Citrus Sinensis ID: 014452

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420----
Protein Sequence
MVVQGNPYPPAAEPFHQRGYAPGYHSRGYSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVTS
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHHcccEEEccccccccccEEEEEEccccccccHHHHHHHHHHHcccccccccccccEEEEEEEccccEEEEEccccccHHHHHHHHcccEEEEccccccccccccccEEEEcccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccccccEEccccccHHHHHHHHccEEEEcccccccccEEEEEEccHHHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHcccEEEEcccccccccEEEEEEccccHHHHHHHHHHHHHHHHHHHccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHcccEEEEEccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEccccccEEEccccHHHHHHHHHcccEEEEEccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
mvvqgnpyppaaepfhqrgyapgyhsrgyssgpghetvggrnrmfYEEEVVFKLLCHLDKvgsligkggsiVRTFqnetgasikiadilpdseERIVVISArensemrhspaqDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCllgrgghivSEMRRATgasirvfpkdqaprcgsphdEIVQVIGNYHSVQDALFHITSRLREtifpmkrpgpnnghsylppfpemppppfrprhnpaspgsypspvgpfhsmdrgmgpsqpfdhqaafshgmdpmvppnsdripfpygserpghgptfdrppsprswtpqgvgggdprgfdassgftprnrpvesgnhaailTSTTIEVVIPQLYMAHVygennsnlshirqisganvvvndpkpgategvVMVSGTSDQMRAAQSLIHAFILCGVTS
Flexible Loop (DISEMBL)
mvvqgnpyppaaepFHQRGYAPGYHSRGYSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLigkggsivrtfqnetgasikiadilpdseERIVVISarensemrhspaqDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVTS
Low Complexity Region (SEG)
MVVQGNPYPPAAEPFHQRGYAPGYHSRGYSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLppfpemppppfrprhnpaspGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVTS
Disordered region (IsUnstruct)
**************************************GGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVI****************VMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKD***RCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIF************************************************************************************************************************************HAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN********GVVMV*******RAAQSLIHAFILCGV**
Disordered Region (DISOPRED)
**************************************************VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR*****************ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE****************************************************************AFSHGMDPMVPPNSDRIPFPYGSER***************************GFDA**********************TTIEVVIPQLYMAHVYGENNSNLSHIRQISGA**********ATEGVVMVSGTSDQMRAAQSLIHAFILCG***
Disordered Region (DISEMBL)
MVVQGNPYPPAAEPFHQRGYAPGYHSRGYSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISAREN*********DAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVTS
Disordered Region (DISPRO)
**********************************************EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMK*******HSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVG**DPRGFDASSG***************ILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVVQGNPYPPAAEPFHQRGYAPGYHSRGYSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVTS
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	424	2.2.26 [Sep-21-2011]
P58223	606	KH domain-containing prot	no	no	0.396	0.277	0.331	3e-20
O19048	356	Poly(rC)-binding protein	yes	no	0.771	0.918	0.247	4e-14
P60335	356	Poly(rC)-binding protein	yes	no	0.771	0.918	0.247	4e-14
Q15365	356	Poly(rC)-binding protein	yes	no	0.771	0.918	0.247	4e-14
Q5E9A3	356	Poly(rC)-binding protein	yes	no	0.771	0.918	0.247	4e-14
Q61990	362	Poly(rC)-binding protein	no	no	0.728	0.853	0.241	8e-13
Q15366	365	Poly(rC)-binding protein	no	no	0.721	0.838	0.238	1e-12
Q9UNW9	492	RNA-binding protein Nova-	no	no	0.365	0.315	0.265	5e-09
Q5SF07	592	Insulin-like growth facto	no	no	0.370	0.265	0.298	7e-09
P57721	371	Poly(rC)-binding protein	no	no	0.275	0.315	0.333	9e-09

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

 Score =  100 bits (248), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 61/184 (33%), Positives = 103/184 (55%), Gaps = 16/184 (8%)

Query: 30  SSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADIL 89
           SS P     GG +R    EE+VFK+LC L  +  +IGKGGS ++  +  +G+ I++ D  
Sbjct: 295 SSLPVTHGFGGSSR---SEELVFKVLCPLCNIMRVIGKGGSTIKRIREASGSCIEVNDSR 351

Query: 90  PDS--EERIVVISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGC 147
                +E +++++A E+ +   S A +AV+ +   I +   E  + V  +LLV S+ IGC
Sbjct: 352 TKCGDDECVIIVTATESPDDMKSMAVEAVLLLQEYIND---EDAENVKMQLLVSSKVIGC 408

Query: 148 LLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLR 207
           ++G+ G +++E+R+ T A+I +             D++V+V G   SV+DAL  I  RLR
Sbjct: 409 VIGKSGSVINEIRKRTNANICISK--------GKKDDLVEVSGEVSSVRDALIQIVLRLR 460

Query: 208 ETIF 211
           E + 
Sbjct: 461 EDVL 464

Arabidopsis thaliana (taxid: 3702)

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

 Score = 79.7 bits (195), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 92/372 (24%), Positives = 158/372 (42%), Gaps = 45/372 (12%)

Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMR- 108
           +  +LL H  +VGS+IGK G  V+  + E+GA I I++   +  ERI+ ++   N+  + 
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITLTGPTNAIFKA 71

Query: 109 HSPAQDAVMR-VHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 167
            +   D +   ++S +          V  RL+V + Q G L+G+GG  + E+R +TGA +
Sbjct: 72  FAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQV 131

Query: 168 RVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPP 227
           +V   D  P   +  +  + + G   SV + +  I   + ET+         +    +  
Sbjct: 132 QV-AGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLETL-------SQSPQGRVMT 180

Query: 228 FPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFD-HQAAFSHGMDPMVPPNS 286
            P  P P   P              G  H+     GP  P D +     H + P+     
Sbjct: 181 IPYQPMPASSPVICAGGQDRCSDAAGYPHATHDLEGP--PLDAYSIQGQHTISPL----- 233

Query: 287 DRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAA 346
           D       + +  H                  GG    G D+SS       P   G  A+
Sbjct: 234 DLAKLNQVARQQSHFAMMH-------------GGTGFAGIDSSS-------PEVKGYWAS 273

Query: 347 I--LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTS 404
           +   T TT E+ IP   +  + G   +N++ IRQ+SGA + + +P  G++   V ++G++
Sbjct: 274 LDASTQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSA 333

Query: 405 DQMRAAQSLIHA 416
             +  AQ LI+A
Sbjct: 334 ASISLAQYLINA 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 = 79.7 bits (195), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 92/372 (24%), Positives = 158/372 (42%), Gaps = 45/372 (12%)

Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMR- 108
           +  +LL H  +VGS+IGK G  V+  + E+GA I I++   +  ERI+ ++   N+  + 
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITLTGPTNAIFKA 71

Query: 109 HSPAQDAVMR-VHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 167
            +   D +   ++S +          V  RL+V + Q G L+G+GG  + E+R +TGA +
Sbjct: 72  FAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQV 131

Query: 168 RVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPP 227
           +V   D  P   +  +  + + G   SV + +  I   + ET+         +    +  
Sbjct: 132 QV-AGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLETL-------SQSPQGRVMT 180

Query: 228 FPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFD-HQAAFSHGMDPMVPPNS 286
            P  P P   P              G  H+     GP  P D +     H + P+     
Sbjct: 181 IPYQPMPASSPVICAGGQDRCSDAAGYPHATHDLEGP--PLDAYSIQGQHTISPL----- 233

Query: 287 DRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAA 346
           D       + +  H                  GG    G D+SS       P   G  A+
Sbjct: 234 DLAKLNQVARQQSHFAMMH-------------GGTGFAGIDSSS-------PEVKGYWAS 273

Query: 347 I--LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTS 404
           +   T TT E+ IP   +  + G   +N++ IRQ+SGA + + +P  G++   V ++G++
Sbjct: 274 LDASTQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSA 333

Query: 405 DQMRAAQSLIHA 416
             +  AQ LI+A
Sbjct: 334 ASISLAQYLINA 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 = 79.7 bits (195), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 92/372 (24%), Positives = 158/372 (42%), Gaps = 45/372 (12%)

Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMR- 108
           +  +LL H  +VGS+IGK G  V+  + E+GA I I++   +  ERI+ ++   N+  + 
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITLTGPTNAIFKA 71

Query: 109 HSPAQDAVMR-VHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 167
            +   D +   ++S +          V  RL+V + Q G L+G+GG  + E+R +TGA +
Sbjct: 72  FAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQV 131

Query: 168 RVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPP 227
           +V   D  P   +  +  + + G   SV + +  I   + ET+         +    +  
Sbjct: 132 QV-AGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLETL-------SQSPQGRVMT 180

Query: 228 FPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFD-HQAAFSHGMDPMVPPNS 286
            P  P P   P              G  H+     GP  P D +     H + P+     
Sbjct: 181 IPYQPMPASSPVICAGGQDRCSDAAGYPHATHDLEGP--PLDAYSIQGQHTISPL----- 233

Query: 287 DRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAA 346
           D       + +  H                  GG    G D+SS       P   G  A+
Sbjct: 234 DLAKLNQVARQQSHFAMMH-------------GGTGFAGIDSSS-------PEVKGYWAS 273

Query: 347 I--LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTS 404
           +   T TT E+ IP   +  + G   +N++ IRQ+SGA + + +P  G++   V ++G++
Sbjct: 274 LDASTQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSA 333

Query: 405 DQMRAAQSLIHA 416
             +  AQ LI+A
Sbjct: 334 ASISLAQYLINA 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 = 79.7 bits (195), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 92/372 (24%), Positives = 158/372 (42%), Gaps = 45/372 (12%)

Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMR- 108
           +  +LL H  +VGS+IGK G  V+  + E+GA I I++   +  ERI+ ++   N+  + 
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITLTGPTNAIFKA 71

Query: 109 HSPAQDAVMR-VHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 167
            +   D +   ++S +          V  RL+V + Q G L+G+GG  + E+R +TGA +
Sbjct: 72  FAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQV 131

Query: 168 RVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPP 227
           +V   D  P   +  +  + + G   SV + +  I   + ET+         +    +  
Sbjct: 132 QV-AGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLETL-------SQSPQGRVMT 180

Query: 228 FPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFD-HQAAFSHGMDPMVPPNS 286
            P  P P   P              G  H+     GP  P D +     H + P+     
Sbjct: 181 IPYQPMPASSPVICAGGQDRCSDAAGYPHATHDLEGP--PLDAYSIQGQHTISPL----- 233

Query: 287 DRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAA 346
           D       + +  H                  GG    G D+SS       P   G  A+
Sbjct: 234 DLAKLNQVARQQSHFAMMH-------------GGTGFAGIDSSS-------PEVKGYWAS 273

Query: 347 I--LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTS 404
           +   T TT E+ IP   +  + G   +N++ IRQ+SGA + + +P  G++   V ++G++
Sbjct: 274 LDASTQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSA 333

Query: 405 DQMRAAQSLIHA 416
             +  AQ LI+A
Sbjct: 334 ASISLAQYLINA 345

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

Bos taurus (taxid: 9913)

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

 Score = 75.5 bits (184), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 95/393 (24%), Positives = 167/393 (42%), Gaps = 84/393 (21%)

Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRH 109
           +  +LL H  +VGS+IGK G  V+  + E+GA I I++   +  ERI+ ++   N+  + 
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTNAIFKA 71

Query: 110 SPAQDAVMRVHSRIAEIGFEPGQA----VVARLLVHSQQIGCLLGRGGHIVSEMRRATGA 165
                 + ++   I+        A    V  RL+V + Q G L+G+GG  + E+R +TGA
Sbjct: 72  FAM--IIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGA 129

Query: 166 SIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYL 225
            ++V   D  P   +  +  + + G   S+ + +  I   + E+        P  G +  
Sbjct: 130 QVQV-AGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLES--------PPKGVTI- 176

Query: 226 PPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPN 285
                    P+RP+  P+S     SPV      DR             +S G        
Sbjct: 177 ---------PYRPK--PSS-----SPVIFAGGQDR-------------YSTG-------- 199

Query: 286 SDRIPFPYGSERPGHGPTFDRPPSPRSWTPQG-----------------------VGGGD 322
           SD   FP+ +      P  + PP   ++T QG                       +  G+
Sbjct: 200 SDSASFPHTTPSMCLNPDLEGPP-LEAYTIQGQYAIPQPDLTKLHQLAMQQSHFPMTHGN 258

Query: 323 PRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGA 382
             GF      +P  +   +G  A+  T T+ E+ IP   +  + G   + ++ IRQ+SGA
Sbjct: 259 -TGFSGIESSSPEVKGYWAGLDASAQT-TSHELTIPNDLIGCIIGRQGAKINEIRQMSGA 316

Query: 383 NVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH 415
            + + +P  G+T+  V ++G++  +  AQ LI+
Sbjct: 317 QIKIANPVEGSTDRQVTITGSAASISLAQYLIN 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|Q15366|PCBP2_HUMAN Poly(rC)-binding protein 2 OS=Homo sapiens GN=PCBP2 PE=1 SV=1

 Score = 74.7 bits (182), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 95/399 (23%), Positives = 167/399 (41%), Gaps = 93/399 (23%)

Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRH 109
           +  +LL H  +VGS+IGK G  V+  + E+GA I I++   +  ERI+ ++   N+  + 
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTNAIFKA 71

Query: 110 SPAQDAVMRVHSRIAEIGFEPGQA----VVARLLVHSQQIGCLLGRGGHIVSEMRRATGA 165
                 + ++   I+        A    V  RL+V + Q G L+G+GG  + E+R +TGA
Sbjct: 72  FAM--IIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGA 129

Query: 166 SIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYL 225
            ++V   D  P   +  +  + + G   S+ + +  I   + ET+            S  
Sbjct: 130 QVQV-AGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLETL------------SQS 173

Query: 226 PPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPN 285
           P  P+    P+RP+  P+S     SPV      DR             +S G        
Sbjct: 174 P--PKGVTIPYRPK--PSS-----SPVIFAGGQDR-------------YSTG-------- 203

Query: 286 SDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGV-------------------------GG 320
           SD   FP+ +      P  + PP   ++T QG                          G 
Sbjct: 204 SDSASFPHTTPSMCLNPDLEGPP-LEAYTIQGQYAIPQPDLTKLHQLAMQQSHFPMTHGN 262

Query: 321 GDPRGFDASS----GFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHI 376
               G ++SS    G+   +   ++ +H         E+ IP   +  + G   + ++ I
Sbjct: 263 TGFSGIESSSPEVKGYWGLDASAQTTSH---------ELTIPNDLIGCIIGRQGAKINEI 313

Query: 377 RQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH 415
           RQ+SGA + + +P  G+T+  V ++G++  +  AQ LI+
Sbjct: 314 RQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLIN 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|Q9UNW9|NOVA2_HUMAN RNA-binding protein Nova-2 OS=Homo sapiens GN=NOVA2 PE=1 SV=1

 Score = 62.8 bits (151), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 51/192 (26%), Positives = 83/192 (43%), Gaps = 37/192 (19%)

Query: 41  RNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA---DILPDSEERIV 97
           R+    E E   K+L      GS+IGKGG  +   Q ETGA+IK++   D  P + ER+ 
Sbjct: 24  RSNTGEEGEYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVC 83

Query: 98  VISARENSEMRHSPAQDAVMRVHSRIAE---------------------IGFEPGQAVVA 136
           ++              +A+  VHS IAE                         P +A  A
Sbjct: 84  LVQG----------TAEALNAVHSFIAEKVREIPQAMTKPEVVNILQPQTTMNPDRAKQA 133

Query: 137 RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQ 196
           +L+V +   G ++G+GG  V  +   +GA +++    Q P   +  + +V V G    V 
Sbjct: 134 KLIVPNSTAGLIIGKGGATVKAVMEQSGAWVQL---SQKPEGINLQERVVTVSGEPEQVH 190

Query: 197 DALFHITSRLRE 208
            A+  I  +++E
Sbjct: 191 KAVSAIVQKVQE 202

May regulate RNA splicing or metabolism in a specific subset of developing neurons (By similarity). Binds single strand RNA.

Homo sapiens (taxid: 9606)

>sp|Q5SF07|IF2B2_MOUSE Insulin-like growth factor 2 mRNA-binding protein 2 OS=Mus musculus GN=Igf2bp2 PE=1 SV=1

 Score = 62.4 bits (150), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 89/174 (51%), Gaps = 17/174 (9%)

Query: 46  YEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADIL-PDSEERIVVISAREN 104
           Y E+    L      VG++IGK G+ ++      GASIKIA    PD  ER+V+I+    
Sbjct: 417 YPEQETVSLFIPTQAVGAIIGKKGAHIKQLARFAGASIKIAPAEGPDVSERMVIITGPPE 476

Query: 105 SEMRHSPAQDAVMRVHSRIAEIG-FEPGQAVV--ARLLVHSQQIGCLLGRGGHIVSEMRR 161
           ++ +      A  R+  ++ E   F P + V   A + V S   G ++G+GG  V+E++ 
Sbjct: 477 AQFK------AQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNELQN 530

Query: 162 ATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKR 215
            T A + + P+DQ P      + IV++IG++ + Q A      ++RE +  +K+
Sbjct: 531 LTSAEV-IVPRDQTP--DENEEVIVRIIGHFFASQTA----QRKIREIVQQVKQ 577

Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. May regulate translation of target mRNAs.

Mus musculus (taxid: 10090)

>sp|P57721|PCBP3_HUMAN Poly(rC)-binding protein 3 OS=Homo sapiens GN=PCBP3 PE=2 SV=2

 Score = 62.0 bits (149), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 41/123 (33%), Positives = 67/123 (54%), Gaps = 6/123 (4%)

Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRH 109
           +  +LL H  +VGS+IGK G  V+  + E+GA I I++   +  ERIV I+   ++  + 
Sbjct: 46  LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISE--GNCPERIVTITGPTDAIFK- 102

Query: 110 SPAQDAVMRVHSRIAEIGFEPGQA---VVARLLVHSQQIGCLLGRGGHIVSEMRRATGAS 166
           + A  A       I  +   P  +   V  RL+V + Q G L+G+GG  + E+R +TGA 
Sbjct: 103 AFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQ 162

Query: 167 IRV 169
           ++V
Sbjct: 163 VQV 165

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

Homo sapiens (taxid: 9606)

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	424
225443339	704	PREDICTED: KH domain-containing protein	0.981	0.590	0.664	1e-154
147863214	807	hypothetical protein VITISV_006585 [Viti	0.983	0.516	0.656	1e-154
449492545	716	PREDICTED: KH domain-containing protein	0.931	0.551	0.579	1e-117
449448150	716	PREDICTED: KH domain-containing protein	0.931	0.551	0.579	1e-117
356526304	565	PREDICTED: heterogeneous nuclear ribonuc	0.908	0.681	0.591	1e-111
356522258	559	PREDICTED: KH domain-containing protein	0.903	0.685	0.594	1e-111
15217969	621	RNA-binding KH domain-containing protein	0.912	0.623	0.564	1e-109
297847528	622	KH domain-containing protein [Arabidopsi	0.912	0.622	0.565	1e-108
357159179	629	PREDICTED: poly(rC)-binding protein 2-li	0.955	0.643	0.476	3e-94
326504604	531	predicted protein [Hordeum vulgare subsp	0.945	0.755	0.461	2e-90

>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 =  551 bits (1421), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 283/426 (66%), Positives = 330/426 (77%), Gaps = 10/426 (2%)

Query: 2   VVQGNPYPPAAEPFHQRGYA-----PGYHSRGYSSGPGHETVGGRNRMFYEEEVVFKLLC 56
           ++ GN  P   + F QRGY      P YHSRGYSS PG E +G  +RM  EEEVVFKLLC
Sbjct: 275 MLHGNGMPGQLDSFPQRGYGSSLHGPDYHSRGYSSMPGPENIGANHRMVLEEEVVFKLLC 334

Query: 57  HLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAV 116
           H +KVGSLIGKGGSI+R  Q+ETGASIKIAD  PDS+ER+VVISAREN E +HSPAQDAV
Sbjct: 335 HFEKVGSLIGKGGSIIRFLQSETGASIKIADAAPDSDERVVVISARENLEQKHSPAQDAV 394

Query: 117 MRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAP 176
           +RVH RIAEIGFEPG AVVARLLVHSQQIGCLLG+GG I+SEMRRATGASIR+F K+Q P
Sbjct: 395 IRVHCRIAEIGFEPGAAVVARLLVHSQQIGCLLGKGGIIISEMRRATGASIRIFAKEQVP 454

Query: 177 RCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPN-NGHSYLPPFPEMPPPP 235
           +CGS +DE+VQVIG+  SVQDALF ITSR+RETIFP+K    N NG  Y+  FPE+PPP 
Sbjct: 455 KCGSQNDELVQVIGSLQSVQDALFRITSRIRETIFPLKPSISNVNGPPYMSSFPEIPPPM 514

Query: 236 FRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGS 295
           FRPRH+PASPG Y SPVG  H +DR   P  P DHQ++FSHG+D + P N DR P+PYG 
Sbjct: 515 FRPRHDPASPGHYSSPVGVPHGIDRSAVPGHPLDHQSSFSHGVDRIGPSNLDRAPYPYGG 574

Query: 296 ERPGHGPTFDRP-PSPRSWTPQGVGGGDPRGFDASSG-FTPRNRPVESGNHAAILTSTTI 353
           +RPGHGP FDRP  SPR WT QGV  G+ RG D  SG    RN P  SG+ A  +T+TT+
Sbjct: 575 DRPGHGPPFDRPSSSPRMWT-QGV-SGNLRGTDVGSGSLASRNGPPGSGSQAPNITTTTV 632

Query: 354 EVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSL 413
           EV +PQ  ++HVYGENNSNL+ IRQISGA VV+ DP+ G++EGVV+VSGT DQ RAAQSL
Sbjct: 633 EVAVPQALLSHVYGENNSNLNQIRQISGARVVIQDPRTGSSEGVVVVSGTPDQTRAAQSL 692

Query: 414 IHAFIL 419
           + AFIL
Sbjct: 693 VQAFIL 698

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  550 bits (1418), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 283/431 (65%), Positives = 330/431 (76%), Gaps = 14/431 (3%)

Query: 2   VVQGNPYPPAAEPFHQRGYA-----PGYHSRGYSSGPGHETVGGRNRMFYEEEVVFKLLC 56
           ++ GN  P   + F QRGY      P YHSRGYSS PG E +G  +RM  EEEVVFKLLC
Sbjct: 371 MLHGNGMPGQLDSFPQRGYGSSLHGPDYHSRGYSSMPGPENIGANHRMVLEEEVVFKLLC 430

Query: 57  HLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARE-----NSEMRHSP 111
           H +KVGSLIGKGGSI+R  Q+ETGASIKIAD  PDS+ER+VVISARE     N E +HSP
Sbjct: 431 HFEKVGSLIGKGGSIIRXLQSETGASIKIADAAPDSDERVVVISAREACTLTNXEQKHSP 490

Query: 112 AQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFP 171
           AQDAV+RVH RIAEIGFEPG AVVARLLVHSQQIGCLLG+GG I+SEMRRATGASIR+F 
Sbjct: 491 AQDAVIRVHCRIAEIGFEPGAAVVARLLVHSQQIGCLLGKGGIIISEMRRATGASIRIFA 550

Query: 172 KDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPN-NGHSYLPPFPE 230
           K+Q P+CGS +DE+VQVIG+  SVQDALF ITSR+RETIFP+K    N NG  Y+  FPE
Sbjct: 551 KEQVPKCGSQNDELVQVIGSLQSVQDALFCITSRIRETIFPLKPSISNVNGPPYMSSFPE 610

Query: 231 MPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIP 290
           +PPP FRPRH+PASPG Y SPVG  H +DR   P  P DHQ++FSHG+D + P N DR P
Sbjct: 611 IPPPMFRPRHDPASPGHYSSPVGVPHGIDRSAVPGHPLDHQSSFSHGVDRIGPSNLDRAP 670

Query: 291 FPYGSERPGHGPTFDRP-PSPRSWTPQGVGGGDPRGFDA-SSGFTPRNRPVESGNHAAIL 348
           +PYG +RPGHGP FDRP  SPR WTPQGV  G+ RG D  S G   R+ P  SG+ A  +
Sbjct: 671 YPYGGDRPGHGPPFDRPSSSPRMWTPQGV-SGNLRGTDVGSGGLASRSGPPGSGSQAPNI 729

Query: 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 408
           T TT+EV +PQ  ++HVYGENNSNL+ IRQISGA VV+ DP+ G++EGVV+VSGT DQ R
Sbjct: 730 TXTTVEVAVPQALLSHVYGENNSNLNQIRQISGARVVIQDPRTGSSEGVVVVSGTPDQTR 789

Query: 409 AAQSLIHAFIL 419
           AAQSL+ AFIL
Sbjct: 790 AAQSLVQAFIL 800

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  427 bits (1097), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 233/402 (57%), Positives = 282/402 (70%), Gaps = 7/402 (1%)

Query: 24  YHSRGYSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASI 83
           Y SR YSS PGHE  G   R   EE+VVF+LLC  DKVGSLIGKGG++VR  QNETGASI
Sbjct: 318 YRSRSYSSIPGHENAGAGPRAAMEEDVVFRLLCQPDKVGSLIGKGGTVVRALQNETGASI 377

Query: 84  KIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQ 143
           KI D  PD +ER+VVISARE  E  +SPAQ+AV+R H RIAEIG+EPG AVVARLLVH Q
Sbjct: 378 KIVDT-PDLDERLVVISARETLEQTYSPAQEAVIRAHCRIAEIGYEPGAAVVARLLVHGQ 436

Query: 144 QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHIT 203
           QIG L+GRGGHI+++MRR TG SI++FP+DQ    G   DE+VQVIGN  SVQDALFHIT
Sbjct: 437 QIGYLVGRGGHIINDMRRGTGTSIQIFPRDQIQNGGPMSDEVVQVIGNLPSVQDALFHIT 496

Query: 204 SRLRETIFPMK--RPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRG 261
           +R+R+T FPM+   P  NN   YL P PE PPP FRP  N  SPG YPS  G     +R 
Sbjct: 497 NRIRDTFFPMRPHVPNFNNHPPYLSPHPETPPPLFRPGSNAHSPGYYPSQAGGLRGTERP 556

Query: 262 MGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGG 321
              S P DHQ A+ H +      N D +P+P+G ERPG G +F+R PSPRSWT Q V   
Sbjct: 557 PYHSHPLDHQPAYPHNVSFGGGNNMDGVPYPHGMERPGPG-SFER-PSPRSWTSQ-VSSE 613

Query: 322 DPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISG 381
            P+G     G   RN P  SG     +  T++E+VIPQ  + H+YGENN+N++H++QISG
Sbjct: 614 IPKGPTDGFGMVSRNEPYGSGG-PHFMGGTSMEMVIPQTLICHIYGENNNNIAHVQQISG 672

Query: 382 ANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVT 423
           A +VV+D KPG  +G V++SGT DQ+RAAQ L+HAFILCG T
Sbjct: 673 AMLVVHDAKPGMFDGKVIMSGTPDQIRAAQRLVHAFILCGKT 714

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  427 bits (1097), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 233/402 (57%), Positives = 282/402 (70%), Gaps = 7/402 (1%)

Query: 24  YHSRGYSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASI 83
           Y SR YSS PGHE  G   R   EE+VVF+LLC  DKVGSLIGKGG++VR  QNETGASI
Sbjct: 318 YRSRSYSSIPGHENAGAGPRAAMEEDVVFRLLCQPDKVGSLIGKGGTVVRALQNETGASI 377

Query: 84  KIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQ 143
           KI D  PD +ER+VVISARE  E  +SPAQ+AV+R H RIAEIG+EPG AVVARLLVH Q
Sbjct: 378 KIVDT-PDLDERLVVISARETLEQTYSPAQEAVIRAHCRIAEIGYEPGAAVVARLLVHGQ 436

Query: 144 QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHIT 203
           QIG L+GRGGHI+++MRR TG SI++FP+DQ    G   DE+VQVIGN  SVQDALFHIT
Sbjct: 437 QIGYLVGRGGHIINDMRRGTGTSIQIFPRDQIQNGGPMSDEVVQVIGNLPSVQDALFHIT 496

Query: 204 SRLRETIFPMK--RPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRG 261
           +R+R+T FPM+   P  NN   YL P PE PPP FRP  N  SPG YPS  G     +R 
Sbjct: 497 NRIRDTFFPMRPHVPNFNNHPPYLSPHPETPPPLFRPGSNAHSPGYYPSQAGGLRGTERP 556

Query: 262 MGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGG 321
              S P DHQ A+ H +      N D +P+P+G ERPG G +F+R PSPRSWT Q V   
Sbjct: 557 PYHSHPLDHQPAYPHNVSFGGGNNMDGVPYPHGMERPGPG-SFER-PSPRSWTSQ-VSSE 613

Query: 322 DPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISG 381
            P+G     G   RN P  SG     +  T++E+VIPQ  + H+YGENN+N++H++QISG
Sbjct: 614 IPKGPTDGFGMVSRNEPYGSGG-PHFMGGTSMEMVIPQTLICHIYGENNNNIAHVQQISG 672

Query: 382 ANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVT 423
           A +VV+D KPG  +G V++SGT DQ+RAAQ L+HAFILCG T
Sbjct: 673 AMLVVHDAKPGMFDGKVIMSGTPDQIRAAQRLVHAFILCGKT 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 =  408 bits (1048), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 240/406 (59%), Positives = 287/406 (70%), Gaps = 21/406 (5%)

Query: 22  PGYHSRG-YSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETG 80
           P +HSRG YS   GH +    +RMF EEEVVFKLLC  DKVGSLIGKGGS+VR  QNETG
Sbjct: 175 PDHHSRGAYSESAGHSS----HRMFVEEEVVFKLLCRHDKVGSLIGKGGSVVRALQNETG 230

Query: 81  ASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLV 140
           ASI+I +  PDS+ER+VVISA+E SE +HSPAQ+AV+RVH R+ EIGFEP  AVVA+LLV
Sbjct: 231 ASIQIVEAGPDSDERVVVISAQETSEQKHSPAQEAVIRVHCRLTEIGFEPSAAVVAKLLV 290

Query: 141 HSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALF 200
            S Q+GCLLG+GG ++SEMRRATGASIR+F K+Q     S ++E+VQVIG+  SVQDALF
Sbjct: 291 RSPQVGCLLGKGGLVISEMRRATGASIRIFSKEQIKYI-SQNEEVVQVIGSLQSVQDALF 349

Query: 201 HITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSP-VGPFHSMD 259
           HIT+R+RETIFP++ P   +   + PPFPEMPPP FRPR++  S G  P P VG  H  D
Sbjct: 350 HITNRIRETIFPIRTPPNFSAPPHFPPFPEMPPPLFRPRNHLMSSGHPPPPQVG--HPHD 407

Query: 260 RGMGPSQPFDHQA-AFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGV 318
               P  P DHQ  AF HGM    PPN DR+P+P G         ++ P SPRSW P  V
Sbjct: 408 HSTVPPMPVDHQQHAFVHGMG-RGPPNMDRVPYPRG---------YEGPNSPRSWNPLAV 457

Query: 319 GGGDPRGFDASSGFTPRNR-PVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIR 377
             G+P G   +S  T RN  PV++GN      S TIE+ IP +Y+ HVYGENNSNL+ IR
Sbjct: 458 DRGNPGGTADTSSLTSRNETPVKNGNPLQNPNSLTIEITIPYMYLTHVYGENNSNLTQIR 517

Query: 378 QISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVT 423
           Q SGANV V+D KPGATEG+V+VSG  DQ  AAQ LI  FILCG T
Sbjct: 518 QTSGANVAVHDSKPGATEGLVIVSGAPDQTHAAQCLIQGFILCGQT 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 =  407 bits (1046), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 240/404 (59%), Positives = 288/404 (71%), Gaps = 21/404 (5%)

Query: 24  YHSRG-YSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGAS 82
           +HSRG YS   GH +    +RMF EE+VVFKLLCH +KVGSLIGKGGS+VR  QNETGAS
Sbjct: 171 HHSRGCYSESAGHSS----HRMFLEEDVVFKLLCHHEKVGSLIGKGGSVVRALQNETGAS 226

Query: 83  IKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHS 142
           I+I +  PDS+ER+VVISARE SE +HSPAQ+AV+RVH R+ EIGFEP  AVVA+LLV S
Sbjct: 227 IQIVEAGPDSDERVVVISARETSEQKHSPAQEAVIRVHCRLTEIGFEPSAAVVAKLLVRS 286

Query: 143 QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI 202
            Q+GCLLG+GG ++SEMRR TGASIR+F K+Q     S ++E+VQVIG+  SVQDALFHI
Sbjct: 287 PQVGCLLGKGGLVISEMRRVTGASIRIFSKEQIKYI-SQNEEVVQVIGSLQSVQDALFHI 345

Query: 203 TSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSP-VGPFHSMDRG 261
           TSR+RETIFP++ P   +   +LPPFPEMPPP FRPR++  S G  P P VG  H  D  
Sbjct: 346 TSRIRETIFPIRTPPNFSAPPHLPPFPEMPPPLFRPRNHLMSSGHPPPPQVG--HPHDHS 403

Query: 262 MGPSQPFDHQA-AFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGG 320
             P  P DHQ  AF HGM    PPN DR+P+P G         ++ P SPRSW P  V  
Sbjct: 404 TVPPMPVDHQQHAFVHGMG-RGPPNMDRVPYPRG---------YEGPNSPRSWNPLAVNR 453

Query: 321 GDPRGFDASSGFTPRNRPV-ESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQI 379
           G+  G   +S    RN  + E+GN      + TIE+ IP +Y+ HVYGENNSNL+ IRQ 
Sbjct: 454 GNSGGTADTSSLASRNENLGENGNPLQNPNNLTIEITIPHMYLTHVYGENNSNLTQIRQT 513

Query: 380 SGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVT 423
           SGANVVV+DPKPGATEG+V+VSG  DQ  AAQSLI AFILCG T
Sbjct: 514 SGANVVVHDPKPGATEGLVIVSGAPDQTHAAQSLIQAFILCGQT 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 =  400 bits (1028), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 245/434 (56%), Positives = 278/434 (64%), Gaps = 47/434 (10%)

Query: 2   VVQGNPYPPAAE--PFHQRGYAPGYHSRGYSSGPGH-------ETVGGRNRMFYEEEVVF 52
            +Q +  PP  +  PF Q GY P YHS  Y     H       E VG  NR   EEEV F
Sbjct: 219 CLQESGAPPTWDECPFPQPGYPPEYHSMEYHPQWDHPPPNPMPEDVGPFNRPVVEEEVAF 278

Query: 53  KLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPA 112
           +LLC  DKVGSLIGKGG++VR  QNE+GASIK++D   DSEERI+VISAREN E RHS A
Sbjct: 279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISARENLERRHSLA 338

Query: 113 QDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 172
           QD VMRVH+RI EIGFEP  AVVARLLVHS  IG LLG+GGH++SEMRRATGASIRVF K
Sbjct: 339 QDGVMRVHNRIVEIGFEPSAAVVARLLVHSPYIGRLLGKGGHLISEMRRATGASIRVFAK 398

Query: 173 DQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFP--MKRPGPNNGHSYLPPFPE 230
           DQA +  S HDEIVQVIGN  +VQDALF I  RLRE +FP  +   G             
Sbjct: 399 DQATKYESQHDEIVQVIGNLKTVQDALFQILCRLREAMFPGRLPFQGMGGPPPPFMGPYP 458

Query: 231 MPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIP 290
            PPPPF PR  PASP  Y SPVGPFH                   HG      P  DR P
Sbjct: 459 EPPPPFGPRQYPASPDRYHSPVGPFHER---------------HCHG------PGFDRPP 497

Query: 291 FPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGF---DASSGFTPRNRPVESGNHAAI 347
                     GP FDRPPSP SWTPQ    G P G    D + GF  RN P+ S N   +
Sbjct: 498 ----------GPGFDRPPSPMSWTPQPGIDGHPGGMVPPDVNHGFALRNEPIGSEN--PV 545

Query: 348 LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQM 407
           +TS  +E+VIPQ Y+ HVYGEN SNL++I+Q+SGANVVV+DPK G TEG+V+VSGTSDQ 
Sbjct: 546 MTSANVEIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSDQA 605

Query: 408 RAAQSLIHAFILCG 421
             AQSL+HAFILCG
Sbjct: 606 HFAQSLLHAFILCG 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 =  396 bits (1018), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 245/433 (56%), Positives = 277/433 (63%), Gaps = 46/433 (10%)

Query: 2   VVQGNPYPPAAE--PFHQRGYAPGYHSRGYSSGPGH------ETVGGRNRMFYEEEVVFK 53
            +Q +  PP  +  PF Q GY P YHS  Y     H      E V   NR   EEEV F+
Sbjct: 221 CLQESGAPPTWDECPFPQPGYPPDYHSMEYHPQWDHPPNPMPEDVVPFNRPVVEEEVSFR 280

Query: 54  LLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQ 113
           LLC  DKVGSLIGKGG++VR  QNE+GASIK++D   DSEERI+VISAREN E RHS AQ
Sbjct: 281 LLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISARENLERRHSLAQ 340

Query: 114 DAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKD 173
           D VMRVH+RI EIGFEP  AVVARLLVHS  IG LLG+GGH++SEMRRATGASIRVF KD
Sbjct: 341 DGVMRVHNRIVEIGFEPSAAVVARLLVHSPYIGRLLGKGGHLISEMRRATGASIRVFAKD 400

Query: 174 QAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFP--MKRPGPNNGHSYLPPFPEM 231
           QA +  S HDEIVQVIGN  +VQDALF I  RLRE +FP  +   G              
Sbjct: 401 QATKYESQHDEIVQVIGNLKTVQDALFQILCRLREAMFPGRLPFQGLGGPPPPFMGPYPE 460

Query: 232 PPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPF 291
           PPPPF PR  PASP  Y SPVG FH                   HG      P  DR P 
Sbjct: 461 PPPPFGPRQYPASPDRYHSPVGSFHER---------------HCHG------PGFDRPP- 498

Query: 292 PYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGF---DASSGFTPRNRPVESGNHAAIL 348
                    GP FDRPPSP SWTPQ    G P G    D + GF  RN P+ S N A  +
Sbjct: 499 ---------GPGFDRPPSPMSWTPQPGIDGHPGGMVPPDVNHGFALRNEPIGSENPA--M 547

Query: 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 408
           TS  +E+VIPQ Y+ HVYGEN SNL++I+Q+SGANVVV+DPK GATEG+V+VSGTSDQ  
Sbjct: 548 TSANVEIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGATEGLVVVSGTSDQAH 607

Query: 409 AAQSLIHAFILCG 421
            AQSL+HAFILCG
Sbjct: 608 FAQSLLHAFILCG 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 =  351 bits (901), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 202/424 (47%), Positives = 261/424 (61%), Gaps = 19/424 (4%)

Query: 9   PPAAEPFHQRGYAP----GYHSRGYSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSL 64
           PP  +   QR Y P     YH+R +SS           R F E+E+VF+++C  + VG +
Sbjct: 212 PPGVDSHSQRSYLPPHIPDYHARNFSS----NVAAPGPRFFIEQEIVFRMICLNEMVGGI 267

Query: 65  IGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIA 124
           IGKGG+ +R  Q++TGAS+K+ D + DS+ER++VISARENSEM HSPAQDAV+RV+SRI+
Sbjct: 268 IGKGGATIRALQSDTGASVKVIDAVADSDERVIVISARENSEMMHSPAQDAVLRVYSRIS 327

Query: 125 EIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDE 184
           E   +   AV ARLLV SQ IGCLLG+GG I++EMR  TGASIR+F  +Q PRC   +DE
Sbjct: 328 EASMDKSSAVPARLLVPSQHIGCLLGKGGSIIAEMRNVTGASIRIFGNEQIPRCAQRNDE 387

Query: 185 IVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPAS 244
           +VQV GN+ S+QDAL HIT R+R+ I P K P P+ G S  PP    P  P   R +PA 
Sbjct: 388 LVQVTGNFQSIQDALLHITGRIRDVIIPPK-PHPSGGMSPYPPAGSTPHHPS--RQDPAP 444

Query: 245 P----GSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGH 300
           P    G  P P+ PF   +  MGP    DH+    H   PM    +DRIP+ YG E+ G 
Sbjct: 445 PHHSGGMPPYPMHPFRP-NHPMGPFDVADHRPPGQHPAHPMEHMGADRIPYSYGCEQGGP 503

Query: 301 GPTFDRPPSPRSWTPQGVGGGDPRGF-DASSGFTPRNRPVE-SGNHAAILTSTTIEVVIP 358
            P  ++ PSPR+W P+      PR   D       R   V  S N  A  TSTT EVVIP
Sbjct: 504 RPFLEQ-PSPRTWAPEAQTADAPRSIPDKGLAMDSRKGSVAGSENQVATPTSTTTEVVIP 562

Query: 359 QLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFI 418
             Y+  + G N S+L+ I++ISGA + V+DPKPG T+  V V G  +Q + AQSLIHAFI
Sbjct: 563 CKYIGFICGTNGSDLAEIQKISGAAITVHDPKPGDTDASVFVCGDPEQTKKAQSLIHAFI 622

Query: 419 LCGV 422
            CG+
Sbjct: 623 FCGL 626

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326504604|dbj|BAK06593.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  339 bits (869), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 197/427 (46%), Positives = 260/427 (60%), Gaps = 26/427 (6%)

Query: 9   PPAAEPFHQRGY-----APGYHSRGYSS---GPGHETVGGRNRMFYEEEVVFKLLCHLDK 60
           PP  +P  QR Y      P YH+R +SS    PG        R F E+E+VF+++C  D 
Sbjct: 115 PPGVDPHSQRSYLPPPHVPDYHARNFSSNGAAPG-------PRFFVEQEIVFRMICLNDM 167

Query: 61  VGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVH 120
           VG +IGKGGS +R  Q+ETGAS+K+ D + DS+ERI+VISARENSEM  SP+QDA++RV+
Sbjct: 168 VGGVIGKGGSTIRALQSETGASVKVIDPVADSDERIIVISARENSEMMRSPSQDALLRVY 227

Query: 121 SRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGS 180
           S+I+E   +   +V ARLLV +Q IGCLLG+GG I++EMR+ TGASIR+F  +Q PRC  
Sbjct: 228 SKISEASMDKSSSVPARLLVPAQHIGCLLGKGGSIIAEMRKLTGASIRIFGNEQIPRCAQ 287

Query: 181 PHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRH 240
            +DE+VQV G++ S+QDAL HIT R+R+ I P K P P+ G   +PP+P +  P      
Sbjct: 288 RNDELVQVTGSFQSIQDALLHITGRIRDLIIPPK-PHPSGG---MPPYPPVGNPSHHQSR 343

Query: 241 NPA----SPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSE 296
             A    S G  P P+ PF   +  MGP    D +        PM    +DR+P+PYG E
Sbjct: 344 QEAPSHHSGGMPPYPMHPFRP-NPPMGPFDVADPRPPGPPPSHPMEHMGADRMPYPYGCE 402

Query: 297 RPGHGPTFDRPPSPRSWTPQGVGGGDPRGF-DASSGFTPRNRPVESGNHAAILTSTTIEV 355
           + G  P F   PSPR+W P+      PR   D       R  PV S N  A   +TT EV
Sbjct: 403 QGGPRP-FVEQPSPRTWAPEAPATDAPRSMPDTVPAVDFRKGPVSSENQVATPATTTTEV 461

Query: 356 VIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH 415
           VIP  Y+  V G N S+L  I++ISGA + V+DPKPG T   V++ G  +Q + AQSLIH
Sbjct: 462 VIPCKYIGFVCGTNGSDLDEIKKISGAAITVHDPKPGDTNSTVIICGDPEQTKKAQSLIH 521

Query: 416 AFILCGV 422
           AFI CG+
Sbjct: 522 AFIFCGL 528

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	424
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.504	0.344	0.641	4.5e-107
TAIR|locus:2168367	652	RCF3 "AT5G53060" [Arabidopsis	0.389	0.253	0.337	2.1e-36
TAIR|locus:2161413	644	AT5G46190 "AT5G46190" [Arabido	0.415	0.273	0.322	9.2e-34
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.379	0.293	0.413	8.1e-33
TAIR|locus:2066020	632	AT2G22600 "AT2G22600" [Arabido	0.389	0.261	0.403	1e-30
TAIR|locus:2084908	577	FLK "AT3G04610" [Arabidopsis t	0.405	0.298	0.366	2.3e-29
TAIR|locus:2035807	479	AT1G14170 "AT1G14170" [Arabido	0.455	0.402	0.341	9.6e-25
TAIR|locus:2120755	495	PEP "AT4G26000" [Arabidopsis t	0.375	0.321	0.317	1.3e-20
TAIR|locus:2831364	606	AT4G18375 "AT4G18375" [Arabido	0.570	0.399	0.273	4.7e-18
UNIPROTKB|Q5E9A3	356	PCBP1 "Poly(rC)-binding protei	0.365	0.435	0.282	7.4e-16

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

 Score = 664 (238.8 bits), Expect = 4.5e-107, Sum P(2) = 4.5e-107
 Identities = 143/223 (64%), Positives = 161/223 (72%)

Query:     3 VQGNPYPPAAE--PFHQRGYAPGYHSRGYSS-------GPGHETVGGRNRMFYEEEVVFK 53
             +Q +  PP  +  PF Q GY P YHS  Y          P  E VG  NR   EEEV F+
Sbjct:   220 LQESGAPPTWDECPFPQPGYPPEYHSMEYHPQWDHPPPNPMPEDVGPFNRPVVEEEVAFR 279

Query:    54 LLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQ 113
             LLC  DKVGSLIGKGG++VR  QNE+GASIK++D   DSEERI+VISAREN E RHS AQ
Sbjct:   280 LLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISARENLERRHSLAQ 339

Query:   114 DAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKD 173
             D VMRVH+RI EIGFEP  AVVARLLVHS  IG LLG+GGH++SEMRRATGASIRVF KD
Sbjct:   340 DGVMRVHNRIVEIGFEPSAAVVARLLVHSPYIGRLLGKGGHLISEMRRATGASIRVFAKD 399

Query:   174 QAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRP 216
             QA +  S HDEIVQVIGN  +VQDALF I  RLRE +FP + P
Sbjct:   400 QATKYESQHDEIVQVIGNLKTVQDALFQILCRLREAMFPGRLP 442

