9913)

>sp|Q15366|PCBP2_HUMAN Poly(rC)-binding protein 2 OS=Homo sapiens GN=PCBP2 PE=1 SV=1

 Score = 54.7 bits (130), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 73/311 (23%), Positives = 126/311 (40%), Gaps = 85/311 (27%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
           V  RL+V + Q G L+G+GG  + E+R +TGA ++V   D  P   +  +  + + G   
Sbjct: 98  VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQV-AGDMLP---NSTERAITIAGIPQ 153

Query: 88  SVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVG 147
           S+ + +  I   + ET+            S  PP  +    P+RP+  P+S     SPV 
Sbjct: 154 SIIECVKQICVVMLETL------------SQSPP--KGVTIPYRPK--PSS-----SPVI 192

Query: 148 PFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSW 207
                DR             +S G        SD   FP+ +      P  + PP   ++
Sbjct: 193 FAGGQDR-------------YSTG--------SDSASFPHTTPSMCLNPDLEGPP-LEAY 230

Query: 208 TPQGV-------------------------GGGDPRGFDASS----GFTPRNRPVESGNH 238
           T QG                          G     G ++SS    G+   +   ++ +H
Sbjct: 231 TIQGQYAIPQPDLTKLHQLAMQQSHFPMTHGNTGFSGIESSSPEVKGYWGLDASAQTTSH 290

Query: 239 AAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTS 298
                    E+ IP   +  + G   + ++ IRQ+SGA + + +P  G+T+  V ++G++
Sbjct: 291 ---------ELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSA 341

Query: 299 DQMRAAQSLIH 309
             +  AQ LI+
Sbjct: 342 ASISLAQYLIN 352

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC. Major cellular poly(rC)-binding protein. Binds also poly(rU). Negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitinationa and degradation.

Homo sapiens (taxid: 9606)

>sp|Q61990|PCBP2_MOUSE Poly(rC)-binding protein 2 OS=Mus musculus GN=Pcbp2 PE=1 SV=1

 Score = 54.7 bits (130), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 73/305 (23%), Positives = 126/305 (41%), Gaps = 76/305 (24%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
           V  RL+V + Q G L+G+GG  + E+R +TGA ++V   D  P   +  +  + + G   
Sbjct: 98  VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQV-AGDMLP---NSTERAITIAGIPQ 153

Query: 88  SVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVG 147
           S+ + +  I   + E+        P  G +           P+RP+  P+S     SPV 
Sbjct: 154 SIIECVKQICVVMLES--------PPKGVTI----------PYRPK--PSS-----SPVI 188

Query: 148 PFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSW 207
                DR             +S G        SD   FP+ +      P  + PP   ++
Sbjct: 189 FAGGQDR-------------YSTG--------SDSASFPHTTPSMCLNPDLEGPP-LEAY 226

Query: 208 TPQG-----------------------VGGGDPRGFDASSGFTPRNRPVESGNHAAILTS 244
           T QG                       +  G+  GF      +P  +   +G  A+  T 
Sbjct: 227 TIQGQYAIPQPDLTKLHQLAMQQSHFPMTHGNT-GFSGIESSSPEVKGYWAGLDASAQT- 284

Query: 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 304
           T+ E+ IP   +  + G   + ++ IRQ+SGA + + +P  G+T+  V ++G++  +  A
Sbjct: 285 TSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLA 344

Query: 305 QSLIH 309
           Q LI+
Sbjct: 345 QYLIN 349

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC. Major cellular poly(rC)-binding protein. Binds also poly(rU). Negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitinationa and degradation.

Mus musculus (taxid: 10090)

>sp|O19049|HNRPK_RABIT Heterogeneous nuclear ribonucleoprotein K OS=Oryctolagus cuniculus GN=HNRNPK PE=2 SV=1

 Score = 48.1 bits (113), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 19/64 (29%), Positives = 38/64 (59%)

Query: 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 305
           T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ AQ
Sbjct: 389 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 448

Query: 306 SLIH 309
            L+ 
Sbjct: 449 YLLQ 452

One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single-stranded DNA.

Oryctolagus cuniculus (taxid: 9986)

>sp|P61980|HNRPK_RAT Heterogeneous nuclear ribonucleoprotein K OS=Rattus norvegicus GN=Hnrnpk PE=1 SV=1

 Score = 48.1 bits (113), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 19/64 (29%), Positives = 38/64 (59%)

Query: 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 305
           T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ AQ
Sbjct: 389 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 448

Query: 306 SLIH 309
            L+ 
Sbjct: 449 YLLQ 452

One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single-stranded DNA.

Rattus norvegicus (taxid: 10116)

>sp|P61979|HNRPK_MOUSE Heterogeneous nuclear ribonucleoprotein K OS=Mus musculus GN=Hnrnpk PE=1 SV=1

 Score = 48.1 bits (113), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 19/64 (29%), Positives = 38/64 (59%)

Query: 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 305
           T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ AQ
Sbjct: 389 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 448

Query: 306 SLIH 309
            L+ 
Sbjct: 449 YLLQ 452

One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single-stranded DNA.

Mus musculus (taxid: 10090)

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	318
147863214	807	hypothetical protein VITISV_006585 [Viti	0.977	0.385	0.669	1e-114
225443339	704	PREDICTED: KH domain-containing protein	0.974	0.440	0.669	1e-113
449448150	716	PREDICTED: KH domain-containing protein	0.977	0.434	0.558	1e-85
449492545	716	PREDICTED: KH domain-containing protein	0.977	0.434	0.558	1e-85
356526304	565	PREDICTED: heterogeneous nuclear ribonuc	0.955	0.538	0.566	4e-79
356522258	559	PREDICTED: KH domain-containing protein	0.952	0.542	0.573	9e-79
15217969	621	RNA-binding KH domain-containing protein	0.883	0.452	0.570	2e-78
297847528	622	KH domain-containing protein [Arabidopsi	0.883	0.451	0.573	3e-78
357159179	629	PREDICTED: poly(rC)-binding protein 2-li	0.977	0.494	0.484	6e-67
242045198	371	hypothetical protein SORBIDRAFT_02g02892	0.971	0.832	0.461	2e-64

>gi|147863214|emb|CAN78372.1| hypothetical protein VITISV_006585 [Vitis vinifera]

 Score =  417 bits (1072), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 211/315 (66%), Positives = 248/315 (78%), Gaps = 4/315 (1%)

Query: 2   RHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 61
           +HSPAQDAV+RVH RIAEIGFEPG AVVARLLVHSQQIGCLLG+GG I+SEMRRATGASI
Sbjct: 487 KHSPAQDAVIRVHCRIAEIGFEPGAAVVARLLVHSQQIGCLLGKGGIIISEMRRATGASI 546

Query: 62  RVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPN-NGHSYLP 120
           R+F K+Q P+CGS +DE+VQVIG+  SVQDALF ITSR+RETIFP+K    N NG  Y+ 
Sbjct: 547 RIFAKEQVPKCGSQNDELVQVIGSLQSVQDALFCITSRIRETIFPLKPSISNVNGPPYMS 606

Query: 121 PFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNS 180
            FPE+PPP FRPRH+PASPG Y SPVG  H +DR   P  P DHQ++FSHG+D + P N 
Sbjct: 607 SFPEIPPPMFRPRHDPASPGHYSSPVGVPHGIDRSAVPGHPLDHQSSFSHGVDRIGPSNL 666

Query: 181 DRIPFPYGSERPGHGPTFDRP-PSPRSWTPQGVGGGDPRGFDA-SSGFTPRNRPVESGNH 238
           DR P+PYG +RPGHGP FDRP  SPR WTPQGV  G+ RG D  S G   R+ P  SG+ 
Sbjct: 667 DRAPYPYGGDRPGHGPPFDRPSSSPRMWTPQGV-SGNLRGTDVGSGGLASRSGPPGSGSQ 725

Query: 239 AAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTS 298
           A  +T TT+EV +PQ  ++HVYGENNSNL+ IRQISGA VV+ DP+ G++EGVV+VSGT 
Sbjct: 726 APNITXTTVEVAVPQALLSHVYGENNSNLNQIRQISGARVVIQDPRTGSSEGVVVVSGTP 785

Query: 299 DQMRAAQSLIHAFIL 313
           DQ RAAQSL+ AFIL
Sbjct: 786 DQTRAAQSLVQAFIL 800

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443339|ref|XP_002264125.1| PREDICTED: KH domain-containing protein At4g18375 [Vitis vinifera] gi|297735779|emb|CBI18466.3| unnamed protein product [Vitis vinifera]

 Score =  414 bits (1063), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 211/315 (66%), Positives = 248/315 (78%), Gaps = 5/315 (1%)

Query: 2   RHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 61
           +HSPAQDAV+RVH RIAEIGFEPG AVVARLLVHSQQIGCLLG+GG I+SEMRRATGASI
Sbjct: 386 KHSPAQDAVIRVHCRIAEIGFEPGAAVVARLLVHSQQIGCLLGKGGIIISEMRRATGASI 445

Query: 62  RVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPN-NGHSYLP 120
           R+F K+Q P+CGS +DE+VQVIG+  SVQDALF ITSR+RETIFP+K    N NG  Y+ 
Sbjct: 446 RIFAKEQVPKCGSQNDELVQVIGSLQSVQDALFRITSRIRETIFPLKPSISNVNGPPYMS 505

Query: 121 PFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNS 180
            FPE+PPP FRPRH+PASPG Y SPVG  H +DR   P  P DHQ++FSHG+D + P N 
Sbjct: 506 SFPEIPPPMFRPRHDPASPGHYSSPVGVPHGIDRSAVPGHPLDHQSSFSHGVDRIGPSNL 565

Query: 181 DRIPFPYGSERPGHGPTFDRP-PSPRSWTPQGVGGGDPRGFDASSG-FTPRNRPVESGNH 238
           DR P+PYG +RPGHGP FDRP  SPR WT QGV  G+ RG D  SG    RN P  SG+ 
Sbjct: 566 DRAPYPYGGDRPGHGPPFDRPSSSPRMWT-QGV-SGNLRGTDVGSGSLASRNGPPGSGSQ 623

Query: 239 AAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTS 298
           A  +T+TT+EV +PQ  ++HVYGENNSNL+ IRQISGA VV+ DP+ G++EGVV+VSGT 
Sbjct: 624 APNITTTTVEVAVPQALLSHVYGENNSNLNQIRQISGARVVIQDPRTGSSEGVVVVSGTP 683

Query: 299 DQMRAAQSLIHAFIL 313
           DQ RAAQSL+ AFIL
Sbjct: 684 DQTRAAQSLVQAFIL 698

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448150|ref|XP_004141829.1| PREDICTED: KH domain-containing protein At4g18375-like [Cucumis sativus]

 Score =  322 bits (826), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 177/317 (55%), Positives = 220/317 (69%), Gaps = 6/317 (1%)

Query: 3   HSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIR 62
           +SPAQ+AV+R H RIAEIG+EPG AVVARLLVH QQIG L+GRGGHI+++MRR TG SI+
Sbjct: 402 YSPAQEAVIRAHCRIAEIGYEPGAAVVARLLVHGQQIGYLVGRGGHIINDMRRGTGTSIQ 461

Query: 63  VFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMK--RPGPNNGHSYLP 120
           +FP+DQ    G   DE+VQVIGN  SVQDALFHIT+R+R+T FPM+   P  NN   YL 
Sbjct: 462 IFPRDQIQNGGPMSDEVVQVIGNLPSVQDALFHITNRIRDTFFPMRPHVPNFNNHPPYLS 521

Query: 121 PFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNS 180
           P PE PPP FRP  N  SPG YPS  G     +R    S P DHQ A+ H +      N 
Sbjct: 522 PHPETPPPLFRPGSNAHSPGYYPSQAGGLRGTERPPYHSHPLDHQPAYPHNVSFGGGNNM 581

Query: 181 DRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAA 240
           D +P+P+G ERPG G +F+R PSPRSWT Q V    P+G     G   RN P  SG    
Sbjct: 582 DGVPYPHGMERPGPG-SFER-PSPRSWTSQ-VSSEIPKGPTDGFGMVSRNEPYGSGG-PH 637

Query: 241 ILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQ 300
            +  T++E+VIPQ  + H+YGENN+N++H++QISGA +VV+D KPG  +G V++SGT DQ
Sbjct: 638 FMGGTSMEMVIPQTLICHIYGENNNNIAHVQQISGAMLVVHDAKPGMFDGKVIMSGTPDQ 697

Query: 301 MRAAQSLIHAFILCGVT 317
           +RAAQ L+HAFILCG T
Sbjct: 698 IRAAQRLVHAFILCGKT 714

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449492545|ref|XP_004159029.1| PREDICTED: KH domain-containing protein At4g18375-like [Cucumis sativus]

 Score =  322 bits (826), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 177/317 (55%), Positives = 220/317 (69%), Gaps = 6/317 (1%)

Query: 3   HSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIR 62
           +SPAQ+AV+R H RIAEIG+EPG AVVARLLVH QQIG L+GRGGHI+++MRR TG SI+
Sbjct: 402 YSPAQEAVIRAHCRIAEIGYEPGAAVVARLLVHGQQIGYLVGRGGHIINDMRRGTGTSIQ 461

Query: 63  VFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMK--RPGPNNGHSYLP 120
           +FP+DQ    G   DE+VQVIGN  SVQDALFHIT+R+R+T FPM+   P  NN   YL 
Sbjct: 462 IFPRDQIQNGGPMSDEVVQVIGNLPSVQDALFHITNRIRDTFFPMRPHVPNFNNHPPYLS 521

Query: 121 PFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNS 180
           P PE PPP FRP  N  SPG YPS  G     +R    S P DHQ A+ H +      N 
Sbjct: 522 PHPETPPPLFRPGSNAHSPGYYPSQAGGLRGTERPPYHSHPLDHQPAYPHNVSFGGGNNM 581

Query: 181 DRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAA 240
           D +P+P+G ERPG G +F+R PSPRSWT Q V    P+G     G   RN P  SG    
Sbjct: 582 DGVPYPHGMERPGPG-SFER-PSPRSWTSQ-VSSEIPKGPTDGFGMVSRNEPYGSGG-PH 637

Query: 241 ILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQ 300
            +  T++E+VIPQ  + H+YGENN+N++H++QISGA +VV+D KPG  +G V++SGT DQ
Sbjct: 638 FMGGTSMEMVIPQTLICHIYGENNNNIAHVQQISGAMLVVHDAKPGMFDGKVIMSGTPDQ 697

Query: 301 MRAAQSLIHAFILCGVT 317
           +RAAQ L+HAFILCG T
Sbjct: 698 IRAAQRLVHAFILCGKT 714

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526304|ref|XP_003531758.1| PREDICTED: heterogeneous nuclear ribonucleoprotein K-like [Glycine max]

 Score =  300 bits (769), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 180/318 (56%), Positives = 219/318 (68%), Gaps = 14/318 (4%)

Query: 2   RHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 61
           +HSPAQ+AV+RVH R+ EIGFEP  AVVA+LLV S Q+GCLLG+GG ++SEMRRATGASI
Sbjct: 258 KHSPAQEAVIRVHCRLTEIGFEPSAAVVAKLLVRSPQVGCLLGKGGLVISEMRRATGASI 317

Query: 62  RVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPP 121
           R+F K+Q     S ++E+VQVIG+  SVQDALFHIT+R+RETIFP++ P   +   + PP
Sbjct: 318 RIFSKEQIKYI-SQNEEVVQVIGSLQSVQDALFHITNRIRETIFPIRTPPNFSAPPHFPP 376

Query: 122 FPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQA-AFSHGMDPMVPPNS 180
           FPEMPPP FRPR++  S G +P P    H  D    P  P DHQ  AF HGM    PPN 
Sbjct: 377 FPEMPPPLFRPRNHLMSSG-HPPPPQVGHPHDHSTVPPMPVDHQQHAFVHGMGRG-PPNM 434

Query: 181 DRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNR-PVESGNHA 239
           DR+P+P G         ++ P SPRSW P  V  G+P G   +S  T RN  PV++GN  
Sbjct: 435 DRVPYPRG---------YEGPNSPRSWNPLAVDRGNPGGTADTSSLTSRNETPVKNGNPL 485

Query: 240 AILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSD 299
               S TIE+ IP +Y+ HVYGENNSNL+ IRQ SGANV V+D KPGATEG+V+VSG  D
Sbjct: 486 QNPNSLTIEITIPYMYLTHVYGENNSNLTQIRQTSGANVAVHDSKPGATEGLVIVSGAPD 545

Query: 300 QMRAAQSLIHAFILCGVT 317
           Q  AAQ LI  FILCG T
Sbjct: 546 QTHAAQCLIQGFILCGQT 563

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356522258|ref|XP_003529764.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  300 bits (767), Expect = 9e-79,   Method: Compositional matrix adjust.
 Identities = 183/319 (57%), Positives = 221/319 (69%), Gaps = 16/319 (5%)

Query: 2   RHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 61
           +HSPAQ+AV+RVH R+ EIGFEP  AVVA+LLV S Q+GCLLG+GG ++SEMRR TGASI
Sbjct: 252 KHSPAQEAVIRVHCRLTEIGFEPSAAVVAKLLVRSPQVGCLLGKGGLVISEMRRVTGASI 311

Query: 62  RVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPP 121
           R+F K+Q     S ++E+VQVIG+  SVQDALFHITSR+RETIFP++ P   +   +LPP
Sbjct: 312 RIFSKEQIKYI-SQNEEVVQVIGSLQSVQDALFHITSRIRETIFPIRTPPNFSAPPHLPP 370

Query: 122 FPEMPPPPFRPRHNPASPGSYPSP-VGPFHSMDRGMGPSQPFDHQA-AFSHGMDPMVPPN 179
           FPEMPPP FRPR++  S G  P P VG  H  D    P  P DHQ  AF HGM    PPN
Sbjct: 371 FPEMPPPLFRPRNHLMSSGHPPPPQVG--HPHDHSTVPPMPVDHQQHAFVHGMGRG-PPN 427

Query: 180 SDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPV-ESGNH 238
            DR+P+P G         ++ P SPRSW P  V  G+  G   +S    RN  + E+GN 
Sbjct: 428 MDRVPYPRG---------YEGPNSPRSWNPLAVNRGNSGGTADTSSLASRNENLGENGNP 478

Query: 239 AAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTS 298
                + TIE+ IP +Y+ HVYGENNSNL+ IRQ SGANVVV+DPKPGATEG+V+VSG  
Sbjct: 479 LQNPNNLTIEITIPHMYLTHVYGENNSNLTQIRQTSGANVVVHDPKPGATEGLVIVSGAP 538

Query: 299 DQMRAAQSLIHAFILCGVT 317
           DQ  AAQSLI AFILCG T
Sbjct: 539 DQTHAAQSLIQAFILCGQT 557

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15217969|ref|NP_175569.1| RNA-binding KH domain-containing protein [Arabidopsis thaliana] gi|12321677|gb|AAG50879.1|AC025294_17 hypothetical protein [Arabidopsis thaliana] gi|12325367|gb|AAG52626.1|AC024261_13 hypothetical protein; 15135-12645 [Arabidopsis thaliana] gi|31711718|gb|AAP68215.1| At1g51580 [Arabidopsis thaliana] gi|110735740|dbj|BAE99849.1| hypothetical protein [Arabidopsis thaliana] gi|332194564|gb|AEE32685.1| RNA-binding KH domain-containing protein [Arabidopsis thaliana]

 Score =  298 bits (764), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 182/319 (57%), Positives = 205/319 (64%), Gaps = 38/319 (11%)

Query: 2   RHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 61
           RHS AQD VMRVH+RI EIGFEP  AVVARLLVHS  IG LLG+GGH++SEMRRATGASI
Sbjct: 334 RHSLAQDGVMRVHNRIVEIGFEPSAAVVARLLVHSPYIGRLLGKGGHLISEMRRATGASI 393

Query: 62  RVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFP--MKRPGPNNGHSYL 119
           RVF KDQA +  S HDEIVQVIGN  +VQDALF I  RLRE +FP  +   G        
Sbjct: 394 RVFAKDQATKYESQHDEIVQVIGNLKTVQDALFQILCRLREAMFPGRLPFQGMGGPPPPF 453

Query: 120 PPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPN 179
                 PPPPF PR  PASP  Y SPVGPFH                   HG      P 
Sbjct: 454 MGPYPEPPPPFGPRQYPASPDRYHSPVGPFHER---------------HCHG------PG 492

Query: 180 SDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGF---DASSGFTPRNRPVESG 236
            DR P          GP FDRPPSP SWTPQ    G P G    D + GF  RN P+ S 
Sbjct: 493 FDRPP----------GPGFDRPPSPMSWTPQPGIDGHPGGMVPPDVNHGFALRNEPIGSE 542

Query: 237 NHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG 296
           N   ++TS  +E+VIPQ Y+ HVYGEN SNL++I+Q+SGANVVV+DPK G TEG+V+VSG
Sbjct: 543 N--PVMTSANVEIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSG 600

Query: 297 TSDQMRAAQSLIHAFILCG 315
           TSDQ   AQSL+HAFILCG
Sbjct: 601 TSDQAHFAQSLLHAFILCG 619

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297847528|ref|XP_002891645.1| KH domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297337487|gb|EFH67904.1| KH domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  298 bits (762), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 183/319 (57%), Positives = 205/319 (64%), Gaps = 38/319 (11%)

Query: 2   RHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 61
           RHS AQD VMRVH+RI EIGFEP  AVVARLLVHS  IG LLG+GGH++SEMRRATGASI
Sbjct: 335 RHSLAQDGVMRVHNRIVEIGFEPSAAVVARLLVHSPYIGRLLGKGGHLISEMRRATGASI 394

Query: 62  RVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFP--MKRPGPNNGHSYL 119
           RVF KDQA +  S HDEIVQVIGN  +VQDALF I  RLRE +FP  +   G        
Sbjct: 395 RVFAKDQATKYESQHDEIVQVIGNLKTVQDALFQILCRLREAMFPGRLPFQGLGGPPPPF 454

Query: 120 PPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPN 179
                 PPPPF PR  PASP  Y SPVG FH                   HG      P 
Sbjct: 455 MGPYPEPPPPFGPRQYPASPDRYHSPVGSFHER---------------HCHG------PG 493

Query: 180 SDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGF---DASSGFTPRNRPVESG 236
            DR P          GP FDRPPSP SWTPQ    G P G    D + GF  RN P+ S 
Sbjct: 494 FDRPP----------GPGFDRPPSPMSWTPQPGIDGHPGGMVPPDVNHGFALRNEPIGSE 543

Query: 237 NHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG 296
           N A  +TS  +E+VIPQ Y+ HVYGEN SNL++I+Q+SGANVVV+DPK GATEG+V+VSG
Sbjct: 544 NPA--MTSANVEIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGATEGLVVVSG 601

Query: 297 TSDQMRAAQSLIHAFILCG 315
           TSDQ   AQSL+HAFILCG
Sbjct: 602 TSDQAHFAQSLLHAFILCG 620

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357159179|ref|XP_003578365.1| PREDICTED: poly(rC)-binding protein 2-like [Brachypodium distachyon]

 Score =  260 bits (664), Expect = 6e-67,   Method: Compositional matrix adjust.
 Identities = 156/322 (48%), Positives = 195/322 (60%), Gaps = 11/322 (3%)

Query: 1   MRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGAS 60
           M HSPAQDAV+RV+SRI+E   +   AV ARLLV SQ IGCLLG+GG I++EMR  TGAS
Sbjct: 310 MMHSPAQDAVLRVYSRISEASMDKSSAVPARLLVPSQHIGCLLGKGGSIIAEMRNVTGAS 369

Query: 61  IRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLP 120
           IR+F  +Q PRC   +DE+VQV GN+ S+QDAL HIT R+R+ I P K P P+ G S  P
Sbjct: 370 IRIFGNEQIPRCAQRNDELVQVTGNFQSIQDALLHITGRIRDVIIPPK-PHPSGGMSPYP 428

Query: 121 PFPEMPPPPFRPRHNPASP----GSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMV 176
           P    P  P   R +PA P    G  P P+ PF   +  MGP    DH+    H   PM 
Sbjct: 429 PAGSTPHHP--SRQDPAPPHHSGGMPPYPMHPFRP-NHPMGPFDVADHRPPGQHPAHPME 485

Query: 177 PPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGF-DASSGFTPRNRPVE- 234
              +DRIP+ YG E+ G  P  ++ PSPR+W P+      PR   D       R   V  
Sbjct: 486 HMGADRIPYSYGCEQGGPRPFLEQ-PSPRTWAPEAQTADAPRSIPDKGLAMDSRKGSVAG 544

Query: 235 SGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMV 294
           S N  A  TSTT EVVIP  Y+  + G N S+L+ I++ISGA + V+DPKPG T+  V V
Sbjct: 545 SENQVATPTSTTTEVVIPCKYIGFICGTNGSDLAEIQKISGAAITVHDPKPGDTDASVFV 604

Query: 295 SGTSDQMRAAQSLIHAFILCGV 316
            G  +Q + AQSLIHAFI CG+
Sbjct: 605 CGDPEQTKKAQSLIHAFIFCGL 626

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242045198|ref|XP_002460470.1| hypothetical protein SORBIDRAFT_02g028920 [Sorghum bicolor] gi|241923847|gb|EER96991.1| hypothetical protein SORBIDRAFT_02g028920 [Sorghum bicolor]

 Score =  251 bits (642), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 151/327 (46%), Positives = 200/327 (61%), Gaps = 18/327 (5%)

Query: 1   MRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGAS 60
           M HSPAQDAV+RV+SRI+E   +      ARLLV SQ IGCLLG+GG I++EMR+ TGAS
Sbjct: 54  MMHSPAQDAVVRVYSRISEASMDRSSPTPARLLVPSQHIGCLLGKGGSIITEMRKITGAS 113

Query: 61  IRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLP 120
           IR+F  +Q PRC   +DE+VQV G++ S+QDAL HIT R+R+ I P  +P P+ G   +P
Sbjct: 114 IRIFGNEQIPRCAQRNDEMVQVTGSFQSIQDALLHITGRIRDVILP--KPHPSGG---MP 168

Query: 121 PFPEMPPPPF-RPRHNPASPGSYPS---PVGPFHSM--DRGMGPSQPFDHQAAFSHGMDP 174
           P+P +   P  + R  P  P  +PS   P  P HS   D  MG  +  DH+    H M+ 
Sbjct: 169 PYPPVGNIPVHQSRQEPPPPHLHPSGGMPPYPMHSFRPDAPMGHFETGDHRPPPVHSMEY 228

Query: 175 MVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQG--VGGGDPRGF-DASSGFTPRNR 231
           M    +DR+P+ YG E+ G  P  ++ PSPR+W P+        PR   DA      R  
Sbjct: 229 M---GADRMPYSYGGEQGGPRPFLEQ-PSPRTWPPEAPRTNSEAPRNMPDAVLATDLRKG 284

Query: 232 PVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGV 291
           PV S N  A  TSTT EVVIP  Y+  V G + S +  IRQ+SGA++ V+DPKPG T  +
Sbjct: 285 PVASENQVATPTSTTTEVVIPCKYIGFVCGNSGSEIEEIRQMSGASITVHDPKPGDTNSI 344

Query: 292 VMVSGTSDQMRAAQSLIHAFILCGVTS 318
           V++ G  +Q + AQSLIHAFI CG+ +
Sbjct: 345 VVICGDPEQTKKAQSLIHAFIFCGLQT 371

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	318
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.531	0.272	0.511	6.7e-78
TAIR|locus:2168367	652	RCF3 "AT5G53060" [Arabidopsis	0.261	0.127	0.458	8.4e-25
TAIR|locus:2161413	644	AT5G46190 "AT5G46190" [Arabido	0.339	0.167	0.360	5e-24
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.323	0.187	0.428	4.8e-19
TAIR|locus:2084908	577	FLK "AT3G04610" [Arabidopsis t	0.308	0.169	0.355	5.5e-15
TAIR|locus:2831364	606	AT4G18375 "AT4G18375" [Arabido	0.402	0.211	0.318	9.1e-15
TAIR|locus:2066020	632	AT2G22600 "AT2G22600" [Arabido	0.298	0.150	0.364	2.1e-14
TAIR|locus:2035807	479	AT1G14170 "AT1G14170" [Arabido	0.327	0.217	0.405	5.7e-14
TAIR|locus:2056951	153	AT2G03110 "AT2G03110" [Arabido	0.286	0.594	0.383	7.2e-11
TAIR|locus:2120755	495	PEP "AT4G26000" [Arabidopsis t	0.308	0.197	0.301	9.5e-10

TAIR|locus:2017612 AT1G51580 "AT1G51580" [Arabidopsis thaliana (taxid:3702)]

 Score = 415 (151.1 bits), Expect = 6.7e-78, Sum P(2) = 6.7e-78
 Identities = 92/180 (51%), Positives = 114/180 (63%)

Query:   140 GSYPSP-VGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTF 198
             G  P P +GP+       GP Q   + A+      P+ P +      P G +RP  GP F
Sbjct:   447 GGPPPPFMGPYPEPPPPFGPRQ---YPASPDRYHSPVGPFHERHCHGP-GFDRPP-GPGF 501

Query:   199 DRPPSPRSWTPQGVGGGDPRGF---DASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLY 255
             DRPPSP SWTPQ    G P G    D + GF  RN P+ S N   ++TS  +E+VIPQ Y
Sbjct:   502 DRPPSPMSWTPQPGIDGHPGGMVPPDVNHGFALRNEPIGSEN--PVMTSANVEIVIPQAY 559

Query:   256 MAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG 315
             + HVYGEN SNL++I+Q+SGANVVV+DPK G TEG+V+VSGTSDQ   AQSL+HAFILCG
Sbjct:   560 LGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSDQAHFAQSLLHAFILCG 619

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

TAIR|locus:2168367 RCF3 "AT5G53060" [Arabidopsis thaliana (taxid:3702)]

 Score = 190 (71.9 bits), Expect = 8.4e-25, Sum P(3) = 8.4e-25
 Identities = 39/85 (45%), Positives = 57/85 (67%)

Query:    21 GFEPGQA-VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQ-APRCGSPHDE 78
             G  PG   VV RL+V    +GCLLG+GG I+ +MR  T   IR+ P++   PRC S  +E
Sbjct:   168 GVRPGGGRVVTRLVVSRMHVGCLLGKGGKIIEQMRIETKTHIRILPRESNLPRCVSLSEE 227

Query:    79 IVQVIGNYHSVQDALFHITSRLRET 103
             IVQ++G  ++V++AL  ++SRLRE+
Sbjct:   228 IVQIVGELNAVKNALAIVSSRLRES 252

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2161413 AT5G46190 "AT5G46190" [Arabidopsis thaliana (taxid:3702)]

 Score = 191 (72.3 bits), Expect = 5.0e-24, Sum P(2) = 5.0e-24
 Identities = 40/111 (36%), Positives = 65/111 (58%)

Query:     4 SPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRV 63
             S A +AV+ +  +I +   E    V  +LLV S+ IGC++G+ G I+SE+R+ T A I +
Sbjct:   378 SMAVEAVLLLQEKIND---EDEDKVKMQLLVSSKVIGCIIGKSGSIISEIRKRTKADIHI 434

Query:    64 FPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNN 114
                +  P+C  P+DE+V++ G   +V+DAL  I  RLR+ +   +  G  N
Sbjct:   435 SKGNNTPKCADPNDELVEISGEVSNVRDALIQIVLRLRDDVLRDRETGSRN 485

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2150956 AT5G15270 "AT5G15270" [Arabidopsis thaliana (taxid:3702)]

 Score = 213 (80.0 bits), Expect = 4.8e-19, Sum P(2) = 4.8e-19
 Identities = 45/105 (42%), Positives = 68/105 (64%)

Query:     3 HSPAQDAVMRVHSRIAE-IGFEPGQ-AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGAS 60
             +SP  +AVMR+  + ++ +  + G  +   RLLV S +IGC+LG+GG I++EMRR T A+
Sbjct:   343 YSPTIEAVMRLQPKCSDKVERDSGLVSFTTRLLVPSSRIGCILGKGGAIITEMRRMTKAN 402

Query:    61 IRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIF 105
             IR+  K+  P+  S  DE+VQ+ G     ++AL  ITSRLR  +F
Sbjct:   403 IRILGKENLPKVASDDDEMVQISGELDVAKEALIQITSRLRANVF 447

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2084908 FLK "AT3G04610" [Arabidopsis thaliana (taxid:3702)]

 Score = 137 (53.3 bits), Expect = 5.5e-15, Sum P(2) = 5.5e-15
 Identities = 37/104 (35%), Positives = 54/104 (51%)

Query:     5 PAQDAVMRVHSRIAE-IGFEPGQA-----VVARLLVHSQQIGCLLGRGGHIVSEMRRATG 58
             P+ D ++RVH RI + +  E  QA     V  RLLV + Q G L+G+ G  V  ++ A+ 
Sbjct:   248 PSMDGLLRVHMRIVDGLDGEASQAPPPSKVSTRLLVPASQAGSLIGKQGGTVKAIQEASA 307

Query:    59 ASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 102
               +RV   +  P      D +V+V+G   SV  AL  I S LR+
Sbjct:   308 CIVRVLGSEDLPVFALQDDRVVEVVGEPTSVHRALELIASHLRK 351

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

GO:0009911 "positive regulation of flower development" evidence=IMP

TAIR|locus:2831364 AT4G18375 "AT4G18375" [Arabidopsis thaliana (taxid:3702)]

 Score = 148 (57.2 bits), Expect = 9.1e-15, Sum P(2) = 9.1e-15
 Identities = 44/138 (31%), Positives = 71/138 (51%)

Query:   177 PPNSDRIPFPYGSERPGHG-PTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVES 235
             P  +D   F  GS   G+  P+F    +  S    G G   P G D   G T    P   
Sbjct:   476 PARTDNCSFLSGSSNAGYTLPSFMSSMASTSGF-HGYGSF-PAG-DNVLGSTG---PYSY 529

Query:   236 GNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVS 295
             G    + +S+ +E++IP   M+ V G+   NL +IR+ISGA + ++  K    + + ++S
Sbjct:   530 GR---LPSSSALEILIPAHAMSKVMGKGGGNLENIRRISGAMIEISASKTSHGDHIALLS 586

Query:   296 GTSDQMRAAQSLIHAFIL 313
             GT +QMR A++L+ AF++
Sbjct:   587 GTLEQMRCAENLVQAFVM 604

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2066020 AT2G22600 "AT2G22600" [Arabidopsis thaliana (taxid:3702)]

 Score = 133 (51.9 bits), Expect = 2.1e-14, Sum P(2) = 2.1e-14
 Identities = 39/107 (36%), Positives = 58/107 (54%)

Query:     4 SPAQDAVMRVHSRI-AEIGFEPGQAVV--------ARLLVHSQQIGCLLGRGGHIVSEMR 54
             S AQ A++RV  R    +  + G  VV          +L    QIG +LG GG  V  MR
Sbjct:   107 SAAQTALIRVLERSWVVLAAKDGGGVVDGEDEEAYCGILADRNQIGAVLGLGGKNVEWMR 166

Query:    55 RATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLR 101
             R +GA IRV P    P CG+ +DE++Q+ G+  +V+ AL  ++S ++
Sbjct:   167 RNSGAMIRVLPP---PICGTKNDELIQITGDVLAVKKALVMVSSYIQ 210

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2035807 AT1G14170 "AT1G14170" [Arabidopsis thaliana (taxid:3702)]

 Score = 201 (75.8 bits), Expect = 5.7e-14, P = 5.7e-14
 Identities = 43/106 (40%), Positives = 64/106 (60%)

Query:     4 SPAQDAVMRVHSRIAE-IGFEPGQ-AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 61
             SPA +A +R+  R +E +G +    A+  RLLV S QIGCL+G+GG ++SEMR  T A+I
Sbjct:   328 SPAVNAAIRLQQRCSEKVGKDANDLAISTRLLVSSSQIGCLIGKGGAVISEMRSVTRANI 387

Query:    62 RVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPM 107
             R+  K+  P+     +E+VQ+ G+  +   AL  +  RLR   F M
Sbjct:   388 RILQKEDVPKIAREDEEMVQITGSPDAAMKALTQVILRLRANSFDM 433

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2056951 AT2G03110 "AT2G03110" [Arabidopsis thaliana (taxid:3702)]

 Score = 155 (59.6 bits), Expect = 7.2e-11, P = 7.2e-11
 Identities = 41/107 (38%), Positives = 59/107 (55%)

Query:     5 PAQDAVMRVHSRIAEIGFEP------------GQAVVA-RLLVHSQQIGCLLGRGGHIVS 51
             PA DA+ +VH  +    F+             GQ VV  R+LV S QIG L+G+GG I+ 
Sbjct:    37 PAFDALFKVHDMVVVEEFDDDDDYNDNDEYSEGQTVVTVRMLVPSDQIGYLIGKGGPIIQ 96

Query:    52 EMRRATGASIRVFPKDQAPRCGSP--HDEIVQVIGNYHSVQDALFHI 96
              +R  T A IRV   D  P C     HDE++Q+IG+  +V++AL+ +
Sbjct:    97 TLRNDTNAQIRV-RNDNLPMCALALSHDELLQIIGDPSAVREALYQV 142

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2120755 PEP "AT4G26000" [Arabidopsis thaliana (taxid:3702)]

 Score = 107 (42.7 bits), Expect = 9.5e-10, Sum P(2) = 9.5e-10
 Identities = 32/106 (30%), Positives = 54/106 (50%)

Query:     4 SPAQDAVMRVHSRIAEI------GFEPGQAVVA--RLLVHSQQIGCLLGRGGHIVSEMRR 55
             SPA DAV+RV  R++ +        +   +V +  RLLV S Q   L+G+ G ++  +  
Sbjct:   134 SPAMDAVLRVFRRVSGLPDNDDDDVQNAGSVFSSVRLLVASTQAINLIGKQGSLIKSIVE 193

Query:    56 ATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLR 101
              +GAS+R+  +++ P   +  + IV + G    +  AL  I   LR
Sbjct:   194 NSGASVRILSEEETPFYAAQDERIVDLQGEALKILKALEAIVGHLR 239

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0048367 "shoot system development" evidence=IMP

