Citrus Sinensis ID: 012307

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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-------430-------440-------450-------460------
Protein Sequence
MATAETTDNGSINLPEPDPQPETATTESPTTESEAPPTIGSENTEHTTESDSALPQSTGPDAAAVPEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKESITSSYGQIDTGYRPSYPQLGNSSYPSSSLSTQPYGGYGSSGVGGYTSYRL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHHcccEEEcccccccccEEEEEcccccccccccHHHHHHHHHHHHHcccccccccccccccccEEEEEEEEccccEEEEcccccHHHHHHHHHcccEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccccccccccccccHHHHHHHcccEEEEEcccccccEEEEEEEccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEccccccccccEEEEEcccccHHHHHHHHHHHHHHHHHHcccccccccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHcccEEEEEccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccEEEEEEEccccccEEEccccHHHHHHHHHcccEEEEEccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mataettdngsinlpepdpqpetattesptteseapptigsentehttesdsalpqstgpdaaavpeekkwpgwpghcvfrMIVPVLKvgsiigrkgeLIKKTCEDTRARIkvldgpvsspdrivlisgkeepeapvspaMDAAVRVFKRvsglpendvdakasgaafCSVRLLVPSTQAINLIGKQGSLIKSIqensgasvrvlsadeapfyvtedeRIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQsaisteytpstrreslflerepqlesryrlsgisiygqdpalstirssalgrasgpivTQITQTMQipisyaediigvggtsieNIRRTSGAIITvqesrglpdeitveikgTSSQVQLAQQLIQEYMNNHkesitssygqidtgyrpsypqlgnssypssslstqpyggygssgvggytsyrl
Flexible Loop (DISEMBL)
mataettdngsinlpepdpqpetattesptteseapptIGSENTEHTTESDSALPQSTGPDAAAVPEEKKWPGWPGHCVFRMIVPVLKvgsiigrkgelikktcedtrarikvldgpvsspdRIVLIsgkeepeapvspaMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAatqsaisteytpstrreslflerepqlesryRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAiitvqesrglpDEITVEIKGTSSQVQLAQQLIQEYMNNHKESITSSYGQIDTGYRPSYPQLGNSSYPSsslstqpyggygssgvggytsyrl
Low Complexity Region (SEG)
MATAETTDNGSINLPEPDPQpetattesptteseapptIGSENTEHTTESDSALPQSTGPDAAAVPEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQgeaakvlkaleavvgHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKESITSSYGQIDTGYRPSYPQLGNssypssslsTQPyggygssgvggytsyRL
Disordered region (IsUnstruct)
*********************************************************************KWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPV****RIVLI*****************VRVFKRVSGL****VDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASI***********************************************YRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG****VQLAQQLIQEY*********************************************************
Disordered Region (DISOPRED)
******************************************************************************VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKR********************VRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLF*******************KSSL************************R****E***********************A*GRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGA***********DEITVEIKGTSSQVQLAQQLI************************************************************
Disordered Region (DISEMBL)
*********GSINLPEP************************************************PEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKE********AMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKESITSSYGQIDTGYRPSYPQLGNSSYPSSSLSTQPYGGYGSSGVGGYTSYRL
Disordered Region (DISPRO)
**************************************************************************PGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGL***********AAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIR***********VTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHK******YGQ***GYRP*********************GYGSS******SY**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATAETTDNGSINLPEPDPQPETATTESPTTESEAPPTIGSENTEHTTESDSALPQSTGPDAAAVPEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKESITSSYGQIDTGYRPSYPQLGNSSYPSSSLSTQPYGGYGSSGVGGYTSYRL
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	466	2.2.26 [Sep-21-2011]
P57721	371	Poly(rC)-binding protein	yes	no	0.652	0.819	0.272	5e-17
P57722	371	Poly(rC)-binding protein	yes	no	0.652	0.819	0.272	5e-17
P58223	606	KH domain-containing prot	no	no	0.658	0.506	0.249	2e-13
P57724	403	Poly(rC)-binding protein	no	no	0.618	0.714	0.266	4e-13
Q0VCU0	403	Poly(rC)-binding protein	no	no	0.688	0.796	0.260	7e-13
P57723	403	Poly(rC)-binding protein	no	no	0.618	0.714	0.263	1e-12
Q61990	362	Poly(rC)-binding protein	no	no	0.695	0.895	0.255	2e-12
Q15366	365	Poly(rC)-binding protein	no	no	0.695	0.887	0.261	2e-12
O19048	356	Poly(rC)-binding protein	no	no	0.306	0.401	0.304	2e-11
P60335	356	Poly(rC)-binding protein	no	no	0.306	0.401	0.304	2e-11

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

 Score = 89.4 bits (220), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 93/341 (27%), Positives = 158/341 (46%), Gaps = 37/341 (10%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSP 139
            R+++   +VGSIIG+KGE +KK  E++ ARI + +G  + P+RIV I+G          
Sbjct: 48  IRLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTITG---------- 95

Query: 140 AMDAAVRVFKRVSGLPENDV-----DAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSI 194
             DA  + F  ++   E D+     ++ A+     ++RL+VP++Q  +LIGK GS IK I
Sbjct: 96  PTDAIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEI 155

Query: 195 QENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLF 254
           +E++GA V+V + D  P      ER V + G    +++ ++ +   + +       +P  
Sbjct: 156 RESTGAQVQV-AGDMLP---NSTERAVTISGTPDAIIQCVKQICVVMLESPPKGATIPYR 211

Query: 255 EKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREP-----QLESR 309
            K  +  +        +A   +     Q AI       T+   L +++ P     Q    
Sbjct: 212 PKPASTPV-------IFAGGQAYTIQGQYAIP-HPDQLTKLHQLAMQQTPFPPLGQTNPA 263

Query: 310 YRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIR 369
           +    + ++  + A + +  S+   AS P     T  + IP      IIG  GT I  IR
Sbjct: 264 FPGEKLPLHSSEEAQNLMGQSSGLDASPPAS---THELTIPNDLIGCIIGRQGTKINEIR 320

Query: 370 RTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYM 410
           + SGA I +  +     E  + I GT + + LAQ LI   +
Sbjct: 321 QMSGAQIKIANATEGSSERQITITGTPANISLAQYLINARL 361

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.
Homo sapiens (taxid: 9606)

>sp|P57722|PCBP3_MOUSE Poly(rC)-binding protein 3 OS=Mus musculus GN=Pcbp3 PE=2 SV=3

 Score = 89.4 bits (220), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 93/341 (27%), Positives = 158/341 (46%), Gaps = 37/341 (10%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSP 139
            R+++   +VGSIIG+KGE +KK  E++ ARI + +G  + P+RIV I+G          
Sbjct: 48  IRLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTITGPT-------- 97

Query: 140 AMDAAVRVFKRVSGLPENDV-----DAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSI 194
             DA  + F  ++   E D+     ++ A+     ++RL+VP++Q  +LIGK GS IK I
Sbjct: 98  --DAIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEI 155

Query: 195 QENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLF 254
           +E++GA V+V + D  P      ER V + G    +++ ++ +   + +       +P  
Sbjct: 156 RESTGAQVQV-AGDMLP---NSTERAVTISGTPDAIIQCVKQICVVMLESPPKGATIPYR 211

Query: 255 EKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREP-----QLESR 309
            K  +  +        +A   +     Q AI       T+   L +++ P     Q    
Sbjct: 212 PKPASTPV-------IFAGGQAYTIQGQYAIP-HPDQLTKLHQLAMQQTPFPPLGQTNPA 263

Query: 310 YRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIR 369
           +    + ++  + A + +  S+   AS P     T  + IP      IIG  GT I  IR
Sbjct: 264 FPGEKLPLHSSEEAQNLMGQSSGLDASPPAS---THELTIPNDLIGCIIGRQGTKINEIR 320

Query: 370 RTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYM 410
           + SGA I +  +     E  + I GT + + LAQ LI   +
Sbjct: 321 QMSGAQIKIANATEGSSERQITITGTPANISLAQYLINARL 361

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

Mus musculus (taxid: 10090)

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

 Score = 77.8 bits (190), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 90/361 (24%), Positives = 163/361 (45%), Gaps = 54/361 (14%)

Query: 52  SALPQSTGPDAAAVPEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARI 111
           S+LP + G   ++  EE          VF+++ P+  +  +IG+ G  IK+  E + + I
Sbjct: 295 SSLPVTHGFGGSSRSEE---------LVFKVLCPLCNIMRVIGKGGSTIKRIREASGSCI 345

Query: 112 KVLDGPVSSPDR--IVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFC 169
           +V D      D   +++++  E P+   S A++A + + + +     ND DA+       
Sbjct: 346 EVNDSRTKCGDDECVIIVTATESPDDMKSMAVEAVLLLQEYI-----NDEDAEN-----V 395

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
            ++LLV S     +IGK GS+I  I++ + A++ +           + + +VE+ GE + 
Sbjct: 396 KMQLLVSSKVIGCVIGKSGSVINEIRKRTNANICISKG--------KKDDLVEVSGEVSS 447

Query: 230 VLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEY 289
           V  AL  +V  LR+ +       L +K   A+    R+     D  S  + + +A  T  
Sbjct: 448 VRDALIQIVLRLREDV-------LGDKDSVAT----RKPPARTDNCSFLSGSSNAGYT-- 494

Query: 290 TPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQI 349
            PS             + S    SG   YG  PA   +  S    + G + +     + I
Sbjct: 495 LPSF------------MSSMASTSGFHGYGSFPAGDNVLGSTGPYSYGRLPSSSALEILI 542

Query: 350 PISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEY 409
           P      ++G GG ++ENIRR SGA+I +  S+    +    + GT  Q++ A+ L+Q +
Sbjct: 543 PAHAMSKVMGKGGGNLENIRRISGAMIEISASKTSHGDHIALLSGTLEQMRCAENLVQAF 602

Query: 410 M 410
           +
Sbjct: 603 V 603

Arabidopsis thaliana (taxid: 3702)

>sp|P57724|PCBP4_MOUSE Poly(rC)-binding protein 4 OS=Mus musculus GN=Pcbp4 PE=2 SV=1

 Score = 76.6 bits (187), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 92/345 (26%), Positives = 149/345 (43%), Gaps = 57/345 (16%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSP 139
            RM++   +VGSIIG+KGE +K+  E + ARI + +G  S P+RI  I+G          
Sbjct: 20  LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG--SCPERITTITG---------- 67

Query: 140 AMDAAVRVFKRVS----GLPENDVDAKASGAAF----CSVRLLVPSTQAINLIGKQGSLI 191
              +   VF  VS     L E+   A A+G +      ++RL++P++Q  +LIGK G+ I
Sbjct: 68  ---STAAVFHAVSMIAFKLDEDLCAAPANGGSVSRPPVTLRLVIPASQCGSLIGKAGTKI 124

Query: 192 KSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVL 251
           K I+E +GA V+V + D  P      ER V + G    ++  +  +   + +       +
Sbjct: 125 KEIRETTGAQVQV-AGDLLP---NSTERAVTVSGVPDAIILCVRQICAVILESPPKGATI 180

Query: 252 PLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYR 311
           P     Y+ S+S    +        L A    ++  +Y   T  E   L+         +
Sbjct: 181 P-----YHPSLSLGTVL--------LSANQGFSVQGQYGAVTPAEVTKLQ---------Q 218

Query: 312 LSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRT 371
           LSG ++    P++             P     +Q   +P      +IG  G+ I  IR+ 
Sbjct: 219 LSGHAVPFASPSVVP--------GMDPSTQTSSQEFLVPNDLIGCVIGRQGSKISEIRQM 270

Query: 372 SGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKES 416
           SGA I +        E  V I G+   + LAQ LI   +   K +
Sbjct: 271 SGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITACLETAKST 315

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

Mus musculus (taxid: 10090)

>sp|Q0VCU0|PCBP4_BOVIN Poly(rC)-binding protein 4 OS=Bos taurus GN=PCBP4 PE=2 SV=1

 Score = 75.9 bits (185), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 100/384 (26%), Positives = 161/384 (41%), Gaps = 63/384 (16%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSP 139
            RM++   +VGSIIG+KGE +K+  E + ARI + +G  S P+RI  I+G          
Sbjct: 20  LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG--SCPERITTITG---------- 67

Query: 140 AMDAAVRVFKRVS----GLPENDVDAKASGAAF----CSVRLLVPSTQAINLIGKQGSLI 191
              +   VF  VS     L E+   A A+G        ++RL++P++Q  +LIGK G+ I
Sbjct: 68  ---STAAVFHAVSMIAFKLDEDLCAAPANGGNVSRPPVTLRLVIPASQCGSLIGKAGTKI 124

Query: 192 KSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVL 251
           K I+E +GA V+V + D  P      ER V + G    ++  +  +   + +       +
Sbjct: 125 KEIRETTGAQVQV-AGDLLP---NSTERAVTVSGVPDAIILCVRQICAVILESPPKGATI 180

Query: 252 PLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYR 311
           P     Y+ S+S    + +     S+          +Y   T  E   L+         +
Sbjct: 181 P-----YHPSLSLGTVLLSTNQGFSVQG--------QYGTVTPAEVTKLQ---------Q 218

Query: 312 LSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRT 371
           LSG ++    P++             P     +Q   +P      +IG  G+ I  IR+ 
Sbjct: 219 LSGHAVPFASPSMVP--------GLDPSTQTSSQEFLVPNDLIGCVIGRQGSKISEIRQM 270

Query: 372 SGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKESITSSYGQIDTGYRPS 431
           SGA I +        E  V I G+   + LAQ LI   +   K +   + G   T     
Sbjct: 271 SGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITACLETAKSTSGGTPGSAPTDLPAP 330

Query: 432 YPQLGNSSYPSSSLSTQPYGGYGS 455
           +      S P ++L T P G  G+
Sbjct: 331 F------SPPLTALPTAPPGLLGT 348

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

Bos taurus (taxid: 9913)

>sp|P57723|PCBP4_HUMAN Poly(rC)-binding protein 4 OS=Homo sapiens GN=PCBP4 PE=2 SV=1

 Score = 75.1 bits (183), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 91/345 (26%), Positives = 146/345 (42%), Gaps = 57/345 (16%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSP 139
            RM++   +VGSIIG+KGE +K+  E + ARI + +G  S P+RI  I+G          
Sbjct: 20  LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG--SCPERITTITG---------- 67

Query: 140 AMDAAVRVFKRVS----GLPENDVDAKASGAAF----CSVRLLVPSTQAINLIGKQGSLI 191
              +   VF  VS     L E+   A A+G        ++RL++P++Q  +LIGK G+ I
Sbjct: 68  ---STAAVFHAVSMIAFKLDEDLCAAPANGGNVSRPPVTLRLVIPASQCGSLIGKAGTKI 124

Query: 192 KSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVL 251
           K I+E +GA V+V + D  P      ER V + G    ++  +  +   + +       +
Sbjct: 125 KEIRETTGAQVQV-AGDLLP---NSTERAVTVSGVPDAIILCVRQICAVILESPPKGATI 180

Query: 252 PLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYR 311
           P     Y+ S+S    +        L A    ++  +Y   T  E   L++       + 
Sbjct: 181 P-----YHPSLSLGTVL--------LSANQGFSVQGQYGAVTPAEVTKLQQLSSHAVPFA 227

Query: 312 LSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRT 371
              + + G DP   T                 +Q   +P      +IG  G+ I  IR+ 
Sbjct: 228 TPSV-VPGLDPGTQT----------------SSQEFLVPNDLIGCVIGRQGSKISEIRQM 270

Query: 372 SGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKES 416
           SGA I +        E  V I G+   + LAQ LI   +   K +
Sbjct: 271 SGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITACLETAKST 315

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

Homo sapiens (taxid: 9606)

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

 Score = 74.3 bits (181), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 93/364 (25%), Positives = 166/364 (45%), Gaps = 40/364 (10%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSP 139
            R+++   +VGSIIG+KGE +KK  E++ ARI + +G  + P+RI+ ++G          
Sbjct: 16  IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPT-------- 65

Query: 140 AMDAAVRVFKRVSGLPENDVDAKASGAAFCS-----VRLLVPSTQAINLIGKQGSLIKSI 194
             +A  + F  +    E D+ +  + +   S     +RL+VP++Q  +LIGK G  IK I
Sbjct: 66  --NAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEI 123

Query: 195 QENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLF 254
           +E++GA V+V + D  P      ER + + G    +++ ++ +   + +       +P  
Sbjct: 124 RESTGAQVQV-AGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLESPPKGVTIPYR 179

Query: 255 EKTYNASI----SQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLER-----EPQ 305
            K  ++ +     Q+R   T +D +S    T S            E+  ++      +P 
Sbjct: 180 PKPSSSPVIFAGGQDR-YSTGSDSASFPHTTPSMCLNPDLEGPPLEAYTIQGQYAIPQPD 238

Query: 306 LESRYRL----SGISIYGQDPALSTIRSSA---LGRASGPIVTQITQT--MQIPISYAED 356
           L   ++L    S   +   +   S I SS+    G  +G   +  T +  + IP      
Sbjct: 239 LTKLHQLAMQQSHFPMTHGNTGFSGIESSSPEVKGYWAGLDASAQTTSHELTIPNDLIGC 298

Query: 357 IIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKES 416
           IIG  G  I  IR+ SGA I +        +  V I G+++ + LAQ LI   +++    
Sbjct: 299 IIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSETGG 358

Query: 417 ITSS 420
           + SS
Sbjct: 359 MGSS 362

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 = 73.9 bits (180), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 96/367 (26%), Positives = 167/367 (45%), Gaps = 43/367 (11%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSP 139
            R+++   +VGSIIG+KGE +KK  E++ ARI + +G  + P+RI+ ++G          
Sbjct: 16  IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPT-------- 65

Query: 140 AMDAAVRVFKRVSGLPENDVDAKASGAAFCS-----VRLLVPSTQAINLIGKQGSLIKSI 194
             +A  + F  +    E D+ +  + +   S     +RL+VP++Q  +LIGK G  IK I
Sbjct: 66  --NAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEI 123

Query: 195 QENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVD---QGV- 250
           +E++GA V+V + D  P      ER + + G    +++ ++ +   + + L     +GV 
Sbjct: 124 RESTGAQVQV-AGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLETLSQSPPKGVT 179

Query: 251 LPLFEKTYNASI----SQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLER---- 302
           +P   K  ++ +     Q+R   T +D +S    T S            E+  ++     
Sbjct: 180 IPYRPKPSSSPVIFAGGQDR-YSTGSDSASFPHTTPSMCLNPDLEGPPLEAYTIQGQYAI 238

Query: 303 -EPQLESRYRL----SGISIYGQDPALSTIRSSA---LGRASGPIVTQIT-QTMQIPISY 353
            +P L   ++L    S   +   +   S I SS+    G        Q T   + IP   
Sbjct: 239 PQPDLTKLHQLAMQQSHFPMTHGNTGFSGIESSSPEVKGYWGLDASAQTTSHELTIPNDL 298

Query: 354 AEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH 413
              IIG  G  I  IR+ SGA I +        +  V I G+++ + LAQ LI   +++ 
Sbjct: 299 IGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSE 358

Query: 414 KESITSS 420
              + SS
Sbjct: 359 TGGMGSS 365

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

 Score = 70.9 bits (172), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 50/164 (30%), Positives = 89/164 (54%), Gaps = 21/164 (12%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSP 139
            R+++   +VGSIIG+KGE +K+  E++ ARI + +G  + P+RI+ ++G          
Sbjct: 16  IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEG--NCPERIITLTGPT-------- 65

Query: 140 AMDAAVRVFKRVSGLPENDVDAKASGAAFCS-----VRLLVPSTQAINLIGKQGSLIKSI 194
             +A  + F  +    E D+++  + +   S     +RL+VP+TQ  +LIGK G  IK I
Sbjct: 66  --NAIFKAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEI 123

Query: 195 QENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVV 238
           +E++GA V+V + D  P      ER + + G    V + ++ + 
Sbjct: 124 RESTGAQVQV-AGDMLP---NSTERAITIAGVPQSVTECVKQIC 163

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 = 70.9 bits (172), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 50/164 (30%), Positives = 89/164 (54%), Gaps = 21/164 (12%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSP 139
            R+++   +VGSIIG+KGE +K+  E++ ARI + +G  + P+RI+ ++G          
Sbjct: 16  IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEG--NCPERIITLTGPT-------- 65

Query: 140 AMDAAVRVFKRVSGLPENDVDAKASGAAFCS-----VRLLVPSTQAINLIGKQGSLIKSI 194
             +A  + F  +    E D+++  + +   S     +RL+VP+TQ  +LIGK G  IK I
Sbjct: 66  --NAIFKAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEI 123

Query: 195 QENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVV 238
           +E++GA V+V + D  P      ER + + G    V + ++ + 
Sbjct: 124 RESTGAQVQV-AGDMLP---NSTERAITIAGVPQSVTECVKQIC 163

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

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	466
225445949	466	PREDICTED: KH domain-containing protein	0.935	0.935	0.676	1e-164
356549146	436	PREDICTED: poly(rC)-binding protein 3-li	0.929	0.993	0.656	1e-162
356556240	442	PREDICTED: KH domain-containing protein	0.942	0.993	0.643	1e-159
449463577	468	PREDICTED: LOW QUALITY PROTEIN: poly(rC)	0.918	0.914	0.669	1e-159
356562072	436	PREDICTED: poly(rC)-binding protein 3-li	0.802	0.857	0.738	1e-155
255554418	451	Poly(rC)-binding protein, putative [Rici	0.851	0.880	0.696	1e-154
356530338	443	PREDICTED: KH domain-containing protein	0.858	0.902	0.678	1e-151
297803502	495	hypothetical protein ARALYDRAFT_492216 [	0.894	0.842	0.590	1e-143
15236094	495	RNA-binding KH domain-containing protein	0.948	0.892	0.564	1e-142
357479529	431	Poly(rC)-binding protein [Medicago trunc	0.864	0.935	0.675	1e-139

>gi|225445949|ref|XP_002264417.1| PREDICTED: KH domain-containing protein At4g18375 isoform 1 [Vitis vinifera]

 Score =  584 bits (1506), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 312/461 (67%), Positives = 363/461 (78%), Gaps = 25/461 (5%)

Query: 1   MATAETTD----NGSINLPEPDPQPETATT-----ESPTTESEAPPTIGSENTEHTTESD 51
           MAT  TT+    NG+   P  DP+ E + T      + T ESE  P   SEN E    S+
Sbjct: 1   MATTGTTEPAPVNGAAQSPGSDPKTELSETPLSASNAATAESEQAP---SENLE----SE 53

Query: 52  SALPQSTGPDAAAVPEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARI 111
           S  P  T  +A A   EKKWPGWPG CVFR+IVPVLKVGSIIGRKGELIKK CE+TRARI
Sbjct: 54  STAPPET--EAPAPASEKKWPGWPGDCVFRLIVPVLKVGSIIGRKGELIKKMCEETRARI 111

Query: 112 KVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAA---F 168
           +VLDG V + DRIVLISG+EEPEAP+SPAMDA +RVFKRV+GL E++ D KA GAA   F
Sbjct: 112 RVLDGAVGTSDRIVLISGREEPEAPLSPAMDAVIRVFKRVTGLSESEGDGKAYGAAGVAF 171

Query: 169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAA 228
           CS+RLLV STQAINLIGKQGSLIKSIQE++GASVRVLS DE PFY   DERIVE+QGEA 
Sbjct: 172 CSIRLLVASTQAINLIGKQGSLIKSIQESTGASVRVLSGDEVPFYAAADERIVELQGEAL 231

Query: 229 KVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTE 288
           KV KALEAVVGHLRKFLVD  VLPLFE+TYNA+ISQ+RQ +TWADKS LH  +Q+ + ++
Sbjct: 232 KVQKALEAVVGHLRKFLVDHSVLPLFERTYNATISQDRQSDTWADKSLLHGTSQTGMGSD 291

Query: 289 YTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQ 348
           Y+   +RESL+L+RE Q+E     SG+ +YGQ+  LS IRSS LGRA  PIVTQI QTMQ
Sbjct: 292 YSLPAKRESLYLDRETQMEH----SGLPMYGQEHGLSGIRSSGLGRAGAPIVTQIAQTMQ 347

Query: 349 IPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQE 408
           IP+SYAEDIIG+GG +I  IRRTSGAI+TVQESRGLPDEITVEIKGTSSQVQ AQQLIQE
Sbjct: 348 IPLSYAEDIIGIGGANIAYIRRTSGAILTVQESRGLPDEITVEIKGTSSQVQTAQQLIQE 407

Query: 409 YMNNHKESITSSYGQIDTGYRPSYPQLGNSSYPSSSLSTQP 449
           +++NHKE + SSYG++D+G R SY QLGN+SY SSSLS+QP
Sbjct: 408 FISNHKEPVPSSYGKMDSGLRSSYSQLGNTSYSSSSLSSQP 448

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356549146|ref|XP_003542958.1| PREDICTED: poly(rC)-binding protein 3-like [Glycine max]

 Score =  576 bits (1485), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 308/469 (65%), Positives = 356/469 (75%), Gaps = 36/469 (7%)

Query: 1   MATAETTDNGSINLPEPDPQPETATTESPTTESEAPPTIGSENTEHTTESDSALPQSTGP 60
           MAT +   NG   +   +P    A  E P+T ++ PP                      P
Sbjct: 1   MATLDQIQNG---VSSDNP----AAAEPPSTTADVPP----------------------P 31

Query: 61  DAAAVPEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSS 120
           DAAA   EK+WPGWPGHCVFR+IVPVLKVGSIIGRKGELIKKTCE+T+ARI+VLDG V +
Sbjct: 32  DAAA---EKRWPGWPGHCVFRLIVPVLKVGSIIGRKGELIKKTCEETKARIRVLDGAVGT 88

Query: 121 PDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQA 180
            DRIVLISGKE+ EAP+SPAMDA +RVFKRVSG  E D   KAS  AFCSVRLLV STQA
Sbjct: 89  SDRIVLISGKEDLEAPLSPAMDAVIRVFKRVSGFSEIDAKNKASAVAFCSVRLLVASTQA 148

Query: 181 INLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGH 240
           INLIGKQGSLIKSIQEN+GASVRVLS DE PFY   DERIVE+QGEA KVLKALEAVVGH
Sbjct: 149 INLIGKQGSLIKSIQENTGASVRVLSGDEVPFYAAADERIVELQGEAMKVLKALEAVVGH 208

Query: 241 LRKFLVDQGVLPLFEKTYNASISQERQVE-TWADKSSLHAATQSAISTEYTPSTRRESLF 299
           LRKFLVD  VLPLFEKTYNA+ISQERQ + TW DK SLH+A+Q +I T+   ST+R+SLF
Sbjct: 209 LRKFLVDNSVLPLFEKTYNATISQERQADTTWVDKPSLHSASQPSIVTDIPLSTKRDSLF 268

Query: 300 LEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASG-PIVTQITQTMQIPISYAEDII 358
            +RE QL+S    S +S+YGQD +LS +RSSAL R S  PIVT + QTMQIP+SYAEDII
Sbjct: 269 ADRESQLDSLLPPSTMSMYGQDSSLSGLRSSALSRPSAPPIVTTVIQTMQIPLSYAEDII 328

Query: 359 GVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKESIT 418
           G+ GT+IE IRRTSGAI+TVQESR +PDEI VEIKGTSSQVQ AQQLIQE ++NH E + 
Sbjct: 329 GIQGTNIEYIRRTSGAILTVQESR-VPDEIIVEIKGTSSQVQTAQQLIQEVISNHTEPVA 387

Query: 419 SSYGQIDTGYRPSYPQLG-NSSYPSSSLSTQPYGGYGSSGVGGYTSYRL 466
           S+Y ++DTG R SYPQLG +S   SS  S    GGYGSS +GGY+++RL
Sbjct: 388 SNYSRLDTGLRSSYPQLGSSSYSSSSLSSQPYSGGYGSSALGGYSTFRL 436

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556240|ref|XP_003546434.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  568 bits (1464), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/469 (64%), Positives = 358/469 (76%), Gaps = 30/469 (6%)

Query: 1   MATAETTDNGSINLPEPDPQPETATTESPTTESEAPPTIGSENTEHTTESDSALPQSTGP 60
           MATAE   NG+     PD              +  PPT         TES++A       
Sbjct: 1   MATAEPLQNGTAEPLLPD-----------NVSAAQPPT--------ETESNAAA------ 35

Query: 61  DAAAVPEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSS 120
            AA+ P EK+WPGWPG CVFR+IVPV KVGSIIGRKGELIKK CE+TR+RI+VLD P+ +
Sbjct: 36  -AASTPPEKRWPGWPGDCVFRLIVPVGKVGSIIGRKGELIKKMCEETRSRIRVLDAPLGT 94

Query: 121 PDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAK--ASGAAFCSVRLLVPST 178
           PDRIVL+SGKEEPEA +SPAMDA VR+FKRVSGL E D + K  A+G AFCS+RLLV ST
Sbjct: 95  PDRIVLVSGKEEPEAALSPAMDAVVRIFKRVSGLSETDAENKESAAGLAFCSIRLLVAST 154

Query: 179 QAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVV 238
           QAINLIGKQGSLIKSIQEN+ ASVRVLS DE   Y T DERIVE+QGEA KVLKALEAVV
Sbjct: 155 QAINLIGKQGSLIKSIQENTSASVRVLSGDEVQSYATVDERIVEIQGEALKVLKALEAVV 214

Query: 239 GHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESL 298
           GHLRKFLVD  VLPLFEKTYNAS SQ+RQ ETW+DKS LH  ++++I  +   ST+R+S+
Sbjct: 215 GHLRKFLVDHSVLPLFEKTYNASTSQDRQAETWSDKSLLHTTSRTSIFADIPYSTKRDSV 274

Query: 299 FLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDII 358
             +RE QL+S    S +S+YGQD +LS +RSSALGR   PIVT + QTMQIP+SYAEDII
Sbjct: 275 LADRESQLDSFLPSSTMSLYGQDSSLSGVRSSALGRVGAPIVTTVIQTMQIPLSYAEDII 334

Query: 359 GVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKESIT 418
           G+ GT+IE IRRTSGAI+TVQESR +PDEI VEIKGTSS+VQ AQQLIQ+ +++HKE IT
Sbjct: 335 GIQGTNIEYIRRTSGAILTVQESR-VPDEIVVEIKGTSSEVQTAQQLIQDVISSHKEPIT 393

Query: 419 SSYGQIDTGYRPSYPQLGNS-SYPSSSLSTQPYGGYGSSGVGGYTSYRL 466
           SSYG++D G R SY QLG +   P SSLS+QPY GYG+SG+G Y+++RL
Sbjct: 394 SSYGRLDAGPRSSYSQLGTTSRLPPSSLSSQPYTGYGASGLGDYSTFRL 442

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463577|ref|XP_004149510.1| PREDICTED: LOW QUALITY PROTEIN: poly(rC)-binding protein 3-like [Cucumis sativus]

 Score =  566 bits (1459), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 296/442 (66%), Positives = 345/442 (78%), Gaps = 14/442 (3%)

Query: 1   MATAETTDNGSIN-LPEP--DPQPETATTESPTTESEAPPTIGSENTEHTTE---SDSAL 54
           MAT  TT+NGS + +P P     P  A  E  +TE+    +    + +  +    SDSA 
Sbjct: 1   MATNTTTENGSTDAIPNPLSSTLPSLAAAEPDSTEAGDDDSDSDPSNQDYSSVPPSDSAA 60

Query: 55  PQSTGPDAAAVPEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL 114
            +   P     P +KKWPGWPG CVFR+IVPV+KVGSIIGRKG+LIKK CE+TRARI+VL
Sbjct: 61  HE---PSNHTGPSDKKWPGWPGDCVFRLIVPVVKVGSIIGRKGDLIKKMCEETRARIRVL 117

Query: 115 DGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLL 174
           DG V +PDR+VLISGKEE E+P+SPAMDA +RVFKRVSGL EN+ +AKAS   FCS+RLL
Sbjct: 118 DGAVGTPDRVVLISGKEELESPLSPAMDAVIRVFKRVSGLSENEDEAKAS---FCSIRLL 174

Query: 175 VPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKAL 234
           V STQAINLIGKQGSLIKSIQE++GASVRVLS DE PFY   DER+VE+QGE+ KVLKAL
Sbjct: 175 VASTQAINLIGKQGSLIKSIQESTGASVRVLSGDEMPFYAGADERMVELQGESLKVLKAL 234

Query: 235 EAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTR 294
           E VVGHLRKFLVD  VLPLFEK++N   SQ+RQ ETWADKSSL  A+QS IS EY PST+
Sbjct: 235 EGVVGHLRKFLVDHSVLPLFEKSFNTPASQDRQTETWADKSSLLTASQSIISAEYAPSTK 294

Query: 295 RESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYA 354
           RESLFL+RE   +S    SGIS+YGQD  L TIRSS +GR+ GPIVTQ+TQTMQIP+SYA
Sbjct: 295 RESLFLDREAHFDSHISSSGISLYGQDRVLPTIRSSGVGRSGGPIVTQVTQTMQIPLSYA 354

Query: 355 EDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHK 414
           EDIIGVGGT+I  IRR SGAI+T+QESRGLPDEITVEIKGTSSQVQ+AQQLIQE +N  K
Sbjct: 355 EDIIGVGGTNIAFIRRNSGAILTIQESRGLPDEITVEIKGTSSQVQMAQQLIQEAVNAPK 414

Query: 415 ESIT-SSYGQIDTGYRPSYPQL 435
           E +T SSYG++  G R SY QL
Sbjct: 415 EPVTSSSYGRL-XGLRSSYSQL 435

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356562072|ref|XP_003549298.1| PREDICTED: poly(rC)-binding protein 3-like [Glycine max]

 Score =  553 bits (1426), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 280/379 (73%), Positives = 317/379 (83%), Gaps = 5/379 (1%)

Query: 60  PDAAAVPEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVS 119
           PD AA   EK+WPGWPGHCVFR+IVPVLKVGSIIGRKGELIKKTCE+T+ARI+VLDG V 
Sbjct: 30  PDPAAA--EKRWPGWPGHCVFRLIVPVLKVGSIIGRKGELIKKTCEETKARIRVLDGAVG 87

Query: 120 SPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQ 179
           + DRIVLISGKEEPEAP+SPAM+A +RVFKRVSG  E D + KAS  AFCSVRLLV STQ
Sbjct: 88  TSDRIVLISGKEEPEAPLSPAMNAVIRVFKRVSGFSEIDAENKASAVAFCSVRLLVASTQ 147

Query: 180 AINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVG 239
           AINLIGKQGSLIKSIQEN+GASVRVLS DE PFY   DERIVE+QGEA KVLKALEAVVG
Sbjct: 148 AINLIGKQGSLIKSIQENTGASVRVLSGDEVPFYAAADERIVELQGEAMKVLKALEAVVG 207

Query: 240 HLRKFLVDQGVLPLFEKTYNASISQERQVE-TWADKSSLHAATQSAISTEYTPSTRRESL 298
           HLRKFLVD  VLPLFEKTYNA+ISQE Q + TW DK SLH+A+Q +I T+   ST+R+SL
Sbjct: 208 HLRKFLVDNSVLPLFEKTYNATISQEHQADTTWVDKPSLHSASQPSIVTDLPLSTKRDSL 267

Query: 299 FLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASG-PIVTQITQTMQIPISYAEDI 357
           F +RE QL+S    S +SIYGQD +LS +RSSAL R S  PIVT + QTMQIP+SYAEDI
Sbjct: 268 FADRESQLDSLLPPSTMSIYGQDSSLSGLRSSALSRPSAPPIVTTVIQTMQIPLSYAEDI 327

Query: 358 IGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKESI 417
           IG+ GT+IE IR TSGAI+TVQES  +PDEI VEIKGTSSQVQ AQQLIQE ++NHKE +
Sbjct: 328 IGIQGTNIEYIRCTSGAILTVQES-PVPDEIIVEIKGTSSQVQTAQQLIQEVISNHKEPL 386

Query: 418 TSSYGQIDTGYRPSYPQLG 436
            S+Y ++DTG R SYPQLG
Sbjct: 387 ASNYSRLDTGLRSSYPQLG 405

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255554418|ref|XP_002518248.1| Poly(rC)-binding protein, putative [Ricinus communis] gi|223542595|gb|EEF44134.1| Poly(rC)-binding protein, putative [Ricinus communis]

 Score =  551 bits (1421), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 278/399 (69%), Positives = 332/399 (83%), Gaps = 2/399 (0%)

Query: 70  KWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISG 129
            WPGWPG CVFR+IVPVLKVGSIIGRKG+LIKK C++TRARI+VLD P+ +PDR+VLISG
Sbjct: 53  NWPGWPGDCVFRLIVPVLKVGSIIGRKGDLIKKMCDETRARIRVLDAPIGTPDRVVLISG 112

Query: 130 KEEPEAPVSPAMDAAVRVFKRVSGLPE-NDVDAKASGAAFCSVRLLVPSTQAINLIGKQG 188
           KE+ EAP+SPAMDA +RVFKRVSGLPE N  +  A+G AF S+RLLV STQAINLIGKQG
Sbjct: 113 KEDVEAPLSPAMDAVIRVFKRVSGLPEGNAQELGAAGIAFSSIRLLVASTQAINLIGKQG 172

Query: 189 SLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQ 248
           S+IKSIQE++GASVRVLS +E PFYV  DERIV++QGEA KVL+ALEA+VGHLRKFLVD 
Sbjct: 173 SIIKSIQESTGASVRVLSENEVPFYVATDERIVDLQGEAMKVLEALEAIVGHLRKFLVDH 232

Query: 249 GVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLES 308
            VLPLFEK YNA IS +RQ ETW+D+SS H  +Q  I  +Y  S +R++L LERE   ES
Sbjct: 233 SVLPLFEKNYNALISLDRQAETWSDRSSFHTTSQGRIDIDYPLSGKRDALLLERETPFES 292

Query: 309 RYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENI 368
           +  LS IS+YGQDPA+S++RSS   R+S PIVTQ+TQTMQ+PISYAE+IIG+ G +IE I
Sbjct: 293 QVPLSRISLYGQDPAISSVRSSVFNRSSVPIVTQVTQTMQVPISYAEEIIGIRGNNIEYI 352

Query: 369 RRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH-KESITSSYGQIDTG 427
           RRTSGAIITV ESRGLPDEI VEIKGT+S+VQ+AQQLIQE+++NH KE +TSSY + DTG
Sbjct: 353 RRTSGAIITVNESRGLPDEIIVEIKGTASEVQMAQQLIQEFLSNHNKEPVTSSYSKYDTG 412

Query: 428 YRPSYPQLGNSSYPSSSLSTQPYGGYGSSGVGGYTSYRL 466
            +  Y QL NS Y SSSLS + YG YGSS +GGY+S+RL
Sbjct: 413 LKSVYSQLDNSPYTSSSLSAKSYGEYGSSSLGGYSSFRL 451

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530338|ref|XP_003533739.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  542 bits (1396), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 274/404 (67%), Positives = 330/404 (81%), Gaps = 4/404 (0%)

Query: 66  PEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIV 125
           P EK+WPGWPG CVFR+IVPV KVGSIIGRKGELIKK CE+TR+RI+VLD P+ +PDRIV
Sbjct: 41  PPEKRWPGWPGDCVFRLIVPVGKVGSIIGRKGELIKKMCEETRSRIRVLDAPLGTPDRIV 100

Query: 126 LISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAK--ASGAAFCSVRLLVPSTQAINL 183
           L+SGKE+PEA +SPAMDA VR+FKRVSG  E D + +  A+G AF S+RLLV STQAINL
Sbjct: 101 LVSGKEDPEAALSPAMDAVVRIFKRVSGFSETDAENQESAAGLAFSSIRLLVASTQAINL 160

Query: 184 IGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK 243
           IGKQGSLIKSIQEN+ ASVRVLS DE  FY T +ERIVE+QGEA KVLKALEAVVGHLRK
Sbjct: 161 IGKQGSLIKSIQENTSASVRVLSGDEVQFYATANERIVEIQGEALKVLKALEAVVGHLRK 220

Query: 244 FLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLERE 303
           FLVD  VLPLFEKTYNA  SQ+RQ ETW+DKS LH +++++I  +   ST+R+S+  +RE
Sbjct: 221 FLVDHSVLPLFEKTYNAPTSQDRQAETWSDKSLLHTSSRTSIFADIPLSTKRDSVLADRE 280

Query: 304 PQLESRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGT 363
            QL+     S +S+YGQD +LS + SSALGR   PIVT + QTMQIP+SYAEDIIG+ GT
Sbjct: 281 SQLDLFLPSSTMSLYGQDSSLSGVHSSALGRVGAPIVTTVIQTMQIPLSYAEDIIGIQGT 340

Query: 364 SIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKESITSSYGQ 423
           +IE IRRTSGAI+TVQESR +PDEI VEIKGTSS+VQ AQQLIQ+ +++HKE +TSSYG+
Sbjct: 341 NIEYIRRTSGAILTVQESR-VPDEIVVEIKGTSSEVQTAQQLIQDVISSHKEPVTSSYGR 399

Query: 424 IDTGYRPSYPQLGNS-SYPSSSLSTQPYGGYGSSGVGGYTSYRL 466
           +D   R SY  LG +   P SSLS+QPY GYG+SG+G Y+++RL
Sbjct: 400 LDAVPRSSYSHLGTTSRLPPSSLSSQPYTGYGASGLGDYSTFRL 443

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297803502|ref|XP_002869635.1| hypothetical protein ARALYDRAFT_492216 [Arabidopsis lyrata subsp. lyrata] gi|297315471|gb|EFH45894.1| hypothetical protein ARALYDRAFT_492216 [Arabidopsis lyrata subsp. lyrata]

 Score =  515 bits (1326), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 273/462 (59%), Positives = 331/462 (71%), Gaps = 45/462 (9%)

Query: 49  ESDSALPQSTGPDAAAVPE----------EKKWPGWPGHCVFRMIVPVLKVGSIIGRKGE 98
           E+  A P+   PD+ A  E           ++WPGWPG CVFRMIVPV KVG+IIGRKG+
Sbjct: 35  ENSGAFPELNQPDSLAAAETTAPDTNDFAAERWPGWPGDCVFRMIVPVSKVGAIIGRKGD 94

Query: 99  LIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPEND 158
            IKK CE+TRARIKVLDGPV++PDRIVLISGKEEPEA +SPAMDA +RVF+RVSGLP+ND
Sbjct: 95  FIKKMCEETRARIKVLDGPVNTPDRIVLISGKEEPEAYMSPAMDAVLRVFRRVSGLPDND 154

Query: 159 VD-AKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTED 217
            D  + +G+AFCSVRLLV STQAINLIGKQGSLIKSI ENSGASVR+LS +E PFY  +D
Sbjct: 155 DDDVQNAGSAFCSVRLLVASTQAINLIGKQGSLIKSIVENSGASVRILSEEETPFYAAQD 214

Query: 218 ERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWAD-KSS 276
           ERIV++QGEA K+LKALEA+VGHLRKFLVD  V+PLFEK Y A +SQ RQ E  A+ KSS
Sbjct: 215 ERIVDLQGEALKILKALEAIVGHLRKFLVDHTVVPLFEKQYLARVSQTRQEEPLAESKSS 274

Query: 277 LHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRAS 336
           LH  + + I  +++   RR+ LFL+R+ ++ESR + +G+SIY QDP LS   S  L R S
Sbjct: 275 LHTISSNVIEPDFSLLARRDPLFLDRDARVESRVQPTGVSIYSQDPVLSARHSPGLARVS 334

Query: 337 GPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTS 396
              VTQ++QTMQIP SYAEDIIGV G +I  IRR SGA IT++ES   PD+ITVEIKGTS
Sbjct: 335 SAFVTQVSQTMQIPFSYAEDIIGVEGANIAYIRRRSGATITIKESPH-PDQITVEIKGTS 393

Query: 397 SQVQLAQQLIQEYMNNHKE--SITSSYGQIDTGYRPSYP--------------------- 433
           SQVQ A+QLIQE+++NHKE  S++  Y +IDTGY P+YP                     
Sbjct: 394 SQVQTAEQLIQEFISNHKEPVSVSGGYARIDTGYVPAYPPQLSNRQEPLSNSYMGTETVQ 453