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 295 (108.9 bits), Expect = 2.1e-36, Sum P(2) = 2.1e-36
 Identities = 56/166 (33%), Positives = 102/166 (61%)

Query:    46 YEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENS 105
             Y EE+VF++LC  DK+  ++G+   I+   QNE G  ++++D +  S+E+I+ IS+ E  
Sbjct:   321 YSEELVFQILCPADKIVRVVGESQGIIDLLQNEIGVDVRVSDPVAGSDEQIITISSEEAP 380

Query:   106 EMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGA 165
             +    PAQ+A++ + ++I ++  +    +  RLLV S+   CL G+ G  VSE+ R TG 
Sbjct:   381 DDPFFPAQEALLHIQTQIIDLIPDKDNLITTRLLVPSRDSICLEGKAGS-VSEISRLTGT 439

Query:   166 SIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIF 211
             S+++  +++ PRC S +D ++Q+ G   + ++AL  +T  LR  +F
Sbjct:   440 SVQILAREEIPRCASINDVVIQITGEIRAAREALVELTLLLRSHMF 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:2161413 AT5G46190 "AT5G46190" [Arabidopsis thaliana (taxid:3702)]

 Score = 278 (102.9 bits), Expect = 9.2e-34, Sum P(2) = 9.2e-34
 Identities = 59/183 (32%), Positives = 106/183 (57%)

Query:    39 GGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVV 98
             GG +R    E++  K++C   K+G +IGKGG  ++  +  +G+ I++ D   + ++  V+
Sbjct:   309 GGSSR---SEKLAIKVICSSSKIGRVIGKGGLTIKGIRQASGSHIEVNDSRTNHDDDCVI 365

Query:    99 -ISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVS 157
              ++A E+ +   S A +AV+ +  +I +   E    V  +LLV S+ IGC++G+ G I+S
Sbjct:   366 TVTATESPDDLKSMAVEAVLLLQEKIND---EDEDKVKMQLLVSSKVIGCIIGKSGSIIS 422

Query:   158 EMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPG 217
             E+R+ T A I +   +  P+C  P+DE+V++ G   +V+DAL  I  RLR+ +   +  G
Sbjct:   423 EIRKRTKADIHISKGNNTPKCADPNDELVEISGEVSNVRDALIQIVLRLRDDVLRDRETG 482

Query:   218 PNN 220
               N
Sbjct:   483 SRN 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 = 320 (117.7 bits), Expect = 8.1e-33, Sum P(2) = 8.1e-33
 Identities = 72/174 (41%), Positives = 103/174 (59%)

Query:    48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVI---SAREN 104
             ++ VF+ LC + K+GS+IG+GG IV+  +N+T + I+I + +P  +ER++ I   S   N
Sbjct:    48 DDTVFRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCDERVITIYSPSDETN 107

Query:   105 S----EMRHSPAQDAVMRVHSRI------AEIGFEPGQAVVARLLVHSQQIGCLLGRGGH 154
             +    E   SPAQDA+ R+H R+      +E   E  + V A+LLV S QIGC+LGRGG 
Sbjct:   108 AFGDGEKVLSPAQDALFRIHDRVVADDARSEDSPEGEKQVTAKLLVPSDQIGCILGRGGQ 167

Query:   155 IVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 208
             IV  +R  TGA IR+      P C    DE++Q+ G    V+ AL  I SRL E
Sbjct:   168 IVQNIRSETGAQIRIVKDRNMPLCALNSDELIQISGEVLIVKKALLQIASRLHE 221

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

 Score = 274 (101.5 bits), Expect = 1.0e-30, Sum P(2) = 1.0e-30
 Identities = 71/176 (40%), Positives = 99/176 (56%)

Query:    47 EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSE 106
             E +VVFK++      G +IGK G+I+R  QNETGASI +   L  S ER+V +SAREN E
Sbjct:   274 ERKVVFKIIFTSVVAGGIIGKQGTIIRALQNETGASISVGAPLKVSGERVVTVSARENLE 333

Query:   107 MRHSPAQDAVMRVHSRIAEI----GFEPGQ---AVV-ARLLVHSQQIGCLLGRGGHIVSE 158
              R+S AQ+A+  V +R  EI    G  PG    A+V  +LLV S       G G     E
Sbjct:   334 SRYSHAQNALALVFARSVEIDVEKGLRPGLHNGAIVKTKLLVPSHFANSFNGNGNR---E 390

Query:   159 MRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMK 214
                ATGA + +   +Q     S ++ ++++ G Y  VQ AL H++S+LRE + P K
Sbjct:   391 AIIATGADVHISVGNQVLEWISENEVVIEIKGEYSHVQKALTHVSSKLRENLLPKK 446

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 = 263 (97.6 bits), Expect = 2.3e-29, Sum P(2) = 2.3e-29
 Identities = 66/180 (36%), Positives = 97/180 (53%)

Query:    37 TVGGRNRMF--YEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEE 94
             TVGG  + +  +  E VF++L    KVGS+IG+ G +++    ET A IKI D  P + E
Sbjct:   172 TVGGEEKRWPGWPGETVFRMLVPAQKVGSIIGRKGDVIKKIVEETRARIKILDGPPGTTE 231

Query:    95 RIVVISARENSEMRHSPAQDAVMRVHSRIAE-IGFEPGQA-----VVARLLVHSQQIGCL 148
             R V++S +E  E    P+ D ++RVH RI + +  E  QA     V  RLLV + Q G L
Sbjct:   232 RAVMVSGKEEPESSLPPSMDGLLRVHMRIVDGLDGEASQAPPPSKVSTRLLVPASQAGSL 291

Query:   149 LGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 208
             +G+ G  V  ++ A+   +RV   +  P      D +V+V+G   SV  AL  I S LR+
Sbjct:   292 IGKQGGTVKAIQEASACIVRVLGSEDLPVFALQDDRVVEVVGEPTSVHRALELIASHLRK 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:2035807 AT1G14170 "AT1G14170" [Arabidopsis thaliana (taxid:3702)]

 Score = 293 (108.2 bits), Expect = 9.6e-25, P = 9.6e-25
 Identities = 67/196 (34%), Positives = 105/196 (53%)

Query:    20 YAPGYHSRGYSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNET 79
             + PG      +    H     R  +    E     +C  + VG +IGKGG  +   + ET
Sbjct:   239 HQPGAMLMSAALTSSHRNYAVRRDIADAREFCVCFICPAENVGGVIGKGGGFINQIRQET 298

Query:    80 GASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAE-IGFEPGQ-AVVAR 137
             GA+I++     D ++ I+ IS++E  E + SPA +A +R+  R +E +G +    A+  R
Sbjct:   299 GATIRVNTSETDDDDCIIFISSKEFYEDQ-SPAVNAAIRLQQRCSEKVGKDANDLAISTR 357

Query:   138 LLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQD 197
             LLV S QIGCL+G+GG ++SEMR  T A+IR+  K+  P+     +E+VQ+ G+  +   
Sbjct:   358 LLVSSSQIGCLIGKGGAVISEMRSVTRANIRILQKEDVPKIAREDEEMVQITGSPDAAMK 417

Query:   198 ALFHITSRLRETIFPM 213
             AL  +  RLR   F M
Sbjct:   418 ALTQVILRLRANSFDM 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:2120755 PEP "AT4G26000" [Arabidopsis thaliana (taxid:3702)]

 Score = 206 (77.6 bits), Expect = 1.3e-20, Sum P(2) = 1.3e-20
 Identities = 53/167 (31%), Positives = 91/167 (54%)

Query:    49 EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMR 108
             + VF+++  + KVG++IG+ G  ++    ET A IK+ D   ++ +RIV+IS +E  E  
Sbjct:    73 DCVFRMIVPVTKVGAIIGRKGDFIKKMCEETRARIKVLDGPVNTPDRIVLISGKEEPEAY 132

Query:   109 HSPAQDAVMRVHSRIAEI------GFEPGQAVVA--RLLVHSQQIGCLLGRGGHIVSEMR 160
              SPA DAV+RV  R++ +        +   +V +  RLLV S Q   L+G+ G ++  + 
Sbjct:   133 MSPAMDAVLRVFRRVSGLPDNDDDDVQNAGSVFSSVRLLVASTQAINLIGKQGSLIKSIV 192

Query:   161 RATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLR 207
               +GAS+R+  +++ P   +  + IV + G    +  AL  I   LR
Sbjct:   193 ENSGASVRILSEEETPFYAAQDERIVDLQGEALKILKALEAIVGHLR 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

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

 Score = 245 (91.3 bits), Expect = 4.7e-18, P = 4.7e-18
 Identities = 73/267 (27%), Positives = 131/267 (49%)

Query:    30 SSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADIL 89
             SS P     GG +R    EE+VFK+LC L  +  +IGKGGS ++  +  +G+ I++ D  
Sbjct:   295 SSLPVTHGFGGSSR---SEELVFKVLCPLCNIMRVIGKGGSTIKRIREASGSCIEVNDSR 351

Query:    90 PD--SEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGC 147
                  +E +++++A E+ +   S A +AV+ +   I +   E  + V  +LLV S+ IGC
Sbjct:   352 TKCGDDECVIIVTATESPDDMKSMAVEAVLLLQEYIND---EDAENVKMQLLVSSKVIGC 408

Query:   148 LLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLR 207
             ++G+ G +++E+R+ T A+I +  K +        D++V+V G   SV+DAL  I  RLR
Sbjct:   409 VIGKSGSVINEIRKRTNANICI-SKGKK-------DDLVEVSGEVSSVRDALIQIVLRLR 460

Query:   208 ETIF-------PMKRPGPNNGHSYLXXXXXXXXXXXXXXXXXXXXGSYPSPVGPFHSMDR 260
             E +          K P   +  S+L                      +    G F + D 
Sbjct:   461 EDVLGDKDSVATRKPPARTDNCSFLSGSSNAGYTLPSFMSSMASTSGFHG-YGSFPAGDN 519

Query:   261 GMGPSQPFDH-QAAFSHGMDPMVPPNS 286
              +G + P+ + +   S  ++ ++P ++
Sbjct:   520 VLGSTGPYSYGRLPSSSALEILIPAHA 546

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q5E9A3 PCBP1 "Poly(rC)-binding protein 1" [Bos taurus (taxid:9913)]

 Score = 153 (58.9 bits), Expect = 7.4e-16, Sum P(2) = 7.4e-16
 Identities = 46/163 (28%), Positives = 83/163 (50%)

Query:    50 VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMR- 108
             +  +LL H  +VGS+IGK G  V+  + E+GA I I++   +  ERI+ ++   N+  + 
Sbjct:    14 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITLTGPTNAIFKA 71

Query:   109 HSPAQDAVMR-VHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 167
              +   D +   ++S +          V  RL+V + Q G L+G+GG  + E+R +TGA +
Sbjct:    72 FAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQV 131

Query:   168 RVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETI 210
             +V   D  P   +  +  + + G   SV + +  I   + ET+
Sbjct:   132 QV-AGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLETL 170

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

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

---

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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00029576001 SubName- Full=Chromosome chr9 scaffold_49, whole genome shotgun sequence; (675 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	424
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	5e-18
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	6e-18
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	8e-12
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-11
pfam00013	59	pfam00013, KH_1, KH domain	4e-10
pfam13014	42	pfam13014, KH_3, KH domain	7e-10
pfam00013	59	pfam00013, KH_1, KH domain	1e-09
pfam00013	59	pfam00013, KH_1, KH domain	2e-09
smart00322	68	smart00322, KH, K homology RNA-binding domain	3e-09
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-08
smart00322	68	smart00322, KH, K homology RNA-binding domain	1e-08
TIGR03665	172	TIGR03665, arCOG04150, arCOG04150 universal archae	4e-07
COG0195	190	COG0195, NusA, Transcription elongation factor [Tr	1e-06
smart00322	68	smart00322, KH, K homology RNA-binding domain	3e-06
PRK13763	180	PRK13763, PRK13763, putative RNA-processing protei	3e-06
pfam13014	42	pfam13014, KH_3, KH domain	6e-06
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	4e-05
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	4e-05
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	1e-04
pfam13014	42	pfam13014, KH_3, KH domain	3e-04
COG1094	194	COG1094, COG1094, Predicted RNA-binding protein (c	4e-04
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	5e-04
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.001
PHA03132	580	PHA03132, PHA03132, thymidine kinase; Provisional	0.002
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	0.003

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

 Score = 77.1 bits (191), Expect = 5e-18
 Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 7/71 (9%)

Query: 51  VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIAD-ILPDSEERIVVISARENSEMRH 109
             +LL    + GS+IGKGGS ++  + ETGA I+++  +LP S ER+V IS       + 
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISG------KP 54

Query: 110 SPAQDAVMRVH 120
           S  Q A++ + 
Sbjct: 55  SAVQKALLLIL 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|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 77.1 bits (191), Expect = 6e-18
 Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 4/69 (5%)

Query: 135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHS 194
             RLLV S Q G ++G+GG  + E+R  TGA IRV             + +V + G   +
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLP----GSTERVVTISGKPSA 56

Query: 195 VQDALFHIT 203
           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 = 59.9 bits (146), Expect = 8e-12
 Identities = 18/64 (28%), Positives = 35/64 (54%)

Query: 352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 411
           T  V++P   +  + G+  S +  IR+ +GA + + D   G+ E +V ++GT + +  A+
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60

Query: 412 SLIH 415
            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|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 58.7 bits (143), Expect = 2e-11
 Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 51  VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHS 110
             ++L     VG +IGKGGS ++  + ETGA IKI D    SEERIV I+    +     
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEA----- 55

Query: 111 PAQDAVMRVH 120
             + A   + 
Sbjct: 56  -VEKAKELIL 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 = 54.9 bits (133), Expect = 4e-10
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 9/68 (13%)

Query: 135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHS 194
             R+L+   ++G ++G+GG  + E+R  TG  IR+             D+ V + G    
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR---------DDTVTISGTPEQ 51

Query: 195 VQDALFHI 202
           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|221895 pfam13014, KH_3, KH domain

 Score = 53.7 bits (130), Expect = 7e-10
 Identities = 20/41 (48%), Positives = 27/41 (65%)

Query: 60  KVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVIS 100
            VG++IGKGG  ++  + ETGA I+I    P S ERIV I+
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTIT 41

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|215657 pfam00013, KH_1, KH domain

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 4/51 (7%)

Query: 51  VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISA 101
             ++L   DKVG +IGKGGS ++  + ETG  I+I    PD  +  V IS 
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRI----PDDRDDTVTISG 47

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 = 53.3 bits (129), Expect = 2e-09
 Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 4/63 (6%)

Query: 352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 411
           T  ++IP   +  + G+  SN+  IR+ +G  + + D +    +  V +SGT +Q+  A+
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR----DDTVTISGTPEQVEKAK 56

Query: 412 SLI 414
            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|197652 smart00322, KH, K homology RNA-binding domain

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 28/79 (35%), Positives = 39/79 (49%), Gaps = 12/79 (15%)

Query: 48  EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEM 107
           + V  ++L   DKVG +IGKGGS ++  + ETG  I I    P SEER+V I+       
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--PGSEERVVEITGPP---- 54

Query: 108 RHSPAQDAVMRVHSRIAEI 126
                 + V +    I EI
Sbjct: 55  ------ENVEKAAELILEI 67

Length = 68

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

 Score = 51.0 bits (123), Expect = 1e-08
 Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 5/68 (7%)

Query: 135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHS 194
             R+LV S  +G ++G+GG  + E+R  TGA I++             + IV + G   +
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG-----SGSEERIVTITGTPEA 55

Query: 195 VQDALFHI 202
           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 = 51.1 bits (123), Expect = 1e-08
 Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 408
              TIEV+IP   +  + G+  S +  I + +G  + +  P PG+ E VV ++G  + + 
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI--PGPGSEERVVEITGPPENVE 58

Query: 409 AAQSLI 414
            A  LI
Sbjct: 59  KAAELI 64

Length = 68

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

 Score = 49.1 bits (118), Expect = 4e-07
 Identities = 43/164 (26%), Positives = 63/164 (38%), Gaps = 53/164 (32%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
           D++G LIGKGG   +  +  TG  + I     DSE   V I   +           AVM+
Sbjct: 7   DRIGVLIGKGGETKKEIEERTGVKLDI-----DSETGEVKIEEEDED-------PLAVMK 54

Query: 119 VHSRIAEI--GFEPGQAVVARLLVHSQQI-------------------GCLLGRGGH--- 154
               +  I  GF P +A+  +LL     +                   G ++G GG    
Sbjct: 55  AREVVKAIGRGFSPEKAL--KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRR 112

Query: 155 IVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDA 198
           I+ E+   TG SI V            + + V +IG+   VQ A
Sbjct: 113 IIEEL---TGVSISV------------YGKTVGIIGDPEQVQIA 141

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

>gnl|CDD|223273 COG0195, NusA, Transcription elongation factor [Transcription]

 Score = 48.4 bits (116), Expect = 1e-06
 Identities = 30/117 (25%), Positives = 47/117 (40%), Gaps = 18/117 (15%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
           D VG+ IGK GS V+    E G  I + +   D  E I       N+    +PA      
Sbjct: 85  DPVGACIGKRGSRVKAVSEELGEKIDVVEWSEDPAEFIK------NA---LAPA------ 129

Query: 119 VHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQA 175
               +  +  +     VA ++V   Q+   +G+GG  V    + TG  I +    +A
Sbjct: 130 ---EVLSVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETISEA 183

Length = 190

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

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 7/73 (9%)

Query: 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 193
           V   +L+ + ++G ++G+GG  + ++   TG  I +             + +V++ G   
Sbjct: 3   VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG-------SEERVVEITGPPE 55

Query: 194 SVQDALFHITSRL 206
           +V+ A   I   L
Sbjct: 56  NVEKAAELILEIL 68

Length = 68

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

 Score = 46.8 bits (112), Expect = 3e-06
 Identities = 42/164 (25%), Positives = 67/164 (40%), Gaps = 52/164 (31%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
           D++G LIGK G   +  +  TG  ++I     DSE   V+I   +  +        AV++
Sbjct: 12  DRIGVLIGKKGETKKEIEERTGVKLEI-----DSETGEVIIEPTDGED------PLAVLK 60

Query: 119 VHSRIAEI--GFEPGQAVVARLL-------V-----------HSQQI-GCLLGRGG---H 154
               +  I  GF P +A+  RLL       V             ++I G ++G GG    
Sbjct: 61  ARDIVKAIGRGFSPEKAL--RLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRR 118

Query: 155 IVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDA 198
           I+ E+   TG  I V            + + V +IG+   V+ A
Sbjct: 119 IIEEL---TGVDISV------------YGKTVAIIGDPEQVEIA 147

Length = 180

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

 Score = 42.5 bits (101), Expect = 6e-06
 Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 5/47 (10%)

Query: 144 QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 190
            +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|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

 Score = 41.0 bits (97), Expect = 4e-05
 Identities = 12/29 (41%), Positives = 16/29 (55%)

Query: 59 DKVGSLIGKGGSIVRTFQNETGASIKIAD 87
          DK+  +IG GG  ++    ETG  I I D
Sbjct: 11 DKIRDVIGPGGKTIKKIIEETGVKIDIED 39

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 61

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

 Score = 41.0 bits (97), Expect = 4e-05
 Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 411
           T EV IP+     + G+  SN+  I + +G  +    P PG+    + ++G  + +  A+
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRF--PDPGSKSDTITITGPKENVEKAK 58

Query: 412 SLI 414
             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 = 39.8 bits (94), Expect = 1e-04
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND-PKPGATEGVVMVSGTSDQMRAA 410
           T+ +++P      + G+  S +  IR+ +GA + V+    PG+TE VV +SG    ++ A
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60

Query: 411 QSLIH 415
             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 = 37.9 bits (89), Expect = 3e-04
 Identities = 11/42 (26%), Positives = 24/42 (57%)

Query: 361 YMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG 402
            +  + 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|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH domains) [General function prediction only]

 Score = 40.7 bits (96), Expect = 4e-04
 Identities = 40/178 (22%), Positives = 68/178 (38%), Gaps = 54/178 (30%)

Query: 47  EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSE 106
            E+    +    D++G LIGK G + +  + +TG  ++I     DS+   V I       
Sbjct: 5   AEKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRI-----DSKTGSVTI-----RT 54

Query: 107 MRHSPAQDAVMRVHSRIAEI--GFEPGQAVVARLL--------------------VHSQQ 144
            R +    A+++    +  I  GF P +A+  +LL                       + 
Sbjct: 55  TRKTEDPLALLKARDVVKAIGRGFPPEKAL--KLLEDDYYLEVIDLKDVVTLSGDHLRRI 112

Query: 145 IGCLLGRGGHIVSEMRRA----TGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDA 198
            G ++GR G    + RRA    TG  I V            + + V +IG +  V+ A
Sbjct: 113 KGRIIGREG----KTRRAIEELTGVYISV------------YGKTVAIIGGFEQVEIA 154

Length = 194

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

 Score = 42.0 bits (100), Expect = 5e-04
 Identities = 25/74 (33%), Positives = 34/74 (45%), Gaps = 13/74 (17%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
           DK+  +IG GG  +R    ETGA I I D      +  V I+A  + E     A+ A  R
Sbjct: 563 DKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAA-TDGEA----AEAAKER 611

Query: 119 VHSRIAEIGFEPGQ 132
           +    AE   E G+
Sbjct: 612 IEGITAEP--EVGE 623

Length = 693

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

 Score = 40.6 bits (96), Expect = 0.001
 Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 13/74 (17%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
           DK+  +IG GG ++R    ETGA I I D      +  V I+A  + E     A+ A+  
Sbjct: 560 DKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAA-SDGEA----AEAAIKM 608

Query: 119 VHSRIAEIGFEPGQ 132
           +    AE   E G+
Sbjct: 609 IEGITAEP--EVGK 620

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family) [Transcription, Degradation of RNA]. Length = 684

>gnl|CDD|222997 PHA03132, PHA03132, thymidine kinase; Provisional

 Score = 40.5 bits (95), Expect = 0.002
 Identities = 35/185 (18%), Positives = 43/185 (23%), Gaps = 33/185 (17%)

Query: 169 VFPKDQAPRCGSPHDEIVQVIGNYHSVQ-------DALFHITSRLRETIFPMKRPGPNNG 221
                +  R  +   E    +    S         D L+      RET            
Sbjct: 17  SDESPEGSRDENFDAERDDFLTPLGSTSEATSEDDDDLYPP----RETGSGGGVATSTI- 71

Query: 222 HSYLPPFPEMPPPP------FRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFS 275
             Y  P P   P          P      PG  P P G F    RG    +      A S
Sbjct: 72  --YTVPRPPRGPEQTLDKPDSLPASRELPPGPTPVPPGGF----RGASSPRL----GADS 121

Query: 276 HGMDPMVPPNSDRIPFPYGSERPGHG-----PTFDRPPSPRSWTPQGVGGGDPRGFDASS 330
                +   N   I  P G                RPP   S   +  G   P+GF    
Sbjct: 122 TSPRFLYQVNFPVILAPIGESNSSSEELSEEEEHSRPPPSESLKVKNGGKVYPKGFSKHK 181

Query: 331 GFTPR 335
                
Sbjct: 182 THKRS 186

Length = 580

>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

 Score = 39.9 bits (94), Expect = 0.003
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 31/106 (29%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
           DK+  +IG GG  ++    ETG  I I D   D     V I+A +        A+ A  R
Sbjct: 561 DKIRDVIGPGGKTIKAITEETGVKIDIED---DGT---VKIAASDGES-----AKKAKER 609

Query: 119 VHSRIAEIGFEPGQ---AVVARL---------------LVHSQQIG 146
           + +   E+  E G+     V R+               LVH  Q+ 
Sbjct: 610 IEAITREV--EVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLA 653

Length = 692

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	424
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	100.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.97
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.96
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.95
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.89
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.77
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.7
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.67
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.64
PRK13763	180	putative RNA-processing protein; Provisional	99.63
PRK13763	180	putative RNA-processing protein; Provisional	99.6
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.5
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.41
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.38
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.38
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.35
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.35
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.32
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.19
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.12
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.12
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.06
COG1094	194	Predicted RNA-binding protein (contains KH domains	99.06
smart00322	69	KH K homology RNA-binding domain.	99.04
PF13014	43	KH_3: KH domain	99.0
PF13014	43	KH_3: KH domain	98.98
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.97
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.81
smart00322	69	KH K homology RNA-binding domain.	98.8
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.74
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.61
KOG2113	394	consensus Predicted RNA binding protein, contains	98.61
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.51
KOG2113	394	consensus Predicted RNA binding protein, contains	98.45
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.33
PRK08406	140	transcription elongation factor NusA-like protein;	98.18
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.02
PRK08406	140	transcription elongation factor NusA-like protein;	97.71
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.69
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.67
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.52
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.49
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.31
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.25
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.24
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	97.18
PRK00106	535	hypothetical protein; Provisional	97.14
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.03
KOG2814	345	consensus Transcription coactivator complex, P50 c	97.03
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	97.02
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.0
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.99
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.97
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.92
PRK12704	520	phosphodiesterase; Provisional	96.91
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.88
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.86
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	96.79
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.78
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.77
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.73
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.6
TIGR01953	341	NusA transcription termination factor NusA. This m	96.39
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.35
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.25
PRK00468	75	hypothetical protein; Provisional	96.17
PRK12705	508	hypothetical protein; Provisional	96.04
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.03
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	96.0
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.96
PRK02821	77	hypothetical protein; Provisional	95.92
COG0195	190	NusA Transcription elongation factor [Transcriptio	95.9
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	95.85
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.84
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.78
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.72
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.63
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.43
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.32
PRK01064	78	hypothetical protein; Provisional	95.17
PRK00468	75	hypothetical protein; Provisional	95.1
PRK02821	77	hypothetical protein; Provisional	95.07
TIGR01953	341	NusA transcription termination factor NusA. This m	94.96
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	94.93
PRK00106	535	hypothetical protein; Provisional	94.92
PRK12704	520	phosphodiesterase; Provisional	94.88
PRK12328	374	nusA transcription elongation factor NusA; Provisi	94.7
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	94.67
PRK12327	362	nusA transcription elongation factor NusA; Provisi	94.53
COG1837	76	Predicted RNA-binding protein (contains KH domain)	94.22
PRK09202	470	nusA transcription elongation factor NusA; Validat	94.13
PRK12329	449	nusA transcription elongation factor NusA; Provisi	93.74
PRK01064	78	hypothetical protein; Provisional	93.67
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	93.23
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	93.09
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	92.74
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	92.06
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	91.87
KOG2874	356	consensus rRNA processing protein [Translation, ri	90.93
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	90.47
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	90.38
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	90.27
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	89.61
KOG2874	356	consensus rRNA processing protein [Translation, ri	89.56
PRK12705	508	hypothetical protein; Provisional	89.25
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	88.6
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	88.55
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	88.53
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	88.42
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	87.38
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	87.16
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	85.99
COG1855	604	ATPase (PilT family) [General function prediction	85.07
PRK13764	602	ATPase; Provisional	84.54
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	84.44
COG5166	657	Uncharacterized conserved protein [Function unknow	83.65
PRK06418	166	transcription elongation factor NusA-like protein;	82.7
PRK13764	602	ATPase; Provisional	81.91
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	81.44
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	80.81
COG1855	604	ATPase (PilT family) [General function prediction	80.63

>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=7.2e-40  Score=297.87  Aligned_cols=330  Identities=24%  Similarity=0.394  Sum_probs=229.5

Q ss_pred             CCCcCCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHH
Q 014452           41 RNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVH  120 (424)
Q Consensus        41 ~~~~~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~  120 (424)
                      ..+.+....+.++||+.++.+|+||||+|++||.|+.+++|.|+|++.  +.++|+++|+...+          .+..++
T Consensus        39 ~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~~----------ti~~il  106 (390)
T KOG2192|consen   39 EEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADIE----------TIGEIL  106 (390)
T ss_pred             HHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccHH----------HHHHHH
Confidence            455666678999999999999999999999999999999999999988  58999999998843          444444


Q ss_pred             HHHH---hhcCCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHH
Q 014452          121 SRIA---EIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQD  197 (424)
Q Consensus       121 ~~i~---e~~~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~  197 (424)
                      ..+.   |.++.....|+++|+|..+++|.|||++|+.||+|++++.|+++|+..    .|+.+++|+|.|.|.+++|..
T Consensus       107 k~iip~lee~f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~----c~p~stdrv~l~~g~~k~v~~  182 (390)
T KOG2192|consen  107 KKIIPTLEEGFQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE----CCPHSTDRVVLIGGKPKRVVE  182 (390)
T ss_pred             HHHhhhhhhCCCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc----cCCCCcceEEEecCCcchHHH
Confidence            4432   456777788999999999999999999999999999999999999864    477799999999999999999


Q ss_pred             HHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCC
Q 014452          198 ALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHG  277 (424)
Q Consensus       198 A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g  277 (424)
                      +++.|+++|.+.      |.+...+||.|.|++...          ..+.|..+.+...+      ...|+.++.    |
T Consensus       183 ~i~~il~~i~e~------pikgsa~py~p~fyd~t~----------dyggf~M~f~d~pg------~pgpapqrg----g  236 (390)
T KOG2192|consen  183 CIKIILDLISES------PIKGSAQPYDPNFYDETY----------DYGGFTMMFDDRPG------RPGPAPQRG----G  236 (390)
T ss_pred             HHHHHHHHhhcC------CcCCcCCcCCccccCccc----------ccCCceeecCCCCC------CCCCCCCCC----C
Confidence            999999999987      677888999999877431          11222211111100      001111110    0


Q ss_pred             CCCCCCCCCCCCCCCCCC------CCCCCCCCCC------CCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCC-CCCCC
Q 014452          278 MDPMVPPNSDRIPFPYGS------ERPGHGPTFD------RPPSPRSWTPQGVG-GGDPRGFDASSGFTPRNRP-VESGN  343 (424)
Q Consensus       278 ~~~~~~~~~~~~~~~~g~------~~~g~~~~~~------~~~~p~~~~~~~~~-~g~~~g~~~~~~~~~r~~~-~~~g~  343 (424)
                      .++-++.......+..++      ..-+....+.      ..-.|..|....-- +|..+.+        ...+ .++..
T Consensus       237 qgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydy--------syAG~~GsYG  308 (390)
T KOG2192|consen  237 QGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDY--------SYAGGYGSYG  308 (390)
T ss_pred             CCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCc--------cccccccccC
Confidence            000000000000000000      0000000000      01133334322211 1111111        1111 11100


Q ss_pred             ccccCcceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452          344 HAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       344 ~~~~~~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~  421 (424)
                      ... ..-+|.+|+||.++-|.||||+|.+|++|++++||.|+|+++.+++.+|+|+|+||.+|++.||+|++++|.++
T Consensus       309 dlG-GPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~  385 (390)
T KOG2192|consen  309 DLG-GPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY  385 (390)
T ss_pred             CCC-CceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence            101 23578999999999999999999999999999999999999999999999999999999999999999999865

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

Probab=100.00  E-value=4.7e-34  Score=286.58  Aligned_cols=239  Identities=23%  Similarity=0.363  Sum_probs=192.2

Q ss_pred             CccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccC-C-CCCcccEEEeecccccccccChhHHHHHHHHHHHH
Q 014452           47 EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADI-L-PDSEERIVVISARENSEMRHSPAQDAVMRVHSRIA  124 (424)
Q Consensus        47 ~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~-~-~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~  124 (424)
                      +.+++..|+||.+.+|+||||+|++||+|++++||++.+-+. . .....+.+.|+|.+..++.      +...+++.|.
T Consensus       136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~------a~~lV~dil~  209 (600)
T KOG1676|consen  136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQ------AKQLVADILR  209 (600)
T ss_pred             ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHH------HHHHHHHHHH
Confidence            677899999999999999999999999999999999887633 2 2337789999999987765      3344444444


Q ss_pred             hhcC-----------CCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHH
Q 014452          125 EIGF-----------EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH  193 (424)
Q Consensus       125 e~~~-----------~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~  193 (424)
                      |...           ......++++.||...||.||||+|++||+|+.+||++|+|.++++ |   .+.||.+.|.|+.+
T Consensus       210 e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~-p---~speR~~~IiG~~d  285 (600)
T KOG1676|consen  210 EEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD-P---SSPERPAQIIGTVD  285 (600)
T ss_pred             hcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC-C---CCccceeeeecCHH
Confidence            3211           1223558999999999999999999999999999999999987543 3   47899999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccc
Q 014452          194 SVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAA  273 (424)
Q Consensus       194 ~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~  273 (424)
                      +|+.|.++|.++|++.....                                                            
T Consensus       286 ~ie~Aa~lI~eii~~~~~~~------------------------------------------------------------  305 (600)
T KOG1676|consen  286 QIEHAAELINEIIAEAEAGA------------------------------------------------------------  305 (600)
T ss_pred             HHHHHHHHHHHHHHHHhccC------------------------------------------------------------
Confidence            99999999999999872100                                                            


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEE
Q 014452          274 FSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTI  353 (424)
Q Consensus       274 ~~~g~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~  353 (424)
                         +.                                 .|     ++|..                        .....+
T Consensus       306 ---~~---------------------------------~~-----~~G~P------------------------~~~~~f  320 (600)
T KOG1676|consen  306 ---GG---------------------------------GM-----GGGAP------------------------GLVAQF  320 (600)
T ss_pred             ---CC---------------------------------Cc-----CCCCc------------------------cceeeE
Confidence               00                                 00     00000                        011278


Q ss_pred             EEEeccCcccceeccccchHHHHHHHhCCEEEEeCC--CCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          354 EVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP--KPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       354 ~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~--~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      +|.||...+|+||||+|++||.|..+|||++.+...  .....+++|+|+|++.+|+.|+.||+++|..
T Consensus       321 y~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~  389 (600)
T KOG1676|consen  321 YMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGD  389 (600)
T ss_pred             EEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHHHHHhcc
Confidence            999999999999999999999999999999999843  3456799999999999999999999999864

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

Probab=100.00  E-value=9.6e-33  Score=277.18  Aligned_cols=258  Identities=20%  Similarity=0.260  Sum_probs=198.4

Q ss_pred             CCCCCCCCCCc--CCC-ccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccC
Q 014452           34 GHETVGGRNRM--FYE-EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHS  110 (424)
Q Consensus        34 ~~~~~~~~~~~--~~~-~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~  110 (424)
                      +-+....++++  ... ..++.+..||.+.||.||||+|+.|..|..++||+|++........+|.|.++|.++.+..++
T Consensus        35 ~~~~~~~~l~p~~~~s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK  114 (600)
T KOG1676|consen   35 KGPSEDTDLDPDMDPSDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAK  114 (600)
T ss_pred             cCCCCccccCcccCCcccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHH
Confidence            33344445552  233 445789999999999999999999999999999999988665577899999999998876522


Q ss_pred             hhHHHHHHHHHHHHh-hcC---CCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEE
Q 014452          111 PAQDAVMRVHSRIAE-IGF---EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIV  186 (424)
Q Consensus       111 ~a~~av~~~~~~i~e-~~~---~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v  186 (424)
                         .-+..+.++.+. ..+   ....+++.+++||.+.+|+||||+|++||.|++++||++.+..+.+..   ...++.+
T Consensus       115 ---~li~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~---~~~~Kpl  188 (600)
T KOG1676|consen  115 ---QLIGEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIA---TGADKPL  188 (600)
T ss_pred             ---HhhhhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcC---CCCCCce
Confidence               222222222221 111   123568899999999999999999999999999999999888765432   2478899


Q ss_pred             EEEeCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 014452          187 QVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQ  266 (424)
Q Consensus       187 ~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  266 (424)
                      .|+|+++.|+.|+.||.++|++....                      .|+..      +                    
T Consensus       189 ritGdp~~ve~a~~lV~dil~e~~~~----------------------~~g~~------~--------------------  220 (600)
T KOG1676|consen  189 RITGDPDKVEQAKQLVADILREEDDE----------------------VPGSG------G--------------------  220 (600)
T ss_pred             eecCCHHHHHHHHHHHHHHHHhcccC----------------------CCccc------c--------------------
Confidence            99999999999999999999986110                      00000      0                    


Q ss_pred             CCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccc
Q 014452          267 PFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAA  346 (424)
Q Consensus       267 ~~~~q~~~~~g~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~  346 (424)
                                               .+|                           ..                       
T Consensus       221 -------------------------~~g---------------------------~~-----------------------  225 (600)
T KOG1676|consen  221 -------------------------HAG---------------------------VR-----------------------  225 (600)
T ss_pred             -------------------------ccC---------------------------cC-----------------------
Confidence                                     000                           00                       


Q ss_pred             cCcceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCC-CCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          347 ILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       347 ~~~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~-~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      .....+.+|.||...||.||||+|++||+|+.+||++|+|-.+ .+.+.||.+.|.|++++|++|.+||.++|++
T Consensus       226 ~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~  300 (600)
T KOG1676|consen  226 GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAE  300 (600)
T ss_pred             ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHH
Confidence            0113589999999999999999999999999999999999733 3357899999999999999999999999985

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

Probab=100.00  E-value=3.4e-31  Score=269.85  Aligned_cols=352  Identities=27%  Similarity=0.382  Sum_probs=217.4

Q ss_pred             ccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHhhc
Q 014452           48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIG  127 (424)
Q Consensus        48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e~~  127 (424)
                      ...++||||+.+.+|.||||+|.+||+|+.+|.++|+|.+..+++.+|+|+|+|..... ..+++.+++.++++++....
T Consensus        41 ~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~-~~~~~~~al~ka~~~iv~~~  119 (485)
T KOG2190|consen   41 ETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL-NLSPATDALFKAFDMIVFKL  119 (485)
T ss_pred             CcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-cCCchHHHHHHHHHHHhhcc
Confidence            33348999999999999999999999999999999999999999999999999952222 55567899999999876521


Q ss_pred             ------C------CCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHH
Q 014452          128 ------F------EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSV  195 (424)
Q Consensus       128 ------~------~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v  195 (424)
                            .      ....+++++|+||..++|+||||+|+.||+|+++|||+|+|.++ .+|.   .++|.|+|.|.+++|
T Consensus       120 ~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av  195 (485)
T KOG2190|consen  120 EEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAV  195 (485)
T ss_pred             cccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHH
Confidence                  1      11225889999999999999999999999999999999999865 7777   588999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCccc
Q 014452          196 QDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPS--QPFDHQAA  273 (424)
Q Consensus       196 ~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~--~~~~~q~~  273 (424)
                      .+|+..|..+|.+..-. ..+......+|.|+.+...+....-.+...   .+. +.+. ....+.....  .|.+. ..
T Consensus       196 ~~al~~Is~~L~~~~~~-~~~~~~st~~y~P~~~~~~~~~~s~~~~~~---~~~-~~~~-~~~~~e~~~~~~~p~~~-~~  268 (485)
T KOG2190|consen  196 KKALVQISSRLLENPPR-SPPPLVSTIPYRPSASQGGPVLPSTAQTSP---DAH-PFGG-IVPEEELVFKLICPSDK-VG  268 (485)
T ss_pred             HHHHHHHHHHHHhcCCc-CCCCCCCcccCCCcccccCccccccccCCc---ccc-cccc-cccchhhhhhhcCchhh-ce
Confidence            99999999999996321 223334455665521111111111000000   000 0000 0000000000  00000 00


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCccccCcc
Q 014452          274 FSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGV---GGGDPRGFDASSGFTPRNRPVESGNHAAILTS  350 (424)
Q Consensus       274 ~~~g~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~~~~---~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~  350 (424)
                      ...|.+...-......        .+..-.+..+.....-+.++.   ...-.+..++......+-.+  .....+ ...
T Consensus       269 ~v~g~~~~~i~~l~~~--------~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~--~~~~~~-~~~  337 (485)
T KOG2190|consen  269 SVIGKGGLVIRALRNE--------TGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISE--NAGDDL-TQT  337 (485)
T ss_pred             eeecCCCccchhhhhh--------cCCceEeccccCcceeeeccccCcccccccchhhhhhccccccc--cccccc-cce
Confidence            0000000000000000        000000000000000000000   00000000000000000000  000111 346


Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCC--CCCCcEEEEEcCHHHHHHHHHHHHHHHHcCc
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP--GATEGVVMVSGTSDQMRAAQSLIHAFILCGV  422 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~--~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~~  422 (424)
                      ++.++.||.+++|+||||+|++|.+||+.|||.|.|.+..+  ...++.++|+|+..+...|+++|..++....
T Consensus       338 v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~  411 (485)
T KOG2190|consen  338 VTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSAPK  411 (485)
T ss_pred             eeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhcccccccCc
Confidence            88999999999999999999999999999999999997655  6789999999999999999999988877543

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

Probab=99.97  E-value=2.5e-30  Score=248.50  Aligned_cols=285  Identities=19%  Similarity=0.294  Sum_probs=203.5

Q ss_pred             CCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEecc-CCCCCcccEEEeecccccccccChhHHHHHHHHHHHH
Q 014452           46 YEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIAD-ILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIA  124 (424)
Q Consensus        46 ~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~-~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~  124 (424)
                      ...++.+|++||...||.||||.|+|||.|-..|.|+|.|.. ...+..|+.++|-++++...+      |+..+++.+.
T Consensus       195 q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~------Ac~~ILeimq  268 (584)
T KOG2193|consen  195 QLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSK------ACKMILEIMQ  268 (584)
T ss_pred             cccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHH------HHHHHHHHHH
Confidence            357788999999999999999999999999999999999983 334788999999999887544      5666665554


Q ss_pred             hhc--CCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHH
Q 014452          125 EIG--FEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI  202 (424)
Q Consensus       125 e~~--~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I  202 (424)
                      ...  .+...++.++++-.+.+||++|||.|.+||+|+.+||++|.|.+--++-.  -..||.+++.|+.|+|..|..+|
T Consensus       269 kEA~~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~--ynpERTItVkGsiEac~~AE~eI  346 (584)
T KOG2193|consen  269 KEAVDDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSL--YNPERTITVKGSIEACVQAEAEI  346 (584)
T ss_pred             HhhhccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcc--cCccceEEecccHHHHHHHHHHH
Confidence            332  22346677889999999999999999999999999999999987544422  25699999999999999999999


Q ss_pred             HHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCC
Q 014452          203 TSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMV  282 (424)
Q Consensus       203 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~  282 (424)
                      ..+|++...++-.. .+...+++|                   +.+..-.|.|.+......|+.+-.+            
T Consensus       347 mkKlre~yEnDl~a-~s~q~~l~P-------------------~l~~~~l~~f~ssS~~~~Ph~~Ps~------------  394 (584)
T KOG2193|consen  347 MKKLRECYENDLAA-MSLQCHLPP-------------------GLNLPALGLFPSSSAVSPPHFPPSP------------  394 (584)
T ss_pred             HHHHHHHHhhhHHH-hhccCCCCc-------------------ccCccccCCCCcccccCCCCCCCCc------------
Confidence            99999874332110 011111111                   0000000111000000000000000            


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcc
Q 014452          283 PPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYM  362 (424)
Q Consensus       283 ~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~  362 (424)
                                      .+   |. ++.|...                                ...+.....+.||...+
T Consensus       395 ----------------v~---~a-~p~~~~h--------------------------------q~pe~e~V~~fiP~~~v  422 (584)
T KOG2193|consen  395 ----------------VT---FA-SPYPLFH--------------------------------QNPEQEQVRMFIPAQAV  422 (584)
T ss_pred             ----------------cc---cC-CCchhhh--------------------------------cCcchhheeeeccHHHH
Confidence                            00   00 0000000                                01235678999999999


Q ss_pred             cceeccccchHHHHHHHhCCEEEEeCC-CCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcCc
Q 014452          363 AHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSDQMRAAQSLIHAFILCGV  422 (424)
Q Consensus       363 g~IIGk~G~~Ik~Ir~~SGa~I~i~~~-~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~~  422 (424)
                      |.|||+.|.+||+|.+.+||.|+|..+ -++..+|+|+|+|.+++.-+|+..|..+|+++-
T Consensus       423 GAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEen  483 (584)
T KOG2193|consen  423 GAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEEN  483 (584)
T ss_pred             HHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhc
Confidence            999999999999999999999999754 355789999999999999999999999998764

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

Probab=99.96  E-value=1.1e-28  Score=237.36  Aligned_cols=243  Identities=22%  Similarity=0.372  Sum_probs=190.2

Q ss_pred             CcCCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEec---cCCCCCcccEEEeecccccccccChh-HHHHHH
Q 014452           43 RMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA---DILPDSEERIVVISARENSEMRHSPA-QDAVMR  118 (424)
Q Consensus        43 ~~~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~---~~~~~~~er~v~I~G~~~~~~~~~~a-~~av~~  118 (424)
                      +....+++.++++-++.+||++|||.|++||+|+++||++|.|+   +-..-++||.|+|.|..++|..+... +..+.+
T Consensus       273 ~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre  352 (584)
T KOG2193|consen  273 DDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRE  352 (584)
T ss_pred             ccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHH
Confidence            34455889999999999999999999999999999999999998   33345679999999987776542111 111222


Q ss_pred             HHHH-HHhh---------------c-CC-----------C---------------CcceEEEEEecCCCcceeeccCCch
Q 014452          119 VHSR-IAEI---------------G-FE-----------P---------------GQAVVARLLVHSQQIGCLLGRGGHI  155 (424)
Q Consensus       119 ~~~~-i~e~---------------~-~~-----------~---------------~~~~t~~l~IP~~~vg~IIGkgG~~  155 (424)
                      +++. +...               + +.           +               .....++|.||...+|.|||++|..
T Consensus       353 ~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~h  432 (584)
T KOG2193|consen  353 CYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQH  432 (584)
T ss_pred             HHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchh
Confidence            2221 0000               0 00           0               1234578999999999999999999


Q ss_pred             HHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCC
Q 014452          156 VSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPP  235 (424)
Q Consensus       156 Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (424)
                      ||.|.+.+||.|+|.+.+ .   +...+|.|+|+|++++..+|...|+.+|.|+.+-            .|         
T Consensus       433 IKql~RfagASiKIappE-~---pdvseRMViItGppeaqfKAQgrifgKikEenf~------------~P---------  487 (584)
T KOG2193|consen  433 IKQLSRFAGASIKIAPPE-I---PDVSERMVIITGPPEAQFKAQGRIFGKIKEENFF------------LP---------  487 (584)
T ss_pred             HHHHHHhccceeeecCCC-C---CCcceeEEEecCChHHHHhhhhhhhhhhhhhccC------------Cc---------
Confidence            999999999999998753 3   3478999999999999999999999999998210            00         