GO:0048467 "gynoecium development" evidence=IMP

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	318
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	1e-18
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-12
pfam00013	59	pfam00013, KH_1, KH domain	1e-10
pfam00013	59	pfam00013, KH_1, KH domain	5e-10
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	3e-09
smart00322	68	smart00322, KH, K homology RNA-binding domain	3e-09
smart00322	68	smart00322, KH, K homology RNA-binding domain	8e-07
pfam13014	42	pfam13014, KH_3, KH domain	2e-06
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	2e-05
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	5e-05
pfam13014	42	pfam13014, KH_3, KH domain	1e-04
PHA03132	580	PHA03132, PHA03132, thymidine kinase; Provisional	0.002

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

 Score = 77.9 bits (193), Expect = 1e-18
 Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 4/69 (5%)

Query: 29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHS 88
            RLLV S Q G ++G+GG  + E+R  TGA IRV             + +V + G   +
Sbjct: 1  TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLP----GSTERVVTISGKPSA 56

Query: 89 VQDALFHIT 97
          VQ AL  I 
Sbjct: 57 VQKALLLIL 65

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

 Score = 61.0 bits (149), Expect = 2e-12
 Identities = 18/64 (28%), Positives = 35/64 (54%)

Query: 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 305
           T  V++P   +  + G+  S +  IR+ +GA + + D   G+ E +V ++GT + +  A+
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60

Query: 306 SLIH 309
            LI 
Sbjct: 61  ELIL 64

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 = 56.0 bits (136), Expect = 1e-10
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 9/68 (13%)

Query: 29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHS 88
            R+L+   ++G ++G+GG  + E+R  TG  IR+             D+ V + G    
Sbjct: 1  TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR---------DDTVTISGTPEQ 51

Query: 89 VQDALFHI 96
          V+ A   I
Sbjct: 52 VEKAKELI 59

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

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

 Score = 54.5 bits (132), Expect = 5e-10
 Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 4/63 (6%)

Query: 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 305
           T  ++IP   +  + G+  SN+  IR+ +G  + + D +    +  V +SGT +Q+  A+
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR----DDTVTISGTPEQVEKAK 56

Query: 306 SLI 308
            LI
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|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 52.2 bits (126), Expect = 3e-09
 Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 5/68 (7%)

Query: 29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHS 88
            R+LV S  +G ++G+GG  + E+R  TGA I++             + IV + G   +
Sbjct: 1  TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG-----SGSEERIVTITGTPEA 55

Query: 89 VQDALFHI 96
          V+ A   I
Sbjct: 56 VEKAKELI 63

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

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

 Score = 52.3 bits (126), Expect = 3e-09
 Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 302
              TIEV+IP   +  + G+  S +  I + +G  + +  P PG+ E VV ++G  + + 
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI--PGPGSEERVVEITGPPENVE 58

Query: 303 AAQSLI 308
            A  LI
Sbjct: 59  KAAELI 64

Length = 68

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

 Score = 45.4 bits (108), Expect = 8e-07
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 7/73 (9%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
           V   +L+ + ++G ++G+GG  + ++   TG  I +             + +V++ G   
Sbjct: 3   VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG-------SEERVVEITGPPE 55

Query: 88  SVQDALFHITSRL 100
           +V+ A   I   L
Sbjct: 56  NVEKAAELILEIL 68

Length = 68

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

 Score = 43.3 bits (103), Expect = 2e-06
 Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 5/47 (10%)

Query: 38 QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 84
           +G ++G+GG  + E+R  TGA I++             + IV + G
Sbjct: 1  LVGAIIGKGGETIKEIREETGAKIQIPKP-----EPGSGERIVTITG 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|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 41.3 bits (98), Expect = 2e-05
 Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 305
           T EV IP+     + G+  SN+  I + +G  +    P PG+    + ++G  + +  A+
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRF--PDPGSKSDTITITGPKENVEKAK 58

Query: 306 SLI 308
             I
Sbjct: 59  EEI 61

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

 Score = 40.2 bits (95), Expect = 5e-05
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND-PKPGATEGVVMVSGTSDQMRAA 304
           T+ +++P      + G+  S +  IR+ +GA + V+    PG+TE VV +SG    ++ A
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60

Query: 305 QSLIH 309
             LI 
Sbjct: 61  LLLIL 65

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 = 38.3 bits (90), Expect = 1e-04
 Identities = 11/42 (26%), Positives = 24/42 (57%)

Query: 255 YMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG 296
            +  + G+    +  IR+ +GA + +  P+PG+ E +V ++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|222997 PHA03132, PHA03132, thymidine kinase; Provisional

 Score = 39.4 bits (92), Expect = 0.002
 Identities = 35/185 (18%), Positives = 43/185 (23%), Gaps = 33/185 (17%)

Query: 63  VFPKDQAPRCGSPHDEIVQVIGNYHSVQ-------DALFHITSRLRETIFPMKRPGPNNG 115
                +  R  +   E    +    S         D L+      RET            
Sbjct: 17  SDESPEGSRDENFDAERDDFLTPLGSTSEATSEDDDDLYPP----RETGSGGGVATSTI- 71

Query: 116 HSYLPPFPEMPPPP------FRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFS 169
             Y  P P   P          P      PG  P P G F    RG    +      A S
Sbjct: 72  --YTVPRPPRGPEQTLDKPDSLPASRELPPGPTPVPPGGF----RGASSPRL----GADS 121

Query: 170 HGMDPMVPPNSDRIPFPYGSERPGHG-----PTFDRPPSPRSWTPQGVGGGDPRGFDASS 224
                +   N   I  P G                RPP   S   +  G   P+GF    
Sbjct: 122 TSPRFLYQVNFPVILAPIGESNSSSEELSEEEEHSRPPPSESLKVKNGGKVYPKGFSKHK 181

Query: 225 GFTPR 229
                
Sbjct: 182 THKRS 186

Length = 580

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	318
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	100.0
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.96
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.96
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.94
KOG1676	600	consensus K-homology type RNA binding proteins [RN	99.93
KOG1676	600	consensus K-homology type RNA binding proteins [RN	99.93
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.88
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.83
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.8
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.75
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.71
PRK13763	180	putative RNA-processing protein; Provisional	99.71
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.59
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.59
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.45
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.43
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.41
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.38
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.36
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.36
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.36
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.29
PF13014	43	KH_3: KH domain	99.17
PF13014	43	KH_3: KH domain	99.13
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.11
smart00322	69	KH K homology RNA-binding domain.	99.11
smart00322	69	KH K homology RNA-binding domain.	99.05
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.93
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.67
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.59
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.57
PRK13763	180	putative RNA-processing protein; Provisional	98.55
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.22
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.22
PRK08406	140	transcription elongation factor NusA-like protein;	98.17
KOG2113	394	consensus Predicted RNA binding protein, contains	98.14
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.05
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.01
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.92
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.76
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.75
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	97.73
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.71
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	97.69
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.63
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.62
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	97.42
PRK00106	535	hypothetical protein; Provisional	97.41
KOG2814	345	consensus Transcription coactivator complex, P50 c	97.4
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.4
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.38
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	97.37
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.36
PRK12704	520	phosphodiesterase; Provisional	97.27
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	97.24
COG1094	194	Predicted RNA-binding protein (contains KH domains	97.18
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	97.17
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	97.13
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.08
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.97
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.8
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.73
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.72
PRK00468	75	hypothetical protein; Provisional	96.68
COG1837	76	Predicted RNA-binding protein (contains KH domain)	96.65
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.58
PRK12705	508	hypothetical protein; Provisional	96.47
PRK01064	78	hypothetical protein; Provisional	96.45
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	96.44
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.41
PRK02821	77	hypothetical protein; Provisional	96.33
PRK00468	75	hypothetical protein; Provisional	96.33
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	96.24
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.22
PRK02821	77	hypothetical protein; Provisional	96.18
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.05
TIGR01953	341	NusA transcription termination factor NusA. This m	96.03
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.01
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.61
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.59
PRK01064	78	hypothetical protein; Provisional	95.46
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.37
PRK12704	520	phosphodiesterase; Provisional	95.34
KOG2113	394	consensus Predicted RNA binding protein, contains	95.32
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	95.28
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	95.26
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.15
PRK00106	535	hypothetical protein; Provisional	95.12
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	94.78
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	94.32
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	94.15
PRK08406	140	transcription elongation factor NusA-like protein;	93.94
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	93.52
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	93.51
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	93.48
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	92.87
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	92.16
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	92.04
PRK12705	508	hypothetical protein; Provisional	92.0
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	91.93
PRK13764	602	ATPase; Provisional	91.7
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	91.53
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	91.41
COG1855	604	ATPase (PilT family) [General function prediction	91.2
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	91.13
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	91.08
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	90.8
PRK06418	166	transcription elongation factor NusA-like protein;	90.6
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	90.56
PRK12328	374	nusA transcription elongation factor NusA; Provisi	89.65
TIGR01953	341	NusA transcription termination factor NusA. This m	89.53
COG1855	604	ATPase (PilT family) [General function prediction	88.58
PRK13764	602	ATPase; Provisional	88.28
COG0195	190	NusA Transcription elongation factor [Transcriptio	88.25
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	88.15
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	87.58
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	87.49
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	87.45
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	87.03
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	86.95
KOG2874	356	consensus rRNA processing protein [Translation, ri	86.03
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	84.5
PRK12327	362	nusA transcription elongation factor NusA; Provisi	84.17
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	84.16
PRK09202	470	nusA transcription elongation factor NusA; Validat	84.11
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	83.07
KOG2874	356	consensus rRNA processing protein [Translation, ri	82.46
TIGR00436	270	era GTP-binding protein Era. Era is an essential G	82.16
PRK12329	449	nusA transcription elongation factor NusA; Provisi	80.74

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

Probab=100.00  E-value=1e-35  Score=259.41  Aligned_cols=273  Identities=22%  Similarity=0.362  Sum_probs=176.9

Q ss_pred             HHHHHHHHHHHHHhh---ccCCCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEE
Q 021032            6 AQDAVMRVHSRIAEI---GFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQV   82 (318)
Q Consensus         6 a~~a~~~v~~~i~~~---~~e~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I   82 (318)
                      ..+-+..|+..|+-.   ++...+++++||||+.+++|.|||++|++||+|||++.|+++|...    ||+.++||+|.|
T Consensus        98 d~~ti~~ilk~iip~lee~f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~----c~p~stdrv~l~  173 (390)
T KOG2192|consen   98 DIETIGEILKKIIPTLEEGFQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE----CCPHSTDRVVLI  173 (390)
T ss_pred             cHHHHHHHHHHHhhhhhhCCCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc----cCCCCcceEEEe
Confidence            344555555555543   3446788999999999999999999999999999999999999977    999999999999


Q ss_pred             EecHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032           83 IGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPF  162 (318)
Q Consensus        83 ~G~~~~V~~A~~~I~~~l~e~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~  162 (318)
                      .|++.+|..+++.|++.|.|.      +++.++.+|+|.|.+ +.+.|...         ..+.+..+..  ....+.+.
T Consensus       174 ~g~~k~v~~~i~~il~~i~e~------pikgsa~py~p~fyd-~t~dyggf---------~M~f~d~pg~--pgpapqrg  235 (390)
T KOG2192|consen  174 GGKPKRVVECIKIILDLISES------PIKGSAQPYDPNFYD-ETYDYGGF---------TMMFDDRPGR--PGPAPQRG  235 (390)
T ss_pred             cCCcchHHHHHHHHHHHhhcC------CcCCcCCcCCccccC-cccccCCc---------eeecCCCCCC--CCCCCCCC
Confidence            999999999999999999997      788899999999843 22222111         0000000000  00000000


Q ss_pred             CCcccccCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCC----CCC-----CCCCCCCC-CCCCCCCCCCCCCCCCCCC
Q 021032          163 DHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHG---PTFD----RPP-----SPRSWTPQ-GVGGGDPRGFDASSGFTPR  229 (318)
Q Consensus       163 ~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~---~~~~----~~~-----~~~~~~~~-~~~~~~~~g~~~~~~~~~~  229 (318)
                              |-++-+++..+...+..++..+...   .+|.    .|.     .|..|.+. ..-+++.+.+.....+.+.
T Consensus       236 --------gqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsY  307 (390)
T KOG2192|consen  236 --------GQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSY  307 (390)
T ss_pred             --------CCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCcccccccccc
Confidence                    0000000111111111111000000   0111    011     22333211 1101111111111101100


Q ss_pred             CCCCCCCCccccCcceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHH
Q 021032          230 NRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH  309 (318)
Q Consensus       230 ~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~  309 (318)
                       .++       .....|.+|.||.++-|.||||+|.+|++|++++||+|+|+++.+++.||+++|+||.+|++.||+|++
T Consensus       308 -Gdl-------GGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQ  379 (390)
T KOG2192|consen  308 -GDL-------GGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQ  379 (390)
T ss_pred             -CCC-------CCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHH
Confidence             111       124678999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHcCc
Q 021032          310 AFILCGV  316 (318)
Q Consensus       310 ~~i~~~~  316 (318)
                      ++|+.++
T Consensus       380 n~Vkq~r  386 (390)
T KOG2192|consen  380 NSVKQYR  386 (390)
T ss_pred             HHHHhhh
Confidence            9998754

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

Probab=99.96  E-value=3e-28  Score=236.21  Aligned_cols=279  Identities=25%  Similarity=0.293  Sum_probs=169.2

Q ss_pred             CCChHHHHHHHHHHHHHhhcc------C------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCC
Q 021032            2 RHSPAQDAVMRVHSRIAEIGF------E------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQA   69 (318)
Q Consensus         2 ~~s~a~~a~~~v~~~i~~~~~------e------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~   69 (318)
                      .+|++++|++++|++|....+      +      +..++++|||||++++|+||||+|++||+|+|+|||+|+|++. ++
T Consensus       100 ~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~l  178 (485)
T KOG2190|consen  100 NLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-ML  178 (485)
T ss_pred             cCCchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CC
Confidence            468999999999999998521      1      1225899999999999999999999999999999999999854 88


Q ss_pred             CCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032           70 PRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPF  149 (318)
Q Consensus        70 p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~  149 (318)
                      |.|   ++|.|+|.|++++|.+|+..|+.+|+++.-. ..+...++.+|.|+.++.-+....              ++..
T Consensus       179 P~s---ter~V~IsG~~~av~~al~~Is~~L~~~~~~-~~~~~~st~~y~P~~~~~~~~~~s--------------~~~~  240 (485)
T KOG2190|consen  179 PNS---TERAVTISGEPDAVKKALVQISSRLLENPPR-SPPPLVSTIPYRPSASQGGPVLPS--------------TAQT  240 (485)
T ss_pred             Ccc---cceeEEEcCchHHHHHHHHHHHHHHHhcCCc-CCCCCCCcccCCCcccccCccccc--------------cccC
Confidence            874   8999999999999999999999999997311 112344666777621110000000              0000


Q ss_pred             CCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----CCCCCCC-CCCCCCCCCCCCCCCC
Q 021032          150 HSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDR-----PPSPRSW-TPQGVGGGDPRGFDAS  223 (318)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~~~~~-~~~~~~~~~~~g~~~~  223 (318)
                      .. +..++......++.    .....       .|....+...|-+.....     ....... .+..........   .
T Consensus       241 ~~-~~~~~~~~~~~~e~----~~~~~-------~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~~i~~s~---~  305 (485)
T KOG2190|consen  241 SP-DAHPFGGIVPEEEL----VFKLI-------CPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTDRIVTISA---R  305 (485)
T ss_pred             Cc-ccccccccccchhh----hhhhc-------CchhhceeeecCCCccchhhhhhcCCceEeccccCcceeeecc---c
Confidence            00 00000000000000    00000       000000000000000000     0000000 000000000000   0


Q ss_pred             CCCCCC----CCCC--------CCCCccccCcceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCC--CCCC
Q 021032          224 SGFTPR----NRPV--------ESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP--GATE  289 (318)
Q Consensus       224 ~~~~~~----~~~~--------~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~--~~~e  289 (318)
                      ....++    ...+        ......+ ...++.++.||.+++|+||||+|++|.+||+.|||.|+|.+...  ...|
T Consensus       306 e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e  384 (485)
T KOG2190|consen  306 ENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVRE  384 (485)
T ss_pred             cCcccccccchhhhhhccccccccccccc-cceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcce
Confidence            000000    0000        0001111 34588999999999999999999999999999999999998776  8899


Q ss_pred             eEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          290 GVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       290 r~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      +.++|+|+..+...|++++..++...
T Consensus       385 ~~~~I~~~~~~~~~~~~~~~~~~~~~  410 (485)
T KOG2190|consen  385 ALVQITGMLREDLLAQYLIRARLSAP  410 (485)
T ss_pred             eEEEecchhHHHHhhhhhcccccccC
Confidence            99999999999999999998887764

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

Probab=99.96  E-value=6e-28  Score=216.26  Aligned_cols=167  Identities=23%  Similarity=0.376  Sum_probs=137.8

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcCC
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFP  106 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~  106 (318)
                      .+.+|+|||+..+|+||||||++|.+||.+|||+|++++..+  +|++.+||+|.|+|+.+++......|.++|||....
T Consensus        38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~d--fyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~  115 (402)
T KOG2191|consen   38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKD--FYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQA  115 (402)
T ss_pred             ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccc--cCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHh
Confidence            499999999999999999999999999999999999986443  777899999999999999999999999999997321


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCC
Q 021032          107 MKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFP  186 (318)
Q Consensus       107 ~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~  186 (318)
                      ...                +..+|.                                                       
T Consensus       116 ~~k----------------~v~~~~-------------------------------------------------------  124 (402)
T KOG2191|consen  116 VAK----------------PVDILQ-------------------------------------------------------  124 (402)
T ss_pred             hcC----------------CccccC-------------------------------------------------------
Confidence            100                000000                                                       


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccccccccccccch
Q 021032          187 YGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSN  266 (318)
Q Consensus       187 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~  266 (318)
                                            ++..                             ......++.+|++.+|.||||+|++
T Consensus       125 ----------------------pqt~-----------------------------~r~kqikivvPNstag~iigkggAt  153 (402)
T KOG2191|consen  125 ----------------------PQTP-----------------------------DRIKQIKIVVPNSTAGMIIGKGGAT  153 (402)
T ss_pred             ----------------------CCCc-----------------------------cccceeEEeccCCcccceecCCcch
Confidence                                  0000                             0123488999999999999999999


Q ss_pred             HHHHHHHhCCEEEEcCCCC---CCCCeEEEEEcCHHHHHHHHHHHHHHHHcCcC
Q 021032          267 LSHIRQISGANVVVNDPKP---GATEGVVMVSGTSDQMRAAQSLIHAFILCGVT  317 (318)
Q Consensus       267 Ik~Ir~~SGA~I~i~~~~~---~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~~~  317 (318)
                      ||.|++++||.|+|+...+   .-.||.|+++|++|+..+|..||.++|.++..
T Consensus       154 iK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq  207 (402)
T KOG2191|consen  154 IKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ  207 (402)
T ss_pred             HHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence            9999999999999984332   45799999999999999999999999998754

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

Probab=99.94  E-value=6.5e-27  Score=215.35  Aligned_cols=225  Identities=19%  Similarity=0.306  Sum_probs=156.1

Q ss_pred             HHHHHHHHHHHHHhhccC--CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEE
Q 021032            6 AQDAVMRVHSRIAEIGFE--PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI   83 (318)
Q Consensus         6 a~~a~~~v~~~i~~~~~e--~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~   83 (318)
                      +..|+..|++-|..+..+  -.+.+.||+|-++++||.||||.|.+||+|+.+||++|.|++-.++..|  ..||.++|.
T Consensus       256 ~s~Ac~~ILeimqkEA~~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~y--npERTItVk  333 (584)
T KOG2193|consen  256 TSKACKMILEIMQKEAVDDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLY--NPERTITVK  333 (584)
T ss_pred             hHHHHHHHHHHHHHhhhccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhccc--CccceEEec
Confidence            345666666665544322  2478899999999999999999999999999999999999986666555  679999999


Q ss_pred             ecHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032           84 GNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFD  163 (318)
Q Consensus        84 G~~~~V~~A~~~I~~~l~e~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~  163 (318)
                      |..|+|.+|..+|+.+|+|+...+ ....+..+.+.|                   +.....++.|++.  |++      
T Consensus       334 GsiEac~~AE~eImkKlre~yEnD-l~a~s~q~~l~P-------------------~l~~~~l~~f~ss--S~~------  385 (584)
T KOG2193|consen  334 GSIEACVQAEAEIMKKLRECYEND-LAAMSLQCHLPP-------------------GLNLPALGLFPSS--SAV------  385 (584)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHhhh-HHHhhccCCCCc-------------------ccCccccCCCCcc--ccc------
Confidence            999999999999999999974322 222221111111                   1111111111110  000      


Q ss_pred             CcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCc
Q 021032          164 HQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILT  243 (318)
Q Consensus       164 ~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~  243 (318)
                                  .+                  |.|         +|..+.+..+        ++       ....  ..+
T Consensus       386 ------------~~------------------Ph~---------~Ps~v~~a~p--------~~-------~~hq--~pe  409 (584)
T KOG2193|consen  386 ------------SP------------------PHF---------PPSPVTFASP--------YP-------LFHQ--NPE  409 (584)
T ss_pred             ------------CC------------------CCC---------CCCccccCCC--------ch-------hhhc--Ccc
Confidence                        00                  000         0000000000        00       0000  124


Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCC-CCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcCc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSDQMRAAQSLIHAFILCGV  316 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~-~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~~  316 (318)
                      ..++++.||...+|+||||+|.+||+|.+.+||+|+|..+ .++..||+|+|+|.+++.-+||..|..+|+++-
T Consensus       410 ~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEen  483 (584)
T KOG2193|consen  410 QEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEEN  483 (584)
T ss_pred             hhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhc
Confidence            5678999999999999999999999999999999999865 467899999999999999999999999998753

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

Probab=99.93  E-value=8.6e-25  Score=209.97  Aligned_cols=163  Identities=21%  Similarity=0.333  Sum_probs=134.7

Q ss_pred             CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcC
Q 021032           26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIF  105 (318)
Q Consensus        26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~  105 (318)
                      ..++..++||.+.+|+||||+|++||.|+|+|||++.+........   ..++.+.|+|+++.|+.|..+|.++|+|.. 
T Consensus       137 ~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~---~~~KplritGdp~~ve~a~~lV~dil~e~~-  212 (600)
T KOG1676|consen  137 VETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT---GADKPLRITGDPDKVEQAKQLVADILREED-  212 (600)
T ss_pred             cceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC---CCCCceeecCCHHHHHHHHHHHHHHHHhcc-
Confidence            3489999999999999999999999999999999999987654432   478999999999999999999999999741 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCC
Q 021032          106 PMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPF  185 (318)
Q Consensus       106 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  185 (318)
                       +..                    +      .+.+                             |               
T Consensus       213 -~~~--------------------~------g~~~-----------------------------~---------------  221 (600)
T KOG1676|consen  213 -DEV--------------------P------GSGG-----------------------------H---------------  221 (600)
T ss_pred             -cCC--------------------C------cccc-----------------------------c---------------
Confidence             100                    0      0000                             0               


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccccccccccccc
Q 021032          186 PYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNS  265 (318)
Q Consensus       186 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~  265 (318)
                       +|.                               +                   .....+.+|.||.+.||.||||+|+
T Consensus       222 -~g~-------------------------------~-------------------~g~~~~~~V~VPr~~VG~IIGkgGE  250 (600)
T KOG1676|consen  222 -AGV-------------------------------R-------------------GGGSATREVKVPRSKVGIIIGKGGE  250 (600)
T ss_pred             -cCc-------------------------------C-------------------ccccceeEEeccccceeeEEecCch
Confidence             000                               0                   0112489999999999999999999


Q ss_pred             hHHHHHHHhCCEEEEcCCCC-CCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          266 NLSHIRQISGANVVVNDPKP-GATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       266 ~Ik~Ir~~SGA~I~i~~~~~-~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      +||+|+.+||++|+|..+.+ .+.||++.|.|++++|+.|..||.++|++
T Consensus       251 ~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~  300 (600)
T KOG1676|consen  251 MIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAE  300 (600)
T ss_pred             HHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHH
Confidence            99999999999999976544 78999999999999999999999999986

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

Probab=99.93  E-value=7.9e-25  Score=210.23  Aligned_cols=179  Identities=22%  Similarity=0.312  Sum_probs=142.6

Q ss_pred             HHHHHHHHHHHHhhccC-----------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCC
Q 021032            7 QDAVMRVHSRIAEIGFE-----------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSP   75 (318)
Q Consensus         7 ~~a~~~v~~~i~~~~~e-----------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~   75 (318)
                      +.|-.+|++-|.|...+           .....+++|.||.+.||.||||+|++||+|+.+||+||+|.+ |+.|   ++
T Consensus       198 e~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkp-Dd~p---~s  273 (600)
T KOG1676|consen  198 EQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKP-DDDP---SS  273 (600)
T ss_pred             HHHHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeec-CCCC---CC
Confidence            34556666666654332           123458999999999999999999999999999999999975 4444   47


Q ss_pred             CCceEEEEecHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032           76 HDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRG  155 (318)
Q Consensus        76 ~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~  155 (318)
                      .||.+.|.|.+++|..|..+|.++|.+...-                          +         ..+|+        
T Consensus       274 peR~~~IiG~~d~ie~Aa~lI~eii~~~~~~--------------------------~---------~~~~~--------  310 (600)
T KOG1676|consen  274 PERPAQIIGTVDQIEHAAELINEIIAEAEAG--------------------------A---------GGGMG--------  310 (600)
T ss_pred             ccceeeeecCHHHHHHHHHHHHHHHHHHhcc--------------------------C---------CCCcC--------
Confidence            8999999999999999999999999986100                          0         00000        


Q ss_pred             CCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032          156 MGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVES  235 (318)
Q Consensus       156 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~  235 (318)
                                                                         |           |      .         
T Consensus       311 ---------------------------------------------------~-----------G------~---------  313 (600)
T KOG1676|consen  311 ---------------------------------------------------G-----------G------A---------  313 (600)
T ss_pred             ---------------------------------------------------C-----------C------C---------
Confidence                                                               0           0      0         


Q ss_pred             CCccccCcceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCC--CCCCCCeEEEEEcCHHHHHHHHHHHHHHHH
Q 021032          236 GNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP--KPGATEGVVMVSGTSDQMRAAQSLIHAFIL  313 (318)
Q Consensus       236 ~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~--~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~  313 (318)
                           ......+++.||.+.+|.||||+|++||.|.++|||++.+...  ..+..||+++|+|++.||.-|+.||+++|.
T Consensus       314 -----P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg  388 (600)
T KOG1676|consen  314 -----PGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVG  388 (600)
T ss_pred             -----ccceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHHHHHhc
Confidence                 0001268999999999999999999999999999999999865  346789999999999999999999999986


Q ss_pred             c
Q 021032          314 C  314 (318)
Q Consensus       314 ~  314 (318)
                      .
T Consensus       389 ~  389 (600)
T KOG1676|consen  389 D  389 (600)
T ss_pred             c
Confidence            4

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

Probab=99.88  E-value=3.5e-22  Score=194.02  Aligned_cols=159  Identities=27%  Similarity=0.416  Sum_probs=132.7

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEe---------cHHHHHHHHHH
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG---------NYHSVQDALFH   95 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G---------~~~~V~~A~~~   95 (318)
                      +...++|||++.+++|.||||+|..||+||.+|.++|+|..  ..+.   ..||+|+|+|         ..+++.+|..+
T Consensus        40 ~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~--~~~~---c~eRIiti~g~~~~~~~~~~~~al~ka~~~  114 (485)
T KOG2190|consen   40 DETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNE--SLPG---CPERIITITGNRVELNLSPATDALFKAFDM  114 (485)
T ss_pred             CCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeec--CCCC---CCcceEEEecccccccCCchHHHHHHHHHH
Confidence            45566899999999999999999999999999999999953  2444   4899999999         99999999999


Q ss_pred             HHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCC
Q 021032           96 ITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPM  175 (318)
Q Consensus        96 I~~~l~e~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  175 (318)
                      |...+.+.....                       ..                                           
T Consensus       115 iv~~~~~d~~~~-----------------------~d-------------------------------------------  128 (485)
T KOG2190|consen  115 IVFKLEEDDEAA-----------------------ED-------------------------------------------  128 (485)
T ss_pred             Hhhccccccccc-----------------------cc-------------------------------------------
Confidence            988776431000                       00                                           


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccc
Q 021032          176 VPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLY  255 (318)
Q Consensus       176 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~  255 (318)
                                 .                               +.+.                  .....+.+|+||.+.
T Consensus       129 -----------~-------------------------------~~~~------------------~~~~v~~RLlVp~sq  148 (485)
T KOG2190|consen  129 -----------N-------------------------------GEDA------------------SGPEVTCRLLVPSSQ  148 (485)
T ss_pred             -----------C-------------------------------Cccc------------------cCCceEEEEEechhh
Confidence                       0                               0000                  011479999999999


Q ss_pred             cccccccccchHHHHHHHhCCEEEEcCC-CCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          256 MAHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       256 vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~-~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      +|+||||+|+.||+||+.|||+|+|..+ .+.++||.|+|+|.+++|.+|...|..+|.+
T Consensus       149 ~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~  208 (485)
T KOG2190|consen  149 VGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLE  208 (485)
T ss_pred             eeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999876 7889999999999999999999999999987

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

Probab=99.83  E-value=1e-20  Score=174.70  Aligned_cols=152  Identities=18%  Similarity=0.295  Sum_probs=131.4

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcCC
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFP  106 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~  106 (318)
                      ...+|+|||...+|.||||.|++||.|-..|-|+|+|-.++.    .+..|+.++|.|.+|...+|+.+|++++...-.+
T Consensus       198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken----~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~  273 (584)
T KOG2193|consen  198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN----AGAAEKIITVHSTPEGTSKACKMILEIMQKEAVD  273 (584)
T ss_pred             CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc----CCcccCceEEecCccchHHHHHHHHHHHHHhhhc
Confidence            478999999999999999999999999999999999987644    3578999999999999999999999999876221


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCC
Q 021032          107 MKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFP  186 (318)
Q Consensus       107 ~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~  186 (318)
                      ++                                                                              
T Consensus       274 ~k------------------------------------------------------------------------------  275 (584)
T KOG2193|consen  274 DK------------------------------------------------------------------------------  275 (584)
T ss_pred             cc------------------------------------------------------------------------------
Confidence            10                                                                              


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccccccccccccch
Q 021032          187 YGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSN  266 (318)
Q Consensus       187 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~  266 (318)
                                                                            ....+.+++.-.+.+||++|||.|++
T Consensus       276 ------------------------------------------------------~~~e~pLk~lAHN~lvGRLIGKeGrn  301 (584)
T KOG2193|consen  276 ------------------------------------------------------VAEEIPLKILAHNNLVGRLIGKEGRN  301 (584)
T ss_pred             ------------------------------------------------------hhhhcchhhhhhcchhhhhhhhcccc
Confidence                                                                  01234577778899999999999999


Q ss_pred             HHHHHHHhCCEEEEcCCCC---CCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          267 LSHIRQISGANVVVNDPKP---GATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       267 Ik~Ir~~SGA~I~i~~~~~---~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ||+|.+.||.+|.|+.-.+   ...||+|+++|+-|+|..|..+|..+|++
T Consensus       302 lKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre  352 (584)
T KOG2193|consen  302 LKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRE  352 (584)
T ss_pred             HHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHH
Confidence            9999999999999987532   45799999999999999999999998864

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

Probab=99.80  E-value=4.1e-19  Score=155.62  Aligned_cols=148  Identities=22%  Similarity=0.378  Sum_probs=129.8

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhc
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETI  104 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~  104 (318)
                      ...+++||||.++.+|.||||||++||.|+.+.+|.|+|...       +..+|+++|+.+.+.|-+-++.|.-.|++..
T Consensus        45 ~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds-------~~peri~tisad~~ti~~ilk~iip~lee~f  117 (390)
T KOG2192|consen   45 RSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS-------SGPERILTISADIETIGEILKKIIPTLEEGF  117 (390)
T ss_pred             hcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC-------CCCceeEEEeccHHHHHHHHHHHhhhhhhCC
Confidence            457999999999999999999999999999999999999643       2569999999999999999888888887751


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCC
Q 021032          105 FPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIP  184 (318)
Q Consensus       105 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  184 (318)
                      .                                                                               
T Consensus       118 ~-------------------------------------------------------------------------------  118 (390)
T KOG2192|consen  118 Q-------------------------------------------------------------------------------  118 (390)
T ss_pred             C-------------------------------------------------------------------------------
Confidence            1                                                                               


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccccccccccccc
Q 021032          185 FPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENN  264 (318)
Q Consensus       185 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G  264 (318)
                                                                              ......++++|..+++|.|||++|
T Consensus       119 --------------------------------------------------------~~~pce~rllihqs~ag~iigrng  142 (390)
T KOG2192|consen  119 --------------------------------------------------------LPSPCELRLLIHQSLAGGIIGRNG  142 (390)
T ss_pred             --------------------------------------------------------CCCchhhhhhhhhhhccceecccc
Confidence                                                                    000135788999999999999999


Q ss_pred             chHHHHHHHhCCEEEEc-CCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          265 SNLSHIRQISGANVVVN-DPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       265 ~~Ik~Ir~~SGA~I~i~-~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ++||+||+.+.|+++|- +..+.+++|+|.|.|.+..|..+...|.+.|++
T Consensus       143 skikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e  193 (390)
T KOG2192|consen  143 SKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISE  193 (390)
T ss_pred             hhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhc
Confidence            99999999999999986 568899999999999999999999999888875

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.75  E-value=1.3e-17  Score=142.55  Aligned_cols=61  Identities=21%  Similarity=0.311  Sum_probs=54.4

Q ss_pred             EEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEE---EecHHHHHHHHHHHHHHHHh
Q 021032           32 LLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQV---IGNYHSVQDALFHITSRLRE  102 (318)
Q Consensus        32 llVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I---~G~~~~V~~A~~~I~~~l~e  102 (318)
                      |-||.+.+|.|||+||++||+|+++|||+|+|..          .+..|.|   +++++++.+|...|..+.+.
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 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS----------ETGEVKIEEEDEDPLAVMKAREVVKAIGRG   65 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc----------CCceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence            5689999999999999999999999999999953          2467888   89999999999999987765

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.

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

Probab=99.71  E-value=1.8e-16  Score=142.83  Aligned_cols=203  Identities=20%  Similarity=0.296  Sum_probs=143.1

Q ss_pred             HHHHHHHHHHHHHhhccC----------------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCC
Q 021032            6 AQDAVMRVHSRIAEIGFE----------------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQA   69 (318)
Q Consensus         6 a~~a~~~v~~~i~~~~~e----------------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~   69 (318)
                      -.++|+-+|+.|.++..|                .+..-.+|++||++-+|.||||||.+||.|+|++||.|+|++  ..
T Consensus        94 t~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisP--qk  171 (402)
T KOG2191|consen   94 TVEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISP--QK  171 (402)
T ss_pred             cHHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecc--cC
Confidence            468888888888876433                122356999999999999999999999999999999999985  23


Q ss_pred             CCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032           70 PRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPF  149 (318)
Q Consensus        70 p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~  149 (318)
                      |..-+..||+|++.|++++..+|+.+|+++|.|+..  -    .. + .+-+|                 +....|+.++
T Consensus       172 pt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq--s----~s-c-ln~sy-----------------a~vsGpvaNs  226 (402)
T KOG2191|consen  172 PTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ--S----GS-C-LNISY-----------------ANVSGPVANS  226 (402)
T ss_pred             CCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc--c----cc-e-eccch-----------------hcccCccccc
Confidence            455567899999999999999999999999999721  0    00 0 00000                 0000010000


Q ss_pred             CCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032          150 HSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPR  229 (318)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  229 (318)
                      .+                                   .|                           .++++..       
T Consensus       227 nP-----------------------------------tG---------------------------spya~~~-------  237 (402)
T KOG2191|consen  227 NP-----------------------------------TG---------------------------SPYAYQA-------  237 (402)
T ss_pred             CC-----------------------------------CC---------------------------CCCCCCC-------
Confidence            00                                   00                           0000000       


Q ss_pred             CCCCCCCCccccCcceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCC---CCCCCeEEEEEcCHHHHHHHHH
Q 021032          230 NRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPK---PGATEGVVMVSGTSDQMRAAQS  306 (318)
Q Consensus       230 ~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~---~~~~er~v~I~Gt~~~v~~A~~  306 (318)
                               .......+....++...+|..-|.+|.++..|...+|+.|.+....   .+...+ ..+.|.+-++..|..
T Consensus       238 ---------~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~g~gy~-~n~~g~~ls~~aa~g  307 (402)
T KOG2191|consen  238 ---------HVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMAGYGYN-TNILGLGLSILAAEG  307 (402)
T ss_pred             ---------ccccccchhhccccccccccccccccccceeeecccccceeeccccccccccccc-ccccchhhhhhhhhh
Confidence                     0011234456678889999999999999999999999999997653   245566 789999999999999


Q ss_pred             HHHHHHHc
Q 021032          307 LIHAFILC  314 (318)
Q Consensus       307 lI~~~i~~  314 (318)
                      +|...+..
T Consensus       308 ~L~~~~~~  315 (402)
T KOG2191|consen  308 VLAAKVAS  315 (402)
T ss_pred             HHHHhhcc
Confidence            99887754

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.71  E-value=1.7e-16  Score=136.51  Aligned_cols=65  Identities=18%  Similarity=0.244  Sum_probs=58.2

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEE----ecHHHHHHHHHHHHHHHHh
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI----GNYHSVQDALFHITSRLRE  102 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~----G~~~~V~~A~~~I~~~l~e  102 (318)
                      +...|.||.+.+|.|||++|++||.|+++|||+|+|..          .+..|.|.    ++++++.+|...|..+++.
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~----------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g   71 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS----------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRG   71 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC----------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence            46789999999999999999999999999999999953          24788885    8999999999999988875

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.59  E-value=2.7e-15  Score=107.68  Aligned_cols=64  Identities=30%  Similarity=0.488  Sum_probs=59.5

Q ss_pred             EEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCC-CCCCeEEEEEcCHHHHHHHHHHHH
Q 021032          246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP-GATEGVVMVSGTSDQMRAAQSLIH  309 (318)
Q Consensus       246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~-~~~er~v~I~Gt~~~v~~A~~lI~  309 (318)
                      +.++.||.+.+|+||||+|++|++|++.|||+|.+.+... +..+|.|+|+|++++++.|..||+
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence            3689999999999999999999999999999999987654 788999999999999999999984

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

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.59  E-value=4.1e-15  Score=106.74  Aligned_cols=64  Identities=39%  Similarity=0.597  Sum_probs=58.0

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHH
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI   96 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I   96 (318)
                      ++||+||.+.+|+||||+|++|++|+++|||+|++.+.+.    ....+|+|+|.|++++|.+|+.+|
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhh
Confidence            4799999999999999999999999999999999975432    346799999999999999999987

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.45  E-value=1.3e-13  Score=97.17  Aligned_cols=60  Identities=23%  Similarity=0.511  Sum_probs=55.4

Q ss_pred             EEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHH
Q 021032          246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLI  308 (318)
Q Consensus       246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI  308 (318)
                      |.+|.||.+++|+|||++|++|++|++.|||+|.|++.  + .+..|+|+|++++++.|+.+|
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            67899999999999999999999999999999999765  3 555999999999999999987

; 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 ....