Query: 434 -------QLGNSSYPSSSLSTQPYGG--YGSSGVGGYTSYRL 466
                  QLG  S  + SL+ Q YG     +S VGGY+SY L
Sbjct: 454 YRPTAYSQLGGPSTYTPSLNGQTYGSEYRPASDVGGYSSYNL 495

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15236094|ref|NP_194330.1| RNA-binding KH domain-containing protein [Arabidopsis thaliana] gi|4538929|emb|CAB39665.1| putative nucleic acid binding protein [Arabidopsis thaliana] gi|7269451|emb|CAB79455.1| putative nucleic acid binding protein [Arabidopsis thaliana] gi|15810499|gb|AAL07137.1| putative nucleic acid binding protein [Arabidopsis thaliana] gi|20466386|gb|AAM20510.1| putative nucleic acid binding protein [Arabidopsis thaliana] gi|21280915|gb|AAM45112.1| putative nucleic acid binding protein [Arabidopsis thaliana] gi|332659742|gb|AEE85142.1| RNA-binding KH domain-containing protein [Arabidopsis thaliana]

 Score =  512 bits (1319), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 284/503 (56%), Positives = 345/503 (68%), Gaps = 61/503 (12%)

Query: 8   DNGSINLPEPDPQPETATTESPTTESEAPPTIGSENTEHTTESDSALPQSTGPDAAAVPE 67
           +NGSINLPE               E+  P   G        E+  A P+   PD+ A  E
Sbjct: 10  NNGSINLPE--------------NENLIP--AGFSAAALLDENSGAFPELNQPDSLAAAE 53

Query: 68  ----------EKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGP 117
                     E++WPGWPG CVFRMIVPV KVG+IIGRKG+ IKK CE+TRARIKVLDGP
Sbjct: 54  TTFPDTNDSAEERWPGWPGDCVFRMIVPVTKVGAIIGRKGDFIKKMCEETRARIKVLDGP 113

Query: 118 VSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPEN-DVDAKASGAAFCSVRLLVP 176
           V++PDRIVLISGKEEPEA +SPAMDA +RVF+RVSGLP+N D D + +G+ F SVRLLV 
Sbjct: 114 VNTPDRIVLISGKEEPEAYMSPAMDAVLRVFRRVSGLPDNDDDDVQNAGSVFSSVRLLVA 173

Query: 177 STQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEA 236
           STQAINLIGKQGSLIKSI ENSGASVR+LS +E PFY  +DERIV++QGEA K+LKALEA
Sbjct: 174 STQAINLIGKQGSLIKSIVENSGASVRILSEEETPFYAAQDERIVDLQGEALKILKALEA 233

Query: 237 VVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWAD-KSSLHAATQSAISTEYTPSTRR 295
           +VGHLR+FLVD  V+PLFEK Y A +SQ RQ E  A+ KSSLH  + + +  +++   RR
Sbjct: 234 IVGHLRRFLVDHTVVPLFEKQYLARVSQTRQEEPLAESKSSLHTISSNLMEPDFSLLARR 293

Query: 296 ESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAE 355
           E LFLER+ +++SR + SG+SIY QDP LS   S  L R S   VTQ++QTMQIP SYAE
Sbjct: 294 EPLFLERDSRVDSRVQPSGVSIYSQDPVLSARHSPGLARVSSAFVTQVSQTMQIPFSYAE 353

Query: 356 DIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE 415
           DIIGV G +I  IRR SGA IT++ES   PD+ITVEIKGT+SQVQ A+QLIQE++ NHKE
Sbjct: 354 DIIGVEGANIAYIRRRSGATITIKESPH-PDQITVEIKGTTSQVQTAEQLIQEFIINHKE 412

Query: 416 --SITSSYGQIDTGYRPSY-PQLGNSS--YPSSSLSTQP----------YGG-------- 452
             S++  Y +ID+GY P+Y PQL N     PS+ + T+P           GG        
Sbjct: 413 PVSVSGGYARIDSGYVPAYPPQLSNRQEPLPSTYMGTEPVQYRPTAYSQLGGPSTYTPTL 472

Query: 453 ----YGS-----SGVGGYTSYRL 466
               YGS     S VGGY+SY L
Sbjct: 473 TGQTYGSEYRPASDVGGYSSYNL 495

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357479529|ref|XP_003610050.1| Poly(rC)-binding protein [Medicago truncatula] gi|355511105|gb|AES92247.1| Poly(rC)-binding protein [Medicago truncatula]

 Score =  500 bits (1287), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 279/413 (67%), Positives = 334/413 (80%), Gaps = 10/413 (2%)

Query: 61  DAAAVP-----EEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLD 115
           DAAA P      EK+WPGWPGHCVFR+IVPV+KVG IIGRKGELIKKTCE+T ARI+VLD
Sbjct: 22  DAAANPTDESESEKRWPGWPGHCVFRLIVPVVKVGIIIGRKGELIKKTCEETHARIRVLD 81

Query: 116 GPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVD-AKASGAAFCSVRLL 174
            PV +PDRIVLISGKE+ EAP+SPAMDA +R+FKRVSGL E D +   A+G A CS+RLL
Sbjct: 82  APVGTPDRIVLISGKEDLEAPLSPAMDAILRIFKRVSGLSETDNNNTAAAGVALCSIRLL 141

Query: 175 VPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKAL 234
           V STQAINLIGKQGS IK+IQEN+GA +RVLS DE P Y   DERI+++QGE  KVLKAL
Sbjct: 142 VASTQAINLIGKQGSSIKAIQENTGAVIRVLSGDELPSYAGADERIIDLQGETLKVLKAL 201

Query: 235 EAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTR 294
           EAVVGHLRKFLVD  V+PLFEKT NA+ISQ+RQ + WADK SL++A+Q +I  +    T+
Sbjct: 202 EAVVGHLRKFLVDSSVIPLFEKTCNATISQDRQTDAWADKPSLYSASQPSIVADI--PTK 259

Query: 295 RESLFLEREPQLESRYRLSGISIYGQD-PALSTIRSSALGRASGPIVTQITQTMQIPISY 353
           R+S F +RE QL+S    S +S+YGQD  ++S +RSSA  RAS  IVT + QTMQIP+SY
Sbjct: 260 RDSFFADRESQLDSLLSSSTMSLYGQDSSSISGLRSSAFNRASASIVTTVIQTMQIPLSY 319

Query: 354 AEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH 413
           AEDIIG+ GT+I+ IRRTSGAI+TVQESR +PDEI VEIKGTS+QVQ AQQLIQE + NH
Sbjct: 320 AEDIIGIQGTNIDYIRRTSGAILTVQESR-VPDEIIVEIKGTSTQVQTAQQLIQEVITNH 378

Query: 414 KESITSSYGQIDTGYRPSYPQLGNSSYPSSSLSTQPYGGYGSSGVGGYTSYRL 466
            E+I S+Y ++DTG R SY QLG+SSYPSSSL +QPY GYGSSG G Y+++RL
Sbjct: 379 NETIASNYARLDTGLRSSYSQLGSSSYPSSSLPSQPYNGYGSSGPGDYSTFRL 431

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	466
TAIR|locus:2120755	495	PEP "AT4G26000" [Arabidopsis t	0.918	0.864	0.575	5.2e-120
TAIR|locus:2084908	577	FLK "AT3G04610" [Arabidopsis t	0.757	0.611	0.434	2.3e-71
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.332	0.249	0.335	1.5e-19
UNIPROTKB|E2RCH9	370	PCBP3 "Uncharacterized protein	0.263	0.332	0.374	3.8e-18
TAIR|locus:2831364	606	AT4G18375 "AT4G18375" [Arabido	0.291	0.224	0.342	1.5e-17
UNIPROTKB|J3QT27	322	PCBP3 "Poly(rC)-binding protei	0.263	0.381	0.374	5.2e-17
ZFIN|ZDB-GENE-070424-78	350	zgc:162999 "zgc:162999" [Danio	0.263	0.351	0.374	5.6e-17
RGD|1307430	319	Pcbp3 "poly(rC) binding protei	0.263	0.385	0.374	6.1e-17
FB|FBgn0262737	557	mub "mushroom-body expressed"	0.244	0.204	0.380	7.8e-17
UNIPROTKB|F1NPL4	326	PCBP3 "Uncharacterized protein	0.253	0.361	0.389	9.7e-17

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

 Score = 1181 (420.8 bits), Expect = 5.2e-120, P = 5.2e-120
 Identities = 255/443 (57%), Positives = 311/443 (70%)

Query:     2 ATAETTDN-GSINLPEPDPQXXXXXXXXXXXXXXXXXXIGSENTEHTTESDS-ALPQSTG 59
             A A++ +N GSINLPE +                      S       + DS A  ++T 
Sbjct:     3 AVADSVENNGSINLPENENLIPAGFSAAALLDE------NSGAFPELNQPDSLAAAETTF 56

Query:    60 PDAAAVPEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVS 119
             PD     EE+ WPGWPG CVFRMIVPV KVG+IIGRKG+ IKK CE+TRARIKVLDGPV+
Sbjct:    57 PDTNDSAEER-WPGWPGDCVFRMIVPVTKVGAIIGRKGDFIKKMCEETRARIKVLDGPVN 115

Query:   120 SPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVD-AKASGAAFCSVRLLVPST 178
             +PDRIVLISGKEEPEA +SPAMDA +RVF+RVSGLP+ND D  + +G+ F SVRLLV ST
Sbjct:   116 TPDRIVLISGKEEPEAYMSPAMDAVLRVFRRVSGLPDNDDDDVQNAGSVFSSVRLLVAST 175

Query:   179 QAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQXXXXXXXXXXXXXX 238
             QAINLIGKQGSLIKSI ENSGASVR+LS +E PFY  +DERIV++Q              
Sbjct:   176 QAINLIGKQGSLIKSIVENSGASVRILSEEETPFYAAQDERIVDLQGEALKILKALEAIV 235

Query:   239 XHLRKFLVDQGVLPLFEKTYNASISQERQVETWAD-KSSLHAATQSAISTEYTPSTRRES 297
              HLR+FLVD  V+PLFEK Y A +SQ RQ E  A+ KSSLH  + + +  +++   RRE 
Sbjct:   236 GHLRRFLVDHTVVPLFEKQYLARVSQTRQEEPLAESKSSLHTISSNLMEPDFSLLARREP 295

Query:   298 LFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDI 357
             LFLER+ +++SR + SG+SIY QDP LS   S  L R S   VTQ++QTMQIP SYAEDI
Sbjct:   296 LFLERDSRVDSRVQPSGVSIYSQDPVLSARHSPGLARVSSAFVTQVSQTMQIPFSYAEDI 355

Query:   358 IGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE-- 415
             IGV G +I  IRR SGA IT++ES   PD+ITVEIKGT+SQVQ A+QLIQE++ NHKE  
Sbjct:   356 IGVEGANIAYIRRRSGATITIKESPH-PDQITVEIKGTTSQVQTAEQLIQEFIINHKEPV 414

Query:   416 SITSSYGQIDTGYRPSYP-QLGN 437
             S++  Y +ID+GY P+YP QL N
Sbjct:   415 SVSGGYARIDSGYVPAYPPQLSN 437

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

 Score = 722 (259.2 bits), Expect = 2.3e-71, P = 2.3e-71
 Identities = 166/382 (43%), Positives = 229/382 (59%)

Query:    45 EHTTESDSALPQSTGPDAAAVPEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTC 104
             EH      + P+    DA    EEK+WPGWPG  VFRM+VP  KVGSIIGRKG++IKK  
Sbjct:   157 EHLESLQKSEPEE---DATVGGEEKRWPGWPGETVFRMLVPAQKVGSIIGRKGDVIKKIV 213

Query:   105 EDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKR-VSGLPENDVDA-K 162
             E+TRARIK+LDGP  + +R V++SGKEEPE+ + P+MD  +RV  R V GL   D +A +
Sbjct:   214 EETRARIKILDGPPGTTERAVMVSGKEEPESSLPPSMDGLLRVHMRIVDGL---DGEASQ 270

Query:   163 ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVE 222
             A   +  S RLLVP++QA +LIGKQG  +K+IQE S   VRVL +++ P +  +D+R+VE
Sbjct:   271 APPPSKVSTRLLVPASQAGSLIGKQGGTVKAIQEASACIVRVLGSEDLPVFALQDDRVVE 330

Query:   223 MQXXXXXXXXXXXXXXXHLRKFLVDQGVLPLFEKTYNASISQERQV----ETWADKSSLH 278
             +                HLRKFLVD+ ++P FE        Q   +    ++W      H
Sbjct:   331 VVGEPTSVHRALELIASHLRKFLVDRSIIPFFENQMQKPTRQMDHMPPPHQSWGPPQG-H 389

Query:   279 AATQSAISTEYTPST------RRESLFLE---REPQLESRYRLSGISIYGQDPALSTIRS 329
             A +       + P        R +S +     R+P +E +    GIS YG++P ++   S
Sbjct:   390 APSVGGGGYGHNPPPYMQPPPRHDSYYPPPEMRQPPMEKQPH-QGISAYGREPPMNVHVS 448

Query:   330 SALGRASGPIVTQ-ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEI 388
             SA      P+V Q +TQ MQIP+SYA+ +IG  G++I   RR SGA +T+QE+RG+P E+
Sbjct:   449 SA-----PPMVAQQVTQQMQIPLSYADAVIGTSGSNISYTRRLSGATVTIQETRGVPGEM 503

Query:   389 TVEIKGTSSQVQLAQQLIQEYM 410
             TVE+ GT SQVQ A QLIQ +M
Sbjct:   504 TVEVSGTGSQVQTAVQLIQNFM 525

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

 Score = 206 (77.6 bits), Expect = 1.5e-19, Sum P(2) = 1.5e-19
 Identities = 57/170 (33%), Positives = 90/170 (52%)

Query:    54 LPQSTGPDAAAVPEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKV 113
             +P+  GP    V EE+          FR++ P  KVGS+IG+ G +++    ++ A IKV
Sbjct:   260 MPEDVGPFNRPVVEEE--------VAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKV 311

Query:   114 LDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRL 173
              D    S +RI++IS +E  E   S A D  +RV  R+      ++  + S A     RL
Sbjct:   312 SDPTHDSEERIIVISARENLERRHSLAQDGVMRVHNRIV-----EIGFEPSAAVVA--RL 364

Query:   174 LVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEM 223
             LV S     L+GK G LI  ++  +GAS+RV + D+A  Y ++ + IV++
Sbjct:   365 LVHSPYIGRLLGKGGHLISEMRRATGASIRVFAKDQATKYESQHDEIVQV 414

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|E2RCH9 PCBP3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 182 (69.1 bits), Expect = 3.8e-18, Sum P(2) = 3.8e-18
 Identities = 49/131 (37%), Positives = 81/131 (61%)

Query:    81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPA 140
             R+++   +VGSIIG+KGE +KK  E++ ARI + +G  + P+RIV I+G   P   +  A
Sbjct:    49 RLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTITG---PTDAIFKA 103

Query:   141 MDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGA 200
                A+  +K    +  +  ++ A+     ++RL+VP++Q  +LIGK GS IK I+E++GA
Sbjct:   104 F--AMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGA 161

Query:   201 SVRVLSADEAP 211
              V+V + D  P
Sbjct:   162 QVQV-AGDMLP 171

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 170 (64.9 bits), Expect = 1.5e-17, Sum P(2) = 1.5e-17
 Identities = 51/149 (34%), Positives = 80/149 (53%)

Query:    79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLI--SGKEEPEA- 135
             V+R++ P+  VG +IG+ G++I     +T+A+IKV D       R++ I  S KE+ E  
Sbjct:    37 VYRILCPIDVVGGVIGKSGKVINAIRHNTKAKIKVFDQLHGCSQRVITIYCSVKEKQEEI 96

Query:   136 --------PVSPAMDAAVRVFKR-VSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGK 186
                     P+  A DA ++V+   V+   EN+             RLLVP +Q+ +LIGK
Sbjct:    97 GFTKSENEPLCCAQDALLKVYDAIVASDEENNTKTNVDRDDNKECRLLVPFSQSSSLIGK 156

Query:   187 QGSLIKSIQENSGASVRVLSADEA-PFYV 214
              G  IK I+  + ASV+V+S D + P +V
Sbjct:   157 AGENIKRIRRRTRASVKVVSKDVSDPSHV 185

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|J3QT27 PCBP3 "Poly(rC)-binding protein 3" [Homo sapiens (taxid:9606)]

 Score = 182 (69.1 bits), Expect = 5.2e-17, Sum P(2) = 5.2e-17
 Identities = 49/131 (37%), Positives = 81/131 (61%)

Query:    81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPA 140
             R+++   +VGSIIG+KGE +KK  E++ ARI + +G  + P+RIV I+G   P   +  A
Sbjct:    25 RLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTITG---PTDAIFKA 79

Query:   141 MDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGA 200
                A+  +K    +  +  ++ A+     ++RL+VP++Q  +LIGK GS IK I+E++GA
Sbjct:    80 F--AMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGA 137

Query:   201 SVRVLSADEAP 211
              V+V + D  P
Sbjct:   138 QVQV-AGDMLP 147

GO:0003723 "RNA binding" evidence=IEA

ZFIN|ZDB-GENE-070424-78 zgc:162999 "zgc:162999" [Danio rerio (taxid:7955)]

 Score = 183 (69.5 bits), Expect = 5.6e-17, Sum P(2) = 5.6e-17
 Identities = 49/131 (37%), Positives = 82/131 (62%)

Query:    81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPA 140
             R+++   +VGSIIG+KGE +KK  E++ ARI V +G  + P+RIV I+G   P   +  A
Sbjct:    19 RLLMHGKEVGSIIGKKGETVKKMREESSARINVSEG--NCPERIVTITG---PTDAIFKA 73

Query:   141 MDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGA 200
                A+  +K    +  +  +++A+     ++RL+VP++Q  +LIGK GS IK ++E++GA
Sbjct:    74 F--AMIAYKFEEDIINSMSNSQATSKPPVTLRLVVPASQCGSLIGKGGSKIKEMRESTGA 131

Query:   201 SVRVLSADEAP 211
              V+V + D  P
Sbjct:   132 QVQV-AGDMLP 141

GO:0003723 "RNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

RGD|1307430 Pcbp3 "poly(rC) binding protein 3" [Rattus norvegicus (taxid:10116)]

 Score = 182 (69.1 bits), Expect = 6.1e-17, Sum P(2) = 6.1e-17
 Identities = 49/131 (37%), Positives = 81/131 (61%)

Query:    81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPA 140
             R+++   +VGSIIG+KGE +KK  E++ ARI + +G  + P+RIV I+G   P   +  A
Sbjct:    17 RLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTITG---PTDAIFKA 71

Query:   141 MDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGA 200
                A+  +K    +  +  ++ A+     ++RL+VP++Q  +LIGK GS IK I+E++GA
Sbjct:    72 F--AMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGA 129

Query:   201 SVRVLSADEAP 211
              V+V + D  P
Sbjct:   130 QVQV-AGDMLP 139

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0005829 "cytosol" evidence=IEA;ISO

GO:0043231 "intracellular membrane-bounded organelle" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

FB|FBgn0262737 mub "mushroom-body expressed" [Drosophila melanogaster (taxid:7227)]

 Score = 181 (68.8 bits), Expect = 7.8e-17, Sum P(2) = 7.8e-17
 Identities = 48/126 (38%), Positives = 74/126 (58%)

Query:    81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPA 140
             R+I+   +VGSIIG+KGE++ +  E++ A+I + DG  S P+RIV +SG       +  A
Sbjct:    27 RLIMQGKEVGSIIGKKGEIVNRFREESGAKINISDG--SCPERIVTVSGTTNA---IFSA 81

Query:   141 MDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGA 200
                  + F+       NDV  K  G     +RL+VP++Q  +LIGK GS IK I++ +G 
Sbjct:    82 FTLITKKFEEF-----NDV-GKV-GKTQIPIRLIVPASQCGSLIGKSGSKIKEIRQTTGC 134

Query:   201 SVRVLS 206
             S++V S
Sbjct:   135 SIQVAS 140

GO:0017130 "poly(C) RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=IC

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IMP

UNIPROTKB|F1NPL4 PCBP3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 190 (71.9 bits), Expect = 9.7e-17, Sum P(2) = 9.7e-17
 Identities = 53/136 (38%), Positives = 82/136 (60%)

Query:    81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPA 140
             R+++   +VGSIIG+KGE +KK  E++ ARI + +G  S P+RIV I+G      P    
Sbjct:    17 RLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--SCPERIVTITG------PT--- 65

Query:   141 MDAAVRVFKRVSGLPENDVDAKASGAAFCS-----VRLLVPSTQAINLIGKQGSLIKSIQ 195
              DA  + F  ++   E D++A  + +   S     +RL+VP++Q  +LIGK GS IK I+
Sbjct:    66 -DAIFKAFSMIALKFEEDINASMTNSTVTSKPPVTLRLVVPASQCGSLIGKGGSKIKEIR 124

Query:   196 ENSGASVRVLSADEAP 211
             E++GA V+V + D  P
Sbjct:   125 ESTGAQVQV-AGDMLP 139

GO:0003723 "RNA binding" 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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	466
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	3e-16
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	3e-16
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-11
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	5e-11
pfam00013	59	pfam00013, KH_1, KH domain	3e-10
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-09
smart00322	68	smart00322, KH, K homology RNA-binding domain	4e-09
pfam00013	59	pfam00013, KH_1, KH domain	5e-09
smart00322	68	smart00322, KH, K homology RNA-binding domain	8e-09
pfam13014	42	pfam13014, KH_3, KH domain	8e-09
pfam00013	59	pfam00013, KH_1, KH domain	1e-08
smart00322	68	smart00322, KH, K homology RNA-binding domain	6e-08
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	4e-05
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	4e-05
pfam13014	42	pfam13014, KH_3, KH domain	1e-04
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	1e-04
pfam13014	42	pfam13014, KH_3, KH domain	4e-04

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

 Score = 72.5 bits (179), Expect = 3e-16
 Identities = 29/69 (42%), Positives = 44/69 (63%), Gaps = 4/69 (5%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           ++RLLVPS+QA ++IGK GS IK I+E +GA +RV  +          ER+V + G+ + 
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPG----STERVVTISGKPSA 56

Query: 230 VLKALEAVV 238
           V KAL  ++
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|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 72.5 bits (179), Expect = 3e-16
 Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 79  VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG-PVSSPDRIVLISGKEEPEAPV 137
             R++VP  + GSIIG+ G  IK+  E+T A+I+V       S +R+V ISGK       
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK------P 54

Query: 138 SPAMDAAVRVF 148
           S    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|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 59.5 bits (145), Expect = 1e-11
 Identities = 24/54 (44%), Positives = 33/54 (61%)

Query: 79  VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
             R++VP   VG IIG+ G  IK+  E+T A+IK+ D    S +RIV I+G  E
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPE 54

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 = 57.6 bits (140), Expect = 5e-11
 Identities = 24/64 (37%), Positives = 37/64 (57%)

Query: 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQ 403
           T+ + +P S    IIG GG++I+ IR  +GA I + +S    +E  V I GT   V+ A+
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60

Query: 404 QLIQ 407
           +LI 
Sbjct: 61  ELIL 64

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

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

 Score = 55.6 bits (135), Expect = 3e-10
 Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 4/63 (6%)

Query: 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQ 403
           T+ + IP      IIG GG++I+ IR  +G  I + + R    + TV I GT  QV+ A+
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR----DDTVTISGTPEQVEKAK 56

Query: 404 QLI 406
           +LI
Sbjct: 57  ELI 59

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

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

 Score = 53.3 bits (129), Expect = 2e-09
 Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 5/68 (7%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           + R+LVPS+    +IGK GS IK I+E +GA +++  +         +ERIV + G    
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEA 55

Query: 230 VLKALEAV 237
           V KA E +
Sbjct: 56  VEKAKELI 63

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

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

 Score = 52.3 bits (126), Expect = 4e-09
 Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQ 400
             +T  + IP      IIG GG++I+ I   +G  I +       +E  VEI G    V+
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI--PGPGSEERVVEITGPPENVE 58

Query: 401 LAQQLIQE 408
            A +LI E
Sbjct: 59  KAAELILE 66

Length = 68

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

 Score = 51.8 bits (125), Expect = 5e-09
 Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 4/54 (7%)

Query: 79  VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
             R+++P  KVG IIG+ G  IK+  E+T  +I++ D      D  V ISG  E
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD----DRDDTVTISGTPE 50

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 = 51.5 bits (124), Expect = 8e-09
 Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 2/52 (3%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            +++P  KVG IIG+ G  IKK  E+T  +I +      S +R+V I+G  E
Sbjct: 6   EVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGP--GSEERVVEITGPPE 55

Length = 68

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

 Score = 51.0 bits (123), Expect = 8e-09
 Identities = 19/42 (45%), Positives = 28/42 (66%)

Query: 88  KVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISG 129
            VG+IIG+ GE IK+  E+T A+I++      S +RIV I+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|215657 pfam00013, KH_1, KH domain

 Score = 50.6 bits (122), Expect = 1e-08
 Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 9/68 (13%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           + R+L+P  +   +IGK GS IK I+E +G  +R+           + +  V + G   +
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD---------DRDDTVTISGTPEQ 51

Query: 230 VLKALEAV 237
           V KA E +
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|197652 smart00322, KH, K homology RNA-binding domain

 Score = 49.2 bits (118), Expect = 6e-08
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 7/72 (9%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           ++ +L+P+ +   +IGK GS IK I+E +G  + +            +ER+VE+ G    
Sbjct: 4   TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG-------SEERVVEITGPPEN 56

Query: 230 VLKALEAVVGHL 241
           V KA E ++  L
Sbjct: 57  VEKAAELILEIL 68

Length = 68

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

 Score = 40.9 bits (97), Expect = 4e-05
 Identities = 24/56 (42%), Positives = 32/56 (57%), Gaps = 3/56 (5%)

Query: 349 IPISYAEDIIGVGGTSIENIRRTSGAIITVQESR--GLPDEITVEIKGTSSQVQLA 402
           +P S A  IIG GG++I+ IR  +GA I V +S   G  + + V I G  S VQ A
Sbjct: 6   VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERV-VTISGKPSAVQKA 60

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

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

 Score = 41.0 bits (97), Expect = 4e-05
 Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQ 403
           T+ ++IP      IIG  G++I  I   +G  I   +     D IT  I G    V+ A+
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTIT--ITGPKENVEKAK 58

Query: 404 QLIQ 407
           + I 
Sbjct: 59  EEIL 62

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

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

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 5/43 (11%)

Query: 183 LIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG 225
           +IGK G  IK I+E +GA +++   +         ERIV + G
Sbjct: 5   IIGKGGETIKEIREETGAKIQIPKPEP-----GSGERIVTITG 42

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

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

 Score = 39.4 bits (93), Expect = 1e-04
 Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 2/52 (3%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            + +P      IIG+KG  I+K  E+T  +I+       S    + I+G +E
Sbjct: 3   EVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRF--PDPGSKSDTITITGPKE 52

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|221895 pfam13014, KH_3, KH domain

 Score = 37.5 bits (88), Expect = 4e-04
 Identities = 15/38 (39%), Positives = 20/38 (52%)

Query: 357 IIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG 394
           IIG GG +I+ IR  +GA I + +      E  V I G
Sbjct: 5   IIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	466
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	100.0
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	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
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.97
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.95
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.95
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.92
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.79
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.72
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.67
PRK13763	180	putative RNA-processing protein; Provisional	99.63
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.57
PRK13763	180	putative RNA-processing protein; Provisional	99.54
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.48
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.4
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.33
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	99.32
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.28
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.26
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.1
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.07
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.02
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.01
PF13014	43	KH_3: KH domain	98.99
smart00322	69	KH K homology RNA-binding domain.	98.97
PF13014	43	KH_3: KH domain	98.96
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.91
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.9
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.81
smart00322	69	KH K homology RNA-binding domain.	98.73
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.72
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.69
KOG2113	394	consensus Predicted RNA binding protein, contains	98.68
KOG2113	394	consensus Predicted RNA binding protein, contains	98.47
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.46
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.19
PRK08406	140	transcription elongation factor NusA-like protein;	98.05
PRK08406	140	transcription elongation factor NusA-like protein;	97.92
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.85
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.58
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.58
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.47
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.25
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.24
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.2
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.06
COG0195	190	NusA Transcription elongation factor [Transcriptio	97.04
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.02
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.96
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.92
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	96.89
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.86
PRK00106	535	hypothetical protein; Provisional	96.82
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	96.78
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.76
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.7
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	96.64
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.63
PRK12704	520	phosphodiesterase; Provisional	96.62
TIGR01953	341	NusA transcription termination factor NusA. This m	96.56
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.55
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.46
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.43
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.35
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.33
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.22
PRK00468	75	hypothetical protein; Provisional	96.03
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.02
KOG2814	345	consensus Transcription coactivator complex, P50 c	95.96
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	95.95
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.82
PRK02821	77	hypothetical protein; Provisional	95.74
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.52
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.48
TIGR01953	341	NusA transcription termination factor NusA. This m	95.46
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.33
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.3
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.26
PRK01064	78	hypothetical protein; Provisional	95.19
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	95.17
PRK00468	75	hypothetical protein; Provisional	95.15
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.08
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.01
PRK02821	77	hypothetical protein; Provisional	94.87
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	94.8
COG1837	76	Predicted RNA-binding protein (contains KH domain)	94.72
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	94.67
PRK12705	508	hypothetical protein; Provisional	94.62
PRK12329	449	nusA transcription elongation factor NusA; Provisi	94.49
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	94.42
PRK12704	520	phosphodiesterase; Provisional	94.34
PRK00106	535	hypothetical protein; Provisional	94.33
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	94.27
PRK01064	78	hypothetical protein; Provisional	93.87
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	92.75
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	92.36
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	91.53
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	89.65
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	89.32
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	88.92
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	88.67
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	87.91
PRK12705	508	hypothetical protein; Provisional	87.59
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	87.51
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	87.34
COG1855	604	ATPase (PilT family) [General function prediction	87.22
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	87.17
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	86.72
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	86.52
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	86.5
KOG2874	356	consensus rRNA processing protein [Translation, ri	86.32
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	86.3
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	85.93
COG1855	604	ATPase (PilT family) [General function prediction	85.43
COG1782	637	Predicted metal-dependent RNase, consists of a met	85.04
PRK13764	602	ATPase; Provisional	84.81
PRK06418	166	transcription elongation factor NusA-like protein;	83.77
KOG2874	356	consensus rRNA processing protein [Translation, ri	83.37
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	83.05
PRK13764	602	ATPase; Provisional	82.7
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	82.27
COG5166	657	Uncharacterized conserved protein [Function unknow	81.69
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	81.64
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	80.98
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	80.84

>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=1.3e-39  Score=301.19  Aligned_cols=312  Identities=25%  Similarity=0.402  Sum_probs=228.8

Q ss_pred             CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHh-cCC
Q 012307           76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRV-SGL  154 (466)
Q Consensus        76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i-~~l  154 (466)
                      +.+.+|||+.++.+|.||||+|++||.|+.+++|.|+|++.  +.++|+++|+...          +.|..+++++ ..|
T Consensus        46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~----------~ti~~ilk~iip~l  113 (390)
T KOG2192|consen   46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADI----------ETIGEILKKIIPTL  113 (390)
T ss_pred             cceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccH----------HHHHHHHHHHhhhh
Confidence            56899999999999999999999999999999999999988  6899999999876          4566666665 333


Q ss_pred             CCCCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHH
Q 012307          155 PENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKAL  234 (466)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~  234 (466)
                      .++...     ...|.+||||..+.+|.|||++|++||+|++++.++++|.. +.+|   .+++|+|.|.|.+..|..++
T Consensus       114 ee~f~~-----~~pce~rllihqs~ag~iigrngskikelrekcsarlkift-~c~p---~stdrv~l~~g~~k~v~~~i  184 (390)
T KOG2192|consen  114 EEGFQL-----PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT-ECCP---HSTDRVVLIGGKPKRVVECI  184 (390)
T ss_pred             hhCCCC-----CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh-ccCC---CCcceEEEecCCcchHHHHH
Confidence            333221     35699999999999999999999999999999999999984 4445   89999999999999999999


Q ss_pred             HHHHHHhhhccccCccccccccccCCcccccccccccccCCCcccC-CCCCCCCCCCCCccCCCc--ccCCCccc----c
Q 012307          235 EAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAA-TQSAISTEYTPSTRRESL--FLEREPQL----E  307 (466)
Q Consensus       235 ~~I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~-~~~~~~~~y~~p~~~~~~--~~~~~~~~----~  307 (466)
                      +.|++.|.+...+.+..||.+.-|.+.-.++...-++.+.|.-... ++.+   ...+|..+.++  .++|....    +
T Consensus       185 ~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrg---gqgpp~~~~sdlmay~r~GrpG~ryd  261 (390)
T KOG2192|consen  185 KIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRG---GQGPPPPRGSDLMAYDRRGRPGDRYD  261 (390)
T ss_pred             HHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCC---CCCCCCCCccccceeccCCCCCcccc
Confidence            9999999999999999999887776654444333223332221110 1100   11112111111  12221110    0


Q ss_pred             c------------cccCCCccc----CCC------CCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchH
Q 012307          308 S------------RYRLSGISI----YGQ------DPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSI  365 (466)
Q Consensus       308 ~------------~~~~~~~~~----yg~------~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~I  365 (466)
                      .            .++...++-    |.+      +++..+.. ..|+..++|+   +|.++.||.++-|.||||+|.+|
T Consensus       262 g~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~-GsYGdlGGPi---tTaQvtip~dlggsiigkggqri  337 (390)
T KOG2192|consen  262 GMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGY-GSYGDLGGPI---TTAQVTIPKDLGGSIIGKGGQRI  337 (390)
T ss_pred             ccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccc-cccCCCCCce---eeeeEecccccCcceecccchhh
Confidence            0            011111111    111      11111111 1234444554   46789999999999999999999


Q ss_pred             HHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          366 ENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       366 k~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      ++||+++||.|+|+++.+++.+|+++|+||.+|++.||+|+|+.+...++
T Consensus       338 ~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~re  387 (390)
T KOG2192|consen  338 KQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYRE  387 (390)
T ss_pred             hhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhhhc
Confidence            99999999999999998889999999999999999999999999986443

>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=5.5e-35  Score=302.93  Aligned_cols=335  Identities=28%  Similarity=0.373  Sum_probs=223.6

Q ss_pred             eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCC-
Q 012307           78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPE-  156 (466)
Q Consensus        78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~-  156 (466)
                      .++||||+...+|.||||+|..||+||.+|.++|+|.+..++++||+++|+|..... ....+.++++++++++-...+ 
T Consensus        43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~-~~~~~~~al~ka~~~iv~~~~~  121 (485)
T KOG2190|consen   43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL-NLSPATDALFKAFDMIVFKLEE  121 (485)
T ss_pred             ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-cCCchHHHHHHHHHHHhhcccc
Confidence            348999999999999999999999999999999999999999999999999953332 677889999999998743211 


Q ss_pred             CC---cccc-cCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHH
Q 012307          157 ND---VDAK-ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLK  232 (466)
Q Consensus       157 ~~---~~~~-~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~  232 (466)
                      ..   .+.. ......+++||+||..++|+||||+|+.||+|+++|||+|++.++ .+|   ..++|.|+|.|.+++|.+
T Consensus       122 d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP---~ster~V~IsG~~~av~~  197 (485)
T KOG2190|consen  122 DDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLP---NSTERAVTISGEPDAVKK  197 (485)
T ss_pred             cccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCC---cccceeEEEcCchHHHHH
Confidence            11   1111 111225899999999999999999999999999999999999954 888   578999999999999999


Q ss_pred             HHHHHHHHhhhc-----cccCccccccc--cccCCcccccccccc----ccc-----CCC---cccC-CCCCCCCCCCCC
Q 012307          233 ALEAVVGHLRKF-----LVDQGVLPLFE--KTYNASISQERQVET----WAD-----KSS---LHAA-TQSAISTEYTPS  292 (466)
Q Consensus       233 A~~~I~~~l~~~-----~~~~~~~p~~~--~~~~~~~~~~r~~~~----~~~-----~~~---~~~~-~~~~~~~~y~~p  292 (466)
                      |+..|..+|.++     ....+.++|++  ..+++.+...++.-.    +..     ...   +... ...+....++.+
T Consensus       198 al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~  277 (485)
T KOG2190|consen  198 ALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLV  277 (485)
T ss_pred             HHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCcc
Confidence            999999999984     33566777777  222222211111000    000     000   0000 000000000000


Q ss_pred             cc-----CCCcccCCCccccccccCCCcccCC------CCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccc
Q 012307          293 TR-----RESLFLEREPQLESRYRLSGISIYG------QDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVG  361 (466)
Q Consensus       293 ~~-----~~~~~~~~~~~~~~~~~~~~~~~yg------~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkg  361 (466)
                      ..     ....+.-.....+..+..+....+.      ++..+.............. ...++.+|.||.+++|+||||+
T Consensus       278 i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~  356 (485)
T KOG2190|consen  278 IRALRNETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKG  356 (485)
T ss_pred             chhhhhhcCCceEeccccCcceeeeccccCcccccccchhhhhhccccccccccccc-cceeeeeeccCccccceeeccc
Confidence            00     0000000000000000000000111      0000000000000000011 3457899999999999999999


Q ss_pred             cchHHHHHhHhCCeEEEecCCC--CCCceEEEEEcCHHHHHHHHHHHHHHHhcCcCCCC
Q 012307          362 GTSIENIRRTSGAIITVQESRG--LPDEITVEIKGTSSQVQLAQQLIQEYMNNHKESIT  418 (466)
Q Consensus       362 G~~Ik~Ir~~SGA~I~I~~~~~--~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~~~~  418 (466)
                      |.+|.+||+.|||.|+|.+...  ..+++.++|+|+..+...|+++|..++...+....
T Consensus       357 G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~  415 (485)
T KOG2190|consen  357 GAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSAPKSSMG  415 (485)
T ss_pred             ccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhcccccccCccCCC
Confidence            9999999999999999988665  67899999999999999999999999998776543

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

Probab=100.00  E-value=4.4e-35  Score=299.06  Aligned_cols=252  Identities=23%  Similarity=0.369  Sum_probs=198.5

Q ss_pred             CCceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC-C-CCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhc
Q 012307           75 PGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG-P-VSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVS  152 (466)
Q Consensus        75 ~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~-~-~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~  152 (466)
                      +.+++.+|+||.+++|+||||+|++||+|++.+||++.+..+ . .....+.+.|+|.++.   +..|...+.+++..-.
T Consensus       136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~---ve~a~~lV~dil~e~~  212 (600)
T KOG1676|consen  136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDK---VEQAKQLVADILREED  212 (600)
T ss_pred             ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHH---HHHHHHHHHHHHHhcc
Confidence            467899999999999999999999999999999999888755 2 2236788999999976   4556666666665421


Q ss_pred             CCCCCCcccc-cCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHH
Q 012307          153 GLPENDVDAK-ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVL  231 (466)
Q Consensus       153 ~l~~~~~~~~-~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~  231 (466)
                      +-........ .......+.+|.||...||.||||+|++||+|+.+||++|+|.+++ .|   .+.||++.|.|+.+.|.
T Consensus       213 ~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd-~p---~speR~~~IiG~~d~ie  288 (600)
T KOG1676|consen  213 DEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDD-DP---SSPERPAQIIGTVDQIE  288 (600)
T ss_pred             cCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCC-CC---CCccceeeeecCHHHHH
Confidence            1111110000 1223455899999999999999999999999999999999999655 34   58899999999999999


Q ss_pred             HHHHHHHHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCcccccccc
Q 012307          232 KALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYR  311 (466)
Q Consensus       232 ~A~~~I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~  311 (466)
                      +|.++|.++|++...-.                   ...|                                        
T Consensus       289 ~Aa~lI~eii~~~~~~~-------------------~~~~----------------------------------------  309 (600)
T KOG1676|consen  289 HAAELINEIIAEAEAGA-------------------GGGM----------------------------------------  309 (600)
T ss_pred             HHHHHHHHHHHHHhccC-------------------CCCc----------------------------------------
Confidence            99999999998752110                   0000                                        


Q ss_pred             CCCcccCCCCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecC--CCCCCceE
Q 012307          312 LSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQES--RGLPDEIT  389 (466)
Q Consensus       312 ~~~~~~yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~--~~~~~er~  389 (466)
                                            ..+.|... ..++|.||.+++|.||||+|++||.|.++|||++.+.+.  .++++|++
T Consensus       310 ----------------------~~G~P~~~-~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ekt  366 (600)
T KOG1676|consen  310 ----------------------GGGAPGLV-AQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKT  366 (600)
T ss_pred             ----------------------CCCCccce-eeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceE
Confidence                                  00111111 267899999999999999999999999999999999875  34678999


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          390 VEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       390 V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      |+|+|+..||+.|++||+++|.....
T Consensus       367 f~IrG~~~QIdhAk~LIr~kvg~~~~  392 (600)
T KOG1676|consen  367 FVIRGDKRQIDHAKQLIRDKVGDIAP  392 (600)
T ss_pred             EEEecCcccchHHHHHHHHHhcccCC
Confidence            99999999999999999999998544

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

Probab=100.00  E-value=1.1e-33  Score=288.84  Aligned_cols=251  Identities=26%  Similarity=0.321  Sum_probs=203.7

Q ss_pred             ceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCC
Q 012307           77 HCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPE  156 (466)
Q Consensus        77 ~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~  156 (466)
                      -.+.+..||.++||+||||+|+.|..|+.++||+|++.....+..+|.|.+.|.+++   ++.|...|..+..+.+ ...
T Consensus        53 ~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~---v~~aK~li~evv~r~~-~~~  128 (600)
T KOG1676|consen   53 VQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPEN---VEVAKQLIGEVVSRGR-PPG  128 (600)
T ss_pred             ccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCccc---HHHHHHhhhhhhhccC-CCC
Confidence            357788899999999999999999999999999999887777789999999999987   5566667777766654 111


Q ss_pred             CCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHH
Q 012307          157 NDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEA  236 (466)
Q Consensus       157 ~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~  236 (466)
                      ...++  .....++.+++||...+|+||||+|++||+|++++||++.+..+....   ....+.+.|+|++++|+.|..|
T Consensus       129 ~~~~~--q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~---~~~~KplritGdp~~ve~a~~l  203 (600)
T KOG1676|consen  129 GFPDN--QGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIA---TGADKPLRITGDPDKVEQAKQL  203 (600)
T ss_pred             Ccccc--CCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcC---CCCCCceeecCCHHHHHHHHHH
Confidence            11111  113668999999999999999999999999999999999999765543   4478899999999999999999


Q ss_pred             HHHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcc
Q 012307          237 VVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGIS  316 (466)
Q Consensus       237 I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~  316 (466)
                      |.++|++.....                      +            +                .             ..
T Consensus       204 V~dil~e~~~~~----------------------~------------g----------------~-------------~~  220 (600)
T KOG1676|consen  204 VADILREEDDEV----------------------P------------G----------------S-------------GG  220 (600)
T ss_pred             HHHHHHhcccCC----------------------C------------c----------------c-------------cc
Confidence            999999742110                      0            0                0             00


Q ss_pred             cCCCCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC-CCCceEEEEEcC
Q 012307          317 IYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG-LPDEITVEIKGT  395 (466)
Q Consensus       317 ~yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~-~~~er~V~I~Gt  395 (466)
                      .+|.+                 .....+.+|.||.+.||.||||+|++||+|+.+||++|+|..+.+ .+.||.+.|.|+
T Consensus       221 ~~g~~-----------------~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~  283 (600)
T KOG1676|consen  221 HAGVR-----------------GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGT  283 (600)
T ss_pred             ccCcC-----------------ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecC
Confidence            01111                 012247899999999999999999999999999999999987665 577999999999


Q ss_pred             HHHHHHHHHHHHHHHhcCcCC
Q 012307          396 SSQVQLAQQLIQEYMNNHKES  416 (466)
Q Consensus       396 ~~~V~~A~~lI~~~i~~~~~~  416 (466)
                      .++|+.|.+||.++|++....
T Consensus       284 ~d~ie~Aa~lI~eii~~~~~~  304 (600)
T KOG1676|consen  284 VDQIEHAAELINEIIAEAEAG  304 (600)
T ss_pred             HHHHHHHHHHHHHHHHHHhcc
Confidence            999999999999999987654