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 014452          236 FRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTP  315 (424)
Q Consensus       236 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~  315 (424)
                                                                                                 .    
T Consensus       488 ---------------------------------------------------------------------------k----  488 (584)
T KOG2193|consen  488 ---------------------------------------------------------------------------K----  488 (584)
T ss_pred             ---------------------------------------------------------------------------h----
Confidence                                                                                       0    


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCC--CCCC
Q 014452          316 QGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP--KPGA  393 (424)
Q Consensus       316 ~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~--~~~~  393 (424)
                                                     ..-....+|.||...+|+||||||.++++|+..|+|.|.|+.+  .++.
T Consensus       489 -------------------------------eevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEn  537 (584)
T KOG2193|consen  489 -------------------------------EEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDEN  537 (584)
T ss_pred             -------------------------------hhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCcc
Confidence                                           0124678999999999999999999999999999999999843  2334


Q ss_pred             CCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          394 TEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       394 ~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      +.-+|.|+|...+.+.|++.|.++|.+
T Consensus       538 d~vivriiGhfyatq~aQrki~~iv~q  564 (584)
T KOG2193|consen  538 DQVIVRIIGHFYATQNAQRKIAHIVNQ  564 (584)
T ss_pred             ceeeeeeechhhcchHHHHHHHHHHHH
Confidence            556888999999999999999998864

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

Probab=99.95  E-value=4.8e-26  Score=213.37  Aligned_cols=268  Identities=21%  Similarity=0.333  Sum_probs=189.9

Q ss_pred             CCcCCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEec---cCCCCCcccEEEeecccccccccChhHHHHHH
Q 014452           42 NRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA---DILPDSEERIVVISARENSEMRHSPAQDAVMR  118 (424)
Q Consensus        42 ~~~~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~---~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~  118 (424)
                      +.-..+..+++|||||+..+|+||||+|++|.+|+++|||+|+++   +..|++.||+|.|+|+.+++.      ..+..
T Consensus        31 ~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~------av~ef  104 (402)
T KOG2191|consen   31 TNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALN------AVHEF  104 (402)
T ss_pred             ccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHH------HHHHH
Confidence            334444559999999999999999999999999999999999998   678999999999999954421      12233


Q ss_pred             HHHHHHhhc---------CC---CCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEE
Q 014452          119 VHSRIAEIG---------FE---PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIV  186 (424)
Q Consensus       119 ~~~~i~e~~---------~~---~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v  186 (424)
                      +.++|+|.-         ++   ++..-.+++.||++.+|.||||+|.+||.|+|+++|.|+|.+..  |..-.-.+|+|
T Consensus       105 I~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk--pt~~sLqervv  182 (402)
T KOG2191|consen  105 IADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK--PTGISLQERVV  182 (402)
T ss_pred             HHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC--CCCccceeEEE
Confidence            344444321         11   12224589999999999999999999999999999999998532  23334679999


Q ss_pred             EEEeCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 014452          187 QVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQ  266 (424)
Q Consensus       187 ~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  266 (424)
                      ++.|++++..+|+.+|+.+|.+..      .+..+  +..+|                    ..                
T Consensus       183 t~sge~e~~~~A~~~IL~Ki~eDp------qs~sc--ln~sy--------------------a~----------------  218 (402)
T KOG2191|consen  183 TVSGEPEQNMKAVSLILQKIQEDP------QSGSC--LNISY--------------------AN----------------  218 (402)
T ss_pred             EecCCHHHHHHHHHHHHHHhhcCC------cccce--eccch--------------------hc----------------
Confidence            999999999999999999999871      11000  00000                    00                


Q ss_pred             CCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccc
Q 014452          267 PFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAA  346 (424)
Q Consensus       267 ~~~~q~~~~~g~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~  346 (424)
                                ..++  .-+                  ++           +.+  ++|++..                ..
T Consensus       219 ----------vsGp--vaN------------------sn-----------PtG--spya~~~----------------~~  239 (402)
T KOG2191|consen  219 ----------VSGP--VAN------------------SN-----------PTG--SPYAYQA----------------HV  239 (402)
T ss_pred             ----------ccCc--ccc------------------cC-----------CCC--CCCCCCC----------------cc
Confidence                      0000  000                  00           000  0000000                00


Q ss_pred             cCcceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCC---CCCCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452          347 ILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPK---PGATEGVVMVSGTSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       347 ~~~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~---~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~  421 (424)
                      ..+..+..+-++....|..-|.+|.++-.|-..+|+.+.+.+..   .+..++ .-+.|.+-.+..|-.+|...+.+-
T Consensus       240 ~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~~~~a  316 (402)
T KOG2191|consen  240 LPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMAGYGYN-TNILGLGLSILAAEGVLAAKVASA  316 (402)
T ss_pred             ccccchhhccccccccccccccccccceeeecccccceeeccccccccccccc-ccccchhhhhhhhhhHHHHhhccc
Confidence            12234566778899999999999999999999999999997532   334455 788899999999999998887654

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

Probab=99.89  E-value=3.5e-22  Score=187.52  Aligned_cols=166  Identities=23%  Similarity=0.362  Sum_probs=134.6

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhcC
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIF  211 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~  211 (424)
                      ....++++||...+|.||||+|++|.+++.+|||+|+++...+  .+++.+||+|.|+|+.+++....+.|.++|++...
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~d--fyPGTTeRvcli~Gt~eai~av~efI~dKire~p~  114 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKD--FYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQ  114 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccc--cCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHH
Confidence            3488999999999999999999999999999999999986544  35569999999999999999999999999999732


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCC
Q 014452          212 PMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPF  291 (424)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~~  291 (424)
                      ....+                ...+                                .+|                    
T Consensus       115 ~~~k~----------------v~~~--------------------------------~pq--------------------  126 (402)
T KOG2191|consen  115 AVAKP----------------VDIL--------------------------------QPQ--------------------  126 (402)
T ss_pred             hhcCC----------------cccc--------------------------------CCC--------------------
Confidence            11000                0000                                000                    


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceeccccc
Q 014452          292 PYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNS  371 (424)
Q Consensus       292 ~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G~  371 (424)
                                               .               +              .....+++.||...+|.||||+|.
T Consensus       127 -------------------------t---------------~--------------~r~kqikivvPNstag~iigkggA  152 (402)
T KOG2191|consen  127 -------------------------T---------------P--------------DRIKQIKIVVPNSTAGMIIGKGGA  152 (402)
T ss_pred             -------------------------C---------------c--------------cccceeEEeccCCcccceecCCcc
Confidence                                     0               0              011348899999999999999999


Q ss_pred             hHHHHHHHhCCEEEEeCCCCC---CCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452          372 NLSHIRQISGANVVVNDPKPG---ATEGVVMVSGTSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       372 ~Ik~Ir~~SGa~I~i~~~~~~---~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~  421 (424)
                      +||.|+|++||+|+|...++.   -.+|+||++|++|+..+|..||.++|.+.
T Consensus       153 tiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eD  205 (402)
T KOG2191|consen  153 TIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQED  205 (402)
T ss_pred             hHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcC
Confidence            999999999999999843322   24799999999999999999999999865

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

Probab=99.77  E-value=7.1e-18  Score=172.52  Aligned_cols=159  Identities=27%  Similarity=0.424  Sum_probs=131.6

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe---------CHHHHHHHHHH
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG---------NYHSVQDALFH  201 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G---------~~~~v~~A~~~  201 (424)
                      +...+++++++...+|.||||+|..||+|+.++.++|+|...  .+   +..+|+|+|+|         ..+++.+|..+
T Consensus        40 ~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~--~~---~c~eRIiti~g~~~~~~~~~~~~al~ka~~~  114 (485)
T KOG2190|consen   40 DETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNES--LP---GCPERIITITGNRVELNLSPATDALFKAFDM  114 (485)
T ss_pred             CCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecC--CC---CCCcceEEEecccccccCCchHHHHHHHHHH
Confidence            344558999999999999999999999999999999999643  33   35899999999         99999999999


Q ss_pred             HHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCC
Q 014452          202 ITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPM  281 (424)
Q Consensus       202 I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~  281 (424)
                      |...+++.....            .   +                                                   
T Consensus       115 iv~~~~~d~~~~------------~---d---------------------------------------------------  128 (485)
T KOG2190|consen  115 IVFKLEEDDEAA------------E---D---------------------------------------------------  128 (485)
T ss_pred             Hhhccccccccc------------c---c---------------------------------------------------
Confidence            998877431100            0   0                                                   


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCc
Q 014452          282 VPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLY  361 (424)
Q Consensus       282 ~~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~  361 (424)
                                 .                               +.+.                  ....+++.+.||...
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                  011478999999999


Q ss_pred             ccceeccccchHHHHHHHhCCEEEEeCC-CCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          362 MAHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       362 ~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~-~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      +|+||||+|++||+||++|||+|.|... .+.+++|.|+|+|++++|.+|...|..+|.+
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            9999999999999999999999999854 6789999999999999999999999999986

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

Probab=99.70  E-value=9.2e-17  Score=147.18  Aligned_cols=151  Identities=24%  Similarity=0.487  Sum_probs=123.9

Q ss_pred             ccEEEEEEecccccceeeccCchHHHHHHHHhCceEEec-cCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHhh
Q 014452           48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA-DILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEI  126 (424)
Q Consensus        48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~-~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e~  126 (424)
                      +.-.+||||+.+++|.|||++|+.||.|++++.|+++|- +..|.+.+|+|.|.|.+.++..      .+..+++.+.|.
T Consensus       121 ~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~------~i~~il~~i~e~  194 (390)
T KOG2192|consen  121 SPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVE------CIKIILDLISES  194 (390)
T ss_pred             CchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHH------HHHHHHHHhhcC
Confidence            445789999999999999999999999999999999987 7778899999999999866432      333333333221


Q ss_pred             c----------------------------------------------------------------------C--------
Q 014452          127 G----------------------------------------------------------------------F--------  128 (424)
Q Consensus       127 ~----------------------------------------------------------------------~--------  128 (424)
                      .                                                                      |        
T Consensus       195 pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~s  274 (390)
T KOG2192|consen  195 PIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPS  274 (390)
T ss_pred             CcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCC
Confidence            0                                                                      0        


Q ss_pred             --------------C---------------------CCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCC
Q 014452          129 --------------E---------------------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKD  173 (424)
Q Consensus       129 --------------~---------------------~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~  173 (424)
                                    +                     .....|.++.||.++-|.||||+|++|++|+.++||.|++... 
T Consensus       275 aidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikidep-  353 (390)
T KOG2192|consen  275 AIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEP-  353 (390)
T ss_pred             cCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCc-
Confidence                          0                     0124678999999999999999999999999999999999642 


Q ss_pred             CCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          174 QAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       174 ~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                          ..++.+|+++|+|+.++++.|..++...++.+
T Consensus       354 ----leGsedrIitItGTqdQIqnAQYLlQn~Vkq~  385 (390)
T KOG2192|consen  354 ----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY  385 (390)
T ss_pred             ----CCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence                33588999999999999999999999999865

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.67  E-value=3.9e-16  Score=140.11  Aligned_cols=61  Identities=21%  Similarity=0.315  Sum_probs=53.9

Q ss_pred             EEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEE---EeCHHHHHHHHHHHHHHHHh
Q 014452          138 LLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQV---IGNYHSVQDALFHITSRLRE  208 (424)
Q Consensus       138 l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I---~G~~~~v~~A~~~I~~~l~~  208 (424)
                      +.||.+.+|.|||++|++|+.|+++|||+|++..+          +..|.|   +++++++.+|+.+|..+...
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~----------~g~V~I~~~t~d~~~i~kA~~~I~~i~~g   65 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE----------TGEVKIEEEDEDPLAVMKAREVVKAIGRG   65 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC----------CceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence            57899999999999999999999999999999643          245888   78999999999999987664

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.

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.64  E-value=1.4e-15  Score=136.62  Aligned_cols=129  Identities=29%  Similarity=0.445  Sum_probs=96.9

Q ss_pred             EEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEee---cccccccccChhHHHHHHHHHHHHhh--cC
Q 014452           54 LLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVIS---ARENSEMRHSPAQDAVMRVHSRIAEI--GF  128 (424)
Q Consensus        54 i~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~---G~~~~~~~~~~a~~av~~~~~~i~e~--~~  128 (424)
                      |.||.+.+|.|||++|++|+.|+++|||+|++.+     ++..|.|+   +.+.          ++.++.+.+...  ++
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~----------~i~kA~~~I~~i~~gf   66 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPL----------AVMKAREVVKAIGRGF   66 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHH----------HHHHHHHHHHHHHcCC
Confidence            5689999999999999999999999999999953     34678883   3332          344444433321  11


Q ss_pred             CC-------CcceEEE-EEecC---------CCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC
Q 014452          129 EP-------GQAVVAR-LLVHS---------QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN  191 (424)
Q Consensus       129 ~~-------~~~~t~~-l~IP~---------~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~  191 (424)
                      ++       .+.++.+ +.|+.         ..+|+|||++|++++.|++.|||+|.|..            +.|.|.|+
T Consensus        67 ~~e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~  134 (172)
T TIGR03665        67 SPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGD  134 (172)
T ss_pred             CHHHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECC
Confidence            11       2233333 33443         36899999999999999999999998852            46999999


Q ss_pred             HHHHHHHHHHHHHHHHhh
Q 014452          192 YHSVQDALFHITSRLRET  209 (424)
Q Consensus       192 ~~~v~~A~~~I~~~l~~~  209 (424)
                      +++++.|+.+|.++++..
T Consensus       135 ~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665       135 PEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             HHHHHHHHHHHHHHHcCC
Confidence            999999999999999554

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=99.63  E-value=6.1e-15  Score=133.29  Aligned_cols=65  Identities=18%  Similarity=0.248  Sum_probs=57.2

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEE----eCHHHHHHHHHHHHHHHHh
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI----GNYHSVQDALFHITSRLRE  208 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~----G~~~~v~~A~~~I~~~l~~  208 (424)
                      +...+.||.+.++.|||++|++|+.|+++|||+|++..+          +..|.|.    ++++++.+|+.+|..++..
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 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE----------TGEVIIEPTDGEDPLAVLKARDIVKAIGRG   71 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC----------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence            356899999999999999999999999999999999643          2468885    8999999999999988774

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.60  E-value=1e-14  Score=131.83  Aligned_cols=133  Identities=25%  Similarity=0.385  Sum_probs=98.0

Q ss_pred             EEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEee----cccccccccChhHHHHHHHHHHHHh
Q 014452           50 VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVIS----ARENSEMRHSPAQDAVMRVHSRIAE  125 (424)
Q Consensus        50 ~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~----G~~~~~~~~~~a~~av~~~~~~i~e  125 (424)
                      +...+.||.+.+|.|||++|++|+.|+++|||+|++.+     ++..|.|.    +.++          ++.++.+.+..
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~-----~~g~V~I~~~~~~d~~----------~i~kA~~~I~a   67 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS-----ETGEVIIEPTDGEDPL----------AVLKARDIVKA   67 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC-----CCCeEEEEeCCCCCHH----------HHHHHHHHHHH
Confidence            45689999999999999999999999999999999953     34678886    3433          33333333322


Q ss_pred             hc--CC-------CCcceEEEE-Eec---------CCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEE
Q 014452          126 IG--FE-------PGQAVVARL-LVH---------SQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIV  186 (424)
Q Consensus       126 ~~--~~-------~~~~~t~~l-~IP---------~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v  186 (424)
                      ..  ++       ..+.+..++ .|.         ...+|+|||++|++++.|++.|||+|.|..            +.|
T Consensus        68 i~~gf~~e~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------------~~v  135 (180)
T PRK13763         68 IGRGFSPEKALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------------KTV  135 (180)
T ss_pred             HhcCCCHHHHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC------------CEE
Confidence            11  11       112222221 121         137899999999999999999999999852            239


Q ss_pred             EEEeCHHHHHHHHHHHHHHHHhh
Q 014452          187 QVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       187 ~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      .|.|++++++.|+..|.++++..
T Consensus       136 ~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        136 AIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             EEEeCHHHHHHHHHHHHHHHcCC
Confidence            99999999999999999998554

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.50  E-value=4.6e-14  Score=106.21  Aligned_cols=63  Identities=29%  Similarity=0.482  Sum_probs=58.5

Q ss_pred             EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCC-CCCCcEEEEEcCHHHHHHHHHHHH
Q 014452          353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP-GATEGVVMVSGTSDQMRAAQSLIH  415 (424)
Q Consensus       353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~-~~~~r~i~I~Gt~e~v~~A~~lI~  415 (424)
                      .+|.||.+.+|+|||++|++|++|+++|||+|.+.+... ...+|+|+|+|++++|+.|+.||.
T Consensus         2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence            689999999999999999999999999999999986544 678899999999999999999984

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

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

Probab=99.41  E-value=1.8e-12  Score=130.05  Aligned_cols=294  Identities=17%  Similarity=0.240  Sum_probs=181.2

Q ss_pred             cCCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHH
Q 014452           44 MFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRI  123 (424)
Q Consensus        44 ~~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i  123 (424)
                      ....+++.++++|+...|-.+|||.|++|+.|+..++++|.+.+.. -.+++...+.|.+..+..   +.+++.+   .+
T Consensus        62 ~e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~v~~---a~a~~~~---~~  134 (608)
T KOG2279|consen   62 QKPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQVCK---AKAAIHQ---IL  134 (608)
T ss_pred             cCchhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCCCCh---HHHHHHH---HH
Confidence            3445889999999999999999999999999999999999997442 245566666665544332   3333322   22


Q ss_pred             HhhcCCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHH
Q 014452          124 AEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHIT  203 (424)
Q Consensus       124 ~e~~~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~  203 (424)
                      .+     +..+...+.+|...+++|+|++|.+++.|+..++|+|.+.....     ..-.+...|.+...-+..|+.++.
T Consensus       135 ~~-----~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr-----~g~~~~~~i~~qqk~~~~a~~~~~  204 (608)
T KOG2279|consen  135 TE-----NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR-----LGLSRLIKISGQQKEVAAAKHLIL  204 (608)
T ss_pred             hc-----CCcccccccchhhhcccccccchhhhcchhcccccccccccccc-----cccccceecccccchHHHHHhhhh
Confidence            21     34567789999999999999999999999999999998754311     145778888888888889999999


Q ss_pred             HHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCC
Q 014452          204 SRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVP  283 (424)
Q Consensus       204 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~  283 (424)
                      +.+.+.....+.......... | .. .+...++.  ++..+                                      
T Consensus       205 ~~~~edeelv~~~~e~~q~rv-p-rk-~p~n~~~~--~m~~~--------------------------------------  241 (608)
T KOG2279|consen  205 EKVSEDEELVKRIAESAQTRV-P-RK-QPINVRRE--DMTEP--------------------------------------  241 (608)
T ss_pred             ccccchhHHhhhchhhcccCC-C-CC-CCccccch--hhccc--------------------------------------
Confidence            988764222111111110000 0 00 00000000  00000                                      


Q ss_pred             CCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCccccCcceEEEEEe
Q 014452          284 PNSDRIPFPYGSERPGHGPTF----DRPPSPRSWTPQGVGGGDPRGFDAS--SGFTPRNRPVESGNHAAILTSTTIEVVI  357 (424)
Q Consensus       284 ~~~~~~~~~~g~~~~g~~~~~----~~~~~p~~~~~~~~~~g~~~g~~~~--~~~~~r~~~~~~g~~~~~~~~~t~~v~I  357 (424)
                                +...++|....    +.|..|..     ..+|..+.....  ..|.    +..-|+..........+|.+
T Consensus       242 ----------~~s~~~h~~~~t~~s~spg~~~~-----~~eg~dm~v~vsk~~s~~----~~~d~s~~k~~~l~i~e~e~  302 (608)
T KOG2279|consen  242 ----------GGAGEPHLWKNTSSSMSPGAPLV-----TKEGGDMAVVVSKEGSWE----KPSDDSFQKSEALAIPEMEM  302 (608)
T ss_pred             ----------ccCCccccCccchhccCCCCCCc-----ccCCCcceeEEecccccC----Cccccccccccccccceeec
Confidence                      00000000000    00000000     000111110000  0000    01112223334567789999


Q ss_pred             ccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCC---CcEEEEEcCHHHHHHHHHHHHH
Q 014452          358 PQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGAT---EGVVMVSGTSDQMRAAQSLIHA  416 (424)
Q Consensus       358 P~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~---~r~i~I~Gt~e~v~~A~~lI~~  416 (424)
                      |...+|.+||+.|++++.+...|++.+.|........   -.++.+.|+..-+..|..||..
T Consensus       303 p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkqh~~n~vl~ml~~  364 (608)
T KOG2279|consen  303 PEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQHYENSVLEMLTV  364 (608)
T ss_pred             CcccccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecchhHHHHHHHhhhhc
Confidence            9999999999999999999999999999974322211   2578899999999999999974

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.38  E-value=6.9e-13  Score=98.77  Aligned_cols=61  Identities=23%  Similarity=0.425  Sum_probs=56.3

Q ss_pred             EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHH
Q 014452          353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH  415 (424)
Q Consensus       353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~  415 (424)
                      .+|.||.+++++|||++|++|++|+++|||+|.|++..  ..++.|+|+|++++|+.|+.+|+
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            67999999999999999999999999999999997543  67899999999999999999884

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.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.38  E-value=5.3e-13  Score=98.71  Aligned_cols=60  Identities=23%  Similarity=0.511  Sum_probs=55.4

Q ss_pred             EEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHH
Q 014452          352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLI  414 (424)
Q Consensus       352 t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI  414 (424)
                      |.+|.||.+++|+|||++|++|++|+++|||+|.|++.  + .+..|+|+|++++|+.|+.+|
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            67899999999999999999999999999999999865  2 455999999999999999987

; 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 ....

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

Probab=99.35  E-value=2.7e-12  Score=95.96  Aligned_cols=63  Identities=27%  Similarity=0.545  Sum_probs=58.3

Q ss_pred             EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHH
Q 014452          353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH  415 (424)
Q Consensus       353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~  415 (424)
                      .+|.||.+++++|||++|++|++|+++|||+|.|++..+...++.|+|+|+.++++.|+.+|+
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            679999999999999999999999999999999987655567899999999999999999874

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=99.35  E-value=2.7e-12  Score=95.16  Aligned_cols=59  Identities=19%  Similarity=0.385  Sum_probs=54.0

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcC-HHHHHHHHHHHH
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT-SDQMRAAQSLIH  415 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt-~e~v~~A~~lI~  415 (424)
                      .+..|.||.+++|+|||++|++|++|+++|||+|.|++      ++.|+|+|+ +++++.|+.+|+
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            35789999999999999999999999999999999964      468999998 999999999984

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.

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.32  E-value=4.9e-12  Score=95.11  Aligned_cols=65  Identities=38%  Similarity=0.581  Sum_probs=57.9

Q ss_pred             EEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHH
Q 014452          135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHIT  203 (424)
Q Consensus       135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~  203 (424)
                      +++|.||.+.+|.|||++|++|++|+++|||+|.+.+...    ....+|+|+|+|+++++.+|+.+|.
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhhC
Confidence            3689999999999999999999999999999999976432    2467999999999999999999873

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.19  E-value=2.8e-11  Score=90.04  Aligned_cols=61  Identities=16%  Similarity=0.288  Sum_probs=55.2

Q ss_pred             EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHH
Q 014452          136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHIT  203 (424)
Q Consensus       136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~  203 (424)
                      .++.||.+++++|||++|++|++|+++|||+|.+++.+       +.++.|+|+|+.++|..|+.+|.
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            57899999999999999999999999999999997542       56789999999999999998873

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=99.12  E-value=2.4e-10  Score=84.72  Aligned_cols=58  Identities=19%  Similarity=0.324  Sum_probs=52.3

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHH
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHI  202 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I  202 (424)
                      ....+.||.+++++|||++|++|++|+++|||+|.+..           ++.|.|+|+ .++++.|+.+|
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHh
Confidence            35678999999999999999999999999999999852           346999998 99999999887

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.12  E-value=6e-11  Score=87.65  Aligned_cols=60  Identities=27%  Similarity=0.433  Sum_probs=54.1

Q ss_pred             EEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHH
Q 014452          135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI  202 (424)
Q Consensus       135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I  202 (424)
                      |.+|.||.+++++|||++|++|++|+++|||+|+++++        ..+..|+|+|+.++|++|+++|
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            57899999999999999999999999999999999643        2345899999999999999886

; 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 ....

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

Probab=99.06  E-value=5.8e-10  Score=83.19  Aligned_cols=62  Identities=32%  Similarity=0.559  Sum_probs=55.7

Q ss_pred             EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHH
Q 014452          136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI  202 (424)
Q Consensus       136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I  202 (424)
                      .++.||.++++.|||++|++|++|+++|||+|.|.+...     ...++.|.|.|+.+++..|+.+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----CCCceEEEEEcCHHHHHHHHHHh
Confidence            579999999999999999999999999999999975432     35789999999999999999876

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.

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

Probab=99.06  E-value=3.4e-09  Score=94.76  Aligned_cols=140  Identities=24%  Similarity=0.395  Sum_probs=104.9

Q ss_pred             ccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHh--
Q 014452           48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAE--  125 (424)
Q Consensus        48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e--  125 (424)
                      ......+.||.+.++.+||+.|++.+.|++.++++|.+     +..+..|.|.......+     ..+++++.+.+..  
T Consensus         6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~i-----D~~~~~V~i~~~~~t~D-----p~~~~ka~d~VkAIg   75 (194)
T COG1094           6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRI-----DSKTGSVTIRTTRKTED-----PLALLKARDVVKAIG   75 (194)
T ss_pred             ccceeeeecCchhheeeecccccchHHHHhhcCeEEEE-----ECCCCeEEEEecCCCCC-----hHHHHHHHHHHHHHh
Confidence            34456799999999999999999999999999999999     67888999987732111     2234555444332  


Q ss_pred             hcCCCC-------cceEEE-EEe------cC----CCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEE
Q 014452          126 IGFEPG-------QAVVAR-LLV------HS----QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQ  187 (424)
Q Consensus       126 ~~~~~~-------~~~t~~-l~I------P~----~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~  187 (424)
                      .+|+++       +.+.+. +.+      +.    ...|+|||++|.+.+.|++.|+|.|.|..+            .|.
T Consensus        76 rGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~------------tVa  143 (194)
T COG1094          76 RGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK------------TVA  143 (194)
T ss_pred             cCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc------------EEE
Confidence            244321       122222 222      11    245999999999999999999999988643            499


Q ss_pred             EEeCHHHHHHHHHHHHHHHHhh
Q 014452          188 VIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       188 I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      |.|.+++|+.|+..|++++...
T Consensus       144 iiG~~~~v~iAr~AVemli~G~  165 (194)
T COG1094         144 IIGGFEQVEIAREAVEMLINGA  165 (194)
T ss_pred             EecChhhhHHHHHHHHHHHcCC
Confidence            9999999999999999999765

>smart00322 KH K homology RNA-binding domain

Probab=99.04  E-value=1.3e-09  Score=81.60  Aligned_cols=67  Identities=25%  Similarity=0.440  Sum_probs=60.3

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHH
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~  419 (424)
                      .+.+|.||...++++||++|++|++|++.|||+|.+....  .....|+|.|+.++++.|+.+|.+.++
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~--~~~~~v~i~g~~~~v~~a~~~i~~~~~   69 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG--SEERVVEITGPPENVEKAAELILEILE   69 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC--CCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence            5789999999999999999999999999999999996432  256899999999999999999998763

>PF13014 KH_3: KH domain

Probab=99.00  E-value=6.4e-10  Score=76.38  Aligned_cols=42  Identities=29%  Similarity=0.659  Sum_probs=38.2

Q ss_pred             cccceeccccchHHHHHHHhCCEEEEeC-CCCCCCCcEEEEEc
Q 014452          361 YMAHVYGENNSNLSHIRQISGANVVVND-PKPGATEGVVMVSG  402 (424)
Q Consensus       361 ~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~-~~~~~~~r~i~I~G  402 (424)
                      ++|+|||++|++|++|+++|||+|+|++ ..++..+++|+|+|
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            5799999999999999999999999986 45667899999998

>PF13014 KH_3: KH domain

Probab=98.98  E-value=8.1e-10  Score=75.86  Aligned_cols=42  Identities=48%  Similarity=0.772  Sum_probs=38.7

Q ss_pred             ccceeeccCchHHHHHHHHhCceEEecc-CCCCCcccEEEeec
Q 014452           60 KVGSLIGKGGSIVRTFQNETGASIKIAD-ILPDSEERIVVISA  101 (424)
Q Consensus        60 ~vg~IIGk~G~~Ik~I~~~tga~I~v~~-~~~~~~er~v~I~G  101 (424)
                      +||+|||++|++|++|+++|+|+|+|++ ..++..++.|+|+|
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            4899999999999999999999999997 56688999999987

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.97  E-value=2.3e-09  Score=116.22  Aligned_cols=224  Identities=19%  Similarity=0.281  Sum_probs=156.7

Q ss_pred             ccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccc-cChhHHH-----------
Q 014452           48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMR-HSPAQDA-----------  115 (424)
Q Consensus        48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~-~~~a~~a-----------  115 (424)
                      .-+..++.+....+.+|||++|.+++.+++++.+.|.|++..  .......|.+....... ....+++           
T Consensus       199 r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn--~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~  276 (753)
T KOG2208|consen  199 RSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSN--KSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYD  276 (753)
T ss_pred             eeEEEEeeccccchhhhccccccccccccccceeEEEccccc--ccchhhhhccccccceehhhhhHHHHHHhcChhhhh
Confidence            346778999999999999999999999999999999998542  22222223332111100 0000001           


Q ss_pred             ------------------HHHHHHHHHhh-----c------------CC-----------------CCcceEEEEEecCC
Q 014452          116 ------------------VMRVHSRIAEI-----G------------FE-----------------PGQAVVARLLVHSQ  143 (424)
Q Consensus       116 ------------------v~~~~~~i~e~-----~------------~~-----------------~~~~~t~~l~IP~~  143 (424)
                                        +..+.+...+.     .            .+                 ....+.+.+.|-..
T Consensus       277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~  356 (753)
T KOG2208|consen  277 EIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPE  356 (753)
T ss_pred             hhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHH
Confidence                              01110000000     0            00                 01246677888889


Q ss_pred             CcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCC
Q 014452          144 QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHS  223 (424)
Q Consensus       144 ~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~  223 (424)
                      .+..|+||+|.+|.+|++++.|.|.+...       ++.+..+.++|...++.+|...++....+...            
T Consensus       357 ~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n------------  417 (753)
T KOG2208|consen  357 ELKFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN------------  417 (753)
T ss_pred             hhhhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc------------
Confidence            99999999999999999999999988642       25678899999999999999999998888721            


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 014452          224 YLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPT  303 (424)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~~~~g~~~~g~~~~  303 (424)
                                                                                                      
T Consensus       418 --------------------------------------------------------------------------------  417 (753)
T KOG2208|consen  418 --------------------------------------------------------------------------------  417 (753)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceeccccchHHHHHHHhCCE
Q 014452          304 FDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGAN  383 (424)
Q Consensus       304 ~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~  383 (424)
                                                                   .....++.||..++.++||.+|..|+.|...+++ 
T Consensus       418 ---------------------------------------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~-  451 (753)
T KOG2208|consen  418 ---------------------------------------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGG-  451 (753)
T ss_pred             ---------------------------------------------ccccceeecCccchhhhhccccccHHHHHhhcCc-
Confidence                                                         0134678999999999999999999999999995 


Q ss_pred             EEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 014452          384 VVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFI  418 (424)
Q Consensus       384 I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i  418 (424)
                      +.|..+........+++.|....+..++.++..+.
T Consensus       452 v~i~f~~~~~~~~~~~~~~~~~dv~~~~~~~~~~~  486 (753)
T KOG2208|consen  452 VHIKFQNNNNSSDMVTIRGISKDVEKSVSLLKALK  486 (753)
T ss_pred             EEEecCCCCcccccceEeccccccchhHHHHHhhh
Confidence            44443444455567888887777777666655443

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

Probab=98.81  E-value=2.9e-09  Score=107.34  Aligned_cols=145  Identities=20%  Similarity=0.321  Sum_probs=121.4

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhc
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETI  210 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  210 (424)
                      .+.+.+++.|+...+-+++|+.|++|+.|+..++++|.+.+++ .     ..++.-.+.|-+.++..|..+++.++.+.-
T Consensus        65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~-----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~  138 (608)
T KOG2279|consen   65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-V-----GDERVLLISGFPVQVCKAKAAIHQILTENT  138 (608)
T ss_pred             hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-C-----CcccchhhccCCCCCChHHHHHHHHHhcCC
Confidence            3567889999999999999999999999999999999886543 1     355666677789999999999998887650


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCC
Q 014452          211 FPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIP  290 (424)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~  290 (424)
                                                                                                      
T Consensus       139 --------------------------------------------------------------------------------  138 (608)
T KOG2279|consen  139 --------------------------------------------------------------------------------  138 (608)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceecccc
Q 014452          291 FPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENN  370 (424)
Q Consensus       291 ~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G  370 (424)
                                                                                 .+..+..+|...+++|+||+|
T Consensus       139 -----------------------------------------------------------pvk~~lsvpqr~~~~i~grgg  159 (608)
T KOG2279|consen  139 -----------------------------------------------------------PVSEQLSVPQRSVGRIIGRGG  159 (608)
T ss_pred             -----------------------------------------------------------cccccccchhhhcccccccch
Confidence                                                                       133556778889999999999


Q ss_pred             chHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          371 SNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       371 ~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      .++..|+..|+|+|.++..--....+.+.|.+...-++.|+.++.++++.
T Consensus       160 et~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~e  209 (608)
T KOG2279|consen  160 ETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSE  209 (608)
T ss_pred             hhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccc
Confidence            99999999999999998653334568899999999999999999998875

>smart00322 KH K homology RNA-binding domain

Probab=98.80  E-value=3.2e-08  Score=74.00  Aligned_cols=66  Identities=23%  Similarity=0.475  Sum_probs=58.9

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHH
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL  206 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  206 (424)
                      .+.++.||...++.+||++|++|++|++.++++|.+....       .....|.|.|+.+++..|..+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            5678999999999999999999999999999999986432       25678999999999999999998876

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.74  E-value=2.1e-08  Score=108.72  Aligned_cols=146  Identities=16%  Similarity=0.272  Sum_probs=112.8

Q ss_pred             CCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHh
Q 014452           46 YEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAE  125 (424)
Q Consensus        46 ~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e  125 (424)
                      .+..+...+.+-...+..|+||+|.+|.+|++++.|.|.++..  +..+..+++++...++.+   +.+.+.++...+.+
T Consensus       343 ~~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~~k---a~~~v~~~~~ei~n  417 (753)
T KOG2208|consen  343 EENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSANDEK---AVEDVEKIIAEILN  417 (753)
T ss_pred             hccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccchhH---HHHHHHHHHHhhhc
Confidence            3444677888999999999999999999999999999999874  577788999998766554   34444444433322


Q ss_pred             hcCCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcC-ceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHH
Q 014452          126 IGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATG-ASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITS  204 (424)
Q Consensus       126 ~~~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tg-a~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~  204 (424)
                            ......+.||...+..|||.+|..|++|.++++ .+|+.....       .....+++.|....+..++.++..
T Consensus       418 ------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~-------~~~~~~~~~~~~~dv~~~~~~~~~  484 (753)
T KOG2208|consen  418 ------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN-------NSSDMVTIRGISKDVEKSVSLLKA  484 (753)
T ss_pred             ------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC-------cccccceEeccccccchhHHHHHh
Confidence                  145567999999999999999999999999999 666664332       445668999999888887777666


Q ss_pred             HHHhh
Q 014452          205 RLRET  209 (424)
Q Consensus       205 ~l~~~  209 (424)
                      +....
T Consensus       485 ~~~~a  489 (753)
T KOG2208|consen  485 LKADA  489 (753)
T ss_pred             hhhhh
Confidence            55543

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

Probab=98.61  E-value=5.8e-07  Score=80.57  Aligned_cols=53  Identities=17%  Similarity=0.290  Sum_probs=48.6

Q ss_pred             cccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          361 YMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       361 ~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      .-|+|||++|.+.+.|++.|||+|.|..       .+|.|.|.+++|+.|+..|..+|..
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g-------~tVaiiG~~~~v~iAr~AVemli~G  164 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVYG-------KTVAIIGGFEQVEIAREAVEMLING  164 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEeC-------cEEEEecChhhhHHHHHHHHHHHcC
Confidence            4599999999999999999999999963       4799999999999999999999864

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

Probab=98.61  E-value=5.5e-08  Score=91.81  Aligned_cols=149  Identities=23%  Similarity=0.288  Sum_probs=112.3

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhcC
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIF  211 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~  211 (424)
                      +.++..+.||..+++.|+|++|.+||.|+.+|...|+-+.+.        .+-++.++|..+.|+.|+..|...-++.-.
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~--------eePiF~vTg~~edv~~aRrei~saaeH~~l   95 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG--------EEPIFPVTGRHEDVRRARREIPSAAEHFGL   95 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC--------CCCcceeccCchhHHHHhhcCccccceeee
Confidence            678889999999999999999999999999999999776553        446799999999999999877655444310


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCC
Q 014452          212 PMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPF  291 (424)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~~  291 (424)
                      .          .|.+++                                              +.|.             
T Consensus        96 ~----------~~s~s~----------------------------------------------Sgg~-------------  106 (394)
T KOG2113|consen   96 I----------RASRSF----------------------------------------------SGGT-------------  106 (394)
T ss_pred             e----------eecccc----------------------------------------------cCCC-------------
Confidence            0          000000                                              0000             


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceeccccc
Q 014452          292 PYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNS  371 (424)
Q Consensus       292 ~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G~  371 (424)
                                +                      ++.                   ...+.+.++.+|.+.+|.|.|..|.
T Consensus       107 ----------~----------------------~~s-------------------~s~qt~sy~svP~rvvglvv~~~~~  135 (394)
T KOG2113|consen  107 ----------N----------------------GAS-------------------ASGQTTSYVSVPLRVVGLVVGPKGA  135 (394)
T ss_pred             ----------c----------------------ccc-------------------ccCCCceeeeccceeeeeccccccC
Confidence                      0                      000                   0125678899999999999999999


Q ss_pred             hHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHH-HHHHH
Q 014452          372 NLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQ-MRAAQ  411 (424)
Q Consensus       372 ~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~-v~~A~  411 (424)
                      +|+.|++.+...|...-+   ..+.++.++|-+++ +++|+
T Consensus       136 ti~~iqq~tnt~I~T~v~---~~~~Vf~Vtg~~~nC~kra~  173 (394)
T KOG2113|consen  136 TIKRIQQFTNTYIATPVR---CGEPVFCVTGAPKNCVKRAR  173 (394)
T ss_pred             ccchheecccceEeeecc---CCCceEEEecCCcchhhhcc
Confidence            999999999999988533   46789999998877 77776

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

Probab=98.51  E-value=2.9e-07  Score=77.47  Aligned_cols=61  Identities=13%  Similarity=0.258  Sum_probs=50.8

Q ss_pred             CcccceeccccchHHHHHHHhCCEEEEeCCCC-----------------CCCCcEEEEEc-C--HHHHHHHHHHHHHHHH
Q 014452          360 LYMAHVYGENNSNLSHIRQISGANVVVNDPKP-----------------GATEGVVMVSG-T--SDQMRAAQSLIHAFIL  419 (424)
Q Consensus       360 ~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~-----------------~~~~r~i~I~G-t--~e~v~~A~~lI~~~i~  419 (424)
                      +++|.|||++|++||+|+++|||+|.|...-.                 ..+.-.|.|++ +  .+++++|..+|++++.
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            78899999999999999999999999974311                 11235789999 4  6999999999999887


Q ss_pred             c
Q 014452          420 C  420 (424)
Q Consensus       420 ~  420 (424)
                      .
T Consensus        95 ~   95 (120)
T cd02395          95 P   95 (120)
T ss_pred             c
Confidence            4

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.

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

Probab=98.45  E-value=1.3e-07  Score=89.25  Aligned_cols=151  Identities=17%  Similarity=0.219  Sum_probs=108.5

Q ss_pred             CCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHH
Q 014452           45 FYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIA  124 (424)
Q Consensus        45 ~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~  124 (424)
                      .-++.++..+.+|..+|+.|.|++|.+||.|+.+|.++|+-+..   ..+-++.++|..+++..++...++...-+..+.
T Consensus        21 ~~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~edv~~aRrei~saaeH~~l~~   97 (394)
T KOG2113|consen   21 SIGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRHEDVRRARREIPSAAEHFGLIR   97 (394)
T ss_pred             CCCCccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCchhHHHHhhcCccccceeeeee
Confidence            33477888999999999999999999999999999999998744   344778899997765542222221111111111


Q ss_pred             hh--------cCCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHH-H
Q 014452          125 EI--------GFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHS-V  195 (424)
Q Consensus       125 e~--------~~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~-v  195 (424)
                      ..        .+......+...-+|...+|.|.|..|.+|+.|++.++..|.-.-+        ..+.++.++|.+++ +
T Consensus        98 ~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--------~~~~Vf~Vtg~~~nC~  169 (394)
T KOG2113|consen   98 ASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--------CGEPVFCVTGAPKNCV  169 (394)
T ss_pred             ecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--------CCCceEEEecCCcchh
Confidence            00        1112345677888999999999999999999999999999966543        35778999999888 5


Q ss_pred             HHHH-HHHHHHH
Q 014452          196 QDAL-FHITSRL  206 (424)
Q Consensus       196 ~~A~-~~I~~~l  206 (424)
                      ++|. ..|+..+
T Consensus       170 kra~s~eie~ta  181 (394)
T KOG2113|consen  170 KRARSCEIEQTA  181 (394)
T ss_pred             hhccccchhhhh
Confidence            5565 4554443

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

Probab=98.33  E-value=1.9e-06  Score=72.62  Aligned_cols=73  Identities=18%  Similarity=0.298  Sum_probs=54.6

Q ss_pred             EEEecCC------CcceeeccCCchHHHHHhhcCceEEEecCCCCC-----------C-CCCCCCcEEEEEeC---HHHH
Q 014452          137 RLLVHSQ------QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAP-----------R-CGSPHDEIVQVIGN---YHSV  195 (424)
Q Consensus       137 ~l~IP~~------~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p-----------~-~~~~~~r~v~I~G~---~~~v  195 (424)
                      ++.||.+      ++|.|||++|++||+|+++|||+|.|..+....           . ......-.|.|++.   .+++
T Consensus         3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~   82 (120)
T cd02395           3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEAL   82 (120)
T ss_pred             EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHH
Confidence            4555554      789999999999999999999999997542110           0 00122356899996   4999


Q ss_pred             HHHHHHHHHHHHhh
Q 014452          196 QDALFHITSRLRET  209 (424)
Q Consensus       196 ~~A~~~I~~~l~~~  209 (424)
                      .+|+.+|..++...
T Consensus        83 ~~A~~~I~~ll~~~   96 (120)
T cd02395          83 AKAVEAIEELLKPA   96 (120)
T ss_pred             HHHHHHHHHHhccC
Confidence            99999999998854

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.