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.43  E-value=2.3e-13  Score=96.58  Aligned_cols=61  Identities=23%  Similarity=0.425  Sum_probs=56.3

Q ss_pred             EEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHH
Q 021032          247 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH  309 (318)
Q Consensus       247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~  309 (318)
                      .++.||.+++|+|||++|++|++|++.|||+|.+.+..  ..++.|+|+|+++++..|+.+|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHhC
Confidence            57889999999999999999999999999999997654  67899999999999999999874

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=99.41  E-value=7.7e-13  Score=94.19  Aligned_cols=63  Identities=27%  Similarity=0.545  Sum_probs=58.8

Q ss_pred             EEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHH
Q 021032          247 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH  309 (318)
Q Consensus       247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~  309 (318)
                      .++.||.+++|+|||++|++|++|++.|||+|.|.+..++..++.|+|.|+.+++..|+.+|+
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~   64 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL   64 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence            578999999999999999999999999999999988766778999999999999999999873

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.

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

Probab=99.38  E-value=1.6e-12  Score=91.96  Aligned_cols=59  Identities=19%  Similarity=0.385  Sum_probs=53.9

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcC-HHHHHHHHHHHH
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT-SDQMRAAQSLIH  309 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt-~~~v~~A~~lI~  309 (318)
                      .+..+.||.+++|+||||+|++|++|++.|||+|.|++      ++.|.|+|+ +++++.|+.+|.
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~~~v~~A~~~I~   61 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDKEAAEKAKKMIE   61 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCHHHHHHHHHHhC
Confidence            35778899999999999999999999999999999964      468999998 999999999873

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.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.36  E-value=9.8e-13  Score=92.69  Aligned_cols=60  Identities=27%  Similarity=0.433  Sum_probs=54.1

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHH
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI   96 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I   96 (318)
                      |.+|+||.+++|+||||+|++|++|+++|||+|+|...        +.+..|+|+|+.++|.+|+.+|
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--------DERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--------TEEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--------CCcEEEEEEeCHHHHHHHHhhC
Confidence            68999999999999999999999999999999999643        2345999999999999999876

; 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 ....

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.36  E-value=1.7e-12  Score=92.15  Aligned_cols=60  Identities=17%  Similarity=0.300  Sum_probs=54.7

Q ss_pred             EEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHH
Q 021032           30 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI   96 (318)
Q Consensus        30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I   96 (318)
                      .+|.||..++|.|||++|++|++|+++|||+|+|.+.+       +.++.|+|+|+.++|.+|..+|
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i   61 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEI   61 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHh
Confidence            67999999999999999999999999999999996432       4689999999999999999876

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.

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

Probab=99.36  E-value=3.5e-12  Score=90.16  Aligned_cols=58  Identities=19%  Similarity=0.331  Sum_probs=52.8

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEec-HHHHHHHHHHH
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHI   96 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~-~~~V~~A~~~I   96 (318)
                      .+..|-||.+++|.||||||++||+|+++|||+|.|.           .++.|.|.|+ .+++.+|..+|
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~-----------~~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIE-----------DDGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeC-----------CCCEEEEEeCCHHHHHHHHHHh
Confidence            5678999999999999999999999999999999994           2578999998 99999999876

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.

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

Probab=99.29  E-value=1.3e-11  Score=87.71  Aligned_cols=63  Identities=32%  Similarity=0.550  Sum_probs=56.0

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHH
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI   96 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I   96 (318)
                      +.+|.||.+++|.|||++|++|++|+++|||+|.|.....     .+.++.|.|.|..+++.+|...|
T Consensus         1 ~~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             CEEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----CCCceEEEEEcCHHHHHHHHHHh
Confidence            3689999999999999999999999999999999965322     35789999999999999998876

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.

>PF13014 KH_3: KH domain

Probab=99.17  E-value=5.2e-11  Score=78.13  Aligned_cols=43  Identities=30%  Similarity=0.696  Sum_probs=37.8

Q ss_pred             cceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEe
Q 021032           38 QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG   84 (318)
Q Consensus        38 ~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G   84 (318)
                      ++|+||||+|++|++|+++|||+|+|.+ +   .+..+.+|.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~---~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPP-E---NEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECC-c---cCCCCCceEEEEEC
Confidence            5899999999999999999999999976 2   34457899999997

>PF13014 KH_3: KH domain

Probab=99.13  E-value=9.4e-11  Score=76.87  Aligned_cols=42  Identities=29%  Similarity=0.659  Sum_probs=38.8

Q ss_pred             ccccccccccchHHHHHHHhCCEEEEcC-CCCCCCCeEEEEEc
Q 021032          255 YMAHVYGENNSNLSHIRQISGANVVVND-PKPGATEGVVMVSG  296 (318)
Q Consensus       255 ~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~-~~~~~~er~v~I~G  296 (318)
                      ++|+||||+|++|++|+++|||+|+|.+ ..++..+|.|+|+|
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            5799999999999999999999999987 45678999999998

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

Probab=99.11  E-value=3.9e-11  Score=115.13  Aligned_cols=147  Identities=20%  Similarity=0.325  Sum_probs=123.6

Q ss_pred             CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ..+.+.++++|+...+-++|||+|++||.|++.++++|.+-.+ +.+     .++...+.|-+.++..|.+.++.++.+.
T Consensus        64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e-d~g-----~e~~~~~~~~p~~v~~a~a~~~~~~~~~  137 (608)
T KOG2279|consen   64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE-DVG-----DERVLLISGFPVQVCKAKAAIHQILTEN  137 (608)
T ss_pred             chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcc-cCC-----cccchhhccCCCCCChHHHHHHHHHhcC
Confidence            3467889999999999999999999999999999999999643 333     4677777779999999999999888764


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCC
Q 021032          104 IFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRI  183 (318)
Q Consensus       104 ~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  183 (318)
                      -                                                                               
T Consensus       138 ~-------------------------------------------------------------------------------  138 (608)
T KOG2279|consen  138 T-------------------------------------------------------------------------------  138 (608)
T ss_pred             C-------------------------------------------------------------------------------
Confidence            0                                                                               


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccccccccccc
Q 021032          184 PFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGEN  263 (318)
Q Consensus       184 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~  263 (318)
                                                                                  .+..++.+|...+++|+|++
T Consensus       139 ------------------------------------------------------------pvk~~lsvpqr~~~~i~grg  158 (608)
T KOG2279|consen  139 ------------------------------------------------------------PVSEQLSVPQRSVGRIIGRG  158 (608)
T ss_pred             ------------------------------------------------------------cccccccchhhhcccccccc
Confidence                                                                        12345558888999999999


Q ss_pred             cchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          264 NSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       264 G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      |.++.+|+..|+|+|.+...--.-..+.+.|.|...-++.|+.++.+.++..
T Consensus       159 get~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~ed  210 (608)
T KOG2279|consen  159 GETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSED  210 (608)
T ss_pred             hhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccch
Confidence            9999999999999999987644456788999999999999999999888763

>smart00322 KH K homology RNA-binding domain

Probab=99.11  E-value=5.2e-10  Score=79.72  Aligned_cols=66  Identities=26%  Similarity=0.458  Sum_probs=59.8

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFI  312 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i  312 (318)
                      .+.++.||.+++|.+||++|++|++|++.+|++|.+.....  ....|+|.|+.++++.|..+|.+.+
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            57899999999999999999999999999999999964332  6788999999999999999998876

>smart00322 KH K homology RNA-binding domain

Probab=99.05  E-value=1.2e-09  Score=77.75  Aligned_cols=67  Identities=22%  Similarity=0.470  Sum_probs=59.4

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHH
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL  100 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  100 (318)
                      .++.++.||...+|.|||++|++|++|++.||++|.+....       .....|.|.|+.+++..|...|.+.+
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            46789999999999999999999999999999999995321       25789999999999999999998765

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

Probab=98.93  E-value=1.3e-08  Score=86.94  Aligned_cols=67  Identities=16%  Similarity=0.221  Sum_probs=55.7

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEe-----cHHHHHHHHHHHHHHHH
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-----NYHSVQDALFHITSRLR  101 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G-----~~~~V~~A~~~I~~~l~  101 (318)
                      .....+.||...+|.|||+.|++-+.|.+.+++++.+..          .+..|.|.-     ++-.+.+|...|..+-+
T Consensus         7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~----------~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgr   76 (194)
T COG1094           7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS----------KTGSVTIRTTRKTEDPLALLKARDVVKAIGR   76 (194)
T ss_pred             cceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC----------CCCeEEEEecCCCCChHHHHHHHHHHHHHhc
Confidence            445779999999999999999999999999999999963          356677664     57788899988877666


Q ss_pred             hh
Q 021032          102 ET  103 (318)
Q Consensus       102 e~  103 (318)
                      .+
T Consensus        77 GF   78 (194)
T COG1094          77 GF   78 (194)
T ss_pred             CC
Confidence            64

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

Probab=98.67  E-value=1e-07  Score=76.47  Aligned_cols=67  Identities=21%  Similarity=0.352  Sum_probs=51.7

Q ss_pred             ccceeeeCCCCchHHHHHHHhCCeEEEecCCCC-----------CCCCC-CCCceEEEEecH---HHHHHHHHHHHHHHH
Q 021032           37 QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQA-----------PRCGS-PHDEIVQVIGNY---HSVQDALFHITSRLR  101 (318)
Q Consensus        37 ~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~-----------p~~~~-~~er~V~I~G~~---~~V~~A~~~I~~~l~  101 (318)
                      +++|.|||.+|++||+|+++|||+|.|......           |.+.. +..-.|.|++..   +++.+|+..|..++.
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            568999999999999999999999999754221           11111 223568999965   899999999998887


Q ss_pred             hh
Q 021032          102 ET  103 (318)
Q Consensus       102 e~  103 (318)
                      ..
T Consensus        95 ~~   96 (120)
T cd02395          95 PA   96 (120)
T ss_pred             cC
Confidence            54

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.

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

Probab=98.59  E-value=1.3e-07  Score=75.85  Aligned_cols=61  Identities=11%  Similarity=0.244  Sum_probs=51.3

Q ss_pred             cccccccccccchHHHHHHHhCCEEEEcCCCC-----------------CCCCeEEEEEcC---HHHHHHHHHHHHHHHH
Q 021032          254 LYMAHVYGENNSNLSHIRQISGANVVVNDPKP-----------------GATEGVVMVSGT---SDQMRAAQSLIHAFIL  313 (318)
Q Consensus       254 ~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~-----------------~~~er~v~I~Gt---~~~v~~A~~lI~~~i~  313 (318)
                      +++|.|||.+|++||+|+++|||+|.|.....                 ....-.|.|++.   .+++++|..+|..++.
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            78999999999999999999999999976411                 112367999995   5999999999999887


Q ss_pred             c
Q 021032          314 C  314 (318)
Q Consensus       314 ~  314 (318)
                      .
T Consensus        95 ~   95 (120)
T cd02395          95 P   95 (120)
T ss_pred             c
Confidence            5

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.

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.57  E-value=7.8e-08  Score=82.24  Aligned_cols=60  Identities=17%  Similarity=0.266  Sum_probs=54.0

Q ss_pred             EEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEE---EcCHHHHHHHHHHHHHHHH
Q 021032          249 VVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMV---SGTSDQMRAAQSLIHAFIL  313 (318)
Q Consensus       249 v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I---~Gt~~~v~~A~~lI~~~i~  313 (318)
                      +.||.+.+|.|||++|++|+.|++.|||+|+|+.     ++..|.|   +++++++.+|+.+|..+..
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~~i~kA~~~I~~i~~   64 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPLAVMKAREVVKAIGR   64 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence            5699999999999999999999999999999974     2367888   7899999999999998655

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

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.55  E-value=1.7e-07  Score=80.68  Aligned_cols=64  Identities=16%  Similarity=0.245  Sum_probs=57.7

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEE----cCHHHHHHHHHHHHHHHH
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVS----GTSDQMRAAQSLIHAFIL  313 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~----Gt~~~v~~A~~lI~~~i~  313 (318)
                      ....+.||.+.+|.|||++|.+|+.|++.|||+|+|.+     +++.|.|.    ++++++++|+.+|.+++.
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 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS-----ETGEVIIEPTDGEDPLAVLKARDIVKAIGR   70 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC-----CCCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence            46789999999999999999999999999999999974     24788895    899999999999998765

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.22  E-value=4.9e-06  Score=86.07  Aligned_cols=139  Identities=16%  Similarity=0.250  Sum_probs=111.8

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcCCC
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPM  107 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~~  107 (318)
                      +.+.+-+.......++||+|.+|.+|++++.+.|.+..       .++.+..|.++|...++.+|...|.....+.+.+ 
T Consensus       347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~-------~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~-  418 (753)
T KOG2208|consen  347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK-------QGSNNKKVVITGVSANDEKAVEDVEKIIAEILNS-  418 (753)
T ss_pred             eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc-------ccCCCCCeEEeccccchhHHHHHHHHHHHhhhcc-
Confidence            77888899999999999999999999999999999953       2467899999999999999999999888775110 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCC
Q 021032          108 KRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPY  187 (318)
Q Consensus       108 ~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~  187 (318)
                                                                                                      
T Consensus       419 --------------------------------------------------------------------------------  418 (753)
T KOG2208|consen  419 --------------------------------------------------------------------------------  418 (753)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccccccccccccchH
Q 021032          188 GSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNL  267 (318)
Q Consensus       188 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~I  267 (318)
                                                                              .....+.||...+.+|||.+|..|
T Consensus       419 --------------------------------------------------------~~~~~~~iP~k~~~~iig~~g~~i  442 (753)
T KOG2208|consen  419 --------------------------------------------------------IVKEEVQIPTKSHKRIIGTKGALI  442 (753)
T ss_pred             --------------------------------------------------------cccceeecCccchhhhhccccccH
Confidence                                                                    123567799999999999999999


Q ss_pred             HHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHH
Q 021032          268 SHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAF  311 (318)
Q Consensus       268 k~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~  311 (318)
                      .+|...+|+ +.+......+....+++.|.-.-+..++.++..+
T Consensus       443 ~~I~~k~~~-v~i~f~~~~~~~~~~~~~~~~~dv~~~~~~~~~~  485 (753)
T KOG2208|consen  443 NYIMGKHGG-VHIKFQNNNNSSDMVTIRGISKDVEKSVSLLKAL  485 (753)
T ss_pred             HHHHhhcCc-EEEecCCCCcccccceEeccccccchhHHHHHhh
Confidence            999999995 5555455555666677888766666555554443

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.22  E-value=6.3e-06  Score=83.88  Aligned_cols=87  Identities=22%  Similarity=0.272  Sum_probs=73.3

Q ss_pred             hHHHHHHHHHHHHHhhccCC-----CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCce
Q 021032            5 PAQDAVMRVHSRIAEIGFEP-----GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEI   79 (318)
Q Consensus         5 ~a~~a~~~v~~~i~~~~~e~-----~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~   79 (318)
                      -|.++..+|++.+.+...++     ..+....|-||.+.+|.|||.||.+||+|+++|||+|.|.           .+..
T Consensus       550 ~A~~g~~~Il~~m~~al~~p~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~-----------d~G~  618 (719)
T TIGR02696       550 QARDARLAILDVMAEAIDTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE-----------DDGT  618 (719)
T ss_pred             HHHHHHHHHHHHHHHHHhCccccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe-----------cCcE
Confidence            46788888888777765433     3467899999999999999999999999999999999994           3688


Q ss_pred             EEEEe-cHHHHHHHHHHHHHHHHh
Q 021032           80 VQVIG-NYHSVQDALFHITSRLRE  102 (318)
Q Consensus        80 V~I~G-~~~~V~~A~~~I~~~l~e  102 (318)
                      |.|.+ +.+.+.+|+.+|..++..
T Consensus       619 V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       619 VYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             EEEEeCCHHHHHHHHHHHHHhhCc
Confidence            99888 578999999999887774

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.

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.17  E-value=4.9e-06  Score=68.63  Aligned_cols=62  Identities=15%  Similarity=0.249  Sum_probs=46.1

Q ss_pred             CChHHHHHHHHHHHHHhhccCC--CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEe
Q 021032            3 HSPAQDAVMRVHSRIAEIGFEP--GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVF   64 (318)
Q Consensus         3 ~s~a~~a~~~v~~~i~~~~~e~--~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~   64 (318)
                      ++..+=....+|+.+-....-.  .+.-.+.++|+...+|..||++|++|+.|++..|-+|.|.
T Consensus         5 l~~~~~~~i~~fe~~t~~~~~dc~~d~~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv   68 (140)
T PRK08406          5 LTTEEIRYIALFESITGATVKDCIIDDDRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV   68 (140)
T ss_pred             ECHHHHHHHHHHHHHhCCCceEEEEeCCEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence            4445555667777765442100  1114588999999999999999999999999999999986

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

Probab=98.14  E-value=3.4e-06  Score=76.45  Aligned_cols=65  Identities=26%  Similarity=0.360  Sum_probs=56.8

Q ss_pred             CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHH
Q 021032           26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITS   98 (318)
Q Consensus        26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~   98 (318)
                      +.++..+-||..+++.|.|++|.+||.||.+|...|+-....        .|-+..++|..+.|+.|..+|-.
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~--------eePiF~vTg~~edv~~aRrei~s   88 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG--------EEPIFPVTGRHEDVRRARREIPS   88 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC--------CCCcceeccCchhHHHHhhcCcc
Confidence            678899999999999999999999999999999999976542        35678899999999999888743

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.05  E-value=1.3e-05  Score=82.50  Aligned_cols=86  Identities=20%  Similarity=0.363  Sum_probs=68.4

Q ss_pred             HHHHHHHHHHHHHhhccC------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCce
Q 021032            6 AQDAVMRVHSRIAEIGFE------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEI   79 (318)
Q Consensus         6 a~~a~~~v~~~i~~~~~e------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~   79 (318)
                      |.++..+|++.+.+...+      +-.+....+-||...+|.|||+||++||+|+++|||+|.|.           .+..
T Consensus       523 a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~-----------ddG~  591 (684)
T TIGR03591       523 AKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE-----------DDGT  591 (684)
T ss_pred             HHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe-----------cCeE
Confidence            556677777766665432      34577889999999999999999999999999999999994           3567


Q ss_pred             EEEEe-cHHHHHHHHHHHHHHHHh
Q 021032           80 VQVIG-NYHSVQDALFHITSRLRE  102 (318)
Q Consensus        80 V~I~G-~~~~V~~A~~~I~~~l~e  102 (318)
                      |.|.+ ..+.+.+|...|..+..+
T Consensus       592 V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       592 VKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             EEEEECcHHHHHHHHHHHHhhhcc
Confidence            77776 567888998888777543

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).

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

Probab=98.01  E-value=3.4e-05  Score=74.93  Aligned_cols=74  Identities=22%  Similarity=0.395  Sum_probs=62.1

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      +..+...+-+|...++.|+|++|.+|.+|+.-++|+|.+...  ..   ...++...|.|...-++.|..++.+++.+.
T Consensus       137 ~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n--gr---~g~~~~~~i~~qqk~~~~a~~~~~~~~~ed  210 (608)
T KOG2279|consen  137 NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN--GR---LGLSRLIKISGQQKEVAAAKHLILEKVSED  210 (608)
T ss_pred             CCcccccccchhhhcccccccchhhhcchhcccccccccccc--cc---cccccceecccccchHHHHHhhhhccccch
Confidence            466778888999999999999999999999999999999543  21   145788999998888888988888887664

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.92  E-value=2.3e-05  Score=79.89  Aligned_cols=64  Identities=25%  Similarity=0.430  Sum_probs=58.1

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHH
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL  313 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~  313 (318)
                      .....+.||.+.+|.|||.||.+||.|.++|||+|+|.+      +..|.|.+ +.+++++|+.+|..++.
T Consensus       577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~  641 (719)
T TIGR02696       577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIAN  641 (719)
T ss_pred             CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence            356788899999999999999999999999999999953      67899999 67999999999999877

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.

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.76  E-value=9.7e-05  Score=60.86  Aligned_cols=62  Identities=16%  Similarity=0.295  Sum_probs=46.2

Q ss_pred             CChHHHHHHHHHHHHHhhcc-C--CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEe
Q 021032            3 HSPAQDAVMRVHSRIAEIGF-E--PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVF   64 (318)
Q Consensus         3 ~s~a~~a~~~v~~~i~~~~~-e--~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~   64 (318)
                      +++.+=..+.+|+.+..... +  -++..-+=++|....+|..||++|++|+.|+|..|-+|.|.
T Consensus         5 l~~e~~~~i~lfe~~t~~~~~dc~~d~~~riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV   69 (141)
T TIGR01952         5 LSTEAIKYIALFEDMTGATVVDCLIDDRNRVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI   69 (141)
T ss_pred             ECHHHHHHHHHHHHHhCCceEEEEecCCcEEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence            45555666778877765421 0  01111677889999999999999999999999999999885

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.

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

Probab=97.75  E-value=9.8e-05  Score=70.95  Aligned_cols=76  Identities=14%  Similarity=0.247  Sum_probs=57.1

Q ss_pred             eeEEEEEEec------ccceeeeCCCCchHHHHHHHhCCeEEEecCCC----------CCCCCCCC-CceEEEEecH-HH
Q 021032           27 AVVARLLVHS------QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQ----------APRCGSPH-DEIVQVIGNY-HS   88 (318)
Q Consensus        27 ~~~~rllVp~------~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~----------~p~~~~~~-er~V~I~G~~-~~   88 (318)
                      .++-||.||.      +++|+|||-.|.|.|+|+++|||+|.|..+..          +..-..+. +--+.|+++. |.
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            6788999985      46999999999999999999999999975211          11111122 2347888865 68


Q ss_pred             HHHHHHHHHHHHHh
Q 021032           89 VQDALFHITSRLRE  102 (318)
Q Consensus        89 V~~A~~~I~~~l~e  102 (318)
                      |.+|+..|..+|.+
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            88999988888865

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=97.73  E-value=0.00015  Score=75.25  Aligned_cols=70  Identities=20%  Similarity=0.237  Sum_probs=61.1

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      ..-..+.|-..+...|+||+|.+|.+|++++.+.|.+..  .++++..+.++|....++.|...++..+.+-
T Consensus       346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei  415 (753)
T KOG2208|consen  346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVSANDEKAVEDVEKIIAEI  415 (753)
T ss_pred             ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccccchhHHHHHHHHHHHhh
Confidence            356777888999999999999999999999999999965  4567888999999999999999988877653

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.71  E-value=7.3e-05  Score=77.91  Aligned_cols=87  Identities=17%  Similarity=0.270  Sum_probs=71.6

Q ss_pred             hHHHHHHHHHHHHHhhccC------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCe-EEEecCCCCCCCCCCCC
Q 021032            5 PAQDAVMRVHSRIAEIGFE------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGAS-IRVFPKDQAPRCGSPHD   77 (318)
Q Consensus         5 ~a~~a~~~v~~~i~~~~~e------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~-I~i~~~~~~p~~~~~~e   77 (318)
                      -|.++..+|++.+.+...+      +..+....|-||.+++|.|||.||.+||+|+++||++ |.|.           .+
T Consensus       656 ~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-----------dd  724 (891)
T PLN00207        656 QAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-----------DD  724 (891)
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------CC
Confidence            4677778888777665332      3567889999999999999999999999999999999 9983           36


Q ss_pred             ceEEEEe-cHHHHHHHHHHHHHHHHh
Q 021032           78 EIVQVIG-NYHSVQDALFHITSRLRE  102 (318)
Q Consensus        78 r~V~I~G-~~~~V~~A~~~I~~~l~e  102 (318)
                      -.|.|.+ +.+.+.+|+..|..+..+
T Consensus       725 g~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        725 GTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             eeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            7788888 678999999998877754

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

Probab=97.69  E-value=0.00028  Score=63.15  Aligned_cols=81  Identities=15%  Similarity=0.292  Sum_probs=54.1

Q ss_pred             CeeEEEEEEecc------cceeeeCCCCchHHHHHHHhCCeEEEecCCCC------------CCCCCCCCc---eEEEEe
Q 021032           26 QAVVARLLVHSQ------QIGCLLGRGGHIVSEMRRATGASIRVFPKDQA------------PRCGSPHDE---IVQVIG   84 (318)
Q Consensus        26 ~~~~~rllVp~~------~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~------------p~~~~~~er---~V~I~G   84 (318)
                      -.++.||+||-.      +||.|+|..|.++|+|+++|||+|.|..+.++            |.|+.-.+.   .|+...
T Consensus        90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~  169 (259)
T KOG1588|consen   90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEA  169 (259)
T ss_pred             eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeC
Confidence            357899999965      69999999999999999999999999754332            344433332   456666


Q ss_pred             cHHHHHHHHHHHHHHHHhhcCC
Q 021032           85 NYHSVQDALFHITSRLRETIFP  106 (318)
Q Consensus        85 ~~~~V~~A~~~I~~~l~e~~~~  106 (318)
                      ++.-+..=+.+-.+.|++.|.|
T Consensus       170 p~~ea~~rl~~AleeI~klL~P  191 (259)
T KOG1588|consen  170 PPAEAYARLAYALEEIKKLLVP  191 (259)
T ss_pred             CHHHHHHHHHHHHHHHHHhcCC
Confidence            6654443333333444444443

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

Probab=97.63  E-value=0.00016  Score=69.48  Aligned_cols=72  Identities=17%  Similarity=0.328  Sum_probs=57.0

Q ss_pred             ceEEEEEecc------cccccccccccchHHHHHHHhCCEEEEcCC---------------CCCCC-CeEEEEEc-CHHH
Q 021032          244 STTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVNDP---------------KPGAT-EGVVMVSG-TSDQ  300 (318)
Q Consensus       244 ~~t~~v~IP~------~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~---------------~~~~~-er~v~I~G-t~~~  300 (318)
                      ..+-+|.||.      +|||.|||-.|.+.|+|.++|||+|.|-..               .+... +=-+.|++ |.|.
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            4566777775      699999999999999999999999999541               11222 23477888 6799


Q ss_pred             HHHHHHHHHHHHHcC
Q 021032          301 MRAAQSLIHAFILCG  315 (318)
Q Consensus       301 v~~A~~lI~~~i~~~  315 (318)
                      |++|..+|+.+|.+.
T Consensus       217 i~~Ai~vienli~~a  231 (554)
T KOG0119|consen  217 IKKAIAVIENLIQSA  231 (554)
T ss_pred             HHHHHHHHHHHHHhh
Confidence            999999999999864

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.62  E-value=0.0001  Score=75.97  Aligned_cols=65  Identities=18%  Similarity=0.290  Sum_probs=56.8

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~  314 (318)
                      .....+.||.+.+|.|||++|.+||+|.++|||+|.|.+      +..|.|.+ ..+.+++|+.+|..+...
T Consensus       550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            456788999999999999999999999999999999953      57788887 578999999999887653

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).

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=97.42  E-value=0.00041  Score=69.13  Aligned_cols=69  Identities=19%  Similarity=0.381  Sum_probs=59.7

Q ss_pred             cceEEEEEecc-cccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 021032          243 TSTTIEVVIPQ-LYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV  316 (318)
Q Consensus       243 ~~~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~~~  316 (318)
                      ...+..|.+|+ ++-|+||||.|.||+-+...||++|-|++..     ..|+|+| .|---+.|+..|..+|..|+
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~fdp~rreia~~~l~~li~dgr  272 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPVRREIARMALEKLIQDGR  272 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC-----CeEEecCCchHHHHHHHHHHHHHHHcCC
Confidence            34667788998 7779999999999999999999999997533     3588999 78888999999999999875

>PRK00106 hypothetical protein; Provisional

Probab=97.41  E-value=0.00045  Score=68.77  Aligned_cols=69  Identities=22%  Similarity=0.406  Sum_probs=60.0

Q ss_pred             cceEEEEEecc-cccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 021032          243 TSTTIEVVIPQ-LYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV  316 (318)
Q Consensus       243 ~~~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~~~  316 (318)
                      ...+..|.+|+ ++-|+||||.|.||+-+...||++|-|++..     ..|+|+| .|---+-|+..|..+|..|+
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~v~lS~fdpvRReiAr~~le~Li~dgr  293 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP-----EVVVLSGFDPIRREIARMTLESLIKDGR  293 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC-----CeEEEeCCChHHHHHHHHHHHHHHHcCC
Confidence            34667788998 7789999999999999999999999997533     3588999 89999999999999999886

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

Probab=97.40  E-value=0.00023  Score=65.49  Aligned_cols=71  Identities=23%  Similarity=0.284  Sum_probs=58.9

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ....-++|+++..|+|||+.|.|-|+|+++|+++|.++...      ...+.++.+.+..++|.+|...|...|.+.
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~  126 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN------TNKEEIKIIGISRNCVIQALERIAKLIDSD  126 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC------CCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence            35678899999999999999999999999999999996542      133455555568899999999999888776

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

Probab=97.40  E-value=0.00015  Score=68.66  Aligned_cols=69  Identities=20%  Similarity=0.326  Sum_probs=57.3

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHH
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLR  101 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~  101 (318)
                      .....+.|-|-+..||.+||+||++||.||..|+++|+|...        ..+-.|+|.|..+--.+|...|-...+
T Consensus        44 ~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~  112 (629)
T KOG0336|consen   44 GGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQD  112 (629)
T ss_pred             CCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhh
Confidence            456788999999999999999999999999999999999743        457889999988866666666644443

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

Probab=97.38  E-value=0.00019  Score=67.96  Aligned_cols=68  Identities=15%  Similarity=0.112  Sum_probs=57.4

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ...+-+.|-.++||.|||++|++|+.|+..+..+|+|.+..   .|-.|+|-|..+--.+|+..|...+..
T Consensus        46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~---~e~kv~ifg~~~m~~kaka~id~~~~k  113 (629)
T KOG0336|consen   46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD---LEVKVTIFGINHMRKKAKASIDRGQDK  113 (629)
T ss_pred             CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC---ceeEEEEechHHHHHHHHhhHhhhhhh
Confidence            34566778899999999999999999999999999997654   467899999998888888887766543

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=97.37  E-value=0.00029  Score=72.74  Aligned_cols=87  Identities=21%  Similarity=0.324  Sum_probs=69.4

Q ss_pred             hHHHHHHHHHHHHHhhccCC------CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCc
Q 021032            5 PAQDAVMRVHSRIAEIGFEP------GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDE   78 (318)
Q Consensus         5 ~a~~a~~~v~~~i~~~~~e~------~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er   78 (318)
                      -|.++..+|++.+.+...++      ..+....+-|+...++.+||.||.+||+|+++||++|.+.           .+.
T Consensus       525 ~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~G  593 (693)
T PRK11824        525 QAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DDG  593 (693)
T ss_pred             HHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CCc
Confidence            46778888888887765432      3455567778999999999999999999999999998882           367


Q ss_pred             eEEEEe-cHHHHHHHHHHHHHHHHh
Q 021032           79 IVQVIG-NYHSVQDALFHITSRLRE  102 (318)
Q Consensus        79 ~V~I~G-~~~~V~~A~~~I~~~l~e  102 (318)
                      .|.|.+ ..+.+.+|...|..+..+
T Consensus       594 ~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        594 TVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             eEEEEcccHHHHHHHHHHHHHhccc
Confidence            788888 678888999988776644

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

Probab=97.36  E-value=0.00064  Score=68.33  Aligned_cols=87  Identities=22%  Similarity=0.309  Sum_probs=71.0

Q ss_pred             HHHHHHHHHHHHHhhccC------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCce
Q 021032            6 AQDAVMRVHSRIAEIGFE------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEI   79 (318)
Q Consensus         6 a~~a~~~v~~~i~~~~~e------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~   79 (318)
                      |-+|-++++..+.+.-.+      +-.+-...+-|+...++-+||+||.+|++|.++|||+|+|.           .+..
T Consensus       524 Ak~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------ddGt  592 (692)
T COG1185         524 AKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DDGT  592 (692)
T ss_pred             HHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CCCc
Confidence            556777777776665332      23456678889999999999999999999999999999993           3678


Q ss_pred             EEEEecH-HHHHHHHHHHHHHHHhh
Q 021032           80 VQVIGNY-HSVQDALFHITSRLRET  103 (318)
Q Consensus        80 V~I~G~~-~~V~~A~~~I~~~l~e~  103 (318)
                      |.|.+.. +.+.+|+..|..+.++.
T Consensus       593 v~i~~s~~~~~~~ak~~I~~i~~e~  617 (692)
T COG1185         593 VKIAASDGESAKKAKERIEAITREV  617 (692)
T ss_pred             EEEEecchHHHHHHHHHHHHHHhhc
Confidence            9999876 78889999999988775

>PRK12704 phosphodiesterase; Provisional

Probab=97.27  E-value=0.00072  Score=67.53  Aligned_cols=69  Identities=17%  Similarity=0.370  Sum_probs=57.7

Q ss_pred             cceEEEEEecc-cccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 021032          243 TSTTIEVVIPQ-LYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV  316 (318)
Q Consensus       243 ~~~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~~~  316 (318)
                      ...+..|.+|+ ++-|+||||.|.||+-+...||++|-|++.     -..|+||| .|-.-+.|+..|..++..|+
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~~~~~rre~a~~~l~~l~~dg~  278 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSGFDPIRREIARLALEKLVQDGR  278 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC-----CCeEEEecCChhhHHHHHHHHHHHHhcCC
Confidence            34566778998 778999999999999999999999999753     34588999 67777789999988888775

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

Probab=97.24  E-value=0.00054  Score=48.21  Aligned_cols=37  Identities=30%  Similarity=0.514  Sum_probs=34.6

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEE
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRV   63 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i   63 (318)
                      .....+.|+..++|..|||+|.+|+.+++.+|-+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            4789999999999999999999999999999988876

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.