>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=2e-30  Score=253.34  Aligned_cols=287  Identities=21%  Similarity=0.309  Sum_probs=203.2

Q ss_pred             CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC-CCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCC
Q 012307           76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG-PVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGL  154 (466)
Q Consensus        76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~-~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l  154 (466)
                      .+..+|+|||..+||.||||.|.+||.|-..|.|||+|... ..+..||+++|-+.+|.   ..+|...|++++.+-.. 
T Consensus       197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg---~s~Ac~~ILeimqkEA~-  272 (584)
T KOG2193|consen  197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG---TSKACKMILEIMQKEAV-  272 (584)
T ss_pred             cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc---hHHHHHHHHHHHHHhhh-
Confidence            44569999999999999999999999999999999999754 45789999999999986   56777777777654211 


Q ss_pred             CCCCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHH
Q 012307          155 PENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKAL  234 (466)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~  234 (466)
                       +.+.      .....++++-.+.+||+||||.|.+||+|+.+||++|.|.+--++.-  -..||.+++.|..++|.+|.
T Consensus       273 -~~k~------~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~--ynpERTItVkGsiEac~~AE  343 (584)
T KOG2193|consen  273 -DDKV------AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSL--YNPERTITVKGSIEACVQAE  343 (584)
T ss_pred             -ccch------hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcc--cCccceEEecccHHHHHHHH
Confidence             1011      14577899999999999999999999999999999999986444332  35699999999999999999


Q ss_pred             HHHHHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCC
Q 012307          235 EAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSG  314 (466)
Q Consensus       235 ~~I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~  314 (466)
                      .+|+.+|+++...+ +.   .......+..+-....++.+++.         +.++.|+..     +..-++.     ..
T Consensus       344 ~eImkKlre~yEnD-l~---a~s~q~~l~P~l~~~~l~~f~ss---------S~~~~Ph~~-----Ps~v~~a-----~p  400 (584)
T KOG2193|consen  344 AEIMKKLRECYEND-LA---AMSLQCHLPPGLNLPALGLFPSS---------SAVSPPHFP-----PSPVTFA-----SP  400 (584)
T ss_pred             HHHHHHHHHHHhhh-HH---HhhccCCCCcccCccccCCCCcc---------cccCCCCCC-----CCccccC-----CC
Confidence            99999999975432 00   00000000000000000000000         001111000     0000000     00


Q ss_pred             cccCCCCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCC-CCCCceEEEEE
Q 012307          315 ISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESR-GLPDEITVEIK  393 (466)
Q Consensus       315 ~~~yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~-~~~~er~V~I~  393 (466)
                      ...+.+                .  ..+....|.||...+|+||||+|.+||.|-+.+||.|+|..+. ++..+|.|+|+
T Consensus       401 ~~~~hq----------------~--pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViIt  462 (584)
T KOG2193|consen  401 YPLFHQ----------------N--PEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIIT  462 (584)
T ss_pred             chhhhc----------------C--cchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEec
Confidence            000000                0  1334678999999999999999999999999999999997654 34679999999


Q ss_pred             cCHHHHHHHHHHHHHHHhcCcCC
Q 012307          394 GTSSQVQLAQQLIQEYMNNHKES  416 (466)
Q Consensus       394 Gt~~~V~~A~~lI~~~i~~~~~~  416 (466)
                      |.+++.-+|+-.|..+|.+....
T Consensus       463 GppeaqfKAQgrifgKikEenf~  485 (584)
T KOG2193|consen  463 GPPEAQFKAQGRIFGKIKEENFF  485 (584)
T ss_pred             CChHHHHhhhhhhhhhhhhhccC
Confidence            99999999999999999986543

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

Probab=99.95  E-value=6.1e-29  Score=242.96  Aligned_cols=247  Identities=23%  Similarity=0.379  Sum_probs=196.8

Q ss_pred             CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC---CCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhc
Q 012307           76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG---PVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVS  152 (466)
Q Consensus        76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~---~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~  152 (466)
                      +++.+||+.++.++|++|||.|.+||+|+.+||++|.|++-   ..-++||.|+|.|..|.|   ..|-..|.+.++++-
T Consensus       278 ~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac---~~AE~eImkKlre~y  354 (584)
T KOG2193|consen  278 EEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEAC---VQAEAEIMKKLRECY  354 (584)
T ss_pred             hhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHH---HHHHHHHHHHHHHHH
Confidence            77899999999999999999999999999999999999864   345789999999987764   345455554443320


Q ss_pred             --C---------CCCCC-------cc-c-----------c----------cCCCcceEEEEEeccCcceeeecCCchhHH
Q 012307          153 --G---------LPEND-------VD-A-----------K----------ASGAAFCSVRLLVPSTQAINLIGKQGSLIK  192 (466)
Q Consensus       153 --~---------l~~~~-------~~-~-----------~----------~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik  192 (466)
                        +         +.++.       +. .           .          ........++|.||...+|.||||+|..||
T Consensus       355 EnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIK  434 (584)
T KOG2193|consen  355 ENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIK  434 (584)
T ss_pred             hhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHH
Confidence              0         11100       00 0           0          012355678999999999999999999999


Q ss_pred             HHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccccCccccccccccCCcccccccccccc
Q 012307          193 SIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWA  272 (466)
Q Consensus       193 ~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~  272 (466)
                      .|.+.+||.|+|.+.+ .|   +..+|.|+|+|.+++..+|...|..+|.+..+-   .                     
T Consensus       435 ql~RfagASiKIappE-~p---dvseRMViItGppeaqfKAQgrifgKikEenf~---~---------------------  486 (584)
T KOG2193|consen  435 QLSRFAGASIKIAPPE-IP---DVSERMVIITGPPEAQFKAQGRIFGKIKEENFF---L---------------------  486 (584)
T ss_pred             HHHHhccceeeecCCC-CC---CcceeEEEecCChHHHHhhhhhhhhhhhhhccC---C---------------------
Confidence            9999999999998643 34   788999999999999999999999999875321   0                     


Q ss_pred             cCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCcccccCCCCCCCCCcccceEEEEEeccC
Q 012307          273 DKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPIS  352 (466)
Q Consensus       273 ~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~  352 (466)
                                         |         +                                    ....+..++.||..
T Consensus       487 -------------------P---------k------------------------------------eevklethirVPs~  502 (584)
T KOG2193|consen  487 -------------------P---------K------------------------------------EEVKLETHIRVPSS  502 (584)
T ss_pred             -------------------c---------h------------------------------------hhheeeeeeeccch
Confidence                               0         0                                    01235678999999


Q ss_pred             cccceeccccchHHHHHhHhCCeEEEecCC--CCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcCCC
Q 012307          353 YAEDIIGVGGTSIENIRRTSGAIITVQESR--GLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKESI  417 (466)
Q Consensus       353 ~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~--~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~~~  417 (466)
                      .+|+||||||.++++|++.|+|.|.|+++.  +..+.-+|.|.|..-+.+.|+..|.++|.+.+...
T Consensus       503 ~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~qvkq~~  569 (584)
T KOG2193|consen  503 AAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVNQVKQSG  569 (584)
T ss_pred             hhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHHHHHHhh
Confidence            999999999999999999999999998754  23456788999999999999999999999987643

>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=1.1e-26  Score=221.33  Aligned_cols=271  Identities=22%  Similarity=0.332  Sum_probs=191.9

Q ss_pred             CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC---CCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhc
Q 012307           76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG---PVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVS  152 (466)
Q Consensus        76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~---~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~  152 (466)
                      +.+++|+|||+..+|.||||+|++|.+|+++|||||++++.   .|++.||+|+|+|+.+.      .+..+.-|.++|+
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~ea------i~av~efI~dKir  110 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEA------LNAVHEFIADKIR  110 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHH------HHHHHHHHHHHHH
Confidence            34999999999999999999999999999999999999864   79999999999999753      1222233444554


Q ss_pred             CCCCCCcc-----cccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCH
Q 012307          153 GLPENDVD-----AKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEA  227 (466)
Q Consensus       153 ~l~~~~~~-----~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~  227 (466)
                      +.......     .+...+....++++||+..+|.||||+|.+||.|+++++|.|+|.+.+  |....-.+|+|++.|++
T Consensus       111 e~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk--pt~~sLqervvt~sge~  188 (402)
T KOG2191|consen  111 EKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK--PTGISLQERVVTVSGEP  188 (402)
T ss_pred             HhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC--CCCccceeEEEEecCCH
Confidence            43322111     111122445699999999999999999999999999999999999633  44447789999999999


Q ss_pred             HHHHHHHHHHHHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCcccc
Q 012307          228 AKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLE  307 (466)
Q Consensus       228 ~~V~~A~~~I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~  307 (466)
                      ++..+|+.+|+++|.+.....+.+.         ++       |+.-        .+...+|.                 
T Consensus       189 e~~~~A~~~IL~Ki~eDpqs~scln---------~s-------ya~v--------sGpvaNsn-----------------  227 (402)
T KOG2191|consen  189 EQNMKAVSLILQKIQEDPQSGSCLN---------IS-------YANV--------SGPVANSN-----------------  227 (402)
T ss_pred             HHHHHHHHHHHHHhhcCCcccceec---------cc-------hhcc--------cCcccccC-----------------
Confidence            9999999999999987533221110         00       0000        00000000                 


Q ss_pred             ccccCCCcccCCCCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC---C
Q 012307          308 SRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG---L  384 (466)
Q Consensus       308 ~~~~~~~~~~yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~---~  384 (466)
                          + ..+.|+.              ...-+....+..+.++....|..-|.+|.++-.|-..+|+.+.|.+-.+   .
T Consensus       228 ----P-tGspya~--------------~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~g  288 (402)
T KOG2191|consen  228 ----P-TGSPYAY--------------QAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMAG  288 (402)
T ss_pred             ----C-CCCCCCC--------------CCccccccchhhccccccccccccccccccceeeecccccceeeccccccccc
Confidence                0 0011110              0000112234456788999999999999999999999999999876433   3


Q ss_pred             CCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          385 PDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       385 ~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      +.++ +-+.|-.-.+..|.-+|...+.....
T Consensus       289 ~gy~-~n~~g~~ls~~aa~g~L~~~~~~a~t  318 (402)
T KOG2191|consen  289 YGYN-TNILGLGLSILAAEGVLAAKVASANT  318 (402)
T ss_pred             cccc-ccccchhhhhhhhhhHHHHhhcccCc
Confidence            4455 77888899999999999888776543

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

Probab=99.92  E-value=3e-24  Score=204.80  Aligned_cols=191  Identities=25%  Similarity=0.354  Sum_probs=149.9

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLV  246 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~  246 (466)
                      ....+++|||+..+|.||||+|++|.+||+++||+|+++...  .++.+.+||+|.|+|+.+++....++|+++|++.+.
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~--dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~  114 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSK--DFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQ  114 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEecccc--ccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHH
Confidence            348899999999999999999999999999999999998533  345599999999999999999999999999998654


Q ss_pred             cCcc-ccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCc
Q 012307          247 DQGV-LPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALS  325 (466)
Q Consensus       247 ~~~~-~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~  325 (466)
                      +... ...++                                    |+.     .+|                       
T Consensus       115 ~~~k~v~~~~------------------------------------pqt-----~~r-----------------------  130 (402)
T KOG2191|consen  115 AVAKPVDILQ------------------------------------PQT-----PDR-----------------------  130 (402)
T ss_pred             hhcCCccccC------------------------------------CCC-----ccc-----------------------
Confidence            3211 00000                                    000     000                       


Q ss_pred             ccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC---CCCceEEEEEcCHHHHHHH
Q 012307          326 TIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG---LPDEITVEIKGTSSQVQLA  402 (466)
Q Consensus       326 ~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~---~~~er~V~I~Gt~~~V~~A  402 (466)
                                      .-..++.||+.-+|.||||+|.+||.|++++||.|+|.+..+   ...||+|+++|++++..+|
T Consensus       131 ----------------~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A  194 (402)
T KOG2191|consen  131 ----------------IKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKA  194 (402)
T ss_pred             ----------------cceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHH
Confidence                            013578999999999999999999999999999999985332   3458999999999999999


Q ss_pred             HHHHHHHHhcCcCCCC---CCCCCCCCCCCCCCCCCCCCCC
Q 012307          403 QQLIQEYMNNHKESIT---SSYGQIDTGYRPSYPQLGNSSY  440 (466)
Q Consensus       403 ~~lI~~~i~~~~~~~~---~~~~~~~~g~~~~~~~~~~~~~  440 (466)
                      ..||.++|.++.....   ..|+.+. |...+|.|.|+++.
T Consensus       195 ~~~IL~Ki~eDpqs~scln~sya~vs-GpvaNsnPtGspya  234 (402)
T KOG2191|consen  195 VSLILQKIQEDPQSGSCLNISYANVS-GPVANSNPTGSPYA  234 (402)
T ss_pred             HHHHHHHhhcCCcccceeccchhccc-CcccccCCCCCCCC
Confidence            9999999999887654   3454443 23456666666653

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

Probab=99.79  E-value=1.4e-18  Score=180.96  Aligned_cols=160  Identities=28%  Similarity=0.408  Sum_probs=131.8

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec---------CHHHHHHHHHHH
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG---------EAAKVLKALEAV  237 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G---------~~~~V~~A~~~I  237 (466)
                      ...+.|||++...+|.||||+|..||+|+.++.++|+|.  +.++   +..+|+|+|+|         ..+++.+|.++|
T Consensus        41 ~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~--~~~~---~c~eRIiti~g~~~~~~~~~~~~al~ka~~~i  115 (485)
T KOG2190|consen   41 ETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVN--ESLP---GCPERIITITGNRVELNLSPATDALFKAFDMI  115 (485)
T ss_pred             CcceEEEEeccccceeEEccCcHHHHHHhhcccccceee--cCCC---CCCcceEEEecccccccCCchHHHHHHHHHHH
Confidence            334489999999999999999999999999999999996  3345   56799999999         999999999999


Q ss_pred             HHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCccc
Q 012307          238 VGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISI  317 (466)
Q Consensus       238 ~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~  317 (466)
                      ...+++.....      +.                                                             
T Consensus       116 v~~~~~d~~~~------~d-------------------------------------------------------------  128 (485)
T KOG2190|consen  116 VFKLEEDDEAA------ED-------------------------------------------------------------  128 (485)
T ss_pred             hhccccccccc------cc-------------------------------------------------------------
Confidence            88665221100      00                                                             


Q ss_pred             CCCCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecC-CCCCCceEEEEEcCH
Q 012307          318 YGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQES-RGLPDEITVEIKGTS  396 (466)
Q Consensus       318 yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~-~~~~~er~V~I~Gt~  396 (466)
                      .+.+               .. ...++.+|.||.+++|+||||+|++||+||++|||+|+|..+ ...+++|.|+|+|.+
T Consensus       129 ~~~~---------------~~-~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~  192 (485)
T KOG2190|consen  129 NGED---------------AS-GPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEP  192 (485)
T ss_pred             CCcc---------------cc-CCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCch
Confidence            0000               00 013789999999999999999999999999999999999876 456789999999999


Q ss_pred             HHHHHHHHHHHHHHhcCc
Q 012307          397 SQVQLAQQLIQEYMNNHK  414 (466)
Q Consensus       397 ~~V~~A~~lI~~~i~~~~  414 (466)
                      ++|.+|...|..+|.+..
T Consensus       193 ~av~~al~~Is~~L~~~~  210 (485)
T KOG2190|consen  193 DAVKKALVQISSRLLENP  210 (485)
T ss_pred             HHHHHHHHHHHHHHHhcC
Confidence            999999999999999965

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

Probab=99.72  E-value=2.5e-16  Score=146.81  Aligned_cols=149  Identities=23%  Similarity=0.322  Sum_probs=126.8

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLV  246 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~  246 (466)
                      ..+.+++|+-+..+|.||||+|++||.|+.++++.|.|+ +.      ...+|+++|+...+.|..-++.|+-.|++...
T Consensus        46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vp-ds------~~peri~tisad~~ti~~ilk~iip~lee~f~  118 (390)
T KOG2192|consen   46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVP-DS------SGPERILTISADIETIGEILKKIIPTLEEGFQ  118 (390)
T ss_pred             cceeEEEEEecccccceeccccccHHHHhhhccceeecc-CC------CCCceeEEEeccHHHHHHHHHHHhhhhhhCCC
Confidence            447899999999999999999999999999999999997 33      34599999999999988887777776665321


Q ss_pred             cCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCcc
Q 012307          247 DQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALST  326 (466)
Q Consensus       247 ~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~  326 (466)
                      ..                                                                              
T Consensus       119 ~~------------------------------------------------------------------------------  120 (390)
T KOG2192|consen  119 LP------------------------------------------------------------------------------  120 (390)
T ss_pred             CC------------------------------------------------------------------------------
Confidence            10                                                                              


Q ss_pred             cccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEe-cCCCCCCceEEEEEcCHHHHHHHHHH
Q 012307          327 IRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQ-ESRGLPDEITVEIKGTSSQVQLAQQL  405 (466)
Q Consensus       327 ~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~-~~~~~~~er~V~I~Gt~~~V~~A~~l  405 (466)
                                    ..+..+|+|..+++|.|||++|++||++|+.+.|+++|- +....+++|+|.|.|.+..|..+.+.
T Consensus       121 --------------~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~  186 (390)
T KOG2192|consen  121 --------------SPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKI  186 (390)
T ss_pred             --------------CchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHH
Confidence                          114667899999999999999999999999999999985 34567899999999999999999999


Q ss_pred             HHHHHhcCc
Q 012307          406 IQEYMNNHK  414 (466)
Q Consensus       406 I~~~i~~~~  414 (466)
                      |.+.|.+..
T Consensus       187 il~~i~e~p  195 (390)
T KOG2192|consen  187 ILDLISESP  195 (390)
T ss_pred             HHHHhhcCC
Confidence            999998753

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.67  E-value=2.3e-16  Score=144.16  Aligned_cols=139  Identities=28%  Similarity=0.400  Sum_probs=107.0

Q ss_pred             EEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEE---ecCHHHHHHHHHHHHHHhhhccccCc
Q 012307          173 LLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEM---QGEAAKVLKALEAVVGHLRKFLVDQG  249 (466)
Q Consensus       173 llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I---~G~~~~V~~A~~~I~~~l~~~~~~~~  249 (466)
                      |.||.+.+|.|||++|++|+.|+++||++|++..          ++..|.|   +++++++.+|.++|..+.+.+..+..
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~----------~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A   71 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS----------ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKA   71 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc----------CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            5689999999999999999999999999999962          2356778   78999999999999987775422100


Q ss_pred             cccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCccccc
Q 012307          250 VLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRS  329 (466)
Q Consensus       250 ~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~~~~  329 (466)
                      .. ++...|.                                                                      
T Consensus        72 ~~-l~gd~y~----------------------------------------------------------------------   80 (172)
T TIGR03665        72 LK-LLDDDYM----------------------------------------------------------------------   80 (172)
T ss_pred             HH-hcCCcce----------------------------------------------------------------------
Confidence            00 0000000                                                                      


Q ss_pred             CCCCCCCCCcccceEEEEEec---------cCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHH
Q 012307          330 SALGRASGPIVTQITQTMQIP---------ISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQ  400 (466)
Q Consensus       330 s~~~~~~~~~~~~~t~~i~IP---------~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~  400 (466)
                                    -.-+.|+         ...+|+|||++|.+++.|++.|||+|.|++       ..|.|.|++++++
T Consensus        81 --------------~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~-------~~v~i~G~~~~~~  139 (172)
T TIGR03665        81 --------------LEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG-------KTVGIIGDPEQVQ  139 (172)
T ss_pred             --------------EEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC-------CEEEEECCHHHHH
Confidence                          0001111         136899999999999999999999999953       6899999999999


Q ss_pred             HHHHHHHHHHhcC
Q 012307          401 LAQQLIQEYMNNH  413 (466)
Q Consensus       401 ~A~~lI~~~i~~~  413 (466)
                      .|+.+|+++|+..
T Consensus       140 ~A~~~i~~li~~~  152 (172)
T TIGR03665       140 IAREAIEMLIEGA  152 (172)
T ss_pred             HHHHHHHHHHcCC
Confidence            9999999999543

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=2.3e-15  Score=138.58  Aligned_cols=152  Identities=28%  Similarity=0.383  Sum_probs=109.7

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEe----cCHHHHHHHHHHHHHHhhhc
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQ----GEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~----G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ....+.||.+.+|.|||++|++|+.|+++||++|++..          ++..|.|.    ++++++.+|+++|..++..+
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~----------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf   72 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS----------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRGF   72 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC----------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCC
Confidence            45789999999999999999999999999999999962          23577785    89999999999999988754


Q ss_pred             cccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCC
Q 012307          245 LVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPAL  324 (466)
Q Consensus       245 ~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~  324 (466)
                      ..+.... ++...|...+                                         -.         +..|+..   
T Consensus        73 ~~e~A~~-l~gd~y~~~V-----------------------------------------i~---------i~~~~~~---   98 (180)
T PRK13763         73 SPEKALR-LLDDDYVLEV-----------------------------------------ID---------LSDYGDS---   98 (180)
T ss_pred             CHHHHHH-HhCCCceEEE-----------------------------------------EE---------hhhccCC---
Confidence            2211000 0000000000                                         00         0000000   


Q ss_pred             cccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHH
Q 012307          325 STIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQ  404 (466)
Q Consensus       325 ~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~  404 (466)
                                   +         ......+|+|||++|.+++.|++.|||+|.|++       ..|.|.|++++++.|+.
T Consensus        99 -------------~---------~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~  149 (180)
T PRK13763         99 -------------P---------NALRRIKGRIIGEGGKTRRIIEELTGVDISVYG-------KTVAIIGDPEQVEIARE  149 (180)
T ss_pred             -------------h---------hHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-------CEEEEEeCHHHHHHHHH
Confidence                         0         011236899999999999999999999999953       45999999999999999


Q ss_pred             HHHHHHhcC
Q 012307          405 LIQEYMNNH  413 (466)
Q Consensus       405 lI~~~i~~~  413 (466)
                      .|+++++..
T Consensus       150 ~I~~li~g~  158 (180)
T PRK13763        150 AIEMLIEGA  158 (180)
T ss_pred             HHHHHHcCC
Confidence            999999543

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.57  E-value=9.6e-15  Score=133.51  Aligned_cols=139  Identities=19%  Similarity=0.227  Sum_probs=97.7

Q ss_pred             EEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEe---cCCCCCCCCCChhHHHHHHHHHHhcCCCCCC
Q 012307           82 MIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLI---SGKEEPEAPVSPAMDAAVRVFKRVSGLPEND  158 (466)
Q Consensus        82 llvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I---~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~  158 (466)
                      |.||.+.+|.|||++|++||+|+++|||+|++.+.     +..|.|   +++++   .+.+|++.|..+...   ....+
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~---~i~kA~~~I~~i~~g---f~~e~   70 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPL---AVMKAREVVKAIGRG---FSPEK   70 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHH---HHHHHHHHHHHHHcC---CCHHH
Confidence            56899999999999999999999999999999864     356888   34332   244444444443221   00000


Q ss_pred             cccccCCCcceEEEEEecc---------CcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHH
Q 012307          159 VDAKASGAAFCSVRLLVPS---------TQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK  229 (466)
Q Consensus       159 ~~~~~~~~~~~~~~llVP~---------~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~  229 (466)
                      .-. ..+......-+.|+.         ..+|+|||++|++++.|++.|||+|.|.            ++.|.|.|.+++
T Consensus        71 A~~-l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~------------~~~v~i~G~~~~  137 (172)
T TIGR03665        71 ALK-LLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY------------GKTVGIIGDPEQ  137 (172)
T ss_pred             HHH-hcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc------------CCEEEEECCHHH
Confidence            000 000111112233333         3689999999999999999999999995            257999999999


Q ss_pred             HHHHHHHHHHHhhhc
Q 012307          230 VLKALEAVVGHLRKF  244 (466)
Q Consensus       230 V~~A~~~I~~~l~~~  244 (466)
                      ++.|..+|.+++.+.
T Consensus       138 ~~~A~~~i~~li~~~  152 (172)
T TIGR03665       138 VQIAREAIEMLIEGA  152 (172)
T ss_pred             HHHHHHHHHHHHcCC
Confidence            999999999988654

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=99.54  E-value=5.1e-14  Score=129.62  Aligned_cols=142  Identities=20%  Similarity=0.243  Sum_probs=99.6

Q ss_pred             eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEec----CCCCCCCCCChhHHHHHHHHHHhcC
Q 012307           78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLIS----GKEEPEAPVSPAMDAAVRVFKRVSG  153 (466)
Q Consensus        78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~----G~~e~~~~v~~A~~ai~~i~~~i~~  153 (466)
                      +...|.||.+.+|.|||++|++||.|+++|||+|++.+.     +..|.|.    ++++   .+.+|++.|..+..-   
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-----TGEVIIEPTDGEDPL---AVLKARDIVKAIGRG---   71 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHH---HHHHHHHHHHHHhcC---
Confidence            467899999999999999999999999999999999864     3567775    3332   244444444443321   


Q ss_pred             CCCCCcccccCCCcceEEE-EEec---------cCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEE
Q 012307          154 LPENDVDAKASGAAFCSVR-LLVP---------STQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEM  223 (466)
Q Consensus       154 l~~~~~~~~~~~~~~~~~~-llVP---------~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I  223 (466)
                      ....+.- ...+.. +..+ +.+.         ...+|+|||++|++++.|++.|||+|.|.            ++.|.|
T Consensus        72 f~~e~A~-~l~gd~-y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~------------~~~v~i  137 (180)
T PRK13763         72 FSPEKAL-RLLDDD-YVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY------------GKTVAI  137 (180)
T ss_pred             CCHHHHH-HHhCCC-ceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc------------CCEEEE
Confidence            0000000 000001 1111 1111         14789999999999999999999999995            234889


Q ss_pred             ecCHHHHHHHHHHHHHHhhhc
Q 012307          224 QGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       224 ~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      .|.++++..|...|..+++.+
T Consensus       138 ~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        138 IGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             EeCHHHHHHHHHHHHHHHcCC
Confidence            999999999999999998765

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.48  E-value=7.3e-14  Score=106.99  Aligned_cols=63  Identities=41%  Similarity=0.483  Sum_probs=58.6

Q ss_pred             EEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC-CCCceEEEEEcCHHHHHHHHHHHH
Q 012307          345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG-LPDEITVEIKGTSSQVQLAQQLIQ  407 (466)
Q Consensus       345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~-~~~er~V~I~Gt~~~V~~A~~lI~  407 (466)
                      .+|.||.+++|+|||++|.+|++|+++|||+|+|.+... ...+|+|+|+|++++|+.|+.||+
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            579999999999999999999999999999999987655 578999999999999999999984

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=99.40  E-value=1.8e-12  Score=132.22  Aligned_cols=292  Identities=18%  Similarity=0.174  Sum_probs=182.5

Q ss_pred             CCceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCC
Q 012307           75 PGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGL  154 (466)
Q Consensus        75 ~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l  154 (466)
                      ++++.++++|+...|-.||||.|.+||.|++.+++||.+.+.. -.+++...+.|.+..   +.+|..++.++...-   
T Consensus        65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~---v~~a~a~~~~~~~~~---  137 (608)
T KOG2279|consen   65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQ---VCKAKAAIHQILTEN---  137 (608)
T ss_pred             hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCC---CChHHHHHHHHHhcC---
Confidence            4789999999999999999999999999999999999997652 234566666666654   666777766654331   


Q ss_pred             CCCCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHH
Q 012307          155 PENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKAL  234 (466)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~  234 (466)
                                  ..+...+-+|...+++|+|++|++++.|+..++++|.+...  .-   ..-.+...|.+..+.+..|.
T Consensus       138 ------------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n--gr---~g~~~~~~i~~qqk~~~~a~  200 (608)
T KOG2279|consen  138 ------------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN--GR---LGLSRLIKISGQQKEVAAAK  200 (608)
T ss_pred             ------------Ccccccccchhhhcccccccchhhhcchhcccccccccccc--cc---cccccceecccccchHHHHH
Confidence                        45677888999999999999999999999999999998632  11   34578888999998999999


Q ss_pred             HHHHHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCC-CCCCCCccCCCcccCC-CccccccccC
Q 012307          235 EAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAIS-TEYTPSTRRESLFLER-EPQLESRYRL  312 (466)
Q Consensus       235 ~~I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~-~~y~~p~~~~~~~~~~-~~~~~~~~~~  312 (466)
                      .++.+.+.+......-+|.-...-     -.|....       ... ..++. +....++..+.....- .++.+     
T Consensus       201 ~~~~~~~~edeelv~~~~e~~q~r-----vprk~p~-------n~~-~~~m~~~~~s~~~h~~~~t~~s~spg~~-----  262 (608)
T KOG2279|consen  201 HLILEKVSEDEELVKRIAESAQTR-----VPRKQPI-------NVR-REDMTEPGGAGEPHLWKNTSSSMSPGAP-----  262 (608)
T ss_pred             hhhhccccchhHHhhhchhhcccC-----CCCCCCc-------ccc-chhhcccccCCccccCccchhccCCCCC-----
Confidence            999988876422111111111100     0000000       000 00000 0000000000000000 00000     


Q ss_pred             CCcccCCCCCCCcccccCC------CCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCC-
Q 012307          313 SGISIYGQDPALSTIRSSA------LGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLP-  385 (466)
Q Consensus       313 ~~~~~yg~~~~~~~~~~s~------~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~-  385 (466)
                       +...-|.+.+  ..++..      ..+.-...+...-.+|.||...+|.+||+.|..|+.+...|++.+.|--..-.. 
T Consensus       263 -~~~~eg~dm~--v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~  339 (608)
T KOG2279|consen  263 -LVTKEGGDMA--VVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSR  339 (608)
T ss_pred             -CcccCCCcce--eEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccch
Confidence             0000000000  000000      000001123345678999999999999999999999999999999885432211 


Q ss_pred             --CceEEEEEcCHHHHHHHHHHHHHHHh
Q 012307          386 --DEITVEIKGTSSQVQLAQQLIQEYMN  411 (466)
Q Consensus       386 --~er~V~I~Gt~~~V~~A~~lI~~~i~  411 (466)
                        .-.++.+.|+...+..|..||...+-
T Consensus       340 v~~~qic~~egkqh~~n~vl~ml~~~~p  367 (608)
T KOG2279|consen  340 VLQLQICVNEGKQHYENSVLEMLTVHVP  367 (608)
T ss_pred             hhhhhhheecchhHHHHHHHhhhhccCC
Confidence              12568899999999999999975543

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.33  E-value=1.7e-12  Score=97.74  Aligned_cols=60  Identities=30%  Similarity=0.527  Sum_probs=55.2

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHH
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLI  406 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI  406 (466)
                      |.+|.||.+++|+|||++|.+|++|+++|||+|.|++.  + ++..|+|+|++++|+.|+.+|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--~-~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--D-ERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHHHHHHHHhhC
Confidence            57899999999999999999999999999999999765  2 456999999999999999987

; 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 ....

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.32  E-value=5.1e-12  Score=96.74  Aligned_cols=64  Identities=47%  Similarity=0.684  Sum_probs=57.9

Q ss_pred             EEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHH
Q 012307          170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAV  237 (466)
Q Consensus       170 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I  237 (466)
                      +++|+||...+|.|||++|++|++|+++|||+|.+.+... +   ...+|+|+|.|++++|.+|+.+|
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-P---GSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-C---CCCceEEEEEeCHHHHHHHHHhh
Confidence            3689999999999999999999999999999999985432 2   57799999999999999999987

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=99.32  E-value=2.5e-12  Score=97.42  Aligned_cols=61  Identities=26%  Similarity=0.400  Sum_probs=55.9

Q ss_pred             EEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 012307          345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQ  407 (466)
Q Consensus       345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~  407 (466)
                      .+|.||.+++++|||++|++|++|+++|||+|.|++..  ..++.|+|+|+.++|..|+.+|+
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            57899999999999999999999999999999997654  46789999999999999999874

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

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

Probab=99.28  E-value=1e-11  Score=94.46  Aligned_cols=63  Identities=37%  Similarity=0.565  Sum_probs=57.9

Q ss_pred             EEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 012307          345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQ  407 (466)
Q Consensus       345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~  407 (466)
                      .+|.||.+++++|||++|++|++|++.|||+|.|.+......++.|+|.|+.++++.|+.+|+
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            478999999999999999999999999999999987655567899999999999999999874

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=99.26  E-value=1.3e-11  Score=93.13  Aligned_cols=58  Identities=31%  Similarity=0.541  Sum_probs=53.2

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcC-HHHHHHHHHHHH
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGT-SSQVQLAQQLIQ  407 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt-~~~V~~A~~lI~  407 (466)
                      +..|.||.+++|+|||++|++|++|+++|||+|.|++      ++.|.|+|+ +++++.|+.+|+
T Consensus         3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~~~v~~A~~~I~   61 (61)
T cd02393           3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDKEAAEKAKKMIE   61 (61)
T ss_pred             EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCHHHHHHHHHHhC
Confidence            5679999999999999999999999999999999965      357999999 899999999883

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.

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.10  E-value=1.4e-10  Score=87.80  Aligned_cols=61  Identities=26%  Similarity=0.421  Sum_probs=55.0

Q ss_pred             EEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHH
Q 012307          171 VRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVV  238 (466)
Q Consensus       171 ~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~  238 (466)
                      .+|.||..+++.|||++|++|++|+++|||+|.+++.       ...++.|+|+|+.++|.+|+.+|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~-------~~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP-------GSKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCC-------CCCCCEEEEEcCHHHHHHHHHHhC
Confidence            5789999999999999999999999999999999743       245789999999999999998873

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=99.07  E-value=1.6e-10  Score=86.89  Aligned_cols=60  Identities=33%  Similarity=0.544  Sum_probs=54.1

Q ss_pred             EEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHH
Q 012307          170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAV  237 (466)
Q Consensus       170 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I  237 (466)
                      |.+|.||..++++|||++|.+|++|+++|||+|.+..+       + ....|+|.|+.++|.+|+++|
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            57899999999999999999999999999999999732       2 355999999999999999886

; 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=99.02  E-value=1.3e-09  Score=82.78  Aligned_cols=62  Identities=40%  Similarity=0.609  Sum_probs=55.7

Q ss_pred             EEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHH
Q 012307          171 VRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAV  237 (466)
Q Consensus       171 ~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I  237 (466)
                      .+|.||..+++.|||++|++|++|+++|||+|.|.....     ...++.|.|.|..+++..|+.+|
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            689999999999999999999999999999999974321     36789999999999999999887

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=99.01  E-value=1.3e-09  Score=82.13  Aligned_cols=58  Identities=21%  Similarity=0.327  Sum_probs=52.4

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecC-HHHHHHHHHHH
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGE-AAKVLKALEAV  237 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I  237 (466)
                      ....+.||..++|+|||++|++|++|+++|||+|.+..           ++.|.|.|+ .+++++|+++|
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            45678999999999999999999999999999999852           357999998 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.

>PF13014 KH_3: KH domain

Probab=98.99  E-value=7e-10  Score=77.57  Aligned_cols=42  Identities=40%  Similarity=0.610  Sum_probs=38.6

Q ss_pred             ccceeeecCChhHHHHHHHhCceEEEeC-CCCCCCCeEEEecC
Q 012307           88 KVGSIIGRKGELIKKTCEDTRARIKVLD-GPVSSPDRIVLISG  129 (466)
Q Consensus        88 ~vG~IIGk~G~~Ik~I~~etga~I~v~~-~~~~~~ervv~I~G  129 (466)
                      +||+||||+|++|++|+++|+|+|+|++ ..++..+|.|+|+|
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            5899999999999999999999999998 45678899999987

>smart00322 KH K homology RNA-binding domain

Probab=98.97  E-value=3.2e-09  Score=80.92  Aligned_cols=67  Identities=34%  Similarity=0.535  Sum_probs=60.0

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMN  411 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~  411 (466)
                      .+.+|.||.++++.+||++|.+|++|++.+|++|.+.....  ....|+|.|+.++++.|..+|.+.++
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~~   69 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEILE   69 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHhC
Confidence            46789999999999999999999999999999999965432  56899999999999999999988763

>PF13014 KH_3: KH domain

Probab=98.96  E-value=1e-09  Score=76.71  Aligned_cols=42  Identities=36%  Similarity=0.605  Sum_probs=37.7

Q ss_pred             cccceeccccchHHHHHhHhCCeEEEec-CCCCCCceEEEEEc
Q 012307          353 YAEDIIGVGGTSIENIRRTSGAIITVQE-SRGLPDEITVEIKG  394 (466)
Q Consensus       353 ~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~-~~~~~~er~V~I~G  394 (466)
                      ++|+|||++|++|++|+++|||+|+|++ ......+++|+|+|
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            5899999999999999999999999987 33456899999998

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

Probab=98.91  E-value=7.2e-09  Score=94.35  Aligned_cols=154  Identities=25%  Similarity=0.286  Sum_probs=111.4

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-----CHHHHHHHHHHHHHHhhh
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-----EAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-----~~~~V~~A~~~I~~~l~~  243 (466)
                      ....+.||...++.|||+.|+.-+.|.+.++++|.+.          ..+..|+|..     ++..+.+|.+.|..+-+.
T Consensus         8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD----------~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG   77 (194)
T COG1094           8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID----------SKTGSVTIRTTRKTEDPLALLKARDVVKAIGRG   77 (194)
T ss_pred             ceeeeecCchhheeeecccccchHHHHhhcCeEEEEE----------CCCCeEEEEecCCCCChHHHHHHHHHHHHHhcC
Confidence            4566899999999999999999999999999999995          4456676654     577899999999988887


Q ss_pred             ccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCC
Q 012307          244 FLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPA  323 (466)
Q Consensus       244 ~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~  323 (466)
                      |..+..+.-+....+-..+...                                                   -+-..  
T Consensus        78 F~pe~A~~LL~d~~~levIdi~---------------------------------------------------~~~~~--  104 (194)
T COG1094          78 FPPEKALKLLEDDYYLEVIDLK---------------------------------------------------DVVTL--  104 (194)
T ss_pred             CCHHHHHHHhcCCcEEEEEEHH---------------------------------------------------HhccC--
Confidence            7544322211110000000000                                                   00000  


Q ss_pred             CcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHH
Q 012307          324 LSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQ  403 (466)
Q Consensus       324 ~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~  403 (466)
                                 .    ...       =....|+|||++|.+-+.|++.|||.|.|..       .+|-|.|.+++|+.|+
T Consensus       105 -----------~----~~~-------l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g-------~tVaiiG~~~~v~iAr  155 (194)
T COG1094         105 -----------S----GDH-------LRRIKGRIIGREGKTRRAIEELTGVYISVYG-------KTVAIIGGFEQVEIAR  155 (194)
T ss_pred             -----------c----hhh-------hhHhhceeeCCCchHHHHHHHHhCCeEEEeC-------cEEEEecChhhhHHHH
Confidence                       0    000       0234699999999999999999999999953       5899999999999999


Q ss_pred             HHHHHHHhcCc
Q 012307          404 QLIQEYMNNHK  414 (466)
Q Consensus       404 ~lI~~~i~~~~  414 (466)
                      ..|..+|+..+
T Consensus       156 ~AVemli~G~~  166 (194)
T COG1094         156 EAVEMLINGAP  166 (194)
T ss_pred             HHHHHHHcCCC
Confidence            99999998754

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.90  E-value=6.9e-09  Score=114.51  Aligned_cols=231  Identities=22%  Similarity=0.277  Sum_probs=161.6

Q ss_pred             eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhc-----
Q 012307           78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVS-----  152 (466)
Q Consensus        78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~-----  152 (466)
                      +..++.+....+.+|||++|.+|+.++.++.+.|+|++..  .......|.|..+..   ..+...+...+.++.     
T Consensus       201 ~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn--~~~~~~~i~~~~~~~---~~~~~~i~~~~~~le~~~~~  275 (753)
T KOG2208|consen  201 VFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSN--KSSPSNKIDGRLNSS---SSINVEIQEALTRLESEFDY  275 (753)
T ss_pred             EEEEeeccccchhhhccccccccccccccceeEEEccccc--ccchhhhhccccccc---eehhhhhHHHHHHhcChhhh
Confidence            6789999999999999999999999999999999999662  222223344432221   111111111111110     


Q ss_pred             ---------CCCCCC-------------------------ccc----------------c-----cCCCcceEEEEEecc
Q 012307          153 ---------GLPEND-------------------------VDA----------------K-----ASGAAFCSVRLLVPS  177 (466)
Q Consensus       153 ---------~l~~~~-------------------------~~~----------------~-----~~~~~~~~~~llVP~  177 (466)
                               .+....                         .+.                .     ........+.+.+-.
T Consensus       276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~  355 (753)
T KOG2208|consen  276 DEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFP  355 (753)
T ss_pred             hhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecH
Confidence                     000000                         000                0     112244677888889


Q ss_pred             CcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccccCccccccccc
Q 012307          178 TQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLFEKT  257 (466)
Q Consensus       178 ~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~p~~~~~  257 (466)
                      ..+..++||+|.+|.+|++++.|.+.+...       +++...+.++|...++.+|...+...+.+.+..          
T Consensus       356 ~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~----------  418 (753)
T KOG2208|consen  356 EELKFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILNS----------  418 (753)
T ss_pred             HhhhhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhcc----------
Confidence            999999999999999999999999999631       467888999999999999999999877765210          


Q ss_pred             cCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCcccccCCCCCCCC
Q 012307          258 YNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASG  337 (466)
Q Consensus       258 ~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~~~~s~~~~~~~  337 (466)
                                                                                                      
T Consensus       419 --------------------------------------------------------------------------------  418 (753)
T KOG2208|consen  419 --------------------------------------------------------------------------------  418 (753)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          338 PIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       338 ~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                          .....+.||...+.+|||.+|..|++|...+|+ |+|...+.......+++.|....+..++.++..+....++
T Consensus       419 ----~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~-v~i~f~~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~a~~  491 (753)
T KOG2208|consen  419 ----IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGG-VHIKFQNNNNSSDMVTIRGISKDVEKSVSLLKALKADAKN  491 (753)
T ss_pred             ----cccceeecCccchhhhhccccccHHHHHhhcCc-EEEecCCCCcccccceEeccccccchhHHHHHhhhhhhhc
Confidence                124568899999999999999999999999995 5554444444556688888887777766666665554443

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

Probab=98.81  E-value=2.4e-09  Score=109.78  Aligned_cols=147  Identities=29%  Similarity=0.448  Sum_probs=122.6

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLV  246 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~  246 (466)
                      ..+.+++.|+...+-+++||.|.+|+.|++.++++|.+.+++      -..+++-.+.|-+.++.+|..+++.++.+.. 
T Consensus        66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed------~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~-  138 (608)
T KOG2279|consen   66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED------VGDERVLLISGFPVQVCKAKAAIHQILTENT-  138 (608)
T ss_pred             hheeeeEeecccceeeeeccccCCcchhhcccccceecCccc------CCcccchhhccCCCCCChHHHHHHHHHhcCC-
Confidence            557789999999999999999999999999999999997543      2346666777789999999999888765421 


Q ss_pred             cCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCcc
Q 012307          247 DQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALST  326 (466)
Q Consensus       247 ~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~  326 (466)
                                                                                                      
T Consensus       139 --------------------------------------------------------------------------------  138 (608)
T KOG2279|consen  139 --------------------------------------------------------------------------------  138 (608)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             cccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHH
Q 012307          327 IRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLI  406 (466)
Q Consensus       327 ~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI  406 (466)
                                     .+..++.+|...+++|+|++|.+|..|+..|+|+|.++...-.-..+.+.|.|..+-++.|+.++
T Consensus       139 ---------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~  203 (608)
T KOG2279|consen  139 ---------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLI  203 (608)
T ss_pred             ---------------cccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhh
Confidence                           13456778999999999999999999999999999997763334578888999999999999999