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.18  E-value=3.9e-06  Score=72.67  Aligned_cols=100  Identities=17%  Similarity=0.324  Sum_probs=70.3

Q ss_pred             EEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHH--hhcC
Q 014452           51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIA--EIGF  128 (424)
Q Consensus        51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~--e~~~  128 (424)
                      .+.++|+...+|+.||++|++|+.|++..|-+|.|-+-           +-.+         .+-+..++..+.  +...
T Consensus        33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~-----------s~d~---------~~fI~n~l~Pa~V~~v~I   92 (140)
T PRK08406         33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY-----------SDDP---------EEFIKNIFAPAAVRSVTI   92 (140)
T ss_pred             EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc-----------CCCH---------HHHHHHHcCCCEEEEEEE
Confidence            45788899999999999999999999999988888322           1111         111111111110  0001


Q ss_pred             -CCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEe
Q 014452          129 -EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVF  170 (424)
Q Consensus       129 -~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~  170 (424)
                       +......+.+.|+.+..|..|||+|++++.++.-++-++.|.
T Consensus        93 ~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         93 KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence             122334567789999999999999999999999999888763

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.02  E-value=3.2e-05  Score=82.81  Aligned_cols=63  Identities=25%  Similarity=0.435  Sum_probs=57.6

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~  419 (424)
                      ....+.||.+.++.|||.||.+||.|.++|||+|.|++      +.+|.|.+ +.+.+++|+.+|+..+.
T Consensus       578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~  641 (719)
T TIGR02696       578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIAN  641 (719)
T ss_pred             eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence            35789999999999999999999999999999999964      47899988 88999999999999876

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=97.71  E-value=6.1e-05  Score=65.26  Aligned_cols=39  Identities=21%  Similarity=0.388  Sum_probs=34.6

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK  172 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~  172 (424)
                      -.+.+.|+...+|..||++|++|+.|++..|-+|.+..-
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~   70 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY   70 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc
Confidence            356788899999999999999999999999999988753

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.69  E-value=0.00015  Score=77.81  Aligned_cols=65  Identities=20%  Similarity=0.292  Sum_probs=57.3

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRE  208 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  208 (424)
                      .....+.||.+.++.|||+||.+||.|+++|||+|.+..           +..|.|.+ ..+.+++|+.+|..++..
T Consensus       577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----------~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-----------DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            455789999999999999999999999999999999953           34699988 588999999999988875

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=97.67  E-value=0.00014  Score=62.81  Aligned_cols=100  Identities=21%  Similarity=0.307  Sum_probs=70.2

Q ss_pred             EEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHH--HHHhh-c
Q 014452           51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHS--RIAEI-G  127 (424)
Q Consensus        51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~--~i~e~-~  127 (424)
                      -+-++|....+|+.||++|++|+.|++..|=+|.|-           .-+..+.         +-+..++.  .+... .
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV-----------eys~D~~---------~fI~N~l~PA~V~~V~i   93 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI-----------EYSENLE---------EFVANKLAPAEVKNVTV   93 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE-----------EcCCCHH---------HHHHHcCCCceEEEEEE
Confidence            567888999999999999999999999899888883           2222210         01111110  00110 0


Q ss_pred             CCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEe
Q 014452          128 FEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVF  170 (424)
Q Consensus       128 ~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~  170 (424)
                      .+.++.....+.|+.+..+..|||+|++++..++-++-++.|.
T Consensus        94 ~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        94 SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            1223345677889999999999999999999999999888663

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=97.52  E-value=0.00067  Score=68.48  Aligned_cols=76  Identities=14%  Similarity=0.244  Sum_probs=57.3

Q ss_pred             ceEEEEEecCC------CcceeeccCCchHHHHHhhcCceEEEecCCC----------CCCCCCCC-CcEEEEEe-CHHH
Q 014452          133 AVVARLLVHSQ------QIGCLLGRGGHIVSEMRRATGASIRVFPKDQ----------APRCGSPH-DEIVQVIG-NYHS  194 (424)
Q Consensus       133 ~~t~~l~IP~~------~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~----------~p~~~~~~-~r~v~I~G-~~~~  194 (424)
                      ..+.++.||.+      +||+|||..|.|.|+|+++|||+|.|..+..          +....... +=-|.|++ +.|.
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            55667888765      8899999999999999999999999976321          11111122 23477888 4779


Q ss_pred             HHHHHHHHHHHHHh
Q 014452          195 VQDALFHITSRLRE  208 (424)
Q Consensus       195 v~~A~~~I~~~l~~  208 (424)
                      |++|+++|..+|++
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999986

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.49  E-value=0.00016  Score=78.50  Aligned_cols=65  Identities=18%  Similarity=0.309  Sum_probs=56.9

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~  419 (424)
                      ......+.||.+.++.|||++|++||.|.++|||+|.|.+      +..|.|.+ +.+.+++|+.+|+....
T Consensus       549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~~~~~~a~~~I~~~~~  614 (684)
T TIGR03591       549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEAAEAAIKMIEGITA  614 (684)
T ss_pred             CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcHHHHHHHHHHHHhhhc
Confidence            3456889999999999999999999999999999999963      35677776 78999999999998765

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

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

Probab=97.31  E-value=0.00057  Score=68.94  Aligned_cols=63  Identities=16%  Similarity=0.340  Sum_probs=50.5

Q ss_pred             CcccceeccccchHHHHHHHhCCEEEEeC------C---------CCCC-CCcEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 014452          360 LYMAHVYGENNSNLSHIRQISGANVVVND------P---------KPGA-TEGVVMVSG-TSDQMRAAQSLIHAFILCGV  422 (424)
Q Consensus       360 ~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~------~---------~~~~-~~r~i~I~G-t~e~v~~A~~lI~~~i~~~~  422 (424)
                      +|+|+|||..|.+.|+|+++|||+|.|--      -         .+.. .+=-+.|+. |.|.|++|..+|+.+|.+..
T Consensus       153 NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~av  232 (554)
T KOG0119|consen  153 NFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSAV  232 (554)
T ss_pred             ceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHhhc
Confidence            78999999999999999999999999942      0         0111 122477888 88999999999999998643

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

Probab=97.25  E-value=0.00027  Score=70.06  Aligned_cols=80  Identities=26%  Similarity=0.351  Sum_probs=57.7

Q ss_pred             CCCCCCCCCC--CCCCCCCCCCCCCCCCcCCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCccc
Q 014452           18 RGYAPGYHSR--GYSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEER   95 (424)
Q Consensus        18 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er   95 (424)
                      +.|+..++.+  .||.+.-.+   ........+++.+.+-|-+++||.|||++|++||+|+..|+++|++-+.   ..+-
T Consensus        16 rd~g~g~~v~rg~~w~g~~~~---~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~   89 (629)
T KOG0336|consen   16 RDYGGGRRVNRGNYWAGHRDS---RDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEV   89 (629)
T ss_pred             ccCCcceecCCCCCccCCCCC---CcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---Ccee
Confidence            4444444444  245433322   2334455678888999999999999999999999999999999999755   3456


Q ss_pred             EEEeeccc
Q 014452           96 IVVISARE  103 (424)
Q Consensus        96 ~v~I~G~~  103 (424)
                      .|+|-|..
T Consensus        90 kv~ifg~~   97 (629)
T KOG0336|consen   90 KVTIFGIN   97 (629)
T ss_pred             EEEEechH
Confidence            67787764

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.24  E-value=0.00093  Score=72.62  Aligned_cols=65  Identities=22%  Similarity=0.388  Sum_probs=55.2

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRE  208 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  208 (424)
                      .....+.||.+.++.|||++|++||.|+++|||+|.|..           +..|.|.+ ..+.+.+|+.+|..+..+
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            456789999999999999999999999999999999953           33577777 578899999999888654

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=97.18  E-value=0.00095  Score=70.09  Aligned_cols=69  Identities=20%  Similarity=0.392  Sum_probs=59.8

Q ss_pred             cceEEEEEeccCcc-cceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 014452          349 TSTTIEVVIPQLYM-AHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV  422 (424)
Q Consensus       349 ~~~t~~v~IP~~~~-g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~~~  422 (424)
                      ..++..|.+|.+-+ |+||||.|.||+.+...||++|.|++.     ...|+||+ +|--=+.|+.-|+.+|..|-
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~fdp~rreia~~~l~~li~dgr  272 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSGFDPVRREIARMALEKLIQDGR  272 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC-----CCeEEecCCchHHHHHHHHHHHHHHHcCC
Confidence            35677899999554 999999999999999999999999854     35788999 99999999999999998763

>PRK00106 hypothetical protein; Provisional

Probab=97.14  E-value=0.0012  Score=69.13  Aligned_cols=69  Identities=22%  Similarity=0.395  Sum_probs=60.0

Q ss_pred             cceEEEEEeccCc-ccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 014452          349 TSTTIEVVIPQLY-MAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV  422 (424)
Q Consensus       349 ~~~t~~v~IP~~~-~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~~~  422 (424)
                      ..++..|.+|.+- -|+||||.|.||+.+...||++|.|++.+     ..|+||| +|--=+.|+.-|..+|..|-
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            3567789999954 59999999999999999999999998533     5688999 99999999999999998773

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

Probab=97.03  E-value=0.00073  Score=67.11  Aligned_cols=70  Identities=20%  Similarity=0.327  Sum_probs=58.6

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  208 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  208 (424)
                      ..+..+.|.|-+++||.|||++|++|+.||..|+++|++...        ..+-.|+|-|..+--.+|+..|...++.
T Consensus        44 ~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~k  113 (629)
T KOG0336|consen   44 GGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQDK  113 (629)
T ss_pred             CCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence            346678899999999999999999999999999999999753        3577899999988777777777665543

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

Probab=97.03  E-value=0.00084  Score=64.81  Aligned_cols=69  Identities=10%  Similarity=0.251  Sum_probs=58.2

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHc
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~  420 (424)
                      .+...+.|+..+.|.|||+.|.+.+.|+++|+|+|.++.+  .+....|+|+| .-++|.+|...|.-+|.+
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids  125 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGISRNCVIQALERIAKLIDS  125 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeehhHHHHHHHHHHHHHHHHh
Confidence            4667789999999999999999999999999999999654  33444556655 889999999999888865

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=97.02  E-value=0.0015  Score=61.76  Aligned_cols=65  Identities=18%  Similarity=0.312  Sum_probs=56.5

Q ss_pred             EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHcCcC
Q 014452          353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGVT  423 (424)
Q Consensus       353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~~~~  423 (424)
                      ..+.||..+++.+||++|.+|+.|.+.++++|.|..      +-.|.|.+ +.+.+++|+.+|++.-++-++
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~  212 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDEEDEEIAIEAIKKIEREAHT  212 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence            668999999999999999999999999999999953      36789988 677999999999987665543

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.00  E-value=0.0015  Score=56.53  Aligned_cols=37  Identities=8%  Similarity=0.135  Sum_probs=33.9

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN  387 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~  387 (424)
                      ....+.||.+..++.|||+|.|++..++.++-++.|.
T Consensus       100 ~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952       100 KVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             EEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            5678999999999999999999999999999998874

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.99  E-value=0.00071  Score=74.35  Aligned_cols=64  Identities=11%  Similarity=0.273  Sum_probs=57.3

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCE-EEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGAN-VVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~-I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~  419 (424)
                      .....+.||.+.++.|||.||.+||.|.++||+. |.|.+      +-.|.|.+ +.+.+++|+.+|++.+.
T Consensus       684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~~~i~~A~~~I~~l~~  749 (891)
T PLN00207        684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDLSSLEKSKAIISSLTM  749 (891)
T ss_pred             CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            4568899999999999999999999999999999 99853      46788888 88999999999998865

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

Probab=96.97  E-value=0.00098  Score=62.60  Aligned_cols=41  Identities=27%  Similarity=0.455  Sum_probs=36.4

Q ss_pred             CCccEEEEEEeccc------ccceeeccCchHHHHHHHHhCceEEec
Q 014452           46 YEEEVVFKLLCHLD------KVGSLIGKGGSIVRTFQNETGASIKIA   86 (424)
Q Consensus        46 ~~~~~~~ri~ip~~------~vg~IIGk~G~~Ik~I~~~tga~I~v~   86 (424)
                      .+-.++.+|+||.+      +||+|+|.+|.++|+|+++|+|+|.|.
T Consensus        88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir  134 (259)
T KOG1588|consen   88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR  134 (259)
T ss_pred             CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence            34566889999986      699999999999999999999999985

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.92  E-value=0.0017  Score=59.10  Aligned_cols=98  Identities=26%  Similarity=0.397  Sum_probs=67.0

Q ss_pred             EEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHH--HHhhcC-C
Q 014452           53 KLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSR--IAEIGF-E  129 (424)
Q Consensus        53 ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~--i~e~~~-~  129 (424)
                      -+.+-.+.+|..||++|++|+.|+++.|=+|.|-+-           +-.+         ..-+..++.-  +..... +
T Consensus        79 ~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-----------s~d~---------~~fI~nal~Pa~v~~V~~~~  138 (190)
T COG0195          79 SNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-----------SEDP---------AEFIKNALAPAEVLSVNIKE  138 (190)
T ss_pred             EeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-----------CCCH---------HHHHHHhcCcceEeEEEEEe
Confidence            444555778999999999999999999977777322           2111         1111111110  000001 1


Q ss_pred             CCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEec
Q 014452          130 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFP  171 (424)
Q Consensus       130 ~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~  171 (424)
                      .+.. ...+.||.+..+..|||+|.+++-+.+-||-++.|..
T Consensus       139 ~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         139 DDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             CCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            1122 6778899999999999999999999999999999964

>PRK12704 phosphodiesterase; Provisional

Probab=96.91  E-value=0.0025  Score=67.05  Aligned_cols=68  Identities=18%  Similarity=0.358  Sum_probs=57.9

Q ss_pred             ceEEEEEeccCc-ccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 014452          350 STTIEVVIPQLY-MAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV  422 (424)
Q Consensus       350 ~~t~~v~IP~~~-~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~~~  422 (424)
                      .++..|.+|.+- -|+||||.|.||+.+...||++|.|++.     ..+|+||| +|--=+.|+.-|...+..|.
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~~~~~rre~a~~~l~~l~~dg~  278 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSGFDPIRREIARLALEKLVQDGR  278 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC-----CCeEEEecCChhhHHHHHHHHHHHHhcCC
Confidence            567788999954 4999999999999999999999999853     35789999 88887889998888887664

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

Probab=96.88  E-value=0.0016  Score=68.73  Aligned_cols=65  Identities=15%  Similarity=0.280  Sum_probs=57.4

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~  419 (424)
                      .....++.|+.+.+..|||++|++|++|.++|||+|.|.      ++-+|.|.+ +.+.+++|+.+|.+..+
T Consensus       550 aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie------ddGtv~i~~s~~~~~~~ak~~I~~i~~  615 (692)
T COG1185         550 APRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE------DDGTVKIAASDGESAKKAKERIEAITR  615 (692)
T ss_pred             CCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec------CCCcEEEEecchHHHHHHHHHHHHHHh
Confidence            445689999999999999999999999999999999995      335789988 45999999999999875

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

Probab=96.86  E-value=0.0017  Score=47.87  Aligned_cols=37  Identities=35%  Similarity=0.461  Sum_probs=34.2

Q ss_pred             cEEEEEEecccccceeeccCchHHHHHHHHhCceEEe
Q 014452           49 EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKI   85 (424)
Q Consensus        49 ~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v   85 (424)
                      ...+.+.|+.+.+|.+|||+|.+|+.+++.++-+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3577999999999999999999999999999988876

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.

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=96.79  E-value=0.042  Score=50.91  Aligned_cols=64  Identities=17%  Similarity=0.255  Sum_probs=53.6

Q ss_pred             EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      +.+.++....-.+...+|..++.|....||+|.+..          .+..+.|+|+...+..+...|.+++...
T Consensus        28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~----------~~~~i~I~g~k~~~~~i~~~i~~~l~~i   91 (210)
T PF14611_consen   28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR----------SENRIRITGTKSTAEYIEASINEILSNI   91 (210)
T ss_pred             eEEEecchheeeeecCCchHHHHHHHhcCceEEEec----------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence            345556778889999999999999888999999964          3457999999999999998888888765

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

Probab=96.78  E-value=0.0043  Score=58.35  Aligned_cols=39  Identities=15%  Similarity=0.472  Sum_probs=34.6

Q ss_pred             cceEEEEEecc------CcccceeccccchHHHHHHHhCCEEEEe
Q 014452          349 TSTTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVN  387 (424)
Q Consensus       349 ~~~t~~v~IP~------~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~  387 (424)
                      ...+.+|.||.      ++||+|+|..|.++|+|+++|||+|.|-
T Consensus        90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir  134 (259)
T KOG1588|consen   90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR  134 (259)
T ss_pred             eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence            35678888885      5999999999999999999999999994

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

Probab=96.77  E-value=0.0027  Score=67.14  Aligned_cols=66  Identities=21%  Similarity=0.351  Sum_probs=57.0

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHHHHHHHhh
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHITSRLRET  209 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  209 (424)
                      .-..++.|+.+.+..+||++|.+|++|.++|||+|++. +          +..|.|.++ .+.+.+|+..|..++++.
T Consensus       551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-d----------dGtv~i~~s~~~~~~~ak~~I~~i~~e~  617 (692)
T COG1185         551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-D----------DGTVKIAASDGESAKKAKERIEAITREV  617 (692)
T ss_pred             CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-C----------CCcEEEEecchHHHHHHHHHHHHHHhhc
Confidence            34567889999999999999999999999999999995 2          234899886 488999999999999776

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.73  E-value=0.0025  Score=70.21  Aligned_cols=65  Identities=20%  Similarity=0.335  Sum_probs=55.9

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhhcCce-EEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGAS-IRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRE  208 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~-I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  208 (424)
                      .....|.||.+.++.|||.||.+||.|.++||++ |.+.+           +-.|.|.+ ..+.+++|+.+|..++.+
T Consensus       684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d-----------dg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD-----------DGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-----------CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            4567899999999999999999999999999999 87742           34588888 588999999999888763

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

Probab=96.60  E-value=0.0031  Score=46.51  Aligned_cols=36  Identities=17%  Similarity=0.346  Sum_probs=33.8

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEE
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV  386 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i  386 (424)
                      ....+.|+.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            578899999999999999999999999999988876

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.

>TIGR01953 NusA transcription termination factor NusA

Probab=96.39  E-value=0.0054  Score=61.01  Aligned_cols=93  Identities=24%  Similarity=0.397  Sum_probs=63.8

Q ss_pred             cccceeeccCchHHHHHHHHh-CceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHH--HHHhh-cCCCCcce
Q 014452           59 DKVGSLIGKGGSIVRTFQNET-GASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHS--RIAEI-GFEPGQAV  134 (424)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~--~i~e~-~~~~~~~~  134 (424)
                      +-+|+.||++|++|+.|.++. |=+|.|-.-.           -.+         ..-+..++.  .+... ..+. ...
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s-----------~d~---------~~fi~nal~Pa~v~~v~i~~~-~~~  301 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYS-----------DDP---------AEFIANALSPAKVISVEVLDE-DKH  301 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcC-----------CCH---------HHHHHHhcCCceEEEEEEEcC-CCc
Confidence            458999999999999999998 8888884321           111         000111000  00000 0011 224


Q ss_pred             EEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452          135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK  172 (424)
Q Consensus       135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~  172 (424)
                      ...+.||..+.+..|||+|.+++-...-||.+|.|...
T Consensus       302 ~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~  339 (341)
T TIGR01953       302 SAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE  339 (341)
T ss_pred             EEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence            67899999999999999999999999999999999753

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.

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

Probab=96.35  E-value=0.0044  Score=59.93  Aligned_cols=65  Identities=23%  Similarity=0.362  Sum_probs=50.7

Q ss_pred             cEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHH
Q 014452           49 EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIA  124 (424)
Q Consensus        49 ~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~  124 (424)
                      +...-+++++...+.|||++|.|.++|+++|+|+|.++.+  ++....|+|+|-.         ++++.++.++|.
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~~---------~~~V~~a~~Ri~  120 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGIS---------RNCVIQALERIA  120 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeehh---------HHHHHHHHHHHH
Confidence            4556788999999999999999999999999999999866  4455667777652         445555555554

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.25  E-value=0.017  Score=57.73  Aligned_cols=94  Identities=20%  Similarity=0.244  Sum_probs=64.2

Q ss_pred             cccceeeccCchHHHHHHHHh-CceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHH--HHHhhcCCCCcceE
Q 014452           59 DKVGSLIGKGGSIVRTFQNET-GASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHS--RIAEIGFEPGQAVV  135 (424)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~--~i~e~~~~~~~~~t  135 (424)
                      +-+|+.||++|++|+.|.++. |=+|.|-.-..+..+                    -+..++.  .+...... .....
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~--------------------fI~Nal~Pa~V~~V~i~-~~~~~  309 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEI--------------------FIARALAPAIISSVKIE-EEEKK  309 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHH--------------------HHHHhCCCceeeEEEEc-CCCcE
Confidence            458999999999999999998 888887432111100                    0000000  00000001 12246


Q ss_pred             EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCC
Q 014452          136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKD  173 (424)
Q Consensus       136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~  173 (424)
                      ..+.||..+.+..|||+|.+++-..+-||.+|+|..-.
T Consensus       310 ~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~  347 (374)
T PRK12328        310 AIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG  347 (374)
T ss_pred             EEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence            78899999999999999999999999999999998644

>PRK00468 hypothetical protein; Provisional

Probab=96.17  E-value=0.0057  Score=47.01  Aligned_cols=34  Identities=26%  Similarity=0.501  Sum_probs=30.0

Q ss_pred             CCccEEEEEEecccccceeeccCchHHHHHHHHh
Q 014452           46 YEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNET   79 (424)
Q Consensus        46 ~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~t   79 (424)
                      .++.+.++|.+..+.+|+||||+|.+|+.||.--
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            3456789999999999999999999999999864

>PRK12705 hypothetical protein; Provisional

Probab=96.04  E-value=0.0081  Score=62.66  Aligned_cols=68  Identities=18%  Similarity=0.331  Sum_probs=57.0

Q ss_pred             ceEEEEEeccCcc-cceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 014452          350 STTIEVVIPQLYM-AHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV  422 (424)
Q Consensus       350 ~~t~~v~IP~~~~-g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~~~  422 (424)
                      .++..|.+|.+-+ |+||||.|.||+.+...||+.|.|++.+     ..|+|++ +|.-=+.|+.-+...|..|.
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            5667788998555 9999999999999999999999998543     4577888 88888888888888887664

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.03  E-value=0.011  Score=59.26  Aligned_cols=94  Identities=24%  Similarity=0.357  Sum_probs=64.0

Q ss_pred             cccceeeccCchHHHHHHHHh-CceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHH--HHhhcCCCCcceE
Q 014452           59 DKVGSLIGKGGSIVRTFQNET-GASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSR--IAEIGFEPGQAVV  135 (424)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~--i~e~~~~~~~~~t  135 (424)
                      +-+|+.||++|++|+.|.++. |=+|.|-.-..+..                    .-+..++.-  +............
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~--------------------~fi~nal~Pa~v~~v~i~~~~~~~  304 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPA--------------------EFVANALSPAKVVSVEVDDEEEKA  304 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHH--------------------HHHHHhCCCceEEEEEEEcCCCcE
Confidence            459999999999999999998 88888843211100                    001110000  0000000022345


Q ss_pred             EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452          136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK  172 (424)
Q Consensus       136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~  172 (424)
                      ..+.||..+.+..|||+|.+++--..-||.+|.|...
T Consensus       305 ~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        305 ARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             EEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            7889999999999999999999999999999999754

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

Probab=96.00  E-value=0.0025  Score=70.07  Aligned_cols=70  Identities=21%  Similarity=0.159  Sum_probs=60.9

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeC-CCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND-PKPGATEGVVMVSGTSDQMRAAQSLIHAFI  418 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~-~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i  418 (424)
                      ......+.+|.....+|||++|++|+.+|..|||.|+|.+ ......||.+++.|+++.+..|..+|.-.|
T Consensus      1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i 1408 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPI 1408 (2131)
T ss_pred             cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhcccccee
Confidence            4456788999999999999999999999999999999986 334468999999999999999998886544

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.96  E-value=0.006  Score=66.55  Aligned_cols=63  Identities=19%  Similarity=0.340  Sum_probs=54.9

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~  419 (424)
                      ....+.||.+.++.+||.||.+||.|.++||+.|.+.      ++-.|.|.+ ..+.+++|+.+|+..+.
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~------d~G~v~i~~~~~~~~~~a~~~I~~~~~  617 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE------DDGTVKIAATDGEAAEAAKERIEGITA  617 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC------CCceEEEEcccHHHHHHHHHHHHHhcc
Confidence            3467888999999999999999999999999988874      246788888 88999999999998765

>PRK02821 hypothetical protein; Provisional

Probab=95.92  E-value=0.0078  Score=46.46  Aligned_cols=34  Identities=24%  Similarity=0.499  Sum_probs=29.9

Q ss_pred             ccEEEEEEecccccceeeccCchHHHHHHHHhCc
Q 014452           48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGA   81 (424)
Q Consensus        48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga   81 (424)
                      +.+.++|.+..+.+|+||||+|.+|+.||.--.+
T Consensus        29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            4577899999999999999999999999987544

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=95.90  E-value=0.019  Score=52.24  Aligned_cols=37  Identities=19%  Similarity=0.325  Sum_probs=34.8

Q ss_pred             EEEEEeccCcccceeccccchHHHHHHHhCCEEEEeC
Q 014452          352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  388 (424)
Q Consensus       352 t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~  388 (424)
                      ...+.||.+..+.+|||+|.+++-+.+.||-+|.|..
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            6889999999999999999999999999999999963

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=95.85  E-value=0.019  Score=54.35  Aligned_cols=63  Identities=17%  Similarity=0.259  Sum_probs=53.1

Q ss_pred             EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHHHHHHHhh
Q 014452          136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHITSRLRET  209 (424)
Q Consensus       136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  209 (424)
                      +.+.||.+.++++||++|.+|+.|.+.++++|.+-.           +-.|.|.+. .+++.+|+.+|..+-++.
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~  210 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREA  210 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence            458899999999999999999999999999998842           346899986 558888998888777665

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.84  E-value=0.0093  Score=60.55  Aligned_cols=92  Identities=28%  Similarity=0.382  Sum_probs=62.7

Q ss_pred             cccceeeccCchHHHHHHHHh-CceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHH--HHHhh-cCCCCcce
Q 014452           59 DKVGSLIGKGGSIVRTFQNET-GASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHS--RIAEI-GFEPGQAV  134 (424)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~--~i~e~-~~~~~~~~  134 (424)
                      +-+|+.||++|++|+.|.++. |=+|.|-.-           +-.+         ..-+..++.  .+... ..+ ....
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~y-----------s~Dp---------~~fI~NaLsPA~V~~V~i~~-~~~k  335 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRW-----------SPDP---------ATYIANALSPARVDEVRLVD-PEGR  335 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEc-----------CCCH---------HHHHHHhcCCceeeEEEEEc-CCCc
Confidence            459999999999999999998 888887422           1111         000111100  00000 001 1223


Q ss_pred             EEEEEecCCCcceeeccCCchHHHHHhhcCceEEEec
Q 014452          135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFP  171 (424)
Q Consensus       135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~  171 (424)
                      ...+.||..+.+..|||+|.+++--..-||.+|.|..
T Consensus       336 ~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        336 HAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             EEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            5688999999999999999999999999999998853

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

Probab=95.78  E-value=0.011  Score=45.44  Aligned_cols=32  Identities=25%  Similarity=0.483  Sum_probs=29.4

Q ss_pred             CccEEEEEEecccccceeeccCchHHHHHHHH
Q 014452           47 EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNE   78 (424)
Q Consensus        47 ~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~   78 (424)
                      +..+.++|.+..+.+|.||||+|.+|+.||.-
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            56678999999999999999999999999975

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.72  E-value=0.015  Score=63.58  Aligned_cols=64  Identities=22%  Similarity=0.343  Sum_probs=53.3

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRE  208 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  208 (424)
                      ....+.||.+.++.+||.||.+||+|.++||++|.+..           +-.|.|.+ ..+.+.+|+.+|..+..+
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d-----------~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED-----------DGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC-----------CceEEEEcccHHHHHHHHHHHHHhccc
Confidence            34567789999999999999999999999999887732           34588888 588999999999887754

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.63  E-value=0.024  Score=58.88  Aligned_cols=93  Identities=23%  Similarity=0.358  Sum_probs=63.4

Q ss_pred             cccceeeccCchHHHHHHHHh-CceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHH--HHhhcCCCCcceE
Q 014452           59 DKVGSLIGKGGSIVRTFQNET-GASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSR--IAEIGFEPGQAVV  135 (424)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~--i~e~~~~~~~~~t  135 (424)
                      +-+|+.||++|++|+.|.++. |=+|.|-.-.           -.+         ..-+..++.-  +.....+ ...-.
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s-----------~d~---------~~fi~nal~pa~v~~v~~~-~~~~~  303 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDIILWS-----------DDP---------AQFIINALSPAEVSSVVVD-EDEHS  303 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEEEcC-----------CCH---------HHHHHHhCCCCEEEEEEEe-CCCCE
Confidence            348999999999999999998 8888884221           111         0000000000  0000001 11236


Q ss_pred             EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452          136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK  172 (424)
Q Consensus       136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~  172 (424)
                      +.+.||..+.+..|||+|.+++-.++.||.+|.|...
T Consensus       304 ~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        304 ADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             EEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            7899999999999999999999999999999999764

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

Probab=95.43  E-value=0.016  Score=52.37  Aligned_cols=40  Identities=28%  Similarity=0.378  Sum_probs=33.7

Q ss_pred             ccEEEEEEecc------cccceeeccCchHHHHHHHHhCceEEecc
Q 014452           48 EEVVFKLLCHL------DKVGSLIGKGGSIVRTFQNETGASIKIAD   87 (424)
Q Consensus        48 ~~~~~ri~ip~------~~vg~IIGk~G~~Ik~I~~~tga~I~v~~   87 (424)
                      ..++-++.||.      ++||+|||+.|+|+|+|++.|+|+|-|..
T Consensus       146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG  191 (269)
T COG5176         146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG  191 (269)
T ss_pred             ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence            34455677774      67999999999999999999999999973

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

Probab=95.32  E-value=0.021  Score=51.72  Aligned_cols=37  Identities=22%  Similarity=0.420  Sum_probs=31.3

Q ss_pred             eEEEEEecc------CcccceeccccchHHHHHHHhCCEEEEe
Q 014452          351 TTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVN  387 (424)
Q Consensus       351 ~t~~v~IP~------~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~  387 (424)
                      .+.++.||-      +++|+|||..|+++|++++.|+|+|-|-
T Consensus       148 ~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIR  190 (269)
T COG5176         148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIR  190 (269)
T ss_pred             ccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEe
Confidence            344555553      7899999999999999999999999995

>PRK01064 hypothetical protein; Provisional

Probab=95.17  E-value=0.024  Score=43.91  Aligned_cols=33  Identities=18%  Similarity=0.496  Sum_probs=29.8

Q ss_pred             CccEEEEEEecccccceeeccCchHHHHHHHHh
Q 014452           47 EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNET   79 (424)
Q Consensus        47 ~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~t   79 (424)
                      .+.+.+++.|..+..|.+|||+|.+|+.||.-.
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            466789999999999999999999999999854

>PRK00468 hypothetical protein; Provisional

Probab=95.10  E-value=0.023  Score=43.68  Aligned_cols=31  Identities=23%  Similarity=0.309  Sum_probs=28.4

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHh
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQIS  380 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S  380 (424)
                      ...+++.+..+-+|+||||+|.+|+.||..-
T Consensus        29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         29 SVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             eEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            4789999999999999999999999999864

>PRK02821 hypothetical protein; Provisional

Probab=95.07  E-value=0.023  Score=43.86  Aligned_cols=32  Identities=19%  Similarity=0.312  Sum_probs=29.0

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhC
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISG  381 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SG  381 (424)
                      ...+++.|.++-+|+||||+|.+|+.||..-.
T Consensus        30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             cEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            47799999999999999999999999998743

>TIGR01953 NusA transcription termination factor NusA

Probab=94.96  E-value=0.056  Score=53.87  Aligned_cols=37  Identities=24%  Similarity=0.419  Sum_probs=35.1

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN  387 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~  387 (424)
                      ....+.||.+..+..|||+|.|++-.++.||.+|.|.
T Consensus       301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~  337 (341)
T TIGR01953       301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVK  337 (341)
T ss_pred             cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEE
Confidence            4688999999999999999999999999999999995

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.

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=94.93  E-value=0.065  Score=56.47  Aligned_cols=65  Identities=17%  Similarity=0.260  Sum_probs=49.2

Q ss_pred             eEEEEEecC-CCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 014452          134 VVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRE  208 (424)
Q Consensus       134 ~t~~l~IP~-~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  208 (424)
                      .+-.+.+|+ ++-|+|||+.|.||+.++..||++|-|.+          +...|+|++ .|---+.|+..|..++.+
T Consensus       204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC----------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            344567888 58899999999999999999999997742          233577888 566666677766666653

>PRK00106 hypothetical protein; Provisional

Probab=94.92  E-value=0.072  Score=56.09  Aligned_cols=65  Identities=17%  Similarity=0.300  Sum_probs=49.5

Q ss_pred             eEEEEEecC-CCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 014452          134 VVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRE  208 (424)
Q Consensus       134 ~t~~l~IP~-~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  208 (424)
                      .+-.+.+|+ ++-|+||||.|.||+.++..||+++-|.+          +...|+|++ .|---+.|+..+..++.+
T Consensus       225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----------tp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD----------TPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC----------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            344577888 58899999999999999999999997742          233588888 666666677666666653

>PRK12704 phosphodiesterase; Provisional

Probab=94.88  E-value=0.072  Score=56.21  Aligned_cols=66  Identities=17%  Similarity=0.255  Sum_probs=49.4

Q ss_pred             eEEEEEecC-CCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHhh
Q 014452          134 VVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRET  209 (424)
Q Consensus       134 ~t~~l~IP~-~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~  209 (424)
                      .+-.+.+|+ ++-|+||||.|.||+.++..||++|-|.   +       +...|.|+| .+-.-+.|+..+..++.+.
T Consensus       210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~~~~~rre~a~~~l~~l~~dg  277 (520)
T PRK12704        210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPIRREIARLALEKLVQDG  277 (520)
T ss_pred             ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---C-------CCCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence            334567787 5889999999999999999999999774   2       233588888 5655556776666666543

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=94.70  E-value=0.049  Score=54.47  Aligned_cols=37  Identities=16%  Similarity=0.217  Sum_probs=34.9

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN  387 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~  387 (424)
                      ....+.||.+..+..|||+|.|++-.++.||.+|.|.
T Consensus       308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~  344 (374)
T PRK12328        308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN  344 (374)
T ss_pred             cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence            4678999999999999999999999999999999996

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=94.67  E-value=0.52  Score=43.61  Aligned_cols=127  Identities=13%  Similarity=0.133  Sum_probs=83.5

Q ss_pred             EEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHhhcCCCCc
Q 014452           53 KLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQ  132 (424)
Q Consensus        53 ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e~~~~~~~  132 (424)
                      .+.++....-.+...+|..++.|-...||+|.+     ..++..+.|+|+...+..       +......+..      .
T Consensus        29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~-----~~~~~~i~I~g~k~~~~~-------i~~~i~~~l~------~   90 (210)
T PF14611_consen   29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEV-----SRSENRIRITGTKSTAEY-------IEASINEILS------N   90 (210)
T ss_pred             EEEecchheeeeecCCchHHHHHHHhcCceEEE-----ecCCcEEEEEccHHHHHH-------HHHHHHHHHh------h
Confidence            344468889999999999999998889999999     456678999999655332       2222222221      1


Q ss_pred             ceEEEEEecCCCcceee----ccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEE-----eCHHHHHHHHHHHH
Q 014452          133 AVVARLLVHSQQIGCLL----GRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI-----GNYHSVQDALFHIT  203 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~II----GkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~-----G~~~~v~~A~~~I~  203 (424)
                      ..+.++.++.-.--...    -.....++.|++.|++.|...+++          ..+.|.     -....+..|+.++.
T Consensus        91 i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~----------~~~~i~~~~~~~~~~~~~~a~RlL~  160 (210)
T PF14611_consen   91 IRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDG----------NKLKISWLASPENEKRADRAKRLLL  160 (210)
T ss_pred             cEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCC----------CeEEEEEEeeccccchHHHHHHHHH
Confidence            23445555532111111    113567899999999999886432          224444     45778888998888


Q ss_pred             HHHH
Q 014452          204 SRLR  207 (424)
Q Consensus       204 ~~l~  207 (424)
                      ..+.
T Consensus       161 ~a~~  164 (210)
T PF14611_consen  161 WALD  164 (210)
T ss_pred             Hhcc
Confidence            8774

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=94.53  E-value=0.08  Score=53.15  Aligned_cols=37  Identities=16%  Similarity=0.366  Sum_probs=35.0

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN  387 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~  387 (424)
                      ....+.||.+..+..|||+|.|++--++.||.+|.|-
T Consensus       303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~  339 (362)
T PRK12327        303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIK  339 (362)
T ss_pred             cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEE
Confidence            4688999999999999999999999999999999996

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

Probab=94.22  E-value=0.052  Score=41.67  Aligned_cols=32  Identities=25%  Similarity=0.397  Sum_probs=28.9

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHh
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQIS  380 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S  380 (424)
                      .....++.+.+.-+|+||||+|.+|+.||..-
T Consensus        28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             CeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            35789999999999999999999999999863

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=94.13  E-value=0.1  Score=54.31  Aligned_cols=38  Identities=18%  Similarity=0.375  Sum_probs=35.4

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeC
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  388 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~  388 (424)
                      ....+.||....+..|||+|.|++..++.||.+|.|-.
T Consensus       302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            46889999999999999999999999999999999963

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=93.74  E-value=0.1  Score=53.20  Aligned_cols=37  Identities=14%  Similarity=0.322  Sum_probs=34.7

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN  387 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~  387 (424)
                      ....+.||.+..+..|||+|.|++--.+.||.+|.|.
T Consensus       335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~  371 (449)
T PRK12329        335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK  371 (449)
T ss_pred             cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence            3578999999999999999999999999999999996

>PRK01064 hypothetical protein; Provisional

Probab=93.67  E-value=0.074  Score=41.19  Aligned_cols=32  Identities=13%  Similarity=0.328  Sum_probs=28.8

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHh
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQIS  380 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S  380 (424)
                      ..+.+++.|..+-.|.+|||+|.+|+.||...
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            35789999999999999999999999999863

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=93.23  E-value=0.042  Score=41.91  Aligned_cols=36  Identities=22%  Similarity=0.284  Sum_probs=30.1

Q ss_pred             ccEEEEEEecccccceeeccCchHHHHHHHHhCceE
Q 014452           48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASI   83 (424)
Q Consensus        48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I   83 (424)
                      +...+.+.+..+..|.||||+|.+++.||.-.+.-+
T Consensus        27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~   62 (73)
T PF13083_consen   27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA   62 (73)
T ss_dssp             TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence            455678888999999999999999999998765543

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

Probab=93.09  E-value=0.34  Score=50.38  Aligned_cols=63  Identities=21%  Similarity=0.195  Sum_probs=54.8

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHc
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~  420 (424)
                      ....+.|+.+..-.+||.+|-+.|+|..+||+.-.++       +.+++|-- ++++.+.|+.+|.+.+.-
T Consensus       597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-------e~t~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-------EGTFSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             eeeEEeecchhhheeecCccceeeeEeeeccceeeec-------CceEEEEecCHHHHHHHHHHHHHHhcC
Confidence            5678999999999999999999999999999666663       35688877 899999999999998765

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

Probab=92.74  E-value=0.23  Score=44.81  Aligned_cols=137  Identities=15%  Similarity=0.229  Sum_probs=84.9

Q ss_pred             EEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHh--hcC
Q 014452           51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAE--IGF  128 (424)
Q Consensus        51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e--~~~  128 (424)
                      +-++.||....-.+--.==....-|-+..+..|.+     +-..|.|.+.-..+..+     ..++.+..+.+..  .+|
T Consensus        75 ~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRm-----NlK~r~VelRt~~~t~D-----~s~Lqk~adfv~Af~lGF  144 (252)
T KOG3273|consen   75 TRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRM-----NLKARSVELRTCKDTED-----PSALQKGADFVRAFILGF  144 (252)
T ss_pred             eeeccCCcccCChHHHhhHhhhhHHHHhhhheeEe-----ecccceeEeecCCCCCC-----hHHHHHHHHHHHHHHhCC
Confidence            44777888776655222122233456667777877     45667787765443222     1122222222211  111


Q ss_pred             CC---------CcceEEEEEe----------cCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEE
Q 014452          129 EP---------GQAVVARLLV----------HSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI  189 (424)
Q Consensus       129 ~~---------~~~~t~~l~I----------P~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~  189 (424)
                      +-         ++-+-..|.|          -+..+|+|+||+|.+--.|++.|.++|.+..            ..+.|-
T Consensus       145 ~i~DAiALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVlad------------~kIHiL  212 (252)
T KOG3273|consen  145 DIDDAIALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLAD------------SKIHIL  212 (252)
T ss_pred             cchhHHHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEecC------------ceEEEe
Confidence            11         1111112222          2347799999999999999999999997742            359999


Q ss_pred             eCHHHHHHHHHHHHHHHHhh
Q 014452          190 GNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       190 G~~~~v~~A~~~I~~~l~~~  209 (424)
                      |..+++..|+..|+.++...
T Consensus       213 G~~~niriAR~avcsLIlGs  232 (252)
T KOG3273|consen  213 GAFQNIRIARDAVCSLILGS  232 (252)
T ss_pred             ecchhhHHHHHhhHhhhccC
Confidence            99999999999999998765

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

Probab=92.06  E-value=0.24  Score=36.40  Aligned_cols=35  Identities=20%  Similarity=0.325  Sum_probs=28.2

Q ss_pred             cEEEEEEecccccceeeccCchHHHHHHHHhCceE
Q 014452           49 EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASI   83 (424)
Q Consensus        49 ~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I   83 (424)
                      .....+.+.....|.+||++|.+|+.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            35556666666799999999999999999988544

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.

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

Probab=91.87  E-value=0.19  Score=56.14  Aligned_cols=56  Identities=29%  Similarity=0.245  Sum_probs=48.5

Q ss_pred             EEEEEecccccceeeccCchHHHHHHHHhCceEEeccCC-CCCcccEEEeecccccc
Q 014452           51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADIL-PDSEERIVVISARENSE  106 (424)
Q Consensus        51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~-~~~~er~v~I~G~~~~~  106 (424)
                      ..++.+|.....+|||++|.+|..++.-||+.|.+.... .+..||.+.+.|.++..
T Consensus      1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~ 1397 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQ 1397 (2131)
T ss_pred             ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhh
Confidence            447889999999999999999999999999999999743 35678999999998553

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

Probab=90.93  E-value=0.48  Score=45.04  Aligned_cols=53  Identities=13%  Similarity=0.259  Sum_probs=48.1

Q ss_pred             cceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcCc
Q 014452          363 AHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGV  422 (424)
Q Consensus       363 g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~~  422 (424)
                      -++||.+|++++.|+-.|.|+|-|..       .+|.+.|.-..++.++..+.++|.+-|
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfkGlkevr~IV~DcM~NiH  213 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFKGLKEVRKIVEDCMKNIH  213 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeC-------cEEEeecCcchHHHHHHHHHHHHhccc
Confidence            57999999999999999999999952       469999999999999999999998754

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

Probab=90.47  E-value=0.51  Score=44.22  Aligned_cols=47  Identities=23%  Similarity=0.389  Sum_probs=40.5

Q ss_pred             EEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeeccccc
Q 014452           53 KLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENS  105 (424)
Q Consensus        53 ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~  105 (424)
                      -+.|+...|.++||++|+.++.|.++|+|+|-|      ...-.|.|.+..+.
T Consensus       149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~V------G~NG~IWV~~~~~~  195 (239)
T COG1097         149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIV------GQNGRIWVDGENES  195 (239)
T ss_pred             EEEEchhhcceEecCCCcHHHHhhhhcCeEEEE------ecCCEEEecCCCcc
Confidence            467899999999999999999999999999999      34456888888663

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

Probab=90.38  E-value=0.19  Score=37.94  Aligned_cols=34  Identities=32%  Similarity=0.558  Sum_probs=27.8

Q ss_pred             EEEecccc-----cceeeccCchHHHHHHHHh-CceEEec
Q 014452           53 KLLCHLDK-----VGSLIGKGGSIVRTFQNET-GASIKIA   86 (424)
Q Consensus        53 ri~ip~~~-----vg~IIGk~G~~Ik~I~~~t-ga~I~v~   86 (424)
                      ++.|-+..     +|..||++|++|+.|+++. |-+|.|-
T Consensus         6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV   45 (69)
T PF13184_consen    6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV   45 (69)
T ss_dssp             EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred             EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence            56666666     9999999999999999999 8888884

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

Probab=90.27  E-value=0.56  Score=43.93  Aligned_cols=47  Identities=26%  Similarity=0.479  Sum_probs=38.4

Q ss_pred             EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHH
Q 014452          353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSD  405 (424)
Q Consensus       353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e  405 (424)
                      .-+.|+...+-++||++|+.++.|.+.++|+|.|..+      -.|=|.+..+
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~  194 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENE  194 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCc
Confidence            5589999999999999999999999999999999632      3455555444

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=89.61  E-value=0.19  Score=38.26  Aligned_cols=33  Identities=21%  Similarity=0.261  Sum_probs=29.1

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCC
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGA  382 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa  382 (424)
                      .....+.|..+..|.||||.|.+++.||.....
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            467889999999999999999999999987643

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

Probab=89.56  E-value=0.55  Score=44.64  Aligned_cols=52  Identities=17%  Similarity=0.289  Sum_probs=45.8

Q ss_pred             ceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          146 GCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       146 g~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      -++||.+|.+++.|+-.|.|.|-|...            .|.+.|....+..+...+.+++...
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG~------------TVsaiGpfkGlkevr~IV~DcM~Ni  212 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQGN------------TVSAIGPFKGLKEVRKIVEDCMKNI  212 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeCc------------EEEeecCcchHHHHHHHHHHHHhcc
Confidence            579999999999999999999988532            4999999999999999999988753

>PRK12705 hypothetical protein; Provisional

Probab=89.25  E-value=0.64  Score=48.77  Aligned_cols=35  Identities=20%  Similarity=0.342  Sum_probs=30.3

Q ss_pred             EEEEecC-CCcceeeccCCchHHHHHhhcCceEEEe
Q 014452          136 ARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVF  170 (424)
Q Consensus       136 ~~l~IP~-~~vg~IIGkgG~~Ik~I~~~tga~I~v~  170 (424)
                      -.+.+|+ ++-|+|||+.|.+|+.++..||+.+-|.
T Consensus       200 s~v~lp~demkGriIGreGrNir~~E~~tGvdliid  235 (508)
T PRK12705        200 SVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID  235 (508)
T ss_pred             eeeecCChHhhccccCccchhHHHHHHhhCCceEec
Confidence            3456777 4779999999999999999999999784

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

Probab=88.60  E-value=1.5  Score=45.82  Aligned_cols=66  Identities=20%  Similarity=0.322  Sum_probs=53.4

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHhh
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRET  209 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~  209 (424)
                      ..+...+.++.+....+||.+|...|+|..+||+.-++.            +..++|.. +..+.++|++.|..++...
T Consensus       595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD------------e~t~~i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD------------EGTFSIFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             CceeeEEeecchhhheeecCccceeeeEeeeccceeeec------------CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence            356778999999999999999999999999999555442            23477766 5778889999998888663

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=88.55  E-value=0.28  Score=37.74  Aligned_cols=34  Identities=21%  Similarity=0.395  Sum_probs=29.6

Q ss_pred             EEEEEecccccceeeccCchHHHHHHHHhCceEE
Q 014452           51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIK   84 (424)
Q Consensus        51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~   84 (424)
                      ...+.+.....|.|||++|++|++|++...-.+.
T Consensus        26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            3578889999999999999999999998777664

; 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 ....

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=88.53  E-value=0.44  Score=36.68  Aligned_cols=35  Identities=23%  Similarity=0.313  Sum_probs=28.4

Q ss_pred             EEEEEecccccceeeccCchHHHHHHHHhCceEEe
Q 014452           51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKI   85 (424)
Q Consensus        51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v   85 (424)
                      .+.+.|..+..|.+|||+|++++.||--+..-++-
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~   59 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR   59 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence            34566778899999999999999999887765553

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.

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

Probab=88.42  E-value=0.82  Score=33.43  Aligned_cols=34  Identities=15%  Similarity=0.232  Sum_probs=27.1

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEE
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANV  384 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I  384 (424)
                      ....+.+...-.|.+||++|.+|+.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            4555666665689999999999999999987544

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.