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

Probab=97.18  E-value=0.001  Score=57.14  Aligned_cols=54  Identities=24%  Similarity=0.405  Sum_probs=49.1

Q ss_pred             cceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           38 QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        38 ~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ..|.|||++|.+-+-|++-|||.|.|.            +..|.|-|.+++|+.|...|..++...
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~------------g~tVaiiG~~~~v~iAr~AVemli~G~  165 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVY------------GKTVAIIGGFEQVEIAREAVEMLINGA  165 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEe------------CcEEEEecChhhhHHHHHHHHHHHcCC
Confidence            469999999999999999999999995            567999999999999999998888664

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=97.17  E-value=0.001  Score=59.76  Aligned_cols=65  Identities=18%  Similarity=0.308  Sum_probs=55.9

Q ss_pred             EEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcC-HHHHHHHHHHHHHHHHcCcC
Q 021032          247 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT-SDQMRAAQSLIHAFILCGVT  317 (318)
Q Consensus       247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt-~~~v~~A~~lI~~~i~~~~~  317 (318)
                      ..+.||.++++++||++|.+|+.|.+.++++|.|.      .+..|.|+++ .+.+.+|+.+|+.+-++-++
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~  212 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG------QNGRIWIKGPDEEDEEIAIEAIKKIEREAHT  212 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence            56779999999999999999999999999999994      3577899995 56999999999987665443

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

Probab=97.13  E-value=0.00063  Score=47.83  Aligned_cols=36  Identities=17%  Similarity=0.346  Sum_probs=33.9

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEE
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV  280 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i  280 (318)
                      ....+.|+.+.+|.+|||+|.+|+.+++.+|-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            578999999999999999999999999999988876

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

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.08  E-value=0.00065  Score=71.00  Aligned_cols=65  Identities=9%  Similarity=0.245  Sum_probs=57.6

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCE-EEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGAN-VVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~-I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~  314 (318)
                      .....+.||.+.+|.|||.||.+|+.|.++||+. |++.      ++..|.|.+ +.+.+++|+.+|.+++..
T Consensus       684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~------ddg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ------DDGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            4567889999999999999999999999999999 9995      367889999 689999999999988653

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

Probab=96.97  E-value=0.0012  Score=66.33  Aligned_cols=65  Identities=15%  Similarity=0.269  Sum_probs=57.6

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCH-HHHHHHHHHHHHHHHc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTS-DQMRAAQSLIHAFILC  314 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~-~~v~~A~~lI~~~i~~  314 (318)
                      ....++.|+.+.++-|||++|.+|++|.++|||+|+|.      ++.+|.|.++. +.+..|+..|.+++.+
T Consensus       551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie------ddGtv~i~~s~~~~~~~ak~~I~~i~~e  616 (692)
T COG1185         551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE------DDGTVKIAASDGESAKKAKERIEAITRE  616 (692)
T ss_pred             CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec------CCCcEEEEecchHHHHHHHHHHHHHHhh
Confidence            45677889999999999999999999999999999994      45679999965 8999999999998754

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.80  E-value=0.002  Score=55.74  Aligned_cols=37  Identities=19%  Similarity=0.325  Sum_probs=34.8

Q ss_pred             EEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032          246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      ...+.||.+..+..|||+|.+++.+++.||-+|.|..
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            6888899999999999999999999999999999954

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

Probab=96.73  E-value=0.0037  Score=53.93  Aligned_cols=78  Identities=12%  Similarity=0.201  Sum_probs=53.6

Q ss_pred             CeeEEEEEEec------ccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCC---------CCce---EEEEecHH
Q 021032           26 QAVVARLLVHS------QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSP---------HDEI---VQVIGNYH   87 (318)
Q Consensus        26 ~~~~~rllVp~------~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~---------~er~---V~I~G~~~   87 (318)
                      ..++-++.||-      ++||+|||..|+|+|+|++.|+|+|.|-.+...-.|-.+         .+.+   +.+.-..+
T Consensus       146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsed  225 (269)
T COG5176         146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSED  225 (269)
T ss_pred             ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhh
Confidence            45677888874      679999999999999999999999999753222122111         1211   22233445


Q ss_pred             HHHHHHHHHHHHHHhh
Q 021032           88 SVQDALFHITSRLRET  103 (318)
Q Consensus        88 ~V~~A~~~I~~~l~e~  103 (318)
                      .+++++..+...++++
T Consensus       226 ki~~~ik~~~n~I~~a  241 (269)
T COG5176         226 KICRLIKSQLNAIREA  241 (269)
T ss_pred             hHHHHHHHHHHHHHHH
Confidence            6777888888888886

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

Probab=96.72  E-value=0.0024  Score=58.95  Aligned_cols=71  Identities=10%  Similarity=0.237  Sum_probs=57.9

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV  316 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~~~  316 (318)
                      .....+.++..+.|.|||++|.+.+.|+++|+++|.++.+.  .....|+|+| ..++|.+|..-|.-+|.+.+
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~--~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN--TNKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC--CCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            45567789999999999999999999999999999996554  3344455555 78999999999988887644

>PRK00468 hypothetical protein; Provisional

Probab=96.68  E-value=0.0019  Score=47.32  Aligned_cols=33  Identities=27%  Similarity=0.529  Sum_probs=29.8

Q ss_pred             CCCeeEEEEEEecccceeeeCCCCchHHHHHHH
Q 021032           24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA   56 (318)
Q Consensus        24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~   56 (318)
                      .++.+.++|-|...-+|.||||+|.+|+.||.-
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            456789999999999999999999999999854

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

Probab=96.65  E-value=0.0044  Score=45.32  Aligned_cols=33  Identities=21%  Similarity=0.456  Sum_probs=29.9

Q ss_pred             CCCeeEEEEEEecccceeeeCCCCchHHHHHHH
Q 021032           24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA   56 (318)
Q Consensus        24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~   56 (318)
                      .+..+.++|-|....+|.+|||+|.+|+.||.-
T Consensus        26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             cCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            467889999999999999999999999999953

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

Probab=96.58  E-value=0.0027  Score=56.93  Aligned_cols=39  Identities=15%  Similarity=0.472  Sum_probs=34.9

Q ss_pred             cceEEEEEecc------cccccccccccchHHHHHHHhCCEEEEc
Q 021032          243 TSTTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVN  281 (318)
Q Consensus       243 ~~~t~~v~IP~------~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~  281 (318)
                      ...+.+|.||.      ++||+|+|..|.++|+|+++|||+|.|-
T Consensus        90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir  134 (259)
T KOG1588|consen   90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR  134 (259)
T ss_pred             eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence            35778888886      5999999999999999999999999994

>PRK12705 hypothetical protein; Provisional

Probab=96.47  E-value=0.004  Score=61.70  Aligned_cols=68  Identities=16%  Similarity=0.326  Sum_probs=56.1

Q ss_pred             ceEEEEEecc-cccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 021032          244 STTIEVVIPQ-LYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV  316 (318)
Q Consensus       244 ~~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~~~  316 (318)
                      ..+..|.+|+ ++-|+||||.|.||+-+...||..|.|++..     ..|+|++ .|.--+.|...+..+|..|+
T Consensus       197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~V~ls~fdp~rreia~~~l~~Li~dgr  266 (508)
T PRK12705        197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP-----EAVVISSFNPIRREIARLTLEKLLADGR  266 (508)
T ss_pred             heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc-----cchhhcccCccchHHHHHHHHHHHhcCC
Confidence            4566678887 6779999999999999999999999997533     3377888 67788888888888888775

>PRK01064 hypothetical protein; Provisional

Probab=96.45  E-value=0.0079  Score=44.40  Aligned_cols=33  Identities=21%  Similarity=0.477  Sum_probs=30.0

Q ss_pred             CCCeeEEEEEEecccceeeeCCCCchHHHHHHH
Q 021032           24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA   56 (318)
Q Consensus        24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~   56 (318)
                      .+..+.+++.|.....|.+|||+|.+|+.||.-
T Consensus        26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l   58 (78)
T PRK01064         26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTL   58 (78)
T ss_pred             CCCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence            467789999999999999999999999999864

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

Probab=96.44  E-value=0.00085  Score=70.34  Aligned_cols=73  Identities=21%  Similarity=0.159  Sum_probs=62.6

Q ss_pred             CcceEEEEEecccccccccccccchHHHHHHHhCCEEEEcC-CCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          242 LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND-PKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       242 ~~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~-~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      .......+.+|.....+|||++|++|+.+|.-+||.|.|.+ ..++..||.+.+.|+++.++.|..+|.-.|..
T Consensus      1337 ~~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1337 VPANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             CcccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeec
Confidence            34455678899999999999999999999999999999987 34457899999999999999999988765543

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.41  E-value=0.0066  Score=54.55  Aligned_cols=63  Identities=17%  Similarity=0.266  Sum_probs=51.5

Q ss_pred             EEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHH-HHHHHHHHHHHHHHhh
Q 021032           30 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH-SVQDALFHITSRLRET  103 (318)
Q Consensus        30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~-~V~~A~~~I~~~l~e~  103 (318)
                      +.+-||...++.|||++|.+|+.|.++++++|.|-           .+-.|.|.+... ++.+|...|..+-++.
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~  210 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-----------QNGRIWIKGPDEEDEEIAIEAIKKIEREA  210 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence            45788999999999999999999999999999993           257788888654 7777777776655554

>PRK02821 hypothetical protein; Provisional

Probab=96.33  E-value=0.0077  Score=44.33  Aligned_cols=33  Identities=24%  Similarity=0.538  Sum_probs=29.2

Q ss_pred             CCCeeEEEEEEecccceeeeCCCCchHHHHHHH
Q 021032           24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA   56 (318)
Q Consensus        24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~   56 (318)
                      .++.+.+.|-|...-+|.||||+|.+|+.||.-
T Consensus        27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtl   59 (77)
T PRK02821         27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTV   59 (77)
T ss_pred             CCCcEEEEEEEChhhCcceeCCCCchHHHHHHH
Confidence            355688999999999999999999999999954

>PRK00468 hypothetical protein; Provisional

Probab=96.33  E-value=0.004  Score=45.62  Aligned_cols=31  Identities=23%  Similarity=0.309  Sum_probs=28.5

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHh
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQIS  274 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S  274 (318)
                      ...+++.+..+-+|+||||+|.+|+.||..-
T Consensus        29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         29 SVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             eEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            4788999999999999999999999999874

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=96.24  E-value=0.43  Score=41.89  Aligned_cols=65  Identities=17%  Similarity=0.237  Sum_probs=54.2

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      .+.+.++....-.|...+|..++.|-...||+|.+..          .+..|.|+|+...+..+...|.+.+...
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~----------~~~~i~I~g~k~~~~~i~~~i~~~l~~i   91 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR----------SENRIRITGTKSTAEYIEASINEILSNI   91 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec----------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence            3455556888899999999999999888899999964          4789999999999988888887777664

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.22  E-value=0.0043  Score=64.23  Aligned_cols=64  Identities=19%  Similarity=0.319  Sum_probs=55.1

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHc
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~  314 (318)
                      ....+.||.+.++.+||.||.+|+.|.+++|+.|++.      ++..|.|.+ ..+.+++|+.+|..++..
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~------d~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE------DDGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence            3456778999999999999999999999999998883      357789999 678999999999987753

>PRK02821 hypothetical protein; Provisional

Probab=96.18  E-value=0.0052  Score=45.21  Aligned_cols=33  Identities=21%  Similarity=0.327  Sum_probs=29.5

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCC
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGA  276 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA  276 (318)
                      ...+++.+..+-+|+||||+|.+|+.||..-.|
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            467899999999999999999999999998544

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

Probab=96.05  E-value=0.012  Score=50.91  Aligned_cols=39  Identities=21%  Similarity=0.400  Sum_probs=32.7

Q ss_pred             ceEEEEEecc------cccccccccccchHHHHHHHhCCEEEEcC
Q 021032          244 STTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       244 ~~t~~v~IP~------~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      ..+-.++||-      ++||.|||..|.++|++++.|+|+|-|-.
T Consensus       147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG  191 (269)
T COG5176         147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG  191 (269)
T ss_pred             cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence            3455566653      79999999999999999999999999954

>TIGR01953 NusA transcription termination factor NusA

Probab=96.03  E-value=0.017  Score=54.73  Aligned_cols=38  Identities=24%  Similarity=0.408  Sum_probs=35.5

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      ....+.||.+..+..|||+|.|++-.++.||.+|.|..
T Consensus       301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            46889999999999999999999999999999999953

This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.01  E-value=0.013  Score=55.80  Aligned_cols=38  Identities=16%  Similarity=0.235  Sum_probs=35.2

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      ....+.||.+..+..|||+|.|++-.++.||.+|+|..
T Consensus       308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s  345 (374)
T PRK12328        308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE  345 (374)
T ss_pred             cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence            46788999999999999999999999999999999954

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

Probab=95.61  E-value=0.013  Score=42.82  Aligned_cols=32  Identities=25%  Similarity=0.397  Sum_probs=28.8

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHh
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQIS  274 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S  274 (318)
                      ....+++.+..+-+|.||||+|.+|+.||..-
T Consensus        28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             CeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            35779999999999999999999999999874

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.59  E-value=0.03  Score=53.40  Aligned_cols=38  Identities=16%  Similarity=0.361  Sum_probs=35.4

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      ....+.||.+..+..|||+|.|++--++.||.+|.|..
T Consensus       303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s  340 (362)
T PRK12327        303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS  340 (362)
T ss_pred             cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence            46889999999999999999999999999999999964

>PRK01064 hypothetical protein; Provisional

Probab=95.46  E-value=0.012  Score=43.46  Aligned_cols=32  Identities=13%  Similarity=0.328  Sum_probs=28.7

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHh
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQIS  274 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S  274 (318)
                      ....+++.|..+-.|++|||+|.+|+.||...
T Consensus        28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            35789999999999999999999999999964

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.37  E-value=0.042  Score=54.22  Aligned_cols=38  Identities=18%  Similarity=0.375  Sum_probs=35.6

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      ....+.||.+..+.-|||+|.|++..++.||.+|.|..
T Consensus       302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            47889999999999999999999999999999999964

>PRK12704 phosphodiesterase; Provisional

Probab=95.34  E-value=0.076  Score=53.22  Aligned_cols=49  Identities=20%  Similarity=0.350  Sum_probs=39.9

Q ss_pred             CeeEEEEEEec-ccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEe
Q 021032           26 QAVVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG   84 (318)
Q Consensus        26 ~~~~~rllVp~-~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G   84 (318)
                      +..+--+-+|+ ..-|.||||.|.+||.++.-||++|-|.          ++-.+|.|+|
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~  257 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSG  257 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc----------CCCCeEEEec
Confidence            34555666787 6789999999999999999999999994          2456777888

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

Probab=95.32  E-value=0.014  Score=53.53  Aligned_cols=65  Identities=18%  Similarity=0.306  Sum_probs=55.5

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHH
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHA  310 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~  310 (318)
                      ..++..+.||..+++.|.|++|.+||.||..|...|+-...   ..|-++.++|.++.|..|++-|..
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~edv~~aRrei~s   88 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRHEDVRRARREIPS   88 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCchhHHHHhhcCcc
Confidence            35788889999999999999999999999999988876422   245889999999999999987754

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

Probab=95.28  E-value=0.01  Score=51.01  Aligned_cols=64  Identities=19%  Similarity=0.271  Sum_probs=54.5

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      .+++=.=-+..+|.|+||+|.+--.|++.|.++|.+.            +..+.|-|..++++-|...||.++...
T Consensus       169 KtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlGs  232 (252)
T KOG3273|consen  169 KTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILGS  232 (252)
T ss_pred             ccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhccC
Confidence            3444444456799999999999999999999999984            567899999999999999999998774

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=95.26  E-value=0.086  Score=52.76  Aligned_cols=50  Identities=20%  Similarity=0.347  Sum_probs=40.2

Q ss_pred             CCeeEEEEEEec-ccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEe
Q 021032           25 GQAVVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG   84 (318)
Q Consensus        25 ~~~~~~rllVp~-~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G   84 (318)
                      .+..+.-+-+|+ ..-|.||||.|.+||.++..||++|-|.          ++-..|.|++
T Consensus       201 ~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~  251 (514)
T TIGR03319       201 AETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSG  251 (514)
T ss_pred             hhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc----------CCCCeEEecC
Confidence            345556677887 6789999999999999999999999994          2345677777

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.15  E-value=0.053  Score=52.57  Aligned_cols=38  Identities=16%  Similarity=0.355  Sum_probs=35.1

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      ....+.||.+..+..|||+|.|++--...||.+|.|..
T Consensus       335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            35789999999999999999999999999999999964

>PRK00106 hypothetical protein; Provisional

Probab=95.12  E-value=0.12  Score=51.79  Aligned_cols=50  Identities=18%  Similarity=0.359  Sum_probs=40.7

Q ss_pred             CCeeEEEEEEec-ccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEe
Q 021032           25 GQAVVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG   84 (318)
Q Consensus        25 ~~~~~~rllVp~-~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G   84 (318)
                      .+..+.-+-+|+ ..-|.||||.|.+|+.++.-||++|-|.          ++-..|.|+|
T Consensus       222 ~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid----------dtp~~v~lS~  272 (535)
T PRK00106        222 TEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID----------DTPEVVVLSG  272 (535)
T ss_pred             hhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc----------CCCCeEEEeC
Confidence            345556677887 5789999999999999999999999994          2446677887

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

Probab=94.78  E-value=0.026  Score=40.65  Aligned_cols=36  Identities=22%  Similarity=0.480  Sum_probs=30.3

Q ss_pred             EEEEEeccc-----ceeeeCCCCchHHHHHHHh-CCeEEEec
Q 021032           30 ARLLVHSQQ-----IGCLLGRGGHIVSEMRRAT-GASIRVFP   65 (318)
Q Consensus        30 ~rllVp~~~-----vG~IIGkgG~~Ik~I~e~t-Ga~I~i~~   65 (318)
                      +++.|-...     +|..||++|++||.|.++. |-+|+|..
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            567777777     9999999999999999999 99999964

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=94.32  E-value=0.11  Score=51.42  Aligned_cols=86  Identities=17%  Similarity=0.265  Sum_probs=65.8

Q ss_pred             HHHHHHHHHHHHHhhccC------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCce
Q 021032            6 AQDAVMRVHSRIAEIGFE------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEI   79 (318)
Q Consensus         6 a~~a~~~v~~~i~~~~~e------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~   79 (318)
                      |.+|-++|++.+.+.-.+      ...++...|-|+.++.-.+||.+|...|+|+.+||+.-++            +|..
T Consensus       569 a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t  636 (760)
T KOG1067|consen  569 AREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGT  636 (760)
T ss_pred             hhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCce
Confidence            455666666665544322      3568889999999999999999999999999999965555            3566


Q ss_pred             EEEEe-cHHHHHHHHHHHHHHHHhh
Q 021032           80 VQVIG-NYHSVQDALFHITSRLRET  103 (318)
Q Consensus        80 V~I~G-~~~~V~~A~~~I~~~l~e~  103 (318)
                      +.|-. +..+.++|...|..++...
T Consensus       637 ~~i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  637 FSIFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             EEEEecCHHHHHHHHHHHHHHhcCc
Confidence            77766 5677789999998887663

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

Probab=94.15  E-value=0.089  Score=36.79  Aligned_cols=35  Identities=14%  Similarity=0.317  Sum_probs=28.4

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeE
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI   61 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I   61 (318)
                      ...+.+.+.....|.+|||+|.+|+.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            45566666666799999999999999999988543

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.

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=93.94  E-value=0.076  Score=43.78  Aligned_cols=38  Identities=16%  Similarity=0.279  Sum_probs=34.4

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      ...-+.|+...+|..||++|++|+.|++..|-+|+|-+
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve   69 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE   69 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence            56778889999999999999999999999999999843

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=93.52  E-value=0.25  Score=48.98  Aligned_cols=65  Identities=20%  Similarity=0.170  Sum_probs=55.5

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV  316 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~~~  316 (318)
                      ....+.|+.+..-.+||.+|-+.|+|..+|||.-.+       +|.++.|.- ++.+.+.|+.+|..++..++
T Consensus       597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v-------De~t~~i~A~~~~am~~Ak~~I~~i~~~~~  662 (760)
T KOG1067|consen  597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV-------DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQ  662 (760)
T ss_pred             eeeEEeecchhhheeecCccceeeeEeeeccceeee-------cCceEEEEecCHHHHHHHHHHHHHHhcCcc
Confidence            456778999999999999999999999999965555       466788887 78999999999999887643

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=93.51  E-value=0.033  Score=40.38  Aligned_cols=34  Identities=12%  Similarity=0.291  Sum_probs=28.5

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhC
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATG   58 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tG   58 (318)
                      .+...+.+-|.....|.||||.|.+++.||--.+
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~   59 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN   59 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence            4556788888999999999999999999985443

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=93.48  E-value=0.038  Score=40.57  Aligned_cols=35  Identities=14%  Similarity=0.351  Sum_probs=29.9

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEE
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIR   62 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~   62 (318)
                      ..+.+.+..++.|.+|||+|++|++|++..+-.+.
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            45788899999999999999999999987765553

; InterPro: IPR004044 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-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=92.87  E-value=0.066  Score=38.80  Aligned_cols=33  Identities=21%  Similarity=0.261  Sum_probs=29.1

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCC
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGA  276 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA  276 (318)
                      ...+.+.+..+..|.+|||.|.+++.||....+
T Consensus        28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             ceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            457888899999999999999999999988754

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=92.16  E-value=0.28  Score=43.73  Aligned_cols=58  Identities=24%  Similarity=0.390  Sum_probs=43.4

Q ss_pred             EEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHH-HHHHHHHHHHH
Q 021032          247 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSD-QMRAAQSLIHA  310 (318)
Q Consensus       247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~-~v~~A~~lI~~  310 (318)
                      .-+.|+...+-++|||+|+.++.|.+.++|+|.|.      ....|-|.|..+ ....|...|..
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG------~NG~IWV~~~~~~~e~~~~~aI~~  206 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVG------QNGRIWVDGENESLEELAIEAIRK  206 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEe------cCCEEEecCCCcchHHHHHHHHHH
Confidence            55779999999999999999999999999999994      334456666555 24444444443

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

Probab=92.04  E-value=0.1  Score=45.00  Aligned_cols=53  Identities=15%  Similarity=0.340  Sum_probs=48.1

Q ss_pred             cccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHH
Q 021032          254 LYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFIL  313 (318)
Q Consensus       254 ~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~  313 (318)
                      ..+|+|+||+|.+---|.+.|..+|.+.       +..|.|-|+.+.++.|+..|..+|.
T Consensus       178 RAIGRiaGk~GkTkfaIEn~trtrIVla-------d~kIHiLG~~~niriAR~avcsLIl  230 (252)
T KOG3273|consen  178 RAIGRIAGKGGKTKFAIENVTRTRIVLA-------DSKIHILGAFQNIRIARDAVCSLIL  230 (252)
T ss_pred             HHHHHhhcCCCcceeeeeccceeEEEec-------CceEEEeecchhhHHHHHhhHhhhc
Confidence            4689999999999999999999999995       3559999999999999999998875

>PRK12705 hypothetical protein; Provisional

Probab=92.00  E-value=0.37  Score=48.03  Aligned_cols=39  Identities=21%  Similarity=0.325  Sum_probs=32.7

Q ss_pred             CeeEEEEEEec-ccceeeeCCCCchHHHHHHHhCCeEEEe
Q 021032           26 QAVVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVF   64 (318)
Q Consensus        26 ~~~~~rllVp~-~~vG~IIGkgG~~Ik~I~e~tGa~I~i~   64 (318)
                      +..+--+-+|+ ..-|.||||.|.+|+.++..||+.|-|.
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid  235 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID  235 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEec
Confidence            34445566776 5789999999999999999999999995

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

Probab=91.93  E-value=0.27  Score=34.28  Aligned_cols=34  Identities=15%  Similarity=0.232  Sum_probs=27.2

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEE
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANV  278 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I  278 (318)
                      ....+.+.....|.+|||+|.+|+.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            4555666665689999999999999999998544

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.

>PRK13764 ATPase; Provisional

Probab=91.70  E-value=0.29  Score=49.83  Aligned_cols=44  Identities=27%  Similarity=0.499  Sum_probs=38.1

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCC
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAP   70 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p   70 (318)
                      .-..-+.||...++.+|||+|.+|++|+++.|.+|.|-+.+..+
T Consensus       480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~  523 (602)
T PRK13764        480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP  523 (602)
T ss_pred             CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence            34567889999999999999999999999999999998765443

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=91.53  E-value=0.22  Score=36.47  Aligned_cols=33  Identities=15%  Similarity=0.409  Sum_probs=26.1

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCCeE
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASI   61 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I   61 (318)
                      .+.+-|.....|.||||.|++++.||-=...-+
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~   57 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL   57 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence            356667788999999999999999996555333

The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. 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 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.

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

Probab=91.41  E-value=0.21  Score=35.90  Aligned_cols=36  Identities=17%  Similarity=0.242  Sum_probs=27.9

Q ss_pred             EEEEecccc-----cccccccccchHHHHHHHh-CCEEEEcC
Q 021032          247 IEVVIPQLY-----MAHVYGENNSNLSHIRQIS-GANVVVND  282 (318)
Q Consensus       247 ~~v~IP~~~-----vG~IIGk~G~~Ik~Ir~~S-GA~I~i~~  282 (318)
                      ..+.|-...     +|..||++|.+|+.|.++. |-+|+|-+
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            444555555     8999999999999999999 99999854

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=91.20  E-value=0.21  Score=48.62  Aligned_cols=38  Identities=29%  Similarity=0.450  Sum_probs=34.8

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK   66 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~   66 (318)
                      .+.+.||...++.+|||+|.+|++|+++.|.+|.|-+.
T Consensus       487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~  524 (604)
T COG1855         487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL  524 (604)
T ss_pred             eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence            46688999999999999999999999999999999754

>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3

Probab=91.13  E-value=0.27  Score=36.52  Aligned_cols=36  Identities=11%  Similarity=0.293  Sum_probs=29.6

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEE
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRV   63 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i   63 (318)
                      -.+++.|....-|.||||+|+.|++|+++-.-...+
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~   65 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF   65 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence            448899999999999999999999999875544433

S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. 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 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.

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=91.08  E-value=0.26  Score=40.65  Aligned_cols=37  Identities=14%  Similarity=0.326  Sum_probs=33.2

Q ss_pred             EEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032          246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      ..-+.|....+|..||++|++|+.|++..|-+|+|-+
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe   70 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE   70 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence            5667788899999999999999999999999999843

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.

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

Probab=90.80  E-value=0.063  Score=57.03  Aligned_cols=69  Identities=20%  Similarity=0.124  Sum_probs=57.4

Q ss_pred             EEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHh
Q 021032           30 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  102 (318)
Q Consensus        30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e  102 (318)
                      -++-+|......+||+||++|..+|+.|||-|.|-.  .-|.  .-.||.+.+.|.++.++-|...|.-.+.+
T Consensus      1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielek--mq~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEK--MQPD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             cccccchhhhhhhhccCcchhhhHhhccceEEehhh--cCCc--cchhhhcccCCCChhhhhhhccccceeec
Confidence            467789899999999999999999999999999843  2221  13589999999999999999888766655

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=90.60  E-value=0.29  Score=41.41  Aligned_cols=34  Identities=35%  Similarity=0.576  Sum_probs=30.3

Q ss_pred             EEEEEecccceeeeCCCCchHHHHHHHhCCeEEEe
Q 021032           30 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVF   64 (318)
Q Consensus        30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~   64 (318)
                      +=++|-... |.-|||+|.+||.+++..|-+|.+.
T Consensus        63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV   96 (166)
T PRK06418         63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV   96 (166)
T ss_pred             EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence            456777777 9999999999999999999999996

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=90.56  E-value=0.19  Score=36.83  Aligned_cols=34  Identities=26%  Similarity=0.307  Sum_probs=29.1

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEE
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANV  278 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I  278 (318)
                      ....+.+-...-|.|||++|++|++|++..+-.+
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l   58 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL   58 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence            4577788889999999999999999998876554

; InterPro: IPR004044 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-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=89.65  E-value=0.55  Score=44.83  Aligned_cols=43  Identities=19%  Similarity=0.118  Sum_probs=38.2

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCC
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQA   69 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~   69 (318)
                      .-.+.+.||..+.+..|||+|.+++-..+-||.+|.|.+-++.
T Consensus       307 ~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~~  349 (374)
T PRK12328        307 EKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGSK  349 (374)
T ss_pred             CcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCCC
Confidence            3467899999999999999999999999999999999875443

>TIGR01953 NusA transcription termination factor NusA

Probab=89.53  E-value=0.41  Score=45.40  Aligned_cols=39  Identities=28%  Similarity=0.399  Sum_probs=36.2

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK   66 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~   66 (318)
                      ..+.+.||..+.+..|||+|.+++-...-||.+|.|.+.
T Consensus       301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~  339 (341)
T TIGR01953       301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE  339 (341)
T ss_pred             cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence            568999999999999999999999999999999999753

This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=88.58  E-value=0.35  Score=47.17  Aligned_cols=39  Identities=21%  Similarity=0.400  Sum_probs=35.4

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      .....+.||.+.++.+|||+|.+|++|.+..|-+|+|..
T Consensus       485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~  523 (604)
T COG1855         485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP  523 (604)
T ss_pred             CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence            355778899999999999999999999999999999964

>PRK13764 ATPase; Provisional

Probab=88.28  E-value=0.46  Score=48.41  Aligned_cols=40  Identities=18%  Similarity=0.345  Sum_probs=36.7

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      ......|.||.+.++.+|||+|.+|++|.+..|.+|+|..
T Consensus       479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~  518 (602)
T PRK13764        479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP  518 (602)
T ss_pred             cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence            4567889999999999999999999999999999999964

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=88.25  E-value=0.46  Score=41.21  Aligned_cols=37  Identities=30%  Similarity=0.416  Sum_probs=34.9

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEec
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFP   65 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~   65 (318)
                      ...+.||.++.+..|||+|.+++-+.+-||-++.|..
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            7888999999999999999999999999999999954

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=88.15  E-value=1.2  Score=39.71  Aligned_cols=45  Identities=18%  Similarity=0.341  Sum_probs=37.6

Q ss_pred             EEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHH
Q 021032           32 LLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH   87 (318)
Q Consensus        32 llVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~   87 (318)
                      +.|+...+-.+|||+|+-++-|.++|+|+|-+-.           ...|-|.++.+
T Consensus       150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~  194 (239)
T COG1097         150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENE  194 (239)
T ss_pred             EEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCc
Confidence            6788899999999999999999999999999953           34566666655

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=87.58  E-value=2.7  Score=36.83  Aligned_cols=65  Identities=15%  Similarity=0.200  Sum_probs=55.2

Q ss_pred             EEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      .+.+.++....-.+...+|..+++|-...||+|.+..     .+..|.|+|+...+..+...|.+++..-
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k~~~~~i~~~i~~~l~~i   91 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTKSTAEYIEASINEILSNI   91 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence            4555566888888999999999999888899999963     5567999999999999999999988753

>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein

Probab=87.49  E-value=0.66  Score=34.69  Aligned_cols=28  Identities=21%  Similarity=0.551  Sum_probs=24.2

Q ss_pred             EEEEEecccceeeeCCCCchHHHHHHHh
Q 021032           30 ARLLVHSQQIGCLLGRGGHIVSEMRRAT   57 (318)
Q Consensus        30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~t   57 (318)
                      +++.|....-|.+|||+|.+|++|++.-
T Consensus        40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l   67 (85)
T cd02411          40 TQITIYAERPGMVIGRGGKNIRELTEIL   67 (85)
T ss_pred             EEEEEEECCCCceECCCchhHHHHHHHH
Confidence            6777777899999999999999998653

S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. 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 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.

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=87.45  E-value=0.67  Score=33.90  Aligned_cols=35  Identities=17%  Similarity=0.241  Sum_probs=28.2

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEE
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVV  279 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~  279 (318)
                      ....+.|..+..|.+|||.|.+++.||-....-+.
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            35667777788899999999999999998765433

The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. 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 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.

>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH)

Probab=87.03  E-value=1.1  Score=36.95  Aligned_cols=38  Identities=24%  Similarity=0.559  Sum_probs=32.0

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK   66 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~   66 (318)
                      +-.+.|-...-|.+|||+|.++++|..+||-+-.|...
T Consensus        77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence            34556666777999999999999999999999988654

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. 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 general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3

Probab=86.95  E-value=0.6  Score=36.68  Aligned_cols=30  Identities=17%  Similarity=0.460  Sum_probs=26.0

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhC
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATG   58 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tG   58 (318)
                      .+++.|....-|.||||.|++|++|++...
T Consensus        62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~   91 (109)
T cd02412          62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ   91 (109)
T ss_pred             CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence            378888889999999999999999986643

S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. 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 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.

>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]

Probab=86.03  E-value=1.6  Score=39.73  Aligned_cols=52  Identities=13%  Similarity=0.277  Sum_probs=47.1

Q ss_pred             ccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          257 AHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       257 G~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      -++||.+|++++.|.=+|.|.|-|+.       .+|.+.|.-.-++.++..+.+|+.+-
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfkGlkevr~IV~DcM~Ni  212 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFKGLKEVRKIVEDCMKNI  212 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeC-------cEEEeecCcchHHHHHHHHHHHHhcc
Confidence            46999999999999999999999963       56999999999999999999998764

>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3

Probab=84.50  E-value=1.1  Score=33.32  Aligned_cols=36  Identities=17%  Similarity=0.289  Sum_probs=28.6

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEE
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV  280 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i  280 (318)
                      ...+|.|-...-|.|||++|.+|++|++.---...+
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~   65 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF   65 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence            347777878888999999999999999876544444

S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. 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 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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=84.17  E-value=1.2  Score=42.65  Aligned_cols=40  Identities=25%  Similarity=0.332  Sum_probs=36.7

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK   66 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~   66 (318)
                      ...+.+.||..+.+..|||+|.+++-...-||.+|.|.+.
T Consensus       302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            3568899999999999999999999999999999999754

>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]

Probab=84.16  E-value=1  Score=40.07  Aligned_cols=37  Identities=19%  Similarity=0.520  Sum_probs=30.3

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHH----HhCC-eEEE
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRR----ATGA-SIRV   63 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e----~tGa-~I~i   63 (318)
                      +..+++.|....-|.||||+|+.|++|++    .+|. .++|
T Consensus        50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I   91 (233)
T COG0092          50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQI   91 (233)
T ss_pred             CCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceE
Confidence            56789999999999999999999999875    4665 3444

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=84.11  E-value=0.93  Score=44.90  Aligned_cols=39  Identities=23%  Similarity=0.372  Sum_probs=36.2

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK   66 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~   66 (318)
                      -.+.+.||..+.+.-|||+|.+|+-..+-||.+|.|...
T Consensus       302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            478899999999999999999999999999999999753

>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH)

Probab=83.07  E-value=1.3  Score=36.43  Aligned_cols=42  Identities=29%  Similarity=0.261  Sum_probs=36.9

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCC
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP  285 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~  285 (318)
                      ..|.+|.|-.+.-|.+|||+|.++++|...+|-.-+|....+
T Consensus        75 ~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP  116 (145)
T cd02410          75 DDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP  116 (145)
T ss_pred             CCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence            457888999999999999999999999999999998865444

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. 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 general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]

Probab=82.46  E-value=2.9  Score=38.11  Aligned_cols=51  Identities=18%  Similarity=0.311  Sum_probs=43.6

Q ss_pred             eeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHh
Q 021032           40 GCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  102 (318)
Q Consensus        40 G~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e  102 (318)
                      -.|||.+|+|+|.|+--|.|-|-|.            -..|.+.|....+.++...|.+++..
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVq------------G~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQ------------GNTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEee------------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence            5799999999999999999999984            35688999999888888887777744

>TIGR00436 era GTP-binding protein Era

Probab=82.16  E-value=1.8  Score=39.45  Aligned_cols=30  Identities=20%  Similarity=0.369  Sum_probs=25.1

Q ss_pred             eeEEEEEEe-cccceeeeCCCCchHHHHHHH
Q 021032           27 AVVARLLVH-SQQIGCLLGRGGHIVSEMRRA   56 (318)
Q Consensus        27 ~~~~rllVp-~~~vG~IIGkgG~~Ik~I~e~   56 (318)
                      .+...++|. .+|-+.||||+|+.||+|..+
T Consensus       220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~  250 (270)
T TIGR00436       220 KIHALISVERESQKKIIIGKNGSMIKAIGIA  250 (270)
T ss_pred             EEEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence            366788888 479999999999999998644

Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=80.74  E-value=1.5  Score=42.85  Aligned_cols=38  Identities=29%  Similarity=0.343  Sum_probs=35.2

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEec
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFP   65 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~   65 (318)
                      ..+.+.||..+.+..|||+|.+++-...-||.+|.|.+
T Consensus       335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            45789999999999999999999999999999999953

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	318
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		5e-05
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		6e-05
1wvn_A	82	Crsytal Structure Of Domain 3 Of Human Alpha Polyc		1e-04
1khm_A	89	C-Terminal Kh Domain Of Hnrnp K (Kh3) Length = 89		1e-04
2p2r_A	76	Crystal Structure Of The Third Kh Domain Of Human P		3e-04

>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 = 45.1 bits (105), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 19/64 (29%), Positives = 38/64 (59%)
Query: 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 305
           T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ AQ
Sbjct: 8   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 67
Query: 306 SLIH 309
            L+ 
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 = 44.7 bits (104), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 19/64 (29%), Positives = 38/64 (59%)
Query: 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 305
           T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ AQ
Sbjct: 15  TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 74
Query: 306 SLIH 309
            L+ 
Sbjct: 75  YLLQ 78

>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding Protein Length = 82

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/68 (32%), Positives = 41/68 (60%)
Query: 243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 302
           + TT E+ IP   +  + G   +N++ IRQ+SGA + + +P  G++   V ++G++  + 
Sbjct: 4   SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASIS 63
Query: 303 AAQSLIHA 310
            AQ LI+A
Sbjct: 64  LAQYLINA 71

>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3) Length = 89

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/64 (29%), Positives = 38/64 (59%)
Query: 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 305
           T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ AQ
Sbjct: 15  TTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 74
Query: 306 SLIH 309
            L+ 
Sbjct: 75  YLLQ 78

>pdb|2P2R|A Chain A, Crystal Structure Of The Third Kh Domain Of Human Poly(C)- Binding Protein-2 In Complex With C-Rich Strand Of Human Telomeric Dna Length = 76

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/66 (30%), Positives = 39/66 (59%)
Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 303
           +T+ E+ IP   +  + G   + ++ IRQ SGA + + +P  G+T+  V ++G++  +  
Sbjct: 4   TTSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASISL 63
Query: 304 AQSLIH 309
           AQ LI+
Sbjct: 64  AQYLIN 69

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	318
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	9e-20
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-10
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-09
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-06
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-19
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-10
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	5e-08
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	7e-08
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-18
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	2e-12
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	3e-18
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	1e-11
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-17
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-11
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-16
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	8e-12
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-07
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	6e-07
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	2e-16
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-11
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-15
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-07
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-15
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-10
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	5e-09
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-08
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	4e-15
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	4e-13
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	7e-15
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	5e-11
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	4e-14
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	2e-08
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	8e-14
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	4e-10
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	8e-10
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	7e-07
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	8e-11
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	7e-08
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-09
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-06
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-09
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	8e-07
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-09
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-09
1we8_A	104	Tudor and KH domain containing protein; structural	1e-08
1we8_A	104	Tudor and KH domain containing protein; structural	1e-07
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-07
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-06
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	8e-06
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	2e-05
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-05
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	4e-05
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	2e-04
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	3e-04
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-04
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-04

>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 = 83.7 bits (207), Expect = 9e-20
 Identities = 23/108 (21%), Positives = 44/108 (40%), Gaps = 12/108 (11%)

Query: 4   SPAQDAVMRVHSRIAEI--------GFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRR 55
           +    A   +  ++ E                V  RL+V + Q G L+G+GG  + E+R 
Sbjct: 57  NAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRE 116

Query: 56  ATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET 103
           +TGA ++V          +  +  + + G   S+ + +  I   + ET
Sbjct: 117 STGAQVQVAGDM----LPNSTERAITIAGIPQSIIECVKQICVVMLET 160

>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 = 57.5 bits (139), Expect = 2e-10
 Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 7/88 (7%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
           +  RLL+H +++G ++G+ G  V +MR  +GA I +         G+  + I+ + G  +
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE-------GNCPERIITLAGPTN 57

Query: 88  SVQDALFHITSRLRETIFPMKRPGPNNG 115
           ++  A   I  +L E I           
Sbjct: 58  AIFKAFAMIIDKLEEDISSSMTNSTAAS 85

>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 = 54.0 bits (130), Expect = 3e-09
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 234 ESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV-NDPKPGATEGVV 292
            + + AA     T+ +V+P      + G+    +  IR+ +GA V V  D  P +TE  +
Sbjct: 78  MTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAI 137

Query: 293 MVSGTSDQMRAAQSLIHAFIL 313
            ++G    +      I   +L
Sbjct: 138 TIAGIPQSIIECVKQICVVML 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 = 46.3 bits (110), Expect = 2e-06
 Identities = 11/70 (15%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 302
            + TI +++    +  + G+   ++  +R+ SGA + +   +    E ++ ++G ++ + 
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLAGPTNAIF 60