Q ss_pred             HHHHhcCcC
Q 012307          407 QEYMNNHKE  415 (466)
Q Consensus       407 ~~~i~~~~~  415 (466)
                      .+.+++...
T Consensus       204 ~~~~~edee  212 (608)
T KOG2279|consen  204 LEKVSEDEE  212 (608)
T ss_pred             hccccchhH
Confidence            999987543

>smart00322 KH K homology RNA-binding domain

Probab=98.73  E-value=7.6e-08  Score=73.20  Aligned_cols=66  Identities=33%  Similarity=0.568  Sum_probs=58.7

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHh
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHL  241 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l  241 (466)
                      .+.++.||..+++.|||++|.+|++|++.++++|.+...       ......|.|.|..+++..|..+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~-------~~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED-------GSEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC-------CCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            578899999999999999999999999999999999632       125788999999999999999998765

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.72  E-value=2.1e-08  Score=110.83  Aligned_cols=216  Identities=18%  Similarity=0.270  Sum_probs=160.0

Q ss_pred             eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCC
Q 012307           78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPEN  157 (466)
Q Consensus        78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~  157 (466)
                      +...+-+-...+..|+||+|.+|.+|++++.|.|.+...  +..+..+.++|...+   +..|++.+..++..+..    
T Consensus       347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~---~~ka~~~v~~~~~ei~n----  417 (753)
T KOG2208|consen  347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAN---DEKAVEDVEKIIAEILN----  417 (753)
T ss_pred             eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccc---hhHHHHHHHHHHHhhhc----
Confidence            677788888999999999999999999999999999984  567778999998865   66788888887777643    


Q ss_pred             CcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhC-CeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHH
Q 012307          158 DVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSG-ASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEA  236 (466)
Q Consensus       158 ~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sg-a~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~  236 (466)
                               ......+.+|...+..+||.+|..|..|..+++ ..|+....       ......+++.|....+.++..+
T Consensus       418 ---------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-------~~~~~~~~~~~~~~dv~~~~~~  481 (753)
T KOG2208|consen  418 ---------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-------NNSSDMVTIRGISKDVEKSVSL  481 (753)
T ss_pred             ---------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-------CcccccceEeccccccchhHHH
Confidence                     134567899999999999999999999999999 55555422       3445668888888888887766


Q ss_pred             HHHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcc
Q 012307          237 VVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGIS  316 (466)
Q Consensus       237 I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~  316 (466)
                      +..+........                      |                                             
T Consensus       482 ~~~~~~~a~~~~----------------------~---------------------------------------------  494 (753)
T KOG2208|consen  482 LKALKADAKNLK----------------------F---------------------------------------------  494 (753)
T ss_pred             HHhhhhhhhcch----------------------h---------------------------------------------
Confidence            665443211000                      0                                             


Q ss_pred             cCCCCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCH
Q 012307          317 IYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTS  396 (466)
Q Consensus       317 ~yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~  396 (466)
                                             ...++.+...|..+.+..+|+.|..+...++..+..+..+     .++..++|.|..
T Consensus       495 -----------------------~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~-----~~~~~i~i~gk~  546 (753)
T KOG2208|consen  495 -----------------------RDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNED-----EDHEKITIEGKL  546 (753)
T ss_pred             -----------------------hhhhhccccchHHhhcccccCceeeeccCCceeecccccc-----cccceeeecccc
Confidence                                   0112334556677777777777766666555554444443     356689999999


Q ss_pred             HHHHHHHHHHHHHHhcC
Q 012307          397 SQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       397 ~~V~~A~~lI~~~i~~~  413 (466)
                      +.|.+|+.+++..+...
T Consensus       547 ~~v~~a~~~L~~~~~~~  563 (753)
T KOG2208|consen  547 ELVLEAPAELKALIEAL  563 (753)
T ss_pred             cchhhhHHHHHhcchhh
Confidence            99999999998887764

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

Probab=98.69  E-value=2e-07  Score=85.02  Aligned_cols=147  Identities=21%  Similarity=0.259  Sum_probs=99.5

Q ss_pred             CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCC---CCCCCCChhHHHHHHHHHHhc
Q 012307           76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKE---EPEAPVSPAMDAAVRVFKRVS  152 (466)
Q Consensus        76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~---e~~~~v~~A~~ai~~i~~~i~  152 (466)
                      ....+.+.||...++.+||+.|+..+.|++.++++|.+.     ..+..|.|....   ++ ..+.+|.+.|..+ .  +
T Consensus         6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp-~~~~ka~d~VkAI-g--r   76 (194)
T COG1094           6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDP-LALLKARDVVKAI-G--R   76 (194)
T ss_pred             ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCCh-HHHHHHHHHHHHH-h--c
Confidence            345677999999999999999999999999999999995     346778886653   32 1223333333222 0  1


Q ss_pred             CCCCCCcccccCCCcceEEEEE-----e-----ccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEE
Q 012307          153 GLPENDVDAKASGAAFCSVRLL-----V-----PSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVE  222 (466)
Q Consensus       153 ~l~~~~~~~~~~~~~~~~~~ll-----V-----P~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~  222 (466)
                      ++.....-. .-........+.     -     -...-|+|||++|.+-+.|++-|+|.|.|.            ...|.
T Consensus        77 GF~pe~A~~-LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~------------g~tVa  143 (194)
T COG1094          77 GFPPEKALK-LLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY------------GKTVA  143 (194)
T ss_pred             CCCHHHHHH-HhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe------------CcEEE
Confidence            111000000 000000000010     0     123569999999999999999999999996            34799


Q ss_pred             EecCHHHHHHHHHHHHHHhhhc
Q 012307          223 MQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       223 I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      |-|..++|..|.+.|..++...
T Consensus       144 iiG~~~~v~iAr~AVemli~G~  165 (194)
T COG1094         144 IIGGFEQVEIAREAVEMLINGA  165 (194)
T ss_pred             EecChhhhHHHHHHHHHHHcCC
Confidence            9999999999999999988764

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

Probab=98.68  E-value=1.7e-08  Score=96.82  Aligned_cols=153  Identities=20%  Similarity=0.196  Sum_probs=112.1

Q ss_pred             CCCceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHH---
Q 012307           74 WPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKR---  150 (466)
Q Consensus        74 ~~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~---  150 (466)
                      .++.++..+-||..+|+.|.|++|.+||.|+.+|..+|+-+..   ..+-++.++|..+.+   .+|+..|...-+.   
T Consensus        22 ~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~edv---~~aRrei~saaeH~~l   95 (394)
T KOG2113|consen   22 IGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRHEDV---RRARREIPSAAEHFGL   95 (394)
T ss_pred             CCCccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCchhH---HHHhhcCccccceeee
Confidence            3578899999999999999999999999999999999988654   345788899999864   3444444442222   


Q ss_pred             hcCCCCCCcccc-cCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHH
Q 012307          151 VSGLPENDVDAK-ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK  229 (466)
Q Consensus       151 i~~l~~~~~~~~-~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~  229 (466)
                      ++.......+.. .......+...-+|...+|.|+|.+|.+|+.|++.++..|.-+-.        ..+.++.++|.+++
T Consensus        96 ~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--------~~~~Vf~Vtg~~~n  167 (394)
T KOG2113|consen   96 IRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--------CGEPVFCVTGAPKN  167 (394)
T ss_pred             eeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--------CCCceEEEecCCcc
Confidence            222211111111 122355677788899999999999999999999999999987632        34678999999888


Q ss_pred             -HHHHH-HHHHHH
Q 012307          230 -VLKAL-EAVVGH  240 (466)
Q Consensus       230 -V~~A~-~~I~~~  240 (466)
                       +++|. ..|...
T Consensus       168 C~kra~s~eie~t  180 (394)
T KOG2113|consen  168 CVKRARSCEIEQT  180 (394)
T ss_pred             hhhhccccchhhh
Confidence             56666 445443

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

Probab=98.47  E-value=2.2e-07  Score=89.34  Aligned_cols=149  Identities=21%  Similarity=0.321  Sum_probs=108.2

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLV  246 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~  246 (466)
                      ..++..+.||..+++.++|++|.+||.|+.+|.+.|+-+....        +-+|.++|..+.|..|+..|...-+.+-.
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e--------ePiF~vTg~~edv~~aRrei~saaeH~~l   95 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE--------EPIFPVTGRHEDVRRARREIPSAAEHFGL   95 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC--------CCcceeccCchhHHHHhhcCccccceeee
Confidence            6688899999999999999999999999999999999875433        45899999999999999888664433211


Q ss_pred             cCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCcc
Q 012307          247 DQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALST  326 (466)
Q Consensus       247 ~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~  326 (466)
                      ..         |      .|   ++           .+                             +...|        
T Consensus        96 ~~---------~------s~---s~-----------Sg-----------------------------g~~~~--------  109 (394)
T KOG2113|consen   96 IR---------A------SR---SF-----------SG-----------------------------GTNGA--------  109 (394)
T ss_pred             ee---------e------cc---cc-----------cC-----------------------------CCccc--------
Confidence            00         0      00   00           00                             00000        


Q ss_pred             cccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHH-HHHHH
Q 012307          327 IRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQ-VQLAQ  403 (466)
Q Consensus       327 ~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~-V~~A~  403 (466)
                                 ....+.+.+..+|...+|.|.|..|.+|+.|++.+...|.-.-..   .+-++.++|-+.. +++|.
T Consensus       110 -----------s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~---~~~Vf~Vtg~~~nC~kra~  173 (394)
T KOG2113|consen  110 -----------SASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC---GEPVFCVTGAPKNCVKRAR  173 (394)
T ss_pred             -----------cccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC---CCceEEEecCCcchhhhcc
Confidence                       011245677899999999999999999999999999888764332   3558888887776 44444

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

Probab=98.46  E-value=5.1e-07  Score=77.41  Aligned_cols=64  Identities=19%  Similarity=0.376  Sum_probs=52.8

Q ss_pred             cCcccceeccccchHHHHHhHhCCeEEEecCCC-----------------CCCceEEEEEcCH---HHHHHHHHHHHHHH
Q 012307          351 ISYAEDIIGVGGTSIENIRRTSGAIITVQESRG-----------------LPDEITVEIKGTS---SQVQLAQQLIQEYM  410 (466)
Q Consensus       351 ~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~-----------------~~~er~V~I~Gt~---~~V~~A~~lI~~~i  410 (466)
                      .+++|.|||.+|.+||+|+++|||+|.|.....                 ..+.-.|.|++..   +.++.|..+|++++
T Consensus        14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll   93 (120)
T cd02395          14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL   93 (120)
T ss_pred             CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence            368899999999999999999999999976410                 1123689999965   89999999999999


Q ss_pred             hcCc
Q 012307          411 NNHK  414 (466)
Q Consensus       411 ~~~~  414 (466)
                      ....
T Consensus        94 ~~~~   97 (120)
T cd02395          94 KPAI   97 (120)
T ss_pred             ccCC
Confidence            8543

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

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

Probab=98.19  E-value=6.1e-06  Score=70.76  Aligned_cols=67  Identities=19%  Similarity=0.305  Sum_probs=51.1

Q ss_pred             CcceeeecCCchhHHHHHHHhCCeEEEecCCCCC-----------CCC-CCCceEEEEecC---HHHHHHHHHHHHHHhh
Q 012307          178 TQAINLIGKQGSLIKSIQENSGASVRVLSADEAP-----------FYV-TEDERIVEMQGE---AAKVLKALEAVVGHLR  242 (466)
Q Consensus       178 ~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p-----------~~~-~~~er~v~I~G~---~~~V~~A~~~I~~~l~  242 (466)
                      .++|.|||++|.+||+|+++|||+|.|..+...-           ... ..+.-.|.|.+.   .+++.+|+.+|..++.
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            5789999999999999999999999997542111           000 122356888885   5899999999999887


Q ss_pred             hc
Q 012307          243 KF  244 (466)
Q Consensus       243 ~~  244 (466)
                      ..
T Consensus        95 ~~   96 (120)
T cd02395          95 PA   96 (120)
T ss_pred             cC
Confidence            54

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

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.05  E-value=1.3e-05  Score=70.77  Aligned_cols=103  Identities=17%  Similarity=0.176  Sum_probs=71.5

Q ss_pred             eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCC
Q 012307           78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPEN  157 (466)
Q Consensus        78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~  157 (466)
                      -.+.++|+...+|..||++|++|+.|++..|-+|.|-.-           +-.         +.+-|..++.-.. +.+-
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~-----------s~d---------~~~fI~n~l~Pa~-V~~v   90 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY-----------SDD---------PEEFIKNIFAPAA-VRSV   90 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc-----------CCC---------HHHHHHHHcCCCE-EEEE
Confidence            467888999999999999999999999999988888543           111         1223333322110 0000


Q ss_pred             CcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEE
Q 012307          158 DVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRV  204 (466)
Q Consensus       158 ~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i  204 (466)
                      ..   ..........+.|+....|.+|||+|.+|+.++.-++-.+.|
T Consensus        91 ~I---~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di  134 (140)
T PRK08406         91 TI---KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             EE---EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence            00   001123566778999999999999999999999999887766

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.92  E-value=3.2e-05  Score=68.28  Aligned_cols=37  Identities=22%  Similarity=0.342  Sum_probs=34.3

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEe
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVL  205 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~  205 (466)
                      ..+.++|+...+|..||++|++|+.|++..|-+|.+.
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv   68 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV   68 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence            5688899999999999999999999999999999886

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.85  E-value=7.1e-05  Score=81.67  Aligned_cols=63  Identities=27%  Similarity=0.446  Sum_probs=56.9

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~  412 (466)
                      ..+|.||.+++|.|||.||.+||.|.++|||+|.|.+      +..|.|.+ ..+.+++|+.+|+.++..
T Consensus       579 ~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       579 IITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             eEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            5679999999999999999999999999999999965      35799988 568999999999999985

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=97.58  E-value=0.00028  Score=62.15  Aligned_cols=100  Identities=19%  Similarity=0.163  Sum_probs=69.6

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCC
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPEND  158 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~  158 (466)
                      .+-++|....+|..||++|++|+.|++..|=+|.|-.-           +..++         +-|..++.      +..
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey-----------s~D~~---------~fI~N~l~------PA~   87 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY-----------SENLE---------EFVANKLA------PAE   87 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc-----------CCCHH---------HHHHHcCC------Cce
Confidence            67788999999999999999999999999988888542           11110         11211111      000


Q ss_pred             cccc--cCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEE
Q 012307          159 VDAK--ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRV  204 (466)
Q Consensus       159 ~~~~--~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i  204 (466)
                      ....  ...+......+.||.+..+..|||+|.+|+...+-++-++.|
T Consensus        88 V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI  135 (141)
T TIGR01952        88 VKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI  135 (141)
T ss_pred             EEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence            0000  001134567788999999999999999999999998877766

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=97.58  E-value=0.00045  Score=70.88  Aligned_cols=76  Identities=14%  Similarity=0.264  Sum_probs=57.5

Q ss_pred             ceEEEEEecc------CcceeeecCCchhHHHHHHHhCCeEEEecCCCC---------CCCC--CCCceEEEEec-CHHH
Q 012307          168 FCSVRLLVPS------TQAINLIGKQGSLIKSIQENSGASVRVLSADEA---------PFYV--TEDERIVEMQG-EAAK  229 (466)
Q Consensus       168 ~~~~~llVP~------~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~---------p~~~--~~~er~v~I~G-~~~~  229 (466)
                      ..+.++.||.      +++|+|||..|.|.|+|+++|||+|.|..+..+         +.+.  ..++--+.|++ +.+.
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            5677888884      578999999999999999999999999862111         1111  12233467777 5778


Q ss_pred             HHHHHHHHHHHhhh
Q 012307          230 VLKALEAVVGHLRK  243 (466)
Q Consensus       230 V~~A~~~I~~~l~~  243 (466)
                      |++|+++|..+|.+
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999886

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.47  E-value=0.00034  Score=76.54  Aligned_cols=66  Identities=18%  Similarity=0.295  Sum_probs=57.8

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~  243 (466)
                      ......+.||.+.++.|||++|.+||.|+++||++|.|..           +..|.|.+ ..+.+++|+.+|..++..
T Consensus       576 aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----------~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       576 APRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-----------DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            4567788999999999999999999999999999999951           45788887 688999999999988874

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.25  E-value=0.00048  Score=76.21  Aligned_cols=64  Identities=27%  Similarity=0.425  Sum_probs=55.5

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~  412 (466)
                      ...++.||.++++.|||+||.+||.|.++|||+|.|.+      +-.|.|.+ ..+.+++|+.+|..+...
T Consensus       551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            35779999999999999999999999999999999965      34677776 567899999999988764

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).

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.24  E-value=0.00085  Score=59.14  Aligned_cols=36  Identities=28%  Similarity=0.412  Sum_probs=33.3

Q ss_pred             EEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEe
Q 012307          170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVL  205 (466)
Q Consensus       170 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~  205 (466)
                      .+-++|....+|..||++|++|+.|++..|-+|.+.
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV   69 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI   69 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence            677889999999999999999999999999888886

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=97.20  E-value=0.00036  Score=71.59  Aligned_cols=73  Identities=22%  Similarity=0.277  Sum_probs=51.8

Q ss_pred             CceEEEEEeccc------ccceeeecCChhHHHHHHHhCceEEEeCC---------------CCCC-CCeEEEecCCCCC
Q 012307           76 GHCVFRMIVPVL------KVGSIIGRKGELIKKTCEDTRARIKVLDG---------------PVSS-PDRIVLISGKEEP  133 (466)
Q Consensus        76 ~~~~~rllvp~~------~vG~IIGk~G~~Ik~I~~etga~I~v~~~---------------~~~~-~ervv~I~G~~e~  133 (466)
                      ..++-||.||.+      +||+|||.+|.+.|+|++||||||.|.-.               .++. ++=.|.|++..+ 
T Consensus       136 ~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~-  214 (554)
T KOG0119|consen  136 AKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQ-  214 (554)
T ss_pred             cccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchH-
Confidence            367889999976      59999999999999999999999999741               1111 223467776554 


Q ss_pred             CCCCChhHHHHHHHHHH
Q 012307          134 EAPVSPAMDAAVRVFKR  150 (466)
Q Consensus       134 ~~~v~~A~~ai~~i~~~  150 (466)
                       +.+.+|+..|..+++.
T Consensus       215 -eki~~Ai~vienli~~  230 (554)
T KOG0119|consen  215 -EKIKKAIAVIENLIQS  230 (554)
T ss_pred             -HHHHHHHHHHHHHHHh
Confidence             3455555555555544

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

Probab=97.06  E-value=0.0017  Score=65.68  Aligned_cols=68  Identities=21%  Similarity=0.303  Sum_probs=56.9

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      ...-+.|-.+++|.|||++|++|+.||..|.++|+|.+..   .+..|+|-|..+--.+|+..|...+...
T Consensus        47 ~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~---~e~kv~ifg~~~m~~kaka~id~~~~k~  114 (629)
T KOG0336|consen   47 FPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD---LEVKVTIFGINHMRKKAKASIDRGQDKD  114 (629)
T ss_pred             CchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC---ceeEEEEechHHHHHHHHhhHhhhhhhh
Confidence            4566789999999999999999999999999999997644   4678999999887777877776666543

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=97.04  E-value=0.0019  Score=59.80  Aligned_cols=100  Identities=22%  Similarity=0.328  Sum_probs=70.1

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCC
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPEND  158 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~  158 (466)
                      .+-+++-.+.+|..||++|.+|+.|.++.|=+|.|-.-.             ++.       ..-|..++.-.      .
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-------------~d~-------~~fI~nal~Pa------~  130 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-------------EDP-------AEFIKNALAPA------E  130 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-------------CCH-------HHHHHHhcCcc------e
Confidence            455566677899999999999999999999778775431             111       12232222211      0


Q ss_pred             cccc--cCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEe
Q 012307          159 VDAK--ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVL  205 (466)
Q Consensus       159 ~~~~--~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~  205 (466)
                      ..+.  ... ......+.||.++.+.+|||+|.+++-+.+-||-++.|.
T Consensus       131 v~~V~~~~~-d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~  178 (190)
T COG0195         131 VLSVNIKED-DGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE  178 (190)
T ss_pred             EeEEEEEeC-CCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence            0000  000 112788899999999999999999999999999999996

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

Probab=97.02  E-value=0.00032  Score=70.74  Aligned_cols=56  Identities=29%  Similarity=0.383  Sum_probs=48.9

Q ss_pred             CCCceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCC
Q 012307           74 WPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE  132 (466)
Q Consensus        74 ~~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e  132 (466)
                      +.+++.+.+-|-+++||.|||++|++||+||..|+++|++-+.   ..+-.|+|.|..+
T Consensus        43 g~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~   98 (629)
T KOG0336|consen   43 GGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINH   98 (629)
T ss_pred             CCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHH
Confidence            3567888999999999999999999999999999999999866   4566788888764

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

Probab=96.96  E-value=0.00081  Score=64.31  Aligned_cols=42  Identities=31%  Similarity=0.509  Sum_probs=37.4

Q ss_pred             CCceEEEEEeccc------ccceeeecCChhHHHHHHHhCceEEEeCC
Q 012307           75 PGHCVFRMIVPVL------KVGSIIGRKGELIKKTCEDTRARIKVLDG  116 (466)
Q Consensus        75 ~~~~~~rllvp~~------~vG~IIGk~G~~Ik~I~~etga~I~v~~~  116 (466)
                      +-..+.||+||.+      .||.|+|.+|.++|+|+++|+|+|.|.-.
T Consensus        89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr  136 (259)
T KOG1588|consen   89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR  136 (259)
T ss_pred             ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence            3457889999998      69999999999999999999999998744

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.92  E-value=0.002  Score=72.17  Aligned_cols=63  Identities=24%  Similarity=0.356  Sum_probs=56.1

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCe-EEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAI-ITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~-I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~  412 (466)
                      ...|.||.++++.|||.||.+||.|.++||+. |.|.+      +-.|.|.+ ..+.++.|+.+|++++..
T Consensus       686 i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        686 IHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             eEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            56799999999999999999999999999999 99964      35788888 568999999999999874

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=96.89  E-value=0.06  Score=50.80  Aligned_cols=88  Identities=13%  Similarity=0.232  Sum_probs=65.4

Q ss_pred             HHHHHHHHHhcCCCCCCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEE
Q 012307          142 DAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIV  221 (466)
Q Consensus       142 ~ai~~i~~~i~~l~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v  221 (466)
                      ..+.+|+..+.++.-.+..     .....+.+.++....-.|...+|..++.|....|++|.+.          ..+..+
T Consensus         4 ~l~~~Il~d~W~l~v~e~v-----~~~g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~----------~~~~~i   68 (210)
T PF14611_consen    4 KLAERILRDCWNLEVSEEV-----DELGDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVS----------RSENRI   68 (210)
T ss_pred             HHHHHHHHHhcCCccccee-----eccceeEEEecchheeeeecCCchHHHHHHHhcCceEEEe----------cCCcEE
Confidence            4567777777665432211     0223445556688888999999999999988889999996          335689


Q ss_pred             EEecCHHHHHHHHHHHHHHhhhc
Q 012307          222 EMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       222 ~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      .|+|+...+..+...|.+++...
T Consensus        69 ~I~g~k~~~~~i~~~i~~~l~~i   91 (210)
T PF14611_consen   69 RITGTKSTAEYIEASINEILSNI   91 (210)
T ss_pred             EEEccHHHHHHHHHHHHHHHhhc
Confidence            99999999999998888877653

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

Probab=96.86  E-value=0.0017  Score=48.84  Aligned_cols=37  Identities=22%  Similarity=0.370  Sum_probs=34.4

Q ss_pred             ceEEEEEecccccceeeecCChhHHHHHHHhCceEEE
Q 012307           77 HCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKV  113 (466)
Q Consensus        77 ~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v  113 (466)
                      ...+.+.|+.+.+|.+|||+|.+|+.+++.++-+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3688999999999999999999999999999988876

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.

>PRK00106 hypothetical protein; Provisional

Probab=96.82  E-value=0.0072  Score=64.59  Aligned_cols=66  Identities=17%  Similarity=0.363  Sum_probs=51.7

Q ss_pred             eEEEEEeccC-cccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcC
Q 012307          343 ITQTMQIPIS-YAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       343 ~t~~i~IP~~-~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~~  413 (466)
                      .+..+.+|++ +-|+||||.|.||+.+...||+.|.|++..+     .|+|+| .|---+-|+.-|..+|.+.
T Consensus       225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~-----~v~lS~fdpvRReiAr~~le~Li~dg  292 (535)
T PRK00106        225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPE-----VVVLSGFDPIRREIARMTLESLIKDG  292 (535)
T ss_pred             eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCCC-----eEEEeCCChHHHHHHHHHHHHHHHcC
Confidence            3456889995 4599999999999999999999999987443     788998 6655566666666666543

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=96.78  E-value=0.0023  Score=70.94  Aligned_cols=66  Identities=18%  Similarity=0.325  Sum_probs=55.2

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~  243 (466)
                      ......+.||.+.++.|||++|++||+|+++||++|.|..           +..|.|.+ ..+.+.+|..+|..+..+
T Consensus       549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------dG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------DGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            4567789999999999999999999999999999999951           34566665 678899999999877553

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).

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

Probab=96.76  E-value=0.0019  Score=69.43  Aligned_cols=65  Identities=25%  Similarity=0.431  Sum_probs=57.5

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHhcCc
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTS-SQVQLAQQLIQEYMNNHK  414 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~-~~V~~A~~lI~~~i~~~~  414 (466)
                      ..++.|+.+.++.|||++|.+|++|.++|||+|+|.+      +-+|.|.++. +.+..|+.+|.++.++..
T Consensus       553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied------dGtv~i~~s~~~~~~~ak~~I~~i~~e~e  618 (692)
T COG1185         553 IETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED------DGTVKIAASDGESAKKAKERIEAITREVE  618 (692)
T ss_pred             eEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC------CCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence            5679999999999999999999999999999999963      3379999976 789999999999997643

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.70  E-value=0.0042  Score=66.51  Aligned_cols=66  Identities=15%  Similarity=0.352  Sum_probs=51.5

Q ss_pred             eEEEEEeccCc-ccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcC
Q 012307          343 ITQTMQIPISY-AEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       343 ~t~~i~IP~~~-~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~~  413 (466)
                      .+..+.+|++- -|+||||.|.||+.+...||+.|.|++..+     .|+|+| .|---+.|+.-|..+|...
T Consensus       204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp~-----~v~ls~fdp~rreia~~~l~~li~dg  271 (514)
T TIGR03319       204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPE-----AVILSGFDPVRREIARMALEKLIQDG  271 (514)
T ss_pred             eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCCC-----eEEecCCchHHHHHHHHHHHHHHHcC
Confidence            44568999965 599999999999999999999999987443     788888 5655566666666666543

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

Probab=96.64  E-value=0.0015  Score=72.83  Aligned_cols=102  Identities=10%  Similarity=-0.067  Sum_probs=78.8

Q ss_pred             ccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCceEEEEEecccccceeeecCChhH
Q 012307           24 ATTESPTTESEAPPTIGSENTEHTTESDSALPQSTGPDAAAVPEEKKWPGW---PGHCVFRMIVPVLKVGSIIGRKGELI  100 (466)
Q Consensus        24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~rllvp~~~vG~IIGk~G~~I  100 (466)
                      -.-+++|+++.+...+....++++++.++..       |..-+..+|...|   -..-.++.-.+..++.+||++.+.+|
T Consensus       731 r~~~e~t~~slskS~~~~id~~Te~n~~t~L-------T~acaggh~e~vellv~rganiehrdkkgf~plImaatagh~  803 (2131)
T KOG4369|consen  731 RLEGEVTPNSLSKSYKTVIDPLTEPNIKTNL-------TSACAGGHREEVELLVVRGANIEHRDKKGFVPLIMAATAGHI  803 (2131)
T ss_pred             hhhccccchhhccccceeeccccCccccccc-------cccccCccHHHHHHHHHhcccccccccccchhhhhhcccCch
Confidence            3456888999888888888888888888777       5555556665544   22235667788999999999999999


Q ss_pred             HHHHHHhCceEEEeCCCCCCCCeEEEecCCCC
Q 012307          101 KKTCEDTRARIKVLDGPVSSPDRIVLISGKEE  132 (466)
Q Consensus       101 k~I~~etga~I~v~~~~~~~~ervv~I~G~~e  132 (466)
                      +-++.-+++.+.|......+.|+.+.|.+.-+
T Consensus       804 tvV~~llk~ha~veaQsdrtkdt~lSlacsgg  835 (2131)
T KOG4369|consen  804 TVVQDLLKAHADVEAQSDRTKDTMLSLACSGG  835 (2131)
T ss_pred             HHHHHHHhhhhhhhhhcccccCceEEEecCCC
Confidence            99999999999998665567888888876543

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

Probab=96.63  E-value=0.014  Score=55.91  Aligned_cols=42  Identities=19%  Similarity=0.408  Sum_probs=37.2

Q ss_pred             CcceEEEEEeccC------cceeeecCCchhHHHHHHHhCCeEEEecC
Q 012307          166 AAFCSVRLLVPST------QAINLIGKQGSLIKSIQENSGASVRVLSA  207 (466)
Q Consensus       166 ~~~~~~~llVP~~------~vg~IIGk~G~~Ik~I~~~sga~I~i~~~  207 (466)
                      ....+.+|+||..      +||+|+|.+|.++|+|+++|||+|-|..+
T Consensus        89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr  136 (259)
T KOG1588|consen   89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR  136 (259)
T ss_pred             ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence            3567788999965      79999999999999999999999999864

>PRK12704 phosphodiesterase; Provisional

Probab=96.62  E-value=0.0053  Score=65.84  Aligned_cols=66  Identities=15%  Similarity=0.331  Sum_probs=51.4

Q ss_pred             eEEEEEeccCc-ccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcC
Q 012307          343 ITQTMQIPISY-AEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       343 ~t~~i~IP~~~-~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~~  413 (466)
                      .+..+.+|++- -|+||||.|.||+.+...||+.|.|++..     ..|+|+| .+---+.|+..+...+...
T Consensus       210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~~~~~rre~a~~~l~~l~~dg  277 (520)
T PRK12704        210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPIRREIARLALEKLVQDG  277 (520)
T ss_pred             ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC-----CeEEEecCChhhHHHHHHHHHHHHhcC
Confidence            44568899855 59999999999999999999999998744     3788999 5555556666666665543

>TIGR01953 NusA transcription termination factor NusA

Probab=96.56  E-value=0.0085  Score=60.71  Aligned_cols=93  Identities=19%  Similarity=0.278  Sum_probs=63.8

Q ss_pred             ccceeeecCChhHHHHHHHh-CceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccc-cCC
Q 012307           88 KVGSIIGRKGELIKKTCEDT-RARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAK-ASG  165 (466)
Q Consensus        88 ~vG~IIGk~G~~Ik~I~~et-ga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~-~~~  165 (466)
                      -+|..||++|.+|+.|.++. |=+|.|-.-..+           +         ..-|..++.      +...... ...
T Consensus       244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d-----------~---------~~fi~nal~------Pa~v~~v~i~~  297 (341)
T TIGR01953       244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSDD-----------P---------AEFIANALS------PAKVISVEVLD  297 (341)
T ss_pred             cceeeECCCCchHHHHHHHhCCCeEEEEEcCCC-----------H---------HHHHHHhcC------CceEEEEEEEc
Confidence            49999999999999999998 778887543100           0         011111111      0000000 000


Q ss_pred             CcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEec
Q 012307          166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLS  206 (466)
Q Consensus       166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~  206 (466)
                      .......+.||..+.+..|||+|.+++-..+-||.+|.|.+
T Consensus       298 ~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       298 EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            12357889999999999999999999999999999999974

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

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.55  E-value=0.0089  Score=60.73  Aligned_cols=97  Identities=16%  Similarity=0.168  Sum_probs=65.8

Q ss_pred             cccceeeecCChhHHHHHHHh-CceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccccCC
Q 012307           87 LKVGSIIGRKGELIKKTCEDT-RARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASG  165 (466)
Q Consensus        87 ~~vG~IIGk~G~~Ik~I~~et-ga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~~~~  165 (466)
                      +-+|..||++|.+|+.|.++. |=+|.|-.-.             .+.       ..-|..++.      +.........
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s-------------~D~-------~~fI~Nal~------Pa~V~~V~i~  304 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYS-------------NVP-------EIFIARALA------PAIISSVKIE  304 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC-------------CCH-------HHHHHHhCC------CceeeEEEEc
Confidence            359999999999999999998 7788875431             110       011111111      0000000000


Q ss_pred             CcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCC
Q 012307          166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADE  209 (466)
Q Consensus       166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~  209 (466)
                      .......+.||..+.+..|||+|.+++-..+-||.+|.|.+-.+
T Consensus       305 ~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~  348 (374)
T PRK12328        305 EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS  348 (374)
T ss_pred             CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence            13357889999999999999999999999999999999986443

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.46  E-value=0.0081  Score=55.64  Aligned_cols=37  Identities=19%  Similarity=0.304  Sum_probs=34.0

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE  380 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~  380 (466)
                      ...+.||.+..+.+|||+|.|++.+.+.||-++.|..
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            4567899999999999999999999999999999954

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

Probab=96.43  E-value=0.0036  Score=61.60  Aligned_cols=73  Identities=14%  Similarity=0.172  Sum_probs=60.7

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      .....+.++..+.|.|||+.|.+-+.|+++|++.|.++.+... .+.++.+.+..++|..|...|.-+|.+..-
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n-~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~  128 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTN-KEEIKIIGISRNCVIQALERIAKLIDSDRK  128 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCC-cceEEEeehhHHHHHHHHHHHHHHHHhhhh
Confidence            4556789999999999999999999999999999999776642 344444555778999999999999998763

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

Probab=96.35  E-value=0.0051  Score=46.22  Aligned_cols=36  Identities=19%  Similarity=0.277  Sum_probs=33.1

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEE
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITV  378 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I  378 (466)
                      ....+.|+.+..|.+|||+|.+|+.+++.+|-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            356789999999999999999999999999988876

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.33  E-value=0.012  Score=59.94  Aligned_cols=94  Identities=18%  Similarity=0.261  Sum_probs=64.6

Q ss_pred             cccceeeecCChhHHHHHHHh-CceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccc-cC
Q 012307           87 LKVGSIIGRKGELIKKTCEDT-RARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAK-AS  164 (466)
Q Consensus        87 ~~vG~IIGk~G~~Ik~I~~et-ga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~-~~  164 (466)
                      +-+|..||++|.+|+.|.++. |=+|.|-.-..+           +         ...|..++.      +...... ..
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d-----------~---------~~fi~nal~------Pa~v~~v~i~  298 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSED-----------P---------AEFVANALS------PAKVVSVEVD  298 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCCC-----------H---------HHHHHHhCC------CceEEEEEEE
Confidence            359999999999999999998 778888543100           0         011111111      0000000 00


Q ss_pred             CCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEec
Q 012307          165 GAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLS  206 (466)
Q Consensus       165 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~  206 (466)
                      ........+.||..+.+..|||+|.+++-..+-||.+|.|.+
T Consensus       299 ~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s  340 (362)
T PRK12327        299 DEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS  340 (362)
T ss_pred             cCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence            013357889999999999999999999999999999999974

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.22  E-value=0.011  Score=61.25  Aligned_cols=93  Identities=22%  Similarity=0.304  Sum_probs=63.2

Q ss_pred             cccceeeecCChhHHHHHHHh-CceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccc-cC
Q 012307           87 LKVGSIIGRKGELIKKTCEDT-RARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAK-AS  164 (466)
Q Consensus        87 ~~vG~IIGk~G~~Ik~I~~et-ga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~-~~  164 (466)
                      +-+|..||++|.+|+.|.++. |=+|.|-.-.             .+.       ..-|..++.      +...... ..
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys-------------~Dp-------~~fI~NaLs------PA~V~~V~i~  330 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS-------------PDP-------ATYIANALS------PARVDEVRLV  330 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC-------------CCH-------HHHHHHhcC------CceeeEEEEE
Confidence            359999999999999999998 7788775331             110       011111111      0000000 00


Q ss_pred             CCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEe
Q 012307          165 GAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVL  205 (466)
Q Consensus       165 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~  205 (466)
                      ........+.||..+.+..|||+|.+++-..+-||.+|.|.
T Consensus       331 ~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~  371 (449)
T PRK12329        331 DPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK  371 (449)
T ss_pred             cCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence            01235678999999999999999999999999999999985

>PRK00468 hypothetical protein; Provisional

Probab=96.03  E-value=0.007  Score=47.41  Aligned_cols=32  Identities=19%  Similarity=0.379  Sum_probs=29.0

Q ss_pred             CCceEEEEEecccccceeeecCChhHHHHHHH
Q 012307           75 PGHCVFRMIVPVLKVGSIIGRKGELIKKTCED  106 (466)
Q Consensus        75 ~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~e  106 (466)
                      .+.+.++|.|..+.+|.||||+|.+|+.||.-
T Consensus        27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             CCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            35588999999999999999999999999965

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.02  E-value=0.012  Score=56.70  Aligned_cols=63  Identities=21%  Similarity=0.301  Sum_probs=53.6

Q ss_pred             EEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHhcC
Q 012307          345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTS-SQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~-~~V~~A~~lI~~~i~~~  413 (466)
                      ..+.||.++++++||++|.+|+.|.+.+++.|.|..      +-.|-|.++. +.+++|+.+|+++-++.
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            458899999999999999999999999999999954      2478888865 58999999998766654

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

Probab=95.96  E-value=0.01  Score=58.55  Aligned_cols=72  Identities=26%  Similarity=0.237  Sum_probs=58.3

Q ss_pred             ceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhcc
Q 012307          168 FCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFL  245 (466)
Q Consensus       168 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~  245 (466)
                      .....+.|+....+.|||++|.+-++|+++|+++|.++...      +..+.++.+.+..++|.+|.+.|..+|.+.-
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN------TNKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC------CCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            35567889999999999999999999999999999997432      2334455555588999999999988887653

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=95.95  E-value=0.0086  Score=67.23  Aligned_cols=66  Identities=20%  Similarity=0.232  Sum_probs=55.8

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCe-EEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGAS-VRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~-I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~  243 (466)
                      ......+.||.+.++.|||.+|.+||.|.++||++ |.+.  +         +-.|.|.+ ..+.+.+|+.+|..+..+
T Consensus       683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~--d---------dg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ--D---------DGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC--C---------CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            45678889999999999999999999999999999 8773  1         45677777 688999999999887653

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.82  E-value=0.021  Score=60.41  Aligned_cols=93  Identities=18%  Similarity=0.310  Sum_probs=63.7

Q ss_pred             ccceeeecCChhHHHHHHHh-CceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccccCCC
Q 012307           88 KVGSIIGRKGELIKKTCEDT-RARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGA  166 (466)
Q Consensus        88 ~vG~IIGk~G~~Ik~I~~et-ga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~~~~~  166 (466)
                      -+|..||++|.+|+.|.++. |=+|.|-.-..   +        +         ..-|...+.      +..........
T Consensus       246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~---d--------~---------~~fi~nal~------pa~v~~v~~~~  299 (470)
T PRK09202        246 PVGACVGMRGSRIQAISNELGGEKIDIILWSD---D--------P---------AQFIINALS------PAEVSSVVVDE  299 (470)
T ss_pred             hhHccCCCCCchHHHHHHHhCCCeEEEEEcCC---C--------H---------HHHHHHhCC------CCEEEEEEEeC
Confidence            49999999999999999998 77888753310   0        0         011111111      00000000001


Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEec
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLS  206 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~  206 (466)
                      ......+.||..+.+..|||+|.+++...+-||.+|.|..
T Consensus       300 ~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        300 DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            2247889999999999999999999999999999999975

>PRK02821 hypothetical protein; Provisional

Probab=95.74  E-value=0.01  Score=46.62  Aligned_cols=33  Identities=18%  Similarity=0.177  Sum_probs=29.3

Q ss_pred             CceEEEEEecccccceeeecCChhHHHHHHHhC
Q 012307           76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTR  108 (466)
Q Consensus        76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etg  108 (466)
                      +.+.++|.|..+.+|.||||+|.+|+.||.--.
T Consensus        29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             CcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            457899999999999999999999999997643

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

Probab=95.52  E-value=0.037  Score=51.03  Aligned_cols=41  Identities=24%  Similarity=0.360  Sum_probs=34.7

Q ss_pred             cceEEEEEec------cCcceeeecCCchhHHHHHHHhCCeEEEecC
Q 012307          167 AFCSVRLLVP------STQAINLIGKQGSLIKSIQENSGASVRVLSA  207 (466)
Q Consensus       167 ~~~~~~llVP------~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~  207 (466)
                      ...+-++.||      ..+||+|||..|.+.|+|++.|+|+|-|-..
T Consensus       146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            3455667777      4689999999999999999999999999753

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

Probab=95.48  E-value=0.015  Score=53.61  Aligned_cols=42  Identities=29%  Similarity=0.492  Sum_probs=36.9

Q ss_pred             CCceEEEEEeccc------ccceeeecCChhHHHHHHHhCceEEEeCC
Q 012307           75 PGHCVFRMIVPVL------KVGSIIGRKGELIKKTCEDTRARIKVLDG  116 (466)
Q Consensus        75 ~~~~~~rllvp~~------~vG~IIGk~G~~Ik~I~~etga~I~v~~~  116 (466)
                      |..+.-++.||..      .||+|||..|.++|+|++.|+|+|-|...
T Consensus       145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            4567788899875      69999999999999999999999999754

>TIGR01953 NusA transcription termination factor NusA

Probab=95.46  E-value=0.04  Score=55.90  Aligned_cols=37  Identities=22%  Similarity=0.322  Sum_probs=34.3

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE  380 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~  380 (466)
                      ...+.||.+..+..|||+|.|++-..+.||.+|.|..
T Consensus       302 ~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       302 SAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             EEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            5678999999999999999999999999999999954

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.33  E-value=0.015  Score=64.72  Aligned_cols=63  Identities=29%  Similarity=0.495  Sum_probs=54.5

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~  412 (466)
                      ...+.||.+.++.+||.||.+||.|.++||+.|.|.+      +-.|.|.+ ..+.+++|+.+|+.+...
T Consensus       555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccHHHHHHHHHHHHHhccc
Confidence            4568889999999999999999999999999988843      34688888 567899999999998865

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.30  E-value=0.034  Score=56.61  Aligned_cols=37  Identities=19%  Similarity=0.224  Sum_probs=34.1

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE  380 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~  380 (466)
                      ...+.||.+..+..|||+|.|++-..+.||.+|.|..
T Consensus       309 ~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s  345 (374)
T PRK12328        309 KAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE  345 (374)
T ss_pred             EEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence            4568899999999999999999999999999999964

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

Probab=95.26  E-value=0.022  Score=44.50  Aligned_cols=32  Identities=19%  Similarity=0.310  Sum_probs=29.0

Q ss_pred             CCceEEEEEecccccceeeecCChhHHHHHHH
Q 012307           75 PGHCVFRMIVPVLKVGSIIGRKGELIKKTCED  106 (466)
Q Consensus        75 ~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~e  106 (466)
                      +..+.++|-+..+.+|.||||+|.+|+.||.-
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            45678999999999999999999999999965

>PRK01064 hypothetical protein; Provisional

Probab=95.19  E-value=0.023  Score=44.81  Aligned_cols=32  Identities=25%  Similarity=0.441  Sum_probs=29.0

Q ss_pred             CCceEEEEEecccccceeeecCChhHHHHHHH
Q 012307           75 PGHCVFRMIVPVLKVGSIIGRKGELIKKTCED  106 (466)
Q Consensus        75 ~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~e  106 (466)
                      .+.+.+++.|..+..|.+|||+|.+|+.||.-
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l   58 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTL   58 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence            35688999999999999999999999999974

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

Probab=95.17  E-value=0.026  Score=60.91  Aligned_cols=69  Identities=23%  Similarity=0.312  Sum_probs=58.5