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

Probab=87.38  E-value=0.57  Score=35.38  Aligned_cols=36  Identities=17%  Similarity=0.242  Sum_probs=28.3

Q ss_pred             EEEEeccCc-----ccceeccccchHHHHHHHh-CCEEEEeC
Q 014452          353 IEVVIPQLY-----MAHVYGENNSNLSHIRQIS-GANVVVND  388 (424)
Q Consensus       353 ~~v~IP~~~-----~g~IIGk~G~~Ik~Ir~~S-Ga~I~i~~  388 (424)
                      ..+.|-...     +|..||++|++|+.|.++. |-+|.|-+
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            455665655     8999999999999999999 99998853

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

Probab=87.16  E-value=0.32  Score=43.98  Aligned_cols=53  Identities=17%  Similarity=0.353  Sum_probs=47.8

Q ss_pred             CcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHH
Q 014452          360 LYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       360 ~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~  419 (424)
                      ..+|+|+||+|.+--.|...|.++|.+.+       ..|-|-|+-++++.|+..|-.+|.
T Consensus       178 RAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~niriAR~avcsLIl  230 (252)
T KOG3273|consen  178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQNIRIARDAVCSLIL  230 (252)
T ss_pred             HHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchhhHHHHHhhHhhhc
Confidence            57899999999999999999999999954       469999999999999998887775

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=85.99  E-value=0.49  Score=36.36  Aligned_cols=34  Identities=26%  Similarity=0.307  Sum_probs=28.5

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEE
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANV  384 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I  384 (424)
                      ....+.+-...-|.|||++|++|++|++..+-.+
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            4577888889999999999999999988765444

; 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 ....

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

Probab=85.07  E-value=0.61  Score=47.72  Aligned_cols=36  Identities=19%  Similarity=0.370  Sum_probs=33.5

Q ss_pred             EEEEecccccceeeccCchHHHHHHHHhCceEEecc
Q 014452           52 FKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIAD   87 (424)
Q Consensus        52 ~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~   87 (424)
                      ..+.||.+..+.+|||+|.+|++|+++.|-+|.|..
T Consensus       488 avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~  523 (604)
T COG1855         488 AVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP  523 (604)
T ss_pred             EEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence            567889999999999999999999999999999973

>PRK13764 ATPase; Provisional

Probab=84.54  E-value=2.3  Score=45.66  Aligned_cols=42  Identities=26%  Similarity=0.465  Sum_probs=37.6

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCC
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQA  175 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~  175 (424)
                      -...+.||...++.+|||+|.+|++|.++.|.+|.|-+.++.
T Consensus       481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~  522 (602)
T PRK13764        481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEE  522 (602)
T ss_pred             CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcccc
Confidence            356788999999999999999999999999999999887654

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

Probab=84.44  E-value=1.1  Score=34.92  Aligned_cols=35  Identities=9%  Similarity=0.266  Sum_probs=30.5

Q ss_pred             EEEEEecccccceeeccCchHHHHHHHHhCceEEe
Q 014452           51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKI   85 (424)
Q Consensus        51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v   85 (424)
                      .+++.|....-|.|||++|+.|++|+++-.-...+
T Consensus        31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~   65 (81)
T cd02413          31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF   65 (81)
T ss_pred             eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence            36888899999999999999999999987766655

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.

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=83.65  E-value=1.6  Score=45.01  Aligned_cols=120  Identities=13%  Similarity=0.135  Sum_probs=78.3

Q ss_pred             EEEEEecccccceeeccCchHHHHHHHHhCceEEeccC---CCCCcccEEEeecccccccccChhHHHHHHHHHH---HH
Q 014452           51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADI---LPDSEERIVVISARENSEMRHSPAQDAVMRVHSR---IA  124 (424)
Q Consensus        51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~---~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~---i~  124 (424)
                      .+.+.||...+-.|||.+|..|.+++.+.++.|++...   ....-...|.|..+..+....+-+...++.+...   +.
T Consensus       450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~  529 (657)
T COG5166         450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQQCRFN  529 (657)
T ss_pred             heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhhhcccc
Confidence            46688999999999999999999999999999999732   1122334588888876655444444433333221   10


Q ss_pred             hhc---C----------C----------CCc------ceEEEEEecCCCcceeec---cCCchHHHHHhhcCceEEEe
Q 014452          125 EIG---F----------E----------PGQ------AVVARLLVHSQQIGCLLG---RGGHIVSEMRRATGASIRVF  170 (424)
Q Consensus       125 e~~---~----------~----------~~~------~~t~~l~IP~~~vg~IIG---kgG~~Ik~I~~~tga~I~v~  170 (424)
                      -.+   +          +          ...      +....+-+|.+.++..+|   -.|++|..+.....-.|...
T Consensus       530 ~Kgdirf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~~  607 (657)
T COG5166         530 LKGDIRFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEFS  607 (657)
T ss_pred             cccceEEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcccccccchhhhhhhhhccceee
Confidence            000   0          0          011      122335567777788888   77888888888877777654

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=82.70  E-value=1.6  Score=38.84  Aligned_cols=44  Identities=23%  Similarity=0.506  Sum_probs=32.6

Q ss_pred             CCcCCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEecc
Q 014452           42 NRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIAD   87 (424)
Q Consensus        42 ~~~~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~   87 (424)
                      ++....+... -++|-... |.-|||+|++|++|++..|-+|.+-+
T Consensus        54 ~k~~~~ddrv-IfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE   97 (166)
T PRK06418         54 KKAYEVDDLV-ILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE   97 (166)
T ss_pred             EEEEEeCCEE-EEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence            3333333333 45555566 99999999999999999999999843

>PRK13764 ATPase; Provisional

Probab=81.91  E-value=1  Score=48.30  Aligned_cols=37  Identities=19%  Similarity=0.390  Sum_probs=34.0

Q ss_pred             EEEEEecccccceeeccCchHHHHHHHHhCceEEecc
Q 014452           51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIAD   87 (424)
Q Consensus        51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~   87 (424)
                      ...+.||.+.++.+|||+|.+|++|+++.|.+|.|..
T Consensus       482 ~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~  518 (602)
T PRK13764        482 KAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP  518 (602)
T ss_pred             eEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence            4567899999999999999999999999999999973

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=81.44  E-value=1.8  Score=33.23  Aligned_cols=33  Identities=15%  Similarity=0.409  Sum_probs=26.9

Q ss_pred             EEEEEecCCCcceeeccCCchHHHHHhhcCceE
Q 014452          135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASI  167 (424)
Q Consensus       135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I  167 (424)
                      .+.+.|..+..|.+|||.|++++.||--.+.-+
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            356677778899999999999999997766544

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=80.81  E-value=2.8  Score=36.35  Aligned_cols=87  Identities=18%  Similarity=0.373  Sum_probs=52.9

Q ss_pred             ccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHH------hhcCCCCcceEEEEE
Q 014452           66 GKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIA------EIGFEPGQAVVARLL  139 (424)
Q Consensus        66 Gk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~------e~~~~~~~~~t~~l~  139 (424)
                      =..|..|++|-++..-+|.|...              +.....   ..+|...+.+.+-      +.-|+.   .+-++.
T Consensus        22 ~~~~dli~~lAk~lrKRIvvR~d--------------ps~l~~---~e~A~~~I~~ivP~ea~i~di~Fd~---~tGEV~   81 (145)
T cd02410          22 AEDGDLVKDLAKDLRKRIVIRPD--------------PSVLKP---PEEAIKIILEIVPEEAGITDIYFDD---DTGEVI   81 (145)
T ss_pred             hcccHHHHHHHHHHhceEEEcCC--------------hhhcCC---HHHHHHHHHHhCCCccCceeeEecC---CCcEEE
Confidence            34577888888888777777421              111100   1223333333221      112222   233455


Q ss_pred             ecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452          140 VHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK  172 (424)
Q Consensus       140 IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~  172 (424)
                      |-.+.-|.+||++|.++++|..+||-.-.|...
T Consensus        82 IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          82 IEAEKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             EEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence            556677999999999999999999999888654

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.

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

Probab=80.63  E-value=1.2  Score=45.64  Aligned_cols=37  Identities=22%  Similarity=0.424  Sum_probs=34.3

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN  387 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~  387 (424)
                      ....+.||..+++.||||+|.+|++|++..|-+|.|-
T Consensus       486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~  522 (604)
T COG1855         486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVK  522 (604)
T ss_pred             CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEE
Confidence            4567899999999999999999999999999999996

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	424
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		2e-07
3krm_A	163	Imp1 Kh34 Length = 163		2e-07
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		8e-07
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		1e-06
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		8e-05
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		1e-04
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		2e-04
2p2r_A	76	Crystal Structure Of The Third Kh Domain Of Human P		5e-04

>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains Length = 160

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 45/164 (27%), Positives = 81/164 (49%), Gaps = 12/164 (7%)
Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRH 109
           +  +LL H  +VGS+IGK G  V+  + E+GA I I++   +  ERI+ ++   N+  + 
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTNAIFKA 62
Query: 110 SPAQDAVMRVHSRIAEIGFEPGQA----VVARLLVHSQQIGCLLGRGGHIVSEMRRATGA 165
                 + ++   I+        A    V  RL+V + Q G L+G+GG  + E+R +TGA
Sbjct: 63  FAM--IIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGA 120
Query: 166 SIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET 209
            ++V   D  P   +  +  + + G   S+ + +  I   + ET
Sbjct: 121 QVQV-AGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLET 160

>pdb|3KRM|A Chain A, Imp1 Kh34 Length = 163

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 51/167 (30%), Positives = 89/167 (53%), Gaps = 20/167 (11%)
Query: 47  EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA-DILPDSEERIVVISARENS 105
           E+E+V ++      VG++IGK G  ++       ASIKIA    PDS+ R+V+I+    +
Sbjct: 1   EQEMV-QVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEA 59
Query: 106 EMRHSPAQDAVMRVHSRIAEIG-FEPGQAVVARLLVH----SQQIGCLLGRGGHIVSEMR 160
           + +      A  R++ ++ E   F P + V  +L  H    +   G ++G+GG  V+E++
Sbjct: 60  QFK------AQGRIYGKLKEENFFGPKEEV--KLETHIRVPASAAGRVIGKGGKTVNELQ 111
Query: 161 RATGASIRVFPKDQAPRCGSPHDE-IVQVIGNYHSVQDALFHITSRL 206
             T A + V P+DQ P     +D+ IV++IG++++ Q A   I   L
Sbjct: 112 NLTAAEV-VVPRDQTP---DENDQVIVKIIGHFYASQMAQRKIRDIL 154

>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH 25NT RNA Hairpin Length = 178

Iteration: 1
 Score = 51.6 bits (122), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 43/171 (25%), Positives = 78/171 (45%), Gaps = 17/171 (9%)
Query: 52  FKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA---DILPDSEERIVVISARENS--- 105
            K+L      GS+IGKGG  +   Q ETGA+IK++   D  P + ER+ +I     +   
Sbjct: 8   LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNA 67
Query: 106 -------EMRHSPAQDAVMRVHSRIA-EIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVS 157
                  ++R  P   A     S +  +    P +A   +++V +   G ++G+GG  V 
Sbjct: 68  VHGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVK 127
Query: 158 EMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 208
            +   +GA +++    Q P   +  + +V V G     + A+  I  +++E
Sbjct: 128 AIXEQSGAWVQL---SQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQE 175

>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH 25 NT RNA Hairpin Length = 178

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 43/171 (25%), Positives = 78/171 (45%), Gaps = 17/171 (9%)
Query: 52  FKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA---DILPDSEERIVVISARENS--- 105
            K+L      GS+IGKGG  +   Q ETGA+IK++   D  P + ER+ +I     +   
Sbjct: 8   LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNA 67
Query: 106 -------EMRHSPAQDAVMRVHSRIA-EIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVS 157
                  ++R  P   A     S +  +    P +A   +++V +   G ++G+GG  V 
Sbjct: 68  VHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVK 127
Query: 158 EMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 208
            +   +GA +++    Q P   +  + +V V G     + A+  I  +++E
Sbjct: 128 AIMEQSGAWVQL---SQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQE 175

>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 = 8e-05,   Method: Composition-based stats.
 Identities = 19/64 (29%), Positives = 38/64 (59%)
Query: 352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 411
           T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ AQ
Sbjct: 8   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 67
Query: 412 SLIH 415
            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 = 1e-04,   Method: Composition-based stats.
 Identities = 19/64 (29%), Positives = 38/64 (59%)
Query: 352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 411
           T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ AQ
Sbjct: 15  TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 74
Query: 412 SLIH 415
            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: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 41/68 (60%)
Query: 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 408
           + TT E+ IP   +  + G   +N++ IRQ+SGA + + +P  G++   V ++G++  + 
Sbjct: 4   SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASIS 63
Query: 409 AAQSLIHA 416
            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 = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/64 (29%), Positives = 38/64 (59%)
Query: 352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQ 411
           T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ AQ
Sbjct: 15  TTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 74
Query: 412 SLIH 415
            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 = 5e-04,   Method: Composition-based stats.
 Identities = 20/66 (30%), Positives = 39/66 (59%)
Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 409
           +T+ E+ IP   +  + G   + ++ IRQ SGA + + +P  G+T+  V ++G++  +  
Sbjct: 4   TTSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASISL 63
Query: 410 AQSLIH 415
           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	424
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	8e-41
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-09
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-07
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-07
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	1e-40
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	8e-09
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	4e-06
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-37
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-11
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-10
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	5e-07
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-06
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-35
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	1e-09
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	1e-08
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	8e-08
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	4e-31
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	4e-11
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-09
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-09
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-06
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	6e-18
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	4e-12
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	4e-11
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	1e-17
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	3e-11
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-10
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	4e-17
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	7e-13
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	3e-11
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	5e-16
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	6e-13
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	3e-11
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	4e-15
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-14
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	6e-07
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-14
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-12
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	3e-11
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	2e-14
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-10
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-10
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	8e-14
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-08
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	4e-08
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	7e-13
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	1e-10
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	7e-08
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	1e-07
1tua_A	191	Hypothetical protein APE0754; structural genomics,	4e-10
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-09
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	7e-07
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-06
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	2e-09
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	2e-09
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	2e-06
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	3e-09
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	4e-09
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	5e-09
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	7e-09
1we8_A	104	Tudor and KH domain containing protein; structural	2e-08
1we8_A	104	Tudor and KH domain containing protein; structural	9e-08
1we8_A	104	Tudor and KH domain containing protein; structural	2e-07
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	5e-07
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-06
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	3e-05
2cxc_A	144	NUSA; transcription termination, RNA binding prote	3e-05
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	4e-05
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	4e-05
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	5e-05
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	5e-05
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	5e-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	4e-04
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	6e-04
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	2e-04
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	4e-04
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-04
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	6e-04

>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 =  141 bits (358), Expect = 8e-41
 Identities = 45/165 (27%), Positives = 81/165 (49%), Gaps = 13/165 (7%)

Query: 48  EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADI-LPDSEERIVVISARENSE 106
           E+ + ++      VG++IGK G  ++       ASIKIA    PDS+ R+V+I+    + 
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEA- 59

Query: 107 MRHSPAQDAVMRVHSRIAE---IGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRAT 163
                   A  R++ ++ E    G +    +   + V +   G ++G+GG  V+E++  T
Sbjct: 60  -----QFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLT 114

Query: 164 GASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 208
            A + V P+DQ P        IV++IG++++ Q A   I   L +
Sbjct: 115 AAEVVV-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 = 55.9 bits (135), Expect = 1e-09
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 8/82 (9%)

Query: 47  EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA-DILPDS-EERIVVISAREN 104
           E ++   +       G +IGKGG  V   QN T A + +  D  PD  ++ IV I     
Sbjct: 82  EVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFY 141

Query: 105 SEMRHSPAQDAVMRVHSRIAEI 126
           +      +Q A  ++   +A++
Sbjct: 142 A------SQMAQRKIRDILAQV 157

>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 = 49.8 bits (119), Expect = 1e-07
 Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 2/71 (2%)

Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV-NDPKPGAT-EGVVMVSGTSDQM 407
                + +P      V G+    ++ ++ ++ A VVV  D  P    + +V + G     
Sbjct: 84  KLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYAS 143

Query: 408 RAAQSLIHAFI 418
           + 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 = 49.4 bits (118), Expect = 2e-07
 Identities = 12/69 (17%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSDQMRA 409
             ++V IP   +  + G+   ++  + + + A++ +  P  P +   +V+++G  +    
Sbjct: 3   EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFK 62

Query: 410 AQSLIHAFI 418
           AQ  I+  +
Sbjct: 63  AQGRIYGKL 71

>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 =  141 bits (357), Expect = 1e-40
 Identities = 43/171 (25%), Positives = 76/171 (44%), Gaps = 20/171 (11%)

Query: 47  EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSE 106
              +  +LL H  +VGS+IGK G  V+  + E+GA I I++   +  ERI+ ++   N  
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTN-- 57

Query: 107 MRHSPAQDAVMRVHSRIAEI--------GFEPGQAVVARLLVHSQQIGCLLGRGGHIVSE 158
                   A   +  ++ E                V  RL+V + Q G L+G+GG  + E
Sbjct: 58  ----AIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKE 113

Query: 159 MRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET 209
           +R +TGA ++V          +  +  + + G   S+ + +  I   + ET
Sbjct: 114 IRESTGAQVQVAGDM----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 = 53.6 bits (129), Expect = 8e-09
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 340 ESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV-NDPKPGATEGVV 398
            + + AA     T+ +V+P      + G+    +  IR+ +GA V V  D  P +TE  +
Sbjct: 78  MTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAI 137

Query: 399 MVSGTSDQMRAAQSLIHAFIL 419
            ++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 = 45.5 bits (108), Expect = 4e-06
 Identities = 11/70 (15%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 408
            + TI +++    +  + G+   ++  +R+ SGA + +   +    E ++ ++G ++ + 
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLAGPTNAIF 60

Query: 409 AAQSLIHAFI 418
            A ++I   +
Sbjct: 61  KAFAMIIDKL 70

>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 =  133 bits (337), Expect = 1e-37
 Identities = 42/175 (24%), Positives = 78/175 (44%), Gaps = 17/175 (9%)

Query: 48  EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA---DILPDSEERIVVISA-RE 103
            +   K+L      GS+IGKGG  +   Q ETGA+IK++   D  P + ER+ +I    E
Sbjct: 4   SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIE 63

Query: 104 NSEMRHSPAQDAVMRVHSRIAEI----------GFEPGQAVVARLLVHSQQIGCLLGRGG 153
                H    + +  +   +A+              P +A   +++V +   G ++G+GG
Sbjct: 64  ALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGG 123

Query: 154 HIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 208
             V  +   +GA +++    Q P   +  + +V V G     + A+  I  +++E
Sbjct: 124 ATVKAIMEQSGAWVQL---SQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQE 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 = 61.4 bits (149), Expect = 2e-11
 Identities = 18/108 (16%), Positives = 45/108 (41%), Gaps = 2/108 (1%)

Query: 130 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI 189
            G     ++L+ S   G ++G+GG  + ++++ TGA+I++  K +    G+  + +  + 
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKL-SKSKDFYPGTT-ERVCLIQ 59

Query: 190 GNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFR 237
           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 = 59.1 bits (143), Expect = 1e-10
 Identities = 19/105 (18%), Positives = 42/105 (40%), Gaps = 12/105 (11%)

Query: 25  HSRGYSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIK 84
             +  +       +  +  +  +     K++      G +IGKGG+ V+    ++GA ++
Sbjct: 79  MPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQ 138

Query: 85  IA--DILPDSEERIVVISARENSEMRHSPAQ--DAVMRVHSRIAE 125
           ++      + + R+V +S          P Q   AV  +  +I E
Sbjct: 139 LSQKPDGINLQNRVVTVS--------GEPEQNRKAVELIIQKIQE 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 = 48.7 bits (116), Expect = 5e-07
 Identities = 19/93 (20%), Positives = 35/93 (37%), Gaps = 2/93 (2%)

Query: 324 RGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGAN 383
           R    +   T     ++         +  +++++P      + G+  + +  I + SGA 
Sbjct: 77  REMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAW 136

Query: 384 VVV--NDPKPGATEGVVMVSGTSDQMRAAQSLI 414
           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 = 47.5 bits (113), Expect = 1e-06
 Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 3/72 (4%)

Query: 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV---NDPKPGATEGVVMVSGTSDQM 407
             ++V+IP      + G+    +  +++ +GA + +    D  PG TE V ++ GT + +
Sbjct: 6   YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEAL 65

Query: 408 RAAQSLIHAFIL 419
            A    I   I 
Sbjct: 66  NAVHGFIAEKIR 77

>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 =  128 bits (322), Expect = 2e-35
 Identities = 30/175 (17%), Positives = 61/175 (34%), Gaps = 19/175 (10%)

Query: 49  EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISAR------ 102
             +  +      VG +IG+ G +++  QN+ G  I+       + ERI  I+        
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 103 -----------ENSEMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGR 151
                        +     P      R   +       PG       +V + + G ++G+
Sbjct: 62  AAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGK 121

Query: 152 GGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL 206
           GG  +  + + +GA I +      P    P+ ++  + G    +  A   I  ++
Sbjct: 122 GGETIKSISQQSGARIELQR--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 = 56.4 bits (136), Expect = 1e-09
 Identities = 22/88 (25%), Positives = 33/88 (37%), Gaps = 6/88 (6%)

Query: 16  HQRGYAPGYHSRGYSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTF 75
            Q G   G    G   G G    G  N         F  +    K G +IGKGG  +++ 
Sbjct: 73  VQAGNPGGPGPGGRGRGRGQ---GNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSI 129

Query: 76  QNETGASIKIADILP---DSEERIVVIS 100
             ++GA I++    P   D   ++  I 
Sbjct: 130 SQQSGARIELQRNPPPNADPNMKLFTIR 157

>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 = 53.3 bits (128), Expect = 1e-08
 Identities = 19/100 (19%), Positives = 31/100 (31%), Gaps = 3/100 (3%)

Query: 322 DPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISG 381
                    G   R R   + N            ++P      + G+    +  I Q SG
Sbjct: 75  AGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSG 134

Query: 382 ANVVVN---DPKPGATEGVVMVSGTSDQMRAAQSLIHAFI 418
           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 = 51.0 bits (122), Expect = 8e-08
 Identities = 15/69 (21%), Positives = 29/69 (42%)

Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 409
           S  I+V IP+  +  V G N   +  I+  +G  +          E +  ++G  D+ + 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 410 AQSLIHAFI 418
           A  +I   +
Sbjct: 62  AAEIITDLL 70

>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 =  116 bits (291), Expect = 4e-31
 Identities = 28/166 (16%), Positives = 60/166 (36%), Gaps = 16/166 (9%)

Query: 51  VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDS--EERIVVISARENSEMR 108
           V +++    K G +IGKGG  ++  Q   G  + +      +   ++ + I         
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKV-- 60

Query: 109 HSPAQDAVMRVHSRI------AEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA 162
              A + VM +              +         + V    +G ++GR G ++ +++  
Sbjct: 61  -QQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQND 119

Query: 163 TGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 208
            G  I+    D     G+  ++I  ++G     + A   I   L+ 
Sbjct: 120 AGVRIQFKQDD-----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 = 60.2 bits (146), Expect = 4e-11
 Identities = 15/62 (24%), Positives = 24/62 (38%)

Query: 39  GGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVV 98
           G RN           +      VG +IG+ G +++  QN+ G  I+         E+I  
Sbjct: 80  GDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAH 139

Query: 99  IS 100
           I 
Sbjct: 140 IM 141

>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 = 56.3 bits (136), Expect = 1e-09
 Identities = 13/83 (15%), Positives = 28/83 (33%)

Query: 336 NRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATE 395
                  N         I+V +P+  +  V G +   +  I+  +G  +          E
Sbjct: 76  QGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE 135

Query: 396 GVVMVSGTSDQMRAAQSLIHAFI 418
            +  + 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 = 55.2 bits (133), Expect = 2e-09
 Identities = 16/89 (17%), Positives = 37/89 (41%), Gaps = 3/89 (3%)

Query: 133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNY 192
             V  +++ + + G ++G+GG  + +++   G  + +             D+ +++IG+ 
Sbjct: 1   GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNV---DKPLRIIGDP 57

Query: 193 HSVQDALFHITSRLRETIFPMKRPGPNNG 221
           + 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 = 46.7 bits (111), Expect = 2e-06
 Identities = 9/72 (12%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV--NDPKPGATEGVVMVSGTSDQMR 408
           T  E++IP      V G+    +  +++ +G  +++  +  +    +  + + G   +++
Sbjct: 2   TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQ 61

Query: 409 AAQSLIHAFILC 420
            A  ++   +  
Sbjct: 62  QACEMVMDILRE 73

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

 Score = 77.0 bits (190), Expect = 6e-18
 Identities = 20/69 (28%), Positives = 41/69 (59%)

Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 409
           +T+ E+ IP   +  + G   + ++ IRQ+SGA + + +P  G+T+  V ++G++  +  
Sbjct: 4   TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISL 63

Query: 410 AQSLIHAFI 418
           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 = 60.4 bits (147), Expect = 4e-12
 Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 190
            Q     L + +  IGC++GR G  ++E+R+ +GA I++     A       D  V + G
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKI-----ANPVEGSTDRQVTITG 56

Query: 191 NYHSVQDALFHITSRLRE 208
           +  S+  A + I  RL  
Sbjct: 57  SAASISLAQYLINVRLSS 74

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

 Score = 57.7 bits (140), Expect = 4e-11
 Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 47  EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVIS-ARENS 105
            +    +L    D +G +IG+ G+ +   +  +GA IKIA+ +  S +R V I+ +  + 
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASI 61

Query: 106 EMRHSPAQDAVMRVHSRIAE 125
            +       A   ++ R++ 
Sbjct: 62  SL-------AQYLINVRLSS 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 = 76.5 bits (189), Expect = 1e-17
 Identities = 22/70 (31%), Positives = 42/70 (60%)

Query: 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 408
           + TT E+ IP   +  + G   +N++ IRQ+SGA + + +P  G++   V ++G++  + 
Sbjct: 4   SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASIS 63

Query: 409 AAQSLIHAFI 418
            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 = 3e-11
 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 5/79 (6%)

Query: 130 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI 189
            G      L + +  IGC++GR G  ++E+R+ +GA I++     A          V + 
Sbjct: 2   LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKI-----ANPVEGSSGRQVTIT 56

Query: 190 GNYHSVQDALFHITSRLRE 208
           G+  S+  A + I +RL  
Sbjct: 57  GSAASISLAQYLINARLSS 75

>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 = 56.1 bits (136), Expect = 2e-10
 Identities = 15/53 (28%), Positives = 28/53 (52%)

Query: 48  EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVIS 100
            +   +L    + +G +IG+ G+ +   +  +GA IKIA+ +  S  R V I+
Sbjct: 4   SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTIT 56

>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 = 74.6 bits (184), Expect = 4e-17
 Identities = 19/69 (27%), Positives = 39/69 (56%)

Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 409
             T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ 
Sbjct: 6   IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQN 65

Query: 410 AQSLIHAFI 418
           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 = 62.7 bits (153), Expect = 7e-13
 Identities = 23/76 (30%), Positives = 43/76 (56%), Gaps = 6/76 (7%)

Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRH 109
           +  ++    D  GS+IGKGG  ++  ++E+GASIKI + L  SE+RI+ I+  ++     
Sbjct: 7   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ---- 62

Query: 110 SPAQDAVMRVHSRIAE 125
              Q+A   + + + +
Sbjct: 63  --IQNAQYLLQNSVKQ 76

>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 = 58.1 bits (141), Expect = 3e-11
 Identities = 15/79 (18%), Positives = 38/79 (48%), Gaps = 5/79 (6%)

Query: 130 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI 189
            G  +  ++ +     G ++G+GG  + ++R  +GASI++             D I+ + 
Sbjct: 3   MGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-----DEPLEGSEDRIITIT 57

Query: 190 GNYHSVQDALFHITSRLRE 208
           G    +Q+A + + + +++
Sbjct: 58  GTQDQIQNAQYLLQNSVKQ 76

>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 = 72.0 bits (177), Expect = 5e-16
 Identities = 19/69 (27%), Positives = 39/69 (56%)

Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 409
             T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ 
Sbjct: 13  IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQN 72

Query: 410 AQSLIHAFI 418
           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 = 63.1 bits (154), Expect = 6e-13
 Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 6/79 (7%)

Query: 47  EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSE 106
              +  ++    D  GS+IGKGG  ++  ++E+GASIKI + L  SE+RI+ I+  ++  
Sbjct: 11  GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ- 69

Query: 107 MRHSPAQDAVMRVHSRIAE 125
                 Q+A   + + + +
Sbjct: 70  -----IQNAQYLLQNSVKQ 83

>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 = 58.5 bits (142), Expect = 3e-11
 Identities = 16/85 (18%), Positives = 39/85 (45%), Gaps = 5/85 (5%)

Query: 124 AEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHD 183
              G   G  +  ++ +     G ++G+GG  + ++R  +GASI++             D
Sbjct: 4   MSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-----DEPLEGSED 58

Query: 184 EIVQVIGNYHSVQDALFHITSRLRE 208
            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 = 4e-15
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 12/79 (15%)

Query: 48  EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEM 107
             +  +LL H  +VGS+IGK G  V+  + E+GA I I++   +  ERI+ ++       
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAG------ 54

Query: 108 RHSPAQDAVMRVHSRIAEI 126
                 +A+ +  + I + 
Sbjct: 55  ----PTNAIFKAFAMIIDK 69

>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 = 67.7 bits (166), Expect = 1e-14
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 7/75 (9%)

Query: 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 193
           +  RLL+H +++G ++G+ G  V +MR  +GA I +         G+  + I+ + G  +
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE-------GNCPERIITLAGPTN 57

Query: 194 SVQDALFHITSRLRE 208
           ++  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 = 45.7 bits (109), Expect = 6e-07
 Identities = 11/65 (16%), Positives = 34/65 (52%), Gaps = 2/65 (3%)

Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 409
           + TI +++    +  + G+   ++  +R+ SGA + +   +    E ++ ++G ++ +  
Sbjct: 4   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLAGPTNAIFK 61

Query: 410 AQSLI 414
           A ++I
Sbjct: 62  AFAMI 66

>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 = 67.3 bits (165), Expect = 1e-14
 Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV---NDPKPGATEGVVMVSGTSDQ 406
              +E+ +P+  +  + G+    L   ++++GA + +    +  PG     V ++G+   
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

Query: 407 MRAAQSLIHAFI 418
            +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 = 61.9 bits (151), Expect = 1e-12
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 137 RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQ 196
            + V    +G +LG+GG  + E +  TGA I++  K      G+  +  V + G+  + Q
Sbjct: 6   EMAVPENLVGAILGKGGKTLVEYQELTGARIQI-SKKGEFLPGTR-NRRVTITGSPAATQ 63

Query: 197 DALFHITSRLRE 208
            A + I+ R+  
Sbjct: 64  AAQYLISQRVTY 75

>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 = 58.1 bits (141), Expect = 3e-11
 Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 3/55 (5%)

Query: 49  EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA---DILPDSEERIVVIS 100
           + + ++    + VG+++GKGG  +  +Q  TGA I+I+   + LP +  R V I+
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTIT 56

>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 = 67.7 bits (166), Expect = 2e-14
 Identities = 15/72 (20%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN---DPKPGATEGVVMVSGTSDQ 406
              +E+ +P+  +  + G+    L   ++++GA + ++   +  PG     V ++G+   
Sbjct: 2   KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

Query: 407 MRAAQSLIHAFI 418
            +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 = 57.0 bits (138), Expect = 1e-10
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 137 RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQ 196
            + V    +G +LG+GG  + E +  TGA I++  K      G+  +  V + G+  + Q
Sbjct: 6   EIAVPENLVGAILGKGGKTLVEYQELTGARIQI-SKKGEFLPGTR-NRRVTITGSPAATQ 63

Query: 197 DALFHITSRLRE 208
            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 = 56.6 bits (137), Expect = 1e-10
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 13/81 (16%)

Query: 49  EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA---DILPDSEERIVVISARENS 105
           + + ++    + VG+++GKGG  +  +Q  TGA I+I+   + LP +  R V I+     
Sbjct: 2   KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITG---- 57

Query: 106 EMRHSPAQDAVMRVHSRIAEI 126
                 +  A       I++ 
Sbjct: 58  ------SPAATQAAQYLISQR 72

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

 Score = 65.9 bits (161), Expect = 8e-14
 Identities = 18/78 (23%), Positives = 35/78 (44%)

Query: 341 SGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMV 400
           S  H    +  T E  +P   +  + G     +S I+Q SG  + +     G  E   M+
Sbjct: 5   SSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCML 64

Query: 401 SGTSDQMRAAQSLIHAFI 418
           +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 = 51.3 bits (123), Expect = 1e-08
 Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 8/75 (10%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVIS-ARENSEMRHSPAQDAVM 117
             VG +IG+GG  +   Q E+G  I+IA       ER  +++   E+ +        A  
Sbjct: 24  GMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQS-------AKR 76

Query: 118 RVHSRIAEIGFEPGQ 132
            +   + +    P  
Sbjct: 77  LLDQIVEKGRSGPSS 91

>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 = 4e-08
 Identities = 21/93 (22%), Positives = 40/93 (43%), Gaps = 10/93 (10%)

Query: 129 EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQV 188
           +    +     V    +G ++GRGG  +S +++ +G  I++     AP  G   +    +
Sbjct: 10  QQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQI-----APDSGGLPERSCML 64

Query: 189 IGNYHSVQDALFHITSRLRETIFPMKRPGPNNG 221
            G   SVQ A   +   + +      R GP++G
Sbjct: 65  TGTPESVQSAKRLLDQIVEK-----GRSGPSSG 92

>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 = 64.6 bits (157), Expect = 7e-13
 Identities = 18/141 (12%), Positives = 44/141 (31%), Gaps = 22/141 (15%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
           D +G  IG  G+ ++  +   G    +  I  D +     I   +   ++ + +      
Sbjct: 13  DLMGLAIGTHGANIQQARKVPG----VTAIDLDEDTCTFHIYGEDQDAVKKARSFLEFAE 68

Query: 119 VHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRC 178
                              + V    +G ++G+ G ++ E+   +G        +     
Sbjct: 69  DV-----------------IQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV 111

Query: 179 GSPHDEI-VQVIGNYHSVQDA 198
                 +    +G   S+ +A
Sbjct: 112 PQEEGMVPFVFVGTKDSIANA 132

>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 = 56.7 bits (137), Expect = 1e-10
 Identities = 13/80 (16%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 341 SGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV--NDPKPGATEGVV 398
           S  H     +   E++IP      V G+    +  +++ +G  +V+  + P+    +  +
Sbjct: 5   SSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPL 64

Query: 399 MVSGTSDQMRAAQSLIHAFI 418
            ++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 = 49.0 bits (117), Expect = 7e-08
 Identities = 18/97 (18%), Positives = 31/97 (31%), Gaps = 8/97 (8%)

Query: 39  GGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA--DILPDSEERI 96
           G           V +++    K G +IGKGG  ++  Q   G  + +          ++ 
Sbjct: 4   GSSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKP 63

Query: 97  VVISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQA 133
           + I+            Q A   V   I + G  P   
Sbjct: 64  LRITGDPYK------VQQAKEMVLELIRDQGSGPSSG 94

>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 = 1e-07
 Identities = 16/88 (18%), Positives = 43/88 (48%), Gaps = 8/88 (9%)

Query: 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 193
            V  +++ + + G ++G+GG  + +++   G  + +    Q     +  D+ +++ G+ +
Sbjct: 15  AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVM---IQDGPQNTGADKPLRITGDPY 71

Query: 194 SVQDALFHITSRLRETIFPMKRPGPNNG 221
            VQ A   +   +R+     +  GP++G
Sbjct: 72  KVQQAKEMVLELIRD-----QGSGPSSG 94

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

 Score = 58.1 bits (140), Expect = 4e-10
 Identities = 27/167 (16%), Positives = 49/167 (29%), Gaps = 42/167 (25%)

Query: 52  FKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSP 111
             +    +++G++IG  G +       TG  I +     D+E  +V++            
Sbjct: 6   IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITV-----DTENSMVIVEPE-----AEGI 55

Query: 112 AQDAVMRVHSRIAEIGFEPGQAVVARLL--------------------VHSQQIGCLLGR 151
               +M+    +  I          RLL                       +  G ++G 
Sbjct: 56  PPVNLMKAAEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGE 115

Query: 152 GGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDA 198
           GG     +   T   I V             +  V +IG+Y     A
Sbjct: 116 GGRARRTIEEMTDTYINV------------GEYEVAIIGDYERAMAA 150

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

 Score = 54.5 bits (131), Expect = 1e-09
 Identities = 24/105 (22%), Positives = 43/105 (40%), Gaps = 3/105 (2%)

Query: 130 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI 189
                     + + + G ++GRGG  V  + + TGA + +    Q P  G P+ ++  + 
Sbjct: 3   MAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEI--SRQLPPNGDPNFKLFIIR 60

Query: 190 GNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPP 234
           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 = 46.4 bits (110), Expect = 7e-07
 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 3/77 (3%)

Query: 345 AAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN---DPKPGATEGVVMVS 401
            A+     +   IP      V G    N+  I Q +GA V ++    P       + ++ 
Sbjct: 1   GAMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR 60

Query: 402 GTSDQMRAAQSLIHAFI 418
           G+  Q+  A+ LI   I
Sbjct: 61  GSPQQIDHAKQLIEEKI 77

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

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 52  FKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILP---DSEERIVVIS 100
                   K G +IG+GG  V+    +TGA ++I+  LP   D   ++ +I 
Sbjct: 9   MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR 60

>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 = 2e-09
 Identities = 12/70 (17%), Positives = 27/70 (38%)

Query: 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 408
               I+V +P+  +  V G +   +  I+  +G  +          E +  + G  D+  
Sbjct: 9   IGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCE 68

Query: 409 AAQSLIHAFI 418
            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 = 54.0 bits (130), Expect = 2e-09
 Identities = 17/103 (16%), Positives = 30/103 (29%), Gaps = 13/103 (12%)

Query: 53  KLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPA 112
            +      VG +IG+ G +++  QN+ G  I+         E+I  I             
Sbjct: 14  DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMG----------P 63

Query: 113 QDAVMRVHSRIAEI---GFEPGQAVVARLLVHSQQIGCLLGRG 152
            D        I ++                +     G   G+G
Sbjct: 64  PDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQG 106

>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 = 2e-06
 Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 8/97 (8%)

Query: 137 RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQ 196
            + V    +G ++GR G ++ +++   G  I+    D     G+  ++I  ++G     +
Sbjct: 14  DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-----GTGPEKIAHIMGPPDRCE 68

Query: 197 DALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPP 233
            A   I   L+        P    G   +PP      
Sbjct: 69  HAARIINDLLQS---LRSGPPGPPGGPGMPPGGRGRG 102

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

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 14/82 (17%), Positives = 29/82 (35%), Gaps = 10/82 (12%)

Query: 47  EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA--DILPDSEERIVVIS-ARE 103
           +   V +++    K G +IGKGG  ++  Q   G  + +        + ++ + I     
Sbjct: 11  QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPY 70

Query: 104 NSEMRHSPAQDAVMRVHSRIAE 125
             +        A   V   + E
Sbjct: 71  KVQQ-------ACEMVMDILRE 85

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

 Score = 52.4 bits (126), Expect = 4e-09
 Identities = 15/78 (19%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 190
               V  +++ + + G ++G+GG  + +++   G  + +          +  D+ +++IG
Sbjct: 11  QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDKPLRIIG 67

Query: 191 NYHSVQDALFHITSRLRE 208
           + + VQ A   +   LRE
Sbjct: 68  DPYKVQQACEMVMDILRE 85

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

 Score = 52.0 bits (125), Expect = 5e-09
 Identities = 9/71 (12%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV--NDPKPGATEGVVMVSGTSDQM 407
            T  E++IP      V G+    +  +++ +G  +++  +  +    +  + + G   ++
Sbjct: 13  GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKV 72

Query: 408 RAAQSLIHAFI 418
           + A  ++   +
Sbjct: 73  QQACEMVMDIL 83

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

 Score = 54.7 bits (131), Expect = 7e-09
 Identities = 30/156 (19%), Positives = 54/156 (34%), Gaps = 33/156 (21%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSE------------ 106
           D++  LIGK G   +  +  T   I I     DSE   V I++ + +E            
Sbjct: 43  DRIAVLIGKKGQTKKEIEKRTKTKITI-----DSETGEVWITSTKETEDPLAVWKARDIV 97

Query: 107 ---MRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLVH-SQQIGCLLGRGGHIVSEMRRA 162
               R    + A   ++             ++        +  G ++GR G     +   
Sbjct: 98  LAIGRGFSPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEM 157

Query: 163 TGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDA 198
           +GAS+ V            + + V +IGN   ++ A
Sbjct: 158 SGASVSV------------YGKTVAIIGNPIQIEIA 181

>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 = 51.0 bits (122), Expect = 2e-08
 Identities = 19/100 (19%), Positives = 37/100 (37%), Gaps = 6/100 (6%)

Query: 128 FEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQ 187
                 V  +L V  + +G ++GRGG  +  + +A+GA I     D+          +++
Sbjct: 9   LTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITC---DKESEGTLLLSRLIK 65

Query: 188 VIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPP 227
           + 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 = 49.1 bits (117), Expect = 9e-08
 Identities = 18/89 (20%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 39  GGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDS--EERI 96
           G    +     V  +L      VG +IG+GG  +R+    +GA I        +    R+
Sbjct: 4   GSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRL 63

Query: 97  VVISARENSEMRHSPAQDAVMRVHSRIAE 125
           + IS  +           A   +  +++E
Sbjct: 64  IKISGTQKE------VAAAKHLILEKVSE 86

>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 = 48.3 bits (115), Expect = 2e-07
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPG--ATEGVVMVSGTSDQ 406
           T    ++ +PQ  +  + G     +  I + SGA +  +    G      ++ +SGT  +
Sbjct: 13  TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE 72

Query: 407 MRAAQSLIHAFI 418
           + 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 = 46.6 bits (111), Expect = 5e-07
 Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 408
           T  +  V IP+ +   V G+N   L  +   +   + +  P+P      + ++GT + + 
Sbjct: 15  TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSNQIKITGTKEGIE 72

Query: 409 AAQSLIHAFI 418
            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 = 44.3 bits (105), Expect = 4e-06
 Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 2/42 (4%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVIS 100
           +    +IGK G  ++  + +T   I+I    PD     + I+
Sbjct: 26  EHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKIT 65

>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 = 44.0 bits (104), Expect = 4e-06
 Identities = 17/98 (17%), Positives = 37/98 (37%), Gaps = 10/98 (10%)

Query: 124 AEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHD 183
            +I         A + +  +    ++G+ G  + ++   T   I++      PR   P  
Sbjct: 7   GDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI------PRPDDP-S 59

Query: 184 EIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNG 221
             +++ 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 = 41.6 bits (98), Expect = 2e-05
 Identities = 10/68 (14%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 410
             +E+ I   +  H+ G++ +N++ I+     +V +  P       ++ + G    ++ A
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI--PPDSEKSNLIRIEGDPQGVQQA 62

Query: 411 QSLIHAFI 418
           +  +    
Sbjct: 63  KRELLELA 70

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 45.6 bits (107), Expect = 2e-05
 Identities = 45/339 (13%), Positives = 79/339 (23%), Gaps = 119/339 (35%)

Query: 78  ETGA-SIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSR--IAEIGFEPGQAV 134
           ETG    +  DIL   E+  V     +N + +    QD    + S+  I  I        
Sbjct: 10  ETGEHQYQYKDILSVFEDAFV-----DNFDCKD--VQDMPKSILSKEEIDHIIMSKDAVS 62

Query: 135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHS 194
               L        LL +   +V   ++     +R+                     NY  
Sbjct: 63  GTLRL-----FWTLLSKQEEMV---QKFVEEVLRI---------------------NYKF 93

Query: 195 VQDALFHITSR---LRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNP--------- 242
           +         R   +   ++  +R   +  ++    F +        R  P         
Sbjct: 94  LMSP-IKTEQRQPSMMTRMYIEQR---DRLYNDNQVFAKY----NVSRLQPYLKLRQALL 145

Query: 243 -ASPGSYPSPVGPFHSMDRGMGPS---------------QPF-----------------D 269
              P      V     +  G G +                 F                 +
Sbjct: 146 ELRPAKN---VL-IDGV-LGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLE 200

Query: 270 HQAAFSHGMDPMVPPNSD---RIPFPYGSERPGHGPTFDRPPSPRS-------WTPQGVG 319
                 + +DP     SD    I     S +          P              +   
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW- 259

Query: 320 GGDPRGFDASSG--FTPRNRPVESGNHAAILTSTTIEVV 356
                 F+ S     T R + V        L++ T   +
Sbjct: 260 ----NAFNLSCKILLTTRFKQV-----TDFLSAATTTHI 289

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 45.2 bits (108), Expect = 3e-05
 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 16/84 (19%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
           DK+  +IG GG ++R     TGA + I D      + +V +SA  +        + A+  
Sbjct: 579 DKIREVIGSGGKVIREIVATTGAKVDIND------DGVVKVSA-SDGAK----IKAAIDW 627

Query: 119 VHSRIAEIGFEPGQ---AVVARLL 139
           + S   E   E G+     V +++
Sbjct: 628 IKSITDEA--EVGKIYDGKVVKVV 649

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A Length = 144

 Score = 42.7 bits (101), Expect = 3e-05
 Identities = 18/109 (16%), Positives = 36/109 (33%), Gaps = 17/109 (15%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
            + G  IG+GG +++  +   G +I++ +   D E  +      +N        +  +  
Sbjct: 45  GEAGRAIGRGGRLIKLLREALGKNIEVVEYSSDLERIV------KNL---FPGVK--IES 93

Query: 119 VHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 167
           +         E        + V     G  +G+GG  V   R       
Sbjct: 94  I------NVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLF 136

>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 = 41.7 bits (98), Expect = 4e-05
 Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 2/42 (4%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVIS 100
           D    +IG+ GS +R   +E   +I +    P+ +  I+ I+
Sbjct: 26  DLHRYVIGQKGSGIRKMMDEFEVNIHVPA--PELQSDIIAIT 65

>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 = 41.7 bits (98), Expect = 4e-05
 Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 348 LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQM 407
           L   TIEV +P     +V G+  S +  +      N+ V  P P     ++ ++G +  +
Sbjct: 14  LVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAITGLAANL 71

Query: 408 RAAQSLIHAFI 418
             A++ +   +
Sbjct: 72  DRAKAGLLERV 82

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 44.8 bits (107), Expect = 5e-05
 Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 13/74 (17%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
           DK+  +IGKGGS++R    ETG +I+I D      +  V I+A  + E     A+ A+ R
Sbjct: 569 DKIKDVIGKGGSVIRALTEETGTTIEIED------DGTVKIAA-TDGEK----AKHAIRR 617