Query: 303 AAQSLIHAFI 312
            A ++I   +
Sbjct: 61  KAFAMIIDKL 70

>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 = 82.9 bits (205), Expect = 2e-19
 Identities = 26/106 (24%), Positives = 48/106 (45%), Gaps = 10/106 (9%)

Query: 4   SPAQDAVMRVHSRIAEI-------GFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA 56
           +   +A  +   RI          G +    +   + V +   G ++G+GG  V+E++  
Sbjct: 54  TGPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNL 113

Query: 57  TGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 102
           T A + V P+DQ P        IV++IG++++ Q A   I   L +
Sbjct: 114 TAAEVVV-PRDQTP--DENDQVIVKIIGHFYASQMAQRKIRDILAQ 156

>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 = 58.2 bits (141), Expect = 1e-10
 Identities = 15/77 (19%), Positives = 36/77 (46%), Gaps = 4/77 (5%)

Query: 26  QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN 85
           +  + ++ + +Q +G ++G+ G  + ++ R   ASI++    + P        +V + G 
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKI-APPETPDS---KVRMVIITGP 56

Query: 86  YHSVQDALFHITSRLRE 102
             +   A   I  +L+E
Sbjct: 57  PEAQFKAQGRIYGKLKE 73

>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 = 50.9 bits (122), Expect = 5e-08
 Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 2/71 (2%)

Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV-NDPKPGAT-EGVVMVSGTSDQM 301
                + +P      V G+    ++ ++ ++ A VVV  D  P    + +V + G     
Sbjct: 84  KLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYAS 143

Query: 302 RAAQSLIHAFI 312
           + AQ  I   +
Sbjct: 144 QMAQRKIRDIL 154

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

 Score = 50.1 bits (120), Expect = 7e-08
 Identities = 12/69 (17%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSDQMRA 303
             ++V IP   +  + G+   ++  + + + A++ +  P  P +   +V+++G  +    
Sbjct: 3   EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFK 62

Query: 304 AQSLIHAFI 312
           AQ  I+  +
Sbjct: 63  AQGRIYGKL 71

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

 Score = 77.7 bits (192), Expect = 1e-18
 Identities = 20/69 (28%), Positives = 41/69 (59%)

Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 303
           +T+ E+ IP   +  + G   + ++ IRQ+SGA + + +P  G+T+  V ++G++  +  
Sbjct: 4   TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISL 63

Query: 304 AQSLIHAFI 312
           AQ LI+  +
Sbjct: 64  AQYLINVRL 72

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

 Score = 61.2 bits (149), Expect = 2e-12
 Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 25  GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 84
            Q     L + +  IGC++GR G  ++E+R+ +GA I++     A       D  V + G
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKI-----ANPVEGSTDRQVTITG 56

Query: 85  NYHSVQDALFHITSRLRE 102
           +  S+  A + I  RL  
Sbjct: 57  SAASISLAQYLINVRLSS 74

>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 = 76.9 bits (190), Expect = 3e-18
 Identities = 22/70 (31%), Positives = 42/70 (60%)

Query: 243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 302
           + TT E+ IP   +  + G   +N++ IRQ+SGA + + +P  G++   V ++G++  + 
Sbjct: 4   SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASIS 63

Query: 303 AAQSLIHAFI 312
            AQ LI+A +
Sbjct: 64  LAQYLINARL 73

>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 = 58.4 bits (142), Expect = 1e-11
 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 5/79 (6%)

Query: 24  PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI 83
            G      L + +  IGC++GR G  ++E+R+ +GA I++     A          V + 
Sbjct: 2   LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKI-----ANPVEGSSGRQVTIT 56

Query: 84  GNYHSVQDALFHITSRLRE 102
           G+  S+  A + I +RL  
Sbjct: 57  GSAASISLAQYLINARLSS 75

>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 = 75.4 bits (186), Expect = 1e-17
 Identities = 19/69 (27%), Positives = 39/69 (56%)

Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 303
             T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ 
Sbjct: 6   IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQN 65

Query: 304 AQSLIHAFI 312
           AQ L+   +
Sbjct: 66  AQYLLQNSV 74

>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 = 58.8 bits (143), Expect = 1e-11
 Identities = 15/79 (18%), Positives = 38/79 (48%), Gaps = 5/79 (6%)

Query: 24  PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI 83
            G  +  ++ +     G ++G+GG  + ++R  +GASI++             D I+ + 
Sbjct: 3   MGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-----DEPLEGSEDRIITIT 57

Query: 84  GNYHSVQDALFHITSRLRE 102
           G    +Q+A + + + +++
Sbjct: 58  GTQDQIQNAQYLLQNSVKQ 76

>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 = 75.7 bits (186), Expect = 1e-16
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 21  GFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIV 80
              P +A   +++V +   G ++G+GG  V  +   +GA +++    Q P   +  + +V
Sbjct: 97  TVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQL---SQKPDGINLQNRVV 153

Query: 81  QVIGNYHSVQDALFHITSRLRE 102
            V G     + A+  I  +++E
Sbjct: 154 TVSGEPEQNRKAVELIIQKIQE 175

>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 = 62.2 bits (151), Expect = 8e-12
 Identities = 18/108 (16%), Positives = 45/108 (41%), Gaps = 2/108 (1%)

Query: 24  PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI 83
            G     ++L+ S   G ++G+GG  + ++++ TGA+I++  K +    G+  + +  + 
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKL-SKSKDFYPGTT-ERVCLIQ 59

Query: 84  GNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFR 131
           G   ++      I  ++RE    + +  P +                +
Sbjct: 60  GTIEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVK 107

>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 = 49.1 bits (117), Expect = 2e-07
 Identities = 19/93 (20%), Positives = 35/93 (37%), Gaps = 2/93 (2%)

Query: 218 RGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGAN 277
           R    +   T     ++         +  +++++P      + G+  + +  I + SGA 
Sbjct: 77  REMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAW 136

Query: 278 VVV--NDPKPGATEGVVMVSGTSDQMRAAQSLI 308
           V +            VV VSG  +Q R A  LI
Sbjct: 137 VQLSQKPDGINLQNRVVTVSGEPEQNRKAVELI 169

>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 = 47.9 bits (114), Expect = 6e-07
 Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 3/72 (4%)

Query: 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV---NDPKPGATEGVVMVSGTSDQM 301
             ++V+IP      + G+    +  +++ +GA + +    D  PG TE V ++ GT + +
Sbjct: 6   YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEAL 65

Query: 302 RAAQSLIHAFIL 313
            A    I   I 
Sbjct: 66  NAVHGFIAEKIR 77

>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 = 72.4 bits (178), Expect = 2e-16
 Identities = 19/69 (27%), Positives = 39/69 (56%)

Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 303
             T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ 
Sbjct: 13  IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQN 72

Query: 304 AQSLIHAFI 312
           AQ L+   +
Sbjct: 73  AQYLLQNSV 81

>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 = 58.9 bits (143), Expect = 1e-11
 Identities = 16/85 (18%), Positives = 39/85 (45%), Gaps = 5/85 (5%)

Query: 18  AEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHD 77
              G   G  +  ++ +     G ++G+GG  + ++R  +GASI++             D
Sbjct: 4   MSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-----DEPLEGSED 58

Query: 78  EIVQVIGNYHSVQDALFHITSRLRE 102
            I+ + G    +Q+A + + + +++
Sbjct: 59  RIITITGTQDQIQNAQYLLQNSVKQ 83

>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 = 68.8 bits (169), Expect = 2e-15
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 7/75 (9%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
           +  RLL+H +++G ++G+ G  V +MR  +GA I +         G+  + I+ + G  +
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE-------GNCPERIITLAGPTN 57

Query: 88  SVQDALFHITSRLRE 102
           ++  A   I  +L E
Sbjct: 58  AIFKAFAMIIDKLEE 72

>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 = 46.5 bits (111), Expect = 2e-07
 Identities = 11/65 (16%), Positives = 34/65 (52%), Gaps = 2/65 (3%)

Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 303
           + TI +++    +  + G+   ++  +R+ SGA + +   +    E ++ ++G ++ +  
Sbjct: 4   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLAGPTNAIFK 61

Query: 304 AQSLI 308
           A ++I
Sbjct: 62  AFAMI 66

>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 = 71.4 bits (175), Expect = 4e-15
 Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 2/98 (2%)

Query: 3   HSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIR 62
             P      R   +       PG       +V + + G ++G+GG  +  + + +GA I 
Sbjct: 79  GGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIE 138

Query: 63  VFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL 100
           +      P    P+ ++  + G    +  A   I  ++
Sbjct: 139 LQR--NPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 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 = 57.6 bits (139), Expect = 3e-10
 Identities = 21/105 (20%), Positives = 37/105 (35%), Gaps = 6/105 (5%)

Query: 25  GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 84
           G  ++  + +    +G ++GR G ++ +++   G  I+  P D     G+  + I Q+ G
Sbjct: 1   GSHMI-DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-----GTTPERIAQITG 54

Query: 85  NYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPP 129
                Q A   IT  LR             G             P
Sbjct: 55  PPDRAQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGP 99

>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 = 54.1 bits (130), Expect = 5e-09
 Identities = 19/100 (19%), Positives = 31/100 (31%), Gaps = 3/100 (3%)

Query: 216 DPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISG 275
                    G   R R   + N            ++P      + G+    +  I Q SG
Sbjct: 75  AGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSG 134

Query: 276 ANVVVN---DPKPGATEGVVMVSGTSDQMRAAQSLIHAFI 312
           A + +     P       +  + GT  Q+  A+ LI   I
Sbjct: 135 ARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 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 = 51.4 bits (123), Expect = 4e-08
 Identities = 15/69 (21%), Positives = 29/69 (42%)

Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 303
           S  I+V IP+  +  V G N   +  I+  +G  +          E +  ++G  D+ + 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 304 AQSLIHAFI 312
           A  +I   +
Sbjct: 62  AAEIITDLL 70

>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 = 68.5 bits (168), Expect = 4e-15
 Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV---NDPKPGATEGVVMVSGTSDQ 300
              +E+ +P+  +  + G+    L   ++++GA + +    +  PG     V ++G+   
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

Query: 301 MRAAQSLIHAFI 312
            +AAQ LI   +
Sbjct: 62  TQAAQYLISQRV 73

>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 = 62.7 bits (153), Expect = 4e-13
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 31  RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQ 90
            + V    +G +LG+GG  + E +  TGA I++  K      G+  +  V + G+  + Q
Sbjct: 6   EMAVPENLVGAILGKGGKTLVEYQELTGARIQI-SKKGEFLPGTR-NRRVTITGSPAATQ 63

Query: 91  DALFHITSRLRE 102
            A + I+ R+  
Sbjct: 64  AAQYLISQRVTY 75

>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 = 68.1 bits (167), Expect = 7e-15
 Identities = 15/72 (20%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN---DPKPGATEGVVMVSGTSDQ 300
              +E+ +P+  +  + G+    L   ++++GA + ++   +  PG     V ++G+   
Sbjct: 2   KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

Query: 301 MRAAQSLIHAFI 312
            +AAQ LI   +
Sbjct: 62  TQAAQYLISQRV 73

>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 = 57.3 bits (139), Expect = 5e-11
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 31  RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQ 90
            + V    +G +LG+GG  + E +  TGA I++  K      G+  +  V + G+  + Q
Sbjct: 6   EIAVPENLVGAILGKGGKTLVEYQELTGARIQI-SKKGEFLPGTR-NRRVTITGSPAATQ 63

Query: 91  DALFHITSRLRE 102
            A + I+ R+  
Sbjct: 64  AAQYLISQRVTY 75

>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 = 65.9 bits (161), Expect = 4e-14
 Identities = 18/78 (23%), Positives = 35/78 (44%)

Query: 235 SGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMV 294
           S  H    +  T E  +P   +  + G     +S I+Q SG  + +     G  E   M+
Sbjct: 5   SSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCML 64

Query: 295 SGTSDQMRAAQSLIHAFI 312
           +GT + +++A+ L+   +
Sbjct: 65  TGTPESVQSAKRLLDQIV 82

>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 = 49.7 bits (119), Expect = 2e-08
 Identities = 21/93 (22%), Positives = 40/93 (43%), Gaps = 10/93 (10%)

Query: 23  EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQV 82
           +    +     V    +G ++GRGG  +S +++ +G  I++     AP  G   +    +
Sbjct: 10  QQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQI-----APDSGGLPERSCML 64

Query: 83  IGNYHSVQDALFHITSRLRETIFPMKRPGPNNG 115
            G   SVQ A   +   + +      R GP++G
Sbjct: 65  TGTPESVQSAKRLLDQIVEK-----GRSGPSSG 92

>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 = 67.1 bits (164), Expect = 8e-14
 Identities = 17/105 (16%), Positives = 37/105 (35%), Gaps = 11/105 (10%)

Query: 4   SPAQDAVMRVHSRI------AEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRAT 57
             A + VM +              +         + V    +G ++GR G ++ +++   
Sbjct: 61  QQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDA 120

Query: 58  GASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 102
           G  I+    D     G+  ++I  ++G     + A   I   L+ 
Sbjct: 121 GVRIQFKQDD-----GTGPEKIAHIMGPPDRCEHAARIINDLLQS 160

>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 = 56.7 bits (137), Expect = 4e-10
 Identities = 13/83 (15%), Positives = 28/83 (33%)

Query: 230 NRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATE 289
                  N         I+V +P+  +  V G +   +  I+  +G  +          E
Sbjct: 76  QGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE 135

Query: 290 GVVMVSGTSDQMRAAQSLIHAFI 312
            +  + G  D+   A  +I+  +
Sbjct: 136 KIAHIMGPPDRCEHAARIINDLL 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 = 55.9 bits (135), Expect = 8e-10
 Identities = 16/89 (17%), Positives = 37/89 (41%), Gaps = 3/89 (3%)

Query: 27  AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNY 86
             V  +++ + + G ++G+GG  + +++   G  + +             D+ +++IG+ 
Sbjct: 1   GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNV---DKPLRIIGDP 57

Query: 87  HSVQDALFHITSRLRETIFPMKRPGPNNG 115
           + VQ A   +   LRE            G
Sbjct: 58  YKVQQACEMVMDILRERDQGGFGDRNEYG 86

>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 = 47.5 bits (113), Expect = 7e-07
 Identities = 9/72 (12%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV--NDPKPGATEGVVMVSGTSDQMR 302
           T  E++IP      V G+    +  +++ +G  +++  +  +    +  + + G   +++
Sbjct: 2   TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQ 61

Query: 303 AAQSLIHAFILC 314
            A  ++   +  
Sbjct: 62  QACEMVMDILRE 73

>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 = 57.0 bits (138), Expect = 8e-11
 Identities = 13/80 (16%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 235 SGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV--NDPKPGATEGVV 292
           S  H     +   E++IP      V G+    +  +++ +G  +V+  + P+    +  +
Sbjct: 5   SSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPL 64

Query: 293 MVSGTSDQMRAAQSLIHAFI 312
            ++G   +++ A+ ++   I
Sbjct: 65  RITGDPYKVQQAKEMVLELI 84

>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 = 48.6 bits (116), Expect = 7e-08
 Identities = 16/88 (18%), Positives = 43/88 (48%), Gaps = 8/88 (9%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
            V  +++ + + G ++G+GG  + +++   G  + +    Q     +  D+ +++ G+ +
Sbjct: 15  AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVM---IQDGPQNTGADKPLRITGDPY 71

Query: 88  SVQDALFHITSRLRETIFPMKRPGPNNG 115
            VQ A   +   +R+     +  GP++G
Sbjct: 72  KVQQAKEMVLELIRD-----QGSGPSSG 94

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

 Score = 54.0 bits (130), Expect = 1e-09
 Identities = 12/70 (17%), Positives = 27/70 (38%)

Query: 243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 302
               I+V +P+  +  V G +   +  I+  +G  +          E +  + G  D+  
Sbjct: 9   IGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCE 68

Query: 303 AAQSLIHAFI 312
            A  +I+  +
Sbjct: 69  HAARIINDLL 78

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

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 8/97 (8%)

Query: 31  RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQ 90
            + V    +G ++GR G ++ +++   G  I+    D     G+  ++I  ++G     +
Sbjct: 14  DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-----GTGPEKIAHIMGPPDRCE 68

Query: 91  DALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPP 127
            A   I   L+        P    G   +PP      
Sbjct: 69  HAARIINDLLQS---LRSGPPGPPGGPGMPPGGRGRG 102

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

 Score = 53.7 bits (129), Expect = 1e-09
 Identities = 24/105 (22%), Positives = 43/105 (40%), Gaps = 3/105 (2%)

Query: 24  PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI 83
                     + + + G ++GRGG  V  + + TGA + +    Q P  G P+ ++  + 
Sbjct: 3   MAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEI--SRQLPPNGDPNFKLFIIR 60

Query: 84  GNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPP 128
           G+   +  A   I  ++   + P+  PGP       P  P  P P
Sbjct: 61  GSPQQIDHAKQLIEEKIEGPLCPVG-PGPGGPGPAGPMGPFNPGP 104

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

 Score = 46.0 bits (109), Expect = 8e-07
 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 3/77 (3%)

Query: 239 AAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN---DPKPGATEGVVMVS 295
            A+     +   IP      V G    N+  I Q +GA V ++    P       + ++ 
Sbjct: 1   GAMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR 60

Query: 296 GTSDQMRAAQSLIHAFI 312
           G+  Q+  A+ LI   I
Sbjct: 61  GSPQQIDHAKQLIEEKI 77

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

 Score = 52.7 bits (127), Expect = 2e-09
 Identities = 15/78 (19%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 25  GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 84
               V  +++ + + G ++G+GG  + +++   G  + +          +  D+ +++IG
Sbjct: 11  QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDKPLRIIG 67

Query: 85  NYHSVQDALFHITSRLRE 102
           + + VQ A   +   LRE
Sbjct: 68  DPYKVQQACEMVMDILRE 85

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

 Score = 52.7 bits (127), Expect = 2e-09
 Identities = 9/71 (12%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV--NDPKPGATEGVVMVSGTSDQM 301
            T  E++IP      V G+    +  +++ +G  +++  +  +    +  + + G   ++
Sbjct: 13  GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKV 72

Query: 302 RAAQSLIHAFI 312
           + A  ++   +
Sbjct: 73  QQACEMVMDIL 83

>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 = 51.4 bits (123), Expect = 1e-08
 Identities = 19/100 (19%), Positives = 37/100 (37%), Gaps = 6/100 (6%)

Query: 22  FEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQ 81
                 V  +L V  + +G ++GRGG  +  + +A+GA I     D+          +++
Sbjct: 9   LTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITC---DKESEGTLLLSRLIK 65

Query: 82  VIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPP 121
           + G    V  A   I  ++ E     +        +  P 
Sbjct: 66  ISGTQKEVAAAKHLILEKVSE---DEELRKRIAHSASGPS 102

>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 = 48.7 bits (116), Expect = 1e-07
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPG--ATEGVVMVSGTSDQ 300
           T    ++ +PQ  +  + G     +  I + SGA +  +    G      ++ +SGT  +
Sbjct: 13  TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE 72

Query: 301 MRAAQSLIHAFI 312
           + AA+ LI   +
Sbjct: 73  VAAAKHLILEKV 84

>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 = 47.0 bits (112), Expect = 2e-07
 Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 302
           T  +  V IP+ +   V G+N   L  +   +   + +  P+P      + ++GT + + 
Sbjct: 15  TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSNQIKITGTKEGIE 72

Query: 303 AAQSLIHAFI 312
            A+  +    
Sbjct: 73  KARHEVLLIS 82

>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 = 44.7 bits (106), Expect = 2e-06
 Identities = 17/98 (17%), Positives = 37/98 (37%), Gaps = 10/98 (10%)

Query: 18  AEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHD 77
            +I         A + +  +    ++G+ G  + ++   T   I++      PR   P  
Sbjct: 7   GDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI------PRPDDP-S 59

Query: 78  EIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNG 115
             +++ G    ++ A   +     E     KR GP++G
Sbjct: 60  NQIKITGTKEGIEKARHEVLLISAEQ---DKRSGPSSG 94

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

 Score = 42.0 bits (99), Expect = 8e-06
 Identities = 10/68 (14%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 304
             +E+ I   +  H+ G++ +N++ I+     +V +  P       ++ + G    ++ A
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI--PPDSEKSNLIRIEGDPQGVQQA 62

Query: 305 QSLIHAFI 312
           +  +    
Sbjct: 63  KRELLELA 70

>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 = 42.1 bits (99), Expect = 2e-05
 Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 242 LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQM 301
           L   TIEV +P     +V G+  S +  +      N+ V  P P     ++ ++G +  +
Sbjct: 14  LVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAITGLAANL 71

Query: 302 RAAQSLIHAFI 312
             A++ +   +
Sbjct: 72  DRAKAGLLERV 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 = 41.7 bits (98), Expect = 2e-05
 Identities = 20/110 (18%), Positives = 44/110 (40%), Gaps = 16/110 (14%)

Query: 6   AQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFP 65
           +  +  R+   + ++       V   + +  +    ++G  G  + ++       IR   
Sbjct: 2   SSGSSGRIVGELEQM-------VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-- 52

Query: 66  KDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNG 115
               P+ G+P    V V G   +V++A+ HI +   E    +   GP++G
Sbjct: 53  ----PQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY---LADSGPSSG 95

>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 = 40.7 bits (95), Expect = 4e-05
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 236 GNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVS 295
           G+  +    TTI+V +P   +  V G   + +  I+Q +   +V         E V  V+
Sbjct: 1   GSSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD---KEPVFAVT 57

Query: 296 GTSDQMRAAQSLIHAFI 312
           G  + +  A+  I 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 = 39.0 bits (91), Expect = 2e-04
 Identities = 17/98 (17%), Positives = 40/98 (40%), Gaps = 7/98 (7%)

Query: 18  AEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHD 77
            E      ++    + V  +    ++GR G +++++R     +I+   KD     G+   
Sbjct: 7   GEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD----GNQPQ 62

Query: 78  EIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNG 115
           + + + G   + + A   I   + E     +  GP++G
Sbjct: 63  DQITITGYEKNTEAARDAILRIVGE---LEQMSGPSSG 97

>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 = 38.7 bits (90), Expect = 3e-04
 Identities = 13/73 (17%), Positives = 26/73 (35%), Gaps = 1/73 (1%)

Query: 241 ILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSD 299
            L S  + V +   Y   + G   + ++ IR     N+   D       +  + ++G   
Sbjct: 13  ALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK 72

Query: 300 QMRAAQSLIHAFI 312
              AA+  I   +
Sbjct: 73  NTEAARDAILRIV 85

>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 = 40.0 bits (93), Expect = 2e-04
 Identities = 9/76 (11%), Positives = 25/76 (32%), Gaps = 1/76 (1%)

Query: 18  AEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHD 77
            +      +     + V    +G ++G+ G ++ E+   +G        +          
Sbjct: 57  VKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEG 116

Query: 78  EI-VQVIGNYHSVQDA 92
            +    +G   S+ +A
Sbjct: 117 MVPFVFVGTKDSIANA 132

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 40.8 bits (95), Expect = 5e-04
 Identities = 32/141 (22%), Positives = 44/141 (31%), Gaps = 13/141 (9%)

Query: 110  PGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYP-----SPVGPFHS-MDRGMGPSQPFD 163
             G  +      PF      P  P    +SPG  P     SP  P +S       P+ P  
Sbjct: 1511 YGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSP-- 1568

Query: 164  HQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDAS 223
              +  S    P  P  S   P  Y    P + PT    PS    +P       P     S
Sbjct: 1569 SYSPTSPSYSPTSPSYSPTSP-SYSPTSPSYSPT---SPSYSPTSP-SYSPTSPSYSPTS 1623

Query: 224  SGFTPRNRPVESGNHAAILTS 244
              ++P +      + +   TS
Sbjct: 1624 PSYSPTSPSYSPTSPSYSPTS 1644

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	318
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.96
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.96
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.96
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.96
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.96
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.86
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.77
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.75
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.73
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.73
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.72
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.7
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.7
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.69
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.68
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.68
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.68
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.64
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.64
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.64
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.64
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.63
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.63
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.62
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.61
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.61
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.61
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.6
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.6
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.58
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.58
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.57
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.57
1we8_A	104	Tudor and KH domain containing protein; structural	99.57
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.56
1we8_A	104	Tudor and KH domain containing protein; structural	99.54
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.54
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.51
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.51
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.5
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.5
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.5
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.49
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.47
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.46
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.46
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.45
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.44
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.42
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.4
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.37
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.34
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.29
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.27
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.25
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.25
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.2
2cpq_A	91	FragIle X mental retardation syndrome related prot	99.1
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.96
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	98.94
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.88
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.82
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.81
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.72
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.57
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.54
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.4
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.39
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.38
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	98.34
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.08
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.98
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.86
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.82
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.33
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	96.44
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.18
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.14
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	95.37
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.09
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	93.8
2cxc_A	144	NUSA; transcription termination, RNA binding prote	91.3
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	87.97
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	86.73
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	85.43
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	84.59
1wh9_A	92	40S ribosomal protein S3; KH domain, structural ge	83.15
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	80.3

>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=99.96  E-value=3.5e-29  Score=211.31  Aligned_cols=159  Identities=19%  Similarity=0.354  Sum_probs=129.9

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcCCC
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPM  107 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~~  107 (318)
                      ++.+|+||.+++|.||||+|++||+|+++|||+|+|.+...   ++...||+|+|+|++++|.+|+.+|.+++.+.... 
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~---~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~~-   77 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS---QNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQG-   77 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTT---SSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSSSC-
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCC---CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhccCC-
Confidence            57899999999999999999999999999999999964321   23467899999999999999999999988764100 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCC
Q 021032          108 KRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPY  187 (318)
Q Consensus       108 ~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~  187 (318)
                                   .|                    .       ..                           .     .|
T Consensus        78 -------------~~--------------------~-------~~---------------------------~-----~~   85 (164)
T 2jvz_A           78 -------------GF--------------------G-------DR---------------------------N-----EY   85 (164)
T ss_dssp             -------------CC--------------------S-------SC---------------------------S-----SC
T ss_pred             -------------CC--------------------C-------Cc---------------------------c-----cc
Confidence                         00                    0       00                           0     00


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccccccccccccchH
Q 021032          188 GSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNL  267 (318)
Q Consensus       188 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~I  267 (318)
                      +                                                    .....+.+|.||.+++|+||||+|++|
T Consensus        86 ~----------------------------------------------------~~~~~~~~i~vp~~~~g~iIGk~G~~I  113 (164)
T 2jvz_A           86 G----------------------------------------------------SRIGGGIDVPVPRHSVGVVIGRSGEMI  113 (164)
T ss_dssp             T----------------------------------------------------TSCSSSBCCEEETTTHHHHHCSSSHHH
T ss_pred             C----------------------------------------------------CCCCceEEEEEChhhccccCCCCcHhH
Confidence            0                                                    000124677899999999999999999


Q ss_pred             HHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          268 SHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       268 k~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ++|++.|||+|+|.+..+.+.+|.|+|+|++++++.|+.+|.+++.+
T Consensus       114 ~~i~~~tg~~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~  160 (164)
T 2jvz_A          114 KKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQS  160 (164)
T ss_dssp             HHHHHHTCCEEEECCCCTTSSEEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCeEEEeCCCCCCCcEEEEEEcCHHHHHHHHHHHHHHHhh
Confidence            99999999999998877677799999999999999999999999875

>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=99.96  E-value=8.2e-29  Score=209.00  Aligned_cols=154  Identities=19%  Similarity=0.323  Sum_probs=129.8

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcCC
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFP  106 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~  106 (318)
                      +-+++|+||.+.+|.||||+|++||+|+++|||+|+|.+.    .++.+.+|+|+|+|+++++.+|..+|.+++.+....
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~----~~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~~   77 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPP----ETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFF   77 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCC----SSTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTSS
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCC----CCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccccc
Confidence            4589999999999999999999999999999999999753    234578999999999999999999999999875100


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCC
Q 021032          107 MKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFP  186 (318)
Q Consensus       107 ~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~  186 (318)
                                                           .|      .                                  
T Consensus        78 -------------------------------------~~------~----------------------------------   80 (163)
T 3krm_A           78 -------------------------------------GP------K----------------------------------   80 (163)
T ss_dssp             -------------------------------------CS------S----------------------------------
T ss_pred             -------------------------------------cc------c----------------------------------
Confidence                                                 00      0                                  


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccccccccccccch
Q 021032          187 YGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSN  266 (318)
Q Consensus       187 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~  266 (318)
                                                                            .....+.++.||.+++|+||||+|++
T Consensus        81 ------------------------------------------------------~~~~~~~~i~vp~~~~g~iIGkgG~~  106 (163)
T 3krm_A           81 ------------------------------------------------------EEVKLETHIRVPASAAGRVIGKGGKT  106 (163)
T ss_dssp             ------------------------------------------------------CCCCEEEEEEEETTTHHHHHCGGGHH
T ss_pred             ------------------------------------------------------cCCceEEEEEcChhheeeEEcCCChH
Confidence                                                                  00125679999999999999999999


Q ss_pred             HHHHHHHhCCEEEEcCCC-CCCC-CeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          267 LSHIRQISGANVVVNDPK-PGAT-EGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       267 Ik~Ir~~SGA~I~i~~~~-~~~~-er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      |++|++.|||+|+|.+.. ++++ ++.|+|+|++++++.|+.+|.++|.+-
T Consensus       107 I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~  157 (163)
T 3krm_A          107 VNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQV  157 (163)
T ss_dssp             HHHHHHHHCCEEECCTTCCCCTTSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCeEEECCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            999999999999997642 3444 458999999999999999999999863

>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=99.96  E-value=6.6e-29  Score=212.57  Aligned_cols=172  Identities=22%  Similarity=0.357  Sum_probs=133.4

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhc
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETI  104 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~  104 (318)
                      ...++++|+||.+++|.||||+|++||+|+++|||+|+|.+..+  ..+.+.+|+|+|+|..++|.+|..+|.+++.+..
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~--~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~   80 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKD--FYPGTTERVCLIQGTIEALNAVHGFIAEKIREMP   80 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTC--BCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCC
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCC--CCCCCCCceEEEEeCHHHHHHHHHHHHHHHhccC
Confidence            45789999999999999999999999999999999999975422  1234679999999999999999999999987751


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCC
Q 021032          105 FPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIP  184 (318)
Q Consensus       105 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  184 (318)
                      ...   .                              ...+..                           +.+       
T Consensus        81 ~~~---~------------------------------~~~~~~---------------------------~~~-------   93 (178)
T 2anr_A           81 QNV---A------------------------------KTEPVS---------------------------ILQ-------   93 (178)
T ss_dssp             CC------------------------------------------------------------------------------
T ss_pred             Ccc---c------------------------------cCCccc---------------------------ccC-------
Confidence            100   0                              000000                           000       


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccccccccccccc
Q 021032          185 FPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENN  264 (318)
Q Consensus       185 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G  264 (318)
                                              ++.       +      .             ......+.++.||.+++|+||||+|
T Consensus        94 ------------------------~~~-------~------~-------------~~~~~~~~~i~Vp~~~vg~iIGkgG  123 (178)
T 2anr_A           94 ------------------------PQT-------T------V-------------NPDRANQVKIIVPNSTAGLIIGKGG  123 (178)
T ss_dssp             --------------------------------------------------------CGGGGEEEEEEEHHHHHHHHCGGG
T ss_pred             ------------------------Ccc-------C------C-------------CCCCceEEEEEEchhheeeeECCCc
Confidence                                    000       0      0             0012367899999999999999999


Q ss_pred             chHHHHHHHhCCEEEEcCCC--CCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          265 SNLSHIRQISGANVVVNDPK--PGATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       265 ~~Ik~Ir~~SGA~I~i~~~~--~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      ++|++|++.|||+|+|.+..  +.+.+|.|+|+|+++++++|+.+|.++|.+.
T Consensus       124 ~~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~  176 (178)
T 2anr_A          124 ATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED  176 (178)
T ss_dssp             HHHHHHHHHSSCEEEECCCC----CCEEEEEEESSHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhC
Confidence            99999999999999998653  3567899999999999999999999999875

>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=99.96  E-value=1.4e-28  Score=206.92  Aligned_cols=157  Identities=24%  Similarity=0.412  Sum_probs=132.8

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhc
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETI  104 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~  104 (318)
                      +.+++++|+||.+.+|.||||||++||+|+++|||+|+|...       .+.+|.|+|+|+.++|.+|+.+|.+++.+.+
T Consensus         2 ~~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~-------~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   74 (160)
T 2jzx_A            2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEEDI   74 (160)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC-------TTTEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC-------CCCceEEEEEeCHHHHHHHHHHHHHHHHhhc
Confidence            467899999999999999999999999999999999999743       2468999999999999999999999998863


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCC
Q 021032          105 FPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIP  184 (318)
Q Consensus       105 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  184 (318)
                      ...                         .     .+.+.                                         
T Consensus        75 ~~~-------------------------~-----~~~~~-----------------------------------------   83 (160)
T 2jzx_A           75 SSS-------------------------M-----TNSTA-----------------------------------------   83 (160)
T ss_dssp             TSC-------------------------C-----CSSSC-----------------------------------------
T ss_pred             ccc-------------------------C-----CCCcc-----------------------------------------
Confidence            100                         0     00000                                         


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccccccccccccc
Q 021032          185 FPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENN  264 (318)
Q Consensus       185 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G  264 (318)
                                                                             ......+.++.||.+++|+||||+|
T Consensus        84 -------------------------------------------------------~~~~~~~~~i~vp~~~~g~iIGkgG  108 (160)
T 2jzx_A           84 -------------------------------------------------------ASRPPVTLRLVVPASQCGSLIGKGG  108 (160)
T ss_dssp             -------------------------------------------------------CCCCSEEEEEEEEHHHHHHHHCGGG
T ss_pred             -------------------------------------------------------CCCCCEEEEEEEChhheeeEECCCC
Confidence                                                                   0001368999999999999999999


Q ss_pred             chHHHHHHHhCCEEEEcC-CCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          265 SNLSHIRQISGANVVVND-PKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       265 ~~Ik~Ir~~SGA~I~i~~-~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ++|++|++.|||+|+|.+ ..++++++.|+|+|++++++.|+.+|.+++.+
T Consensus       109 ~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          109 CKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             HHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCeEEECCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            999999999999999975 34677899999999999999999999999875

>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=99.96  E-value=2.6e-28  Score=208.20  Aligned_cols=170  Identities=22%  Similarity=0.351  Sum_probs=127.7

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcCC
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFP  106 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~  106 (318)
                      ..+++|+||.+++|.||||+|++||+|+++|||+|+|.+.+     ....||+|+|+|+.++|.+|+.+|.+++++..  
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~-----~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~--   74 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-----GTTPERIAQITGPPDRAQHAAEIITDLLRSVQ--   74 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT-----TSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC--
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCC-----CCCCccEEEEEeCHHHHHHHHHHHHHHHHhcc--
Confidence            46799999999999999999999999999999999996431     23678999999999999999999999998861  


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCC
Q 021032          107 MKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFP  186 (318)
Q Consensus       107 ~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~  186 (318)
                      ..                    .|.      .    +.|.+.                      ++.             
T Consensus        75 ~~--------------------~~~------~----~~p~~~----------------------~~~-------------   89 (174)
T 1j4w_A           75 AG--------------------NPG------G----PGPGGR----------------------GRG-------------   89 (174)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cC--------------------CCC------C----CCCCCC----------------------CCC-------------
Confidence            00                    000      0    000000                      000             


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccccccccccccch
Q 021032          187 YGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSN  266 (318)
Q Consensus       187 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~  266 (318)
                      ++.      ..|..                                      .......+.++.||.+++|+||||+|++
T Consensus        90 ~~~------~~~~~--------------------------------------~~~~~~~~~~i~vp~~~~g~iIGkgG~~  125 (174)
T 1j4w_A           90 RGQ------GNWNM--------------------------------------GPPGGLQEFNFIVPTGKTGLIIGKGGET  125 (174)
T ss_dssp             ----------------------------------------------------------CEEEEEEETTTHHHHHCGGGHH
T ss_pred             CCC------Ccccc--------------------------------------CCCCCcEEEEEEEChHHcCeeECCCchH
Confidence            000      00000                                      0001135789999999999999999999


Q ss_pred             HHHHHHHhCCEEEEcCCC---CCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 021032          267 LSHIRQISGANVVVNDPK---PGATEGVVMVSGTSDQMRAAQSLIHAFI  312 (318)
Q Consensus       267 Ik~Ir~~SGA~I~i~~~~---~~~~er~v~I~Gt~~~v~~A~~lI~~~i  312 (318)
                      |++|++.|||+|+|.+..   +++.+|.|+|+|++++++.|+.||+++|
T Consensus       126 Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          126 IKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             HHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            999999999999998653   3477899999999999999999999874

>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=99.86  E-value=1.8e-21  Score=160.53  Aligned_cols=68  Identities=21%  Similarity=0.282  Sum_probs=59.1

Q ss_pred             EEEEecccccccccccccchHHHHHHHhCC-EEEEcCCCCC---CCC--eEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          247 IEVVIPQLYMAHVYGENNSNLSHIRQISGA-NVVVNDPKPG---ATE--GVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA-~I~i~~~~~~---~~e--r~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      .+|.||.+.+|++|||+|.+|+.|++.||| +|+|....+.   .++  +.|+|+|++++|+.|+.||.++|.+
T Consensus        69 ~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A           69 DVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             EEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred             EEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            778899999999999999999999999997 9999754321   233  3589999999999999999999975

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

Probab=99.77  E-value=2.2e-18  Score=151.07  Aligned_cols=67  Identities=16%  Similarity=0.133  Sum_probs=59.1

Q ss_pred             CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEec-----HHHHHHHHHHHHHHH
Q 021032           26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-----YHSVQDALFHITSRL  100 (318)
Q Consensus        26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~-----~~~V~~A~~~I~~~l  100 (318)
                      .+...++.||...+|.|||+||++|+.|+++|||+|+|..          .++.|+|.+.     ++++.+|...|..+.
T Consensus        32 aP~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~----------~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~  101 (219)
T 2e3u_A           32 FKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS----------ETGEVWITSTKETEDPLAVWKARDIVLAIG  101 (219)
T ss_dssp             -CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT----------TTCEEEEEECTTCCSHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc----------CCCEEEEecCCCCCCHHHHHHHHHHHHHHh
Confidence            4567899999999999999999999999999999999942          3688999986     699999999999988