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecC-HHHHHHHHHHHHHHhhhcc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGE-AAKVLKALEAVVGHLRKFL  245 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I~~~l~~~~  245 (466)
                      ......+.|+.+.+.-+||++|.+|++|.++||++|.+.           ++-.|.|.+. .+.+.+|+..|..+.++..
T Consensus       550 aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~e  618 (692)
T COG1185         550 APRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DDGTVKIAASDGESAKKAKERIEAITREVE  618 (692)
T ss_pred             CCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CCCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence            445677889999999999999999999999999999995           2446888875 5889999999999998764


Q ss_pred             c
Q 012307          246 V  246 (466)
Q Consensus       246 ~  246 (466)
                      +
T Consensus       619 v  619 (692)
T COG1185         619 V  619 (692)
T ss_pred             c
Confidence            4

>PRK00468 hypothetical protein; Provisional

Probab=95.15  E-value=0.049  Score=42.64  Aligned_cols=32  Identities=28%  Similarity=0.356  Sum_probs=28.6

Q ss_pred             CcceEEEEEeccCcceeeecCCchhHHHHHHH
Q 012307          166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQEN  197 (466)
Q Consensus       166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~  197 (466)
                      .....+++.|...-+|+||||+|.+|+.|+.-
T Consensus        27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             CCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            35678899999999999999999999999864

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.08  E-value=0.043  Score=58.05  Aligned_cols=37  Identities=16%  Similarity=0.249  Sum_probs=34.4

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE  380 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~  380 (466)
                      ...+.||.+..+..|||+|.||+..++.||.+|.|..
T Consensus       303 ~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        303 SADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             EEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            5678999999999999999999999999999999965

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.01  E-value=0.062  Score=54.89  Aligned_cols=37  Identities=19%  Similarity=0.211  Sum_probs=34.3

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE  380 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~  380 (466)
                      ...+.||.+..+..|||+|.|++-..+.||.+|.|..
T Consensus       304 ~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s  340 (362)
T PRK12327        304 AARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS  340 (362)
T ss_pred             EEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence            4678999999999999999999999999999999964

>PRK02821 hypothetical protein; Provisional

Probab=94.87  E-value=0.058  Score=42.44  Aligned_cols=33  Identities=12%  Similarity=0.155  Sum_probs=28.9

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhC
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSG  199 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sg  199 (466)
                      ....+++.|...-+|+||||+|.+|+.|+.--.
T Consensus        29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             CcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            557899999999999999999999999987543

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=94.80  E-value=0.064  Score=51.68  Aligned_cols=64  Identities=22%  Similarity=0.318  Sum_probs=52.6

Q ss_pred             EEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecC-HHHHHHHHHHHHHHhhhc
Q 012307          170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGE-AAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       170 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I~~~l~~~  244 (466)
                      -..+.||...++.|||++|.+|+.|.+.++++|.+-          . +-.|.|.+. .+++.+|..+|..+-++.
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig----------~-NG~VwI~~~~~~~~~~a~~~I~~~e~~~  210 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG----------Q-NGRIWIKGPDEEDEEIAIEAIKKIEREA  210 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc----------C-CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence            366889999999999999999999999999999983          1 346778775 668888999887765553

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

Probab=94.72  E-value=0.086  Score=41.24  Aligned_cols=32  Identities=28%  Similarity=0.388  Sum_probs=29.2

Q ss_pred             CcceEEEEEeccCcceeeecCCchhHHHHHHH
Q 012307          166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQEN  197 (466)
Q Consensus       166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~  197 (466)
                      ......++-|...-+|.||||+|.+|+.|+.-
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            46788999999999999999999999999975

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=94.67  E-value=0.53  Score=44.36  Aligned_cols=130  Identities=9%  Similarity=0.108  Sum_probs=85.0

Q ss_pred             CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCC
Q 012307           76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLP  155 (466)
Q Consensus        76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~  155 (466)
                      +++.++  ++....-++...+|..++.|-...||+|.+...     +..|.|+|++..+   ..+...|.++++.+    
T Consensus        26 g~l~v~--l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k~~~---~~i~~~i~~~l~~i----   91 (210)
T PF14611_consen   26 GDLDVW--LQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTKSTA---EYIEASINEILSNI----   91 (210)
T ss_pred             ceeEEE--ecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccHHHH---HHHHHHHHHHHhhc----
Confidence            444444  457888999999999999998889999999754     5679999988542   22333334444333    


Q ss_pred             CCCcccccCCCcceEEEEEeccCcceeee----cCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEe-----cC
Q 012307          156 ENDVDAKASGAAFCSVRLLVPSTQAINLI----GKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQ-----GE  226 (466)
Q Consensus       156 ~~~~~~~~~~~~~~~~~llVP~~~vg~II----Gk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~-----G~  226 (466)
                                   .+..+-++.-.--.-.    -.....++.|++.|++.|+..++          ...+.|.     -.
T Consensus        92 -------------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~~~  148 (210)
T PF14611_consen   92 -------------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASPEN  148 (210)
T ss_pred             -------------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeeccc
Confidence                         3344444422111111    12356789999999999998632          2223333     46


Q ss_pred             HHHHHHHHHHHHHHhh
Q 012307          227 AAKVLKALEAVVGHLR  242 (466)
Q Consensus       227 ~~~V~~A~~~I~~~l~  242 (466)
                      .+.+..|+.+++..+.
T Consensus       149 ~~~~~~a~RlL~~a~~  164 (210)
T PF14611_consen  149 EKRADRAKRLLLWALD  164 (210)
T ss_pred             cchHHHHHHHHHHhcc
Confidence            7788999999988774

>PRK12705 hypothetical protein; Provisional

Probab=94.62  E-value=0.044  Score=58.30  Aligned_cols=40  Identities=20%  Similarity=0.354  Sum_probs=34.5

Q ss_pred             eEEEEEeccCcc-cceeccccchHHHHHhHhCCeEEEecCC
Q 012307          343 ITQTMQIPISYA-EDIIGVGGTSIENIRRTSGAIITVQESR  382 (466)
Q Consensus       343 ~t~~i~IP~~~~-G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~  382 (466)
                      .+..+.+|++-+ |+||||.|.||+.+...||+.|.|++..
T Consensus       198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp  238 (508)
T PRK12705        198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP  238 (508)
T ss_pred             eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc
Confidence            345678898655 9999999999999999999999998744

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=94.49  E-value=0.068  Score=55.38  Aligned_cols=37  Identities=19%  Similarity=0.291  Sum_probs=34.0

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE  380 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~  380 (466)
                      ...+.||.+..+..|||+|.||+-..+.||.+|.|..
T Consensus       336 ~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        336 HAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             EEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            3568899999999999999999999999999999954

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=94.42  E-value=0.038  Score=61.52  Aligned_cols=65  Identities=22%  Similarity=0.354  Sum_probs=53.1

Q ss_pred             ceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307          168 FCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       168 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~  243 (466)
                      .....+.||.+.++.+||.+|.+||+|.++||++|.+.  +         +-.|.|.+ ..+.+.+|..+|..+..+
T Consensus       553 p~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~--d---------~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        553 PRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE--D---------DGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             chheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC--C---------CceEEEEcccHHHHHHHHHHHHHhccc
Confidence            34566777999999999999999999999999988773  2         34577777 678899999999887754

>PRK12704 phosphodiesterase; Provisional

Probab=94.34  E-value=0.17  Score=54.41  Aligned_cols=66  Identities=15%  Similarity=0.213  Sum_probs=49.3

Q ss_pred             eEEEEEecc-CcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhhc
Q 012307          169 CSVRLLVPS-TQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       169 ~~~~llVP~-~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~~  244 (466)
                      ....+-+|+ ++-|+||||.|.+|+.++.-||+.|.|.          .+...|.|+| .+-.-+.|...+..++.+.
T Consensus       210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~~~~~rre~a~~~l~~l~~dg  277 (520)
T PRK12704        210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSGFDPIRREIARLALEKLVQDG  277 (520)
T ss_pred             ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc----------CCCCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence            444566776 6889999999999999999999999994          3345677888 4555456666666655554

>PRK00106 hypothetical protein; Provisional

Probab=94.33  E-value=0.2  Score=53.81  Aligned_cols=67  Identities=15%  Similarity=0.283  Sum_probs=50.2

Q ss_pred             cceEEEEEecc-CcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307          167 AFCSVRLLVPS-TQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       167 ~~~~~~llVP~-~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~  243 (466)
                      ......+-+|+ ++-|+||||.|.+|+.++.-||+.+.|.          .+...|.|+| .|---+.|...+..++.+
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid----------dtp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID----------DTPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc----------CCCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            33455567787 6789999999999999999999999994          3345677888 565556666666665553

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=94.27  E-value=0.18  Score=54.14  Aligned_cols=66  Identities=15%  Similarity=0.242  Sum_probs=49.4

Q ss_pred             ceEEEEEecc-CcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307          168 FCSVRLLVPS-TQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       168 ~~~~~llVP~-~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~  243 (466)
                      .....+-+|+ ++-|+||||.|.+|+.++.-||+.|.|.          .+...|.|++ .|---+.|...|..++.+
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc----------CCCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            3445566776 6789999999999999999999999994          2345677888 565555566666665553

>PRK01064 hypothetical protein; Provisional

Probab=93.87  E-value=0.18  Score=39.81  Aligned_cols=32  Identities=28%  Similarity=0.325  Sum_probs=28.8

Q ss_pred             CcceEEEEEeccCcceeeecCCchhHHHHHHH
Q 012307          166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQEN  197 (466)
Q Consensus       166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~  197 (466)
                      .....+++.|...-.|.+|||+|.+|+.|+.-
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l   58 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTL   58 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence            46688999999999999999999999999874

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=92.75  E-value=0.054  Score=42.07  Aligned_cols=33  Identities=12%  Similarity=0.132  Sum_probs=28.3

Q ss_pred             CceEEEEEecccccceeeecCChhHHHHHHHhC
Q 012307           76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTR  108 (466)
Q Consensus        76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etg  108 (466)
                      +...+.+-|..+..|.||||+|.+++.||.-.+
T Consensus        27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~   59 (73)
T PF13083_consen   27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN   59 (73)
T ss_dssp             TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred             CceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence            456778888999999999999999999996544

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

Probab=92.36  E-value=0.22  Score=37.27  Aligned_cols=35  Identities=20%  Similarity=0.272  Sum_probs=28.1

Q ss_pred             ceEEEEEecccccceeeecCChhHHHHHHHhCceE
Q 012307           77 HCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARI  111 (466)
Q Consensus        77 ~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I  111 (466)
                      ...+.+.+.....|.+|||+|.+|+.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            34556666666789999999999999999988544

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=91.53  E-value=0.14  Score=39.42  Aligned_cols=37  Identities=32%  Similarity=0.467  Sum_probs=29.0

Q ss_pred             EEEEecccc-----cceeeecCChhHHHHHHHh-CceEEEeCC
Q 012307           80 FRMIVPVLK-----VGSIIGRKGELIKKTCEDT-RARIKVLDG  116 (466)
Q Consensus        80 ~rllvp~~~-----vG~IIGk~G~~Ik~I~~et-ga~I~v~~~  116 (466)
                      .++.|-...     +|..||++|.+||.|.++. |-+|+|-.-
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            456666666     9999999999999999999 888888543

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

Probab=89.65  E-value=0.4  Score=54.56  Aligned_cols=57  Identities=18%  Similarity=0.144  Sum_probs=49.6

Q ss_pred             ceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC-CCCCCCeEEEecCCCCC
Q 012307           77 HCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG-PVSSPDRIVLISGKEEP  133 (466)
Q Consensus        77 ~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~-~~~~~ervv~I~G~~e~  133 (466)
                      ...-++.+|.....+|||++|.+|..++.-||+-|.|.+- ..+..||.+.+.|.++.
T Consensus      1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~ 1396 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPS 1396 (2131)
T ss_pred             ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChh
Confidence            3455778899999999999999999999999999999873 44578999999999874

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

Probab=89.32  E-value=1.2  Score=39.22  Aligned_cols=93  Identities=20%  Similarity=0.356  Sum_probs=58.6

Q ss_pred             eecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccccCCCcceEEE
Q 012307           93 IGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVR  172 (466)
Q Consensus        93 IGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~~~~~~~~~~~  172 (466)
                      +=.+|..|++|-.+-.-||.|..++.        +.-.++      .|.+.|.++.-.-.++.+-.+       ...+-+
T Consensus        21 ~~~~~dli~~lAk~lrKRIvvR~dps--------~l~~~e------~A~~~I~~ivP~ea~i~di~F-------d~~tGE   79 (145)
T cd02410          21 FAEDGDLVKDLAKDLRKRIVIRPDPS--------VLKPPE------EAIKIILEIVPEEAGITDIYF-------DDDTGE   79 (145)
T ss_pred             HhcccHHHHHHHHHHhceEEEcCChh--------hcCCHH------HHHHHHHHhCCCccCceeeEe-------cCCCcE
Confidence            34568899999999999998864420        111111      233333332210012222122       223456


Q ss_pred             EEeccCcceeeecCCchhHHHHHHHhCCeEEEec
Q 012307          173 LLVPSTQAINLIGKQGSLIKSIQENSGASVRVLS  206 (466)
Q Consensus       173 llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~  206 (466)
                      +.|-...-|.+||++|.++++|..+||-.-++..
T Consensus        80 V~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR  113 (145)
T cd02410          80 VIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR  113 (145)
T ss_pred             EEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence            7777788899999999999999999998888864

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.

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=88.92  E-value=0.21  Score=39.13  Aligned_cols=34  Identities=29%  Similarity=0.515  Sum_probs=29.0

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCceEE
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIK  112 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~  112 (466)
                      ...+.+.....|.|||++|++|++|.++.+-.+.
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            4678889999999999999999999988765553

; 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 ....

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

Probab=88.67  E-value=0.53  Score=49.82  Aligned_cols=66  Identities=27%  Similarity=0.406  Sum_probs=56.4

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcCcC
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~~~~  415 (466)
                      +..+|.++.+..-.+||.+|.+.|.|..+||+.-.+       ++.++.|-- ++...++|+.+|..++.....
T Consensus       597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v-------De~t~~i~A~~~~am~~Ak~~I~~i~~~~~~  663 (760)
T KOG1067|consen  597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV-------DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQV  663 (760)
T ss_pred             eeeEEeecchhhheeecCccceeeeEeeeccceeee-------cCceEEEEecCHHHHHHHHHHHHHHhcCccc
Confidence            467799999999999999999999999999977777       445788766 677889999999999887554

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=87.91  E-value=0.53  Score=36.94  Aligned_cols=34  Identities=12%  Similarity=0.224  Sum_probs=26.2

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCceEE
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIK  112 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~  112 (466)
                      .+.+-|..+..|.+|||+|++++.||--.+.-++
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            3455566788999999999999999977664443

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.

>PRK12705 hypothetical protein; Provisional

Probab=87.59  E-value=1.1  Score=47.98  Aligned_cols=37  Identities=19%  Similarity=0.349  Sum_probs=31.3

Q ss_pred             eEEEEEecc-CcceeeecCCchhHHHHHHHhCCeEEEe
Q 012307          169 CSVRLLVPS-TQAINLIGKQGSLIKSIQENSGASVRVL  205 (466)
Q Consensus       169 ~~~~llVP~-~~vg~IIGk~G~~Ik~I~~~sga~I~i~  205 (466)
                      ....+-+|+ ++-|+||||.|.+|+.++..||+.|.|.
T Consensus       198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid  235 (508)
T PRK12705        198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID  235 (508)
T ss_pred             eeeeeecCChHhhccccCccchhHHHHHHhhCCceEec
Confidence            344455665 6789999999999999999999999994

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

Probab=87.51  E-value=0.9  Score=33.83  Aligned_cols=33  Identities=12%  Similarity=0.243  Sum_probs=26.2

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeE
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAII  376 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I  376 (466)
                      ...+.+.....|.+||++|.+|+.|+..++-.+
T Consensus        26 ~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          26 EIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            444555555689999999999999999988554

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

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

Probab=87.34  E-value=0.43  Score=43.96  Aligned_cols=55  Identities=16%  Similarity=0.272  Sum_probs=49.7

Q ss_pred             CcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          352 SYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       352 ~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      ..+|+|+||+|.+--.|.+.|..+|.+.+       ..|-|-|+.+++..|+..|+.+|...
T Consensus       178 RAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~niriAR~avcsLIlGs  232 (252)
T KOG3273|consen  178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQNIRIARDAVCSLILGS  232 (252)
T ss_pred             HHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchhhHHHHHhhHhhhccC
Confidence            46799999999999999999999999953       47999999999999999999999863

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

Probab=87.22  E-value=0.4  Score=49.81  Aligned_cols=38  Identities=24%  Similarity=0.242  Sum_probs=34.3

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG  116 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~  116 (466)
                      ...+.||.++++.+|||+|.+|++|++..|.+|.|...
T Consensus       487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~  524 (604)
T COG1855         487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL  524 (604)
T ss_pred             eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence            35577899999999999999999999999999999754

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=87.17  E-value=0.32  Score=37.64  Aligned_cols=33  Identities=21%  Similarity=0.232  Sum_probs=28.4

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhC
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSG  199 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sg  199 (466)
                      ....+.+-+.....|.||||+|.+++.||.-.+
T Consensus        27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~   59 (73)
T PF13083_consen   27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN   59 (73)
T ss_dssp             TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred             CceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence            456788889999999999999999999986544

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

Probab=86.72  E-value=0.29  Score=45.00  Aligned_cols=56  Identities=16%  Similarity=0.169  Sum_probs=49.3

Q ss_pred             cCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          177 STQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       177 ~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      +..+|+|+||+|.+--.|+..|.++|.+.            +..|.|-|..+++..|...|+.+|-..
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlGs  232 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILGS  232 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhccC
Confidence            46789999999999999999999999985            346889999999999999999988654

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

Probab=86.52  E-value=1.5  Score=46.49  Aligned_cols=65  Identities=28%  Similarity=0.328  Sum_probs=53.1

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~  243 (466)
                      ......|.|+.+....+||.+|...|+|+.+||+.-.+            ++..|.|.. +....++|++.|..++.+
T Consensus       595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             CceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence            45677889999999999999999999999999954444            245677766 677889999999887765

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

Probab=86.50  E-value=0.86  Score=43.48  Aligned_cols=48  Identities=27%  Similarity=0.400  Sum_probs=39.9

Q ss_pred             EEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCC
Q 012307           80 FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEP  133 (466)
Q Consensus        80 ~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~  133 (466)
                      .-+.|+...|-++||++|..++.|.++|+|+|-|-..      -.|-|.+..+.
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~~  195 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENES  195 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCcc
Confidence            3466899999999999999999999999999999543      24778887763

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

Probab=86.32  E-value=1.3  Score=42.83  Aligned_cols=51  Identities=22%  Similarity=0.405  Sum_probs=46.8

Q ss_pred             cceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 012307          355 EDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       355 G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~  412 (466)
                      -++||.+|++++.|+-.|.|.|-|+.       .+|.+.|....++.+...+.++|.+
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeC-------cEEEeecCcchHHHHHHHHHHHHhc
Confidence            57999999999999999999999964       4799999999999999999999886

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

Probab=86.30  E-value=0.8  Score=36.42  Aligned_cols=36  Identities=17%  Similarity=0.325  Sum_probs=30.4

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCceEEEe
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL  114 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~  114 (466)
                      .+++.|....-|.|||++|+.|++|+++-.-...+.
T Consensus        31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~   66 (81)
T cd02413          31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP   66 (81)
T ss_pred             eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence            478888999999999999999999998876666553

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.

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

Probab=85.93  E-value=0.75  Score=35.40  Aligned_cols=35  Identities=26%  Similarity=0.328  Sum_probs=27.2

Q ss_pred             EEEeccCc-----ccceeccccchHHHHHhHh-CCeEEEec
Q 012307          346 TMQIPISY-----AEDIIGVGGTSIENIRRTS-GAIITVQE  380 (466)
Q Consensus       346 ~i~IP~~~-----~G~IIGkgG~~Ik~Ir~~S-GA~I~I~~  380 (466)
                      .+.|-...     +|..||++|.+|+.|.++. |-+|+|-+
T Consensus         6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            34455555     8999999999999999999 99999854

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

Probab=85.43  E-value=1.8  Score=45.27  Aligned_cols=40  Identities=28%  Similarity=0.390  Sum_probs=36.4

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCC
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSAD  208 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~  208 (466)
                      ....+.||...++.+|||+|.+|++|+++.|.+|.|.+.+
T Consensus       486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e  525 (604)
T COG1855         486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE  525 (604)
T ss_pred             CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence            4577899999999999999999999999999999998644

>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]

Probab=85.04  E-value=2.3  Score=44.85  Aligned_cols=93  Identities=23%  Similarity=0.379  Sum_probs=63.3

Q ss_pred             ceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHh---cCCCCCCcccccCCC
Q 012307           90 GSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRV---SGLPENDVDAKASGA  166 (466)
Q Consensus        90 G~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i---~~l~~~~~~~~~~~~  166 (466)
                      ..+|=+.|..||+|-++-.-||.|..++.      +.  -+         ..+|+..+++.+   .++.+-.+       
T Consensus        41 P~~~~~~~dlik~lAk~lrKRI~iR~dPs------vl--~~---------~e~A~~~I~eivP~ea~i~~i~F-------   96 (637)
T COG1782          41 PELFAKDGDLIKDLAKDLRKRIIIRPDPS------VL--KP---------PEEARKIILEIVPEEAGITDIYF-------   96 (637)
T ss_pred             HHHhccchhHHHHHHHHHhhceEeccCch------hc--CC---------HHHHHHHHHHhCccccCceeEEe-------
Confidence            44567889999999999999999965520      11  11         123444444433   22222222       


Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEec
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLS  206 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~  206 (466)
                      ...+-+++|-...-|.+|||+|++.++|..++|-.-+|..
T Consensus        97 d~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR  136 (637)
T COG1782          97 DDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR  136 (637)
T ss_pred             cCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence            2245678888889999999999999999999998777764

>PRK13764 ATPase; Provisional

Probab=84.81  E-value=1.7  Score=47.49  Aligned_cols=45  Identities=31%  Similarity=0.459  Sum_probs=39.3

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCC
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAP  211 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p  211 (466)
                      ......+.||...++.+|||+|.+|++|.++.|.+|.|-+.++.+
T Consensus       479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~  523 (602)
T PRK13764        479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP  523 (602)
T ss_pred             cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence            345678999999999999999999999999999999998765543

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=83.77  E-value=1.6  Score=39.56  Aligned_cols=37  Identities=16%  Similarity=0.311  Sum_probs=31.1

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG  116 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~  116 (466)
                      .+-++|-... |.-|||+|.+|+++++..|-+|.+-+.
T Consensus        62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~   98 (166)
T PRK06418         62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK   98 (166)
T ss_pred             EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence            4556666666 999999999999999999999988653

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

Probab=83.37  E-value=2  Score=41.62  Aligned_cols=51  Identities=20%  Similarity=0.247  Sum_probs=45.2

Q ss_pred             eeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhh
Q 012307          181 INLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       181 g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  243 (466)
                      -+|||.+|.++|.|+--|.|.|-|.            -..|.+.|....+..+...|.+++..
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVq------------G~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQ------------GNTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEee------------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence            4699999999999999999999986            23688999999999999999988875

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=83.05  E-value=0.62  Score=36.46  Aligned_cols=33  Identities=24%  Similarity=0.292  Sum_probs=27.7

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeE
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAII  376 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I  376 (466)
                      ...+.+-....|.|||++|++|+.|+...+-.+
T Consensus        26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l   58 (78)
T PF07650_consen   26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKEL   58 (78)
T ss_dssp             EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence            356788889999999999999999988776544

; 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 ....

>PRK13764 ATPase; Provisional

Probab=82.70  E-value=0.93  Score=49.53  Aligned_cols=39  Identities=26%  Similarity=0.248  Sum_probs=35.0

Q ss_pred             eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC
Q 012307           78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG  116 (466)
Q Consensus        78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~  116 (466)
                      ....+.||.+.++.+|||+|.+|++|+++.|.+|.|...
T Consensus       481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~  519 (602)
T PRK13764        481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL  519 (602)
T ss_pred             CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence            355678999999999999999999999999999999754

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

Probab=82.27  E-value=2  Score=37.89  Aligned_cols=38  Identities=26%  Similarity=0.429  Sum_probs=32.5

Q ss_pred             EEEecccccceeeecCChhHHHHHHHhCceEEEeCCCC
Q 012307           81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPV  118 (466)
Q Consensus        81 rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~  118 (466)
                      ++.|-.+.-|.+|||+|.++++|..+||-+-.|...+|
T Consensus        79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP  116 (145)
T cd02410          79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP  116 (145)
T ss_pred             EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence            56666788999999999999999999999988876543

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.

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=81.69  E-value=3  Score=43.89  Aligned_cols=72  Identities=18%  Similarity=0.098  Sum_probs=55.7

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC--CCCC-CCeEEEecCCCCCCCCCChhHHHHHHHHHH
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG--PVSS-PDRIVLISGKEEPEAPVSPAMDAAVRVFKR  150 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~--~~~~-~ervv~I~G~~e~~~~v~~A~~ai~~i~~~  150 (466)
                      .+-+.||...|-.|||.+|..|.+++...++.|++...  .+.+ -..-|.|..+..+.+++.-+.+.++++.+.
T Consensus       450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~  524 (657)
T COG5166         450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ  524 (657)
T ss_pred             heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhh
Confidence            45678999999999999999999999999999999854  1222 223378888877777777777777666653

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

Probab=81.64  E-value=4  Score=39.02  Aligned_cols=47  Identities=23%  Similarity=0.439  Sum_probs=37.9

Q ss_pred             EEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHH
Q 012307          345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSS  397 (466)
Q Consensus       345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~  397 (466)
                      +-+.|+..++-++||++|+.++.+.+.++|+|-|..+-      .|=|.|..+
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG------~IWV~~~~~  194 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG------RIWVDGENE  194 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCC------EEEecCCCc
Confidence            34789999999999999999999999999999996422      455555444

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=80.98  E-value=1.8  Score=33.85  Aligned_cols=35  Identities=20%  Similarity=0.265  Sum_probs=27.5

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEE
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVR  203 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~  203 (466)
                      ..+.+-|.....|.||||.|++++.||--.+.-++
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            34667777889999999999999999876654443

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.

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

Probab=80.84  E-value=1.4  Score=37.02  Aligned_cols=31  Identities=26%  Similarity=0.402  Sum_probs=26.2

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCc
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRA  109 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga  109 (466)
                      .+++.|....-|.|||++|+.|++|++....
T Consensus        62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~   92 (109)
T cd02412          62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQK   92 (109)
T ss_pred             CEEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence            3677788888999999999999999977543

S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	466
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		4e-11
1khm_A	89	C-Terminal Kh Domain Of Hnrnp K (Kh3) Length = 89		3e-05
3krm_A	163	Imp1 Kh34 Length = 163		8e-05
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		9e-05
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		1e-04
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		1e-04
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		2e-04
1j4w_A	174	Complex Of The Kh3 And Kh4 Domains Of Fbp With A Si		3e-04
3vke_A	76	Contribution Of The First K-Homology Domain Of Poly		6e-04

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 46/137 (33%), Positives = 78/137 (56%), Gaps = 18/137 (13%)
Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSP 139
            R+++   +VGSIIG+KGE +KK  E++ ARI + +G  + P+RI+ ++G          
Sbjct: 7   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAG---------- 54
Query: 140 AMDAAVRVFKRVSGLPENDVDAKASGAAFCS-----VRLLVPSTQAINLIGKQGSLIKSI 194
             +A  + F  +    E D+ +  + +   S     +RL+VP++Q  +LIGK G  IK I
Sbjct: 55  PTNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEI 114
Query: 195 QENSGASVRVLSADEAP 211
           +E++GA V+V + D  P
Sbjct: 115 RESTGAQVQV-AGDMLP 130

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 32/85 (37%), Positives = 45/85 (52%), Gaps = 5/85 (5%)
Query: 330 SALGRASGPIVT-QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEI 388
           ++ G   GPI+T Q+T    IP   A  IIG GG  I+ IR  SGA I + E     ++ 
Sbjct: 4   NSYGDLGGPIITTQVT----IPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDR 59
Query: 389 TVEIKGTSSQVQLAQQLIQEYMNNH 413
            + I GT  Q+Q AQ L+Q  +  +
Sbjct: 60  IITITGTQDQIQNAQYLLQNSVKQY 84

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 42/136 (30%), Positives = 68/136 (50%), Gaps = 16/136 (11%)
Query: 79  VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPD---RIVLISGKEEPEA 135
           + ++ +P   VG+IIG+KG+ IK+      A IK+   P  +PD   R+V+I+G   PEA
Sbjct: 4   MVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKI--APPETPDSKVRMVIITG--PPEA 59
Query: 136 PVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQ 195
                  A  R++ ++    EN    K        +R  VP++ A  +IGK G  +  +Q
Sbjct: 60  ----QFKAQGRIYGKLK--EENFFGPKEEVKLETHIR--VPASAAGRVIGKGGKTVNELQ 111
Query: 196 ENSGASVRVLSADEAP 211
             + A V V+  D+ P
Sbjct: 112 NLTAAEV-VVPRDQTP 126

>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 = 45.1 bits (105), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 32/84 (38%), Positives = 44/84 (52%), Gaps = 5/84 (5%)
Query: 331 ALGRASGPIVT-QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEIT 389
           + G   GPI+T Q+T    IP   A  IIG GG  I+ IR  SGA I + E     ++  
Sbjct: 5   SYGDLGGPIITTQVT----IPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRI 60
Query: 390 VEIKGTSSQVQLAQQLIQEYMNNH 413
           + I GT  Q+Q AQ L+Q  +  +
Sbjct: 61  ITITGTQDQIQNAQYLLQNSVKQY 84

>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 = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 32/80 (40%), Positives = 43/80 (53%), Gaps = 5/80 (6%)
Query: 335 ASGPIVT-QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIK 393
           A GPI+T Q+T    IP   A  IIG GG  I+ IR  SGA I + E     ++  + I 
Sbjct: 2   AMGPIITTQVT----IPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITIT 57
Query: 394 GTSSQVQLAQQLIQEYMNNH 413
           GT  Q+Q AQ L+Q  +  +
Sbjct: 58  GTQDQIQNAQYLLQNSVKQY 77

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 43/153 (28%), Positives = 75/153 (49%), Gaps = 18/153 (11%)
Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSP---DRIVLISGKEEPEAP 136
            ++++P    GSIIG+ G+ I +  ++T A IK+       P   +R+ LI G  E    
Sbjct: 8   LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNA 67
Query: 137 VSPAMDAAVRVFKR-------VSGL-PENDVDAKASGAAFCSVRLLVPSTQAINLIGKQG 188
           V   +   +R   +       VS L P+  V+   +      V+++VP++ A  +IGK G
Sbjct: 68  VHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRAN----QVKIIVPNSTAGLIIGKGG 123
Query: 189 SLIKSIQENSGASVRVLSADEAPFYVTEDERIV 221
           + +K+I E SGA V++    + P  +    R+V
Sbjct: 124 ATVKAIMEQSGAWVQL---SQKPDGINLQNRVV 153

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 42/158 (26%), Positives = 74/158 (46%), Gaps = 28/158 (17%)
Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSP---DRIVLISGKEEP--- 133
            ++++P    GSIIG+ G+ I +  ++T A IK+       P   +R+ LI G  E    
Sbjct: 8   LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNA 67
Query: 134 ----------EAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINL 183
                     E P + A    V + +     P+  V+   +      V+++VP++ A  +
Sbjct: 68  VHGFIAEKIREXPQNVAKTEPVSILQ-----PQTTVNPDRAN----QVKIIVPNSTAGLI 118
Query: 184 IGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIV 221
           IGK G+ +K+I E SGA V++    + P  +    R+V
Sbjct: 119 IGKGGATVKAIXEQSGAWVQL---SQKPDGINLQNRVV 153

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 37/142 (26%), Positives = 57/142 (40%), Gaps = 16/142 (11%)
Query: 76  GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEA 135
           G  +  + +P   VG +IGR GE+IKK   D   RI+      ++P+RI  I+G   P  
Sbjct: 1   GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITG---PPD 57
Query: 136 PVSPAMDAAVRVFKRVSGLPENDVDAKASG-------------AAFCSVRLLVPSTQAIN 182
               A +    + + V             G                     +VP+ +   
Sbjct: 58  RAQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGL 117
Query: 183 LIGKQGSLIKSIQENSGASVRV 204
           +IGK G  IKSI + SGA + +
Sbjct: 118 IIGKGGETIKSISQQSGARIEL 139

>pdb|3VKE|A Chain A, Contribution Of The First K-Homology Domain Of Poly(C)-Binding Protein 1 To Its Affinity And Specificity For C-Rich Oligonucleotides Length = 76

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 21/49 (42%), Positives = 37/49 (75%), Gaps = 2/49 (4%)
Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISG 129
           R+++   +VGSIIG+KGE +K+  E++ ARI + +G  +SP+RI+ ++G
Sbjct: 6   RLLMHGKEVGSIIGKKGESVKRIREESGARINISEG--NSPERIITLTG 52

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	466
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-39
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	1e-11
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	8e-11
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-08
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-08
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-38
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-10
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-10
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	5e-09
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-36
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-10
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-09
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	1e-08
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	9e-07
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	7e-34
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	6e-11
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-09
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-08
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-33
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-11
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-07
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	4e-21
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	5e-09
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	3e-07
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	2e-19
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	6e-10
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	7e-08
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-19
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	3e-10
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	6e-08
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-16
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-08
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	3e-07
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	9e-16
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	3e-08
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-07
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	2e-15
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-08
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-05
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	4e-14
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	7e-12
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	9e-14
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	7e-10
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	9e-09
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	2e-13
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-08
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	6e-08
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	3e-13
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	1e-09
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	1e-08
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	8e-13
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	5e-09
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-08
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	5e-12
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	2e-10
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	3e-08
1we8_A	104	Tudor and KH domain containing protein; structural	1e-10
1we8_A	104	Tudor and KH domain containing protein; structural	2e-06
1we8_A	104	Tudor and KH domain containing protein; structural	8e-06
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	7e-10
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	1e-09
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	8e-07
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-04
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	6e-09
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	6e-05
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	2e-04
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	1e-08
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	2e-05
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	3e-04
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	1e-07
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	8e-07
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	7e-05
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-07
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-04
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	8e-04
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	2e-06
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	3e-06
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	6e-04
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	3e-06
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	1e-04
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	2e-04
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	2e-04
1tua_A	191	Hypothetical protein APE0754; structural genomics,	7e-04

>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 =  139 bits (351), Expect = 2e-39
 Identities = 37/176 (21%), Positives = 70/176 (39%), Gaps = 12/176 (6%)

Query: 76  GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEA 135
           G  +  + +P   VG +IGR GE+IKK   D   RI+      ++P+RI  I+G  +   
Sbjct: 1   GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQ 60

Query: 136 PVSPAMDAAVRVFKRVSGLPE----------NDVDAKASGAAFCSVRLLVPSTQAINLIG 185
             +  +   +R  +  +                               +VP+ +   +IG
Sbjct: 61  HAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIG 120

Query: 186 KQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHL 241
           K G  IKSI + SGA + +      P     + ++  ++G   ++  A + +   +
Sbjct: 121 KGGETIKSISQQSGARIEL--QRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 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 = 62.2 bits (151), Expect = 1e-11
 Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 333 GRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESR---GLPDEIT 389
               GP          +P      IIG GG +I++I + SGA I +Q +      P+   
Sbjct: 94  NWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKL 153

Query: 390 VEIKGTSSQVQLAQQLIQE 408
             I+GT  Q+  A+QLI+E
Sbjct: 154 FTIRGTPQQIDYARQLIEE 172

>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 = 59.9 bits (145), Expect = 8e-11
 Identities = 20/109 (18%), Positives = 36/109 (33%), Gaps = 5/109 (4%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
            + + +P      +IG+ G +IK IQ ++G  ++    D      T  ERI ++ G   +
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG-----TTPERIAQITGPPDR 58

Query: 230 VLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLH 278
              A E +   LR         P               +         +
Sbjct: 59  AQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFN 107

>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 = 2e-08
 Identities = 18/100 (18%), Positives = 32/100 (32%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQL 401
                + IP      +IG  G  I+ I+  +G  I  +   G   E   +I G   + Q 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 402 AQQLIQEYMNNHKESITSSYGQIDTGYRPSYPQLGNSSYP 441
           A ++I + + + +       G    G              
Sbjct: 62  AAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPG 101

>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 = 52.2 bits (125), Expect = 3e-08
 Identities = 27/128 (21%), Positives = 40/128 (31%), Gaps = 7/128 (5%)

Query: 11  SINLPEPDPQ-PETATTESPTTES--EAPPTIGSENTEHTTESDSALPQSTGPDAAAVPE 67
            I     D   PE     +   +    A   I ++        +   P   G        
Sbjct: 35  RIQFKPDDGTTPERIAQITGPPDRAQHAAEII-TDLLRSVQAGNPGGPGPGGRGRGRGQG 93

Query: 68  EKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKV---LDGPVSSPDRI 124
                   G   F  IVP  K G IIG+ GE IK   + + ARI++            ++
Sbjct: 94  NWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKL 153

Query: 125 VLISGKEE 132
             I G  +
Sbjct: 154 FTIRGTPQ 161

>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 =  137 bits (346), Expect = 1e-38
 Identities = 43/176 (24%), Positives = 83/176 (47%), Gaps = 10/176 (5%)

Query: 75  PGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL---DGPVSSPDRIVLISGKE 131
                 ++++P    GSIIG+ G+ I +  ++T A IK+    D    + +R+ LI G  
Sbjct: 3   GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI 62

Query: 132 EPEAPVSPAMDAAVRVFKR----VSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQ 187
           E    V   +   +R   +       +         +      V+++VP++ A  +IGK 
Sbjct: 63  EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKG 122

Query: 188 GSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK 243
           G+ +K+I E SGA V++    + P  +    R+V + GE  +  KA+E ++  +++
Sbjct: 123 GATVKAIMEQSGAWVQL---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 = 59.5 bits (144), Expect = 1e-10
 Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 55  PQSTGPDAAAVPEEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL 114
                 +  ++ + +           ++IVP    G IIG+ G  +K   E + A +++ 
Sbjct: 81  QNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLS 140

Query: 115 DGP--VSSPDRIVLISGKEE 132
             P  ++  +R+V +SG+ E
Sbjct: 141 QKPDGINLQNRVVTVSGEPE 160

>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 = 58.3 bits (141), Expect = 3e-10
 Identities = 21/98 (21%), Positives = 39/98 (39%), Gaps = 2/98 (2%)

Query: 320 QDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQ 379
           Q+ A +   S    + +          + +P S A  IIG GG +++ I   SGA + + 
Sbjct: 81  QNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLS 140

Query: 380 ESRGLP--DEITVEIKGTSSQVQLAQQLIQEYMNNHKE 415
           +           V + G   Q + A +LI + +    +
Sbjct: 141 QKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDPQ 178

>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 = 54.9 bits (132), Expect = 5e-09
 Identities = 21/105 (20%), Positives = 42/105 (40%), Gaps = 3/105 (2%)

Query: 338 PIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLP---DEITVEIKG 394
           P+ +Q    + IP   A  IIG GG +I  +++ +GA I + +S+       E    I+G
Sbjct: 1   PLGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQG 60

Query: 395 TSSQVQLAQQLIQEYMNNHKESITSSYGQIDTGYRPSYPQLGNSS 439
           T   +      I E +    +++  +        + +      + 
Sbjct: 61  TIEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQ 105

>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 =  130 bits (329), Expect = 2e-36
 Identities = 44/164 (26%), Positives = 86/164 (52%), Gaps = 11/164 (6%)

Query: 79  VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVS 138
             R+++   +VGSIIG+KGE +KK  E++ ARI + +G  + P+RI+ ++G       + 
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTN---AIF 60

Query: 139 PAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENS 198
            A    +   +    +  +  ++ A+     ++RL+VP++Q  +LIGK G  IK I+E++
Sbjct: 61  KAFAMIIDKLEE--DISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIREST 118

Query: 199 GASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLR 242
           GA V+V             ER + + G    +++ ++ +   + 
Sbjct: 119 GAQVQVAGDMLP----NSTERAITIAGIPQSIIECVKQICVVML 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 = 57.1 bits (138), Expect = 5e-10
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 72  PGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL-DGPVSSPDRIVLISGK 130
                    R++VP  + GS+IG+ G  IK+  E T A+++V  D   +S +R + I+G 
Sbjct: 83  AASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGI 142

Query: 131 EE 132
            +
Sbjct: 143 PQ 144

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

 Score = 54.8 bits (132), Expect = 3e-09
 Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 7/74 (9%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           ++RLL+   +  ++IGK+G  +K ++E SGA + +   +         ERI+ + G    
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC-------PERIITLAGPTNA 58

Query: 230 VLKALEAVVGHLRK 243
           + KA   ++  L +
Sbjct: 59  IFKAFAMIIDKLEE 72

>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 = 53.2 bits (128), Expect = 1e-08
 Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 1/70 (1%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITV-QESRGLPDEITVEIKGTSSQVQ 400
            +T  + +P S    +IG GG  I+ IR ++GA + V  +      E  + I G    + 
Sbjct: 88  PVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSII 147

Query: 401 LAQQLIQEYM 410
              + I   M
Sbjct: 148 ECVKQICVVM 157

>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 = 47.8 bits (114), Expect = 9e-07
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 2/76 (2%)

Query: 341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQ 400
             +T  + +       IIG  G S++ +R  SGA I + E      E  + + G ++ + 
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC--PERIITLAGPTNAIF 60

Query: 401 LAQQLIQEYMNNHKES 416
            A  +I + +     S
Sbjct: 61  KAFAMIIDKLEEDISS 76

>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 =  124 bits (312), Expect = 7e-34
 Identities = 39/167 (23%), Positives = 67/167 (40%), Gaps = 14/167 (8%)

Query: 79  VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVS-SPDRIVLISGKEEPEAPV 137
           + ++ +P   VG+IIG+KG+ IK+      A IK+       S  R+V+I+G  E     
Sbjct: 4   MVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPE----- 58

Query: 138 SPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQEN 197
                A  +   R+ G  + +              + VP++ A  +IGK G  +  +Q  
Sbjct: 59  -----AQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNL 113

Query: 198 SGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF 244
           + A V V            D+ IV++ G       A   +   L + 
Sbjct: 114 TAAEVVVPRDQTPD---ENDQVIVKIIGHFYASQMAQRKIRDILAQV 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 = 59.8 bits (145), Expect = 6e-11
 Identities = 18/76 (23%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLP--DEITVEIKGTSSQV 399
           ++   +++P S A  +IG GG ++  ++  + A + V   +     D++ V+I G     
Sbjct: 84  KLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYAS 143

Query: 400 QLAQQLIQEYMNNHKE 415
           Q+AQ+ I++ +   K+
Sbjct: 144 QMAQRKIRDILAQVKQ 159

>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 = 55.5 bits (134), Expect = 2e-09
 Identities = 16/68 (23%), Positives = 24/68 (35%), Gaps = 2/68 (2%)

Query: 67  EEKKWPGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL--DGPVSSPDRI 124
           E    P         + VP    G +IG+ G+ + +    T A + V     P  +   I
Sbjct: 74  ENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVI 133

Query: 125 VLISGKEE 132
           V I G   
Sbjct: 134 VKIIGHFY 141

>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 = 52.5 bits (126), Expect = 2e-08
 Identities = 18/86 (20%), Positives = 27/86 (31%), Gaps = 1/86 (1%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGL-PDEITVEIKGTSSQVQ 400
           Q    + IP      IIG  G  I+ + R + A I +            V I G      
Sbjct: 2   QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQF 61

Query: 401 LAQQLIQEYMNNHKESITSSYGQIDT 426
            AQ  I   +            +++T
Sbjct: 62  KAQGRIYGKLKEENFFGPKEEVKLET 87

>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 =  123 bits (311), Expect = 1e-33
 Identities = 34/167 (20%), Positives = 66/167 (39%), Gaps = 11/167 (6%)

Query: 79  VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG--PVSSPDRIVLISGKEEPEAP 136
           V  +++P  K G +IG+ GE IK+  E    ++ ++      ++ D+ + I G       
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPY---K 59