Query: 119 VHSRIAEIGFEPGQ 132
           +    AEI  E G+
Sbjct: 618 IEEITAEI--EVGR 629

>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 = 5e-05
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 342 GNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVS 401
           G+  +    TTI+V +P   +  V G   + +  I+Q +   +V         E V  V+
Sbjct: 1   GSSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD---KEPVFAVT 57

Query: 402 GTSDQMRAAQSLIHAFI 418
           G  + +  A+  I A I
Sbjct: 58  GMPENVDRAREEIEAHI 74

>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 = 40.9 bits (96), Expect = 5e-05
 Identities = 20/110 (18%), Positives = 44/110 (40%), Gaps = 16/110 (14%)

Query: 112 AQDAVMRVHSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFP 171
           +  +  R+   + ++       V   + +  +    ++G  G  + ++       IR   
Sbjct: 2   SSGSSGRIVGELEQM-------VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-- 52

Query: 172 KDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNG 221
               P+ G+P    V V G   +V++A+ HI +   E    +   GP++G
Sbjct: 53  ----PQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY---LADSGPSSG 95

>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 = 39.4 bits (92), Expect = 2e-04
 Identities = 17/84 (20%), Positives = 39/84 (46%), Gaps = 8/84 (9%)

Query: 47  EEEVVFKLLCHLDK--VGSLIGKGGSIVRTFQNETGASIKIAD-ILPDSEERIVVIS-AR 102
                FKL   +D      +IG+ G+++   + E   +I+  D    +  +  + I+   
Sbjct: 12  RALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYE 71

Query: 103 ENSEMRHSPAQDAVMRVHSRIAEI 126
           +N+E     A+DA++R+   + ++
Sbjct: 72  KNTEA----ARDAILRIVGELEQM 91

>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 = 4e-04
 Identities = 17/98 (17%), Positives = 40/98 (40%), Gaps = 7/98 (7%)

Query: 124 AEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHD 183
            E      ++    + V  +    ++GR G +++++R     +I+   KD     G+   
Sbjct: 7   GEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD----GNQPQ 62

Query: 184 EIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNG 221
           + + + 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 = 37.9 bits (88), Expect = 6e-04
 Identities = 13/73 (17%), Positives = 26/73 (35%), Gaps = 1/73 (1%)

Query: 347 ILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSD 405
            L S  + V +   Y   + G   + ++ IR     N+   D       +  + ++G   
Sbjct: 13  ALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK 72

Query: 406 QMRAAQSLIHAFI 418
              AA+  I   +
Sbjct: 73  NTEAARDAILRIV 85

>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 Length = 757

 Score = 42.6 bits (101), Expect = 2e-04
 Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 11/74 (14%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
           DK+G +IG    ++   Q +TGA I I D      +  + I A  +       A+ A   
Sbjct: 607 DKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGA-ADGPA----AEAARAT 655

Query: 119 VHSRIAEIGFEPGQ 132
           ++        E G+
Sbjct: 656 INGIANPTSPEVGE 669

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Length = 630

 Score = 41.7 bits (99), Expect = 4e-04
 Identities = 16/68 (23%), Positives = 23/68 (33%), Gaps = 15/68 (22%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
            K    +G GG  ++  Q ETG +I   D      E    +          +P   A+  
Sbjct: 576 SKRAKFVGPGGYNLKKLQAETGVTISQVD------EETFSVF---------APTPSAMHE 620

Query: 119 VHSRIAEI 126
               I EI
Sbjct: 621 ARDFITEI 628

>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 = 41.6 bits (97), Expect = 5e-04
 Identities = 32/141 (22%), Positives = 44/141 (31%), Gaps = 13/141 (9%)

Query: 216  PGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYP-----SPVGPFHS-MDRGMGPSQPFD 269
             G  +      PF      P  P    +SPG  P     SP  P +S       P+ P  
Sbjct: 1511 YGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSP-- 1568

Query: 270  HQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDAS 329
              +  S    P  P  S   P  Y    P + PT    PS    +P       P     S
Sbjct: 1569 SYSPTSPSYSPTSPSYSPTSP-SYSPTSPSYSPT---SPSYSPTSP-SYSPTSPSYSPTS 1623

Query: 330  SGFTPRNRPVESGNHAAILTS 350
              ++P +      + +   TS
Sbjct: 1624 PSYSPTSPSYSPTSPSYSPTS 1644

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 41.3 bits (96), Expect = 6e-04
 Identities = 16/108 (14%), Positives = 32/108 (29%), Gaps = 5/108 (4%)

Query: 216 PGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFS 275
            G + G   +PP   +P    +    PA    +        SM+     + P     A+ 
Sbjct: 38  AGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYM 97

Query: 276 HGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDP 323
               P+              ++P   P + +P +      + +    P
Sbjct: 98  QPQVPVQMGTP-----LQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYP 140

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	424
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.94
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.93
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.93
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.93
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.93
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.93
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.92
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.92
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.91
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.91
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.9
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.79
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.77
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.68
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.67
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.66
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.66
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.65
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.62
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.62
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.6
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.59
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.57
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.56
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.56
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.56
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.55
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.55
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.54
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.54
1we8_A	104	Tudor and KH domain containing protein; structural	99.5
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.48
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.46
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.46
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.46
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.45
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.44
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.44
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.42
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.42
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.4
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.4
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.39
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.39
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.38
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.36
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.36
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.36
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.35
1we8_A	104	Tudor and KH domain containing protein; structural	99.33
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.31
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.3
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.3
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.29
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.27
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.26
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.23
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.19
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.11
2cpq_A	91	FragIle X mental retardation syndrome related prot	99.06
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.04
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
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.68
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.51
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.42
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.25
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	98.02
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.0
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.97
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.75
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.71
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.65
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.21
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.01
2cxc_A	144	NUSA; transcription termination, RNA binding prote	96.88
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.21
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.9
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.06
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	94.9
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	94.57
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	94.48
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	94.23
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	94.02
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	92.05

>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=99.94  E-value=3.2e-26  Score=203.30  Aligned_cols=159  Identities=20%  Similarity=0.386  Sum_probs=128.9

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhcCCC
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPM  213 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~  213 (424)
                      ++.+|+||.+++|.||||+|++|++|+++|||+|++.++..   .....+|.|+|+|++++|.+|+.+|.+++.+.... 
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            57899999999999999999999999999999999975432   22367899999999999999999999988765100 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCC
Q 014452          214 KRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPY  293 (424)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~~~~  293 (424)
                                           .|.+..                                                   .|
T Consensus        78 ---------------------~~~~~~---------------------------------------------------~~   85 (164)
T 2jvz_A           78 ---------------------GFGDRN---------------------------------------------------EY   85 (164)
T ss_dssp             ---------------------CCSSCS---------------------------------------------------SC
T ss_pred             ---------------------CCCCcc---------------------------------------------------cc
Confidence                                 000000                                                   00


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceeccccchH
Q 014452          294 GSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNL  373 (424)
Q Consensus       294 g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G~~I  373 (424)
                      +                                       ++             ...+.+|.||.+++|+||||+|++|
T Consensus        86 ~---------------------------------------~~-------------~~~~~~i~vp~~~~g~iIGk~G~~I  113 (164)
T 2jvz_A           86 G---------------------------------------SR-------------IGGGIDVPVPRHSVGVVIGRSGEMI  113 (164)
T ss_dssp             T---------------------------------------TS-------------CSSSBCCEEETTTHHHHHCSSSHHH
T ss_pred             C---------------------------------------CC-------------CCceEEEEEChhhccccCCCCcHhH
Confidence            0                                       00             0134678999999999999999999


Q ss_pred             HHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          374 SHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       374 k~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      ++|+++|||+|.|++..+...++.|+|+|++++|+.|+.+|+++|++
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            99999999999998765556689999999999999999999999874

>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=99.93  E-value=1.5e-25  Score=198.85  Aligned_cols=153  Identities=20%  Similarity=0.327  Sum_probs=128.6

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhcCCC
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPM  213 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~  213 (424)
                      .+++|+||.+.+|.||||+|++|++|+++|||+|+|.+. .   .+++.+|.|+|+|+++++.+|+.+|.+++.+.... 
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~-~---~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~~-   77 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPP-E---TPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFF-   77 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCC-S---STTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTSS-
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCC-C---CCCCCceEEEEEcCHHHHHHHHHHHHHHHhccccc-
Confidence            478999999999999999999999999999999999753 2   23478999999999999999999999999876100 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCC
Q 014452          214 KRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPY  293 (424)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~~~~  293 (424)
                                 .|                                                                   
T Consensus        78 -----------~~-------------------------------------------------------------------   79 (163)
T 3krm_A           78 -----------GP-------------------------------------------------------------------   79 (163)
T ss_dssp             -----------CS-------------------------------------------------------------------
T ss_pred             -----------cc-------------------------------------------------------------------
Confidence                       00                                                                   


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceeccccchH
Q 014452          294 GSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNL  373 (424)
Q Consensus       294 g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G~~I  373 (424)
                                       .                                   .....+.+|.||.+++|+||||+|++|
T Consensus        80 -----------------~-----------------------------------~~~~~~~~i~vp~~~~g~iIGkgG~~I  107 (163)
T 3krm_A           80 -----------------K-----------------------------------EEVKLETHIRVPASAAGRVIGKGGKTV  107 (163)
T ss_dssp             -----------------S-----------------------------------CCCCEEEEEEEETTTHHHHHCGGGHHH
T ss_pred             -----------------c-----------------------------------cCCceEEEEEcChhheeeEEcCCChHH
Confidence                             0                                   001357799999999999999999999


Q ss_pred             HHHHHHhCCEEEEeCCC-CCCC-CcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452          374 SHIRQISGANVVVNDPK-PGAT-EGVVMVSGTSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       374 k~Ir~~SGa~I~i~~~~-~~~~-~r~i~I~Gt~e~v~~A~~lI~~~i~~~  421 (424)
                      ++|+++|||+|.|++.. +..+ ++.|+|+|++++|++|+.+|+++|.+-
T Consensus       108 ~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~  157 (163)
T 3krm_A          108 NELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQV  157 (163)
T ss_dssp             HHHHHHHCCEEECCTTCCCCTTSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCeEEECCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            99999999999998532 3333 458999999999999999999999753

>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=99.93  E-value=1.2e-25  Score=202.39  Aligned_cols=172  Identities=21%  Similarity=0.343  Sum_probs=132.4

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhc
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETI  210 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  210 (424)
                      ...++++|+||.+++|.||||+|++|++|+++|||+|+|.+..+.  .++..+|.|+|+|+.++|.+|+.+|.+++.+..
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 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDF--YPGTTERVCLIQGTIEALNAVHGFIAEKIREMP   80 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCB--CTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCC
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCC--CCCCCCceEEEEeCHHHHHHHHHHHHHHHhccC
Confidence            356889999999999999999999999999999999999754321  224679999999999999999999999987751


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCC
Q 014452          211 FPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIP  290 (424)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~  290 (424)
                      ...         ..                        ..+...+                                  +
T Consensus        81 ~~~---------~~------------------------~~~~~~~----------------------------------~   93 (178)
T 2anr_A           81 QNV---------AK------------------------TEPVSIL----------------------------------Q   93 (178)
T ss_dssp             CC------------------------------------------------------------------------------
T ss_pred             Ccc---------cc------------------------CCccccc----------------------------------C
Confidence            100         00                        0000000                                  0


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceecccc
Q 014452          291 FPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENN  370 (424)
Q Consensus       291 ~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G  370 (424)
                                         |. +           .      .             ......+.+|.||.+++|+||||+|
T Consensus        94 -------------------~~-~-----------~------~-------------~~~~~~~~~i~Vp~~~vg~iIGkgG  123 (178)
T 2anr_A           94 -------------------PQ-T-----------T------V-------------NPDRANQVKIIVPNSTAGLIIGKGG  123 (178)
T ss_dssp             --------------------------------------------------------CGGGGEEEEEEEHHHHHHHHCGGG
T ss_pred             -------------------Cc-c-----------C------C-------------CCCCceEEEEEEchhheeeeECCCc
Confidence                               00 0           0      0             0012468899999999999999999


Q ss_pred             chHHHHHHHhCCEEEEeCCC--CCCCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452          371 SNLSHIRQISGANVVVNDPK--PGATEGVVMVSGTSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       371 ~~Ik~Ir~~SGa~I~i~~~~--~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~  421 (424)
                      ++|++|+++|||+|.|++..  +..++++|+|+|++++|++|+.||.++|.+.
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            99999999999999998542  2356799999999999999999999999863

>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=99.93  E-value=2.2e-25  Score=200.04  Aligned_cols=170  Identities=24%  Similarity=0.390  Sum_probs=127.1

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhcCC
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFP  212 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~  212 (424)
                      ..+++|+||.+++|.||||+|++|++|+++|||+|+|.+.+     ....+|.|+|+|++++|.+|+.+|.+++.+....
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~-----~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~   76 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-----GTTPERIAQITGPPDRAQHAAEIITDLLRSVQAG   76 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT-----TSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC--
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCC-----CCCCccEEEEEeCHHHHHHHHHHHHHHHHhcccC
Confidence            46789999999999999999999999999999999997532     1367899999999999999999999999886100


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCC
Q 014452          213 MKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFP  292 (424)
Q Consensus       213 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~~~  292 (424)
                                            .|..          +.|.+             +         +.              
T Consensus        77 ----------------------~~~~----------~~p~~-------------~---------~~--------------   88 (174)
T 1j4w_A           77 ----------------------NPGG----------PGPGG-------------R---------GR--------------   88 (174)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ----------------------CCCC----------CCCCC-------------C---------CC--------------
Confidence                                  0000          00000             0         00              


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceeccccch
Q 014452          293 YGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSN  372 (424)
Q Consensus       293 ~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G~~  372 (424)
                       +.   +.          ..|..                          +   +.....+.+|.||.+++|+||||+|++
T Consensus        89 -~~---~~----------~~~~~--------------------------~---~~~~~~~~~i~vp~~~~g~iIGkgG~~  125 (174)
T 1j4w_A           89 -GR---GQ----------GNWNM--------------------------G---PPGGLQEFNFIVPTGKTGLIIGKGGET  125 (174)
T ss_dssp             ----------------------------------------------------------CEEEEEEETTTHHHHHCGGGHH
T ss_pred             -CC---CC----------Ccccc--------------------------C---CCCCcEEEEEEEChHHcCeeECCCchH
Confidence             00   00          00000                          0   001246789999999999999999999


Q ss_pred             HHHHHHHhCCEEEEeCCC---CCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 014452          373 LSHIRQISGANVVVNDPK---PGATEGVVMVSGTSDQMRAAQSLIHAFI  418 (424)
Q Consensus       373 Ik~Ir~~SGa~I~i~~~~---~~~~~r~i~I~Gt~e~v~~A~~lI~~~i  418 (424)
                      |++|+++|||+|.|++..   .+..++.|+|+|++++|++|+.||+++|
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            999999999999998542   2356799999999999999999999875

>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=99.93  E-value=1.2e-25  Score=198.95  Aligned_cols=156  Identities=24%  Similarity=0.415  Sum_probs=131.2

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhcC
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIF  211 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~  211 (424)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|...       +..+|.|+|+|+.++|.+|+.+|.+++.+...
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~-------~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~   75 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEEDIS   75 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC-------TTTEEEEEEEEEHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC-------CCCceEEEEEeCHHHHHHHHHHHHHHHHhhcc
Confidence            45789999999999999999999999999999999999753       25689999999999999999999999988631


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCC
Q 014452          212 PMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPF  291 (424)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~~  291 (424)
                      ..          . +                       .                                  .      
T Consensus        76 ~~----------~-~-----------------------~----------------------------------~------   81 (160)
T 2jzx_A           76 SS----------M-T-----------------------N----------------------------------S------   81 (160)
T ss_dssp             SC----------C-C-----------------------S----------------------------------S------
T ss_pred             cc----------C-C-----------------------C----------------------------------C------
Confidence            00          0 0                       0                                  0      


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceeccccc
Q 014452          292 PYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNS  371 (424)
Q Consensus       292 ~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G~  371 (424)
                                  .                    .                    ......+.+|.||.+++|+||||+|+
T Consensus        82 ------------~--------------------~--------------------~~~~~~~~~i~vp~~~~g~iIGkgG~  109 (160)
T 2jzx_A           82 ------------T--------------------A--------------------ASRPPVTLRLVVPASQCGSLIGKGGC  109 (160)
T ss_dssp             ------------S--------------------C--------------------CCCCSEEEEEEEEHHHHHHHHCGGGH
T ss_pred             ------------c--------------------c--------------------CCCCCEEEEEEEChhheeeEECCCCH
Confidence                        0                    0                    00013689999999999999999999


Q ss_pred             hHHHHHHHhCCEEEEeC-CCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          372 NLSHIRQISGANVVVND-PKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       372 ~Ik~Ir~~SGa~I~i~~-~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      +|++|+++|||+|.|++ ..+..+++.|+|+|++++|+.|+.+|.+.|.+
T Consensus       110 ~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          110 KIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             HHHHHHHHHSSEECCCCCCSTTCCEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCeEEECCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            99999999999999984 34567889999999999999999999998865

>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=99.93  E-value=2.6e-25  Score=197.35  Aligned_cols=152  Identities=28%  Similarity=0.446  Sum_probs=125.7

Q ss_pred             cEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccC-CCCCcccEEEeecccccccccChhHHHHHHHHHHHHhhc
Q 014452           49 EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADI-LPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIG  127 (424)
Q Consensus        49 ~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~-~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e~~  127 (424)
                      +-+++|+||.+.+|.||||+|++||+|+++|||+|+|++. .+++.+|+|+|+|.++++.      .|...+.+.+.+..
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~v~------~A~~~I~~~~~e~~   75 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQF------KAQGRIYGKLKEEN   75 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHHHH------HHHHHHHHHHHHTT
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHHHH------HHHHHHHHHHhccc
Confidence            3478999999999999999999999999999999999964 5688999999999876543      34555555555442


Q ss_pred             C-C--CCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHH
Q 014452          128 F-E--PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITS  204 (424)
Q Consensus       128 ~-~--~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~  204 (424)
                      . .  .....+.+|.||.+++|+||||+|++|++|+++|||+|+|.+ +..|.  ...++.|+|+|++++|.+|+.+|.+
T Consensus        76 ~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~-~~~~~--~~~~~~v~I~G~~~~v~~A~~~I~~  152 (163)
T 3krm_A           76 FFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR-DQTPD--ENDQVIVKIIGHFYASQMAQRKIRD  152 (163)
T ss_dssp             SSCSSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCT-TCCCC--TTSEEEEEEEECHHHHHHHHHHHHH
T ss_pred             ccccccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECC-CCCCC--CCCceEEEEEeCHHHHHHHHHHHHH
Confidence            2 2  234567899999999999999999999999999999999964 33343  2344589999999999999999999


Q ss_pred             HHHhh
Q 014452          205 RLRET  209 (424)
Q Consensus       205 ~l~~~  209 (424)
                      ++++.
T Consensus       153 ~i~~~  157 (163)
T 3krm_A          153 ILAQV  157 (163)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99986

>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=99.92  E-value=2.1e-25  Score=200.77  Aligned_cols=154  Identities=25%  Similarity=0.410  Sum_probs=124.1

Q ss_pred             CccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccC---CCCCcccEEEeecccccccccChhHHHHHHHHHHH
Q 014452           47 EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADI---LPDSEERIVVISARENSEMRHSPAQDAVMRVHSRI  123 (424)
Q Consensus        47 ~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~---~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i  123 (424)
                      +.+++++|+||.+.+|.||||+|++||+|+++|||+|+|++.   .+++.+|+|+|+|..+++..      |...+.+.+
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~------A~~~I~~~~   76 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNA------VHGFIAEKI   76 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHH------HHHHHHHHH
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHH------HHHHHHHHH
Confidence            467999999999999999999999999999999999999843   46788999999998655432      333333333


Q ss_pred             HhhcC-----------------CCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEE
Q 014452          124 AEIGF-----------------EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIV  186 (424)
Q Consensus       124 ~e~~~-----------------~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v  186 (424)
                      .+...                 ......+++|.||.+++|+||||+|++|++|+++|||+|+|.+...   +..+.++.|
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~---~~~~~~~~v  153 (178)
T 2anr_A           77 REMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD---GINLQNRVV  153 (178)
T ss_dssp             TCCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC-------CCEEEE
T ss_pred             hccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCC---CCCCCceEE
Confidence            22110                 1123478899999999999999999999999999999999976543   233678999


Q ss_pred             EEEeCHHHHHHHHHHHHHHHHhh
Q 014452          187 QVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       187 ~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      +|+|++++|.+|+.+|.++|++.
T Consensus       154 ~I~G~~~~v~~A~~~I~~~i~e~  176 (178)
T 2anr_A          154 TVSGEPEQNRKAVELIIQKIQED  176 (178)
T ss_dssp             EEESSHHHHHHHHHHHHHHHHSC
T ss_pred             EEEcCHHHHHHHHHHHHHHHHhC
Confidence            99999999999999999999876

>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=99.92  E-value=3e-25  Score=196.40  Aligned_cols=149  Identities=30%  Similarity=0.489  Sum_probs=123.6

Q ss_pred             ccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHhhc
Q 014452           48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIG  127 (424)
Q Consensus        48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e~~  127 (424)
                      ..++++|+||.+.+|.||||+|++||+|+++|||+|+|++.  ++++|.|+|+|+.+++..      |...+.+.+.+..
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~~v~~------A~~~I~~~i~e~~   74 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFK------AFAMIIDKLEEDI   74 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHHHHHH------HHHHHHHHHHHHH
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHHHHHH------HHHHHHHHHHhhc
Confidence            56889999999999999999999999999999999999875  578899999999655433      3333443333321


Q ss_pred             C--------CCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHH
Q 014452          128 F--------EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDAL  199 (424)
Q Consensus       128 ~--------~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~  199 (424)
                      .        .....++++|.||.+++|+||||+|++|++|+++|||+|+|.+ +..|   .+.++.|+|+|++++|.+|+
T Consensus        75 ~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~-~~~~---~~~~~~v~I~G~~~~v~~A~  150 (160)
T 2jzx_A           75 SSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG-DMLP---NSTERAITIAGIPQSIIECV  150 (160)
T ss_dssp             TSCCCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCC-CCST---TCCEEEEEEEECHHHHHHHH
T ss_pred             cccCCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECC-CCCC---CCCceEEEEEcCHHHHHHHH
Confidence            1        1233588999999999999999999999999999999999964 3333   36899999999999999999


Q ss_pred             HHHHHHHHh
Q 014452          200 FHITSRLRE  208 (424)
Q Consensus       200 ~~I~~~l~~  208 (424)
                      .+|.+++.+
T Consensus       151 ~~I~~~i~e  159 (160)
T 2jzx_A          151 KQICVVMLE  159 (160)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhc
Confidence            999999876

>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=99.91  E-value=9.5e-25  Score=195.83  Aligned_cols=153  Identities=19%  Similarity=0.347  Sum_probs=119.7

Q ss_pred             cEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHhhcC
Q 014452           49 EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIGF  128 (424)
Q Consensus        49 ~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e~~~  128 (424)
                      ..+++|+||.+.+|.||||+|++||+|+++|||+|+|.+..++..+|+|+|+|+.+++..   |.+.+..+........+
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~---A~~~I~~~~~~~~~~~~   78 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH---AAEIITDLLRSVQAGNP   78 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHH---HHHHHHHHHHHHC----
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHH---HHHHHHHHHHhcccCCC
Confidence            457899999999999999999999999999999999986666788999999999766554   23333222222110000


Q ss_pred             --------------------CCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEE
Q 014452          129 --------------------EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQV  188 (424)
Q Consensus       129 --------------------~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I  188 (424)
                                          .+....+++|.||.+++|+||||+|++|++|+++|||+|+|.+..  +.+..+.++.|+|
T Consensus        79 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~--~~~~~~~~~~v~I  156 (174)
T 1j4w_A           79 GGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP--PPNADPNMKLFTI  156 (174)
T ss_dssp             -------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCC--TTTSCTTEEEEEE
T ss_pred             CCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCC--CCCCCCCceEEEE
Confidence                                011246889999999999999999999999999999999997532  2234467899999


Q ss_pred             EeCHHHHHHHHHHHHHHH
Q 014452          189 IGNYHSVQDALFHITSRL  206 (424)
Q Consensus       189 ~G~~~~v~~A~~~I~~~l  206 (424)
                      +|++++|.+|+.+|.++|
T Consensus       157 ~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          157 RGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             ECCHHHHHHHHHHHHHHC
T ss_pred             ECCHHHHHHHHHHHHHhC
Confidence            999999999999998864

>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=99.91  E-value=6.9e-24  Score=188.23  Aligned_cols=149  Identities=19%  Similarity=0.325  Sum_probs=119.8

Q ss_pred             EEEEEEecccccceeeccCchHHHHHHHHhCceEEeccC--CCCCcccEEEeecccccccccChhHHHHHHHHHHHHhhc
Q 014452           50 VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADI--LPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIG  127 (424)
Q Consensus        50 ~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~--~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e~~  127 (424)
                      ++++|+||.+.+|+||||+|++||+|+++|||+|+|.+.  .++..+|+|+|+|.++++..      |...+.+.+.+..
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~~------A~~~I~~ii~e~~   75 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ------ACEMVMDILRERD   75 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHHH------HHHHHHHHTTCSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHHH------HHHHHHHHHHhcc
Confidence            578999999999999999999999999999999999743  24577899999998655332      3333333333221


Q ss_pred             ---CCC------CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHH
Q 014452          128 ---FEP------GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDA  198 (424)
Q Consensus       128 ---~~~------~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A  198 (424)
                         +.+      ....+++|.||.+++|+||||+|++|++|+++|||+|+|.+.+     ..+.++.|+|+|++++|..|
T Consensus        76 ~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~-----~~~~~~~v~I~G~~~~v~~A  150 (164)
T 2jvz_A           76 QGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-----GTGPEKIAHIMGPPDRCEHA  150 (164)
T ss_dssp             SCCCSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC-----TTSSEEEEEEESCHHHHHHH
T ss_pred             CCCCCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC-----CCCCcEEEEEEcCHHHHHHH
Confidence               111      1134578999999999999999999999999999999997543     13568999999999999999


Q ss_pred             HHHHHHHHHhh
Q 014452          199 LFHITSRLRET  209 (424)
Q Consensus       199 ~~~I~~~l~~~  209 (424)
                      +.+|.+++++.
T Consensus       151 ~~~I~~~i~~~  161 (164)
T 2jvz_A          151 ARIINDLLQSL  161 (164)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHhhh
Confidence            99999999875

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

Probab=99.90  E-value=1.8e-23  Score=205.54  Aligned_cols=220  Identities=11%  Similarity=0.083  Sum_probs=160.8

Q ss_pred             CccEEEEEEecccccceeeccCc--hHHHHHHHHhCceEEeccCC-----CCCcccEEEeecccccccccChhHHHHHHH
Q 014452           47 EEEVVFKLLCHLDKVGSLIGKGG--SIVRTFQNETGASIKIADIL-----PDSEERIVVISARENSEMRHSPAQDAVMRV  119 (424)
Q Consensus        47 ~~~~~~ri~ip~~~vg~IIGk~G--~~Ik~I~~~tga~I~v~~~~-----~~~~er~v~I~G~~~~~~~~~~a~~av~~~  119 (424)
                      ...+++++.||..+++.||||+|  ++|++|+++|||+|+|++..     +......|+|+|..++          +.++
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~en----------VE~A   96 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGD----------VDRA   96 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHH----------HHHH
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHH----------HHHH
Confidence            57899999999999999999999  99999999999999999764     1235578999999655          4444


Q ss_pred             HHHHHhhcCCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHH
Q 014452          120 HSRIAEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDAL  199 (424)
Q Consensus       120 ~~~i~e~~~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~  199 (424)
                      ..+|.+.     -.+++.+.+|...+..  ..-...|.. ++.++++|.+++..+.   .+.....|+|+|...++..|+
T Consensus        97 R~~I~~l-----~Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~---~~~~sd~V~IrG~~~nv~~ak  165 (376)
T 3n89_A           97 RMLMRRN-----CHFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEK---NGIVTTYLRITAREKNQHELI  165 (376)
T ss_dssp             HHHHHHS-----CEEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC--------CEEEEEEEEEGGGHHHHH
T ss_pred             HHHHHhc-----CCceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCcccc---cCCCCCEEEEEcChhhHHHHH
Confidence            4455442     2456677777654332  111234544 5689999988654221   112356899999999888888


Q ss_pred             HHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCC
Q 014452          200 FHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMD  279 (424)
Q Consensus       200 ~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~  279 (424)
                      +.+..+++......          +                                                       
T Consensus       166 eA~~~Ll~~l~~~e----------~-------------------------------------------------------  180 (376)
T 3n89_A          166 EAAKRLNEILFRES----------P-------------------------------------------------------  180 (376)
T ss_dssp             HHHHHHHHHHCC------------C-------------------------------------------------------
T ss_pred             HHHHHHHHHHHhhh----------c-------------------------------------------------------
Confidence            88777777651000          0                                                       


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecc
Q 014452          280 PMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQ  359 (424)
Q Consensus       280 ~~~~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~  359 (424)
                                                                                        .....++.+|.|+.
T Consensus       181 ------------------------------------------------------------------~~~~~~s~~v~V~~  194 (376)
T 3n89_A          181 ------------------------------------------------------------------APENNFTLHFTLST  194 (376)
T ss_dssp             ------------------------------------------------------------------CCSSCEEEEEEEEG
T ss_pred             ------------------------------------------------------------------ccccceEEEEEeCH
Confidence                                                                              00124789999999


Q ss_pred             Ccccceecccc--chHHHHHHHhCCEEEEeCCCCC----CCCcEEEEEcCHHHHHHHHHHHHHHH
Q 014452          360 LYMAHVYGENN--SNLSHIRQISGANVVVNDPKPG----ATEGVVMVSGTSDQMRAAQSLIHAFI  418 (424)
Q Consensus       360 ~~~g~IIGk~G--~~Ik~Ir~~SGa~I~i~~~~~~----~~~r~i~I~Gt~e~v~~A~~lI~~~i  418 (424)
                      .++..|||++|  ..|++|+++|||+|.+++....    .+...|+|+|+.++|+.|+.+|+++|
T Consensus       195 ~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lL  259 (376)
T 3n89_A          195 YYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLL  259 (376)
T ss_dssp             GGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTS
T ss_pred             HHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhC
Confidence            99999999999  5569999999999999753221    23468999999999999999999875

>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=99.79  E-value=3.3e-19  Score=154.44  Aligned_cols=68  Identities=22%  Similarity=0.330  Sum_probs=58.7

Q ss_pred             EEEEeccCcccceeccccchHHHHHHHhCC-EEEEeCCCCC---CCCc--EEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          353 IEVVIPQLYMAHVYGENNSNLSHIRQISGA-NVVVNDPKPG---ATEG--VVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa-~I~i~~~~~~---~~~r--~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      .+|.||.+.+|++|||+|.+|+.|++.||| +|.|....+.   .+++  .|+|+|++++|+.|+.||++.|.+
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            779999999999999999999999999997 9999842211   2333  589999999999999999999976

>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=99.77  E-value=2.1e-18  Score=149.40  Aligned_cols=137  Identities=17%  Similarity=0.275  Sum_probs=101.5

Q ss_pred             cEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeec-ccccccccChhHHHHHHHHHHHHhhc
Q 014452           49 EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISA-RENSEMRHSPAQDAVMRVHSRIAEIG  127 (424)
Q Consensus        49 ~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G-~~~~~~~~~~a~~av~~~~~~i~e~~  127 (424)
                      .++.+|+||.+.+|++||++|++|++|++++|+.|.....   .+++ +.+.+ .++          ++.++.. +.+. 
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~~---~~~~-~i~~~~~p~----------~v~~~~~-~l~~-   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE---DTCT-FHIYGEDQD----------AVKKARS-FLEF-   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEET---TTTE-EEEEESSHH----------HHHHHHH-HHCE-
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccCC---Cchh-eeeccCCHH----------HHHHHHH-hhhc-
Confidence            4678999999999999999999999999999944333222   2333 44544 332          3333322 1111 


Q ss_pred             CCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCc-eEEEecCCCCCCCCCCCCc--EEEEEeCHHHHHHHHHHHHH
Q 014452          128 FEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGA-SIRVFPKDQAPRCGSPHDE--IVQVIGNYHSVQDALFHITS  204 (424)
Q Consensus       128 ~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga-~I~v~~~~~~p~~~~~~~r--~v~I~G~~~~v~~A~~~I~~  204 (424)
                            ...++.||.+++|++|||+|++|+.|++.||| +|+|.+.++.. . ...++  .|+|+|+.++|+.|+.+|.+
T Consensus        67 ------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~-~-~~~~~~~~vtI~G~~~~v~~Ak~li~~  138 (144)
T 2qnd_A           67 ------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKN-V-PQEEGMVPFVFVGTKDSIANATVLLDY  138 (144)
T ss_dssp             ------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTC-C-CCCTTEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             ------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCC-c-cccCCeeEEEEEeCHHHHHHHHHHHHH
Confidence                  13789999999999999999999999999997 99998754321 1 12333  58999999999999999999


Q ss_pred             HHHhh
Q 014452          205 RLRET  209 (424)
Q Consensus       205 ~l~~~  209 (424)
                      +|.+.
T Consensus       139 ~l~~l  143 (144)
T 2qnd_A          139 HLNYL  143 (144)
T ss_dssp             HHHTC
T ss_pred             HHHhc
Confidence            99763

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

Probab=99.68  E-value=1.4e-16  Score=146.62  Aligned_cols=66  Identities=17%  Similarity=0.149  Sum_probs=57.4

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-----HHHHHHHHHHHHHHHH
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-----YHSVQDALFHITSRLR  207 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-----~~~v~~A~~~I~~~l~  207 (424)
                      +...++.||.+.++.|||++|++|+.|+++|||+|++..          .++.|+|.++     ++++.+|+.+|..+++
T Consensus        33 P~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~----------~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~r  102 (219)
T 2e3u_A           33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS----------ETGEVWITSTKETEDPLAVWKARDIVLAIGR  102 (219)
T ss_dssp             CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT----------TTCEEEEEECTTCCSHHHHHHHHHHHHHHHT
T ss_pred             CEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc----------CCCEEEEecCCCCCCHHHHHHHHHHHHHHhc
Confidence            345689999999999999999999999999999999953          2456889886     6999999999999884


Q ss_pred             h
Q 014452          208 E  208 (424)
Q Consensus       208 ~  208 (424)
                      .
T Consensus       103 g  103 (219)
T 2e3u_A          103 G  103 (219)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=99.67  E-value=2e-16  Score=123.65  Aligned_cols=72  Identities=26%  Similarity=0.507  Sum_probs=67.6

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|+++.+++++|.|+|+|++++|++|+.||+++|.+
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            368899999999999999999999999999999999999776677889999999999999999999999874

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

Probab=99.66  E-value=1.1e-16  Score=123.35  Aligned_cols=72  Identities=28%  Similarity=0.511  Sum_probs=68.3

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~  421 (424)
                      .++.+|.||.+++|+||||+|++|++|+++|||+|+|+++.+++.+|.|+|+|++++|++|+.||+++|.++
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            578999999999999999999999999999999999998777788999999999999999999999999865

>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=99.66  E-value=1.3e-16  Score=124.77  Aligned_cols=74  Identities=30%  Similarity=0.503  Sum_probs=67.2

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcCc
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGV  422 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~~  422 (424)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|+++.+++.+|.|+|+|++++|++|+.||+++|.+.+
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   77 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSEK   77 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC---
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhhh
Confidence            36889999999999999999999999999999999999976677889999999999999999999999987653

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

Probab=99.65  E-value=5.2e-16  Score=142.86  Aligned_cols=137  Identities=25%  Similarity=0.326  Sum_probs=102.2

Q ss_pred             EEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHhhc--C
Q 014452           51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIG--F  128 (424)
Q Consensus        51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e~~--~  128 (424)
                      ..++.||.+.+|.|||++|++|+.|+++|||+|+++     .+++.|+|.+.....+     .+++.++.+.+....  +
T Consensus        35 i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~-----~~~g~V~I~~~~~t~d-----~~~i~kA~~~I~~i~rg~  104 (219)
T 2e3u_A           35 EEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITID-----SETGEVWITSTKETED-----PLAVWKARDIVLAIGRGF  104 (219)
T ss_dssp             EEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEEC-----TTTCEEEEEECTTCCS-----HHHHHHHHHHHHHHHTTC
T ss_pred             EEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEE-----cCCCEEEEecCCCCCC-----HHHHHHHHHHHHHHhccC
Confidence            458999999999999999999999999999999994     3568899988642111     223344433333211  1


Q ss_pred             C--------CCcceEEEEEecC-----------CCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEE
Q 014452          129 E--------PGQAVVARLLVHS-----------QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI  189 (424)
Q Consensus       129 ~--------~~~~~t~~l~IP~-----------~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~  189 (424)
                      +        .++.....+.|+.           ..+|+||||+|++|+.|++.|||+|.|..            +.|+|.
T Consensus       105 ~~e~g~~ll~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~~------------~~v~i~  172 (219)
T 2e3u_A          105 SPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG------------KTVAII  172 (219)
T ss_dssp             CHHHHGGGGSTTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEET------------TEEEEE
T ss_pred             CccccceeccCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEECC------------eEEEEE
Confidence            1        1222223344442           26899999999999999999999999952            359999


Q ss_pred             eCHHHHHHHHHHHHHHHHhh
Q 014452          190 GNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       190 G~~~~v~~A~~~I~~~l~~~  209 (424)
                      |+.++++.|+.+|++++...
T Consensus       173 G~~~~i~~A~~~i~~li~g~  192 (219)
T 2e3u_A          173 GNPIQIEIAKTAIEKLARGS  192 (219)
T ss_dssp             ECHHHHHHHHHHHHHHHTTC
T ss_pred             eCHHHHHHHHHHHHHHHcCC
Confidence            99999999999999999653

>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=99.62  E-value=6.1e-16  Score=123.53  Aligned_cols=74  Identities=23%  Similarity=0.399  Sum_probs=69.1

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcCcC
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVT  423 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~~~  423 (424)
                      .++.+|.||.+++|+||||+|++|++|+++|||+|+|++..++..+|.|+|+|++++|++|+.||+++|++..+
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            58899999999999999999999999999999999999766667889999999999999999999999987654

>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=99.62  E-value=4.7e-16  Score=123.42  Aligned_cols=72  Identities=26%  Similarity=0.507  Sum_probs=67.7

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|+|+++.+++++|.|+|+|++++|++|+.||+++|.+
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            368899999999999999999999999999999999999776778899999999999999999999999875

>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=99.60  E-value=1e-15  Score=117.87  Aligned_cols=71  Identities=21%  Similarity=0.438  Sum_probs=64.2

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCC---CCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP---KPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~---~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      ..+.+|.||.+++|+||||+|++|++|+++|||+|+|++.   .+++.++.|+|+|++++|++|+.||+++|.+
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            3678999999999999999999999999999999999853   3456789999999999999999999998865

>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=99.59  E-value=1.4e-15  Score=116.03  Aligned_cols=69  Identities=16%  Similarity=0.325  Sum_probs=64.7

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      .++.+|.||.+.+|+||||+|++|++|+++|||+|+|++.  +..+|+|+|+|++++|++|+.+|.++|++
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC--CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            5789999999999999999999999999999999999864  56789999999999999999999999975

>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=99.57  E-value=1.7e-15  Score=118.19  Aligned_cols=69  Identities=26%  Similarity=0.344  Sum_probs=62.7

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      ...+.+|.||.+++|+||||+|++||+|+++|||+|+|+..   .++++|+|+|++++|++|+.+|++++..
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 GQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR---DKEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS---SSCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC---CCCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            46899999999999999999999999999999999999743   2468999999999999999999998763

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

Probab=99.56  E-value=3.8e-15  Score=121.76  Aligned_cols=72  Identities=17%  Similarity=0.295  Sum_probs=65.4

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcCc
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGV  422 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~~  422 (424)
                      .+.+|.||.+++++||||+|++||+|+++|||+|+|++..+...+|+|+|+|++++|++|+.||+++|.+..
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~   82 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLR   82 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhccc
Confidence            468999999999999999999999999999999999865556678999999999999999999999997643

>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=99.56  E-value=1.4e-14  Score=130.07  Aligned_cols=139  Identities=18%  Similarity=0.184  Sum_probs=110.5

Q ss_pred             EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEE-----eCHHHHHHHHHHHHHHHHhhc
Q 014452          136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI-----GNYHSVQDALFHITSRLRETI  210 (424)
Q Consensus       136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~-----G~~~~v~~A~~~I~~~l~~~~  210 (424)
                      .++.||.+.+|.|||++|++++.|++.++++|++..          .++.|+|+     |++.++.+|..+|..+.+..-
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          46678888     999999999999988877541


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCC
Q 014452          211 FPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIP  290 (424)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~  290 (424)
                      .+.                                                           +..              .
T Consensus        76 ~e~-----------------------------------------------------------A~~--------------L   82 (191)
T 1tua_A           76 PEK-----------------------------------------------------------AFR--------------L   82 (191)
T ss_dssp             HHH-----------------------------------------------------------HGG--------------G
T ss_pred             HHH-----------------------------------------------------------hhh--------------c
Confidence            000                                                           000              0


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEec----------cC
Q 014452          291 FPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIP----------QL  360 (424)
Q Consensus       291 ~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP----------~~  360 (424)
                                                                 ++            .......+.|+          .+
T Consensus        83 -------------------------------------------l~------------Dd~~~e~i~i~~~~~~~~~~~~r  107 (191)
T 1tua_A           83 -------------------------------------------LE------------EDQILVVVDLKQVVGDSQNHLKR  107 (191)
T ss_dssp             -------------------------------------------GS------------TTEEEEEEETHHHHTTCHHHHHH
T ss_pred             -------------------------------------------cc------------CcceeEEEEcccccccCchhHHH
Confidence                                                       00            00112223333          34


Q ss_pred             cccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHH
Q 014452          361 YMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       361 ~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~  419 (424)
                      ..|+||||+|++|+.|+..|||+|.|++       .+|.|.|++++++.|+..|.++|.
T Consensus       108 ~~GrIIGk~G~tik~iE~~Tg~~I~v~~-------~~v~i~G~~~~i~~Ar~~i~~li~  159 (191)
T 1tua_A          108 IKGRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGDYERAMAAKQAIEMLAE  159 (191)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS-------SEEEEEEEHHHHHHHHHHHHHHHT
T ss_pred             HhhheeCCCccHHHHHHHHHCceEEEcC-------CEEEEEeChHHHHHHHHHHHHHHc
Confidence            6799999999999999999999999963       389999999999999999999996

>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=99.56  E-value=3.6e-15  Score=117.80  Aligned_cols=71  Identities=21%  Similarity=0.441  Sum_probs=65.1

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCC---CCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP---KPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~---~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~  421 (424)
                      .+.+|.||.+++|+|||++|++|++|+++|||+|.|++.   .+++.++.|+|+|++++|+.|+.||+++|.+.
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 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            578999999999999999999999999999999999853   24667899999999999999999999998764

>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=99.55  E-value=5.7e-15  Score=118.35  Aligned_cols=73  Identities=15%  Similarity=0.328  Sum_probs=66.1

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCC--CCCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP--GATEGVVMVSGTSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~--~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~  421 (424)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|+|++...  ...+|.|+|+|++++|++|+.||+++|.+.
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            4689999999999999999999999999999999999986432  347899999999999999999999999764

>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=99.55  E-value=3.1e-15  Score=134.36  Aligned_cols=135  Identities=20%  Similarity=0.345  Sum_probs=101.4

Q ss_pred             EEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHhh--cCC
Q 014452           52 FKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEI--GFE  129 (424)
Q Consensus        52 ~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e~--~~~  129 (424)
                      ++++||.+.+|.|||++|++++.|++++|++|++     +..++.|+|+.......     ..++.++.+.+...  +++
T Consensus         6 ~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~i-----d~~~~~V~i~t~~~t~d-----p~~i~KA~dlI~ai~rgf~   75 (191)
T 1tua_A            6 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITV-----DTENSMVIVEPEAEGIP-----PVNLMKAAEVVKAISLGFP   75 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEE-----ETTTTEEEEEESSTTSC-----HHHHHHHHHHHHHHHHTCC
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEE-----EcCCCeEEEEeCCCCCC-----HHHHHHHHHHHHHHHcCCC
Confidence            5899999999999999999999999999999999     45678899883321111     22344444433221  111


Q ss_pred             --------CCcceEEEEEecC----------CCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC
Q 014452          130 --------PGQAVVARLLVHS----------QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN  191 (424)
Q Consensus       130 --------~~~~~t~~l~IP~----------~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~  191 (424)
                              .++.+...+.|+.          ...|+|||++|.+|+.|++.|||+|.|..            +.|.|.|+
T Consensus        76 ~e~A~~Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~~------------~~v~i~G~  143 (191)
T 1tua_A           76 PEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGE------------YEVAIIGD  143 (191)
T ss_dssp             HHHHGGGGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEECS------------SEEEEEEE
T ss_pred             HHHhhhcccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEcC------------CEEEEEeC
Confidence                    1222333454552          35799999999999999999999998842            26999999


Q ss_pred             HHHHHHHHHHHHHHHHh
Q 014452          192 YHSVQDALFHITSRLRE  208 (424)
Q Consensus       192 ~~~v~~A~~~I~~~l~~  208 (424)
                      .++++.|+..|++++..
T Consensus       144 ~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          144 YERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             HHHHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHHcC
Confidence            99999999999999964

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

Probab=99.54  E-value=7.9e-15  Score=120.31  Aligned_cols=71  Identities=23%  Similarity=0.290  Sum_probs=63.9

Q ss_pred             EEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCC---CCCCCcEEEEEcCHHHHHHHHHHHHHHHHcCc
Q 014452          352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPK---PGATEGVVMVSGTSDQMRAAQSLIHAFILCGV  422 (424)
Q Consensus       352 t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~---~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~~  422 (424)
                      +.+|.||.+++|+||||+|++|++|+++|||+|+|++..   .+..+++|+|+|++++|++|+.||+++|.+..
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~   81 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhccc
Confidence            689999999999999999999999999999999998642   23467999999999999999999999987643