Q ss_pred             Hh
Q 021032          101 RE  102 (318)
Q Consensus       101 ~e  102 (318)
                      +.
T Consensus       102 rg  103 (219)
T 2e3u_A          102 RG  103 (219)
T ss_dssp             TT
T ss_pred             cc
Confidence            54

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

Probab=99.75  E-value=1.2e-17  Score=156.17  Aligned_cols=76  Identities=16%  Similarity=0.195  Sum_probs=63.8

Q ss_pred             CCCeeEEEEEEecccceeeeCCCC--chHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHH
Q 021032           24 PGQAVVARLLVHSQQIGCLLGRGG--HIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSR   99 (318)
Q Consensus        24 ~~~~~~~rllVp~~~vG~IIGkgG--~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~   99 (318)
                      +.+.+|+++.||..+++.||||||  ++|++|+++|||+|++...+.-.....+....|+|+|.+++|++|...|.++
T Consensus        26 ~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l  103 (376)
T 3n89_A           26 NPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRN  103 (376)
T ss_dssp             CTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHS
T ss_pred             cCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhc
Confidence            578999999999999999999999  9999999999999999654300011124567899999999999999999874

>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=99.73  E-value=7.4e-18  Score=125.63  Aligned_cols=73  Identities=30%  Similarity=0.517  Sum_probs=67.7

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      ...+.+|.||.+++|+||||+|++|++|++.|||+|+|.++.+++.+|.|+|+|+++++++|+.||.+++.+.
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            3578999999999999999999999999999999999998778889999999999999999999999998775

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

Probab=99.73  E-value=7.8e-18  Score=123.67  Aligned_cols=72  Identities=28%  Similarity=0.511  Sum_probs=68.6

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      ..+.+|.||.+++|+||||+|++|++|++.|||+|+|.++.+++.+|.|+|+|++++++.|+.||.+++.++
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            578999999999999999999999999999999999998888889999999999999999999999999864

>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=99.72  E-value=1.9e-17  Score=123.39  Aligned_cols=72  Identities=26%  Similarity=0.507  Sum_probs=68.1

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|+++.+++.+|.|+|+|+++++++|+.||++++.+
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   76 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   76 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            358899999999999999999999999999999999999877788999999999999999999999999875

>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=99.70  E-value=5.1e-17  Score=139.07  Aligned_cols=138  Identities=17%  Similarity=0.196  Sum_probs=111.2

Q ss_pred             EEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEE-----ecHHHHHHHHHHHHHHHHhhc
Q 021032           30 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI-----GNYHSVQDALFHITSRLRETI  104 (318)
Q Consensus        30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~-----G~~~~V~~A~~~I~~~l~e~~  104 (318)
                      .+++||...+|.|||++|++++.|++++|++|++..          .++.|+|.     |++.++.+|...|....+.+-
T Consensus         6 ~~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            6 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT----------ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFP   75 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET----------TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCC
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc----------CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCC
Confidence            689999999999999999999999999999999963          47889999     999999999999999888751


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCC
Q 021032          105 FPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIP  184 (318)
Q Consensus       105 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  184 (318)
                      .++                                                           |    ..           
T Consensus        76 ~e~-----------------------------------------------------------A----~~-----------   81 (191)
T 1tua_A           76 PEK-----------------------------------------------------------A----FR-----------   81 (191)
T ss_dssp             HHH-----------------------------------------------------------H----GG-----------
T ss_pred             HHH-----------------------------------------------------------h----hh-----------
Confidence            100                                                           0    00           


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEE-EEec----------c
Q 021032          185 FPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIE-VVIP----------Q  253 (318)
Q Consensus       185 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~-v~IP----------~  253 (318)
                                                                      +       .......+ +.++          .
T Consensus        82 ------------------------------------------------L-------l~Dd~~~e~i~i~~~~~~~~~~~~  106 (191)
T 1tua_A           82 ------------------------------------------------L-------LEEDQILVVVDLKQVVGDSQNHLK  106 (191)
T ss_dssp             ------------------------------------------------G-------GSTTEEEEEEETHHHHTTCHHHHH
T ss_pred             ------------------------------------------------c-------ccCcceeEEEEcccccccCchhHH
Confidence                                                            0       00001111 1122          3


Q ss_pred             cccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHH
Q 021032          254 LYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFIL  313 (318)
Q Consensus       254 ~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~  313 (318)
                      ...|+||||+|.+|+.|++.|||+|.|.+       ++|.|.|++++++.|+.+|.++|.
T Consensus       107 r~~GrIIGk~G~tik~iE~~Tg~~I~v~~-------~~v~i~G~~~~i~~Ar~~i~~li~  159 (191)
T 1tua_A          107 RIKGRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGDYERAMAAKQAIEMLAE  159 (191)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHTCEEEECS-------SEEEEEEEHHHHHHHHHHHHHHHT
T ss_pred             HHhhheeCCCccHHHHHHHHHCceEEEcC-------CEEEEEeChHHHHHHHHHHHHHHc
Confidence            46899999999999999999999999953       489999999999999999999996

>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=99.70  E-value=2.2e-17  Score=120.25  Aligned_cols=72  Identities=26%  Similarity=0.515  Sum_probs=65.5

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      +.+++++|+||++++|.||||||++||+|+++|||+|+|.+.       ...+|+|+|.|++++|.+|+.+|.++|+++
T Consensus         2 ~~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~-------~~~er~v~I~G~~~~v~~A~~~I~~~l~ed   73 (73)
T 2axy_A            2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEED   73 (73)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-------CCSEEEEEEEECHHHHHHHHHHHHHHHHC-
T ss_pred             CceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-------CCCcEEEEEEeCHHHHHHHHHHHHHHHhcC
Confidence            457899999999999999999999999999999999999753       246999999999999999999999999873

>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=99.69  E-value=4.2e-17  Score=124.16  Aligned_cols=74  Identities=23%  Similarity=0.399  Sum_probs=69.7

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcCcC
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVT  317 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~~~  317 (318)
                      ..+.+|.||.+++|+||||+|++|++|+++|||+|+|.+..++..+|.|+|+|+++++++|+.||+++|.+.++
T Consensus        14 ~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~~   87 (92)
T 1x4n_A           14 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGRS   87 (92)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTC
T ss_pred             CEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhccc
Confidence            57899999999999999999999999999999999999877778899999999999999999999999998664

>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=99.68  E-value=6.7e-17  Score=118.63  Aligned_cols=71  Identities=21%  Similarity=0.438  Sum_probs=64.9

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCC---CCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP---KPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~---~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ..+.++.||.+++|+||||+|++|++|++.|||+|+|.+.   .+++.+|.|+|+|++++++.|+.+|.+++.+
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            3688999999999999999999999999999999999864   3577899999999999999999999998865

>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=99.68  E-value=5.4e-17  Score=122.81  Aligned_cols=72  Identities=26%  Similarity=0.507  Sum_probs=68.2

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|+++.+++.+|.|+|+|+++++++|+.+|++++.+
T Consensus        12 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e   83 (89)
T 1j5k_A           12 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   83 (89)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHHh
Confidence            368899999999999999999999999999999999999877788999999999999999999999999875

>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=99.68  E-value=8.7e-17  Score=117.07  Aligned_cols=70  Identities=16%  Similarity=0.321  Sum_probs=65.0

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      ..+.++.||.+.+|.||||+|++|++|++.|||+|+|++.  +..||.|+|+|+++++..|+.+|.++|.++
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l~ed   73 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEED   73 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHHHHHHHHHHHHHHHC-
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC--CCCcEEEEEEeCHHHHHHHHHHHHHHHhcC
Confidence            4789999999999999999999999999999999999865  568999999999999999999999999863

>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=99.64  E-value=2.5e-16  Score=118.66  Aligned_cols=70  Identities=21%  Similarity=0.451  Sum_probs=65.4

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCC---CCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP---KPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~---~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      .+.++.||.+++|+||||+|++|++|++.|||+|+|.+.   .+++.+|.|+|+|++++++.|+.||.+++.+
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~   75 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999874   3577899999999999999999999999876

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

Probab=99.64  E-value=2e-16  Score=116.04  Aligned_cols=74  Identities=28%  Similarity=0.505  Sum_probs=66.2

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ...++++|+||.+++|.||||||++||+|+++|||+|+|.+     .++.+.+|.|+|+|++++|.+|..+|.+++.+.
T Consensus         2 ~~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~-----~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            2 AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIAN-----PVEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             -CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECC-----CCTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             CCceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcC-----CCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            35688999999999999999999999999999999999964     234578999999999999999999999998763

>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=99.64  E-value=4.1e-16  Score=114.42  Aligned_cols=74  Identities=24%  Similarity=0.408  Sum_probs=64.3

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHh
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  102 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e  102 (318)
                      ..+++|+||.+.+|.||||||++||+|+++|||+|+|.+.++  .++++.+|.|+|+|++++|.+|..+|.+++.+
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~--~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGE--FLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTC--CSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCC--CCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            367899999999999999999999999999999999975422  22346789999999999999999999988754

>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=99.64  E-value=7.2e-16  Score=114.77  Aligned_cols=74  Identities=20%  Similarity=0.517  Sum_probs=66.9

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ...++++|+||.+++|.||||+|++||+|+++|||+|+|.+.     ++.+.+|.|+|+|++++|.+|..+|.+++.+.
T Consensus         4 g~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~-----~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            4 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT-----TSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC-----CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            457899999999999999999999999999999999999632     23467899999999999999999999999886

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

Probab=99.63  E-value=4.1e-16  Score=121.53  Aligned_cols=71  Identities=17%  Similarity=0.309  Sum_probs=65.8

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      .+.+|.||.+++|+||||+|++||+|+++|||+|+|.+..+.+.||.|+|+|+++++++|+.||++++.+.
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            46899999999999999999999999999999999987666778999999999999999999999999763

>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=99.63  E-value=3.4e-16  Score=116.58  Aligned_cols=74  Identities=27%  Similarity=0.508  Sum_probs=65.6

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ...++++|+||.+++|.||||||++||+|+++|||+|+|.+.     ++.+.+|.|+|+|++++|.+|+.+|.+++.+.
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~-----~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-----VEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC-----CTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC-----CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            457899999999999999999999999999999999999642     24468999999999999999999999998775

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

Probab=99.62  E-value=6.7e-16  Score=120.72  Aligned_cols=71  Identities=23%  Similarity=0.276  Sum_probs=64.7

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCC---CCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPK---PGATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~---~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|.+..   .+..+|.|+|+|+++++++|+.||+++|.+.
T Consensus         7 ~~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            7 GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CCEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             CeEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            3789999999999999999999999999999999998753   3457899999999999999999999998764

>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=99.61  E-value=9.7e-16  Score=117.03  Aligned_cols=73  Identities=15%  Similarity=0.328  Sum_probs=66.7

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCC--CCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP--GATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~--~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|.+..+  ...+|.|+|+|++++++.|+.||++++.+.
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           13 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            4689999999999999999999999999999999999987533  457999999999999999999999999763

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

Probab=99.61  E-value=2.4e-15  Score=112.72  Aligned_cols=71  Identities=13%  Similarity=0.254  Sum_probs=64.7

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCC--CCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPK--PGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~--~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ..+.+|.||.+++|+||||+|++|++|++.|||+|+|.+..  +.+.||.|+|+|++++++.|+.+|.+++.+
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            46789999999999999999999999999999999998753  357899999999999999999999998853

>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=99.61  E-value=7.3e-16  Score=114.71  Aligned_cols=69  Identities=26%  Similarity=0.348  Sum_probs=62.6

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ...+.+|.||.+++|.||||+|++||+|+++|||+|+|....   +++.|+|+|+++++++|+++|.+++..
T Consensus         8 ~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~---~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            8 GQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD---KEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS---SCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC---CCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            457899999999999999999999999999999999997532   368999999999999999999998764

>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=99.60  E-value=1.2e-15  Score=115.31  Aligned_cols=75  Identities=20%  Similarity=0.503  Sum_probs=67.8

Q ss_pred             CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ....++++|+||.+++|.||||+|++||+|+++|||+|+|.+.     ++.+.+|.|+|+|++++|.+|+.+|.+++.+.
T Consensus        10 ~~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~-----~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC-----CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC-----CCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            3568999999999999999999999999999999999999632     23467999999999999999999999999886

>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=99.60  E-value=1.1e-15  Score=115.08  Aligned_cols=74  Identities=24%  Similarity=0.410  Sum_probs=65.8

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ++++|+||.+.+|.||||||++||+|+++|||+|+|.+.++  .++++.+|.|+|+|++++|.+|..+|.+++.+.
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~--~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGE--FLPGTRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTC--BSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCC--CCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            57899999999999999999999999999999999975422  223467899999999999999999999999875

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

Probab=99.58  E-value=5.3e-15  Score=110.83  Aligned_cols=74  Identities=20%  Similarity=0.437  Sum_probs=64.8

Q ss_pred             CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHh
Q 021032           26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  102 (318)
Q Consensus        26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e  102 (318)
                      ...+.+|+||.+++|.||||||++||+|+++|||+|+|.+....   ..+.||.|.|+|+++++.+|+.+|.++++|
T Consensus        12 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~---~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           12 NGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ---NTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCS---STTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCC---CCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            45789999999999999999999999999999999999753221   236799999999999999999999988764

>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=99.58  E-value=1.1e-15  Score=113.68  Aligned_cols=70  Identities=17%  Similarity=0.249  Sum_probs=63.2

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHh
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  102 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e  102 (318)
                      ...++++|.||.+++|+||||+|++||+||++|||+|+|.+.        ..+++|+|+|++++|++|..+|.+++..
T Consensus         7 ~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~--------~~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            7 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR--------DKEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS--------SSCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC--------CCCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            356889999999999999999999999999999999999643        2478999999999999999999997665

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

Probab=99.57  E-value=3.3e-15  Score=116.74  Aligned_cols=73  Identities=21%  Similarity=0.396  Sum_probs=64.2

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      +++|+||.+++|+||||+|++||+|+++|||+|+|.+.. .+ .....+|+|+|+|+.++|.+|+.+|.+++.+.
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~-~~-~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQL-PP-NGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCC-CT-TCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCcc-CC-CCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            789999999999999999999999999999999996432 22 23357899999999999999999999988775

>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=99.57  E-value=4.4e-15  Score=112.93  Aligned_cols=74  Identities=22%  Similarity=0.401  Sum_probs=66.9

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ...++++|+||.+.+|.||||+|++||+|+++|||+|+|.+..     ....+|.|+|+|++++|.+|+.+|.+++.+.
T Consensus        12 ~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~-----~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~   85 (92)
T 1x4n_A           12 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS-----GGLPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC-----TTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC-----CCCCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            4678999999999999999999999999999999999996432     2357899999999999999999999999885

>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=99.57  E-value=6.9e-15  Score=114.38  Aligned_cols=71  Identities=21%  Similarity=0.350  Sum_probs=64.9

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCC--CCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPG--ATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~--~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ..+.+|.||.+++|+||||+|++|++|+++|||+|+|.+..++  +.+|.|+|+|+++++++|+.||.+++..
T Consensus        14 p~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T 1we8_A           14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             EEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            4789999999999999999999999999999999999875443  3689999999999999999999999864

>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=99.56  E-value=3.6e-15  Score=113.83  Aligned_cols=76  Identities=16%  Similarity=0.379  Sum_probs=66.5

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ...++++|+||.+++|.||||+|++||+|+++|||+|+|.+....   ....+|+|+|+|++++|.+|+.+|.+++.+.
T Consensus        12 p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           12 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQ---NTGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCC---SSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCC---CCCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            356899999999999999999999999999999999999643211   1247899999999999999999999999874

>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=99.54  E-value=1.6e-14  Score=112.36  Aligned_cols=77  Identities=22%  Similarity=0.388  Sum_probs=67.2

Q ss_pred             CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ...+++++|+||.+++|.||||||++||+|+++|||+|+|.+...  . ..+.+|.|+|+|+.++|.+|+.+|.+++.+.
T Consensus        11 ~~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~--~-~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE--G-TLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSC--C-SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCC--C-CCCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            356789999999999999999999999999999999999975321  1 1246899999999999999999999999775

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

Probab=99.54  E-value=1.2e-14  Score=113.28  Aligned_cols=72  Identities=19%  Similarity=0.382  Sum_probs=63.9

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ..+++|+||.+++|.||||+|++||+|+++|||+|+|.+.+     ..+.||+|+|+|++++|++|+.+|.+++.+.
T Consensus        10 ~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~-----~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-----GTGPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC-----SSSSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC-----CCCceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            34789999999999999999999999999999999996432     2356899999999999999999999999886

>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=99.51  E-value=2.8e-14  Score=119.39  Aligned_cols=74  Identities=31%  Similarity=0.524  Sum_probs=66.6

Q ss_pred             CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ..++++|+||.+++|+||||||++||+|+++|||+|+|.+ +..|   .+.++.|+|+|++++|.+|+.+|.+++.|+
T Consensus        87 ~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~-~~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~  160 (160)
T 2jzx_A           87 PPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG-DMLP---NSTERAITIAGIPQSIIECVKQICVVMLET  160 (160)
T ss_dssp             CSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCC-CCST---TCCEEEEEEEECHHHHHHHHHHHHHHHHHC
T ss_pred             CCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECC-CCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Confidence            4689999999999999999999999999999999999964 3333   468999999999999999999999998873

>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=99.51  E-value=3e-14  Score=121.33  Aligned_cols=74  Identities=22%  Similarity=0.368  Sum_probs=65.6

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      .++++|+||.+++|+||||+|++||+|+++|||+|+|.+.+.   ++.+.+|.|+|+|+.++|.+|+.+|.++|+++
T Consensus       103 ~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~---~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~  176 (178)
T 2anr_A          103 ANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD---GINLQNRVVTVSGEPEQNRKAVELIIQKIQED  176 (178)
T ss_dssp             GGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC-------CCEEEEEEESSHHHHHHHHHHHHHHHHSC
T ss_pred             ceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCC---CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhC
Confidence            478999999999999999999999999999999999975432   34467899999999999999999999999986

>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=99.50  E-value=3e-14  Score=108.72  Aligned_cols=76  Identities=12%  Similarity=0.199  Sum_probs=67.7

Q ss_pred             ccCCCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHH
Q 021032           21 GFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL  100 (318)
Q Consensus        21 ~~e~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  100 (318)
                      +.+....++.+|.||...+|.||||||++||+|+++|||+|+|.+.+       +.++.|+|+|+.++|.+|..+|..++
T Consensus        10 v~~l~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-------~~~~~V~I~G~~e~v~~A~~~I~~i~   82 (94)
T 2cte_A           10 VARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEGIEKARHEVLLIS   82 (94)
T ss_dssp             CCCCCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-------SSCCEEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHhCCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-------CCCCeEEEEECHHHHHHHHHHHHHHh
Confidence            34456789999999999999999999999999999999999996431       24689999999999999999999999


Q ss_pred             Hhh
Q 021032          101 RET  103 (318)
Q Consensus       101 ~e~  103 (318)
                      .+.
T Consensus        83 ~~~   85 (94)
T 2cte_A           83 AEQ   85 (94)
T ss_dssp             HHH
T ss_pred             hcc
Confidence            886

>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=99.50  E-value=3.8e-14  Score=108.21  Aligned_cols=80  Identities=21%  Similarity=0.236  Sum_probs=70.5

Q ss_pred             hhccCCCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHH
Q 021032           19 EIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITS   98 (318)
Q Consensus        19 ~~~~e~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~   98 (318)
                      +++.+....+++.|.||..++|.||||||++||+|+++|||+|+|....      ...+|.|+|+|..++|.+|+.+|..
T Consensus         8 ~iv~~l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g------~~~~~~V~I~G~~e~v~~A~~~I~~   81 (95)
T 2ctm_A            8 RIVGELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG------APDPNCVTVTGLPENVEEAIDHILN   81 (95)
T ss_dssp             CCCCCTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT------CSCTTEEEEESCHHHHHHHHHHHHH
T ss_pred             HHHHhhcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC------CCCCcEEEEEcCHHHHHHHHHHHHH
Confidence            4455678899999999999999999999999999999999999996431      1347899999999999999999999


Q ss_pred             HHHhhc
Q 021032           99 RLRETI  104 (318)
Q Consensus        99 ~l~e~~  104 (318)
                      ++.+..
T Consensus        82 i~~e~~   87 (95)
T 2ctm_A           82 LEEEYL   87 (95)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            998874

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

Probab=99.50  E-value=3.2e-14  Score=102.82  Aligned_cols=67  Identities=13%  Similarity=0.308  Sum_probs=61.0

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFI  312 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i  312 (318)
                      ..+.++.||.+++|.|||++|++|++|+++|||+|+|.++  +..+|.|+|+|+++++++|+.+|.+++
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~--g~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD--SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC--CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCC--CCcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            4689999999999999999999999999999999999753  347899999999999999999998764

>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=99.49  E-value=6.3e-14  Score=107.46  Aligned_cols=72  Identities=17%  Similarity=0.271  Sum_probs=64.8

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCC-CCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPK-PGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~-~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ...+..|.||.+++|.||||+|++|++|+++|||+|+|.+.. +...+|.|+|+|+++++++|+.+|..++..
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            357899999999999999999999999999999999997653 234789999999999999999999998864

>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=99.47  E-value=2.5e-13  Score=113.94  Aligned_cols=95  Identities=26%  Similarity=0.390  Sum_probs=75.0

Q ss_pred             HHHHHHHHHHHHHhhcc---CCCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEE
Q 021032            6 AQDAVMRVHSRIAEIGF---EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQV   82 (318)
Q Consensus         6 a~~a~~~v~~~i~~~~~---e~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I   82 (318)
                      +..|...+++.+.+...   .....++++|+||.+++|+||||||++||+|+++|||+|+|.. +..|.  ...++.|+|
T Consensus        60 v~~A~~~I~~~~~e~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~-~~~~~--~~~~~~v~I  136 (163)
T 3krm_A           60 QFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR-DQTPD--ENDQVIVKI  136 (163)
T ss_dssp             HHHHHHHHHHHHHHTTSSCSSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCT-TCCCC--TTSEEEEEE
T ss_pred             HHHHHHHHHHHHhcccccccccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECC-CCCCC--CCCceEEEE
Confidence            34555666666655421   1234678899999999999999999999999999999999964 44443  233458999


Q ss_pred             EecHHHHHHHHHHHHHHHHhh
Q 021032           83 IGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        83 ~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      +|++++|.+|..+|.+++++.
T Consensus       137 ~G~~~~v~~A~~~I~~~i~~~  157 (163)
T 3krm_A          137 IGHFYASQMAQRKIRDILAQV  157 (163)
T ss_dssp             EECHHHHHHHHHHHHHHHHHH
T ss_pred             EeCHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999886

>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=99.46  E-value=8.7e-14  Score=106.12  Aligned_cols=70  Identities=17%  Similarity=0.301  Sum_probs=63.4

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ...+.+|.||.+++|.|||++|.+|++|+++|||+|+|++..  ..++.|+|+|+++++++|+.+|.+++.+
T Consensus        15 ~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~--~~~~~V~I~G~~e~v~~A~~~I~~i~~~   84 (94)
T 2cte_A           15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD--DPSNQIKITGTKEGIEKARHEVLLISAE   84 (94)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT--SSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC--CCCCeEEEEECHHHHHHHHHHHHHHhhc
Confidence            468999999999999999999999999999999999997532  3468999999999999999999999875

>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=99.46  E-value=1.2e-13  Score=105.83  Aligned_cols=74  Identities=18%  Similarity=0.277  Sum_probs=65.1

Q ss_pred             CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ..++++|.||...+|.||||||++||+|+++|||+|+|.+...    ++..+|.|+|+|..+++.+|..+|..++.+.
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~----~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~   88 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD----GNQPQDQITITGYEKNTEAARDAILRIVGEL   88 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT----CSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC----CCCCccEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            3578999999999999999999999999999999999965321    2246899999999999999999999988774

>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=99.45  E-value=1.6e-13  Score=104.78  Aligned_cols=71  Identities=13%  Similarity=0.140  Sum_probs=63.8

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ...+.++.||.+++|.|||++|++|++|+++|||+|+|.+.. ..++|.|+|+|+++++++|+.+|.+++.+
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   85 (95)
T 2ctm_A           15 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPENVEEAIDHILNLEEE   85 (95)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-CSCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC-CCCCcEEEEEcCHHHHHHHHHHHHHHHHH
Confidence            357899999999999999999999999999999999996532 23578999999999999999999999875

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

Probab=99.44  E-value=1.2e-13  Score=99.74  Aligned_cols=67  Identities=15%  Similarity=0.295  Sum_probs=59.9

Q ss_pred             CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHH
Q 021032           26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSR   99 (318)
Q Consensus        26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~   99 (318)
                      ...+..|.||...+|.||||||++|++|+++|||+|+|.+.+       ..+|.|+|+|+.+++.+|+.+|..+
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-------~~~~~V~I~G~~~~v~~A~~~I~~i   69 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-------SSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-------CcccEEEEEcCHHHHHHHHHHHHHH
Confidence            457899999999999999999999999999999999996431       3578999999999999999999764

>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=99.42  E-value=2.5e-13  Score=115.22  Aligned_cols=70  Identities=20%  Similarity=0.381  Sum_probs=65.9

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|.+..++..||.|+|+|+++++++|+.+|.+++..
T Consensus         3 ~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~   72 (174)
T 1j4w_A            3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRS   72 (174)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            6789999999999999999999999999999999998766678899999999999999999999999875

>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=99.40  E-value=4.2e-13  Score=104.10  Aligned_cols=69  Identities=19%  Similarity=0.261  Sum_probs=62.4

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ..+.++.||.+++|.|||++|++|++|+++|||+|+|.+.  +...+.|+|+|++++++.|+.+|..++..
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~--g~~~~~V~I~G~~e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP--ELQSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT--TTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCC--CCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            3789999999999999999999999999999999999753  33467999999999999999999998865

>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=99.37  E-value=1.1e-12  Score=109.99  Aligned_cols=71  Identities=13%  Similarity=0.248  Sum_probs=64.7

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCC--CCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPK--PGATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~--~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      .+.++.||.+++|+||||+|++|++|++.|||+|+|.+..  ++..+|.|+|+|+++++..|+.+|.+++.+.
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~   74 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRER   74 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHHHHHHHHHHHTTCS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Confidence            5789999999999999999999999999999999997543  4577999999999999999999999998753

>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=99.34  E-value=1.4e-12  Score=101.22  Aligned_cols=71  Identities=17%  Similarity=0.216  Sum_probs=63.1

Q ss_pred             CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      .+++..|.||...+|.|||+||++||+|+++|||+|+|.+..       ...+.|+|+|..++|.+|+.+|..++.+.
T Consensus        15 ap~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g-------~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   85 (104)
T 2ctk_A           15 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAANLDRAKAGLLERVKEL   85 (104)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-------TTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-------CCcceEEEEcCHHHHHHHHHHHHHHHhhH
Confidence            468899999999999999999999999999999999996431       23569999999999999999999988664

>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=99.29  E-value=2.1e-12  Score=98.36  Aligned_cols=78  Identities=14%  Similarity=0.205  Sum_probs=69.4

Q ss_pred             hhccCCCCeeEEEEEEecccceeeeCCCCchHHHHHHHh-CCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHH
Q 021032           19 EIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRAT-GASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHIT   97 (318)
Q Consensus        19 ~~~~e~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~t-Ga~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~   97 (318)
                      ++..|.++.++..|.||...++.|||+||.+||+|+++| ||+|+|...       ++..+.|+|.|+.++|.+|+.+|.
T Consensus         8 ~i~~e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~-------g~~~~~V~I~G~~~~v~~A~~~I~   80 (95)
T 2ctj_A            8 SIQKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-------GSGSDTVVIRGPSSDVEKAKKQLL   80 (95)
T ss_dssp             CCCCCCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-------TTTCCEEEEESCHHHHHHHHHHHH
T ss_pred             HHHHHHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC-------CCCcceEEEEcCHHHHHHHHHHHH
Confidence            445677889999999999999999999999999999999 999999532       245679999999999999999999


Q ss_pred             HHHHhh
Q 021032           98 SRLRET  103 (318)
Q Consensus        98 ~~l~e~  103 (318)
                      .++.+.
T Consensus        81 ~iv~e~   86 (95)
T 2ctj_A           81 HLAEEK   86 (95)
T ss_dssp             HHHHHH
T ss_pred             HHHhhh
Confidence            999875

>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=99.27  E-value=6.5e-12  Score=95.66  Aligned_cols=70  Identities=17%  Similarity=0.262  Sum_probs=63.8

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHh-CCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQIS-GANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S-GA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ...+..|.||.++++.|||++|.+|++|+++| ||+|+|.+  +++..+.|+|+|+.+++++|+.+|+.++..
T Consensus        15 ~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~--~g~~~~~V~I~G~~~~v~~A~~~I~~iv~e   85 (95)
T 2ctj_A           15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV--EGSGSDTVVIRGPSSDVEKAKKQLLHLAEE   85 (95)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCC--TTTTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCC--CCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            45788999999999999999999999999999 99999954  456678999999999999999999999875

>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=99.25  E-value=1.5e-11  Score=94.91  Aligned_cols=65  Identities=20%  Similarity=0.341  Sum_probs=60.2

Q ss_pred             eEEEEEecccccccccccccchHHHHHHH-hCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQI-SGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~-SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      .+.+|.||.++++.|||++|++|++|++. ++++|.+++     .++.|+|+|++++|.+|+..|+.++++
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-----~~~~ItI~G~~~~V~~a~~~I~~~v~e   92 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTEDVSVAQEQIEGMVKD   92 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-----CCCEEEEECCHHHHHHHHHHHHHHHHH
Confidence            78999999999999999999999999997 599999965     467999999999999999999999875

>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=99.25  E-value=1.3e-11  Score=95.24  Aligned_cols=69  Identities=13%  Similarity=0.192  Sum_probs=62.0

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHH-hCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA-TGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~-tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ...++.+|.||+.+++.||||+|++||+|+++ ++++|+|+.          .++.|+|+|+++.|.+|..+|..++.+.
T Consensus        24 ~~~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~----------~~~~ItI~G~~~~V~~a~~~I~~~v~el   93 (102)
T 2ctf_A           24 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVKDL   93 (102)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cCeEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC----------CCCEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            34588999999999999999999999999997 589999853          3689999999999999999999998775

>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=99.20  E-value=2.3e-11  Score=99.89  Aligned_cols=72  Identities=15%  Similarity=0.326  Sum_probs=60.4

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCC-eEEEecCCCCCCCCCCCCc--eEEEEecHHHHHHHHHHHHHHHHh
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGA-SIRVFPKDQAPRCGSPHDE--IVQVIGNYHSVQDALFHITSRLRE  102 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa-~I~i~~~~~~p~~~~~~er--~V~I~G~~~~V~~A~~~I~~~l~e  102 (318)
                      ++++.||.+++|++|||+|.+||+|++.||| +|+|.+.++...  ...++  .|+|+|++++|++|..+|..+|.+
T Consensus        68 e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~--~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A           68 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV--PQEEGMVPFVFVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             EEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC--CCCTTEEEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc--cccCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            3899999999999999999999999999997 999986433211  12344  489999999999999999998865

>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=99.10  E-value=8.1e-11  Score=88.26  Aligned_cols=65  Identities=18%  Similarity=0.393  Sum_probs=58.2

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCE-EEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHH
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGAN-VVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFI  312 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~-I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i  312 (318)
                      .....++.||.+++|.|||++|.+|++|++.|||+ |.|.+     ++++|+|.| +.+++++|+.+|..+.
T Consensus        13 ~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e-----ddG~V~I~g~~~ea~~~A~~~I~~ie   79 (91)
T 2cpq_A           13 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-----DTGTFRIYGESADAVKKARGFLEFVE   79 (91)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHSCCC
T ss_pred             CceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc-----CCCEEEEEECCHHHHHHHHHHHHhhh
Confidence            35789999999999999999999999999999998 99963     358999999 8999999999997543

>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=98.96  E-value=5.4e-10  Score=83.76  Aligned_cols=63  Identities=17%  Similarity=0.321  Sum_probs=56.6

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCe-EEEecCCCCCCCCCCCCceEEEEe-cHHHHHHHHHHHH
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGAS-IRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHIT   97 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~-I~i~~~~~~p~~~~~~er~V~I~G-~~~~V~~A~~~I~   97 (318)
                      ...+...|.||...+|.+||+||++||+|+++|||+ |.|..          .+..|+|.| +.+++.+|+.+|.
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e----------ddG~V~I~g~~~ea~~~A~~~I~   76 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----------DTGTFRIYGESADAVKKARGFLE   76 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----------TTTEEEEEESSHHHHHHHHHHHS
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc----------CCCEEEEEECCHHHHHHHHHHHH
Confidence            456889999999999999999999999999999998 99942          359999999 8999999998884

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

Probab=98.94  E-value=7.2e-10  Score=103.70  Aligned_cols=70  Identities=17%  Similarity=0.245  Sum_probs=62.0

Q ss_pred             CcceEEEEEeccccccccccccc--chHHHHHHHhCCEEEEcCCC-----CCCCCeEEEEEcCHHHHHHHHHHHHHH
Q 021032          242 LTSTTIEVVIPQLYMAHVYGENN--SNLSHIRQISGANVVVNDPK-----PGATEGVVMVSGTSDQMRAAQSLIHAF  311 (318)
Q Consensus       242 ~~~~t~~v~IP~~~vG~IIGk~G--~~Ik~Ir~~SGA~I~i~~~~-----~~~~er~v~I~Gt~~~v~~A~~lI~~~  311 (318)
                      .+.+|.++.||..+++.||||+|  ++|++|+++|||+|++.+..     +......|+|+|.++.|++|+..|.++
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l  103 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRN  103 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHS
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhc
Confidence            35789999999999999999999  99999999999999997654     124557899999999999999999874

>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=98.88  E-value=5.4e-09  Score=84.04  Aligned_cols=73  Identities=18%  Similarity=0.270  Sum_probs=61.7

Q ss_pred             CcceEEEEEeccc------ccccccccccchHHHHHHHhCCEEEEcCCC----------------CCCCCeEEEEEc-CH
Q 021032          242 LTSTTIEVVIPQL------YMAHVYGENNSNLSHIRQISGANVVVNDPK----------------PGATEGVVMVSG-TS  298 (318)
Q Consensus       242 ~~~~t~~v~IP~~------~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~----------------~~~~er~v~I~G-t~  298 (318)
                      ....+..|.||.+      ++|.|||.+|.+||+|+++|||+|.|...-                ....+-.|.|++ +.
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            3468899999987      899999999999999999999999996421                112366899999 68


Q ss_pred             HHHHHHHHHHHHHHHc
Q 021032          299 DQMRAAQSLIHAFILC  314 (318)
Q Consensus       299 ~~v~~A~~lI~~~i~~  314 (318)
                      +.+++|..+|..++..
T Consensus        84 e~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           84 ENVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhc
Confidence            9999999999999965

>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=98.82  E-value=1.1e-08  Score=82.36  Aligned_cols=78  Identities=18%  Similarity=0.284  Sum_probs=62.9

Q ss_pred             CeeEEEEEEecc------cceeeeCCCCchHHHHHHHhCCeEEEecCCCCC-----------CCCCCCCceEEEEe-cHH
Q 021032           26 QAVVARLLVHSQ------QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAP-----------RCGSPHDEIVQVIG-NYH   87 (318)
Q Consensus        26 ~~~~~rllVp~~------~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p-----------~~~~~~er~V~I~G-~~~   87 (318)
                      ..++.+|.||..      ++|.|||.+|.+||+|+++|||+|.|..+....           ......+-.|.|++ +.+
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e   84 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTME   84 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHH
Confidence            468899999988      899999999999999999999999997543211           11123356788999 578


Q ss_pred             HHHHHHHHHHHHHHhh
Q 021032           88 SVQDALFHITSRLRET  103 (318)
Q Consensus        88 ~V~~A~~~I~~~l~e~  103 (318)
                      ++.+|+..|..+|.+.
T Consensus        85 ~~~~A~~~I~~ll~~~  100 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQG  100 (131)
T ss_dssp             HHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhcc
Confidence            9999999999998774

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

Probab=98.81  E-value=1.9e-08  Score=79.38  Aligned_cols=71  Identities=18%  Similarity=0.194  Sum_probs=57.6

Q ss_pred             ceEEEEEeccc-------ccccccccccchHHHHHHHhCCEEEEcCCC----------CCCCCeEEEEEc-CHHHHHHHH
Q 021032          244 STTIEVVIPQL-------YMAHVYGENNSNLSHIRQISGANVVVNDPK----------PGATEGVVMVSG-TSDQMRAAQ  305 (318)
Q Consensus       244 ~~t~~v~IP~~-------~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~----------~~~~er~v~I~G-t~~~v~~A~  305 (318)
                      ..+.+|.||.+       ++|.|||.+|.+||+|+++|||+|.|...-          +..++-.|.|++ +++++++|+
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            46777888764       889999999999999999999999996321          112345788887 689999999


Q ss_pred             HHHHHHHHc
Q 021032          306 SLIHAFILC  314 (318)
Q Consensus       306 ~lI~~~i~~  314 (318)
                      .||.+++..
T Consensus        91 ~~Ie~Ll~~   99 (119)
T 2yqr_A           91 KLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhhc
Confidence            999999874

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

Probab=98.72  E-value=3.6e-08  Score=77.73  Aligned_cols=77  Identities=14%  Similarity=0.082  Sum_probs=58.4

Q ss_pred             CeeEEEEEEecc-------cceeeeCCCCchHHHHHHHhCCeEEEecCCCC-----CCCCCCCCceEEEEe-cHHHHHHH
Q 021032           26 QAVVARLLVHSQ-------QIGCLLGRGGHIVSEMRRATGASIRVFPKDQA-----PRCGSPHDEIVQVIG-NYHSVQDA   92 (318)
Q Consensus        26 ~~~~~rllVp~~-------~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~-----p~~~~~~er~V~I~G-~~~~V~~A   92 (318)
                      ..++.||.||-.       ++|.|||++|.+||+|+++|||+|.|..+...     .......+-.|.|.+ +.+++.+|
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A   89 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA   89 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHH
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHH
Confidence            357789999865       69999999999999999999999999643211     000112344677776 58999999