Query: 137 VSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQE 196
           V  A +  + +  R           +        + + VP      +IG+ G +IK IQ 
Sbjct: 60  VQQACEMVMDIL-RERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQN 118

Query: 197 NSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK 243
           ++G  ++    D      T  E+I  + G   +   A   +   L+ 
Sbjct: 119 DAGVRIQFKQDDG-----TGPEKIAHIMGPPDRCEHAARIINDLLQS 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 = 61.7 bits (150), Expect = 2e-11
 Identities = 15/82 (18%), Positives = 31/82 (37%)

Query: 333 GRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEI 392
            R            + +P      +IG  G  I+ I+  +G  I  ++  G   E    I
Sbjct: 81  DRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHI 140

Query: 393 KGTSSQVQLAQQLIQEYMNNHK 414
            G   + + A ++I + + + +
Sbjct: 141 MGPPDRCEHAARIINDLLQSLR 162

>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 = 60.6 bits (147), Expect = 4e-11
 Identities = 19/58 (32%), Positives = 27/58 (46%)

Query: 75  PGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
                  + VP   VG +IGR GE+IKK   D   RI+      + P++I  I G  +
Sbjct: 88  RIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPD 145

>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 = 50.6 bits (121), Expect = 1e-07
 Identities = 15/86 (17%), Positives = 36/86 (41%), Gaps = 2/86 (2%)

Query: 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPD--EITVEIKGTSSQVQL 401
            Q + IP   A  +IG GG +I+ ++  +G  + + +        +  + I G   +VQ 
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 62

Query: 402 AQQLIQEYMNNHKESITSSYGQIDTG 427
           A +++ + +    +       +  + 
Sbjct: 63  ACEMVMDILRERDQGGFGDRNEYGSR 88

>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 = 86.2 bits (214), Expect = 4e-21
 Identities = 25/79 (31%), Positives = 39/79 (49%)

Query: 338 PIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSS 397
           P+ +Q T  + IP +    IIG  G +I  IR+ SGA I +           V I G+++
Sbjct: 1   PLGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAA 60

Query: 398 QVQLAQQLIQEYMNNHKES 416
            + LAQ LI   +++ K  
Sbjct: 61  SISLAQYLINARLSSEKGM 79

>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 = 51.9 bits (125), Expect = 5e-09
 Identities = 16/52 (30%), Positives = 27/52 (51%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            + +P   +G IIGR+G  I +  + + A+IK+ +    S  R V I+G   
Sbjct: 9   ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAA 60

>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 = 47.3 bits (113), Expect = 3e-07
 Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 5/68 (7%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           +  L +P+     +IG+QG+ I  I++ SGA +++ +  E         R V + G AA 
Sbjct: 7   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGS-----SGRQVTITGSAAS 61

Query: 230 VLKALEAV 237
           +  A   +
Sbjct: 62  ISLAQYLI 69

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

 Score = 82.0 bits (203), Expect = 2e-19
 Identities = 30/86 (34%), Positives = 41/86 (47%), Gaps = 3/86 (3%)

Query: 330 SALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEIT 389
            + G   GP    IT  + IP   A  IIG GG  I+ IR  SGA I + E     ++  
Sbjct: 4   MSYGDLGGP---IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRI 60

Query: 390 VEIKGTSSQVQLAQQLIQEYMNNHKE 415
           + I GT  Q+Q AQ L+Q  +  +  
Sbjct: 61  ITITGTQDQIQNAQYLLQNSVKQYSG 86

>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 = 55.0 bits (133), Expect = 6e-10
 Identities = 18/53 (33%), Positives = 32/53 (60%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            ++ +P    GSIIG+ G+ IK+   ++ A IK+ +    S DRI+ I+G ++
Sbjct: 16  TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD 68

>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 = 48.9 bits (117), Expect = 7e-08
 Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 5/82 (6%)

Query: 163 ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVE 222
             G    + ++ +P   A ++IGK G  IK I+  SGAS+++    E       ++RI+ 
Sbjct: 8   DLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGS-----EDRIIT 62

Query: 223 MQGEAAKVLKALEAVVGHLRKF 244
           + G   ++  A   +   ++++
Sbjct: 63  ITGTQDQIQNAQYLLQNSVKQY 84

>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 = 81.6 bits (202), Expect = 2e-19
 Identities = 30/81 (37%), Positives = 41/81 (50%), Gaps = 3/81 (3%)

Query: 335 ASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG 394
           A GPI+T     + IP   A  IIG GG  I+ IR  SGA I + E     ++  + I G
Sbjct: 2   AMGPIITT---QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG 58

Query: 395 TSSQVQLAQQLIQEYMNNHKE 415
           T  Q+Q AQ L+Q  +  +  
Sbjct: 59  TQDQIQNAQYLLQNSVKQYSG 79

>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 = 55.4 bits (134), Expect = 3e-10
 Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 73  GWPGHCV-FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKE 131
           G  G  +  ++ +P    GSIIG+ G+ IK+   ++ A IK+ +    S DRI+ I+G +
Sbjct: 1   GAMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 60

Query: 132 E 132
           +
Sbjct: 61  D 61

>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 = 48.8 bits (117), Expect = 6e-08
 Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 5/82 (6%)

Query: 163 ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVE 222
            +     + ++ +P   A ++IGK G  IK I+  SGAS+++    E       ++RI+ 
Sbjct: 1   GAMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGS-----EDRIIT 55

Query: 223 MQGEAAKVLKALEAVVGHLRKF 244
           + G   ++  A   +   ++++
Sbjct: 56  ITGTQDQIQNAQYLLQNSVKQY 77

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

 Score = 73.9 bits (182), Expect = 1e-16
 Identities = 21/71 (29%), Positives = 33/71 (46%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQL 401
             +  + IP      IIG  G  I  IR+ SGA I +        +  V I G+++ + L
Sbjct: 4   TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISL 63

Query: 402 AQQLIQEYMNN 412
           AQ LI   +++
Sbjct: 64  AQYLINVRLSS 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 = 50.8 bits (122), Expect = 1e-08
 Identities = 17/52 (32%), Positives = 28/52 (53%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            + +P   +G IIGR+G  I +  + + A+IK+ +    S DR V I+G   
Sbjct: 8   ELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAA 59

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

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           S  L +P+     +IG+QG+ I  I++ SGA +++ +  E        +R V + G AA 
Sbjct: 6   SHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEG-----STDRQVTITGSAAS 60

Query: 230 VLKALEAVVGHLR 242
           +  A   +   L 
Sbjct: 61  ISLAQYLINVRLS 73

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

 Score = 72.2 bits (177), Expect = 9e-16
 Identities = 26/110 (23%), Positives = 46/110 (41%), Gaps = 7/110 (6%)

Query: 337 GPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQ---ESRGLPDEITVEIK 393
           G +      T  IP      +IG GG +++ I + +GA + +       G P+     I+
Sbjct: 1   GAMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR 60

Query: 394 GTSSQVQLAQQLIQEYMNNHKESITSSYGQIDTGYRPSYPQLGNSSYPSS 443
           G+  Q+  A+QLI+E +      +    G    G  P+ P    +  P +
Sbjct: 61  GSPQQIDHAKQLIEEKIEGPLCPVGPGPG----GPGPAGPMGPFNPGPFN 106

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

 Score = 50.6 bits (121), Expect = 3e-08
 Identities = 13/75 (17%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 163 ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVE 222
            + A    +   +P+ +   +IG+ G  +K+I + +GA V +  + + P     + ++  
Sbjct: 1   GAMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEI--SRQLPPNGDPNFKLFI 58

Query: 223 MQGEAAKVLKALEAV 237
           ++G   ++  A + +
Sbjct: 59  IRGSPQQIDHAKQLI 73

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

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 3/56 (5%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPD---RIVLISGKEE 132
               +P  K G +IGR GE +K   + T A +++      + D   ++ +I G  +
Sbjct: 9   MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQ 64

>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 = 70.5 bits (173), Expect = 2e-15
 Identities = 21/82 (25%), Positives = 37/82 (45%)

Query: 330 SALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEIT 389
           S+         + +T+  ++P      IIG GG  I  I++ SG  I +    G   E +
Sbjct: 2   SSGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERS 61

Query: 390 VEIKGTSSQVQLAQQLIQEYMN 411
             + GT   VQ A++L+ + + 
Sbjct: 62  CMLTGTPESVQSAKRLLDQIVE 83

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

 Score = 51.7 bits (124), Expect = 1e-08
 Identities = 16/52 (30%), Positives = 27/52 (51%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
              VP   VG IIGR GE I +  +++  +I++       P+R  +++G  E
Sbjct: 18  EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPE 69

>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 = 42.8 bits (101), Expect = 1e-05
 Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 5/68 (7%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           +    VP      +IG+ G  I  IQ+ SG  +++             ER   + G    
Sbjct: 16  TEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGG-----LPERSCMLTGTPES 70

Query: 230 VLKALEAV 237
           V  A   +
Sbjct: 71  VQSAKRLL 78

>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 = 66.1 bits (162), Expect = 4e-14
 Identities = 21/57 (36%), Positives = 36/57 (63%), Gaps = 2/57 (3%)

Query: 76  GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
                R+++   +VGSIIG+KGE +KK  E++ ARI + +G  + P+RI+ ++G   
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTN 57

>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 = 60.0 bits (146), Expect = 7e-12
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           ++RLL+   +  ++IGK+G  +K ++E SGA + +             ERI+ + G    
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNA 58

Query: 230 VLKALEAVVGHLR 242
           + KA   ++  L 
Sbjct: 59  IFKAFAMIIDKLE 71

>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 = 53.8 bits (130), Expect = 1e-09
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQL 401
            +T  + +       IIG  G S++ +R  SGA I + E    P+ I + + G ++ +  
Sbjct: 4   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-NCPERI-ITLAGPTNAIFK 61

Query: 402 AQQLIQEYMNN 412
           A  +I + +  
Sbjct: 62  AFAMIIDKLEE 72

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

 Score = 65.9 bits (161), Expect = 9e-14
 Identities = 18/86 (20%), Positives = 37/86 (43%), Gaps = 2/86 (2%)

Query: 333 GRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITV--QESRGLPDEITV 390
               G       Q + IP S A  +IG GG +I+ ++  +G  + +     +    +  +
Sbjct: 5   SSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPL 64

Query: 391 EIKGTSSQVQLAQQLIQEYMNNHKES 416
            I G   +VQ A++++ E + +    
Sbjct: 65  RITGDPYKVQQAKEMVLELIRDQGSG 90

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

 Score = 54.7 bits (132), Expect = 7e-10
 Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 3/81 (3%)

Query: 163 ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVE 222
             G       +++P+++A  +IGK G  IK +QE +G  + ++         T  ++ + 
Sbjct: 9   GDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLR 65

Query: 223 MQGEAAKVLKALEAVVGHLRK 243
           + G+  KV +A E V+  +R 
Sbjct: 66  ITGDPYKVQQAKEMVLELIRD 86

>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 = 51.6 bits (124), Expect = 9e-09
 Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 75  PGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL--DGPVSSPDRIVLISGKEE 132
           PG+ V  +++P  K G +IG+ GE IK+  E    ++ ++      +  D+ + I+G   
Sbjct: 12  PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPY 71

>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 = 65.1 bits (159), Expect = 2e-13
 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 3/78 (3%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPD---EITVEIKGTSSQ 398
           +    + +P +    I+G GG ++   +  +GA I + +            V I G+ + 
Sbjct: 2   KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

Query: 399 VQLAQQLIQEYMNNHKES 416
            Q AQ LI + +   +  
Sbjct: 62  TQAAQYLISQRVTYEQGV 79

>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 = 51.2 bits (123), Expect = 1e-08
 Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 2/66 (3%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
            V + VP      ++GK G  +   QE +GA +++  + +  F      R V + G  A 
Sbjct: 4   LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQI--SKKGEFLPGTRNRRVTITGSPAA 61

Query: 230 VLKALE 235
              A  
Sbjct: 62  TQAAQY 67

>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 = 49.3 bits (118), Expect = 6e-08
 Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 3/53 (5%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL---DGPVSSPDRIVLISG 129
             + VP   VG+I+G+ G+ + +  E T ARI++    +    + +R V I+G
Sbjct: 5   VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITG 57

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

 Score = 63.9 bits (156), Expect = 3e-13
 Identities = 16/72 (22%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITV--QESRGLPDEITVEIKGTSSQV 399
              Q + IP   A  +IG GG +I+ ++  +G  + +    S+    +  + I G   +V
Sbjct: 13  GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKV 72

Query: 400 QLAQQLIQEYMN 411
           Q A +++ + + 
Sbjct: 73  QQACEMVMDILR 84

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

 Score = 53.9 bits (130), Expect = 1e-09
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 3/83 (3%)

Query: 160 DAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDER 219
           D    G       +++P+ +A  +IGK G  IK +QE +G  + ++         T  ++
Sbjct: 5   DNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDK 61

Query: 220 IVEMQGEAAKVLKALEAVVGHLR 242
            + + G+  KV +A E V+  LR
Sbjct: 62  PLRIIGDPYKVQQACEMVMDILR 84

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

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 2/63 (3%)

Query: 72  PGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL--DGPVSSPDRIVLISG 129
            G     V  +++P  K G +IG+ GE IK+  E    ++ ++      ++ D+ + I G
Sbjct: 8   NGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIG 67

Query: 130 KEE 132
              
Sbjct: 68  DPY 70

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

 Score = 62.7 bits (153), Expect = 8e-13
 Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPD---EITVEIKGTSSQ 398
           +    M +P +    I+G GG ++   +  +GA I + +            V I G+ + 
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

Query: 399 VQLAQQLIQEYMN 411
            Q AQ LI + + 
Sbjct: 62  TQAAQYLISQRVT 74

>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 = 51.9 bits (125), Expect = 5e-09
 Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 2/66 (3%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
            V + VP      ++GK G  +   QE +GA +++  + +  F      R V + G  A 
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQI--SKKGEFLPGTRNRRVTITGSPAA 61

Query: 230 VLKALE 235
              A  
Sbjct: 62  TQAAQY 67

>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 = 50.3 bits (121), Expect = 2e-08
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 79  VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL---DGPVSSPDRIVLISGKEE 132
           +  M VP   VG+I+G+ G+ + +  E T ARI++    +    + +R V I+G   
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPA 60

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

 Score = 61.3 bits (149), Expect = 5e-12
 Identities = 18/106 (16%), Positives = 35/106 (33%), Gaps = 2/106 (1%)

Query: 333 GRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEI 392
           G  +          + +P      +IG  G  I+ I+  +G  I  ++  G   E    I
Sbjct: 1   GAMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHI 60

Query: 393 KGTSSQVQLAQQLIQEYMNNHKESITSSYGQIDTGYRPSYPQLGNS 438
            G   + + A ++I + + + +            G  P     G  
Sbjct: 61  MGPPDRCEHAARIINDLLQSLRSG--PPGPPGGPGMPPGGRGRGRG 104

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

 Score = 57.1 bits (138), Expect = 2e-10
 Identities = 19/52 (36%), Positives = 27/52 (51%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            + VP   VG +IGR GE+IKK   D   RI+      + P++I  I G  +
Sbjct: 14  DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPD 65

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

 Score = 50.6 bits (121), Expect = 3e-08
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 5/81 (6%)

Query: 163 ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVE 222
                   + + VP      +IG+ G +IK IQ ++G  ++    D      T  E+I  
Sbjct: 5   TGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG-----TGPEKIAH 59

Query: 223 MQGEAAKVLKALEAVVGHLRK 243
           + G   +   A   +   L+ 
Sbjct: 60  IMGPPDRCEHAARIINDLLQS 80

>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 = 57.5 bits (139), Expect = 1e-10
 Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPD--EITVEIKGTSSQ 398
           T + + + +P      IIG GG +I +I + SGA IT  +           ++I GT  +
Sbjct: 13  TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE 72

Query: 399 VQLAQQLIQE 408
           V  A+ LI E
Sbjct: 73  VAAAKHLILE 82

>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 = 45.2 bits (107), Expect = 2e-06
 Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)

Query: 79  VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSP--DRIVLISGKEE 132
             ++ VP   VG IIGR GE I+  C+ + A+I        +    R++ ISG ++
Sbjct: 16  FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQK 71

>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 = 43.7 bits (103), Expect = 8e-06
 Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 3/66 (4%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
             +L VP      +IG+ G  I+SI + SGA +     D+         R++++ G   +
Sbjct: 16  FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITC---DKESEGTLLLSRLIKISGTQKE 72

Query: 230 VLKALE 235
           V  A  
Sbjct: 73  VAAAKH 78

>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 = 56.2 bits (135), Expect = 7e-10
 Identities = 33/166 (19%), Positives = 53/166 (31%), Gaps = 32/166 (19%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPA 140
           + IV    +G  IG  G  I++  +        LD                E        
Sbjct: 7   QFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLD----------------EDTCTF--- 47

Query: 141 MDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGA 200
                     + G  ++ V    S   F    + VP      +IGK G LI+ I + SG 
Sbjct: 48  ---------HIYGEDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGV 98

Query: 201 S-VRVLSADEAPFYVTEDERIVEMQGEAAKVLKA---LEAVVGHLR 242
             VR+ + +E      E        G    +  A   L+  + +L+
Sbjct: 99  VRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNYLK 144

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

 Score = 46.5 bits (110), Expect = 2e-06
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 339 IVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPD------EITVEI 392
            +      +Q+P +    +IG  G  I+ I   SG +    E+    +       +    
Sbjct: 63  FLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVF 122

Query: 393 KGTSSQVQLAQQLIQEYMNNHK 414
            GT   +  A  L+  ++N  K
Sbjct: 123 VGTKDSIANATVLLDYHLNYLK 144

>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 = 54.4 bits (131), Expect = 1e-09
 Identities = 19/93 (20%), Positives = 37/93 (39%), Gaps = 3/93 (3%)

Query: 329 SSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEI 388
           S + G     + TQ + T+ IP  +   +IG  G  ++++   +   I +          
Sbjct: 3   SGSSGDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD--PSN 60

Query: 389 TVEIKGTSSQVQLAQQLIQEYMNN-HKESITSS 420
            ++I GT   ++ A+  +        K S  SS
Sbjct: 61  QIKITGTKEGIEKARHEVLLISAEQDKRSGPSS 93

>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 = 46.3 bits (110), Expect = 8e-07
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 2/52 (3%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            + +P      +IG+ GE ++     T  +I++       P   + I+G +E
Sbjct: 20  TVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP--DDPSNQIKITGTKE 69

>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 = 38.6 bits (90), Expect = 4e-04
 Identities = 11/75 (14%), Positives = 29/75 (38%), Gaps = 7/75 (9%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           S  + +P      +IGK G  ++ ++  +   +++   D       +    +++ G    
Sbjct: 18  SATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEG 70

Query: 230 VLKALEAVVGHLRKF 244
           + KA   V+    + 
Sbjct: 71  IEKARHEVLLISAEQ 85

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

 Score = 51.6 bits (124), Expect = 6e-09
 Identities = 14/73 (19%), Positives = 27/73 (36%), Gaps = 2/73 (2%)

Query: 339 IVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQ 398
           I       + I   +   +IG  G +I  I+      + +       + I   I+G    
Sbjct: 1   INRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIR--IEGDPQG 58

Query: 399 VQLAQQLIQEYMN 411
           VQ A++ + E  +
Sbjct: 59  VQQAKRELLELAS 71

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

 Score = 40.4 bits (95), Expect = 6e-05
 Identities = 7/52 (13%), Positives = 20/52 (38%), Gaps = 2/52 (3%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            + +       +IG+ G  I +  +  +  +++     S    ++ I G  +
Sbjct: 8   EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD--SEKSNLIRIEGDPQ 57

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 7/64 (10%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
            V + +      +LIGK G+ I  I++    SVR+    E          ++ ++G+   
Sbjct: 6   YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEK-------SNLIRIEGDPQG 58

Query: 230 VLKA 233
           V +A
Sbjct: 59  VQQA 62

>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 = 51.7 bits (124), Expect = 1e-08
 Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 2/68 (2%)

Query: 341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQ 400
             +T  +++P      +IG  G+ I  +       I V       D I   I G ++ + 
Sbjct: 15  VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIA--ITGLAANLD 72

Query: 401 LAQQLIQE 408
            A+  + E
Sbjct: 73  RAKAGLLE 80

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

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 2/51 (3%)

Query: 82  MIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
           + VP      +IG+KG  I+K  ++    I V          I+ I+G   
Sbjct: 21  VEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAITGLAA 69

>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 = 39.0 bits (91), Expect = 3e-04
 Identities = 14/79 (17%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           ++ + VP      +IG++GS I+ + +    ++ V + +           I+ + G AA 
Sbjct: 18  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQ-------SDIIAITGLAAN 70

Query: 230 VLKALEAVVGHLRKFLVDQ 248
           + +A   ++  +++   +Q
Sbjct: 71  LDRAKAGLLERVKELQAEQ 89

>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 = 48.7 bits (116), Expect = 1e-07
 Identities = 19/94 (20%), Positives = 31/94 (32%), Gaps = 2/94 (2%)

Query: 329 SSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITV-QESRGLPDE 387
           S + G      +     ++ +   Y   IIG  G  I  IR      I    +  G   +
Sbjct: 3   SGSSGEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQ 62

Query: 388 ITVEIKGTSSQVQLAQQLIQEYMNN-HKESITSS 420
             + I G     + A+  I   +    + S  SS
Sbjct: 63  DQITITGYEKNTEAARDAILRIVGELEQMSGPSS 96

>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 = 46.4 bits (110), Expect = 8e-07
 Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 82  MIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLD-GPVSSPDRIVLISGKEE 132
           + V       IIGRKG +I +   +    I+  D    + P   + I+G E+
Sbjct: 21  VTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK 72

>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 = 40.6 bits (95), Expect = 7e-05
 Identities = 10/74 (13%), Positives = 31/74 (41%), Gaps = 4/74 (5%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
            + + V       +IG++G++I  I+     +++    D+      + +  + + G    
Sbjct: 18  KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGN----QPQDQITITGYEKN 73

Query: 230 VLKALEAVVGHLRK 243
              A +A++  + +
Sbjct: 74  TEAARDAILRIVGE 87

>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 = 48.2 bits (115), Expect = 2e-07
 Identities = 22/93 (23%), Positives = 34/93 (36%), Gaps = 2/93 (2%)

Query: 329 SSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEI 388
           S + GR  G +   +++ + +       IIG  G +I  I       I      G PD  
Sbjct: 3   SGSSGRIVGELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-PQSGAPDPN 61

Query: 389 TVEIKGTSSQVQLAQQLIQEYMNNH-KESITSS 420
            V + G    V+ A   I      +  +S  SS
Sbjct: 62  CVTVTGLPENVEEAIDHILNLEEEYLADSGPSS 94

>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 = 39.8 bits (93), Expect = 2e-04
 Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 82  MIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
           + +       IIG +G+ I+K  ++ +  I+        P+  V ++G  E
Sbjct: 21  VPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPN-CVTVTGLPE 70

>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 = 37.8 bits (88), Expect = 8e-04
 Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 6/84 (7%)

Query: 166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG 225
               S  + +       +IG +G  I+ I +     +R       P     D   V + G
Sbjct: 14  EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF------PQSGAPDPNCVTVTG 67

Query: 226 EAAKVLKALEAVVGHLRKFLVDQG 249
               V +A++ ++    ++L D G
Sbjct: 68  LPENVEEAIDHILNLEEEYLADSG 91

>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 = 44.9 bits (106), Expect = 2e-06
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 335 ASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG 394
           +SG    Q T  +++P      ++G  G +I+ I++ +   I          E    + G
Sbjct: 2   SSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR---DKEPVFAVTG 58

Query: 395 TSSQVQLAQQLIQEYMN 411
               V  A++ I+ ++ 
Sbjct: 59  MPENVDRAREEIEAHIT 75

>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 = 44.2 bits (104), Expect = 3e-06
 Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 3/61 (4%)

Query: 72  PGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKE 131
               G    ++ VP   VG ++G KG  IK+  + T   I     P    + +  ++G  
Sbjct: 4   GSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVT---PGRDKEPVFAVTGMP 60

Query: 132 E 132
           E
Sbjct: 61  E 61

>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 = 38.0 bits (88), Expect = 6e-04
 Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 8/72 (11%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           ++++ VP      ++G +G+ IK IQ+ +   +     D+        E +  + G    
Sbjct: 11  TIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDK--------EPVFAVTGMPEN 62

Query: 230 VLKALEAVVGHL 241
           V +A E +  H+
Sbjct: 63  VDRAREEIEAHI 74

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

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 20/95 (21%), Positives = 33/95 (34%), Gaps = 3/95 (3%)

Query: 329 SSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAI-ITVQESRGLPDE 387
           S + G     +       + IP      +IG  G  I +I    G + I         D 
Sbjct: 3   SGSSGSIQKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDT 62

Query: 388 ITVEIKGTSSQVQLAQQLIQEYMNNHKESITSSYG 422
           +   I+G SS V+ A++ +       +     S G
Sbjct: 63  VV--IRGPSSDVEKAKKQLLHLAEEKQTKSGPSSG 95

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

 Score = 43.0 bits (100), Expect = 1e-04
 Identities = 29/256 (11%), Positives = 74/256 (28%), Gaps = 40/256 (15%)

Query: 170 SVRLLVPSTQAINLIGKQGSL--IKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEA 227
           ++ +   S     +    G    + SI   +   +++              + V + G  
Sbjct: 31  TLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYF 90

Query: 228 AKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAIST 287
             V +A   +                  +  + ++                   Q+ I  
Sbjct: 91  GDVDRARMLM-----------------RRNCHFTVFMALSKMKMPLHELQAHVRQNPIQN 133

Query: 288 EYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSA------LGRASGPIVT 341
                   E  F++     ++    + + I  ++     +  +A      L R S     
Sbjct: 134 -------VEMSFVDAPE--KNGIVTTYLRITAREKNQHELIEAAKRLNEILFRESPAPEN 184

Query: 342 QITQTMQIPISYAEDIIGVGGTS--IENIRRTSGAIITV----QESRGLPDEITVEIKGT 395
             T    +   Y + ++G   T+  +  I R +  II+       +    +   +++ G 
Sbjct: 185 NFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGN 244

Query: 396 SSQVQLAQQLIQEYMN 411
              V  A++ I + + 
Sbjct: 245 IDNVLKARRYIMDLLP 260

>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 = 41.6 bits (97), Expect = 2e-04
 Identities = 17/73 (23%), Positives = 27/73 (36%), Gaps = 7/73 (9%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQL 401
            I             IIG  G + + I   SGA ++V          TV I G   Q+++
Sbjct: 128 IIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYGK-------TVAIIGNPIQIEI 180

Query: 402 AQQLIQEYMNNHK 414
           A+  I++      
Sbjct: 181 AKTAIEKLARGSP 193

>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 = 41.6 bits (97), Expect = 2e-04
 Identities = 32/168 (19%), Positives = 61/168 (36%), Gaps = 28/168 (16%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPA 140
            + +P  ++  +IG+KG+  K+  + T+ +I      + S    V I+  +E E P++  
Sbjct: 37  YVKIPKDRIAVLIGKKGQTKKEIEKRTKTKIT-----IDSETGEVWITSTKETEDPLA-V 90

Query: 141 MDAAVRVFKRVSGLPENDVDAKASGAAFCSV----------RLLVPSTQAINLIGKQGSL 190
             A   V     G          +   +  +                     +IG++G  
Sbjct: 91  WKARDIVLAIGRGFSPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRT 150

Query: 191 IKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVV 238
            + I+E SGASV V              + V + G   ++  A  A+ 
Sbjct: 151 RQIIEEMSGASVSV------------YGKTVAIIGNPIQIEIAKTAIE 186

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

 Score = 39.6 bits (92), Expect = 7e-04
 Identities = 23/129 (17%), Positives = 47/129 (36%), Gaps = 13/129 (10%)

Query: 84  VPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSP---- 139
           V   ++G++IG +GE+  +    T   I      V + + +V++  + E   PV+     
Sbjct: 10  VKPERLGAVIGPRGEVKAEIMRRTGTVIT-----VDTENSMVIVEPEAEGIPPVNLMKAA 64

Query: 140 ----AMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQ 195
               A+       K    L E+ +                       +IG+ G   ++I+
Sbjct: 65  EVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIE 124

Query: 196 ENSGASVRV 204
           E +   + V
Sbjct: 125 EMTDTYINV 133

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	466
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.93
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.93
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.93
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.92
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.92
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	99.92
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.91
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.9
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.88
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	99.7
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.65
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.63
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.63
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.63
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.62
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.61
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.6
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.59
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.58
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.58
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.54
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.53
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.53
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.53
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.49
1we8_A	104	Tudor and KH domain containing protein; structural	99.47
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.43
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.42
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.41
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.41
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.41
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.4
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.4
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.39
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.38
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.37
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.37
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.36
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.35
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.35
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.34
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.33
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.33
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.3
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.29
1we8_A	104	Tudor and KH domain containing protein; structural	99.27
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.21
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.19
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.19
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.18
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.18
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.16
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.15
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.05
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.05
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.98
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.92
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.79
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.7
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.58
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.37
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.34
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.28
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.05
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	98.0
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.92
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.61
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.5
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.46
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.32
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.23
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.5
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.02
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.01
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.4
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	94.74
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	94.69
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	94.07
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	92.62
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	92.49
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	91.11
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	88.76

>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=1.4e-25  Score=202.68  Aligned_cols=155  Identities=24%  Similarity=0.402  Sum_probs=130.4

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccccC
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQ  248 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~  248 (466)
                      .+++|+||...+|.||||+|++||+|+++|||+|+|... ..|   +..+|+|+|+|+++++.+|+.+|++++.+.....
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~-~~~---~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~~~   78 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPP-ETP---DSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFG   78 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCC-SST---TCSEEEEEEEECHHHHHHHHHHHHHHHHHTTSSC
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCC-CCC---CCCceEEEEEcCHHHHHHHHHHHHHHHhcccccc
Confidence            578999999999999999999999999999999999743 233   6889999999999999999999999887641100


Q ss_pred             ccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCcccc
Q 012307          249 GVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIR  328 (466)
Q Consensus       249 ~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~~~  328 (466)
                                                                 |                            .       
T Consensus        79 -------------------------------------------~----------------------------~-------   80 (163)
T 3krm_A           79 -------------------------------------------P----------------------------K-------   80 (163)
T ss_dssp             -------------------------------------------S----------------------------S-------
T ss_pred             -------------------------------------------c----------------------------c-------
Confidence                                                       0                            0       


Q ss_pred             cCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCC-C-CCCceEEEEEcCHHHHHHHHHHH
Q 012307          329 SSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESR-G-LPDEITVEIKGTSSQVQLAQQLI  406 (466)
Q Consensus       329 ~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~-~-~~~er~V~I~Gt~~~V~~A~~lI  406 (466)
                                .....+.+|.||.+++|+||||+|.+|++|++.|||+|+|.+.. . ..+++.|+|+|++++|+.|+.+|
T Consensus        81 ----------~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I  150 (163)
T 3krm_A           81 ----------EEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKI  150 (163)
T ss_dssp             ----------CCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEEEEEECHHHHHHHHHHH
T ss_pred             ----------cCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEEEEEeCHHHHHHHHHHH
Confidence                      00124678999999999999999999999999999999997643 2 23456899999999999999999


Q ss_pred             HHHHhcCcC
Q 012307          407 QEYMNNHKE  415 (466)
Q Consensus       407 ~~~i~~~~~  415 (466)
                      +++|++.++
T Consensus       151 ~~~i~~~~~  159 (163)
T 3krm_A          151 RDILAQVKQ  159 (163)
T ss_dssp             HHHHHHHTC
T ss_pred             HHHHHHHHH
Confidence            999998655

>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=99.93  E-value=1.2e-25  Score=203.25  Aligned_cols=161  Identities=23%  Similarity=0.375  Sum_probs=130.5

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccccC
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQ  248 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~  248 (466)
                      ++.+|+||..++|.||||+|++||+|+++|||+|++.++...+   ...+|.|+|+|++++|.+|+.+|.+++.+.....
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~~~   78 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDKPLRIIGDPYKVQQACEMVMDILRERDQGG   78 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSS---SSSCEEEEEEECHHHHHHHHHHHHHHTTCSSSCC
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHHhccCCC
Confidence            5789999999999999999999999999999999997533222   5678999999999999999999999887542100


Q ss_pred             ccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCcccc
Q 012307          249 GVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIR  328 (466)
Q Consensus       249 ~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~~~  328 (466)
                               +                               .          ++             ..|+..       
T Consensus        79 ---------~-------------------------------~----------~~-------------~~~~~~-------   88 (164)
T 2jvz_A           79 ---------F-------------------------------G----------DR-------------NEYGSR-------   88 (164)
T ss_dssp             ---------C-------------------------------S----------SC-------------SSCTTS-------
T ss_pred             ---------C-------------------------------C----------Cc-------------cccCCC-------
Confidence                     0                               0          00             001100       


Q ss_pred             cCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 012307          329 SSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQE  408 (466)
Q Consensus       329 ~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~  408 (466)
                                  ...+.+|.||.+++|+||||+|.+|++|+++|||+|+|.+..+...++.|+|+|++++|+.|+.+|++
T Consensus        89 ------------~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~  156 (164)
T 2jvz_A           89 ------------IGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIIND  156 (164)
T ss_dssp             ------------CSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEESCHHHHHHHHHHHHH
T ss_pred             ------------CCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEEcCHHHHHHHHHHHHH
Confidence                        01245688999999999999999999999999999999876555668999999999999999999999


Q ss_pred             HHhcCc
Q 012307          409 YMNNHK  414 (466)
Q Consensus       409 ~i~~~~  414 (466)
                      +|++.+
T Consensus       157 ~i~~~~  162 (164)
T 2jvz_A          157 LLQSLR  162 (164)
T ss_dssp             HHHHHH
T ss_pred             HHhhhh
Confidence            998643

>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=1.6e-25  Score=205.16  Aligned_cols=171  Identities=23%  Similarity=0.330  Sum_probs=133.3

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCC-CCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhcc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADE-APFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFL  245 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~-~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~  245 (466)
                      ..++++|+||..++|.||||+|++||+|+++|||+|+|....+ .|   +..+|+|+|+|+.++|.+|+.+|.+++.+..
T Consensus         4 ~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~---~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~   80 (178)
T 2anr_A            4 SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP---GTTERVCLIQGTIEALNAVHGFIAEKIREMP   80 (178)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCT---TSSEEEEEEEECHHHHHHHHHHHHHHHTCCC
T ss_pred             CCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCC---CCCCceEEEEeCHHHHHHHHHHHHHHHhccC
Confidence            5688999999999999999999999999999999999975322 33   6789999999999999999999999887653


Q ss_pred             ccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCc
Q 012307          246 VDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALS  325 (466)
Q Consensus       246 ~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~  325 (466)
                      ....        .+..+.                                                     .+.+..   
T Consensus        81 ~~~~--------~~~~~~-----------------------------------------------------~~~~~~---   96 (178)
T 2anr_A           81 QNVA--------KTEPVS-----------------------------------------------------ILQPQT---   96 (178)
T ss_dssp             CC------------------------------------------------------------------------------
T ss_pred             Cccc--------cCCccc-----------------------------------------------------ccCCcc---
Confidence            2100        000000                                                     000000   


Q ss_pred             ccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC--CCCceEEEEEcCHHHHHHHH
Q 012307          326 TIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG--LPDEITVEIKGTSSQVQLAQ  403 (466)
Q Consensus       326 ~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~--~~~er~V~I~Gt~~~V~~A~  403 (466)
                      .          .......+.+|.||.+++|+||||+|.+|++|++.|||+|+|.+...  ..+++.|+|+|++++|+.|+
T Consensus        97 ~----------~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~  166 (178)
T 2anr_A           97 T----------VNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAV  166 (178)
T ss_dssp             -------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEEEEEEESSHHHHHHHH
T ss_pred             C----------CCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEcCHHHHHHHH
Confidence            0          00012357899999999999999999999999999999999976532  34689999999999999999


Q ss_pred             HHHHHHHhcCc
Q 012307          404 QLIQEYMNNHK  414 (466)
Q Consensus       404 ~lI~~~i~~~~  414 (466)
                      .+|.++|.++.
T Consensus       167 ~~I~~~i~e~p  177 (178)
T 2anr_A          167 ELIIQKIQEDP  177 (178)
T ss_dssp             HHHHHHHHSCC
T ss_pred             HHHHHHHHhCC
Confidence            99999998753

>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=99.92  E-value=2.7e-25  Score=200.74  Aligned_cols=155  Identities=26%  Similarity=0.325  Sum_probs=124.9

Q ss_pred             ceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC-CCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCC
Q 012307           77 HCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG-PVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLP  155 (466)
Q Consensus        77 ~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~-~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~  155 (466)
                      .-+++|+||.+++|.||||+|++||+|+++|||+|+|.+. .+++.+|+|+|+|.++.   +..|...|..++.......
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~---v~~A~~~I~~~~~e~~~~~   78 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEA---QFKAQGRIYGKLKEENFFG   78 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHH---HHHHHHHHHHHHHHTTSSC
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHH---HHHHHHHHHHHHhcccccc
Confidence            3489999999999999999999999999999999999876 56889999999998754   3444444444443321110


Q ss_pred             CCCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHH
Q 012307          156 ENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALE  235 (466)
Q Consensus       156 ~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~  235 (466)
                             .......+.+|+||..++|+||||+|++|++|+++|||+|.|.. +..|.  ..+++.|+|+|++++|.+|+.
T Consensus        79 -------~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~-~~~~~--~~~~~~v~I~G~~~~v~~A~~  148 (163)
T 3krm_A           79 -------PKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR-DQTPD--ENDQVIVKIIGHFYASQMAQR  148 (163)
T ss_dssp             -------SSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCT-TCCCC--TTSEEEEEEEECHHHHHHHHH
T ss_pred             -------cccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECC-CCCCC--CCCceEEEEEeCHHHHHHHHH
Confidence                   01124567899999999999999999999999999999999974 44442  344568999999999999999


Q ss_pred             HHHHHhhhc
Q 012307          236 AVVGHLRKF  244 (466)
Q Consensus       236 ~I~~~l~~~  244 (466)
                      +|.+++++.
T Consensus       149 ~I~~~i~~~  157 (163)
T 3krm_A          149 KIRDILAQV  157 (163)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999875

>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=99.92  E-value=4.5e-25  Score=201.49  Aligned_cols=170  Identities=26%  Similarity=0.377  Sum_probs=127.1

Q ss_pred             ceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhcccc
Q 012307          168 FCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVD  247 (466)
Q Consensus       168 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~  247 (466)
                      ..+.+|+||.+++|.||||+|++||+|+++|||+|+|.+.+  +   ...+|+|+|+|+.++|.+|+.+|.+++++....
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--G---TTPERIAQITGPPDRAQHAAEIITDLLRSVQAG   76 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT--T---SCSEEEEEEEECHHHHHHHHHHHHHHHHHHC--
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCC--C---CCCccEEEEEeCHHHHHHHHHHHHHHHHhcccC
Confidence            46789999999999999999999999999999999997432  2   467899999999999999999999998875211


Q ss_pred             CccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCccc
Q 012307          248 QGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTI  327 (466)
Q Consensus       248 ~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~~  327 (466)
                      .         ++.              +        +       |..+  . +.+.           ...|...      
T Consensus        77 ~---------~~~--------------~--------~-------p~~~--~-~~~~-----------~~~~~~~------   98 (174)
T 1j4w_A           77 N---------PGG--------------P--------G-------PGGR--G-RGRG-----------QGNWNMG------   98 (174)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             C---------CCC--------------C--------C-------CCCC--C-CCCC-----------CCccccC------
Confidence            0         000              0        0       0000  0 0000           0001000      


Q ss_pred             ccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCC---CCCCceEEEEEcCHHHHHHHHH
Q 012307          328 RSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESR---GLPDEITVEIKGTSSQVQLAQQ  404 (466)
Q Consensus       328 ~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~---~~~~er~V~I~Gt~~~V~~A~~  404 (466)
                               .+ ....+.+|.||.+++|+||||+|.+|++|++.|||+|+|.+..   ..++++.|+|+|++++|+.|+.
T Consensus        99 ---------~~-~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~  168 (174)
T 1j4w_A           99 ---------PP-GGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQ  168 (174)
T ss_dssp             ---------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHH
T ss_pred             ---------CC-CCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHH
Confidence                     00 1235788999999999999999999999999999999998753   2356899999999999999999


Q ss_pred             HHHHHH
Q 012307          405 LIQEYM  410 (466)
Q Consensus       405 lI~~~i  410 (466)
                      ||+++|
T Consensus       169 ~I~~~i  174 (174)
T 1j4w_A          169 LIEEKI  174 (174)
T ss_dssp             HHHHHC
T ss_pred             HHHHhC
Confidence            999875

>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=3.1e-25  Score=203.28  Aligned_cols=161  Identities=25%  Similarity=0.418  Sum_probs=126.7

Q ss_pred             CCceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC---CCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHh
Q 012307           75 PGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG---PVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRV  151 (466)
Q Consensus        75 ~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~---~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i  151 (466)
                      +++++++|+||.+++|.||||+|++||+|+++|||+|+|.+.   .+++.+|+|+|+|..++   +.+|++.|.+++   
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 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEA---LNAVHGFIAEKI---   76 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHH---HHHHHHHHHHHH---
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHH---HHHHHHHHHHHH---
Confidence            578999999999999999999999999999999999999864   46788999999998754   444554444443   


Q ss_pred             cCCCCCCccc----------ccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEE
Q 012307          152 SGLPENDVDA----------KASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIV  221 (466)
Q Consensus       152 ~~l~~~~~~~----------~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v  221 (466)
                      .+........          ........+.+|+||.+++|+||||+|++||+|+++|||+|+|.+....+   ...++.|
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~---~~~~~~v  153 (178)
T 2anr_A           77 REMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGI---NLQNRVV  153 (178)
T ss_dssp             TCCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC-------CCEEEE
T ss_pred             hccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCC---CCCceEE
Confidence            3222111000          00112457899999999999999999999999999999999998544333   5678999


Q ss_pred             EEecCHHHHHHHHHHHHHHhhhc
Q 012307          222 EMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       222 ~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      +|+|+.++|.+|+.+|.++|++.
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            99999999999999999999864

>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=7.3e-25  Score=197.31  Aligned_cols=156  Identities=24%  Similarity=0.397  Sum_probs=129.7

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLV  246 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~  246 (466)
                      ...+.+|+||...+|.||||+|++||+|+++|||+|+|...       +..+|.|+|.|+.++|.+|+.+|.+++.+...
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            46789999999999999999999999999999999999742       35689999999999999999999998876421


Q ss_pred             cCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCcc
Q 012307          247 DQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALST  326 (466)
Q Consensus       247 ~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~  326 (466)
                      ..                 +                         +   .                .    +.       
T Consensus        76 ~~-----------------~-------------------------~---~----------------~----~~-------   83 (160)
T 2jzx_A           76 SS-----------------M-------------------------T---N----------------S----TA-------   83 (160)
T ss_dssp             SC-----------------C-------------------------C---S----------------S----SC-------
T ss_pred             cc-----------------C-------------------------C---C----------------C----cc-------
Confidence            10                 0                         0   0                0    00       


Q ss_pred             cccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecC-CCCCCceEEEEEcCHHHHHHHHHH
Q 012307          327 IRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQES-RGLPDEITVEIKGTSSQVQLAQQL  405 (466)
Q Consensus       327 ~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~-~~~~~er~V~I~Gt~~~V~~A~~l  405 (466)
                             .    ....++.+|.||.+++|+||||+|.+|++|++.|||+|+|.+. .+..+++.|+|+|++++|+.|+.+
T Consensus        84 -------~----~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G~~~~v~~A~~~  152 (160)
T 2jzx_A           84 -------A----SRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQ  152 (160)
T ss_dssp             -------C----CCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEECHHHHHHHHHH
T ss_pred             -------C----CCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEEEcCHHHHHHHHHH
Confidence                   0    0012578899999999999999999999999999999999753 234678999999999999999999