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

Probab=99.54  E-value=2.4e-14  Score=112.52  Aligned_cols=70  Identities=13%  Similarity=0.272  Sum_probs=63.8

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCC--CCCCCcEEEEEcCHHHHHHHHHHHHHHHH
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPK--PGATEGVVMVSGTSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~--~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~  419 (424)
                      ..+.+|.||.+++|+||||+|++|++|+++|||+|.|++..  +...+|.|+|+|+++++++|+.+|++++.
T Consensus        13 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~   84 (85)
T 2opv_A           13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILR   84 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhc
Confidence            46789999999999999999999999999999999998642  34678999999999999999999999885

>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=99.50  E-value=4.9e-14  Score=115.05  Aligned_cols=72  Identities=22%  Similarity=0.356  Sum_probs=64.7

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCC--CCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPG--ATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~--~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|++..++  ..++.|+|+|++++|++|+.||+++|..
T Consensus        13 ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T 1we8_A           13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            35789999999999999999999999999999999999864332  2589999999999999999999999864

>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=99.48  E-value=3.1e-14  Score=108.52  Aligned_cols=70  Identities=27%  Similarity=0.527  Sum_probs=64.5

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHh
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  208 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  208 (424)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|.+.       +..+|.|+|+|+++++.+|+.+|.++|++
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~-------~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-------CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            45789999999999999999999999999999999999754       25689999999999999999999999976

>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=99.46  E-value=1.5e-13  Score=107.13  Aligned_cols=73  Identities=19%  Similarity=0.494  Sum_probs=65.9

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ..++.+|.||.+++|.||||+|++|++|+++|||+|+|.+.     ++++.+|.|+|+|++++|++|+.+|.+++.+.
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~-----~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT-----TSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC-----CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            46789999999999999999999999999999999999642     22467899999999999999999999999876

>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=99.46  E-value=9.3e-14  Score=106.79  Aligned_cols=73  Identities=25%  Similarity=0.420  Sum_probs=63.9

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHh
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  208 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  208 (424)
                      .+.+|.||.+.+|+|||++|++|++|+++|||+|+|.+.++.  .+++.++.|+|+|+++++.+|+.+|.+++.+
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~--~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEF--LPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCC--STTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCC--CCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999764332  2346789999999999999999999998765

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

Probab=99.46  E-value=8.2e-14  Score=105.59  Aligned_cols=67  Identities=13%  Similarity=0.308  Sum_probs=61.2

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFI  418 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i  418 (424)
                      ..+.+|.||.+++|.|||++|++|++|+++|||+|.|++.  +..++.|+|+|++++|++|+.+|++.+
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            5789999999999999999999999999999999999753  346789999999999999999998753

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

Probab=99.45  E-value=8e-14  Score=107.16  Aligned_cols=73  Identities=29%  Similarity=0.511  Sum_probs=65.8

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ..++.+|.||.+++|.|||++|++|++|+++|||+|+|.+.     ++++.+|.|+|+|+++++.+|+.+|.+++.++
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~-----~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP-----VEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC-----CTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC-----CCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            45788999999999999999999999999999999999742     23478999999999999999999999998764

>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=99.44  E-value=1.2e-13  Score=107.82  Aligned_cols=74  Identities=27%  Similarity=0.508  Sum_probs=65.1

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ...++.+|.||.+++|.||||+|++|++|+++|||+|+|.+.     ++++.+|.|+|+|+++++.+|+.+|.+++.+.
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            346789999999999999999999999999999999999753     23468999999999999999999999998776

>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=99.44  E-value=2.4e-13  Score=109.34  Aligned_cols=72  Identities=17%  Similarity=0.271  Sum_probs=64.1

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCC-CCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPK-PGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~-~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      ..++.+|.||.++++.|||++|++|++|+++|||+|.|++.. +...++.|+|+|++++|++|+.+|++.+..
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            467999999999999999999999999999999999998542 223678999999999999999999998763

>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=99.42  E-value=2e-13  Score=109.32  Aligned_cols=71  Identities=17%  Similarity=0.289  Sum_probs=63.8

Q ss_pred             CcceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          348 LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       348 ~~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      .++++.+|.||.+++|.|||++|++|++|+++|||+|.|++..  ..++.|+|+|++++|++|+.+|++.+..
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~--~~~~~V~I~G~~e~v~~A~~~I~~i~~~   84 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD--DPSNQIKITGTKEGIEKARHEVLLISAE   84 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT--SSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC--CCCCeEEEEECHHHHHHHHHHHHHHhhc
Confidence            3568999999999999999999999999999999999997432  3458999999999999999999998864

>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=99.42  E-value=2.9e-13  Score=108.43  Aligned_cols=71  Identities=13%  Similarity=0.140  Sum_probs=63.8

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      ..++.+|.||.++++.|||++|++|++|+++|||+|+|++.. ...++.|+|+|++++|++|+.+|+++++.
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            468899999999999999999999999999999999997532 23568999999999999999999998864

>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=99.40  E-value=2.6e-13  Score=107.51  Aligned_cols=74  Identities=20%  Similarity=0.517  Sum_probs=66.7

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ...++.+|.||.+.+|.||||+|++|++|+++|||+|+|.+.     ++.+.+|.|+|+|++++|++|+.+|.+++.+.
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~-----~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC-----CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC-----CCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            456889999999999999999999999999999999999642     22467899999999999999999999999886

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

Probab=99.40  E-value=7e-13  Score=104.11  Aligned_cols=74  Identities=20%  Similarity=0.437  Sum_probs=64.6

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHh
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  208 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  208 (424)
                      ...+.+|.||.+.+|+||||+|++||+|+++|||+|+|..+...   ....+|.|+|+|+++++++|+.+|.+++.+
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            45678999999999999999999999999999999999754321   236789999999999999999999998864

>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=99.39  E-value=2.7e-13  Score=107.03  Aligned_cols=74  Identities=24%  Similarity=0.414  Sum_probs=65.5

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      .+++|.||.+.+|+|||++|++|++|+++|||+|+|.+.++.  .+++.+|.|+|+|+++++.+|+.+|.+++.+.
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 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEF--LPGTRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCB--STTSCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCC--CCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            478999999999999999999999999999999999764321  23467899999999999999999999999875

>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=99.39  E-value=5.3e-13  Score=106.38  Aligned_cols=74  Identities=22%  Similarity=0.401  Sum_probs=66.6

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ...++.+|.||.+++|+||||+|++|++|+++|||+|+|.+..     .+..+|.|+|+|++++|++|+.+|.+++++.
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            3457899999999999999999999999999999999997542     2357899999999999999999999999886

>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=99.38  E-value=2.4e-13  Score=105.94  Aligned_cols=71  Identities=18%  Similarity=0.270  Sum_probs=63.4

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ....+++|.||.+++|.||||+|++||+|+++|||+|+|+..+        .++.|+|+|+++++++|+.+|.+++...
T Consensus         7 ~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~--------~~~~v~ItG~~e~v~~A~~~I~~~i~~r   77 (83)
T 2dgr_A            7 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD--------KEPVFAVTGMPENVDRAREEIEAHITLR   77 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS--------SCCEEEEEECTTTHHHHHHHHHHHHHSC
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC--------CCCeEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            4567899999999999999999999999999999999997532        3688999999999999999999977654

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

Probab=99.36  E-value=6.9e-13  Score=108.69  Aligned_cols=73  Identities=21%  Similarity=0.396  Sum_probs=64.1

Q ss_pred             EEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      +++|.||.+++|+||||+|++||+|+++|||+|+|.++. .+ .....+|.|+|+|+.++|++|+.+|.+++.+.
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            679999999999999999999999999999999997542 22 22357899999999999999999999998776

>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=99.36  E-value=5e-13  Score=106.99  Aligned_cols=76  Identities=16%  Similarity=0.379  Sum_probs=66.7

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ...++.+|.||.+++|+||||+|++||+|+++|||+|+|.++...   ....+|.|+|+|++++|++|+.+|.+++.+.
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            456889999999999999999999999999999999999754321   1247899999999999999999999999775

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

Probab=99.36  E-value=8.5e-13  Score=107.76  Aligned_cols=71  Identities=20%  Similarity=0.385  Sum_probs=63.9

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      .+++|.||.+.+++||||+|++||+|+++|+|+|+|.+++     ....+|.|+|+|++++|++|+.+|.+++.+.
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 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-----GTGPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC-----SSSSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC-----CCCceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            3679999999999999999999999999999999997532     1356899999999999999999999999887

>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=99.35  E-value=9e-13  Score=107.33  Aligned_cols=69  Identities=19%  Similarity=0.261  Sum_probs=62.5

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      ..+.+|.||.+++|.|||++|++|++|+++|||+|.|++.  +...+.|+|+|++++|++|+.+|++.+..
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            4789999999999999999999999999999999999753  33457999999999999999999998864

>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=99.33  E-value=2.9e-12  Score=104.51  Aligned_cols=76  Identities=22%  Similarity=0.402  Sum_probs=65.8

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ....+.+|.||.+.+|+||||+|++|++|+++|||+|+|.+..+.   ..+.++.|+|+|+.+++.+|+.+|.+++.+.
T Consensus        12 ~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~---~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG---TLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC---SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCC---CCCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            345788999999999999999999999999999999999754321   1246899999999999999999999999765

>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=99.31  E-value=3.2e-12  Score=102.35  Aligned_cols=75  Identities=20%  Similarity=0.248  Sum_probs=66.7

Q ss_pred             CCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          130 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       130 ~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ....++.+|.||.++++.|||++|++|++|+++|||+|+|+++.+      ..++.|+|+|.+++|++|+.+|..++++.
T Consensus        13 l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~------~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   86 (95)
T 2ctm_A           13 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA------PDPNCVTVTGLPENVEEAIDHILNLEEEY   86 (95)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC------SCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC------CCCcEEEEEcCHHHHHHHHHHHHHHHHHH
Confidence            355688999999999999999999999999999999999965321      35789999999999999999999999887


Q ss_pred             c
Q 014452          210 I  210 (424)
Q Consensus       210 ~  210 (424)
                      .
T Consensus        87 ~   87 (95)
T 2ctm_A           87 L   87 (95)
T ss_dssp             H
T ss_pred             H
Confidence            4

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

Probab=99.30  E-value=1.9e-12  Score=98.02  Aligned_cols=68  Identities=15%  Similarity=0.285  Sum_probs=60.2

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHH
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL  206 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  206 (424)
                      ...+.+|.||.++++.|||++|++|++|+++|||+|+|++..       ..+|.|+|+|+.+++++|+.+|.+++
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-------~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-------CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            346789999999999999999999999999999999997532       36789999999999999999998753

>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=99.30  E-value=3.3e-12  Score=102.17  Aligned_cols=72  Identities=13%  Similarity=0.245  Sum_probs=65.0

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ...++.+|.||.+.+|.|||++|++|++|+++|||+|+|++.+       ..++.|+|+|+.+++.+|+.+|.+++.+.
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-------~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-------SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-------CCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            4568899999999999999999999999999999999997532       24578999999999999999999999886

>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=99.29  E-value=5.7e-12  Score=101.27  Aligned_cols=73  Identities=18%  Similarity=0.274  Sum_probs=64.7

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      .++++|.||..+++.|||++|++|++|+++|||+|+|++..+    ....+|.|+|+|+.+++.+|+.+|..++.+.
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~----~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~   88 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD----GNQPQDQITITGYEKNTEAARDAILRIVGEL   88 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT----CSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC----CCCCccEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            468899999999999999999999999999999999975431    1246889999999999999999999998765

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

Probab=99.27  E-value=6.1e-12  Score=123.69  Aligned_cols=151  Identities=15%  Similarity=0.117  Sum_probs=103.5

Q ss_pred             cEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCC--CCcccEEEeecccccccccChhHHHHHHHHHHHHhh
Q 014452           49 EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILP--DSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEI  126 (424)
Q Consensus        49 ~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~--~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e~  126 (424)
                      .+++.+.+|...++.  ..-+..|.+ ++.++++|.|+....  +.....|+|+|...++..   +.+|+..+.+.+.+.
T Consensus       105 Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~~nv~~---akeA~~~Ll~~l~~~  178 (376)
T 3n89_A          105 HFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKNGIVTTYLRITAREKNQHE---LIEAAKRLNEILFRE  178 (376)
T ss_dssp             EEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC-----CEEEEEEEEEGGGHHH---HHHHHHHHHHHHCC-
T ss_pred             CceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCcccccCCCCCEEEEEcChhhHHH---HHHHHHHHHHHHHhh
Confidence            345667777654443  122345555 567999999964311  123678999999877654   455555555555443


Q ss_pred             cCCCCcceEEEEEecCCCcceeeccCC--chHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHH
Q 014452          127 GFEPGQAVVARLLVHSQQIGCLLGRGG--HIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITS  204 (424)
Q Consensus       127 ~~~~~~~~t~~l~IP~~~vg~IIGkgG--~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~  204 (424)
                      .......++++|.|+..+|..|||++|  ..|++|+++|||+|.++..++. +........|+|+|+.++|.+|+..|.+
T Consensus       179 e~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~-~d~~~~~~~ItItGs~e~V~~Ark~I~~  257 (376)
T 3n89_A          179 SPAPENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNR-NETRGNIYEIKVVGNIDNVLKARRYIMD  257 (376)
T ss_dssp             -CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC----------CCEEEEEEESCHHHHHHHHHHHHH
T ss_pred             hcccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCc-ccccCCceEEEEEeCHHHHHHHHHHHHh
Confidence            233456789999999999999999999  5669999999999999754321 1111245689999999999999999999


Q ss_pred             HH
Q 014452          205 RL  206 (424)
Q Consensus       205 ~l  206 (424)
                      +|
T Consensus       258 lL  259 (376)
T 3n89_A          258 LL  259 (376)
T ss_dssp             TS
T ss_pred             hC
Confidence            88

>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=99.26  E-value=9.3e-12  Score=99.47  Aligned_cols=72  Identities=17%  Similarity=0.244  Sum_probs=65.0

Q ss_pred             CcceEEEEEeccCcccceeccccchHHHHHHHh-CCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452          348 LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQIS-GANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       348 ~~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S-Ga~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~  421 (424)
                      .+.++.+|.||.++++.|||++|++|++|+++| ||+|.|++  ++...+.|+|.|+.++|++|+.+|++.+..-
T Consensus        14 ~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~--~g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~   86 (95)
T 2ctj_A           14 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV--EGSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   86 (95)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCC--TTTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCC--CCCCcceEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            457889999999999999999999999999999 99999964  4456779999999999999999999998753

>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=99.23  E-value=1.6e-11  Score=99.50  Aligned_cols=66  Identities=20%  Similarity=0.322  Sum_probs=60.4

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHH-hCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQI-SGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~-SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      ..+.+|.||..++++|||++|++|++|+++ ++++|.+++     .++.|+|+|++++|++|+.+|++.+++
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-----~~~~ItI~G~~~~V~~a~~~I~~~v~e   92 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTEDVSVAQEQIEGMVKD   92 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-----CCCEEEEECCHHHHHHHHHHHHHHHHH
Confidence            378999999999999999999999999997 599999974     457999999999999999999998874

>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=99.19  E-value=1.9e-11  Score=99.47  Aligned_cols=70  Identities=17%  Similarity=0.226  Sum_probs=62.5

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ..+.+|.||.+.++.|||++|++|++|+++|||+|+|++..       ...+.|+|+|+.+++++|+.+|..++.+.
T Consensus        16 p~~~~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           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAANLDRAKAGLLERVKEL   85 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-------TTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-------CCcceEEEEcCHHHHHHHHHHHHHHHhhH
Confidence            47889999999999999999999999999999999997532       24568999999999999999999998764

>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=99.11  E-value=6.3e-11  Score=94.62  Aligned_cols=73  Identities=14%  Similarity=0.206  Sum_probs=65.7

Q ss_pred             CCcceEEEEEecCCCcceeeccCCchHHHHHhhc-CceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHh
Q 014452          130 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRAT-GASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  208 (424)
Q Consensus       130 ~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~t-ga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  208 (424)
                      .++.++..|.||.++++.|||++|++|++|+++| ||+|+|++..       +..+.|+|+|+.++|++|+.+|..++.+
T Consensus        13 ~~~~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           13 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-------SGSDTVVIRGPSSDVEKAKKQLLHLAEE   85 (95)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-------TTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             HhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC-------CCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            4567789999999999999999999999999999 9999996432       4567899999999999999999999987


Q ss_pred             h
Q 014452          209 T  209 (424)
Q Consensus       209 ~  209 (424)
                      .
T Consensus        86 ~   86 (95)
T 2ctj_A           86 K   86 (95)
T ss_dssp             H
T ss_pred             h
Confidence            6

>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=99.06  E-value=9.7e-11  Score=92.02  Aligned_cols=66  Identities=18%  Similarity=0.367  Sum_probs=59.3

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCE-EEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGAN-VVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~-I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~  419 (424)
                      ..+..+|.||.+++|.|||++|++|++|+++|||+ |.|++     ++.+|+|.| +.+++++|+.+|+...+
T Consensus        13 ~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e-----ddG~V~I~g~~~ea~~~A~~~I~~ie~   80 (91)
T 2cpq_A           13 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-----DTGTFRIYGESADAVKKARGFLEFVED   80 (91)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHSCCCC
T ss_pred             CceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc-----CCCEEEEEECCHHHHHHHHHHHHhhhe
Confidence            46889999999999999999999999999999998 99963     348999999 99999999999976543

>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=99.04  E-value=4.2e-10  Score=91.08  Aligned_cols=67  Identities=13%  Similarity=0.195  Sum_probs=60.7

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhh-cCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRA-TGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~-tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      .++.+|.||.++|+.|||++|++|++|+++ ++++|+|+.          .++.|+|+|+++.|.+|+.+|..++++.
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~----------~~~~ItI~G~~~~V~~a~~~I~~~v~el   93 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVKDL   93 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC----------CCCEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            378999999999999999999999999997 499999863          3568999999999999999999999876

>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=7.5e-09  Score=87.39  Aligned_cols=73  Identities=18%  Similarity=0.270  Sum_probs=61.5

Q ss_pred             CcceEEEEEeccC------cccceeccccchHHHHHHHhCCEEEEeCCC----------------CCCCCcEEEEEc-CH
Q 014452          348 LTSTTIEVVIPQL------YMAHVYGENNSNLSHIRQISGANVVVNDPK----------------PGATEGVVMVSG-TS  404 (424)
Q Consensus       348 ~~~~t~~v~IP~~------~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~----------------~~~~~r~i~I~G-t~  404 (424)
                      ....+.+|.||.+      ++|.|||++|++||+|+++|||+|.|...-                ....+-.|.|++ +.
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            3568999999988      889999999999999999999999996410                112356888999 89


Q ss_pred             HHHHHHHHHHHHHHHc
Q 014452          405 DQMRAAQSLIHAFILC  420 (424)
Q Consensus       405 e~v~~A~~lI~~~i~~  420 (424)
                      +.+++|+.+|+++|..
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

>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=1.8e-08  Score=83.47  Aligned_cols=71  Identities=18%  Similarity=0.194  Sum_probs=57.2

Q ss_pred             ceEEEEEeccC-------cccceeccccchHHHHHHHhCCEEEEeCCC----------CCCCCcEEEEEc-CHHHHHHHH
Q 014452          350 STTIEVVIPQL-------YMAHVYGENNSNLSHIRQISGANVVVNDPK----------PGATEGVVMVSG-TSDQMRAAQ  411 (424)
Q Consensus       350 ~~t~~v~IP~~-------~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~----------~~~~~r~i~I~G-t~e~v~~A~  411 (424)
                      ..+.+|.||.+       ++|.|||++|++||+|+++|||+|.|...-          +..++-.|.|++ +++++++|+
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            46778887765       789999999999999999999999996221          011334788876 899999999


Q ss_pred             HHHHHHHHc
Q 014452          412 SLIHAFILC  420 (424)
Q Consensus       412 ~lI~~~i~~  420 (424)
                      .||+++|..
T Consensus        91 ~~Ie~Ll~~   99 (119)
T 2yqr_A           91 KLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhhc
Confidence            999999864

>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=98.68  E-value=1.7e-08  Score=79.16  Aligned_cols=67  Identities=16%  Similarity=0.241  Sum_probs=57.4

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCce-EEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGAS-IRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRE  208 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~-I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  208 (424)
                      ..+...|.||.+.++.|||++|++|++|+++|||+ |.+..          .+..|+|.| +.+++++|+.+|..+.+.
T Consensus        13 ~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e----------ddG~V~I~g~~~ea~~~A~~~I~~ie~~   81 (91)
T 2cpq_A           13 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----------DTGTFRIYGESADAVKKARGFLEFVEDF   81 (91)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----------TTTEEEEEESSHHHHHHHHHHHSCCCCC
T ss_pred             CceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc----------CCCEEEEEECCHHHHHHHHHHHHhhheE
Confidence            45778999999999999999999999999999998 99952          246799999 899999999888654433

>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=98.51  E-value=2.8e-07  Score=77.70  Aligned_cols=77  Identities=18%  Similarity=0.280  Sum_probs=61.4

Q ss_pred             ceEEEEEecCC------CcceeeccCCchHHHHHhhcCceEEEecCCCC-----------CCCCCCCCcEEEEEe-CHHH
Q 014452          133 AVVARLLVHSQ------QIGCLLGRGGHIVSEMRRATGASIRVFPKDQA-----------PRCGSPHDEIVQVIG-NYHS  194 (424)
Q Consensus       133 ~~t~~l~IP~~------~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~-----------p~~~~~~~r~v~I~G-~~~~  194 (424)
                      .++.++.||.+      ++|.|||++|.+||+|+++|||+|.|..+...           +......+-.|.|++ +.+.
T Consensus         6 k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~   85 (131)
T 1k1g_A            6 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   85 (131)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             eEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHH
Confidence            46788999988      78899999999999999999999999763211           011112355788999 5889


Q ss_pred             HHHHHHHHHHHHHhh
Q 014452          195 VQDALFHITSRLRET  209 (424)
Q Consensus       195 v~~A~~~I~~~l~~~  209 (424)
                      +.+|+++|.++|.+.
T Consensus        86 ~~~A~~~I~~ll~~~  100 (131)
T 1k1g_A           86 VKKAVEQIRNILKQG  100 (131)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHhcc
Confidence            999999999999775

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

Probab=98.42  E-value=4.4e-07  Score=75.05  Aligned_cols=77  Identities=16%  Similarity=0.108  Sum_probs=57.4

Q ss_pred             ceEEEEEecCC-------CcceeeccCCchHHHHHhhcCceEEEecCCCC---C--CCCCCCCcEEEEEe-CHHHHHHHH
Q 014452          133 AVVARLLVHSQ-------QIGCLLGRGGHIVSEMRRATGASIRVFPKDQA---P--RCGSPHDEIVQVIG-NYHSVQDAL  199 (424)
Q Consensus       133 ~~t~~l~IP~~-------~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~---p--~~~~~~~r~v~I~G-~~~~v~~A~  199 (424)
                      .++.++.||.+       ++|.|||++|.+||+|+++|||+|.|..+...   +  ......+-.|.|.+ +.+++++|+
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            35677888765       67999999999999999999999999643210   0  00112334677776 599999999


Q ss_pred             HHHHHHHHhh
Q 014452          200 FHITSRLRET  209 (424)
Q Consensus       200 ~~I~~~l~~~  209 (424)
                      .+|.+++.+.
T Consensus        91 ~~Ie~Ll~~v  100 (119)
T 2yqr_A           91 KLCENLLQTV  100 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHhhch
Confidence            9999999753

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.25  E-value=7.2e-07  Score=75.65  Aligned_cols=69  Identities=9%  Similarity=0.257  Sum_probs=53.3

Q ss_pred             eEEEEEecc------CcccceeccccchHHHHHHHhCCEEEEeCCCC------------------CCCCcEEEEEc-CHH
Q 014452          351 TTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVNDPKP------------------GATEGVVMVSG-TSD  405 (424)
Q Consensus       351 ~t~~v~IP~------~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~------------------~~~~r~i~I~G-t~e  405 (424)
                      .+.+|.||.      +++|.|||++|+++|+|+++|||+|.|...-.                  ...+=-|.|++ +++
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            456777774      45999999999999999999999999974211                  11123788888 443


Q ss_pred             -----HHHHHHHHHHHHHH
Q 014452          406 -----QMRAAQSLIHAFIL  419 (424)
Q Consensus       406 -----~v~~A~~lI~~~i~  419 (424)
                           .+++|+.+|+.+|.
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                 79999999999875

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

Probab=98.02  E-value=1.5e-05  Score=66.28  Aligned_cols=68  Identities=10%  Similarity=0.234  Sum_probs=60.2

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHH
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~  419 (424)
                      ...-+.|....++.|+|++|+.|++|+..|.|.|+|+.-.+ +.+..|+|.|++..-..|+.||+....
T Consensus        56 dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s-~g~tEVtIfG~~~~Q~rak~MI~sLA~  123 (140)
T 3v69_A           56 DPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP-ERRAEIWIFGPPPFRRDVDRMLTDLAH  123 (140)
T ss_dssp             SCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT-TSCEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC-CCcEEEEEECCHHHHHHHHHHHHHHHH
Confidence            34668899999999999999999999999999999986533 467899999999999999999988754

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.00  E-value=6e-06  Score=69.97  Aligned_cols=74  Identities=20%  Similarity=0.247  Sum_probs=54.2

Q ss_pred             eEEEEEecCCC------cceeeccCCchHHHHHhhcCceEEEecCCCCC------------CC-CCCCCcEEEEEeC-HH
Q 014452          134 VVARLLVHSQQ------IGCLLGRGGHIVSEMRRATGASIRVFPKDQAP------------RC-GSPHDEIVQVIGN-YH  193 (424)
Q Consensus       134 ~t~~l~IP~~~------vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p------------~~-~~~~~r~v~I~G~-~~  193 (424)
                      ++.++.||.+.      +|.|||++|.++|+|+++|||+|.|-.+...-            .. ....+--|.|++. .+
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            46688888764      89999999999999999999999997643210            00 0112236888884 32


Q ss_pred             -----HHHHHHHHHHHHHH
Q 014452          194 -----SVQDALFHITSRLR  207 (424)
Q Consensus       194 -----~v~~A~~~I~~~l~  207 (424)
                           .+.+|+.+|.++|.
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                 78899988888775

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.97  E-value=3.5e-06  Score=88.65  Aligned_cols=62  Identities=23%  Similarity=0.280  Sum_probs=54.5

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHH
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFI  418 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i  418 (424)
                      ....|.||.+.++.|||+||++||.|+++|||+|.|.+      +.+|.|.+ +.+.+++|+.+|++.+
T Consensus       567 ~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d------~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          567 VVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD------EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS------SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             eEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC------CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            46889999999999999999999999999999999953      46899998 5789999999998765

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.75  E-value=2.1e-05  Score=82.73  Aligned_cols=63  Identities=22%  Similarity=0.281  Sum_probs=53.6

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHHHHHH
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHITSRL  206 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l  206 (424)
                      .....|.||.+.++.|||++|++||.|+++|||+|.|..           +..|.|.+. .+.+.+|+.+|..++
T Consensus       566 p~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d-----------~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          566 PVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD-----------EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             CEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS-----------SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             CeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC-----------CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            456789999999999999999999999999999999952           346999996 688999999887654

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

Probab=97.71  E-value=7.4e-05  Score=62.12  Aligned_cols=68  Identities=15%  Similarity=0.151  Sum_probs=60.1

Q ss_pred             EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      +.|.|....++.|+|++|+.|++|+..|++.|++..-+      .+....|+|.|++..-.+|+.+|..++..+
T Consensus        58 lVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~------s~g~tEVtIfG~~~~Q~rak~MI~sLA~~h  125 (140)
T 3v69_A           58 KRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWG------PERRAEIWIFGPPPFRRDVDRMLTDLAHYC  125 (140)
T ss_dssp             EEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC------TTSCEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC------CCCcEEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            57889999999999999999999999999999997532      146778999999999999999999988654

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.65  E-value=1.1e-05  Score=68.71  Aligned_cols=101  Identities=20%  Similarity=0.347  Sum_probs=72.0

Q ss_pred             EEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHH--HHHhhc
Q 014452           50 VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHS--RIAEIG  127 (424)
Q Consensus        50 ~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~--~i~e~~  127 (424)
                      -.+.++|+...+|+.||++|++|+.|+++.|-+|.|-+.           +..+         ..-+..++.  .+....
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~-----------s~d~---------~~fI~naLsPA~V~~V~   95 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEY-----------SSDL---------ERIVKNLFPGVKIESIN   95 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEEC-----------CSSH---------HHHHHHHSTTSCEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEc-----------CCCH---------HHHHHHhcCCceEEEEE
Confidence            356889999999999999999999999999999998432           1111         001111110  000000


Q ss_pred             CC-CCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEe
Q 014452          128 FE-PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVF  170 (424)
Q Consensus       128 ~~-~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~  170 (424)
                      .. .++.....+.||.++.+..|||+|.+++-..+-||.+|.|.
T Consensus        96 i~~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           96 VRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             EEEETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             EeecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            11 02345678899999999999999999999999999988774

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.21  E-value=6.7e-05  Score=79.90  Aligned_cols=62  Identities=29%  Similarity=0.396  Sum_probs=11.7

Q ss_pred             EEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452          352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       352 t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~  419 (424)
                      ...+.||.+.++.|||+||.+||.|.++||++|.|.+      +..|.|.+ +.+.+++|+.+|+.++.
T Consensus       571 ~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d------dG~v~I~~~~~~~~~~A~~~i~~i~~  633 (726)
T 4aid_A          571 IETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND------DGVVKVSASDGAKIKAAIDWIKSITD  633 (726)
T ss_dssp             -------------------------------------------------CCSCHHHHHHHHHC------
T ss_pred             EEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC------CceEEEEeCCHHHHHHHHHHHHHHhh
Confidence            5779999999999999999999999999999999953      35678877 68999999999988764

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.01  E-value=0.00027  Score=75.22  Aligned_cols=66  Identities=23%  Similarity=0.389  Sum_probs=12.1

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHHHHHHHhh
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHITSRLRET  209 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  209 (424)
                      .....+.||.+.++.|||+||.+||.|.++||++|.+..           +..|.|.+. .+++++|+.+|..++.+.
T Consensus       569 p~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d-----------dG~v~I~~~~~~~~~~A~~~i~~i~~~~  635 (726)
T 4aid_A          569 PKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND-----------DGVVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             CC------------------------------------------------------CCSCHHHHHHHHHC--------
T ss_pred             CeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC-----------CceEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence            345788999999999999999999999999999998852           234778775 889999999998888654

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=96.88  E-value=0.00048  Score=58.62  Aligned_cols=39  Identities=31%  Similarity=0.490  Sum_probs=35.5

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK  172 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~  172 (424)
                      -.+.+.|+...+|..||++|++|+.|+++.|-+|++..-
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~   74 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEY   74 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEEC
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEc
Confidence            457889999999999999999999999999999999764

>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=96.21  E-value=0.0052  Score=56.82  Aligned_cols=95  Identities=24%  Similarity=0.279  Sum_probs=64.4

Q ss_pred             cccceeeccCchHHHHH-HHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHH--HHhhcCCCCcceE
Q 014452           59 DKVGSLIGKGGSIVRTF-QNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSR--IAEIGFEPGQAVV  135 (424)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I-~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~--i~e~~~~~~~~~t  135 (424)
                      +-+|+.||++|++|+.| ++..|=+|.|-.-.           -.+         ..-+..++.-  +............
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s-----------~dp---------~~fi~nalsPA~V~~V~i~~~~~~~  185 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD-----------DDP---------ARFVANALSPAKVVSVSVIDQTARA  185 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC-----------SSH---------HHHHHHHTTTSCCSEEEEEETTTTE
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEec-----------CCH---------HHHHHhccCCcceEEEEEEcCCCcE
Confidence            45999999999999999 66678888884321           111         0011111100  0000000112246


Q ss_pred             EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCC
Q 014452          136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKD  173 (424)
Q Consensus       136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~  173 (424)
                      ..+.||..+.+.-|||+|.+++--.+-||.+|.|....
T Consensus       186 a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  223 (251)
T 2asb_A          186 ARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  223 (251)
T ss_dssp             EEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             EEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHH
Confidence            78899999999999999999999999999999997654

>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=95.90  E-value=0.0091  Score=58.29  Aligned_cols=94  Identities=26%  Similarity=0.315  Sum_probs=65.6

Q ss_pred             cccceeeccCchHHHHHHHHh-CceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHH--HHHhh-cCCCCcce
Q 014452           59 DKVGSLIGKGGSIVRTFQNET-GASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHS--RIAEI-GFEPGQAV  134 (424)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~--~i~e~-~~~~~~~~  134 (424)
                      +-+|+.||++|++|+.|.++. |=+|.|-.-.           -.+         ..-+..++.  .+... ..+ ....
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s-----------~dp---------~~fi~nalsPA~V~~V~~~~-~~~~  307 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD-----------DDP---------ARFVANALSPAKVVSVSVID-QTAR  307 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC-----------SSH---------HHHHHHHTTTSCCSEEEEEE-TTTT
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcC-----------CCH---------HHHHHHhcCCcceeEEEEEc-CCCc
Confidence            569999999999999999998 8888884321           111         001111110  00000 011 1234


Q ss_pred             EEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCC
Q 014452          135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKD  173 (424)
Q Consensus       135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~  173 (424)
                      ...+.||..+.+..|||+|.+++-..+-||.+|.|....
T Consensus       308 ~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  346 (366)
T 1k0r_A          308 AARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  346 (366)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESS
T ss_pred             EEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHH
Confidence            678999999999999999999999999999999997654

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=95.06  E-value=0.0038  Score=66.65  Aligned_cols=63  Identities=16%  Similarity=0.292  Sum_probs=0.0

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~  419 (424)
                      ....+.||.+.++.|||++|.+|+.|.++||+.|.|.+      +..|.|++ +.+.+++|+.+|+..+.
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            35778999999999999999999999999999998853      35677776 56788889888876653

>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=94.90  E-value=0.022  Score=52.67  Aligned_cols=38  Identities=16%  Similarity=0.364  Sum_probs=35.6

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeC
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  388 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~  388 (424)
                      .+..+.||.+..+..|||+|.|++--.+.||.+|.|..
T Consensus       184 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~  221 (251)
T 2asb_A          184 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG  221 (251)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             cEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceE
Confidence            46889999999999999999999999999999999973

>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=94.57  E-value=0.017  Score=56.13  Aligned_cols=94  Identities=24%  Similarity=0.417  Sum_probs=64.0

Q ss_pred             cccceeeccCchHHHHHHHHh-CceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHH--HHHhhcCCCCcceE
Q 014452           59 DKVGSLIGKGGSIVRTFQNET-GASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHS--RIAEIGFEPGQAVV  135 (424)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~--~i~e~~~~~~~~~t  135 (424)
                      +-+|+.||.+|.+|+.|.++. |=+|.|-.-           +-.+         ..-+..++.  .+............
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~-----------s~d~---------~~fi~nal~Pa~v~~v~~~d~~~~~  304 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKW-----------SDDP---------KQLIANALAPATVIEVEILDKENKA  304 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEEC-----------CSSH---------HHHHHHHTCSSCCSEEEEEETTTTE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEec-----------CCCH---------HHHHHHhcCccEEEEEEEEcCCCCE
Confidence            458999999999999999997 777877422           1111         001111110  00000010122346


Q ss_pred             EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452          136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK  172 (424)
Q Consensus       136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~  172 (424)
                      ..+.||..+.+.-|||+|.+++--..-||.+|.|...
T Consensus       305 ~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          305 ARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             EEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            7899999999999999999999999999999999754

>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=94.48  E-value=0.035  Score=54.17  Aligned_cols=39  Identities=15%  Similarity=0.364  Sum_probs=36.0

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeC
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND  388 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~  388 (424)
                      .....+.||.+..+..|||+|.|++-..+.||.+|.|..
T Consensus       306 ~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~  344 (366)
T 1k0r_A          306 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG  344 (366)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEE
T ss_pred             CcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeE
Confidence            356889999999999999999999999999999999963

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=94.23  E-value=0.017  Score=61.67  Aligned_cols=64  Identities=19%  Similarity=0.385  Sum_probs=0.0

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHHHHHHHh
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHITSRLRE  208 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~  208 (424)
                      ....+.||.+.++.+||++|.+|+.|.+++|+.|.+..           +..|.|.+. .+.+++|+.+|..++.+
T Consensus       560 ~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~-----------dg~v~I~~~~~~~~~~a~~~i~~i~~~  624 (723)
T 3cdi_A          560 RIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED-----------DGTVKIAATDGEKAKHAIRRIEEITAE  624 (723)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             eEEEEEECHHHhcccccccceeeeeeehhhCceEEecC-----------CccEEEecCCHHHHHHHHHHHHHHhhh
Confidence            44678899999999999999999999999999998842           334677664 56777787777666543

>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=94.02  E-value=0.0027  Score=68.08  Aligned_cols=60  Identities=23%  Similarity=0.444  Sum_probs=21.4

Q ss_pred             EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHH
Q 014452          353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFI  418 (424)
Q Consensus       353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i  418 (424)
                      ..|.||.+.++.|||++|.+||.|.++||+.|.|.+      +..|.|+. +.+..++|+.+|+...
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            458899999999999999999999999999999963      46788877 6788888887777654

>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=92.05  E-value=0.016  Score=62.21  Aligned_cols=61  Identities=16%  Similarity=0.266  Sum_probs=20.4

Q ss_pred             EEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHHHHHH
Q 014452          135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHITSRL  206 (424)
Q Consensus       135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l  206 (424)
                      ...|.||.+.++.+||++|.+||.|.+++|+.|.+..           +..|.|... .+..++|+..|..+.
T Consensus       599 ~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~-----------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          599 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED-----------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CCCC------------------CTTCCCCCSCC-------------------CCCBSSHHHHCC---------
T ss_pred             eEEEEEChHHeehcccccceeeehhhHhhCCEEEecC-----------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            3568899999999999999999999999999998852           334667664 666667766665544

---

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	424
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	4e-15
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	8e-11
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	1e-10
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	8e-15
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-12
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-10
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-13
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	7e-11
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	3e-09
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-13
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	3e-11
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	6e-11
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	3e-13
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	5e-10
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	7e-09
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-12
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-12
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-10
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	7e-12
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	3e-10
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	2e-08
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	7e-12
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-09
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	5e-08
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-11
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-08
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-07
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	4e-11
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-09
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	3e-09
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	6e-11
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-10
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	3e-09
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	8e-11
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	1e-08
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	7e-08
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	2e-10
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	5e-10
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	3e-04
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	1e-09
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	2e-06
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	3e-05
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	5e-09
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	5e-04
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-08
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-06
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-05
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	3e-08
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-06
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	4e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	0.001
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	1e-06
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	0.001
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	2e-06
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	1e-05

>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 = 67.6 bits (165), Expect = 4e-15
 Identities = 22/68 (32%), Positives = 41/68 (60%)

Query: 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 410
           TT E+ IP   +  + G   +N++ IRQ+SGA + + +P  G++   V ++G++  +  A
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLA 61

Query: 411 QSLIHAFI 418
           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 = 8e-11
 Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 6/76 (7%)

Query: 49  EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMR 108
           +   +L    + +G +IG+ G+ +   +  +GA IKIA+ +  S  R V I+    S   
Sbjct: 1   QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS--- 57

Query: 109 HSPAQDAVMRVHSRIA 124
                 A   +++R++
Sbjct: 58  ---ISLAQYLINARLS 70

>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 = 54.8 bits (132), Expect = 1e-10
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 193
               L + +  IGC++GR G  ++E+R+ +GA I++     A          V + G+  
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKI-----ANPVEGSSGRQVTITGSAA 56

Query: 194 SVQDALFHITSRL 206
           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 = 66.7 bits (163), Expect = 8e-15
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 7/75 (9%)

Query: 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 193
           +  RLL+H +++G ++G+ G  V +MR  +GA I +         G+  + I+ + G  +
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE-------GNCPERIITLAGPTN 56

Query: 194 SVQDALFHITSRLRE 208
           ++  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 = 59.4 bits (144), Expect = 3e-12
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 8/76 (10%)

Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRH 109
           +  +LL H  +VGS+IGK G  V+  + E+GA I I++   +  ERI+ ++   N+    
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTNA---- 57

Query: 110 SPAQDAVMRVHSRIAE 125
                A   +  ++ E
Sbjct: 58  --IFKAFAMIIDKLEE 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 = 54.4 bits (131), Expect = 2e-10
 Identities = 11/69 (15%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 409
           + TI +++    +  + G+   ++  +R+ SGA + +   +    E ++ ++G ++ +  
Sbjct: 3   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLAGPTNAIFK 60

Query: 410 AQSLIHAFI 418
           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 = 63.4 bits (154), Expect = 1e-13
 Identities = 19/68 (27%), Positives = 39/68 (57%)

Query: 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 410
            T +V IP+     + G+    +  IR  SGA++ +++P  G+ + ++ ++GT DQ++ A
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 63

Query: 411 QSLIHAFI 418
           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 = 55.7 bits (134), Expect = 7e-11
 Identities = 15/78 (19%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 190
           G  +  ++ +     G ++G+GG  + ++R  +GASI++             D I+ + G
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-----DEPLEGSEDRIITITG 55

Query: 191 NYHSVQDALFHITSRLRE 208
               +Q+A + + + +++
Sbjct: 56  TQDQIQNAQYLLQNSVKQ 73

>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 = 51.0 bits (122), Expect = 3e-09
 Identities = 23/76 (30%), Positives = 43/76 (56%), Gaps = 6/76 (7%)

Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRH 109
           +  ++    D  GS+IGKGG  ++  ++E+GASIKI + L  SE+RI+ I+  ++     
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ---- 59

Query: 110 SPAQDAVMRVHSRIAE 125
              Q+A   + + + +
Sbjct: 60  --IQNAQYLLQNSVKQ 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 = 63.3 bits (154), Expect = 1e-13
 Identities = 16/69 (23%), Positives = 32/69 (46%)

Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 409
             T E  +P   +  + G     +S I+Q SG  + +     G  E   M++GT + +++
Sbjct: 7   VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQS 66

Query: 410 AQSLIHAFI 418
           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 = 56.8 bits (137), Expect = 3e-11
 Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 6/76 (7%)

Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRH 109
           +  +       VG +IG+GG  +   Q E+G  I+IA       ER  +++    S    
Sbjct: 8   MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPES---- 63

Query: 110 SPAQDAVMRVHSRIAE 125
              Q A   +   + +
Sbjct: 64  --VQSAKRLLDQIVEK 77

>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 = 56.0 bits (135), Expect = 6e-11
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 5/75 (6%)

Query: 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 193
           +     V    +G ++GRGG  +S +++ +G  I++     AP  G   +    + G   
Sbjct: 8   MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQI-----APDSGGLPERSCMLTGTPE 62

Query: 194 SVQDALFHITSRLRE 208
           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 = 62.6 bits (152), Expect = 3e-13
 Identities = 15/69 (21%), Positives = 29/69 (42%)

Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRA 409
           S  I+V IP+  +  V G N   +  I+  +G  +          E +  ++G  D+ + 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 410 AQSLIHAFI 418
           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 = 53.3 bits (128), Expect = 5e-10
 Identities = 15/76 (19%), Positives = 28/76 (36%), Gaps = 10/76 (13%)

Query: 51  VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHS 110
           +  +      VG +IG+ G +++  QN+ G  I+       + ERI  I+          
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITG--------- 54

Query: 111 PAQDAVMRVHSRIAEI 126
              D        I ++
Sbjct: 55  -PPDRAQHAAEIITDL 69

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.9 bits (119), Expect = 7e-09
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 190
           G  ++  + +    +G ++GR G ++ +++   G  I        P  G+  + I Q+ G
Sbjct: 1   GSHMI-DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRI-----QFKPDDGTTPERIAQITG 54

Query: 191 NYHSVQDALFHITSRLRE 208
                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 = 60.2 bits (146), Expect = 2e-12
 Identities = 15/70 (21%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV---NDPKPGATEGVVMVSGTSDQMR 408
            +E+ +P+  +  + G+    L   ++++GA + +    +  PG     V ++G+    +
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 409 AAQSLIHAFI 418
           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 = 60.2 bits (146), Expect = 2e-12
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHS 194
           +  + V    +G +LG+GG  + E +  TGA I++  K      G+  +  V + G+  +
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQI-SKKGEFLPGTR-NRRVTITGSPAA 61

Query: 195 VQDALFHITSRL 206
            Q A + I+ R+
Sbjct: 62  TQAAQYLISQRV 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 = 54.8 bits (132), Expect = 2e-10
 Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 9/79 (11%)

Query: 49  EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA---DILPDSEERIVVISARENS 105
           + + ++    + VG+++GKGG  +  +Q  TGA I+I+   + LP +  R V I+    +
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

Query: 106 EMRHSPAQDAVMRVHSRIA 124
                  Q A   +  R+ 
Sbjct: 62  ------TQAAQYLISQRVT 74

>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 = 59.6 bits (144), Expect = 7e-12
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 3/81 (3%)

Query: 128 FEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQ 187
                 V  +L V  + +G ++GRGG  +  + +A+GA I     D+          +++
Sbjct: 9   LTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITC---DKESEGTLLLSRLIK 65

Query: 188 VIGNYHSVQDALFHITSRLRE 208
           + 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 = 55.0 bits (132), Expect = 3e-10
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGA--TEGVVMVSGTSDQ 406
           T    ++ +PQ  +  + G     +  I + SGA +  +    G      ++ +SGT  +
Sbjct: 13  TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE 72

Query: 407 MRAAQSLIHAFI 418
           + AA+ LI   +
Sbjct: 73  VAAAKHLILEKV 84

>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 = 49.6 bits (118), Expect = 2e-08
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 8/78 (10%)

Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILP--DSEERIVVISARENSEM 107
           V  +L      VG +IG+GG  +R+    +GA I             R++ IS  +    
Sbjct: 15  VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE-- 72

Query: 108 RHSPAQDAVMRVHSRIAE 125
                  A   +  +++E
Sbjct: 73  ----VAAAKHLILEKVSE 86

>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 = 58.6 bits (142), Expect = 7e-12
 Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMR 408
           T  +  V IP+ +   V G+N   L  +   +   + +  P+P      + ++GT + + 
Sbjct: 8   TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSNQIKITGTKEGIE 65

Query: 409 AAQSLIHAFI 418
            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 = 51.2 bits (123), Expect = 3e-09
 Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 8/79 (10%)