Q ss_pred             HHHHHHHHHh
Q 021032           93 LFHITSRLRE  102 (318)
Q Consensus        93 ~~~I~~~l~e  102 (318)
                      +.+|..++.+
T Consensus        90 ~~~Ie~Ll~~   99 (119)
T 2yqr_A           90 KKLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHhhc
Confidence            9999888865

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.57  E-value=2.3e-08  Score=80.86  Aligned_cols=75  Identities=21%  Similarity=0.269  Sum_probs=55.0

Q ss_pred             eeEEEEEEeccc------ceeeeCCCCchHHHHHHHhCCeEEEecCCCC------------CCCC-CCCCceEEEEec-H
Q 021032           27 AVVARLLVHSQQ------IGCLLGRGGHIVSEMRRATGASIRVFPKDQA------------PRCG-SPHDEIVQVIGN-Y   86 (318)
Q Consensus        27 ~~~~rllVp~~~------vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~------------p~~~-~~~er~V~I~G~-~   86 (318)
                      +++-||.||.+.      +|.|||.+|.++|+|+++|||+|.|..+.+.            |.+. .+.+--|.|+++ .
T Consensus         1 ~~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~   80 (140)
T 2bl5_A            1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDA   80 (140)
T ss_dssp             CEEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSC
T ss_pred             CceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCc
Confidence            357789999766      9999999999999999999999999854321            1111 122236889884 3


Q ss_pred             -----HHHHHHHHHHHHHHH
Q 021032           87 -----HSVQDALFHITSRLR  101 (318)
Q Consensus        87 -----~~V~~A~~~I~~~l~  101 (318)
                           ..+.+|+..|..+|.
T Consensus        81 ~~~~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           81 QNRAELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             CHHHHHHHHHHHHHHHHHSS
T ss_pred             hhhHHHHHHHHHHHHHHHCC
Confidence                 268888888877664

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

Probab=98.54  E-value=9.4e-08  Score=83.47  Aligned_cols=63  Identities=17%  Similarity=0.252  Sum_probs=57.3

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcC-----HHHHHHHHHHHHHHH
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT-----SDQMRAAQSLIHAFI  312 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt-----~~~v~~A~~lI~~~i  312 (318)
                      .+.++.||.+.+|.|||++|.+|+.|++.|||+|+|+.     .++.|+|+|+     ++++++|+.+|.+++
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~-----~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~  101 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS-----ETGEVWITSTKETEDPLAVWKARDIVLAIG  101 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT-----TTCEEEEEECTTCCSHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc-----CCCEEEEecCCCCCCHHHHHHHHHHHHHHh
Confidence            46789999999999999999999999999999999952     3678999986     699999999999987

>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=98.40  E-value=4.8e-07  Score=77.16  Aligned_cols=63  Identities=19%  Similarity=0.252  Sum_probs=58.0

Q ss_pred             EEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEE-----cCHHHHHHHHHHHHHHHH
Q 021032          246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVS-----GTSDQMRAAQSLIHAFIL  313 (318)
Q Consensus       246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~-----Gt~~~v~~A~~lI~~~i~  313 (318)
                      ..++.||.+.+|.|||++|+.++.|++.+|++|+++     ..++.|+|+     |+|.++++|+.+|.++..
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id-----~~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~r   72 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVD-----TENSMVIVEPEAEGIPPVNLMKAAEVVKAISL   72 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEE-----TTTTEEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEE-----cCCCeEEEEeCCCCCCHHHHHHHHHHHHHHHc
Confidence            368999999999999999999999999999999996     357889999     999999999999988765

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=98.39  E-value=3.2e-07  Score=91.69  Aligned_cols=85  Identities=20%  Similarity=0.221  Sum_probs=69.3

Q ss_pred             hHHHHHHHHHHHHHhhccCC------CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCc
Q 021032            5 PAQDAVMRVHSRIAEIGFEP------GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDE   78 (318)
Q Consensus         5 ~a~~a~~~v~~~i~~~~~e~------~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er   78 (318)
                      -|.++..+|++.+.+...+.      -.+....|-||...+|.|||+||++||+|+++|||+|.|.           .+.
T Consensus       538 ~A~~g~~~I~~~m~~al~~~~~~~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~-----------d~G  606 (630)
T 3u1k_A          538 QASVAKKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV-----------DEE  606 (630)
T ss_dssp             HHHHHHHHHHHHHHHHCSSCCSSCCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC-----------SSS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc-----------CCc
Confidence            36777888887777765432      4577899999999999999999999999999999999993           368


Q ss_pred             eEEEEec-HHHHHHHHHHHHHHH
Q 021032           79 IVQVIGN-YHSVQDALFHITSRL  100 (318)
Q Consensus        79 ~V~I~G~-~~~V~~A~~~I~~~l  100 (318)
                      .|.|.|. .+++.+|+..|..++
T Consensus       607 ~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          607 TFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEEESSHHHHHHHHHHTTC--
T ss_pred             EEEEEeCCHHHHHHHHHHHHHHh
Confidence            8999996 678899998886543

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.38  E-value=2.9e-07  Score=74.44  Aligned_cols=69  Identities=9%  Similarity=0.256  Sum_probs=53.8

Q ss_pred             eEEEEEecc------cccccccccccchHHHHHHHhCCEEEEcCCCC------------------CCCCeEEEEEcC-HH
Q 021032          245 TTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVNDPKP------------------GATEGVVMVSGT-SD  299 (318)
Q Consensus       245 ~t~~v~IP~------~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~------------------~~~er~v~I~Gt-~~  299 (318)
                      .+.+|.||.      +++|+|||.+|.++|+|+++|||+|.|...-.                  ...+-.|.|++. ++
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            456777875      45999999999999999999999999975321                  112237889983 43


Q ss_pred             -----HHHHHHHHHHHHHH
Q 021032          300 -----QMRAAQSLIHAFIL  313 (318)
Q Consensus       300 -----~v~~A~~lI~~~i~  313 (318)
                           .++.|..+|..++.
T Consensus        82 ~~~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             hhHHHHHHHHHHHHHHHCC
Confidence                 79999999999876

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

Probab=98.34  E-value=1.8e-06  Score=68.54  Aligned_cols=68  Identities=10%  Similarity=0.231  Sum_probs=61.0

Q ss_pred             EEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      -..+.+..+.++.|||++|+.|+.|++.|.|.|+|..-.+ +++..|+|.|++..-+.|+.||+.+...
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s-~g~tEVtIfG~~~~Q~rak~MI~sLA~~  124 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP-ERRAEIWIFGPPPFRRDVDRMLTDLAHY  124 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT-TSCEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC-CCcEEEEEECCHHHHHHHHHHHHHHHHH
Confidence            3667799999999999999999999999999999987644 4788999999999999999999987653

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=98.08  E-value=1.9e-06  Score=86.17  Aligned_cols=62  Identities=19%  Similarity=0.242  Sum_probs=54.6

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcC-HHHHHHHHHHHHHHH
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT-SDQMRAAQSLIHAFI  312 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt-~~~v~~A~~lI~~~i  312 (318)
                      ....+.||.+.+|.|||++|.+||+|+++|||+|+|.      ++..|.|.|+ ++++++|+.+|.+++
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 VVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV------DEETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC------SSSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             eEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc------CCcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            4678899999999999999999999999999999995      3578999996 689999999998765

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

Probab=97.98  E-value=1.6e-05  Score=63.19  Aligned_cols=68  Identities=16%  Similarity=0.176  Sum_probs=58.3

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHh
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  102 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e  102 (318)
                      .+.|.|...+++.|||++|+.|++|++.|++.|+|..-      .++.+--|+|.|++..=.+|..+|..+..-
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~------~s~g~tEVtIfG~~~~Q~rak~MI~sLA~~  124 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVW------GPERRAEIWIFGPPPFRRDVDRMLTDLAHY  124 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECC------CTTSCEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEecc------CCCCcEEEEEECCHHHHHHHHHHHHHHHHH
Confidence            47788999999999999999999999999999999643      124577899999999999999988776643

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.86  E-value=6e-06  Score=83.52  Aligned_cols=88  Identities=19%  Similarity=0.310  Sum_probs=26.8

Q ss_pred             hHHHHHHHHHHHHHhhccCC------CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCc
Q 021032            5 PAQDAVMRVHSRIAEIGFEP------GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDE   78 (318)
Q Consensus         5 ~a~~a~~~v~~~i~~~~~e~------~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er   78 (318)
                      -|.++..+|++.+.+...+.      ..+....|-||...+|.|||+||.+||+|+++||++|.|.           .+.
T Consensus       541 ~A~~g~~~I~~~m~~al~~~r~~~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~-----------ddG  609 (726)
T 4aid_A          541 QAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN-----------DDG  609 (726)
T ss_dssp             HHHHHHHHHHHHHHTTCSSCCSSCCSSCCC--------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE-----------CCc
Confidence            46778888888877765432      3466788999999999999999999999999999999993           356


Q ss_pred             eEEEEec-HHHHHHHHHHHHHHHHhh
Q 021032           79 IVQVIGN-YHSVQDALFHITSRLRET  103 (318)
Q Consensus        79 ~V~I~G~-~~~V~~A~~~I~~~l~e~  103 (318)
                      .|.|.+. .+++.+|+..|..++.+.
T Consensus       610 ~v~I~~~~~~~~~~A~~~i~~i~~~~  635 (726)
T 4aid_A          610 VVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             ----CCSCHHHHHHHHHC--------
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence            7777775 788899999888777653

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.82  E-value=3e-05  Score=62.93  Aligned_cols=64  Identities=23%  Similarity=0.333  Sum_probs=48.9

Q ss_pred             CCChHHHHHHHHHHHHHhhcc----CCCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEec
Q 021032            2 RHSPAQDAVMRVHSRIAEIGF----EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFP   65 (318)
Q Consensus         2 ~~s~a~~a~~~v~~~i~~~~~----e~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~   65 (318)
                      +++..+=..+.+|+.+.....    ..++.-.+.++|+...+|..||++|++|+.|+++.|-+|.|..
T Consensus         6 ~l~~~~~r~i~lfe~~t~a~~~dcvid~~~dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~   73 (144)
T 2cxc_A            6 RITLEELRYISVFHSITGVTAYRCIVDEENNRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVE   73 (144)
T ss_dssp             -CCHHHHHHHHHHHHHHSCCEEEEEEEGGGTEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEE
T ss_pred             EeCHHHHHHHHHHHHHhCCCeeeEEEeCCCCEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEE
Confidence            355566667777877755421    1122345889999999999999999999999999999999974

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.33  E-value=4e-05  Score=77.51  Aligned_cols=63  Identities=27%  Similarity=0.357  Sum_probs=11.6

Q ss_pred             EEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcC-HHHHHHHHHHHHHHHHc
Q 021032          246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT-SDQMRAAQSLIHAFILC  314 (318)
Q Consensus       246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt-~~~v~~A~~lI~~~i~~  314 (318)
                      ...+.||.+.++.|||+||.+|+.|.++||++|.|.      ++..|.|.++ .+++++|+.+|..++..
T Consensus       571 ~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~------ddG~v~I~~~~~~~~~~A~~~i~~i~~~  634 (726)
T 4aid_A          571 IETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN------DDGVVKVSASDGAKIKAAIDWIKSITDE  634 (726)
T ss_dssp             -------------------------------------------------CCSCHHHHHHHHHC-------
T ss_pred             EEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE------CCceEEEEeCCHHHHHHHHHHHHHHhhh
Confidence            567789999999999999999999999999999995      3567888885 88999999999887653

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=96.44  E-value=0.001  Score=67.43  Aligned_cols=86  Identities=16%  Similarity=0.298  Sum_probs=12.4

Q ss_pred             hHHHHHHHHHHHHHhhccCC------CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCc
Q 021032            5 PAQDAVMRVHSRIAEIGFEP------GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDE   78 (318)
Q Consensus         5 ~a~~a~~~v~~~i~~~~~e~------~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er   78 (318)
                      -|.++..++++.+.+...+.      -.+....+-||...++.+||+||.+|++|.++||+.|.|-           .+.
T Consensus       531 ~A~~~~~~I~~~m~~al~~~~~~~~~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~-----------~dg  599 (723)
T 3cdi_A          531 QAKGARLHILGVMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIE-----------DDG  599 (723)
T ss_dssp             HHHHHHHHHHHHHHHHCC--------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHhhhcchhccccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEec-----------CCc
Confidence            36677778887777665332      3456788889999999999999999999999999999983           256


Q ss_pred             eEEEEec-HHHHHHHHHHHHHHHH
Q 021032           79 IVQVIGN-YHSVQDALFHITSRLR  101 (318)
Q Consensus        79 ~V~I~G~-~~~V~~A~~~I~~~l~  101 (318)
                      .|.|.+. .+.+.+|...|..+..
T Consensus       600 ~v~I~~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          600 TVKIAATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             ------------------------
T ss_pred             cEEEecCCHHHHHHHHHHHHHHhh
Confidence            6777654 4566677666655443

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=96.18  E-value=0.0098  Score=52.35  Aligned_cols=39  Identities=15%  Similarity=0.348  Sum_probs=36.0

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP  283 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~  283 (318)
                      .+..+.||.+..+.-|||+|.|++--.++||.+|.|...
T Consensus       184 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  222 (251)
T 2asb_A          184 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  222 (251)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             cEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEH
Confidence            468899999999999999999999999999999999643

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=96.14  E-value=0.01  Score=55.16  Aligned_cols=39  Identities=15%  Similarity=0.348  Sum_probs=36.0

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP  283 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~  283 (318)
                      .+..+.||.+..+..|||+|.|++-..++||.+|.|...
T Consensus       307 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          307 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             cEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            478899999999999999999999999999999999643

>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=95.37  E-value=0.0013  Score=67.01  Aligned_cols=83  Identities=18%  Similarity=0.269  Sum_probs=34.4

Q ss_pred             hHHHHHHHHHHHHHhhccCC-----CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCce
Q 021032            5 PAQDAVMRVHSRIAEIGFEP-----GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEI   79 (318)
Q Consensus         5 ~a~~a~~~v~~~i~~~~~e~-----~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~   79 (318)
                      -|.++..+|++.+.+...+.     ..+....|-||...+|-+||++|.+||+|++++|+.|.|.           .+..
T Consensus       570 ~A~~~~~~I~~~m~~al~~~~~~~~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~-----------~dG~  638 (757)
T 1e3p_A          570 QARDARLHILDVMMEAIDTPDEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE-----------DDGT  638 (757)
T ss_dssp             HHHHHHHHHHHHHHHHCSSCCCCCTTSCBCCCC------------------CTTCCCCCSCC------------------
T ss_pred             HHHHHHHHHHHHHHHHhcccccccccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEec-----------CCce
Confidence            36677777887777654332     2355567889999999999999999999999999999984           2456


Q ss_pred             EEEEec-HHHHHHHHHHHHH
Q 021032           80 VQVIGN-YHSVQDALFHITS   98 (318)
Q Consensus        80 V~I~G~-~~~V~~A~~~I~~   98 (318)
                      |.|... .+...+|...|..
T Consensus       639 v~Is~~~~~~~~~a~~~i~~  658 (757)
T 1e3p_A          639 IYIGAADGPAAEAARATING  658 (757)
T ss_dssp             -CCCBSSHHHHCC-------
T ss_pred             EEEecCCHHHHHHHHHHHHH
Confidence            666653 4555566555544

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=95.09  E-value=0.0037  Score=63.38  Aligned_cols=63  Identities=17%  Similarity=0.305  Sum_probs=0.0

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcC-HHHHHHHHHHHHHHHH
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT-SDQMRAAQSLIHAFIL  313 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt-~~~v~~A~~lI~~~i~  313 (318)
                      ....+.||.+.++.|||++|.+|+.|.+.+|+.|+|.+      +..|.|.+. .+.+++|+.+|..++.
T Consensus       560 ~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~------dg~v~I~~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          560 RIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED------DGTVKIAATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             ----------------------------------------------------------------------
T ss_pred             eEEEEEECHHHhcccccccceeeeeeehhhCceEEecC------CccEEEecCCHHHHHHHHHHHHHHhh
Confidence            35677899999999999999999999999999999853      567888775 5678888888776653

>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=93.80  E-value=0.0028  Score=64.55  Aligned_cols=60  Identities=23%  Similarity=0.448  Sum_probs=20.5

Q ss_pred             EEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcC-HHHHHHHHHHHHHHH
Q 021032          247 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT-SDQMRAAQSLIHAFI  312 (318)
Q Consensus       247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt-~~~v~~A~~lI~~~i  312 (318)
                      ..+.||.+.+|.+||++|.+|++|++.+|+.|+|.+      +..|.|+.. .+..++|+.+|..+.
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            346699999999999999999999999999999952      567888885 567777877776654

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=91.30  E-value=0.16  Score=40.85  Aligned_cols=38  Identities=13%  Similarity=0.240  Sum_probs=35.0

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      ....+.|+...+|+.||++|++|+.|+++.|-+|+|-+
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~   73 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVE   73 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEE
Confidence            57888999999999999999999999999999999854

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=87.97  E-value=0.31  Score=42.76  Aligned_cols=39  Identities=26%  Similarity=0.306  Sum_probs=36.2

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK   66 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~   66 (318)
                      ..+.+.||..+.+.-|||+|.+|+--..-||.+|.|.+.
T Consensus       184 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  222 (251)
T 2asb_A          184 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  222 (251)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             cEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEH
Confidence            468899999999999999999999999999999999754

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=86.73  E-value=0.42  Score=43.98  Aligned_cols=40  Identities=30%  Similarity=0.439  Sum_probs=36.6

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK   66 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~   66 (318)
                      ...+.+.||..+.+.-|||+|.+++--..-||.+|.|.+.
T Consensus       302 ~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          302 NKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             TTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             CCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            3468899999999999999999999999999999999754

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=85.43  E-value=0.54  Score=43.31  Aligned_cols=38  Identities=13%  Similarity=0.325  Sum_probs=35.4

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN  281 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~  281 (318)
                      ..+..+.||.+..+.-|||+|.|++--.+.||.+|.|.
T Consensus       302 ~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~  339 (344)
T 1hh2_P          302 NKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIK  339 (344)
T ss_dssp             TTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             CCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEecee
Confidence            35788999999999999999999999999999999985

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=84.59  E-value=0.57  Score=43.39  Aligned_cols=40  Identities=28%  Similarity=0.318  Sum_probs=36.8

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK   66 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~   66 (318)
                      ...+.+.||..+.+..|||+|.+++-...-||.+|.|...
T Consensus       306 ~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          306 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             CcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            3468999999999999999999999999999999999754

>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens} SCOP: d.52.3.1

Probab=83.15  E-value=0.4  Score=35.47  Aligned_cols=29  Identities=14%  Similarity=0.347  Sum_probs=24.9

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHH
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRA   56 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~   56 (318)
                      -.+++.|....-|.||||+|..|++|+.+
T Consensus        35 ~~i~I~I~tarPg~vIGkkG~~Ie~L~~~   63 (92)
T 1wh9_A           35 TRTEIIILATRTQNVLGEKGRRIRELTAV   63 (92)
T ss_dssp             SCEEEEEEESCHHHHHCGGGHHHHHHHHH
T ss_pred             CeEEEEEEeCCCceEEcCCcHHHHHHHHH
Confidence            34788899999999999999999988753

>2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori}

Probab=80.30  E-value=0.64  Score=37.68  Aligned_cols=67  Identities=9%  Similarity=0.007  Sum_probs=44.3

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhc
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETI  104 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~  104 (318)
                      ++.+-+.....|.||||.|.|++.||--+...+.-  .     +  ...-.+.|.|=.+.-++.+..++..+.+.+
T Consensus        34 ~i~i~i~ged~glLIGK~G~TL~ALQyL~~~~vn~--~-----~--~~~V~LDve~YRerReetL~~lA~~~A~kV  100 (152)
T 2pt7_G           34 VLLIDIDGEDSALLIGEKGYRYKALSYLLFNWIHP--T-----Y--GYSIRLEISTFLQNQEKVMDTQLQSVIMTV  100 (152)
T ss_dssp             EEEEEEEEGGGTTTTCGGGHHHHHHHHHHHHHHHH--H-----H--SCEEEEEETTHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEecCCcceEECCCCcchHHHHHHHHHHhhh--c-----C--CceEEEEhHHhHHHHHHHHHHHHHHHHHHH
Confidence            36666778899999999999999998554222211  0     0  011224466667777788888877777654

---

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	318
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	1e-15
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	4e-11
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-15
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	6e-11
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	4e-14
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	3e-11
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	5e-14
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-11
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	8e-14
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	3e-09
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	6e-13
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	6e-13
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-12
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-08
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	3e-12
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	2e-10
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	4e-12
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	3e-08
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-11
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	6e-10
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-11
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	5e-11
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-11
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-08
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	2e-10
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	5e-10
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	1e-05
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	2e-09
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	5e-09
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-07
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	6e-09
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	0.002
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	3e-04
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	5e-04

>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 = 68.3 bits (167), Expect = 1e-15
 Identities = 22/68 (32%), Positives = 41/68 (60%)

Query: 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 304
           TT E+ IP   +  + G   +N++ IRQ+SGA + + +P  G++   V ++G++  +  A
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLA 61

Query: 305 QSLIHAFI 312
           Q LI+A +
Sbjct: 62  QYLINARL 69

>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 = 55.6 bits (134), Expect = 4e-11
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
               L + +  IGC++GR G  ++E+R+ +GA I++     A          V + G+  
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKI-----ANPVEGSSGRQVTITGSAA 56

Query: 88  SVQDALFHITSRL 100
           S+  A + I +RL
Sbjct: 57  SISLAQYLINARL 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 = 67.9 bits (166), Expect = 2e-15
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 7/75 (9%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
           +  RLL+H +++G ++G+ G  V +MR  +GA I +         G+  + I+ + G  +
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE-------GNCPERIITLAGPTN 56

Query: 88  SVQDALFHITSRLRE 102
           ++  A   I  +L E
Sbjct: 57  AIFKAFAMIIDKLEE 71

>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 = 55.5 bits (134), Expect = 6e-11
 Identities = 11/69 (15%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 303
           + TI +++    +  + G+   ++  +R+ SGA + +   +    E ++ ++G ++ +  
Sbjct: 3   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLAGPTNAIFK 60

Query: 304 AQSLIHAFI 312
           A ++I   +
Sbjct: 61  AFAMIIDKL 69

>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 = 64.1 bits (156), Expect = 4e-14
 Identities = 19/68 (27%), Positives = 39/68 (57%)

Query: 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 304
            T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ A
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 63

Query: 305 QSLIHAFI 312
           Q L+   +
Sbjct: 64  QYLLQNSV 71

>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 = 56.4 bits (136), Expect = 3e-11
 Identities = 15/78 (19%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 25  GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 84
           G  +  ++ +     G ++G+GG  + ++R  +GASI++             D I+ + G
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-----DEPLEGSEDRIITITG 55

Query: 85  NYHSVQDALFHITSRLRE 102
               +Q+A + + + +++
Sbjct: 56  TQDQIQNAQYLLQNSVKQ 73

>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 = 64.5 bits (157), Expect = 5e-14
 Identities = 16/69 (23%), Positives = 32/69 (46%)

Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 303
             T E  +P   +  + G     +S I+Q SG  + +     G  E   M++GT + +++
Sbjct: 7   VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQS 66

Query: 304 AQSLIHAFI 312
           A+ L+   +
Sbjct: 67  AKRLLDQIV 75

>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 = 57.1 bits (138), Expect = 2e-11
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 5/75 (6%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
           +     V    +G ++GRGG  +S +++ +G  I++     AP  G   +    + G   
Sbjct: 8   MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQI-----APDSGGLPERSCMLTGTPE 62

Query: 88  SVQDALFHITSRLRE 102
           SVQ A   +   + +
Sbjct: 63  SVQSAKRLLDQIVEK 77

>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 = 63.3 bits (154), Expect = 8e-14
 Identities = 15/69 (21%), Positives = 29/69 (42%)

Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 303
           S  I+V IP+  +  V G N   +  I+  +G  +          E +  ++G  D+ + 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 304 AQSLIHAFI 312
           A  +I   +
Sbjct: 62  AAEIITDLL 70

>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 = 51.0 bits (122), Expect = 3e-09
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 25  GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 84
           G  ++  + +    +G ++GR G ++ +++   G  I        P  G+  + I Q+ G
Sbjct: 1   GSHMI-DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRI-----QFKPDDGTTPERIAQITG 54

Query: 85  NYHSVQDALFHITSRLRE 102
                Q A   IT  LR 
Sbjct: 55  PPDRAQHAAEIITDLLRS 72

>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 = 61.0 bits (148), Expect = 6e-13
 Identities = 15/70 (21%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV---NDPKPGATEGVVMVSGTSDQMR 302
            +E+ +P+  +  + G+    L   ++++GA + +    +  PG     V ++G+    +
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 303 AAQSLIHAFI 312
           AAQ LI   +
Sbjct: 64  AAQYLISQRV 73

>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 = 61.0 bits (148), Expect = 6e-13
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 29  VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHS 88
           +  + V    +G +LG+GG  + E +  TGA I++  K      G+  +  V + G+  +
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQI-SKKGEFLPGTR-NRRVTITGSPAA 61

Query: 89  VQDALFHITSRL 100
            Q A + I+ R+
Sbjct: 62  TQAAQYLISQRV 73

>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 = 59.7 bits (145), Expect = 2e-12
 Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 302
           T  +  V IP+ +   V G+N   L  +   +   + +  P+P      + ++GT + + 
Sbjct: 8   TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSNQIKITGTKEGIE 65

Query: 303 AAQSLIHAFI 312
            A+  +    
Sbjct: 66  KARHEVLLIS 75

>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 = 48.9 bits (117), Expect = 2e-08
 Identities = 11/75 (14%), Positives = 28/75 (37%), Gaps = 7/75 (9%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
             A + +  +    ++G+ G  + ++   T   I++      PR   P    +++ G   
Sbjct: 10  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI------PRPDDP-SNQIKITGTKE 62

Query: 88  SVQDALFHITSRLRE 102
            ++ A   +     E
Sbjct: 63  GIEKARHEVLLISAE 77

>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 = 60.0 bits (145), Expect = 3e-12
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 3/81 (3%)

Query: 22  FEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQ 81
                 V  +L V  + +G ++GRGG  +  + +A+GA I     D+          +++
Sbjct: 9   LTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITC---DKESEGTLLLSRLIK 65

Query: 82  VIGNYHSVQDALFHITSRLRE 102
           + G    V  A   I  ++ E
Sbjct: 66  ISGTQKEVAAAKHLILEKVSE 86

>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 = 55.4 bits (133), Expect = 2e-10
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGA--TEGVVMVSGTSDQ 300
           T    ++ +PQ  +  + G     +  I + SGA +  +    G      ++ +SGT  +
Sbjct: 13  TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE 72

Query: 301 MRAAQSLIHAFI 312
           + AA+ LI   +
Sbjct: 73  VAAAKHLILEKV 84

>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 = 59.1 bits (143), Expect = 4e-12
 Identities = 12/73 (16%), Positives = 26/73 (35%), Gaps = 1/73 (1%)

Query: 241 ILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANV-VVNDPKPGATEGVVMVSGTSD 299
            L S  + V +   Y   + G   + ++ IR     N+   +       +  + ++G   
Sbjct: 6   ALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK 65

Query: 300 QMRAAQSLIHAFI 312
              AA+  I   +
Sbjct: 66  NTEAARDAILRIV 78

>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 = 47.9 bits (114), Expect = 3e-08
 Identities = 12/72 (16%), Positives = 30/72 (41%), Gaps = 4/72 (5%)

Query: 31  RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQ 90
            + V  +    ++GR G +++++R     +I+ FP        +   + + + G   + +
Sbjct: 13  SVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQ-FPDKDDG---NQPQDQITITGYEKNTE 68

Query: 91  DALFHITSRLRE 102
            A   I   + E
Sbjct: 69  AARDAILRIVGE 80

>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 = 57.3 bits (138), Expect = 1e-11
 Identities = 16/82 (19%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 21  GFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIV 80
           G  PG   V  +++ + + G ++G+GG  + +++   G  + +    Q     +  D+ +
Sbjct: 2   GDGPGN-AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVM---IQDGPQNTGADKPL 57

Query: 81  QVIGNYHSVQDALFHITSRLRE 102
           ++ G+ + VQ A   +   +R+
Sbjct: 58  RITGDPYKVQQAKEMVLELIRD 79

>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 = 53.0 bits (127), Expect = 6e-10
 Identities = 12/77 (15%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 238 HAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV--NDPKPGATEGVVMVS 295
           H     +   E++IP      V G+    +  +++ +G  +V+  + P+    +  + ++
Sbjct: 1   HGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRIT 60

Query: 296 GTSDQMRAAQSLIHAFI 312
           G   +++ A+ ++   I
Sbjct: 61  GDPYKVQQAKEMVLELI 77

>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 = 56.8 bits (137), Expect = 2e-11
 Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 3/70 (4%)

Query: 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV---NDPKPGATEGVVMVSGTSDQMR 302
               ++P      + G+    +  I Q SGA + +     P       +  + GT  Q+ 
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQID 61

Query: 303 AAQSLIHAFI 312
            A+ LI   I
Sbjct: 62  YARQLIEEKI 71

>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 = 55.7 bits (134), Expect = 5e-11
 Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 2/70 (2%)

Query: 31  RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQ 90
             +V + + G ++G+GG  +  + + +GA I +      P    P+ ++  + G    + 
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP--PPNADPNMKLFTIRGTPQQID 61

Query: 91  DALFHITSRL 100
            A   I  ++
Sbjct: 62  YARQLIEEKI 71

>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 = 57.1 bits (138), Expect = 2e-11
 Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 242 LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQM 301
           L   TIEV +P     +V G+  S +  +      N+ V  P P     ++ ++G +  +
Sbjct: 7   LVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAITGLAANL 64

Query: 302 RAAQSLIHAFI 312
             A++ +   +
Sbjct: 65  DRAKAGLLERV 75

>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 = 48.7 bits (116), Expect = 2e-08
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 7/75 (9%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
           V   + V       ++G+ G  + +M      +I V      P       +I+ + G   
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV------PAPELQ-SDIIAITGLAA 62

Query: 88  SVQDALFHITSRLRE 102
           ++  A   +  R++E
Sbjct: 63  NLDRAKAGLLERVKE 77

>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 = 54.5 bits (131), Expect = 2e-10
 Identities = 12/68 (17%), Positives = 28/68 (41%), Gaps = 3/68 (4%)

Query: 241 ILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQ 300
           +  +   E V+ +  M    G + SN+   R++ G   +  D   G      +   ++D 
Sbjct: 4   LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGT---FRIYGESADA 60

Query: 301 MRAAQSLI 308
           ++ A+  +
Sbjct: 61  VKKARGFL 68

>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 = 52.8 bits (127), Expect = 5e-10
 Identities = 10/64 (15%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 304
             +E+ I   +  H+ G++ +N++ I+     +V +  P       ++ + G    ++ A
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI--PPDSEKSNLIRIEGDPQGVQQA 62

Query: 305 QSLI 308
           +  +
Sbjct: 63  KREL 66

>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 = 40.1 bits (94), Expect = 1e-05
 Identities = 11/67 (16%), Positives = 27/67 (40%), Gaps = 7/67 (10%)

Query: 30 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSV 89
            + +  +    L+G+ G  ++ ++     S+R  P D           ++++ G+   V
Sbjct: 7  VEINIDHKFHRHLIGKSGANINRIKDQYKVSVR-IPPDSEK------SNLIRIEGDPQGV 59

Query: 90 QDALFHI 96
          Q A   +
Sbjct: 60 QQAKREL 66

>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 = 51.8 bits (124), Expect = 2e-09
 Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 1/68 (1%)

Query: 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 304
             +EV IP      + G     +  I +  G  V ++ P  G+    V++ G S  +  A
Sbjct: 10  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECG-GVHIHFPVEGSGSDTVVIRGPSSDVEKA 68

Query: 305 QSLIHAFI 312
           +  +    
Sbjct: 69  KKQLLHLA 76

>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 = 50.2 bits (120), Expect = 5e-09
 Identities = 9/68 (13%), Positives = 19/68 (27%), Gaps = 1/68 (1%)

Query: 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 304
            + +V +     A + G     +  I      ++             V V+G  + +  A
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP-DPNCVTVTGLPENVEEA 68

Query: 305 QSLIHAFI 312
              I    
Sbjct: 69  IDHILNLE 76

>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 = 45.2 bits (107), Expect = 3e-07
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 6/75 (8%)

Query: 28  VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87
           V   + +  +    ++G  G  + ++       IR       P+ G+P    V V G   
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF------PQSGAPDPNCVTVTGLPE 63

Query: 88  SVQDALFHITSRLRE 102
           +V++A+ HI +   E
Sbjct: 64  NVEEAIDHILNLEEE 78

>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 = 50.1 bits (120), Expect = 6e-09
 Identities = 11/66 (16%), Positives = 25/66 (37%), Gaps = 8/66 (12%)

Query: 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 304
             +   I    +  V G+  S +  ++      +VV         G++ V+G   ++  A
Sbjct: 3   RIVA--INPARVPRVIGKKGSMIKLLKSELDVQIVVGQ------NGLIWVNGDRRKVSIA 54

Query: 305 QSLIHA 310
           +  I+ 
Sbjct: 55  EEAIYL 60

>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 = 34.3 bits (79), Expect = 0.002
 Identities = 10/69 (14%), Positives = 26/69 (37%), Gaps = 11/69 (15%)

Query: 34  VHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDAL 93
           ++  ++  ++G+ G ++  ++      I V             + ++ V G+   V  A 
Sbjct: 7   INPARVPRVIGKKGSMIKLLKSELDVQIVV-----------GQNGLIWVNGDRRKVSIAE 55

Query: 94  FHITSRLRE 102
             I    +E
Sbjct: 56  EAIYLIEQE 64

>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 = 11/68 (16%), Positives = 20/68 (29%), Gaps = 9/68 (13%)

Query: 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTS-DQMR 302
              +E  I    +  V G   S L  + + +   + V         G + +   + D   
Sbjct: 2   GKIVE--ISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR------NGRIHLECPNEDLEA 53

Query: 303 AAQSLIHA 310
            A   I  
Sbjct: 54  IAVMAIKI 61

>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 = 35.4 bits (82), Expect = 5e-04
 Identities = 7/36 (19%), Positives = 20/36 (55%)

Query: 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRV 63
           +  + +   +IG ++G    ++++++  TGA I +
Sbjct: 3  RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITI 38

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	318
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.76
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.75
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.74
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.72
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.71
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.7
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.7
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.68
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.67
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.67
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.66
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.66
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.65
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.64
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.63
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.61
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.61
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.56
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.55
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.55
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.54
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.53
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.52
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.52
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.51
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.47
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.45
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.44
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.44
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.42
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.41
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.33
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.32
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.3
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.3
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.15
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.05
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	99.05
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.02
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.98
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.91
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.89
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.82
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.75
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.69
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.48
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.29
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.15
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.82
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	96.19
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	96.14
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	96.02
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.55
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	92.66
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	91.67
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	89.5
d2uubc1	105	Ribosomal protein S3 N-terminal domain {Thermus th	86.94
d1wf3a2	118	GTPase Era C-terminal domain {Thermus thermophilus	86.39
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	84.47
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	84.03
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	83.39

>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=99.76  E-value=5.6e-19  Score=125.92  Aligned_cols=68  Identities=32%  Similarity=0.560  Sum_probs=65.6

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFI  312 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i  312 (318)
                      .|.+|.||++++|+||||+|++|++|++.|||+|+|+++.+++.+|.|+|+|++++|+.|++||+++|
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            68999999999999999999999999999999999998888899999999999999999999999886

>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=99.75  E-value=2.3e-18  Score=124.39  Aligned_cols=71  Identities=27%  Similarity=0.513  Sum_probs=67.9

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ..|.+|.||.+++|+||||+|++|++|++.|||+|+|.++.+++.+|.|+|+|++++++.|+.||+++|++
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            47899999999999999999999999999999999999888889999999999999999999999999875

>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=99.74  E-value=1.5e-18  Score=125.15  Aligned_cols=71  Identities=20%  Similarity=0.360  Sum_probs=67.8

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      .+++|.||.+++|+||||+|++|++|++.|||+|+|.+..+++.+|.|+|+|++++++.|+.+|.++|++-
T Consensus         3 ~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            68999999999999999999999999999999999998888889999999999999999999999999864

>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=99.72  E-value=3.4e-18  Score=122.15  Aligned_cols=70  Identities=27%  Similarity=0.527  Sum_probs=64.3

Q ss_pred             CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHh
Q 021032           26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  102 (318)
Q Consensus        26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e  102 (318)
                      ..+++||+||++++|+||||+|++|++|+++|||+|+|++.       ..+||+|+|+|++++|.+|...|.++|+|
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~-------~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC-------CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            46899999999999999999999999999999999999643       24689999999999999999999999875

>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=99.71  E-value=8.8e-18  Score=119.98  Aligned_cols=67  Identities=21%  Similarity=0.348  Sum_probs=61.3

Q ss_pred             EEEEEecccccccccccccchHHHHHHHhCCEEEEcCC---CCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 021032          246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP---KPGATEGVVMVSGTSDQMRAAQSLIHAFI  312 (318)
Q Consensus       246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~---~~~~~er~v~I~Gt~~~v~~A~~lI~~~i  312 (318)
                      .+++.||++++|+||||+|++|++|++.|||+|+|.+.   .+++.+|+|+|+|++++|+.|+.||+++|
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            47899999999999999999999999999999999754   34568899999999999999999999875

>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=99.70  E-value=1.3e-17  Score=121.56  Aligned_cols=73  Identities=23%  Similarity=0.398  Sum_probs=69.7

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcCc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGV  316 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~~  316 (318)
                      ..|.+|.||.+++|+|||++|.+|++|++.|||+|.|.++.+++.+|.|+|+|++++|+.|+.+|.++|.+++
T Consensus         7 ~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~r   79 (79)
T d1x4na1           7 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGR   79 (79)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             cEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHccC
Confidence            5789999999999999999999999999999999999988888999999999999999999999999998764

>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=99.70  E-value=1.5e-17  Score=119.69  Aligned_cols=68  Identities=22%  Similarity=0.466  Sum_probs=62.9