Q ss_pred             HHHHHhc
Q 012307          406 IQEYMNN  412 (466)
Q Consensus       406 I~~~i~~  412 (466)
                      |.++|.+
T Consensus       153 I~~~i~e  159 (160)
T 2jzx_A          153 ICVVMLE  159 (160)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHhc
Confidence            9999875

>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=99.92  E-value=4.4e-25  Score=201.55  Aligned_cols=161  Identities=24%  Similarity=0.400  Sum_probs=126.6

Q ss_pred             CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCC
Q 012307           76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLP  155 (466)
Q Consensus        76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~  155 (466)
                      +..+++|+||.+++|.||||+|++||+|+++|||+|+|.+..++..+|+|+|+|..++   +.+|++.|.+++.....-.
T Consensus         1 g~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~---v~~A~~~I~~~~~~~~~~~   77 (174)
T 1j4w_A            1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDR---AQHAAEIITDLLRSVQAGN   77 (174)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHH---HHHHHHHHHHHHHHHC---
T ss_pred             CCeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHH---HHHHHHHHHHHHHhcccCC
Confidence            4578999999999999999999999999999999999987666788999999999764   5677777777666542100


Q ss_pred             CCC-----------cccc--cCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEE
Q 012307          156 END-----------VDAK--ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVE  222 (466)
Q Consensus       156 ~~~-----------~~~~--~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~  222 (466)
                      ...           .++.  .......+.+|+||.+++|+||||+|++||+|+++|||+|+|...  .+.+.+..++.|+
T Consensus        78 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~--~~~~~~~~~~~v~  155 (174)
T 1j4w_A           78 PGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRN--PPPNADPNMKLFT  155 (174)
T ss_dssp             --------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECC--CTTTSCTTEEEEE
T ss_pred             CCCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCC--CCCCCCCCceEEE
Confidence            000           0000  001134688999999999999999999999999999999999743  2334467899999


Q ss_pred             EecCHHHHHHHHHHHHHHh
Q 012307          223 MQGEAAKVLKALEAVVGHL  241 (466)
Q Consensus       223 I~G~~~~V~~A~~~I~~~l  241 (466)
                      |+|++++|.+|+.+|.++|
T Consensus       156 I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          156 IRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             EECCHHHHHHHHHHHHHHC
T ss_pred             EECCHHHHHHHHHHHHHhC
Confidence            9999999999999998864

>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=99.91  E-value=4.2e-25  Score=198.88  Aligned_cols=156  Identities=30%  Similarity=0.508  Sum_probs=127.2

Q ss_pred             CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHh-cCC
Q 012307           76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRV-SGL  154 (466)
Q Consensus        76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i-~~l  154 (466)
                      ..++++|+||.+++|.||||+|++||+|+++|||+|+|.+.  ++++|+|+|+|..++   +..|+..|.+.+... ...
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~~---v~~A~~~I~~~i~e~~~~~   77 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNA---IFKAFAMIIDKLEEDISSS   77 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHHH---HHHHHHHHHHHHHHHHTSC
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHHH---HHHHHHHHHHHHHhhcccc
Confidence            45799999999999999999999999999999999999976  678999999998654   556666666554432 111


Q ss_pred             CCCCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHH
Q 012307          155 PENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKAL  234 (466)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~  234 (466)
                      ..   ..........+.+|+||.+++|+||||+|++|++|+++|||+|+|.+ +..|   +..++.|+|+|++++|.+|+
T Consensus        78 ~~---~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~-~~~~---~~~~~~v~I~G~~~~v~~A~  150 (160)
T 2jzx_A           78 MT---NSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG-DMLP---NSTERAITIAGIPQSIIECV  150 (160)
T ss_dssp             CC---SSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCC-CCST---TCCEEEEEEEECHHHHHHHH
T ss_pred             CC---CCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECC-CCCC---CCCceEEEEEcCHHHHHHHH
Confidence            00   00011224588999999999999999999999999999999999973 3444   57899999999999999999


Q ss_pred             HHHHHHhhh
Q 012307          235 EAVVGHLRK  243 (466)
Q Consensus       235 ~~I~~~l~~  243 (466)
                      .+|.+++.+
T Consensus       151 ~~I~~~i~e  159 (160)
T 2jzx_A          151 KQICVVMLE  159 (160)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhc
Confidence            999998865

>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=99.90  E-value=1.7e-23  Score=189.07  Aligned_cols=156  Identities=21%  Similarity=0.353  Sum_probs=121.6

Q ss_pred             eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCC--CCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCC
Q 012307           78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGP--VSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLP  155 (466)
Q Consensus        78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~--~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~  155 (466)
                      ++++|+||.+++|.||||+|++||+|+++|||+|+|.+..  ++..+|+|+|+|.+++   +..|+..|..++.   +..
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 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYK---VQQACEMVMDILR---ERD   75 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHH---HHHHHHHHHHHTT---CSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHH---HHHHHHHHHHHHH---hcc
Confidence            5789999999999999999999999999999999997542  4677899999997654   4444444444333   221


Q ss_pred             CCCccc-cc-CCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHH
Q 012307          156 ENDVDA-KA-SGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKA  233 (466)
Q Consensus       156 ~~~~~~-~~-~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A  233 (466)
                      ...... .. ......+.+|+||..++|+||||+|++|++|+++|||+|.|.+.+  +   ...++.|+|+|++++|.+|
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--G---TGPEKIAHIMGPPDRCEHA  150 (164)
T ss_dssp             SCCCSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC--T---TSSEEEEEEESCHHHHHHH
T ss_pred             CCCCCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC--C---CCCcEEEEEEcCHHHHHHH
Confidence            111000 00 001134688999999999999999999999999999999997532  2   4568999999999999999


Q ss_pred             HHHHHHHhhhc
Q 012307          234 LEAVVGHLRKF  244 (466)
Q Consensus       234 ~~~I~~~l~~~  244 (466)
                      +.+|.+++++.
T Consensus       151 ~~~I~~~i~~~  161 (164)
T 2jvz_A          151 ARIINDLLQSL  161 (164)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHhhh
Confidence            99999998764

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

Probab=99.88  E-value=2.5e-22  Score=200.88  Aligned_cols=221  Identities=13%  Similarity=0.132  Sum_probs=156.7

Q ss_pred             CCceEEEEEecccccceeeecCC--hhHHHHHHHhCceEEEeCCC-----CCCCCeEEEecCCCCCCCCCChhHHHHHHH
Q 012307           75 PGHCVFRMIVPVLKVGSIIGRKG--ELIKKTCEDTRARIKVLDGP-----VSSPDRIVLISGKEEPEAPVSPAMDAAVRV  147 (466)
Q Consensus        75 ~~~~~~rllvp~~~vG~IIGk~G--~~Ik~I~~etga~I~v~~~~-----~~~~ervv~I~G~~e~~~~v~~A~~ai~~i  147 (466)
                      ...+++++.||..+|+.||||+|  ++|++|+++|||+|+|++..     +......|+|+|..++   |.+|+.+|.. 
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~en---VE~AR~~I~~-  102 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGD---VDRARMLMRR-  102 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHH---HHHHHHHHHH-
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHH---HHHHHHHHHh-
Confidence            46799999999999999999999  99999999999999998764     1134578999999976   3344444433 


Q ss_pred             HHHhcCCCCCCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCH
Q 012307          148 FKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEA  227 (466)
Q Consensus       148 ~~~i~~l~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~  227 (466)
                            +            ....+.+.+|...+..  ...+..|.+ ++..+++|.+.+....   .......|+|+|..
T Consensus       103 ------l------------~Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~---~~~~sd~V~IrG~~  158 (376)
T 3n89_A          103 ------N------------CHFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEK---NGIVTTYLRITARE  158 (376)
T ss_dssp             ------S------------CEEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC--------CEEEEEEEEEG
T ss_pred             ------c------------CCceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCcccc---cCCCCCEEEEEcCh
Confidence                  1            2345666666543332  122334554 5678999998643211   01236679999999


Q ss_pred             HHHHHHHHHHHHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCcccc
Q 012307          228 AKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLE  307 (466)
Q Consensus       228 ~~V~~A~~~I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~  307 (466)
                      .+|.+|.+.+..+++......         +                                                 
T Consensus       159 ~nv~~akeA~~~Ll~~l~~~e---------~-------------------------------------------------  180 (376)
T 3n89_A          159 KNQHELIEAAKRLNEILFRES---------P-------------------------------------------------  180 (376)
T ss_dssp             GGHHHHHHHHHHHHHHHCC-----------C-------------------------------------------------
T ss_pred             hhHHHHHHHHHHHHHHHHhhh---------c-------------------------------------------------
Confidence            877777666666555421100         0                                                 


Q ss_pred             ccccCCCcccCCCCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceecccc--chHHHHHhHhCCeEEEecCCCC-
Q 012307          308 SRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGG--TSIENIRRTSGAIITVQESRGL-  384 (466)
Q Consensus       308 ~~~~~~~~~~yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG--~~Ik~Ir~~SGA~I~I~~~~~~-  384 (466)
                                   .                 ....++.+|.|+..++..||||+|  ..|++|+++|||+|.+++..+. 
T Consensus       181 -------------~-----------------~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~  230 (376)
T 3n89_A          181 -------------A-----------------PENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRN  230 (376)
T ss_dssp             -------------C-----------------CSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC------
T ss_pred             -------------c-----------------cccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcc
Confidence                         0                 001267889999999999999999  4569999999999999754321 


Q ss_pred             ---CCceEEEEEcCHHHHHHHHHHHHHHHh
Q 012307          385 ---PDEITVEIKGTSSQVQLAQQLIQEYMN  411 (466)
Q Consensus       385 ---~~er~V~I~Gt~~~V~~A~~lI~~~i~  411 (466)
                         .+...|+|+|+.++|.+|++.|+++|-
T Consensus       231 d~~~~~~~ItItGs~e~V~~Ark~I~~lLP  260 (376)
T 3n89_A          231 ETRGNIYEIKVVGNIDNVLKARRYIMDLLP  260 (376)
T ss_dssp             ---CCEEEEEEESCHHHHHHHHHHHHHTSE
T ss_pred             cccCCceEEEEEeCHHHHHHHHHHHHhhCC
Confidence               235789999999999999999999874

>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=4e-19  Score=156.71  Aligned_cols=135  Identities=19%  Similarity=0.256  Sum_probs=106.8

Q ss_pred             ceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhcccc
Q 012307          168 FCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVD  247 (466)
Q Consensus       168 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~  247 (466)
                      .++.+|+||.+.+|.+||++|++|+.|++++|++|....        ...++.+...+.++.|.+|..++ .    .   
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~--------~~~~~~i~~~~~p~~v~~~~~~l-~----~---   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLD--------EDTCTFHIYGEDQDAVKKARSFL-E----F---   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEE--------TTTTEEEEEESSHHHHHHHHHHH-C----E---
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccC--------CCchheeeccCCHHHHHHHHHhh-h----c---
Confidence            467899999999999999999999999999995444332        12345555556799998886543 1    0   


Q ss_pred             CccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCccc
Q 012307          248 QGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTI  327 (466)
Q Consensus       248 ~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~~  327 (466)
                                                                                                      
T Consensus        67 --------------------------------------------------------------------------------   66 (144)
T 2qnd_A           67 --------------------------------------------------------------------------------   66 (144)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             ccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCC-eEEEecCCCC---CCc--eEEEEEcCHHHHHH
Q 012307          328 RSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGA-IITVQESRGL---PDE--ITVEIKGTSSQVQL  401 (466)
Q Consensus       328 ~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA-~I~I~~~~~~---~~e--r~V~I~Gt~~~V~~  401 (466)
                                     ...+|.||.+++|++|||+|.+|+.|++.||| +|+|....+.   .++  +.|+|+|++++|+.
T Consensus        67 ---------------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~  131 (144)
T 2qnd_A           67 ---------------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIAN  131 (144)
T ss_dssp             ---------------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHH
T ss_pred             ---------------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHH
Confidence                           02468899999999999999999999999997 9999764332   123  35899999999999


Q ss_pred             HHHHHHHHHhcC
Q 012307          402 AQQLIQEYMNNH  413 (466)
Q Consensus       402 A~~lI~~~i~~~  413 (466)
                      |+.||.+.|++-
T Consensus       132 Ak~li~~~l~~l  143 (144)
T 2qnd_A          132 ATVLLDYHLNYL  143 (144)
T ss_dssp             HHHHHHHHHHTC
T ss_pred             HHHHHHHHHHhc
Confidence            999999999763

>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=1.6e-18  Score=152.85  Aligned_cols=139  Identities=22%  Similarity=0.226  Sum_probs=101.9

Q ss_pred             ceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCC
Q 012307           77 HCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPE  156 (466)
Q Consensus        77 ~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~  156 (466)
                      .++.+|+||.+.||.+||++|++|++|++++|+.|...+.   .+++.+...+.++          ++.++...+ .   
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~~---~~~~~i~~~~~p~----------~v~~~~~~l-~---   65 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE---DTCTFHIYGEDQD----------AVKKARSFL-E---   65 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEET---TTTEEEEEESSHH----------HHHHHHHHH-C---
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccCC---CchheeeccCCHH----------HHHHHHHhh-h---
Confidence            4688999999999999999999999999999944433322   3445444444442          232222111 1   


Q ss_pred             CCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCC-eEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHH
Q 012307          157 NDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGA-SVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALE  235 (466)
Q Consensus       157 ~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga-~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~  235 (466)
                                 ....++.||..++|++|||+|.+|+.|++.||+ +|+|.+.++.........+.|+|+|+.++|.+|+.
T Consensus        66 -----------~~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~  134 (144)
T 2qnd_A           66 -----------FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATV  134 (144)
T ss_dssp             -----------EEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHH
T ss_pred             -----------cceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHH
Confidence                       123889999999999999999999999999997 99998654321100112246899999999999999


Q ss_pred             HHHHHhhh
Q 012307          236 AVVGHLRK  243 (466)
Q Consensus       236 ~I~~~l~~  243 (466)
                      +|.++|..
T Consensus       135 li~~~l~~  142 (144)
T 2qnd_A          135 LLDYHLNY  142 (144)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHh
Confidence            99998875

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

Probab=99.70  E-value=3.1e-17  Score=153.77  Aligned_cols=154  Identities=24%  Similarity=0.281  Sum_probs=111.9

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecC-----HHHHHHHHHHHHHHh
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGE-----AAKVLKALEAVVGHL  241 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~-----~~~V~~A~~~I~~~l  241 (466)
                      .....++.||.+.+|.|||++|++|+.|+++||++|++.          ..++.|+|.++     ++++.+|+++|..++
T Consensus        32 aP~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~----------~~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~  101 (219)
T 2e3u_A           32 FKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITID----------SETGEVWITSTKETEDPLAVWKARDIVLAIG  101 (219)
T ss_dssp             -CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEEC----------TTTCEEEEEECTTCCSHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEE----------cCCCEEEEecCCCCCCHHHHHHHHHHHHHHh
Confidence            345679999999999999999999999999999999995          23567888875     699999999999988


Q ss_pred             hhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCC
Q 012307          242 RKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQD  321 (466)
Q Consensus       242 ~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~  321 (466)
                      +.+..+.....+ .                                        |..+.+      . +           
T Consensus       102 rg~~~e~g~~ll-~----------------------------------------dd~~~e------~-i-----------  122 (219)
T 2e3u_A          102 RGFSPERAFRLL-N----------------------------------------EGEYLE------I-I-----------  122 (219)
T ss_dssp             TTCCHHHHGGGG-S----------------------------------------TTCEEE------E-E-----------
T ss_pred             ccCCccccceec-c----------------------------------------CCccce------e-E-----------
Confidence            654322110000 0                                        000000      0 0           


Q ss_pred             CCCcccccCCCCCCCCCcccce--EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHH
Q 012307          322 PALSTIRSSALGRASGPIVTQI--TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQV  399 (466)
Q Consensus       322 ~~~~~~~~s~~~~~~~~~~~~~--t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V  399 (466)
                            .           ...+  ...-..+...+|+||||+|.+|+.|++.|||+|.|++       +.|+|.|+.++|
T Consensus       123 ------~-----------i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~~-------~~v~i~G~~~~i  178 (219)
T 2e3u_A          123 ------N-----------LTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG-------KTVAIIGNPIQI  178 (219)
T ss_dssp             ------E-----------GGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEET-------TEEEEEECHHHH
T ss_pred             ------E-----------cccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEECC-------eEEEEEeCHHHH
Confidence                  0           0000  0000112346899999999999999999999999953       579999999999


Q ss_pred             HHHHHHHHHHHhcC
Q 012307          400 QLAQQLIQEYMNNH  413 (466)
Q Consensus       400 ~~A~~lI~~~i~~~  413 (466)
                      +.|+.+|.++|...
T Consensus       179 ~~A~~~i~~li~g~  192 (219)
T 2e3u_A          179 EIAKTAIEKLARGS  192 (219)
T ss_dssp             HHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHcCC
Confidence            99999999999653

>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=99.65  E-value=2.2e-16  Score=125.60  Aligned_cols=73  Identities=32%  Similarity=0.451  Sum_probs=66.7

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       341 ~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      .+++.+|.||.+++|+||||+|++|++|+++|||+|+|++..+...++.|+|+|++++|+.|+.||+++|.+.
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            4578999999999999999999999999999999999988666678999999999999999999999999876

>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=99.63  E-value=6.5e-16  Score=141.31  Aligned_cols=140  Identities=23%  Similarity=0.285  Sum_probs=113.3

Q ss_pred             EEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEe-----cCHHHHHHHHHHHHHHhhhcc
Q 012307          171 VRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQ-----GEAAKVLKALEAVVGHLRKFL  245 (466)
Q Consensus       171 ~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~-----G~~~~V~~A~~~I~~~l~~~~  245 (466)
                      .+++||...+|.|||++|++++.|++.+|++|++.          ..++.|+|.     |++.++.+|.++|..+.+.|.
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 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVD----------TENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFP   75 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEE----------TTTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCC
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEE----------cCCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCC
Confidence            68999999999999999999999999999999995          346788888     999999999999999888775


Q ss_pred             ccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCc
Q 012307          246 VDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALS  325 (466)
Q Consensus       246 ~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~  325 (466)
                      .+.....+ +                                        |.+                           
T Consensus        76 ~e~A~~Ll-~----------------------------------------Dd~---------------------------   87 (191)
T 1tua_A           76 PEKAFRLL-E----------------------------------------EDQ---------------------------   87 (191)
T ss_dssp             HHHHGGGG-S----------------------------------------TTE---------------------------
T ss_pred             HHHhhhcc-c----------------------------------------Ccc---------------------------
Confidence            43211000 0                                        000                           


Q ss_pred             ccccCCCCCCCCCcccceEEEEEe----------ccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcC
Q 012307          326 TIRSSALGRASGPIVTQITQTMQI----------PISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGT  395 (466)
Q Consensus       326 ~~~~s~~~~~~~~~~~~~t~~i~I----------P~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt  395 (466)
                                       .-..+.|          +....|+||||+|.+|+.|+..|||+|.|++       ..|.|.|+
T Consensus        88 -----------------~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~~-------~~v~i~G~  143 (191)
T 1tua_A           88 -----------------ILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGD  143 (191)
T ss_dssp             -----------------EEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEECS-------SEEEEEEE
T ss_pred             -----------------eeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEcC-------CEEEEEeC
Confidence                             0111222          2356899999999999999999999999953       48999999


Q ss_pred             HHHHHHHHHHHHHHHhc
Q 012307          396 SSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       396 ~~~V~~A~~lI~~~i~~  412 (466)
                      +++++.|+..|.++|..
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            99999999999999974

>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=99.63  E-value=8.2e-16  Score=122.28  Aligned_cols=72  Identities=38%  Similarity=0.517  Sum_probs=67.1

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      .++.+|.||.+++|+||||+|.+|++|+++|||+|+|+++..++++|.|+|+|++++|+.|+.||++++.+.
T Consensus         6 ~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            6 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            478899999999999999999999999999999999987665678899999999999999999999999864

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

Probab=99.63  E-value=4e-16  Score=122.26  Aligned_cols=72  Identities=29%  Similarity=0.433  Sum_probs=67.2

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      .++.+|.||.+++|+||||+|.+|++|++.|||+|+|.++.+++.++.|+|+|++++|+.|+.||+++|.++
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            468899999999999999999999999999999999988666678999999999999999999999999864

>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=1.2e-15  Score=123.92  Aligned_cols=75  Identities=27%  Similarity=0.430  Sum_probs=69.2

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       341 ~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      ..++.+|.||.+++|+||||+|.+|++|+++|||+|+|++..+...++.|+|+|++++|++|+.||+++|++...
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~~   87 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGRS   87 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhccc
Confidence            357899999999999999999999999999999999998866566789999999999999999999999998654

>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=99.61  E-value=5.2e-16  Score=125.40  Aligned_cols=73  Identities=37%  Similarity=0.510  Sum_probs=67.7

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       341 ~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      ..++.+|.||.+++|+||||+|.+|++|+++|||+|+|++.....+++.|+|+|++++|++|+.+|+++|.+.
T Consensus        12 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           12 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            4578899999999999999999999999999999999987666678999999999999999999999999864

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

Probab=99.60  E-value=1.1e-15  Score=127.28  Aligned_cols=72  Identities=19%  Similarity=0.363  Sum_probs=65.9

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      +.+|.||.+++|+||||+|++||+|+++|||+|+|+++.+...+|+|+|+|++++|++|+.||++++.+...
T Consensus        12 ~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~~   83 (106)
T 2hh3_A           12 GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRS   83 (106)
T ss_dssp             CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC-
T ss_pred             EEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhcccc
Confidence            578999999999999999999999999999999998766556789999999999999999999999987544

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

Probab=99.59  E-value=2.4e-15  Score=140.92  Aligned_cols=144  Identities=22%  Similarity=0.240  Sum_probs=102.2

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCC--CCCCChhHHHHHHHHHHhcCCCC
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEP--EAPVSPAMDAAVRVFKRVSGLPE  156 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~--~~~v~~A~~ai~~i~~~i~~l~~  156 (466)
                      ..+|.||.+.+|.|||++|++|+.|+++|||+|++...     ++.|.|.+....  -+.+.+|.+.|..+..   +...
T Consensus        35 i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~-----~g~V~I~~~~~t~d~~~i~kA~~~I~~i~r---g~~~  106 (219)
T 2e3u_A           35 EEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE-----TGEVWITSTKETEDPLAVWKARDIVLAIGR---GFSP  106 (219)
T ss_dssp             EEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT-----TCEEEEEECTTCCSHHHHHHHHHHHHHHHT---TCCH
T ss_pred             EEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC-----CCEEEEecCCCCCCHHHHHHHHHHHHHHhc---cCCc
Confidence            56899999999999999999999999999999999633     567899886521  1224445554444331   1000


Q ss_pred             CCcccccCCCcceEEEEEec-----------cCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec
Q 012307          157 NDVDAKASGAAFCSVRLLVP-----------STQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG  225 (466)
Q Consensus       157 ~~~~~~~~~~~~~~~~llVP-----------~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G  225 (466)
                      ....... .+......+.++           ...+|+||||+|.+|+.|++.|||+|.|.            ++.|.|.|
T Consensus       107 e~g~~ll-~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~------------~~~v~i~G  173 (219)
T 2e3u_A          107 ERAFRLL-NEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY------------GKTVAIIG  173 (219)
T ss_dssp             HHHGGGG-STTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE------------TTEEEEEE
T ss_pred             cccceec-cCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC------------CeEEEEEe
Confidence            0000000 001111223232           23689999999999999999999999996            35699999


Q ss_pred             CHHHHHHHHHHHHHHhhh
Q 012307          226 EAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       226 ~~~~V~~A~~~I~~~l~~  243 (466)
                      +.++|+.|+.+|.++|..
T Consensus       174 ~~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          174 NPIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             CHHHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHHHcC
Confidence            999999999999999965

>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=99.58  E-value=1.9e-15  Score=117.45  Aligned_cols=69  Identities=23%  Similarity=0.332  Sum_probs=64.5

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 012307          342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~  412 (466)
                      .++.+|.||.+++|+||||+|.+|++|+++|||+|+|++.  +..+|+|+|+|++++|+.|+.+|.++|.+
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            4688999999999999999999999999999999999875  35799999999999999999999999986

>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=99.58  E-value=2.6e-15  Score=117.58  Aligned_cols=70  Identities=24%  Similarity=0.349  Sum_probs=63.4

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCC---CCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESR---GLPDEITVEIKGTSSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~---~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~  412 (466)
                      .+.+|.||.+++|+||||+|.+|++|++.|||+|+|++..   ++..++.|+|+|++++|+.|+.+|+++|.+
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            5789999999999999999999999999999999998742   345689999999999999999999999875

>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=99.54  E-value=7.5e-15  Score=116.61  Aligned_cols=70  Identities=19%  Similarity=0.302  Sum_probs=63.2

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       341 ~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      .+++.+|.||.+++|+||||+|++||+|+++|||+|+|....   +++.|+|+|++++|++|+++|.+++...
T Consensus         8 ~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~---~~~~v~ItG~~e~v~~A~~~I~~~i~~r   77 (83)
T 2dgr_A            8 GQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD---KEPVFAVTGMPENVDRAREEIEAHITLR   77 (83)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS---SCCEEEEEECTTTHHHHHHHHHHHHHSC
T ss_pred             CceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC---CCCeEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            457889999999999999999999999999999999997532   4689999999999999999999987753

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

Probab=99.53  E-value=1.1e-14  Score=121.57  Aligned_cols=71  Identities=27%  Similarity=0.434  Sum_probs=64.5

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHhcCc
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG---LPDEITVEIKGTSSQVQLAQQLIQEYMNNHK  414 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~---~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~  414 (466)
                      +.+|.||.+++|+||||+|++|++|+++|||+|+|.+...   ...+++|+|+|++++|++|+.+|+++|.+..
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            6789999999999999999999999999999999987532   3468999999999999999999999998754

>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=99.53  E-value=8.8e-15  Score=117.65  Aligned_cols=73  Identities=22%  Similarity=0.331  Sum_probs=65.9

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCC---CCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESR---GLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~---~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      ++.+|.||.+++|+||||+|.+|++|++.|||+|+|++..   ++..++.|+|+|++++|+.|+.+|+++|.+...
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~   78 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQG   78 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccc
Confidence            5789999999999999999999999999999999998743   345689999999999999999999999987543

>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=99.53  E-value=2.1e-14  Score=117.07  Aligned_cols=74  Identities=23%  Similarity=0.404  Sum_probs=66.5

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC--CCCceEEEEEcCHHHHHHHHHHHHHHHhcCc
Q 012307          341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG--LPDEITVEIKGTSSQVQLAQQLIQEYMNNHK  414 (466)
Q Consensus       341 ~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~--~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~  414 (466)
                      .+++.+|.||.+++|+||||+|.+|++|+++|||+|+|.+...  ...+|.|+|+|++++|+.|+.||+++|.+..
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   88 (94)
T 1x4m_A           13 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQG   88 (94)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCCS
T ss_pred             CcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhccC
Confidence            3578899999999999999999999999999999999987533  3468999999999999999999999998743

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

Probab=99.49  E-value=4.9e-14  Score=112.74  Aligned_cols=70  Identities=21%  Similarity=0.381  Sum_probs=63.4

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC--CCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG--LPDEITVEIKGTSSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~--~~~er~V~I~Gt~~~V~~A~~lI~~~i~~  412 (466)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|.+...  ...+|.|+|+|++++++.|+.+|++++.+
T Consensus        14 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           14 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             EEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             EEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            56789999999999999999999999999999999987532  45789999999999999999999998863

>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=99.47  E-value=6.9e-14  Score=116.20  Aligned_cols=73  Identities=30%  Similarity=0.434  Sum_probs=65.7

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCC--CCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGL--PDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~--~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      .+.+|.||.+++|+||||+|.+|++|+++|||+|+|++..+.  ++++.|+|+|++++|+.|+.+|+++|.+...
T Consensus        15 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~~   89 (104)
T 1we8_A           15 VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEE   89 (104)
T ss_dssp             EEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhChH
Confidence            678999999999999999999999999999999999875432  3589999999999999999999999987543

>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=99.43  E-value=1.5e-13  Score=106.59  Aligned_cols=70  Identities=27%  Similarity=0.534  Sum_probs=64.2

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhh
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  243 (466)
                      .....+|+||.+.+|.||||+|++||+|+++|||+|+|.+.       +..+|+|+|.|++++|.+|+.+|.++|++
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            45789999999999999999999999999999999999743       35699999999999999999999999875

>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=99.42  E-value=1.7e-13  Score=125.23  Aligned_cols=144  Identities=18%  Similarity=0.206  Sum_probs=101.5

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCC--CCCChhHHHHHHHHHHhcCCCC
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPE--APVSPAMDAAVRVFKRVSGLPE  156 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~--~~v~~A~~ai~~i~~~i~~l~~  156 (466)
                      .++++||.+.+|.|||++|++++.|++++|++|++..     .++.|+|.-.....  ..+.+|.+.|..+..   ++..
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~-----~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~r---gf~~   76 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGIPPVNLMKAAEVVKAISL---GFPP   76 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET-----TTTEEEEEESSTTSCHHHHHHHHHHHHHHHH---TCCH
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc-----CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHc---CCCH
Confidence            4699999999999999999999999999999999964     37788887332211  124455555543321   1110


Q ss_pred             CCcccccCCCcceEEEEEec----------cCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecC
Q 012307          157 NDVDAKASGAAFCSVRLLVP----------STQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGE  226 (466)
Q Consensus       157 ~~~~~~~~~~~~~~~~llVP----------~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~  226 (466)
                      .+.-.... +......+.++          ....|+||||+|.+|+.|+..|||+|.|.            ++.|.|.|+
T Consensus        77 e~A~~Ll~-Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~------------~~~v~i~G~  143 (191)
T 1tua_A           77 EKAFRLLE-EDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG------------EYEVAIIGD  143 (191)
T ss_dssp             HHHGGGGS-TTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC------------SSEEEEEEE
T ss_pred             HHhhhccc-CcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc------------CCEEEEEeC
Confidence            00000000 11122223343          24689999999999999999999999995            237999999


Q ss_pred             HHHHHHHHHHHHHHhhh
Q 012307          227 AAKVLKALEAVVGHLRK  243 (466)
Q Consensus       227 ~~~V~~A~~~I~~~l~~  243 (466)
                      .++++.|...|.+++..
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            99999999999998864

>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=99.41  E-value=3.8e-13  Score=105.19  Aligned_cols=73  Identities=22%  Similarity=0.263  Sum_probs=63.8

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhh
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  243 (466)
                      .+.+|+||.+++|.||||+|++|++|+++|||+|.|.+.++.  +.+..+|.|+|.|++++|.+|+.+|.+++.+
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            578999999999999999999999999999999999854321  1267799999999999999999999998764

>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=99.41  E-value=6.9e-13  Score=105.29  Aligned_cols=73  Identities=23%  Similarity=0.455  Sum_probs=65.9

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ...+.+|+||.+++|.||||+|++|++|+++|||+|+|..  ..|   +..+|.|+|+|++++|.+|+.+|.+++.+.
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 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE--PLE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECC--TTS---CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcC--CCC---CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            5688999999999999999999999999999999999963  223   577899999999999999999999998864

>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=99.41  E-value=2.3e-13  Score=110.90  Aligned_cols=73  Identities=18%  Similarity=0.301  Sum_probs=65.5

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       341 ~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      .+++.+|.||.+++|.|||++|.+|++|+++|||+|+|++..+  .++.|+|+|++++|+.|+.+|++++.+...
T Consensus        15 ~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~~--~~~~V~I~G~~e~v~~A~~~I~~i~~~~~~   87 (94)
T 2cte_A           15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD--PSNQIKITGTKEGIEKARHEVLLISAEQDK   87 (94)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTS--SCCEEEEEECHHHHHHHHHHHHHHHHHHHT
T ss_pred             CceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCCC--CCCeEEEEECHHHHHHHHHHHHHHhhcccc
Confidence            5688999999999999999999999999999999999975332  457999999999999999999999987654

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

Probab=99.40  E-value=2.4e-13  Score=104.90  Aligned_cols=67  Identities=18%  Similarity=0.281  Sum_probs=60.6

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 012307          342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYM  410 (466)
Q Consensus       342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i  410 (466)
                      ..+.+|.||.+++|.|||++|.+|++|+++|||+|+|+++.  ..++.|+|+|++++|+.|+.+|.+++
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 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS--EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC--SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC--CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            35788999999999999999999999999999999997643  36789999999999999999998764

>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=99.40  E-value=5.1e-13  Score=106.06  Aligned_cols=73  Identities=25%  Similarity=0.341  Sum_probs=64.8

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ...+.+|+||.+++|.||||+|++|++|+++|||+|+|...  .+   +..+|.|+|+|++++|.+|+.+|.+++.+.
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~--~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP--VE---GSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC--CT---TCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC--CC---CCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            56889999999999999999999999999999999999742  22   678999999999999999999999988764

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

Probab=99.39  E-value=4.7e-13  Score=104.69  Aligned_cols=72  Identities=26%  Similarity=0.357  Sum_probs=65.2

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhh
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  243 (466)
                      ...+.+|+||.+++|.||||+|++|++|+++|||+|.|..  ..+   +..+|.|+|.|++++|.+|+.+|.+++++
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~--~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   74 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIAN--PVE---GSTDRQVTITGSAASISLAQYLINVRLSS   74 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECC--CCT---TCSEEEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcC--CCC---CCCeEEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            4578999999999999999999999999999999999974  223   67899999999999999999999998875

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

Probab=99.38  E-value=1.3e-12  Score=104.37  Aligned_cols=75  Identities=27%  Similarity=0.395  Sum_probs=65.6

Q ss_pred             CcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhh
Q 012307          166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  243 (466)
                      ......+|.||.+++|.||||+|++||+|+++|||+|.|..+...+   ...+|.|+|+|+++++.+|+.+|.+++++
T Consensus        11 ~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~---~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           11 QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             CSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSS---TTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            3567889999999999999999999999999999999998533222   56799999999999999999999988753

>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=99.37  E-value=1.2e-12  Score=106.72  Aligned_cols=75  Identities=20%  Similarity=0.228  Sum_probs=66.8

Q ss_pred             ccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          340 VTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       340 ~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      ..+++.+|.||.+++|.|||++|.+|++|+++|||+|+|+++. ..+++.|+|+|++++|+.|+.+|.+++.+..+
T Consensus        14 ~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g-~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~~   88 (95)
T 2ctm_A           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPENVEEAIDHILNLEEEYLA   88 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-CSCTTEEEEESCHHHHHHHHHHHHHHHHHHHT
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC-CCCCcEEEEEcCHHHHHHHHHHHHHHHHHHHH
Confidence            4567899999999999999999999999999999999997543 23578999999999999999999999987655

>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=99.37  E-value=9.1e-13  Score=107.89  Aligned_cols=74  Identities=18%  Similarity=0.267  Sum_probs=65.6

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC-CCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG-LPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~-~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      ..+.+|.||.++++.|||++|.+|++|+++|||+|+|++... ...++.|+|+|+.++|+.|+.+|..++.+..+
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~e~   90 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGELEQ   90 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHHHHh
Confidence            468899999999999999999999999999999999976432 23578999999999999999999999887543

>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=99.36  E-value=8.5e-13  Score=106.44  Aligned_cols=74  Identities=23%  Similarity=0.451  Sum_probs=66.8

Q ss_pred             CcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ....+.+|+||.+++|.||||+|++||+|+++|||+|+|..  ..|   +..+|.|+|+|++++|.+|+.+|.+++.+.
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 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE--PLE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECS--CCS---SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecC--CCC---CCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            36788999999999999999999999999999999999963  223   577999999999999999999999998875

>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=99.35  E-value=9.2e-13  Score=105.79  Aligned_cols=74  Identities=22%  Similarity=0.242  Sum_probs=65.4

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      .+.+|+||..++|.||||+|++|++|+++|||+|.|.+.++.  +.+..+|.|+|+|++++|.+|+.+|.+++.+.
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            578999999999999999999999999999999999854321  12678999999999999999999999998874

>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=99.35  E-value=4.6e-13  Score=106.26  Aligned_cols=70  Identities=23%  Similarity=0.303  Sum_probs=59.7

Q ss_pred             CCCCCceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHH
Q 012307           72 PGWPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRV  147 (466)
Q Consensus        72 ~~~~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i  147 (466)
                      |..++.++++|.||.+++|.||||+|++||+|+++|||+|+|+..   ..+|+|+|+|..++   +.+|.+.|..+
T Consensus         4 ~~~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~---~~~~~v~ItG~~e~---v~~A~~~I~~~   73 (83)
T 2dgr_A            4 GSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR---DKEPVFAVTGMPEN---VDRAREEIEAH   73 (83)
T ss_dssp             CCSCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS---SSCCEEEEEECTTT---HHHHHHHHHHH
T ss_pred             CCCCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC---CCCCeEEEEcCHHH---HHHHHHHHHHH
Confidence            345688999999999999999999999999999999999999854   34789999999976   55666666664

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

Probab=99.34  E-value=9e-13  Score=107.38  Aligned_cols=76  Identities=25%  Similarity=0.407  Sum_probs=66.8

Q ss_pred             CcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      +...+.+|+||.+++|+||||+|++||+|+++|||+|.|..+....   ...+|+|+|+|++++|.+|+.+|.+++++.
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 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS---SCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            4678999999999999999999999999999999999997432211   357899999999999999999999998764

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

Probab=99.33  E-value=2e-12  Score=107.89  Aligned_cols=73  Identities=16%  Similarity=0.296  Sum_probs=64.1

Q ss_pred             EEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       170 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      +.+|+||.+++|+||||+|++||+|+++|||+|+|..+. .+ ..+..+|.|+|+|+.++|.+|+.+|.+++.+.
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            789999999999999999999999999999999997432 22 22467899999999999999999999988764

>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=99.33  E-value=1.9e-12  Score=105.08  Aligned_cols=73  Identities=22%  Similarity=0.255  Sum_probs=65.9

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ..++.+|+||.+++|.||||+|++|++|+++|||+|+|....  +   +..+|.|+|+|++++|.+|+.+|.+++++.
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~--~---g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~   85 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS--G---GLPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC--T---TCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC--C---CCCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            568899999999999999999999999999999999997432  2   467899999999999999999999998864

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

Probab=99.30  E-value=3.5e-12  Score=105.97  Aligned_cols=72  Identities=24%  Similarity=0.382  Sum_probs=63.6

Q ss_pred             ceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          168 FCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       168 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ..+++|+||.++++.||||+|++||+|+++|+|+|+|.+++  +   ...+|.|+|+|++++|++|+.+|.+++.+.
T Consensus        10 ~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~--~---~~~er~V~I~G~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--G---TGPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC--S---SSSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC--C---CCceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            35789999999999999999999999999999999997432  2   466899999999999999999999998864

>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=99.29  E-value=2.7e-12  Score=106.37  Aligned_cols=70  Identities=17%  Similarity=0.268  Sum_probs=63.2

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCc
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHK  414 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~  414 (466)
                      .+.+|.||.+++|.|||++|.+|++|+++|||+|+|+++..  +.+.|+|+|+.++|+.|+.+|.+++.+..
T Consensus        17 ~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~--~~~~V~I~G~~e~v~~A~~~I~~i~~e~e   86 (104)
T 2ctk_A           17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL--QSDIIAITGLAANLDRAKAGLLERVKELQ   86 (104)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT--TCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCC--CcceEEEEcCHHHHHHHHHHHHHHHhhHH
Confidence            67899999999999999999999999999999999976433  45699999999999999999999988744

>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=99.27  E-value=6.7e-12  Score=104.14  Aligned_cols=75  Identities=23%  Similarity=0.302  Sum_probs=65.5

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ...+.+|+||.+++|.||||+|++||+|+++|||+|.|.......   ...++.|+|.|+.++|.+|+.+|.+++.+.
T Consensus        13 ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~---~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT---LLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS---SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCC---CCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            557899999999999999999999999999999999997432110   346899999999999999999999999764

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

Probab=99.21  E-value=1.3e-11  Score=95.02  Aligned_cols=68  Identities=22%  Similarity=0.346  Sum_probs=60.7

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHh
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHL  241 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l  241 (466)
                      ...+..|.||.+++|.|||++|++|++|+++|||+|.|+++       +..+|.|+|.|..++|.+|+.+|.+++
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 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-------SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC-------CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCC-------CCcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            45788999999999999999999999999999999999742       235789999999999999999998754

>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=99.19  E-value=2e-11  Score=99.46  Aligned_cols=74  Identities=18%  Similarity=0.315  Sum_probs=65.6

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLV  246 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~  246 (466)
                      ..++.+|.||.++++.|||++|++|++|+++|||+|+|+.+.      ...++.|+|+|.+++|.+|+.+|..+++++..
T Consensus        15 ~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g------~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~~   88 (95)
T 2ctm_A           15 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG------APDPNCVTVTGLPENVEEAIDHILNLEEEYLA   88 (95)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT------CSCTTEEEEESCHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC------CCCCcEEEEEcCHHHHHHHHHHHHHHHHHHHH
Confidence            568899999999999999999999999999999999997422      23478999999999999999999999887644

>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=99.19  E-value=3.2e-11  Score=98.11  Aligned_cols=75  Identities=23%  Similarity=0.313  Sum_probs=66.4

Q ss_pred             cccceEEEEEeccCcccceeccccchHHHHHhHh-CCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          339 IVTQITQTMQIPISYAEDIIGVGGTSIENIRRTS-GAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       339 ~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~S-GA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      +...++.+|.||.++++.|||++|.+|++|+++| ||+|+|+++  +...+.|+|.|+.++|++|+.+|++++.+...
T Consensus        13 ~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~--g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~e~   88 (95)
T 2ctj_A           13 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE--GSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQT   88 (95)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT--TTTCCEEEEESCHHHHHHHHHHHHHHHHHHSC
T ss_pred             HhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC--CCCcceEEEEcCHHHHHHHHHHHHHHHhhhhh
Confidence            3466789999999999999999999999999999 999999653  34567999999999999999999999987553

>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=99.18  E-value=3.3e-11  Score=98.54  Aligned_cols=74  Identities=14%  Similarity=0.257  Sum_probs=64.9

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ...+..|.||..+++.|||++|++|++|+++|||+|.|++.. .+   ...++.|+|+|..+++.+|+.+|..++.+.
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g-~~---~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~   88 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKD-DG---NQPQDQITITGYEKNTEAARDAILRIVGEL   88 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTT-TC---SSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCC-CC---CCCccEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            457899999999999999999999999999999999997432 22   346789999999999999999999988764

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

Probab=99.18  E-value=5.3e-11  Score=119.14  Aligned_cols=75  Identities=11%  Similarity=0.041  Sum_probs=62.2

Q ss_pred             CcceEEEEEeccCcceeeecCCc--hhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHH
Q 012307          166 AAFCSVRLLVPSTQAINLIGKQG--SLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGH  240 (466)
Q Consensus       166 ~~~~~~~llVP~~~vg~IIGk~G--~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~  240 (466)
                      ...++.++.||..+++.||||+|  ++|++|+++|||+|+|+..+............|+|+|..++|++|+.+|.++
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l  103 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRN  103 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHS
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhc
Confidence            36799999999999999999999  9999999999999999743300011124567899999999999999999873

>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=99.16  E-value=4e-11  Score=98.87  Aligned_cols=68  Identities=21%  Similarity=0.322  Sum_probs=61.9

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhH-hCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRT-SGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~-SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      ++.+|.||..+++.|||++|++|++|+++ ++++|.|++     +++.|+|+|++++|++|+.+|++++++..+
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-----~~~~ItI~G~~~~V~~a~~~I~~~v~el~~   95 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTEDVSVAQEQIEGMVKDLIN   95 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-----CCCEEEEECCHHHHHHHHHHHHHHHHHHHh
Confidence            67899999999999999999999999997 599999976     356999999999999999999999987654

>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=99.15  E-value=3.2e-11  Score=98.10  Aligned_cols=71  Identities=14%  Similarity=0.257  Sum_probs=63.5

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ...+.+|.||.+.+|.|||++|++||+|+++|||+|.|++.       +..++.|+|+|+.++|.+|+.+|..++.+.
T Consensus        15 ~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~-------~~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-------DDPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-------TSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCC-------CCCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            56889999999999999999999999999999999999742       233579999999999999999999998764