Query: 47  EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSE 106
           + +    +    +    +IGK G  ++  + +T   I+I    PD     + I+  +   
Sbjct: 7   QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKITGTKEG- 63

Query: 107 MRHSPAQDAVMRVHSRIAE 125
                 + A   V    AE
Sbjct: 64  -----IEKARHEVLLISAE 77

>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 = 47.8 bits (114), Expect = 5e-08
 Identities = 11/75 (14%), Positives = 28/75 (37%), Gaps = 7/75 (9%)

Query: 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 193
             A + +  +    ++G+ G  + ++   T   I++      PR   P    +++ G   
Sbjct: 10  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI------PRPDDP-SNQIKITGTKE 62

Query: 194 SVQDALFHITSRLRE 208
            ++ A   +     E
Sbjct: 63  GIEKARHEVLLISAE 77

>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 = 57.9 bits (140), Expect = 2e-11
 Identities = 12/73 (16%), Positives = 26/73 (35%), Gaps = 1/73 (1%)

Query: 347 ILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANV-VVNDPKPGATEGVVMVSGTSD 405
            L S  + V +   Y   + G   + ++ IR     N+   +       +  + ++G   
Sbjct: 6   ALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK 65

Query: 406 QMRAAQSLIHAFI 418
              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 = 49.1 bits (117), Expect = 2e-08
 Identities = 10/75 (13%), Positives = 28/75 (37%), Gaps = 7/75 (9%)

Query: 53  KLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIAD-ILPDSEERIVVISARENSEMRHSP 111
            +         +IG+ G+++   + E   +I+  D    +  +  + I+  E +      
Sbjct: 13  SVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKN------ 66

Query: 112 AQDAVMRVHSRIAEI 126
            + A   +   + E+
Sbjct: 67  TEAARDAILRIVGEL 81

>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 = 46.8 bits (111), Expect = 1e-07
 Identities = 13/72 (18%), Positives = 31/72 (43%), Gaps = 4/72 (5%)

Query: 137 RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQ 196
            + V  +    ++GR G +++++R     +I+   KD     G+   + + + G   + +
Sbjct: 13  SVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKD----DGNQPQDQITITGYEKNTE 68

Query: 197 DALFHITSRLRE 208
            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 = 56.5 bits (136), Expect = 4e-11
 Identities = 16/82 (19%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 127 GFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIV 186
           G  PG   V  +++ + + G ++G+GG  + +++   G  + +    Q     +  D+ +
Sbjct: 2   GDGPGN-AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVM---IQDGPQNTGADKPL 57

Query: 187 QVIGNYHSVQDALFHITSRLRE 208
           ++ 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 = 52.3 bits (125), Expect = 1e-09
 Identities = 12/77 (15%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 344 HAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV--NDPKPGATEGVVMVS 401
           H     +   E++IP      V G+    +  +++ +G  +V+  + P+    +  + ++
Sbjct: 1   HGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRIT 60

Query: 402 GTSDQMRAAQSLIHAFI 418
           G   +++ A+ ++   I
Sbjct: 61  GDPYKVQQAKEMVLELI 77

>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 = 51.5 bits (123), Expect = 3e-09
 Identities = 16/81 (19%), Positives = 29/81 (35%), Gaps = 8/81 (9%)

Query: 49  EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADI--LPDSEERIVVISARENSE 106
             V +++    K G +IGKGG  ++  Q   G  + +          ++ + I+      
Sbjct: 7   NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYK- 65

Query: 107 MRHSPAQDAVMRVHSRIAEIG 127
                 Q A   V   I + G
Sbjct: 66  -----VQQAKEMVLELIRDQG 81

>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 = 6e-11
 Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 3/70 (4%)

Query: 352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV---NDPKPGATEGVVMVSGTSDQMR 408
               ++P      + G+    +  I Q SGA + +     P       +  + GT  Q+ 
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQID 61

Query: 409 AAQSLIHAFI 418
            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 = 54.9 bits (132), Expect = 1e-10
 Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 2/70 (2%)

Query: 137 RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQ 196
             +V + + G ++G+GG  +  + + +GA I +      P    P+ ++  + G    + 
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP--PPNADPNMKLFTIRGTPQQID 61

Query: 197 DALFHITSRL 206
            A   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 = 50.7 bits (121), Expect = 3e-09
 Identities = 15/78 (19%), Positives = 27/78 (34%), Gaps = 13/78 (16%)

Query: 52  FKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA---DILPDSEERIVVISARENSEMR 108
           F  +    K G +IGKGG  +++   ++GA I++        D   ++  I         
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRG------- 55

Query: 109 HSPAQDAVMRVHSRIAEI 126
                  +      I E 
Sbjct: 56  ---TPQQIDYARQLIEEK 70

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.0 bits (135), Expect = 8e-11
 Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 348 LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQM 407
           L   TIEV +P     +V G+  S +  +      N+ V  P P     ++ ++G +  +
Sbjct: 7   LVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAITGLAANL 64

Query: 408 RAAQSLIHAFI 418
             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 = 49.8 bits (119), Expect = 1e-08
 Identities = 14/68 (20%), Positives = 28/68 (41%), Gaps = 8/68 (11%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
           D    +IG+ GS +R   +E   +I +    P+ +  I+ I+    +         A   
Sbjct: 19  DLHRYVIGQKGSGIRKMMDEFEVNIHVPA--PELQSDIIAITGLAAN------LDRAKAG 70

Query: 119 VHSRIAEI 126
           +  R+ E+
Sbjct: 71  LLERVKEL 78

>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 = 47.9 bits (114), Expect = 7e-08
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 7/75 (9%)

Query: 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 193
           V   + V       ++G+ G  + +M      +I V      P       +I+ + G   
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV------PAPELQ-SDIIAITGLAA 62

Query: 194 SVQDALFHITSRLRE 208
           ++  A   +  R++E
Sbjct: 63  NLDRAKAGLLERVKE 77

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 54.8 bits (132), Expect = 2e-10
 Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 14/83 (16%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
           +++G++IG  G +       TG  I +     D+E  +V++                +M+
Sbjct: 12  ERLGAVIGPRGEVKAEIMRRTGTVITV-----DTENSMVIVEPEAE-----GIPPVNLMK 61

Query: 119 VHSRIAEI--GFEPGQAVVARLL 139
               +  I  GF P +A   RLL
Sbjct: 62  AAEVVKAISLGFPPEKAF--RLL 82

>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 = 53.4 bits (128), Expect = 5e-10
 Identities = 12/68 (17%), Positives = 28/68 (41%), Gaps = 3/68 (4%)

Query: 347 ILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQ 406
           +  +   E V+ +  M    G + SN+   R++ G   +  D   G      +   ++D 
Sbjct: 4   LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGT---FRIYGESADA 60

Query: 407 MRAAQSLI 414
           ++ A+  +
Sbjct: 61  VKKARGFL 68

>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 = 36.8 bits (85), Expect = 3e-04
 Identities = 11/68 (16%), Positives = 22/68 (32%), Gaps = 13/68 (19%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
           D +G  IG  GS ++  +   G +      L +      +             + DAV +
Sbjct: 17  DLMGLAIGTHGSNIQQARKVPGVTA---IELDEDTGTFRIY----------GESADAVKK 63

Query: 119 VHSRIAEI 126
               +  +
Sbjct: 64  ARGFLEFV 71

>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 = 52.1 bits (125), Expect = 1e-09
 Identities = 10/64 (15%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 410
             +E+ I   +  H+ G++ +N++ I+     +V +  P       ++ + G    ++ A
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI--PPDSEKSNLIRIEGDPQGVQQA 62

Query: 411 QSLI 414
           +  +
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 = 43.2 bits (102), Expect = 2e-06
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 17/85 (20%)

Query: 42  NRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISA 101
           NRM Y E  +            LIGK G+ +   +++   S++I       +  ++ I  
Sbjct: 2   NRMDYVEINIDH-----KFHRHLIGKSGANINRIKDQYKVSVRIPP--DSEKSNLIRIEG 54

Query: 102 RENSEMRHSPAQDAVMRVHSRIAEI 126
                         V +    + E+
Sbjct: 55  ----------DPQGVQQAKRELLEL 69

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (93), Expect = 3e-05
 Identities = 11/67 (16%), Positives = 27/67 (40%), Gaps = 7/67 (10%)

Query: 136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSV 195
             + +  +    L+G+ G  ++ ++     S+R  P D           ++++ G+   V
Sbjct: 7   VEINIDHKFHRHLIGKSGANINRIKDQYKVSVR-IPPDSEK------SNLIRIEGDPQGV 59

Query: 196 QDALFHI 202
           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 = 50.6 bits (121), Expect = 5e-09
 Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 1/68 (1%)

Query: 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 410
             +EV IP      + G     +  I +  G  V ++ P  G+    V++ G S  +  A
Sbjct: 10  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECG-GVHIHFPVEGSGSDTVVIRGPSSDVEKA 68

Query: 411 QSLIHAFI 418
           +  +    
Sbjct: 69  KKQLLHLA 76

>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 = 36.4 bits (84), Expect = 5e-04
 Identities = 14/81 (17%), Positives = 23/81 (28%), Gaps = 13/81 (16%)

Query: 47  EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNE-TGASIKIADILPDSEERIVVISARENS 105
                 ++        SLIG  G ++R+   E  G  I        S    VVI      
Sbjct: 7   ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV--EGSGSDTVVIRG---- 60

Query: 106 EMRHSPAQDAVMRVHSRIAEI 126
                     V +   ++  +
Sbjct: 61  ------PSSDVEKAKKQLLHL 75

>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 = 49.4 bits (118), Expect = 1e-08
 Identities = 9/68 (13%), Positives = 19/68 (27%), Gaps = 1/68 (1%)

Query: 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 410
            + +V +     A + G     +  I      ++             V V+G  + +  A
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP-DPNCVTVTGLPENVEEA 68

Query: 411 QSLIHAFI 418
              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 = 44.0 bits (104), Expect = 1e-06
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 6/75 (8%)

Query: 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 193
           V   + +  +    ++G  G  + ++       IR       P+ G+P    V V G   
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF------PQSGAPDPNCVTVTGLPE 63

Query: 194 SVQDALFHITSRLRE 208
           +V++A+ HI +   E
Sbjct: 64  NVEEAIDHILNLEEE 78

>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 = 41.3 bits (97), Expect = 1e-05
 Identities = 12/61 (19%), Positives = 19/61 (31%)

Query: 47  EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSE 106
           E+ V   +         +IG  G  +R   +E    I+           + V    EN E
Sbjct: 7   EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVE 66

Query: 107 M 107
            
Sbjct: 67  E 67

>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 = 48.6 bits (116), Expect = 3e-08
 Identities = 11/66 (16%), Positives = 25/66 (37%), Gaps = 8/66 (12%)

Query: 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAA 410
             +   I    +  V G+  S +  ++      +VV         G++ V+G   ++  A
Sbjct: 3   RIVA--INPARVPRVIGKKGSMIKLLKSELDVQIVVGQ------NGLIWVNGDRRKVSIA 54

Query: 411 QSLIHA 416
           +  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 = 44.0 bits (104), Expect = 1e-06
 Identities = 11/68 (16%), Positives = 24/68 (35%), Gaps = 16/68 (23%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
            +V  +IGK GS+++  ++E    I +          ++ ++            +  V  
Sbjct: 10  ARVPRVIGKKGSMIKLLKSELDVQIVVGQ------NGLIWVNG----------DRRKVSI 53

Query: 119 VHSRIAEI 126
               I  I
Sbjct: 54  AEEAIYLI 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 = 47.3 bits (113), Expect = 4e-08
 Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 6/52 (11%)

Query: 50  VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISA 101
            +  +   +DK+G +IG    ++   Q +TGA I I D      +  + I A
Sbjct: 3   RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGA 48

>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 = 35.0 bits (81), Expect = 0.001
 Identities = 7/36 (19%), Positives = 20/36 (55%)

Query: 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRV 169
            +  + +   +IG ++G    ++++++  TGA I +
Sbjct: 3   RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITI 38

>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 = 44.3 bits (105), Expect = 1e-06
 Identities = 14/72 (19%), Positives = 25/72 (34%), Gaps = 15/72 (20%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
            KV  +IG+  S+++T + +T   I +A          + +           P +D    
Sbjct: 10  AKVPRVIGRKMSMLKTLEEKTECKIFVAR------NGRIHLEC---------PNEDLEAI 54

Query: 119 VHSRIAEIGFEP 130
               I  I  E 
Sbjct: 55  AVMAIKIIDEEA 66

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 11/68 (16%), Positives = 20/68 (29%), Gaps = 9/68 (13%)

Query: 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTS-DQMR 408
              +E  I    +  V G   S L  + + +   + V         G + +   + D   
Sbjct: 2   GKIVE--ISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR------NGRIHLECPNEDLEA 53

Query: 409 AAQSLIHA 416
            A   I  
Sbjct: 54  IAVMAIKI 61

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 12/71 (16%), Positives = 21/71 (29%), Gaps = 15/71 (21%)

Query: 61  VGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVH 120
            G +IG+GG   RT +  T   I + +        + +I   E +         A   + 
Sbjct: 24  KGRIIGEGGRARRTIEEMTDTYINVGE------YEVAIIGDYERAMA-------AKQAIE 70

Query: 121 SRIAEIGFEPG 131
                      
Sbjct: 71  MLAEGR--MHS 79

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 15/71 (21%)

Query: 59  DKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMR 118
            KV  +IGK  S+  T  +++G SI +A+         +  +          P++ +   
Sbjct: 10  VKVPRVIGKNKSMYETLTSKSGCSIFVAN------NGRIWATC---------PSRFSEEI 54

Query: 119 VHSRIAEIGFE 129
           +   I +I  E
Sbjct: 55  LIEAIRKIENE 65

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	424
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.71
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.7
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.69
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.65
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.64
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.62
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.62
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.61
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.56
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.53
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.53
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.52
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.51
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.51
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.51
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.51
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.5
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.49
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.49
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.49
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.49
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.44
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.44
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.42
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.42
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.39
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.39
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.38
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.37
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.33
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.32
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.32
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.28
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.14
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.12
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.09
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.05
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.99
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.96
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.72
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.71
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.68
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.66
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.64
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.6
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.42
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.2
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.91
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.6
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.48
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.31
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	95.2
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.96
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.85
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	92.28
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	87.2
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	86.61

>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=99.71  E-value=7.2e-18  Score=125.91  Aligned_cols=68  Identities=32%  Similarity=0.560  Sum_probs=65.3

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFI  418 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i  418 (424)
                      +|.+|.||.+++|+||||+|++|++|+++|||+|.|+++.+++++|+|+|+|++++|++|+.||+++|
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            68999999999999999999999999999999999998888888999999999999999999999987

>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=99.70  E-value=2.5e-17  Score=124.75  Aligned_cols=71  Identities=27%  Similarity=0.513  Sum_probs=67.6

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      .+|.+|.||.+++|+|||++|++|++|+++|||+|+|+++.+++.+|+|+|+|++++|++|+.||+++|++
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            47899999999999999999999999999999999999888888899999999999999999999999975

>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=99.69  E-value=1.5e-17  Score=125.59  Aligned_cols=72  Identities=21%  Similarity=0.365  Sum_probs=67.6

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~  421 (424)
                      ..+++|.||.+++|+||||+|++|++|+++|||+|+|++..+...+|.|+|+|++++|++|+.+|+++|++-
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            367999999999999999999999999999999999998777788999999999999999999999999864

>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=99.65  E-value=9.7e-17  Score=120.06  Aligned_cols=67  Identities=21%  Similarity=0.348  Sum_probs=60.7

Q ss_pred             EEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCC---CCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 014452          352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP---KPGATEGVVMVSGTSDQMRAAQSLIHAFI  418 (424)
Q Consensus       352 t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~---~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i  418 (424)
                      +.+|.||.+++|+||||+|++|++|++.|||+|+|+..   .+++.+|+|+|+|++++|++|+.||+++|
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            47899999999999999999999999999999999742   34457899999999999999999999875

>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=99.64  E-value=1.4e-16  Score=121.72  Aligned_cols=73  Identities=23%  Similarity=0.414  Sum_probs=69.1

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~  421 (424)
                      ..++.+|.||.+++|+|||++|++|++|++.|||+|.|+++.+++.++.|+|+|++++|+.|+.||.++|..+
T Consensus         6 ~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           6 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            3688999999999999999999999999999999999998888888999999999999999999999999865

>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=99.62  E-value=2.5e-16  Score=118.79  Aligned_cols=68  Identities=22%  Similarity=0.466  Sum_probs=62.1

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCC---CCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP---KPGATEGVVMVSGTSDQMRAAQSLIHAFI  418 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~---~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i  418 (424)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|++.   .++.++|+|+|+|++++|++|+.||+++|
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            568999999999999999999999999999999999743   34567899999999999999999999986

>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=99.62  E-value=2.8e-16  Score=117.45  Aligned_cols=69  Identities=16%  Similarity=0.325  Sum_probs=63.9

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      .++.+|.||.+++|+||||+|++|++|++.|||+|+|+++  ...+|+|+|+|++++|++|+.+|.++|++
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            4789999999999999999999999999999999999753  45689999999999999999999999874

>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=99.61  E-value=3.5e-16  Score=120.07  Aligned_cols=72  Identities=15%  Similarity=0.348  Sum_probs=65.8

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeC--CCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND--PKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~--~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      .+++.+|.||..++|+|||++|++|++|+++|||+|.|++  +.+...+|+|+|+|++++|++|+.||+++|.+
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            3689999999999999999999999999999999999974  34456789999999999999999999999865

>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=99.56  E-value=3.5e-15  Score=119.97  Aligned_cols=72  Identities=21%  Similarity=0.308  Sum_probs=64.8

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCC--CCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPK--PGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~--~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      +.++.+|.||.+++|+||||+|++|++|+++|||+|+|++..  ....+|+|+|+|++++|++|+.+|+++|++
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            468899999999999999999999999999999999997543  234679999999999999999999999964

>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=99.53  E-value=3.3e-15  Score=111.51  Aligned_cols=70  Identities=27%  Similarity=0.534  Sum_probs=63.9

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHh
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  208 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  208 (424)
                      ..++++|+||.+++|+|||++|++|++|+++|||+|++.+..       ..+|+|+|+|++++|.+|+.+|.++|+|
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 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-------CPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC-------CSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCC-------CCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            357899999999999999999999999999999999996532       4689999999999999999999999875

>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=99.53  E-value=1.1e-14  Score=109.92  Aligned_cols=73  Identities=19%  Similarity=0.482  Sum_probs=65.9

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      +.+|.++.||..++|+|||++|++|++|+++|||+|+|.+..     ..+.+|.|+|+|++++|.+|+.+|.++++++
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 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL-----EGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT-----SCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCC-----CCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            357889999999999999999999999999999999996432     2367899999999999999999999999886

>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=7e-15  Score=112.64  Aligned_cols=72  Identities=17%  Similarity=0.278  Sum_probs=65.6

Q ss_pred             CcceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452          348 LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       348 ~~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~  421 (424)
                      .+..+.+|.||..++|+|||++|++|++|+++|||+|.+++  .++.++.|+|+|++++|++|+.+|++.+++.
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~--~~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCC--TTSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECC--CCCCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            35689999999999999999999999999999999999964  4567789999999999999999999998763

>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=111.43  Aligned_cols=72  Identities=13%  Similarity=0.120  Sum_probs=64.1

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~  421 (424)
                      +.++.+|.||.+++++|||++|++|++|+++|||+|.|++.. ..+++.|+|+|++++|++|+.+|++.+++-
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 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-CSCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCcc-CCCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999999997543 234579999999999999999999998753

>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=99.51  E-value=1.5e-14  Score=111.65  Aligned_cols=71  Identities=17%  Similarity=0.275  Sum_probs=64.8

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeC-CCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND-PKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~-~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      .++.+|.||..++++|||++|++|++|+++|||+|+|++ ...+..+++|+|+|++++|++|+.+|++.|..
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            578999999999999999999999999999999999974 34456788999999999999999999999875

>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=99.51  E-value=9.2e-15  Score=109.08  Aligned_cols=70  Identities=17%  Similarity=0.374  Sum_probs=61.4

Q ss_pred             EEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHH
Q 014452          135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL  206 (424)
Q Consensus       135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  206 (424)
                      +.+|.||.+++|+||||+|++|++|+++|||+|+|....+  ....+.+|.|+|+|++++|.+|+.+|.++|
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            4689999999999999999999999999999999975432  233467899999999999999999998864

>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=99.51  E-value=8.9e-15  Score=109.11  Aligned_cols=67  Identities=13%  Similarity=0.308  Sum_probs=61.4

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFI  418 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i  418 (424)
                      ....+|.||.+++++|||++|++|++|+++|||+|.|++  +.++++.|+|+|++++|++|+.+|++.+
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            578899999999999999999999999999999999964  4567789999999999999999999864

>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=99.50  E-value=1.8e-14  Score=108.36  Aligned_cols=71  Identities=25%  Similarity=0.445  Sum_probs=62.6

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHH
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL  206 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  206 (424)
                      .+++|.||..++|.||||+|++|++|+++|||+|+|.+.++.  ...+.+|.|+|+|++++|++|+.+|.++|
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            357899999999999999999999999999999999765442  23467999999999999999999998875

>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=99.49  E-value=9.6e-15  Score=111.86  Aligned_cols=76  Identities=16%  Similarity=0.379  Sum_probs=67.2

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ...++.+|+||..++|+|||++|++|++|+++|||+|+|.+.+..   ..+.+|.|+|+|++++|.+|+.+|.++|++.
T Consensus         5 ~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   80 (81)
T d1x4ma1           5 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQ---NTGADKPLRITGDPYKVQQAKEMVLELIRDQ   80 (81)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCC---SSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCC---CCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            456889999999999999999999999999999999999754332   2367899999999999999999999999763

>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=99.49  E-value=1.1e-14  Score=111.77  Aligned_cols=72  Identities=17%  Similarity=0.244  Sum_probs=64.5

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHH-hCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcCc
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQI-SGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGV  422 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~-SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~~  422 (424)
                      +..+.+|.||.+++|+|||++|++|++|+++ ++|+|.+++  .+..++.|+|+|++++|++|+.+|++.+++.+
T Consensus         8 ~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~--~~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~~   80 (82)
T d2ctja1           8 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV--EGSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   80 (82)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCC--TTTTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             CcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeC--CCCCCceEEEeCCHHHHHHHHHHHHHHHhhhh
Confidence            4678999999999999999999999999987 589999854  45677999999999999999999999998754

>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=99.49  E-value=1.6e-14  Score=107.44  Aligned_cols=68  Identities=28%  Similarity=0.507  Sum_probs=61.5

Q ss_pred             eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHH
Q 014452          134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL  206 (424)
Q Consensus       134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  206 (424)
                      .|.+|.||.+++|+||||+|.+|++|+++|||+|+|.+..     ....+|.|+|+|++++|++|+.+|.++|
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 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV-----EGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCC-----TTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCC-----CCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            5789999999999999999999999999999999996432     2367899999999999999999998875

>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=99.49  E-value=1.5e-14  Score=108.81  Aligned_cols=72  Identities=24%  Similarity=0.417  Sum_probs=64.8

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ..+++|.||.+++|.||||+|++|++|+++|||+|+|...+.     ...+|.|+|+|++++|.+|+.+|.++|++.
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 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG-----TTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTT-----SCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCC-----CCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            457899999999999999999999999999999999975432     357899999999999999999999999864

>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=99.44  E-value=8.2e-14  Score=106.07  Aligned_cols=74  Identities=22%  Similarity=0.401  Sum_probs=66.5

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ...++.+|.||..++|+|||++|.+|++|+++|||+|+|.+.+     ..+.++.|+|+|++++|.+|+.+|.++|++.
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~-----~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS-----GGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC-----TTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCC-----CCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            4568899999999999999999999999999999999997532     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=99.44  E-value=1.1e-13  Score=111.12  Aligned_cols=76  Identities=22%  Similarity=0.402  Sum_probs=66.8

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ...++.+|.||..++|+||||+|.+|++|+++|||+|+|.+.++.   ....+|+|+|+|++++|.+|+.+|.++|++.
T Consensus        12 ~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG---TLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC---SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            456889999999999999999999999999999999999754332   2356899999999999999999999999765

>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=99.42  E-value=9.1e-14  Score=108.72  Aligned_cols=69  Identities=19%  Similarity=0.261  Sum_probs=63.7

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      .++.+|.||..++++|||++|++|++|+++|||+|.|++  .+..++.|+|+|++++|++|+.+|++++.+
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            588999999999999999999999999999999999964  455678999999999999999999999874

>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=99.42  E-value=1.2e-13  Score=105.51  Aligned_cols=74  Identities=20%  Similarity=0.262  Sum_probs=65.7

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhc
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETI  210 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  210 (424)
                      +..++.++.||..+++.|||++|++|++|+++|||+|+|++.++      ..++.|+|+|++++|.+|+.+|.+++++++
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~------~~~~~v~I~G~~~~V~~A~~~I~~i~~e~~   80 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA------PDPNCVTVTGLPENVEEAIDHILNLEEEYL   80 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC------SCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC------CCCCEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            45677899999999999999999999999999999999975432      345789999999999999999999999874

>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=99.39  E-value=8.3e-14  Score=105.31  Aligned_cols=67  Identities=19%  Similarity=0.335  Sum_probs=59.5

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~  419 (424)
                      ..++.+|.||.+++|+|||++|++|++|+++|||+|.+++.    ++++|+|.| ++++|++|+.||+.+.+
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~----~~g~v~I~g~~~eav~~A~~~Ie~~~~   73 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGESADAVKKARGFLEFVED   73 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----TTTEEEEEESSHHHHHHHHHHHSCCCC
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC----CCceEEEEECCHHHHHHHHHHHHHhhe
Confidence            35899999999999999999999999999999999999642    347899999 79999999999975543

>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=99.39  E-value=3.3e-13  Score=103.37  Aligned_cols=65  Identities=20%  Similarity=0.252  Sum_probs=59.3

Q ss_pred             EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcCcC
Q 014452          353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGVT  423 (424)
Q Consensus       353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~~~  423 (424)
                      ..+.||.+++|+|||++|++|++|+++|||+|.|++      ++.|+|+|++++|+.|+.+|+..+++.++
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            458999999999999999999999999999999953      46899999999999999999999887654

>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=99.38  E-value=4.5e-13  Score=103.09  Aligned_cols=73  Identities=18%  Similarity=0.274  Sum_probs=65.3

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      .++++|.||..++++|||++|++|++|+++|||+|+|++...    ....++.|+|+|+.++|.+|+.+|.+++.+.
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~----~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD----GNQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT----CSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC----CCCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            467899999999999999999999999999999999975432    2367889999999999999999999999875

>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=99.37  E-value=3.4e-13  Score=103.03  Aligned_cols=72  Identities=13%  Similarity=0.245  Sum_probs=65.5

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ...++.++.||..+++.|||++|++|++|+++|||+|++++.+       +.++.|+|+|+.++|.+|+.+|.+++++.
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-------~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-------SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC-------CCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            4567899999999999999999999999999999999996543       56789999999999999999999999875

>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=99.33  E-value=5.4e-13  Score=99.23  Aligned_cols=67  Identities=15%  Similarity=0.282  Sum_probs=60.1

Q ss_pred             ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHH
Q 014452          133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL  206 (424)
Q Consensus       133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  206 (424)
                      -.+++|.||.++++.|||++|++|++|+++|||+|+|++.+       +.++.|+|+|++++|++|+.+|.+++
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCC-------CCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            45788999999999999999999999999999999996542       56789999999999999999998763

>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=99.32  E-value=6.7e-13  Score=101.61  Aligned_cols=72  Identities=14%  Similarity=0.217  Sum_probs=64.3

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhh-cCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA-TGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~-tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ...++.+|.||..++++|||++|++|++|+++ ++|+|++++.+       +.++.|+|+|++++|++|+.+|.+++++.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~-------~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-------SGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-------TTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCC-------CCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            45678999999999999999999999999987 59999886432       56789999999999999999999999886

>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=1.7e-12  Score=100.93  Aligned_cols=67  Identities=19%  Similarity=0.324  Sum_probs=61.2

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHHH-hCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQI-SGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~-SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      +.+|.+|.||..++++|||++|++|++|+++ ++++|.+++     .+..|+|+|++++|+.|+.+|++.+..
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            4689999999999999999999999999999 589999963     357899999999999999999999875

>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=99.28  E-value=1.8e-12  Score=101.14  Aligned_cols=71  Identities=17%  Similarity=0.216  Sum_probs=64.3

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      -.++.++.||..+++.|||++|++|++|+++|||+|.+++.+       +.++.|+|+|+.++|++|+.+|.+++.+.
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 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAANLDRAKAGLLERVKEL   78 (91)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-------TTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCC-------CCcceEEEECCHHHHHHHHHHHHHHHHHH
Confidence            357899999999999999999999999999999999997543       45778999999999999999999999764

>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=99.14  E-value=4.6e-11  Score=92.69  Aligned_cols=69  Identities=13%  Similarity=0.189  Sum_probs=62.2

Q ss_pred             CcceEEEEEecCCCcceeeccCCchHHHHHhhc-CceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRAT-GASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~t-ga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ...++.++.||..+++.|||++|++|++|++++ +++|.+++          .+..|+|+|++++|++|+.+|.+++.+.
T Consensus        18 ~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~----------~~~~v~i~G~~~~ve~Ak~~I~~iv~el   87 (90)
T d2ctfa1          18 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC----------CCceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            456899999999999999999999999999995 89999863          2457999999999999999999999875

>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=99.12  E-value=3.3e-11  Score=92.02  Aligned_cols=63  Identities=16%  Similarity=0.200  Sum_probs=57.1

Q ss_pred             EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452          136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  209 (424)
                      ..+.||.+.++.|||++|++|++|+++|||+|+|..           +..|+|+|+++++..|+.+|..++++.
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~-----------~g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-----------NGLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT-----------TSEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC-----------CCEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            357899999999999999999999999999999942           347999999999999999999888775

>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=99.09  E-value=3.5e-11  Score=90.62  Aligned_cols=63  Identities=16%  Similarity=0.298  Sum_probs=56.1

Q ss_pred             cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHH
Q 014452          132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHIT  203 (424)
Q Consensus       132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~  203 (424)
                      ..++.+|.||.+++|.|||++|++|++|+++|||+|.+..+         .++.|+|.| +.++|++|+.+|.
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~---------~~g~v~I~g~~~eav~~A~~~Ie   69 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE---------DTGTFRIYGESADAVKKARGFLE   69 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET---------TTTEEEEEESSHHHHHHHHHHHS
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC---------CCceEEEEECCHHHHHHHHHHHH
Confidence            45788999999999999999999999999999999988642         356799999 6999999999984

>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=99.05  E-value=1.8e-11  Score=93.33  Aligned_cols=61  Identities=18%  Similarity=0.236  Sum_probs=51.5

Q ss_pred             EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEE-----EcCHHHHHHHHHHHHHHH
Q 014452          353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMV-----SGTSDQMRAAQSLIHAFI  418 (424)
Q Consensus       353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I-----~Gt~e~v~~A~~lI~~~i  418 (424)
                      ++|.||.+.+|.|||++|++|++|+++|||+|+|++.     +..+.+     .|.++++++|+.+|.+.-
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 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE-----NSMVIVEPEAEGIPPVNLMKAAEVVKAIS   70 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT-----TTEEEEEESSTTSCHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC-----CCeEEEecCCccccHHHHHHHHHHHHHHh
Confidence            4699999999999999999999999999999999732     234444     457899999999998753

>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=98.99  E-value=8.4e-12  Score=91.78  Aligned_cols=62  Identities=16%  Similarity=0.168  Sum_probs=48.4

Q ss_pred             EEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHcC
Q 014452          354 EVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCG  421 (424)
Q Consensus       354 ~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~~  421 (424)
                      -+.||.+.+|+|||++|++|+.|+++|||+|.|++      +..|+|+| ++++++.|+.+|+...++.
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~------~g~v~I~g~~~~~v~~A~~~I~~i~~ea   66 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN------NGRIWATCPSRFSEEILIEAIRKIENES   66 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT------TSEEEC-----CTTCCTHHHHTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC------CCEEEEEeCCHHHHHHHHHHHHHHHHhh
Confidence            48899999999999999999999999999999953      35799999 5789999999998766554

>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=98.96  E-value=8.8e-10  Score=83.96  Aligned_cols=65  Identities=18%  Similarity=0.136  Sum_probs=57.7

Q ss_pred             EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHcCcC
Q 014452          353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGVT  423 (424)
Q Consensus       353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~~~~  423 (424)
                      ..+.||.+.++.|||++|++|+.|+++|||+|.|.+      +-.|.|.| +.+.++.|+.+|+...+..+.
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d------~G~V~I~g~~~~~~~~A~~~I~~I~~ea~v   68 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR------NGRIHLECPNEDLEAIAVMAIKIIDEEAYT   68 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET------TTEEEEECSCHHHHHHHHHHHHHHHHCSCC
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC------CcEEEEEeCCHHHHHHHHHHHHHHHHhchh
Confidence            458999999999999999999999999999999963      24799999 689999999999998876553

>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=98.72  E-value=2.1e-10  Score=84.14  Aligned_cols=62  Identities=13%  Similarity=0.109  Sum_probs=47.1

Q ss_pred             EEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHHHHHHHhh
Q 014452          137 RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHITSRLRET  209 (424)
Q Consensus       137 ~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  209 (424)
                      .+.||.+.+|.|||++|++||+|+++|||+|.|..           +..|+|+|. .+++++|+.+|..+.++.
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~-----------~g~v~I~g~~~~~v~~A~~~I~~i~~ea   66 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN-----------NGRIWATCPSRFSEEILIEAIRKIENES   66 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT-----------TSEEEC-----CTTCCTHHHHTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC-----------CCEEEEEeCCHHHHHHHHHHHHHHHHhh
Confidence            57899999999999999999999999999999942           236999996 679999999997766553

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.71  E-value=1.3e-09  Score=82.85  Aligned_cols=64  Identities=20%  Similarity=0.227  Sum_probs=52.3

Q ss_pred             EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEE-----eCHHHHHHHHHHHHHHHHhh
Q 014452          136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI-----GNYHSVQDALFHITSRLRET  209 (424)
Q Consensus       136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~-----G~~~~v~~A~~~I~~~l~~~  209 (424)
                      +.+.||.+.+|.|||++|++||+|+++|||+|+|..++          ..|.+.     |.+.++.+|..+|.++.+.+
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 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTEN----------SMVIVEPEAEGIPPVNLMKAAEVVKAISLGF   73 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTT----------TEEEEEESSTTSCHHHHHHHHHHHHHHHHTC
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCC----------CeEEEecCCccccHHHHHHHHHHHHHHhCCC
Confidence            46899999999999999999999999999999996432          234444     56888999999998876543

>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=98.68  E-value=8.3e-09  Score=81.12  Aligned_cols=53  Identities=17%  Similarity=0.228  Sum_probs=47.7

Q ss_pred             cccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452          361 YMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC  420 (424)
Q Consensus       361 ~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~  420 (424)
                      ..|+|||++|.+|+.|++.|||+|.|++       ..|.|.|++++++.|+.+|.++|..
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d-------~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS-------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeC-------CeEEEEECchhHHHHHHHHHHHHcC
Confidence            4699999999999999999999999953       3588889999999999999999863

>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=98.66  E-value=8.9e-10  Score=76.13  Aligned_cols=46  Identities=28%  Similarity=0.550  Sum_probs=15.0

Q ss_pred             EEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeeccc
Q 014452           52 FKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARE  103 (424)
Q Consensus        52 ~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~  103 (424)
                      .+|.||.+.+|.|||++|++||+|+++|||+|++.      ++..|+|.|..
T Consensus         5 ~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~------ddg~v~I~a~~   50 (54)
T d1e3ha4           5 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAAD   50 (54)
T ss_dssp             C---------------------CHHHHSCCCC--------------CCCCBS
T ss_pred             EEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEe------CCeEEEEEecC
Confidence            47889999999999999999999999999999994      45789998864

>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=98.64  E-value=2e-08  Score=76.24  Aligned_cols=62  Identities=13%  Similarity=0.094  Sum_probs=54.8

Q ss_pred             EEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHHHHHHHhh
Q 014452          137 RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHITSRLRET  209 (424)
Q Consensus       137 ~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  209 (424)
                      .+.||.+.++.|||++|++|+.|+++|||+|.|..           +-.|.|.|. .+.+..|+.+|..+.++.
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 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-----------NGRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET-----------TTEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC-----------CcEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            57899999999999999999999999999999953           226999995 889999999999887765

>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=98.60  E-value=1.3e-09  Score=75.26  Aligned_cols=45  Identities=22%  Similarity=0.479  Sum_probs=14.3

Q ss_pred             EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcC
Q 014452          353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT  403 (424)
Q Consensus       353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt  403 (424)
                      .+|.||.+.+|.|||++|++||.|+++|||+|.|+      ++.+|+|.|+
T Consensus         5 ~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~------ddg~v~I~a~   49 (54)
T d1e3ha4           5 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAA   49 (54)
T ss_dssp             C---------------------CHHHHSCCCC--------------CCCCB
T ss_pred             EEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEe------CCeEEEEEec
Confidence            56899999999999999999999999999999995      3467888874

>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=98.42  E-value=6.6e-08  Score=75.86  Aligned_cols=53  Identities=25%  Similarity=0.289  Sum_probs=47.0

Q ss_pred             CcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHh
Q 014452          144 QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE  208 (424)
Q Consensus       144 ~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  208 (424)
                      +.|+|||++|.+|+.|++.|||+|.|..            ..|.|.|+++++..|+.+|.+++.+
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d------------~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGE------------YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS------------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeC------------CeEEEEECchhHHHHHHHHHHHHcC
Confidence            3589999999999999999999999842            1478889999999999999999965

>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=98.20  E-value=1.9e-06  Score=69.59  Aligned_cols=71  Identities=18%  Similarity=0.295  Sum_probs=55.7

Q ss_pred             ceEEEEEeccC------cccceeccccchHHHHHHHhCCEEEEeCC----------CC------CCCCcEEEEEc-CHHH
Q 014452          350 STTIEVVIPQL------YMAHVYGENNSNLSHIRQISGANVVVNDP----------KP------GATEGVVMVSG-TSDQ  406 (424)
Q Consensus       350 ~~t~~v~IP~~------~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~----------~~------~~~~r~i~I~G-t~e~  406 (424)
                      ..+.+|.||.+      ++|+|||.+|+++|+|+++|||+|.|--.          .+      ...+=-|.|++ +++.
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            46788888875      58999999999999999999999999410          00      01122566777 8899


Q ss_pred             HHHHHHHHHHHHHc
Q 014452          407 MRAAQSLIHAFILC  420 (424)
Q Consensus       407 v~~A~~lI~~~i~~  420 (424)
                      ++.|..+|+++|..
T Consensus        82 ~~~A~~~i~~ll~~   95 (122)
T d1k1ga_          82 VKKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999953

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.91  E-value=1.9e-05  Score=63.53  Aligned_cols=76  Identities=18%  Similarity=0.284  Sum_probs=57.9

Q ss_pred             eEEEEEecCC------CcceeeccCCchHHHHHhhcCceEEEecCCCC----------CCCCC-CCCcEEEEEeC-HHHH
Q 014452          134 VVARLLVHSQ------QIGCLLGRGGHIVSEMRRATGASIRVFPKDQA----------PRCGS-PHDEIVQVIGN-YHSV  195 (424)
Q Consensus       134 ~t~~l~IP~~------~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~----------p~~~~-~~~r~v~I~G~-~~~v  195 (424)
                      ++.++.||.+      ++|.|||.+|.++|+|+++|||+|.|-.+...          +.... ...=-|.|++. .+.+
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~   82 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENV   82 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHH
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhH
Confidence            5678999987      48999999999999999999999999754321          01111 12235778885 7799


Q ss_pred             HHHHHHHHHHHHhh
Q 014452          196 QDALFHITSRLRET  209 (424)
Q Consensus       196 ~~A~~~I~~~l~~~  209 (424)
                      ..|+.+|..+|...
T Consensus        83 ~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          83 KKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999765

>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=97.60  E-value=5.4e-05  Score=61.55  Aligned_cols=69  Identities=9%  Similarity=0.225  Sum_probs=51.0

Q ss_pred             eEEEEEecc------CcccceeccccchHHHHHHHhCCEEEEeCCC------------------CCCCCcEEEEEcC-H-
Q 014452          351 TTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVNDPK------------------PGATEGVVMVSGT-S-  404 (424)
Q Consensus       351 ~t~~v~IP~------~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~------------------~~~~~r~i~I~Gt-~-  404 (424)
                      .+.+|.||.      +++|+|||.+|+++|+|+++|||+|.|--.-                  ....+==|.|++. + 
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            356677774      6889999999999999999999999995210                  0112335677773 2 


Q ss_pred             ----HHHHHHHHHHHHHHH
Q 014452          405 ----DQMRAAQSLIHAFIL  419 (424)
Q Consensus       405 ----e~v~~A~~lI~~~i~  419 (424)
                          ..+++|..+|+.+|.
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                358899999998874

>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=97.48  E-value=5.6e-05  Score=61.46  Aligned_cols=74  Identities=20%  Similarity=0.202  Sum_probs=52.6

Q ss_pred             eEEEEEecCC------CcceeeccCCchHHHHHhhcCceEEEecCCCCC------------C-CCCCCCcEEEEEeCH--
Q 014452          134 VVARLLVHSQ------QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAP------------R-CGSPHDEIVQVIGNY--  192 (424)
Q Consensus       134 ~t~~l~IP~~------~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p------------~-~~~~~~r~v~I~G~~--  192 (424)
                      ++.++.||.+      ++|+|||++|.++|+|+++|||+|.|-.+....            . .....+=-|.|++..  
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            4567888865      779999999999999999999999997653210            0 001223357888752  


Q ss_pred             ----HHHHHHHHHHHHHHH
Q 014452          193 ----HSVQDALFHITSRLR  207 (424)
Q Consensus       193 ----~~v~~A~~~I~~~l~  207 (424)
                          ..+.+|+.+|..+|.
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                357778888877764

>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=95.31  E-value=0.0049  Score=43.39  Aligned_cols=39  Identities=23%  Similarity=0.186  Sum_probs=35.3

Q ss_pred             ccEEEEEEecccccceeeccCchHHHHHHHHhCceEEec
Q 014452           48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA   86 (424)
Q Consensus        48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~   86 (424)
                      +.-.+.+.||.+..+..|||+|.++|-..+-||.+|.|-
T Consensus        24 ~~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~   62 (67)
T d2asba3          24 TARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIR   62 (67)
T ss_dssp             TTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             CCcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEE
Confidence            334678899999999999999999999999999999995

>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=95.20  E-value=0.0055  Score=43.25  Aligned_cols=37  Identities=30%  Similarity=0.350  Sum_probs=34.4

Q ss_pred             EEEEEEecccccceeeccCchHHHHHHHHhCceEEec
Q 014452           50 VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA   86 (424)
Q Consensus        50 ~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~   86 (424)
                      -.+.+.||.+..+..|||+|.++|-..+-||.+|.|.
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~   63 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIK   63 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeE
Confidence            3578899999999999999999999999999999995

>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=94.96  E-value=0.0083  Score=42.31  Aligned_cols=37  Identities=14%  Similarity=0.326  Sum_probs=34.9

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452          351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN  387 (424)
Q Consensus       351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~  387 (424)
                      ....+.||.+..+..|||+|.|++-..+.||.+|.|.
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~   63 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIK   63 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeE
Confidence            4688999999999999999999999999999999996

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.85  E-value=0.0085  Score=42.09  Aligned_cols=38  Identities=16%  Similarity=0.372  Sum_probs=35.5

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452          350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN  387 (424)
Q Consensus       350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~  387 (424)
                      .....+.||.+.....|||+|.|++-..+.||.+|.|-
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~   62 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIR   62 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEE
Confidence            35788999999999999999999999999999999996

>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=92.28  E-value=0.072  Score=39.03  Aligned_cols=60  Identities=12%  Similarity=0.037  Sum_probs=49.3

Q ss_pred             EEEeccCcccceeccccc-hHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452          354 EVVIPQLYMAHVYGENNS-NLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL  419 (424)
Q Consensus       354 ~v~IP~~~~g~IIGk~G~-~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~  419 (424)
                      -+.|+..++..+||++++ -++.|.+.+.|.|.|..      .-.|-|.| +++..-++...|+++-+
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~------NGrIWi~~~~~~~~i~i~~aI~~~e~   65 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL------NGKIWVKCEELSNTLACYRTIMECCQ   65 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET------TTEEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec------CcEEEEECCCHHHHHHHHHHHHHHHH
Confidence            478999999999999998 79999999999999953      35788888 67777777777766544

>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=87.20  E-value=0.11  Score=38.63  Aligned_cols=34  Identities=9%  Similarity=0.248  Sum_probs=28.6

Q ss_pred             EEEEecccccceeeccCchHHHHHHHHhCceEEe
Q 014452           52 FKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKI   85 (424)
Q Consensus        52 ~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v   85 (424)
                      ++|.|....-|.|||++|+.|++|+++..-++.+
T Consensus        37 i~I~I~tarPGivIGrkG~~I~~L~~~l~k~~~~   70 (92)
T d1wh9a_          37 TEIIILATRTQNVLGEKGRRIRELTAVVQKRFGF   70 (92)
T ss_dssp             EEEEEEESCHHHHHCGGGHHHHHHHHHHHHHHCC
T ss_pred             EEEEEEeCCCceeeccCchhHHHHHHHHHHHHCC
Confidence            5788899999999999999999999876554443

>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=86.61  E-value=0.44  Score=34.56  Aligned_cols=60  Identities=10%  Similarity=-0.029  Sum_probs=46.0

Q ss_pred             EEEecCCCcceeeccCCc-hHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHHHHHHH
Q 014452          137 RLLVHSQQIGCLLGRGGH-IVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHITSRLR  207 (424)
Q Consensus       137 ~l~IP~~~vg~IIGkgG~-~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~  207 (424)
                      -+.|+..++.+++|++++ .++.|.+.+++.|.|-.           .-.|-|.|. .+....+...|...-+
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~-----------NGrIWi~~~~~~~~i~i~~aI~~~e~   65 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL-----------NGKIWVKCEELSNTLACYRTIMECCQ   65 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET-----------TTEEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec-----------CcEEEEECCCHHHHHHHHHHHHHHHH
Confidence            467888999999999998 79999999999998843           336889995 5666555555544443