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCC---CCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP---KPGATEGVVMVSGTSDQMRAAQSLIHAFI  312 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~---~~~~~er~v~I~Gt~~~v~~A~~lI~~~i  312 (318)
                      .++++.||++++|+||||+|++|++|++.|||+|+|.+.   .+++.+|.|+|+|++++++.|+.||.++|
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            578999999999999999999999999999999999764   35678999999999999999999999876

>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=99.68  E-value=2.8e-17  Score=117.29  Aligned_cols=69  Identities=16%  Similarity=0.325  Sum_probs=63.9

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ..|.+|.||.+++|+||||+|++|++|++.|||+|+|.++  +..||.|+|+|+++++.+|+.+|.++|.+
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            4789999999999999999999999999999999999653  46789999999999999999999999864

>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=99.67  E-value=6.4e-17  Score=116.67  Aligned_cols=73  Identities=19%  Similarity=0.494  Sum_probs=66.1

Q ss_pred             CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ..++.+|+||.+++|+||||+|++|++|+++|||+|+|.+.     ...+++|+|+|+|++++|.+|+.+|.++++++
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 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT-----TSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccC-----CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            45789999999999999999999999999999999999642     23467999999999999999999999999885

>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=99.67  E-value=4e-17  Score=117.43  Aligned_cols=71  Identities=25%  Similarity=0.445  Sum_probs=62.7

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHH
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL  100 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  100 (318)
                      .+++|+||++++|+||||+|++||+|+++|||+|+|.+.++.  .+.+++|+|+|+|++++|.+|..+|.++|
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 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEF--LPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCC--STTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCC--CCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            358999999999999999999999999999999999764432  23467999999999999999999998765

>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=99.67  E-value=3.9e-17  Score=116.56  Aligned_cols=70  Identities=17%  Similarity=0.374  Sum_probs=61.3

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHH
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL  100 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  100 (318)
                      +++|+||++.+|+||||+|++||+|+++|||+|+|.+...  .+..+.+|+|+|+|++++|.+|..+|.++|
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 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPP--PNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT--TTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCC--CCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            4789999999999999999999999999999999975322  233467899999999999999999998764

>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=99.66  E-value=5.8e-17  Score=118.64  Aligned_cols=72  Identities=14%  Similarity=0.310  Sum_probs=66.1

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCC--CCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP--KPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~--~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ...+.+|.||.+++|+||||+|++|++|++.|||+|+|.+.  .+...+|.|+|+|++++|++|+.||.++|.+
T Consensus         6 ~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           6 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             ccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            36899999999999999999999999999999999999763  4567899999999999999999999999864

>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=99.66  E-value=5.4e-17  Score=118.84  Aligned_cols=76  Identities=16%  Similarity=0.372  Sum_probs=67.7

Q ss_pred             CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHh
Q 021032           24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  102 (318)
Q Consensus        24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e  102 (318)
                      ....++.+|+||.+++|+||||+|++||+|+++|||+|+|.+.+..   ..+.+|+|+|+|++++|.+|..+|.++|+|
T Consensus         4 ~~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           4 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQ---NTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCC---SSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CCccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCC---CCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            3467899999999999999999999999999999999999754322   346799999999999999999999999876

>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=99.65  E-value=7e-17  Score=114.84  Aligned_cols=69  Identities=28%  Similarity=0.513  Sum_probs=61.9

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHH
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL  100 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  100 (318)
                      +.|.+|+||++++|.||||+|++|++|+++|||+|+|.+.     +..+.+|+|+|+|++++|.+|..+|.++|
T Consensus         1 q~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~-----~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           1 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-----VEGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC-----CTTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCC-----CCCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            3688999999999999999999999999999999999642     23467899999999999999999998765

>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=99.64  E-value=1.1e-16  Score=115.14  Aligned_cols=72  Identities=25%  Similarity=0.452  Sum_probs=64.7

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      .++++|+||.+++|.||||+|++||+|+++|||+|+|...+     ..+.+|+|+|+|++++|.+|..+|.++|++.
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 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-----GTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT-----TSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCC-----CCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            46899999999999999999999999999999999997542     2356899999999999999999999998763

>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=99.63  E-value=4.3e-16  Score=119.38  Aligned_cols=77  Identities=22%  Similarity=0.394  Sum_probs=68.0

Q ss_pred             CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ...+++.+|+||..++|+||||+|.+||+|+++|||+|+|.+.+..   ....+|+|+|+|++++|.+|+.+|.++|.+.
T Consensus        11 ~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG---TLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC---SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            4668999999999999999999999999999999999999654321   2356899999999999999999999999764

>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=99.61  E-value=6.2e-16  Score=112.54  Aligned_cols=75  Identities=21%  Similarity=0.395  Sum_probs=67.6

Q ss_pred             CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ....++.+|+||.+++|+|||++|.+|++|+++|||+|+|.+.+     ..+.+|.|+|+|++++|.+|+.+|.++|.+.
T Consensus         4 ~~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~-----~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           4 QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS-----GGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC-----TTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             cCCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCC-----CCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            45779999999999999999999999999999999999996432     2367899999999999999999999999874

>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=99.61  E-value=9.4e-16  Score=117.45  Aligned_cols=72  Identities=21%  Similarity=0.306  Sum_probs=65.6

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCC--CCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP--GATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~--~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      +.++.+|.||.+++|+||||+|.+|++|++.|||+|+|.+..+  ...+|+|+|+|++++|+.|+.+|+++|.+
T Consensus        13 ~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T d1we8a_          13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhC
Confidence            4578999999999999999999999999999999999976533  45789999999999999999999999975

>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=99.56  E-value=3.3e-15  Score=109.07  Aligned_cols=78  Identities=21%  Similarity=0.218  Sum_probs=68.7

Q ss_pred             ccCCCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHH
Q 021032           21 GFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL  100 (318)
Q Consensus        21 ~~e~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  100 (318)
                      ..+.++.++..+.||...+|.||||+|++|++|+++|||+|+|.+.++      ..++.|+|+|++++|.+|..+|.+++
T Consensus         3 v~e~~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~------~~~~~v~I~G~~~~V~~A~~~I~~i~   76 (81)
T d2ctma1           3 VGELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA------PDPNCVTVTGLPENVEEAIDHILNLE   76 (81)
T ss_dssp             CCCTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC------SCTTEEEEESCHHHHHHHHHHHHHHH
T ss_pred             hhHhhcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC------CCCCEEEEeCCHHHHHHHHHHHHHHH
Confidence            445678889999999999999999999999999999999999964321      24679999999999999999999999


Q ss_pred             Hhhc
Q 021032          101 RETI  104 (318)
Q Consensus       101 ~e~~  104 (318)
                      +|++
T Consensus        77 ~e~~   80 (81)
T d2ctma1          77 EEYL   80 (81)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            9873

>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=99.55  E-value=5.3e-15  Score=108.76  Aligned_cols=71  Identities=17%  Similarity=0.276  Sum_probs=65.4

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCC-CCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~-~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ..+.++.||..++|+|||++|++|++|++.|||+|+|++. .++..++.|+|+|++++|++|+.+|+++|.+
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            4678999999999999999999999999999999999754 4567899999999999999999999999875

>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=99.55  E-value=4.9e-15  Score=108.97  Aligned_cols=74  Identities=18%  Similarity=0.259  Sum_probs=66.0

Q ss_pred             CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      ..++++|.||..++|.||||+|++|++|+++|||+|+|++.+    .....++.|+|+|+.++|.+|..+|.+++.+.
T Consensus         8 ~~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~----~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           8 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKD----DGNQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTT----TCSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCC----CCCCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            457899999999999999999999999999999999996542    23467899999999999999999999998874

>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=99.54  E-value=5.4e-15  Score=107.96  Aligned_cols=70  Identities=17%  Similarity=0.299  Sum_probs=64.4

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      +..+.++.||.+++|+|||++|.+|++|++.|||+|++.+  +++.++.|+|+|++++|++|+.+|++++.+
T Consensus         8 ~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~--~~~~~~~v~I~G~~~~v~~A~~~I~~iv~e   77 (81)
T d2ctea1           8 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKITGTKEGIEKARHEVLLISAE   77 (81)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCC--TTSSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECC--CCCCCCEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            4578999999999999999999999999999999999954  456788999999999999999999999875

>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=99.53  E-value=5.3e-15  Score=108.25  Aligned_cols=73  Identities=18%  Similarity=0.257  Sum_probs=64.3

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHH-hCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcCcC
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQI-SGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVT  317 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~-SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~~~  317 (318)
                      +..+.+|.||.+++|+||||+|++|++|++. +|++|++.  .+++.++.|+|+|++++|++|+.+|++++.+.++
T Consensus         8 ~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~--~~~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~~~   81 (82)
T d2ctja1           8 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFP--VEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQT   81 (82)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECC--CTTTTCCEEEEESCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEe--CCCCCCceEEEeCCHHHHHHHHHHHHHHHhhhhc
Confidence            3568999999999999999999999999987 48888884  4556789999999999999999999999987553

>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=99.52  E-value=8.7e-15  Score=104.07  Aligned_cols=67  Identities=13%  Similarity=0.308  Sum_probs=61.1

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFI  312 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i  312 (318)
                      ..+.++.||.+++++|||++|++|++|++.|||+|+|.+  +++.++.|+|+|++++|++|+.+|++++
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~--~~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPP--DSEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCC--CCSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCC--CCCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            367899999999999999999999999999999999954  4567899999999999999999999864

>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=99.52  E-value=1.1e-14  Score=106.33  Aligned_cols=74  Identities=11%  Similarity=0.211  Sum_probs=66.9

Q ss_pred             CCCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHh
Q 021032           23 EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  102 (318)
Q Consensus        23 e~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e  102 (318)
                      +....++.+|.||..++|.||||+|++|++|+++|||+|+|.+.       .+.++.|+|+|+.++|.+|..+|.+++.+
T Consensus         5 ~~~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-------~~~~~~v~I~G~~~~v~~A~~~I~~iv~e   77 (81)
T d2ctea1           5 RLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-------DDPSNQIKITGTKEGIEKARHEVLLISAE   77 (81)
T ss_dssp             CCCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-------TSSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HhcCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC-------CCCCCEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            45677899999999999999999999999999999999999543       25688999999999999999999999987


Q ss_pred             h
Q 021032          103 T  103 (318)
Q Consensus       103 ~  103 (318)
                      .
T Consensus        78 ~   78 (81)
T d2ctea1          78 Q   78 (81)
T ss_dssp             H
T ss_pred             H
Confidence            5

>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=99.51  E-value=1.1e-14  Score=106.34  Aligned_cols=72  Identities=13%  Similarity=0.119  Sum_probs=63.6

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  315 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~  315 (318)
                      ...+.++.||.+++|+|||++|++|++|++.|||+|+|.+..+ .+++.|+|+|++++|++|+.+|++++++.
T Consensus         8 ~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~-~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           8 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA-PDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC-SCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC-CCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            3467899999999999999999999999999999999975433 34578999999999999999999998764

>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=99.47  E-value=2.5e-14  Score=104.58  Aligned_cols=75  Identities=13%  Similarity=0.197  Sum_probs=66.7

Q ss_pred             cCCCCeeEEEEEEecccceeeeCCCCchHHHHHHH-hCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHH
Q 021032           22 FEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA-TGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL  100 (318)
Q Consensus        22 ~e~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~-tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l  100 (318)
                      .+..+.++.+|.||...+|.||||+|++|++|+++ ++++|++...       .+.++.|+|+|++++|.+|..+|.+++
T Consensus         4 ~e~~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~-------~~~~~~v~I~G~~~~v~~A~~~I~~~v   76 (82)
T d2ctja1           4 KDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-------GSGSDTVVIRGPSSDVEKAKKQLLHLA   76 (82)
T ss_dssp             CCCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-------TTTCCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             hhhcCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC-------CCCCceEEEeCCHHHHHHHHHHHHHHH
Confidence            45677889999999999999999999999999988 5899998542       256899999999999999999999999


Q ss_pred             Hhh
Q 021032          101 RET  103 (318)
Q Consensus       101 ~e~  103 (318)
                      .+.
T Consensus        77 ~e~   79 (82)
T d2ctja1          77 EEK   79 (82)
T ss_dssp             HHH
T ss_pred             hhh
Confidence            875

>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=99.45  E-value=6.3e-14  Score=104.44  Aligned_cols=69  Identities=19%  Similarity=0.261  Sum_probs=63.6

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ..+.++.||.+++|+|||++|.+|++|++.|||+|.|++  .++.++.|+|+|++++|++|+.+|++++.+
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~--~~~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA--PELQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCC--TTTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECC--CCCCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            578999999999999999999999999999999999954  456678999999999999999999999875

>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=99.44  E-value=1.1e-13  Score=101.14  Aligned_cols=65  Identities=20%  Similarity=0.252  Sum_probs=58.8

Q ss_pred             EEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcCcC
Q 021032          247 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVT  317 (318)
Q Consensus       247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~~~  317 (318)
                      ..+.||.+++|+||||+|++|++|++.|||+|+|.+      ++.|+|+|++++++.|+.+|+.++.+.++
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            357799999999999999999999999999999953      56899999999999999999999887654

>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=99.44  E-value=7.2e-14  Score=99.21  Aligned_cols=68  Identities=16%  Similarity=0.301  Sum_probs=60.7

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHH
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSR   99 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~   99 (318)
                      +...+++|.||.+++|.|||++|++|++|+++|||+|+|.+.       .+.++.|+|+|++++|.+|..+|.++
T Consensus         2 ~~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~-------~~~~~~v~I~G~~~~v~~A~~~I~~i   69 (71)
T d1viga_           2 NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-------SEKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CCCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC-------CSSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             CceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC-------CCCCCEEEEECCHHHHHHHHHHHHHH
Confidence            355788999999999999999999999999999999999543       25678999999999999999999764

>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=99.42  E-value=4.4e-14  Score=101.97  Aligned_cols=66  Identities=20%  Similarity=0.362  Sum_probs=58.4

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHH
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFI  312 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i  312 (318)
                      ...+.++.||.+++|+|||++|++|++|++.|||+|.+.+    ..+++|+|.| +++++++|+.||+.+.
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~----~~~g~v~I~g~~~eav~~A~~~Ie~~~   72 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD----EDTGTFRIYGESADAVKKARGFLEFVE   72 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE----TTTTEEEEEESSHHHHHHHHHHHSCCC
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEec----CCCceEEEEECCHHHHHHHHHHHHHhh
Confidence            3578999999999999999999999999999999999864    2457899999 7999999999997543

>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=99.41  E-value=1.2e-13  Score=102.83  Aligned_cols=71  Identities=17%  Similarity=0.204  Sum_probs=64.5

Q ss_pred             CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      -+++..|.||.+.+|.|||++|.+|++|+++|||+|.|.+.       .+.++.|+|+|+.++|.+|..+|.+++.+.
T Consensus         8 ~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-------~~~~~~v~I~G~~~~V~~A~~~I~~~v~e~   78 (91)
T d2ctka1           8 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-------ELQSDIIAITGLAANLDRAKAGLLERVKEL   78 (91)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT-------TTTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC-------CCCcceEEEECCHHHHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999543       256789999999999999999999988764

>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=99.33  E-value=6.5e-13  Score=97.00  Aligned_cols=62  Identities=16%  Similarity=0.214  Sum_probs=56.8

Q ss_pred             EEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032           31 RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        31 rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~  103 (318)
                      -+.||.+.+|.||||||++||+|+++|||+|+|.           .++.|.|.|++++|.+|..+|..++++.
T Consensus         4 vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~-----------~~g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           4 IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVG-----------QNGLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEEC-----------TTSEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeeCCcHHHHHHHHHHHCCEEEEC-----------CCCEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            4789999999999999999999999999999994           2578999999999999999998888774

>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=99.32  E-value=2.1e-12  Score=95.69  Aligned_cols=71  Identities=13%  Similarity=0.194  Sum_probs=64.0

Q ss_pred             CCCCeeEEEEEEecccceeeeCCCCchHHHHHHH-hCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHH
Q 021032           23 EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA-TGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLR  101 (318)
Q Consensus        23 e~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~-tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~  101 (318)
                      +..+.++..|.||...++.|||+||++|++|+++ +|++|++..          .++.|+|+|++++|.+|..+|.+++.
T Consensus        16 ~~~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~----------~~~~v~i~G~~~~ve~Ak~~I~~iv~   85 (90)
T d2ctfa1          16 KANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVK   85 (90)
T ss_dssp             CCCCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             HcCCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC----------CCceEEEeCCHHHHHHHHHHHHHHHH
Confidence            3467899999999999999999999999999999 489999952          36789999999999999999999988


Q ss_pred             hh
Q 021032          102 ET  103 (318)
Q Consensus       102 e~  103 (318)
                      +.
T Consensus        86 el   87 (90)
T d2ctfa1          86 DL   87 (90)
T ss_dssp             HH
T ss_pred             HH
Confidence            74

>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=99.30  E-value=9e-13  Score=94.92  Aligned_cols=63  Identities=16%  Similarity=0.301  Sum_probs=57.1

Q ss_pred             CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEe-cHHHHHHHHHHH
Q 021032           25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHI   96 (318)
Q Consensus        25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G-~~~~V~~A~~~I   96 (318)
                      ...++.+|.||.+.+|.|||+||++||+|+++|||+|.+...         .++.|.|.| +.++|.+|..+|
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~---------~~g~v~I~g~~~eav~~A~~~I   68 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE---------DTGTFRIYGESADAVKKARGFL   68 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET---------TTTEEEEEESSHHHHHHHHHHH
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC---------CCceEEEEECCHHHHHHHHHHH
Confidence            466889999999999999999999999999999999998642         468899999 699999999998

>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=99.30  E-value=3.5e-12  Score=94.48  Aligned_cols=67  Identities=19%  Similarity=0.324  Sum_probs=60.9

Q ss_pred             cceEEEEEecccccccccccccchHHHHHHH-hCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQI-SGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~-SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      ...|.+|.||..++++|||++|++|++|++. +|++|.+.+     .+..|+|+|++++|++|+.+|++++.+
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~-----~~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC-----CCceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            3579999999999999999999999999999 589999963     457899999999999999999999875

>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=99.15  E-value=5.1e-12  Score=91.93  Aligned_cols=66  Identities=14%  Similarity=0.097  Sum_probs=51.6

Q ss_pred             EEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 021032          247 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFI  312 (318)
Q Consensus       247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i  312 (318)
                      +++.||.+.+|.||||+|++|++|++.|||+|+|++.......+.....|.+.++++|+.+|.++-
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g~v~i~~~~~~~~~~a~~~a~~iI~aI~   70 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAIS   70 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTTEEEEEESSTTSCHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCCeEEEecCCccccHHHHHHHHHHHHHHh
Confidence            468899999999999999999999999999999964322111122223467899999999998764

>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=99.05  E-value=3.7e-12  Score=89.41  Aligned_cols=63  Identities=16%  Similarity=0.148  Sum_probs=48.4

Q ss_pred             EEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcC-HHHHHHHHHHHHHHHHcCc
Q 021032          248 EVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT-SDQMRAAQSLIHAFILCGV  316 (318)
Q Consensus       248 ~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt-~~~v~~A~~lI~~~i~~~~  316 (318)
                      -+.||.+.+|+||||+|++|++|++.|||+|.|.+      +..|+|+|. ++.++.|+.+|..+..+.+
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~------~g~v~I~g~~~~~v~~A~~~I~~i~~ea~   67 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN------NGRIWATCPSRFSEEILIEAIRKIENESH   67 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT------TSEEEC-----CTTCCTHHHHTTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC------CCEEEEEeCCHHHHHHHHHHHHHHHHhhc
Confidence            45699999999999999999999999999999943      457999995 7899999999987666543

>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=99.05  E-value=2.7e-10  Score=82.93  Aligned_cols=63  Identities=17%  Similarity=0.138  Sum_probs=56.2

Q ss_pred             EEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 021032          248 EVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV  316 (318)
Q Consensus       248 ~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~~~  316 (318)
                      .+.||.+.+|.|||++|++|+.|++.|||+|.|.+      +..|.|.| +.+.+..|+.+|..+..+.+
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d------~G~V~I~g~~~~~~~~A~~~I~~I~~ea~   67 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR------NGRIHLECPNEDLEAIAVMAIKIIDEEAY   67 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET------TTEEEEECSCHHHHHHHHHHHHHHHHCSC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC------CcEEEEEeCCHHHHHHHHHHHHHHHHhch
Confidence            46799999999999999999999999999999953      35799999 58999999999999887654

>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=99.02  E-value=1.8e-10  Score=83.61  Aligned_cols=64  Identities=20%  Similarity=0.227  Sum_probs=53.3

Q ss_pred             EEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEE-----ecHHHHHHHHHHHHHHHHhh
Q 021032           30 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI-----GNYHSVQDALFHITSRLRET  103 (318)
Q Consensus        30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~-----G~~~~V~~A~~~I~~~l~e~  103 (318)
                      +.+-||.+.+|.||||||++||+|+++|||+|+|.+.          +..|.+.     |.+.++.+|...|.++.+.+
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d----------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~rGf   73 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE----------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGF   73 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT----------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTC
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC----------CCeEEEecCCccccHHHHHHHHHHHHHHhCCC
Confidence            3578999999999999999999999999999999532          4555555     46788999999998877764

>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=98.98  E-value=6.3e-12  Score=88.22  Aligned_cols=61  Identities=13%  Similarity=0.114  Sum_probs=46.5

Q ss_pred             EEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEec-HHHHHHHHHHHHHHHHh
Q 021032           31 RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHITSRLRE  102 (318)
Q Consensus        31 rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~e  102 (318)
                      -+.||.+.+|.||||+|++||+|+++|||+|+|.           .+..|.|.|. .+++.+|...|..+.++
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~-----------~~g~v~I~g~~~~~v~~A~~~I~~i~~e   65 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVA-----------NNGRIWATCPSRFSEEILIEAIRKIENE   65 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEEC-----------TTSEEEC-----CTTCCTHHHHTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEc-----------CCCEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            3678999999999999999999999999999993           2567999996 67899999999765554

>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=98.91  E-value=3.3e-11  Score=79.77  Aligned_cols=48  Identities=17%  Similarity=0.358  Sum_probs=15.1

Q ss_pred             eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEec
Q 021032           27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN   85 (318)
Q Consensus        27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~   85 (318)
                      +...+|.||..++|.|||+||.+||+|+++|||+|+|.           .|..|.|.|.
T Consensus         2 P~~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~-----------ddg~v~I~a~   49 (54)
T d1e3ha4           2 PRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE-----------DDGTIYIGAA   49 (54)
T ss_dssp             CBCC---------------------CHHHHSCCCC-------------------CCCCB
T ss_pred             CeEEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEe-----------CCeEEEEEec
Confidence            34567899999999999999999999999999999994           3566777664

>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=98.89  E-value=1e-09  Score=79.80  Aligned_cols=62  Identities=13%  Similarity=0.102  Sum_probs=54.3

Q ss_pred             EEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEec-HHHHHHHHHHHHHHHHhh
Q 021032           31 RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHITSRLRET  103 (318)
Q Consensus        31 rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~e~  103 (318)
                      -+-||.+.+|.|||+||++||.|+++|||+|.|.           .+-.|.|.|. .+.+..|...|..+.++.
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~-----------d~G~V~I~g~~~~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVA-----------RNGRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEE-----------TTTEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEEC-----------CCcEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            3679999999999999999999999999999995           2467999995 788899999998877764

>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=98.82  E-value=1.8e-09  Score=81.08  Aligned_cols=53  Identities=19%  Similarity=0.234  Sum_probs=47.9

Q ss_pred             ccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032          255 YMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  314 (318)
Q Consensus       255 ~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~  314 (318)
                      +.|+|||++|.+|+.|++.|||+|.|.       +..|.|.|++++++.|+.+|.+++..
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~-------d~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVG-------EYEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEEC-------SSEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEe-------CCeEEEEECchhHHHHHHHHHHHHcC
Confidence            479999999999999999999999995       23588899999999999999999864

>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=98.75  E-value=2.7e-10  Score=75.32  Aligned_cols=46  Identities=22%  Similarity=0.464  Sum_probs=14.6

Q ss_pred             EEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcC
Q 021032          246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT  297 (318)
Q Consensus       246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt  297 (318)
                      ...+.||.+.+|.|||++|.+||+|+++|||+|+|.      +++.|+|.|+
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~------ddg~v~I~a~   49 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAA   49 (54)
T ss_dssp             CC---------------------CHHHHSCCCC--------------CCCCB
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEe------CCeEEEEEec
Confidence            356779999999999999999999999999999995      4677888875

>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=98.69  E-value=8.5e-09  Score=77.34  Aligned_cols=52  Identities=25%  Similarity=0.327  Sum_probs=46.6

Q ss_pred             ceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHh
Q 021032           39 IGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  102 (318)
Q Consensus        39 vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e  102 (318)
                      .|.||||||.+||.|++.|||+|.|.            +..|.|.|+++++..|...|..++.+
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~------------d~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVG------------EYEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEEC------------SSEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEe------------CCeEEEEECchhHHHHHHHHHHHHcC
Confidence            68999999999999999999999993            34577889999999999999988865

>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=98.48  E-value=2.5e-07  Score=71.36  Aligned_cols=77  Identities=18%  Similarity=0.312  Sum_probs=58.5

Q ss_pred             eeEEEEEEeccc------ceeeeCCCCchHHHHHHHhCCeEEEecCCCC----------CCCCCCCC-ceEEEEec-HHH
Q 021032           27 AVVARLLVHSQQ------IGCLLGRGGHIVSEMRRATGASIRVFPKDQA----------PRCGSPHD-EIVQVIGN-YHS   88 (318)
Q Consensus        27 ~~~~rllVp~~~------vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~----------p~~~~~~e-r~V~I~G~-~~~   88 (318)
                      .++-+++||-+.      +|.|||.+|+++|+|+++|||+|.|..+.+.          +.++...+ =-|.|+++ .+.
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~   81 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   81 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhh
Confidence            367889999765      9999999999999999999999999754331          11111222 34777775 568


Q ss_pred             HHHHHHHHHHHHHhh
Q 021032           89 VQDALFHITSRLRET  103 (318)
Q Consensus        89 V~~A~~~I~~~l~e~  103 (318)
                      +.+|+..|..+|...
T Consensus        82 ~~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          82 VKKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999988764

>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=98.29  E-value=1.1e-06  Score=67.53  Aligned_cols=71  Identities=20%  Similarity=0.334  Sum_probs=56.2

Q ss_pred             ceEEEEEeccc------ccccccccccchHHHHHHHhCCEEEEcCC----------C-----C-CCCCeEEEEEc-CHHH
Q 021032          244 STTIEVVIPQL------YMAHVYGENNSNLSHIRQISGANVVVNDP----------K-----P-GATEGVVMVSG-TSDQ  300 (318)
Q Consensus       244 ~~t~~v~IP~~------~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~----------~-----~-~~~er~v~I~G-t~~~  300 (318)
                      ..+..|.||-+      ++|+|||.+|+++|+|+++|||+|.|-..          .     . ...+=-|.|++ +++.
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~   81 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   81 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhh
Confidence            46778888875      69999999999999999999999999421          0     0 11223588888 5789


Q ss_pred             HHHHHHHHHHHHHc
Q 021032          301 MRAAQSLIHAFILC  314 (318)
Q Consensus       301 v~~A~~lI~~~i~~  314 (318)
                      ++.|..+|..+|..
T Consensus        82 ~~~A~~~i~~ll~~   95 (122)
T d1k1ga_          82 VKKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999953

>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=98.15  E-value=5.7e-07  Score=70.12  Aligned_cols=74  Identities=20%  Similarity=0.219  Sum_probs=52.6

Q ss_pred             eEEEEEEec------ccceeeeCCCCchHHHHHHHhCCeEEEecCCCCC------------CCCC-CCCceEEEEecH--
Q 021032           28 VVARLLVHS------QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAP------------RCGS-PHDEIVQVIGNY--   86 (318)
Q Consensus        28 ~~~rllVp~------~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p------------~~~~-~~er~V~I~G~~--   86 (318)
                      ++-|++||.      +++|.|||.+|.++|+|+++|||+|.|..+.+.-            .+.. ..+=-|.|+++.  
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~   81 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcH
Confidence            467888884      4699999999999999999999999998654320            0011 223457888752  


Q ss_pred             ----HHHHHHHHHHHHHHH
Q 021032           87 ----HSVQDALFHITSRLR  101 (318)
Q Consensus        87 ----~~V~~A~~~I~~~l~  101 (318)
                          ..+.+|+..|..+|.
T Consensus        82 ~~a~~kl~~A~~~I~~lL~  100 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLV  100 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHHcC
Confidence                346677777766653

>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=97.82  E-value=1.9e-05  Score=61.24  Aligned_cols=69  Identities=9%  Similarity=0.223  Sum_probs=52.6

Q ss_pred             eEEEEEecc------cccccccccccchHHHHHHHhCCEEEEcCCC------------------CCCCCeEEEEEcCH--
Q 021032          245 TTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVNDPK------------------PGATEGVVMVSGTS--  298 (318)
Q Consensus       245 ~t~~v~IP~------~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~------------------~~~~er~v~I~Gt~--  298 (318)
                      .+..|.||.      +++|+|||.+|+++|+|+++|||+|.|-..-                  ....+=-|.|++.-  
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~   81 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcH
Confidence            356777874      5899999999999999999999999995421                  01234458888852  


Q ss_pred             ----HHHHHHHHHHHHHHH
Q 021032          299 ----DQMRAAQSLIHAFIL  313 (318)
Q Consensus       299 ----~~v~~A~~lI~~~i~  313 (318)
                          ..+..|..+|..++.
T Consensus        82 ~~a~~kl~~A~~~I~~lL~  100 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLV  100 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHHcC
Confidence                358889999988774

>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=96.19  E-value=0.0019  Score=43.65  Aligned_cols=38  Identities=13%  Similarity=0.311  Sum_probs=35.3

Q ss_pred             eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032          245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      ....+.||.+..+..|||+|.|++-..+.||.+|.|..
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            46889999999999999999999999999999999953

>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=96.14  E-value=0.0019  Score=43.51  Aligned_cols=39  Identities=15%  Similarity=0.364  Sum_probs=35.8

Q ss_pred             ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032          244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  282 (318)
Q Consensus       244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~  282 (318)
                      .....+.||.+.....|||+|.|++-..+.||.+|.|..
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            357889999999999999999999999999999999953

>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=96.02  E-value=0.0025  Score=43.05  Aligned_cols=38  Identities=32%  Similarity=0.479  Sum_probs=35.3

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK   66 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~   66 (318)
                      .+.+.||..+.+..|||+|.+||-..+-||.+|.|.+.
T Consensus        28 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~   65 (68)
T d1hh2p3          28 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI   65 (68)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEc
Confidence            57889999999999999999999999999999999754

>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=95.55  E-value=0.0036  Score=42.05  Aligned_cols=39  Identities=26%  Similarity=0.306  Sum_probs=35.8

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK   66 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~   66 (318)
                      -.+.++||..+....|||+|.++|-..+-||.+|.|...
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            467889999999999999999999999999999999753

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

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: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=92.66  E-value=0.074  Score=37.11  Aligned_cols=60  Identities=12%  Similarity=0.052  Sum_probs=48.3

Q ss_pred             EEEecccccccccccccc-hHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHH
Q 021032          248 EVVIPQLYMAHVYGENNS-NLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL  313 (318)
Q Consensus       248 ~v~IP~~~vG~IIGk~G~-~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~  313 (318)
                      -+.|+..++.++||++++ -|+.|.+.+++.|.|-      ....|-|.| +++..-++...|..+-.
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG------~NGrIWi~~~~~~~~i~i~~aI~~~e~   65 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIG------LNGKIWVKCEELSNTLACYRTIMECCQ   65 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEE------TTTEEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEe------cCcEEEEECCCHHHHHHHHHHHHHHHH
Confidence            356899999999999998 7999999999999994      455678999 57777776776765543

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

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: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.67  E-value=0.026  Score=40.12  Aligned_cols=30  Identities=13%  Similarity=0.336  Sum_probs=26.4

Q ss_pred             eEEEEEEecccceeeeCCCCchHHHHHHHh
Q 021032           28 VVARLLVHSQQIGCLLGRGGHIVSEMRRAT   57 (318)
Q Consensus        28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~t   57 (318)
                      -.+++.|....-|.||||+|+.|++|+++-
T Consensus        35 ~~i~I~I~tarPGivIGrkG~~I~~L~~~l   64 (92)
T d1wh9a_          35 TRTEIIILATRTQNVLGEKGRRIRELTAVV   64 (92)
T ss_dssp             SCEEEEEEESCHHHHHCGGGHHHHHHHHHH
T ss_pred             CeEEEEEEeCCCceeeccCchhHHHHHHHH
Confidence            347889999999999999999999998653

>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]}

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: GTPase Era C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.50  E-value=0.051  Score=40.10  Aligned_cols=30  Identities=17%  Similarity=0.259  Sum_probs=25.8

Q ss_pred             eeEEEEEEec-ccceeeeCCCCchHHHHHHH
Q 021032           27 AVVARLLVHS-QQIGCLLGRGGHIVSEMRRA   56 (318)
Q Consensus        27 ~~~~rllVp~-~~vG~IIGkgG~~Ik~I~e~   56 (318)
                      .+...++|+. +|.+.||||+|++||+|..+
T Consensus        48 ~I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~   78 (113)
T d1egaa2          48 DINGLILVEREGQKKMVIGNKGAKIKTIGIE   78 (113)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHH
T ss_pred             EEEEEEEECCcchhhhhhcccchHHHHHHHH
Confidence            4778899986 68999999999999998654

>d2uubc1 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal domain {Thermus thermophilus [TaxId: 274]}

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: Ribosomal protein S3 N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=86.94  E-value=0.08  Score=38.46  Aligned_cols=29  Identities=28%  Similarity=0.532  Sum_probs=25.8

Q ss_pred             EEEEEEecccceeeeCCCCchHHHHHHHh
Q 021032           29 VARLLVHSQQIGCLLGRGGHIVSEMRRAT   57 (318)
Q Consensus        29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~t   57 (318)
                      .+++.|....-|.||||+|+.|++|+++-
T Consensus        62 ~i~I~I~tarPG~iIGkkG~~i~~L~~~l   90 (105)
T d2uubc1          62 NVAVTVHVAKPGVVIGRGGERIRVLREEL   90 (105)
T ss_dssp             CEECCEEESCHHHHHCSTTSHHHHHHHHH
T ss_pred             cEEEEEEECCCceEEcCCchhHHHHHHHH
Confidence            48888999999999999999999998763

>d1wf3a2 d.52.3.1 (A:181-298) GTPase Era C-terminal domain {Thermus thermophilus [TaxId: 274]}

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: GTPase Era C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=86.39  E-value=0.1  Score=38.64  Aligned_cols=37  Identities=24%  Similarity=0.406  Sum_probs=29.1

Q ss_pred             eeEEEEEEec-ccceeeeCCCCchHHHHH--------HHhCCeEEE
Q 021032           27 AVVARLLVHS-QQIGCLLGRGGHIVSEMR--------RATGASIRV   63 (318)
Q Consensus        27 ~~~~rllVp~-~~vG~IIGkgG~~Ik~I~--------e~tGa~I~i   63 (318)
                      .+...++|+. +|.+.||||+|++||+|.        +-.+++|.+
T Consensus        49 ~I~~~I~V~~~sqK~IiIGk~G~~ik~Ig~~aR~~le~~~~~kV~L   94 (118)
T d1wf3a2          49 YIKAILYVERPSQKAIVIGEGGRKIKEIGQATRKQLEALLGKKVYL   94 (118)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHTSEEEE
T ss_pred             EEEEEEEeCccchhhhhhccCchhHHHHHHHHHHHHHHHhCCCeEE
Confidence            4567788986 689999999999999775        446676654

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

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: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.47  E-value=0.17  Score=35.74  Aligned_cols=29  Identities=17%  Similarity=0.348  Sum_probs=24.7

Q ss_pred             EEEEEecccccccccccccchHHHHHHHh
Q 021032          246 TIEVVIPQLYMAHVYGENNSNLSHIRQIS  274 (318)
Q Consensus       246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S  274 (318)
                      ..+|.|-...-|.||||+|+.|++|++.-
T Consensus        36 ~i~I~I~tarPGivIGrkG~~I~~L~~~l   64 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGEKGRRIRELTAVV   64 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHHH
T ss_pred             eEEEEEEeCCCceeeccCchhHHHHHHHH
Confidence            46677888888999999999999998764

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

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: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=84.03  E-value=0.56  Score=32.36  Aligned_cols=49  Identities=10%  Similarity=-0.006  Sum_probs=39.1

Q ss_pred             EEEecccceeeeCCCCc-hHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEec-HHHHHH
Q 021032           32 LLVHSQQIGCLLGRGGH-IVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQD   91 (318)
Q Consensus        32 llVp~~~vG~IIGkgG~-~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~-~~~V~~   91 (318)
                      +-|+.+.+..|||++++ -++.|.+++++.|-|-           ....|-|.|+ .+....
T Consensus         5 ~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG-----------~NGrIWi~~~~~~~~i~   55 (85)
T d2ja9a2           5 IDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIG-----------LNGKIWVKCEELSNTLA   55 (85)
T ss_dssp             EECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEE-----------TTTEEEEECSSHHHHHH
T ss_pred             EEecHHHHHHHHcCCCChHHHHHHhhcCceEEEe-----------cCcEEEEECCCHHHHHH
Confidence            45788889999999998 7899999999999994           2467888885 444433

>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]}

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: GTPase Era C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=83.39  E-value=0.24  Score=36.30  Aligned_cols=31  Identities=10%  Similarity=0.091  Sum_probs=25.7

Q ss_pred             ceEEEEEecc-cccccccccccchHHHHHHHh
Q 021032          244 STTIEVVIPQ-LYMAHVYGENNSNLSHIRQIS  274 (318)
Q Consensus       244 ~~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~S  274 (318)
                      .....+.|+. +.-+-||||+|++|++|...+
T Consensus        48 ~I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~a   79 (113)
T d1egaa2          48 DINGLILVEREGQKKMVIGNKGAKIKTIGIEA   79 (113)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             EEEEEEEECCcchhhhhhcccchHHHHHHHHH
Confidence            4678888987 667999999999999887654