>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=99.05  E-value=9.2e-11  Score=96.71  Aligned_cols=68  Identities=21%  Similarity=0.346  Sum_probs=60.8

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHH-hCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQEN-SGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~-sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ...+.+|.||..+++.|||++|++|++|+++ ++++|.|+.          .++.|+|+|+++.|.+|+.+|..++++.
T Consensus        25 ~~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~----------~~~~ItI~G~~~~V~~a~~~I~~~v~el   93 (102)
T 2ctf_A           25 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVKDL   93 (102)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC----------CCCEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            3478999999999999999999999999997 489999862          3678999999999999999999988764

>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=99.05  E-value=1.8e-10  Score=95.43  Aligned_cols=71  Identities=18%  Similarity=0.316  Sum_probs=63.0

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ......|.||..+++.|||++|++|++|+++|||+|.|.+.       +...+.|+|+|..++|.+|+.+|..++.+.
T Consensus        15 ap~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~-------g~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   85 (104)
T 2ctk_A           15 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-------ELQSDIIAITGLAANLDRAKAGLLERVKEL   85 (104)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT-------TTTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCC-------CCCcceEEEEcCHHHHHHHHHHHHHHHhhH
Confidence            34789999999999999999999999999999999999742       224569999999999999999999998764

>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=98.98  E-value=3.1e-10  Score=90.76  Aligned_cols=67  Identities=21%  Similarity=0.316  Sum_probs=58.5

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHhHhCCe-EEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 012307          341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAI-ITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       341 ~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~-I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~  412 (466)
                      ..+..+|.||.+++|.|||++|.+|++|+++|||+ |.|.+     ++.+|+|.| +.+++++|+.+|...-+.
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            34678899999999999999999999999999998 99975     346999999 889999999999655443

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

Probab=98.92  E-value=1e-09  Score=89.20  Aligned_cols=71  Identities=24%  Similarity=0.367  Sum_probs=63.8

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHh-CCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENS-GASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ..++..|.||..+++.|||++|.+|++|+++| ||+|.|+..       +...+.|+|.|..++|.+|+.+|..++.+.
T Consensus        15 ~~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           15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   86 (95)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-------TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC-------CCCcceEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            66889999999999999999999999999999 999999632       345678999999999999999999998764

>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=98.79  E-value=1e-08  Score=88.19  Aligned_cols=73  Identities=21%  Similarity=0.397  Sum_probs=61.7

Q ss_pred             ccceEEEEEeccC------cccceeccccchHHHHHhHhCCeEEEecCC----------------CCCCceEEEEEc-CH
Q 012307          340 VTQITQTMQIPIS------YAEDIIGVGGTSIENIRRTSGAIITVQESR----------------GLPDEITVEIKG-TS  396 (466)
Q Consensus       340 ~~~~t~~i~IP~~------~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~----------------~~~~er~V~I~G-t~  396 (466)
                      ...++.+|.||.+      ++|.|||.+|.+||+|+++|||+|.|....                +..++-.|.|++ +.
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            4568899999988      899999999999999999999999996521                112367899999 57


Q ss_pred             HHHHHHHHHHHHHHhc
Q 012307          397 SQVQLAQQLIQEYMNN  412 (466)
Q Consensus       397 ~~V~~A~~lI~~~i~~  412 (466)
                      +.+++|+.+|+++|..
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            8999999999999976

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

Probab=98.70  E-value=4.7e-08  Score=82.39  Aligned_cols=74  Identities=12%  Similarity=0.236  Sum_probs=59.3

Q ss_pred             cceEEEEEeccC-------cccceeccccchHHHHHhHhCCeEEEecCC----------CCCCceEEEEEc-CHHHHHHH
Q 012307          341 TQITQTMQIPIS-------YAEDIIGVGGTSIENIRRTSGAIITVQESR----------GLPDEITVEIKG-TSSQVQLA  402 (466)
Q Consensus       341 ~~~t~~i~IP~~-------~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~----------~~~~er~V~I~G-t~~~V~~A  402 (466)
                      ..++.+|.||.+       ++|.|||++|.+||+|+++|||+|.|....          +..++-.|.|.+ +.+++++|
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A   89 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA   89 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHH
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHH
Confidence            446778888865       679999999999999999999999996321          112455788876 58899999


Q ss_pred             HHHHHHHHhcCc
Q 012307          403 QQLIQEYMNNHK  414 (466)
Q Consensus       403 ~~lI~~~i~~~~  414 (466)
                      +.||+++|....
T Consensus        90 ~~~Ie~Ll~~v~  101 (119)
T 2yqr_A           90 KKLCENLLQTVH  101 (119)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHhhchH
Confidence            999999998643

>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=98.58  E-value=2.1e-08  Score=80.16  Aligned_cols=67  Identities=22%  Similarity=0.153  Sum_probs=58.3

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCe-EEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGAS-VRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~-I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~  243 (466)
                      ..+...|.||.+.+|.|||++|.+|++|+++||++ |.+.          .++..|+|.| +.+++.+|+.+|..+-+.
T Consensus        13 ~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~----------eddG~V~I~g~~~ea~~~A~~~I~~ie~~   81 (91)
T 2cpq_A           13 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD----------EDTGTFRIYGESADAVKKARGFLEFVEDF   81 (91)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE----------TTTTEEEEEESSHHHHHHHHHHHSCCCCC
T ss_pred             CceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEE----------cCCCEEEEEECCHHHHHHHHHHHHhhheE
Confidence            56888999999999999999999999999999998 9995          1247899999 899999999999654433

>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=98.37  E-value=9e-07  Score=75.94  Aligned_cols=78  Identities=18%  Similarity=0.242  Sum_probs=61.9

Q ss_pred             cceEEEEEeccC------cceeeecCCchhHHHHHHHhCCeEEEecCCCCC-----------CCCCCCceEEEEec-CHH
Q 012307          167 AFCSVRLLVPST------QAINLIGKQGSLIKSIQENSGASVRVLSADEAP-----------FYVTEDERIVEMQG-EAA  228 (466)
Q Consensus       167 ~~~~~~llVP~~------~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p-----------~~~~~~er~v~I~G-~~~  228 (466)
                      ...+.+|.||.+      ++|.|||++|.+||+|+++|||+|.|..+....           .....++-.|.|.+ ..+
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e   84 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTME   84 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHH
Confidence            457889999988      889999999999999999999999997532211           00123356788888 688


Q ss_pred             HHHHHHHHHHHHhhhc
Q 012307          229 KVLKALEAVVGHLRKF  244 (466)
Q Consensus       229 ~V~~A~~~I~~~l~~~  244 (466)
                      .+.+|+++|..+|.+.
T Consensus        85 ~~~~A~~~I~~ll~~~  100 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQG  100 (131)
T ss_dssp             HHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhcc
Confidence            9999999999998764

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

Probab=98.34  E-value=1.1e-06  Score=73.97  Aligned_cols=78  Identities=15%  Similarity=0.133  Sum_probs=58.9

Q ss_pred             cceEEEEEeccC-------cceeeecCCchhHHHHHHHhCCeEEEecCCCC---C--CCCCCCceEEEEec-CHHHHHHH
Q 012307          167 AFCSVRLLVPST-------QAINLIGKQGSLIKSIQENSGASVRVLSADEA---P--FYVTEDERIVEMQG-EAAKVLKA  233 (466)
Q Consensus       167 ~~~~~~llVP~~-------~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~---p--~~~~~~er~v~I~G-~~~~V~~A  233 (466)
                      ...+.+|.||.+       ++|.|||++|.+||+|+++|||+|.|..+...   +  .....++-.|.|.+ +.+++.+|
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A   89 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA   89 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHH
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHH
Confidence            457788888865       67999999999999999999999999743211   0  00012344566765 69999999


Q ss_pred             HHHHHHHhhhc
Q 012307          234 LEAVVGHLRKF  244 (466)
Q Consensus       234 ~~~I~~~l~~~  244 (466)
                      +.+|.++|.+.
T Consensus        90 ~~~Ie~Ll~~v  100 (119)
T 2yqr_A           90 KKLCENLLQTV  100 (119)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHhhch
Confidence            99999998864

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.28  E-value=9e-07  Score=76.44  Aligned_cols=72  Identities=15%  Similarity=0.354  Sum_probs=55.9

Q ss_pred             eEEEEEeccC------cccceeccccchHHHHHhHhCCeEEEecCCC------------------CCCceEEEEEcC-H-
Q 012307          343 ITQTMQIPIS------YAEDIIGVGGTSIENIRRTSGAIITVQESRG------------------LPDEITVEIKGT-S-  396 (466)
Q Consensus       343 ~t~~i~IP~~------~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~------------------~~~er~V~I~Gt-~-  396 (466)
                      ++.+|.||.+      ++|.|||.+|.++|+|+++|||+|.|.....                  ..++-.|.|++. + 
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            4567788854      5999999999999999999999999975210                  112348889984 3 


Q ss_pred             ----HHHHHHHHHHHHHHhcCc
Q 012307          397 ----SQVQLAQQLIQEYMNNHK  414 (466)
Q Consensus       397 ----~~V~~A~~lI~~~i~~~~  414 (466)
                          ..++.|+.+|+.+|....
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p~~  103 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVPAA  103 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCS
T ss_pred             hhHHHHHHHHHHHHHHHCCCCC
Confidence                279999999999997543

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.05  E-value=2.6e-06  Score=73.56  Aligned_cols=39  Identities=31%  Similarity=0.417  Sum_probs=35.5

Q ss_pred             eEEEEEecccc------cceeeecCChhHHHHHHHhCceEEEeCC
Q 012307           78 CVFRMIVPVLK------VGSIIGRKGELIKKTCEDTRARIKVLDG  116 (466)
Q Consensus        78 ~~~rllvp~~~------vG~IIGk~G~~Ik~I~~etga~I~v~~~  116 (466)
                      +..||.||.+.      +|.|||++|.++|+|+++|||+|.|...
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGk   46 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGK   46 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEEST
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecC
Confidence            56789999776      9999999999999999999999999854

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

Probab=98.00  E-value=1.5e-05  Score=67.45  Aligned_cols=69  Identities=12%  Similarity=0.156  Sum_probs=61.3

Q ss_pred             EEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCc
Q 012307          345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHK  414 (466)
Q Consensus       345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~  414 (466)
                      ..+.|..+.++.|||++|+.|++|+..|.+.|+|+.-. .+++-.|+|-|++..-+.|+.+|+...+-++
T Consensus        58 lVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~-s~g~tEVtIfG~~~~Q~rak~MI~sLA~~hr  126 (140)
T 3v69_A           58 KRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWG-PERRAEIWIFGPPPFRRDVDRMLTDLAHYCR  126 (140)
T ss_dssp             EEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC-TTSCEEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC-CCCcEEEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            45889999999999999999999999999999998653 3578899999999999999999998877553

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.92  E-value=1.1e-05  Score=86.44  Aligned_cols=61  Identities=25%  Similarity=0.458  Sum_probs=53.1

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcC-HHHHHHHHHHHHHHH
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGT-SSQVQLAQQLIQEYM  410 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt-~~~V~~A~~lI~~~i  410 (466)
                      ...|.||.+++|.|||+||.+||.|+++|||+|.|.+      +-.|.|.|+ .+.+++|+.+|.+++
T Consensus       568 ~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d------~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          568 VETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD------EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS------SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             EEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC------CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            5679999999999999999999999999999999963      358999997 578999999997765

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.61  E-value=3.5e-05  Score=66.87  Aligned_cols=102  Identities=21%  Similarity=0.187  Sum_probs=73.4

Q ss_pred             eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCC
Q 012307           78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPEN  157 (466)
Q Consensus        78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~  157 (466)
                      -.+.++|+...+|..||++|++|+.|+++.|-+|.|-.-.           ..+         ...|..++.      +.
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s-----------~d~---------~~fI~naLs------PA   89 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYS-----------SDL---------ERIVKNLFP------GV   89 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECC-----------SSH---------HHHHHHHST------TS
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcC-----------CCH---------HHHHHHhcC------Cc
Confidence            4678999999999999999999999999999999886441           111         012222111      11


Q ss_pred             Ccccc--cCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEe
Q 012307          158 DVDAK--ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVL  205 (466)
Q Consensus       158 ~~~~~--~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~  205 (466)
                      .....  ...+......+.||..+.+..|||+|.+++-..+-||.+|.|.
T Consensus        90 ~V~~V~i~~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           90 KIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             CEEEEEEEEETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             eEEEEEEeecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            10000  0002456788999999999999999999999999999888774

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

Probab=97.50  E-value=0.00021  Score=60.47  Aligned_cols=70  Identities=14%  Similarity=0.050  Sum_probs=61.0

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ....|.|....++.|+|++|+.|+.|+..|++.|++..-+      .+++--|+|.|++..-.+|+.+|.++..-+
T Consensus        56 dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~------s~g~tEVtIfG~~~~Q~rak~MI~sLA~~h  125 (140)
T 3v69_A           56 DPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWG------PERRAEIWIFGPPPFRRDVDRMLTDLAHYC  125 (140)
T ss_dssp             SCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC------TTSCEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC------CCCcEEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            3477899999999999999999999999999999997432      245778999999999999999999887653

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.46  E-value=6.9e-05  Score=80.31  Aligned_cols=64  Identities=16%  Similarity=0.266  Sum_probs=53.9

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecC-HHHHHHHHHHHHHHh
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGE-AAKVLKALEAVVGHL  241 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I~~~l  241 (466)
                      ......|.||.+.++.|||++|++||.|+++|||+|.|.           ++..|.|.+. .+.+.+|+++|..++
T Consensus       565 ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~-----------d~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          565 GPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV-----------DEETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             CCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC-----------SSSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             CCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc-----------CCcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            346788999999999999999999999999999999994           1457888885 678999999987654

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.32  E-value=0.00014  Score=78.94  Aligned_cols=65  Identities=23%  Similarity=0.481  Sum_probs=11.2

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcCc
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGT-SSQVQLAQQLIQEYMNNHK  414 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt-~~~V~~A~~lI~~~i~~~~  414 (466)
                      ...|.||.++++.|||+||.+||.|.++||++|.|.+      +-.|.|.++ .+.+++|+.+|..++...+
T Consensus       571 ~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d------dG~v~I~~~~~~~~~~A~~~i~~i~~~~~  636 (726)
T 4aid_A          571 IETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND------DGVVKVSASDGAKIKAAIDWIKSITDEAE  636 (726)
T ss_dssp             -------------------------------------------------CCSCHHHHHHHHHC---------
T ss_pred             EEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC------CceEEEEeCCHHHHHHHHHHHHHHhhhhc
Confidence            3568999999999999999999999999999999964      346788775 7789999999999887543

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.23  E-value=0.00013  Score=63.21  Aligned_cols=38  Identities=32%  Similarity=0.477  Sum_probs=35.5

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEec
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLS  206 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~  206 (466)
                      ....++|+...+|..||++|++|+.|+++.|-+|.+..
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~   73 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVE   73 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEE
Confidence            57889999999999999999999999999999999874

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=96.50  E-value=0.0011  Score=72.04  Aligned_cols=66  Identities=21%  Similarity=0.362  Sum_probs=12.0

Q ss_pred             ceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhhc
Q 012307          168 FCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       168 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~~  244 (466)
                      .....+.||.+.++.|||++|.+||+|+++||++|.|.  +         +..|.|.+ ..+++.+|+.+|..++.+.
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 PKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN--D---------DGVVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             CC------------------------------------------------------CCSCHHHHHHHHHC--------
T ss_pred             CeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE--C---------CceEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence            45677889999999999999999999999999999984  1         34577776 5889999999998877643

>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=96.02  E-value=0.0045  Score=58.30  Aligned_cols=96  Identities=19%  Similarity=0.278  Sum_probs=65.5

Q ss_pred             cccceeeecCChhHHHH-HHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccc-cC
Q 012307           87 LKVGSIIGRKGELIKKT-CEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAK-AS  164 (466)
Q Consensus        87 ~~vG~IIGk~G~~Ik~I-~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~-~~  164 (466)
                      +-+|..||++|.+|+.| ++-.|=+|.|-.-.             .+.       ...|..++.      +...... ..
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s-------------~dp-------~~fi~nals------PA~V~~V~i~  179 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD-------------DDP-------ARFVANALS------PAKVVSVSVI  179 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC-------------SSH-------HHHHHHHTT------TSCCSEEEEE
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEec-------------CCH-------HHHHHhccC------CcceEEEEEE
Confidence            35999999999999999 56678888885431             110       122222211      1110000 00


Q ss_pred             CCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCC
Q 012307          165 GAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSAD  208 (466)
Q Consensus       165 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~  208 (466)
                      ........+.||..+.+.-|||+|.+++--.+-||.+|.|....
T Consensus       180 ~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  223 (251)
T 2asb_A          180 DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  223 (251)
T ss_dssp             ETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             cCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHH
Confidence            01235788999999999999999999999999999999997543

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=96.01  E-value=0.0048  Score=61.31  Aligned_cols=96  Identities=18%  Similarity=0.277  Sum_probs=67.0

Q ss_pred             cccceeeecCChhHHHHHHHh-CceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccc-cC
Q 012307           87 LKVGSIIGRKGELIKKTCEDT-RARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAK-AS  164 (466)
Q Consensus        87 ~~vG~IIGk~G~~Ik~I~~et-ga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~-~~  164 (466)
                      +-+|..||++|.+|+.|.++. |=+|.|-.-.             .+.       ...|..++.      +...... ..
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s-------------~dp-------~~fi~nals------PA~V~~V~~~  302 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD-------------DDP-------ARFVANALS------PAKVVSVSVI  302 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC-------------SSH-------HHHHHHHTT------TSCCSEEEEE
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcC-------------CCH-------HHHHHHhcC------CcceeEEEEE
Confidence            469999999999999999998 8888885431             110       112222211      1110000 00


Q ss_pred             CCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCC
Q 012307          165 GAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSAD  208 (466)
Q Consensus       165 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~  208 (466)
                      ........+.||..+.+..|||+|.+++-..+-||.+|.|....
T Consensus       303 ~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  346 (366)
T 1k0r_A          303 DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  346 (366)
T ss_dssp             ETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESS
T ss_pred             cCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHH
Confidence            01246789999999999999999999999999999999997543

>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=95.40  E-value=0.017  Score=54.33  Aligned_cols=39  Identities=18%  Similarity=0.181  Sum_probs=35.3

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCC
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESR  382 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~  382 (466)
                      +..+.||.+..+.-|||+|.||+--.+.||.+|.|....
T Consensus       185 ~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  223 (251)
T 2asb_A          185 AARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  223 (251)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             EEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHH
Confidence            567899999999999999999999999999999996543

>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=94.74  E-value=0.026  Score=56.05  Aligned_cols=38  Identities=18%  Similarity=0.191  Sum_probs=35.0

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecC
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQES  381 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~  381 (466)
                      ...+.||.+..+..|||+|.|++-..+.||.+|.|...
T Consensus       308 ~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          308 AARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             EEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            56789999999999999999999999999999999654

>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=94.69  E-value=0.027  Score=55.75  Aligned_cols=95  Identities=21%  Similarity=0.272  Sum_probs=65.2

Q ss_pred             cccceeeecCChhHHHHHHHh-CceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccccC-
Q 012307           87 LKVGSIIGRKGELIKKTCEDT-RARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKAS-  164 (466)
Q Consensus        87 ~~vG~IIGk~G~~Ik~I~~et-ga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~~~-  164 (466)
                      +-+|..||.+|.+|+.|.++. |=+|.|-.-.             .+.       ...|..++.      +.......- 
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s-------------~d~-------~~fi~nal~------Pa~v~~v~~~  298 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWS-------------DDP-------KQLIANALA------PATVIEVEIL  298 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECC-------------SSH-------HHHHHHHTC------SSCCSEEEEE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecC-------------CCH-------HHHHHHhcC------ccEEEEEEEE
Confidence            358999999999999999997 7788775331             110       012222111      100000000 


Q ss_pred             CCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecC
Q 012307          165 GAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSA  207 (466)
Q Consensus       165 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~  207 (466)
                      ........+.||..+.+.-|||+|.+++--.+-||.+|.|.+.
T Consensus       299 d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          299 DKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             ETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             cCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            0134678999999999999999999999999999999999743

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=94.07  E-value=0.0091  Score=64.93  Aligned_cols=63  Identities=27%  Similarity=0.453  Sum_probs=0.0

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGT-SSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt-~~~V~~A~~lI~~~i~~  412 (466)
                      ...|.||.++++.|||++|.+|+.|.+++|+.|.|.+      +..|.|.+. .+.+++|+.+|..++..
T Consensus       561 ~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~------dg~v~I~~~~~~~~~~a~~~i~~i~~~  624 (723)
T 3cdi_A          561 IHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED------DGTVKIAATDGEKAKHAIRRIEEITAE  624 (723)
T ss_dssp             ----------------------------------------------------------------------
T ss_pred             EEEEEECHHHhcccccccceeeeeeehhhCceEEecC------CccEEEecCCHHHHHHHHHHHHHHhhh
Confidence            4568999999999999999999999999999999964      346777765 45778888888777654

>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=92.62  E-value=0.11  Score=51.42  Aligned_cols=37  Identities=19%  Similarity=0.293  Sum_probs=34.3

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE  380 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~  380 (466)
                      +..+.||.+..+.-|||+|.||+--.+.||.+|.|..
T Consensus       304 ~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          304 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            5678999999999999999999999999999999953

>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=92.49  E-value=0.0071  Score=66.06  Aligned_cols=59  Identities=25%  Similarity=0.412  Sum_probs=19.8

Q ss_pred             EEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcC-HHHHHHHHHHHHHHH
Q 012307          346 TMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGT-SSQVQLAQQLIQEYM  410 (466)
Q Consensus       346 ~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt-~~~V~~A~~lI~~~i  410 (466)
                      .|.||.+++|.|||++|.+||.|++++|+.|.|.+      +..|.|+.. ....+.|+.+|..+.
T Consensus       601 ~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          601 TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CC------------------CTTCCCCCSCC--------------CCCBSSHHHHCC---------
T ss_pred             EEEEChHHeehcccccceeeehhhHhhCCEEEecC------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            47899999999999999999999999999999963      357888775 456777877777765

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=91.11  E-value=0.041  Score=59.86  Aligned_cols=64  Identities=17%  Similarity=0.333  Sum_probs=0.0

Q ss_pred             ceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhh
Q 012307          168 FCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLR  242 (466)
Q Consensus       168 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~  242 (466)
                      .....+.||.+.++.+||++|.+|+.|.+++|+.|.+..           +..|.|.+ ..+.+.+|.++|..++.
T Consensus       559 p~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~-----------dg~v~I~~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          559 PRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED-----------DGTVKIAATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             ceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC-----------CccEEEecCCHHHHHHHHHHHHHHhh
Confidence            455678899999999999999999999999999998841           34566655 45677778777766543

>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=88.76  E-value=0.024  Score=61.96  Aligned_cols=62  Identities=18%  Similarity=0.329  Sum_probs=20.6

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHh
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHL  241 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l  241 (466)
                      ....|.||.+..+.+||++|.+||.|++++|+.|.|..           +..|.|.. ......+|+.+|..+.
T Consensus       598 ~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~-----------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          598 RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED-----------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             BCCCC------------------CTTCCCCCSCC-------------------CCCBSSHHHHCC---------
T ss_pred             eeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC-----------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            34567799999999999999999999999999998841           44566666 4566667766665543

---

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	466
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	5e-14
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	4e-10
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	6e-09
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-13
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	9e-10
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-08
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	7e-13
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-08
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-08
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	5e-12
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-10
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-10
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	3e-11
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	1e-10
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	5e-08
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-11
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-07
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-07
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-10
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-09
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-09
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-10
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-07
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-07
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	3e-10
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	3e-09
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	3e-08
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	4e-10
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	5e-07
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	4e-10
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	2e-06
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	4e-10
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	6e-10
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	7e-09
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	7e-10
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-07
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-05
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	1e-09
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	1e-07
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	5e-07
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	8e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	0.002
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	1e-07
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	3e-04
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	7e-04
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-07
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-04
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-04
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	5e-06
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	2e-04
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	0.001
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	3e-04
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	8e-04
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.001
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.001
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	0.002
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	0.004

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.8 bits (158), Expect = 5e-14
 Identities = 20/70 (28%), Positives = 34/70 (48%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQL 401
            +T+  ++P      IIG GG  I  I++ SG  I +    G   E +  + GT   VQ 
Sbjct: 7   VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQS 66

Query: 402 AQQLIQEYMN 411
           A++L+ + + 
Sbjct: 67  AKRLLDQIVE 76

>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 = 53.7 bits (129), Expect = 4e-10
 Identities = 16/52 (30%), Positives = 27/52 (51%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
              VP   VG IIGR GE I +  +++  +I++       P+R  +++G  E
Sbjct: 11  EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPE 62

>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 = 50.6 bits (121), Expect = 6e-09
 Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 5/68 (7%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           +    VP      +IG+ G  I  IQ+ SG  +++             ER   + G    
Sbjct: 9   TEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG-----GLPERSCMLTGTPES 63

Query: 230 VLKALEAV 237
           V  A   +
Sbjct: 64  VQSAKRLL 71

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.9 bits (153), Expect = 2e-13
 Identities = 23/67 (34%), Positives = 32/67 (47%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQL 401
           Q T  + IP +    IIG  G +I  IR+ SGA I +           V I G+++ + L
Sbjct: 1   QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISL 60

Query: 402 AQQLIQE 408
           AQ LI  
Sbjct: 61  AQYLINA 67

>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 = 52.5 bits (126), Expect = 9e-10
 Identities = 16/52 (30%), Positives = 27/52 (51%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            + +P   +G IIGR+G  I +  + + A+IK+ +    S  R V I+G   
Sbjct: 5   ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAA 56

>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 = 48.3 bits (115), Expect = 2e-08
 Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           +  L +P+     +IG+QG+ I  I++ SGA +++ +  E         R V + G AA 
Sbjct: 3   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGS-----SGRQVTITGSAAS 57

Query: 230 VLKALEAVVGHL 241
           +  A   +   L
Sbjct: 58  ISLAQYLINARL 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 = 61.4 bits (149), Expect = 7e-13
 Identities = 30/77 (38%), Positives = 40/77 (51%), Gaps = 3/77 (3%)

Query: 337 GPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTS 396
           GPI   IT  + IP   A  IIG GG  I+ IR  SGA I + E     ++  + I GT 
Sbjct: 1   GPI---ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 57

Query: 397 SQVQLAQQLIQEYMNNH 413
            Q+Q AQ L+Q  +  +
Sbjct: 58  DQIQNAQYLLQNSVKQY 74

>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 = 49.9 bits (119), Expect = 1e-08
 Identities = 18/75 (24%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           + ++ +P   A ++IGK G  IK I+  SGAS+++    E       ++RI+ + G   +
Sbjct: 5   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGS-----EDRIITITGTQDQ 59

Query: 230 VLKALEAVVGHLRKF 244
           +  A   +   ++++
Sbjct: 60  IQNAQYLLQNSVKQY 74

>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 = 49.5 bits (118), Expect = 1e-08
 Identities = 18/52 (34%), Positives = 32/52 (61%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
           ++ +P    GSIIG+ G+ IK+   ++ A IK+ +    S DRI+ I+G ++
Sbjct: 7   QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD 58

>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 = 59.0 bits (143), Expect = 5e-12
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 7/73 (9%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           ++RLL+   +  ++IGK+G  +K ++E SGA + +   +         ERI+ + G    
Sbjct: 5   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-------CPERIITLAGPTNA 57

Query: 230 VLKALEAVVGHLR 242
           + KA   ++  L 
Sbjct: 58  IFKAFAMIIDKLE 70

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.2 bits (133), Expect = 1e-10
 Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 2/69 (2%)

Query: 343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLA 402
           +T  + +       IIG  G S++ +R  SGA I +  S G   E  + + G ++ +  A
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLAGPTNAIFKA 61

Query: 403 QQLIQEYMN 411
             +I + + 
Sbjct: 62  FAMIIDKLE 70

>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 = 54.0 bits (130), Expect = 3e-10
 Identities = 21/53 (39%), Positives = 36/53 (67%), Gaps = 2/53 (3%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            R+++   +VGSIIG+KGE +KK  E++ ARI + +G  + P+RI+ ++G   
Sbjct: 6   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTN 56

>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 = 56.8 bits (137), Expect = 3e-11
 Identities = 20/57 (35%), Positives = 31/57 (54%)

Query: 76  GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
           G  +  + +P   VG +IGR GE+IKK   D   RI+      ++P+RI  I+G  +
Sbjct: 1   GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPD 57

>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 = 55.3 bits (133), Expect = 1e-10
 Identities = 16/67 (23%), Positives = 29/67 (43%)

Query: 346 TMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQL 405
            + IP      +IG  G  I+ I+  +G  I  +   G   E   +I G   + Q A ++
Sbjct: 6   DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEI 65

Query: 406 IQEYMNN 412
           I + + +
Sbjct: 66  ITDLLRS 72

>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 = 47.6 bits (113), Expect = 5e-08
 Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAA 228
             + + +P      +IG+ G +IK IQ ++G  ++    D      T  ERI ++ G   
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG-----TTPERIAQITGPPD 57

Query: 229 KVLKALEAVVGHLR 242
           +   A E +   LR
Sbjct: 58  RAQHAAEIITDLLR 71

>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 = 57.0 bits (138), Expect = 3e-11
 Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 2/68 (2%)

Query: 341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQ 400
           TQ + T+ IP  +   +IG  G  ++++   +   I +       ++I   I GT   ++
Sbjct: 8   TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIK--ITGTKEGIE 65

Query: 401 LAQQLIQE 408
            A+  +  
Sbjct: 66  KARHEVLL 73

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (112), Expect = 1e-07
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 2/52 (3%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            + +P      +IG+ GE ++     T  +I++       P   + I+G +E
Sbjct: 13  TVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSNQIKITGTKE 62

>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 = 45.9 bits (109), Expect = 3e-07
 Identities = 11/68 (16%), Positives = 27/68 (39%), Gaps = 7/68 (10%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           S  + +P      +IGK G  ++ ++  +   +++   D       +    +++ G    
Sbjct: 11  SATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEG 63

Query: 230 VLKALEAV 237
           + KA   V
Sbjct: 64  IEKARHEV 71

>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 = 17/70 (24%), Positives = 30/70 (42%), Gaps = 3/70 (4%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLP---DEITVEIKGTSSQ 398
           +    M +P +    I+G GG ++   +  +GA I + +            V I G+ + 
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

Query: 399 VQLAQQLIQE 408
            Q AQ LI +
Sbjct: 62  TQAAQYLISQ 71

>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 = 52.1 bits (125), Expect = 2e-09
 Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 2/67 (2%)

Query: 171 VRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKV 230
           V + VP      ++GK G  +   QE +GA +++    E  F      R V + G  A  
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGE--FLPGTRNRRVTITGSPAAT 62

Query: 231 LKALEAV 237
             A   +
Sbjct: 63  QAAQYLI 69

>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 = 51.7 bits (124), Expect = 2e-09
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 79  VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL---DGPVSSPDRIVLISGKEE 132
           +  M VP   VG+I+G+ G+ + +  E T ARI++    +    + +R V I+G   
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPA 60

>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 = 55.2 bits (133), Expect = 2e-10
 Identities = 14/74 (18%), Positives = 24/74 (32%), Gaps = 1/74 (1%)

Query: 339 IVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITV-QESRGLPDEITVEIKGTSS 397
            +     ++ +   Y   IIG  G  I  IR      I    +  G   +  + I G   
Sbjct: 6   ALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK 65

Query: 398 QVQLAQQLIQEYMN 411
             + A+  I   + 
Sbjct: 66  NTEAARDAILRIVG 79

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (112), Expect = 1e-07
 Identities = 10/68 (14%), Positives = 28/68 (41%), Gaps = 4/68 (5%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
            + + V       +IG++G++I  I+     +++    D+      + +  + + G    
Sbjct: 11  KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG----NQPQDQITITGYEKN 66

Query: 230 VLKALEAV 237
              A +A+
Sbjct: 67  TEAARDAI 74

>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 = 46.4 bits (110), Expect = 2e-07
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLD-GPVSSPDRIVLISGKEE 132
            + V       IIGRKG +I +   +    I+  D    + P   + I+G E+
Sbjct: 13  SVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK 65

>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 = 53.7 bits (129), Expect = 3e-10
 Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 3/66 (4%)

Query: 346 TMQIPISYAEDIIGVGGTSIENIRRTSGAIITV---QESRGLPDEITVEIKGTSSQVQLA 402
              +P      IIG GG +I++I + SGA I +         P+     I+GT  Q+  A
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYA 63

Query: 403 QQLIQE 408
           +QLI+E
Sbjct: 64  RQLIEE 69

>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 = 51.1 bits (122), Expect = 3e-09
 Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 3/56 (5%)

Query: 80  FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKV---LDGPVSSPDRIVLISGKEE 132
           F  IVP  K G IIG+ GE IK   + + ARI++            ++  I G  +
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQ 58

>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 = 48.0 bits (114), Expect = 3e-08
 Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 171 VRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKV 230
              +VP+ +   +IGK G  IKSI + SGA + +      P     + ++  ++G   ++
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIEL--QRNPPPNADPNMKLFTIRGTPQQI 60

Query: 231 LKALEAV 237
             A + +
Sbjct: 61  DYARQLI 67

>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 = 54.4 bits (131), Expect = 4e-10
 Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 2/68 (2%)

Query: 341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQ 400
             +T  +++P      +IG  G+ I  +       I V           + I G ++ + 
Sbjct: 8   VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL--QSDIIAITGLAANLD 65

Query: 401 LAQQLIQE 408
            A+  + E
Sbjct: 66  RAKAGLLE 73

>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 = 46.7 bits (111), Expect = 2e-07
 Identities = 14/79 (17%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           ++ + VP      +IG++GS I+ + +    ++ V + +           I+ + G AA 
Sbjct: 11  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAAN 63

Query: 230 VLKALEAVVGHLRKFLVDQ 248
           + +A   ++  +++   +Q
Sbjct: 64  LDRAKAGLLERVKELQAEQ 82

>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 = 45.6 bits (108), Expect = 5e-07
 Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 2/52 (3%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            + VP      +IG+KG  I+K  ++    I V          I+ I+G   
Sbjct: 13  EVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAITGLAA 62

>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 = 53.6 bits (129), Expect = 4e-10
 Identities = 12/70 (17%), Positives = 25/70 (35%), Gaps = 2/70 (2%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQL 401
                + I   +   +IG  G +I  I+      + +           + I+G    VQ 
Sbjct: 4   MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI--PPDSEKSNLIRIEGDPQGVQQ 61

Query: 402 AQQLIQEYMN 411
           A++ + E  +
Sbjct: 62  AKRELLELAS 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 = 43.2 bits (102), Expect = 2e-06
 Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 7/68 (10%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
            V + +      +LIGK G+ I  I++    SVR+           E   ++ ++G+   
Sbjct: 6   YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQG 58

Query: 230 VLKALEAV 237
           V +A   +
Sbjct: 59  VQQAKREL 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 = 8/52 (15%), Positives = 21/52 (40%), Gaps = 2/52 (3%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            + +       +IG+ G  I +  +  +  +++   P S    ++ I G  +
Sbjct: 8   EINIDHKFHRHLIGKSGANINRIKDQYKVSVRI--PPDSEKSNLIRIEGDPQ 57

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.8 bits (129), Expect = 4e-10
 Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPD--EITVEIKGTSSQV 399
              Q + IP S A  +IG GG +I+ ++  +G  + + +        +  + I G   +V
Sbjct: 7   NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKV 66

Query: 400 QLAQQLIQEYMNN 412
           Q A++++ E + +
Sbjct: 67  QQAKEMVLELIRD 79

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.4 bits (128), Expect = 6e-10
 Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 75  PGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGP--VSSPDRIVLISGKEE 132
           PG+ V  +++P  K G +IG+ GE IK+  E    ++ ++      +  D+ + I+G   
Sbjct: 5   PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPY 64

>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 = 50.3 bits (120), Expect = 7e-09
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 3/78 (3%)

Query: 165 GAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQ 224
           G       +++P+++A  +IGK G  IK +QE +G  + ++         T  ++ + + 
Sbjct: 4   GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRIT 60

Query: 225 GEAAKVLKALEAVVGHLR 242
           G+  KV +A E V+  +R
Sbjct: 61  GDPYKVQQAKEMVLELIR 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 = 53.3 bits (128), Expect = 7e-10
 Identities = 17/73 (23%), Positives = 27/73 (36%), Gaps = 5/73 (6%)

Query: 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQL 401
            +++ + +       IIG  G +I  I       I      G PD   V + G    V+ 
Sbjct: 9   MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-PQSGAPDPNCVTVTGLPENVEE 67

Query: 402 AQQLI----QEYM 410
           A   I    +EY+
Sbjct: 68  AIDHILNLEEEYL 80

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 6/76 (7%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
           S  + +       +IG +G  I+ I +     +R       P     D   V + G    
Sbjct: 11  SEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF------PQSGAPDPNCVTVTGLPEN 64

Query: 230 VLKALEAVVGHLRKFL 245
           V +A++ ++    ++L
Sbjct: 65  VEEAIDHILNLEEEYL 80

>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 = 40.6 bits (95), Expect = 2e-05
 Identities = 10/52 (19%), Positives = 22/52 (42%), Gaps = 1/52 (1%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
            + +       IIG +G+ I+K  ++ +  I+      +     V ++G  E
Sbjct: 13  DVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-PQSGAPDPNCVTVTGLPE 63

>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 = 53.1 bits (127), Expect = 1e-09
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITV--QESRGLPDEITVEIKGTSSQ 398
           T + + + +P      IIG GG +I +I + SGA IT   +    L     ++I GT  +
Sbjct: 13  TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE 72

Query: 399 VQLAQQLIQEYMNNHKE 415
           V  A+ LI E ++  +E
Sbjct: 73  VAAAKHLILEKVSEDEE 89

>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 = 47.3 bits (112), Expect = 1e-07
 Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 3/73 (4%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229
             +L VP      +IG+ G  I+SI + SGA +     D+         R++++ G   +
Sbjct: 16  FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITC---DKESEGTLLLSRLIKISGTQKE 72

Query: 230 VLKALEAVVGHLR 242
           V  A   ++  + 
Sbjct: 73  VAAAKHLILEKVS 85

>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 = 45.7 bits (108), Expect = 5e-07
 Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 79  VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG--PVSSPDRIVLISGKEE 132
             ++ VP   VG IIGR GE I+  C+ + A+I             R++ ISG ++
Sbjct: 16  FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQK 71

>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 = 46.6 bits (111), Expect = 8e-08
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 6/57 (10%)

Query: 79  VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEA 135
           +  + +PV K+G +IG K ++I +  EDT A I + D      D  + I   + P A
Sbjct: 4   IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADGPAA 54

>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 = 34.2 bits (79), Expect = 0.002
 Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 6/55 (10%)

Query: 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQ 398
             T++IP+    ++IG     I  I+  +GA IT++      D+ T+ I      
Sbjct: 4   IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAADGP 52

>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 = 46.8 bits (111), Expect = 1e-07
 Identities = 16/70 (22%), Positives = 27/70 (38%), Gaps = 1/70 (1%)

Query: 339 IVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQ 398
           +       + IP      +IG  G  I +I    G +  +          TV I+G SS 
Sbjct: 6   LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVH-IHFPVEGSGSDTVVIRGPSSD 64

Query: 399 VQLAQQLIQE 408
           V+ A++ +  
Sbjct: 65  VEKAKKQLLH 74

>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 = 37.1 bits (86), Expect = 3e-04
 Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 3/53 (5%)

Query: 81  RMIVPVLKVGSIIGRKGELIKKTCED-TRARIKVLDGPVSSPDRIVLISGKEE 132
            + +P     S+IG KG LI+   E+     I        S    V+I G   
Sbjct: 13  EVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHF--PVEGSGSDTVVIRGPSS 63

>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 = 7e-04
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 8/69 (11%)

Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENS-GASVRVLSADEAPFYVTEDERIVEMQGEAA 228
            V + +P+    +LIG +G LI+SI E   G  +                  V ++G ++
Sbjct: 11  EVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-------SGSDTVVIRGPSS 63

Query: 229 KVLKALEAV 237
            V KA + +
Sbjct: 64  DVEKAKKQL 72

>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 = 46.7 bits (111), Expect = 1e-07
 Identities = 11/64 (17%), Positives = 27/64 (42%), Gaps = 6/64 (9%)

Query: 345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQ 404
           + + I  +    +IG  G+ I+ ++      I V ++        + + G   +V +A++
Sbjct: 3   RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNG------LIWVNGDRRKVSIAEE 56

Query: 405 LIQE 408
            I  
Sbjct: 57  AIYL 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 = 38.6 bits (90), Expect = 1e-04
 Identities = 10/49 (20%), Positives = 22/49 (44%), Gaps = 6/49 (12%)

Query: 84  VPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
           +   +V  +IG+KG +IK    +   +I V        + ++ ++G   
Sbjct: 7   INPARVPRVIGKKGSMIKLLKSELDVQIVVGQ------NGLIWVNGDRR 49

>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 = 38.6 bits (90), Expect = 1e-04
 Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 11/63 (17%)

Query: 175 VPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKAL 234
           +   +   +IGK+GS+IK ++      + V               ++ + G+  KV  A 
Sbjct: 7   INPARVPRVIGKKGSMIKLLKSELDVQIVV-----------GQNGLIWVNGDRRKVSIAE 55

Query: 235 EAV 237
           EA+
Sbjct: 56  EAI 58

>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 = 42.5 bits (100), Expect = 5e-06
 Identities = 10/63 (15%), Positives = 22/63 (34%)

Query: 346 TMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQL 405
            +++       +IG  G     I R +G +ITV     +              +  A ++
Sbjct: 6   YVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEV 65

Query: 406 IQE 408
           ++ 
Sbjct: 66  VKA 68

>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 = 37.8 bits (88), Expect = 2e-04
 Identities = 14/70 (20%), Positives = 24/70 (34%), Gaps = 5/70 (7%)

Query: 175 VPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKAL 234
           V   +   +IG +G +   I   +G  + V + +       E E           ++KA 
Sbjct: 9   VKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAE-----GIPPVNLMKAA 63

Query: 235 EAVVGHLRKF 244
           E V      F
Sbjct: 64  EVVKAISLGF 73

>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 = 35.9 bits (83), Expect = 0.001
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 5/60 (8%)

Query: 82  MIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAM 141
           + V   ++G++IG +GE+  +    T   I      V + + +V++  + E   PV+   
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVIT-----VDTENSMVIVEPEAEGIPPVNLMK 61

>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 = 37.2 bits (86), Expect = 3e-04
 Identities = 8/70 (11%), Positives = 22/70 (31%), Gaps = 3/70 (4%)

Query: 339 IVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQ 398
           +     +   +        IG  G++I+  R+  G      +              ++  
Sbjct: 4   LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE---DTGTFRIYGESADA 60

Query: 399 VQLAQQLIQE 408
           V+ A+  ++ 
Sbjct: 61  VKKARGFLEF 70

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (84), Expect = 8e-04
 Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 6/69 (8%)

Query: 341 TQITQTMQIPISYAEDIIGVGGTSIENIR-RTSGAIITVQESRGLPDEITVEIKGTSSQV 399
           +    ++  P      IIG  G ++  I  +     I          E  + ++G +  V
Sbjct: 19  SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFT-----EGEDKITLEGPTEDV 73

Query: 400 QLAQQLIQE 408
            +AQ+ I+ 
Sbjct: 74  SVAQEQIEG 82

>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 = 35.5 bits (82), Expect = 0.001
 Identities = 6/68 (8%), Positives = 23/68 (33%), Gaps = 12/68 (17%)

Query: 84  VPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDA 143
           +  +KV  +IG+   + +     +   I V +      +  +  +           + + 
Sbjct: 7   IMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN------NGRIWATCPSR------FSEEI 54

Query: 144 AVRVFKRV 151
            +   +++
Sbjct: 55  LIEAIRKI 62

>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 = 35.1 bits (81), Expect = 0.001
 Identities = 10/65 (15%), Positives = 21/65 (32%), Gaps = 7/65 (10%)

Query: 345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTS-SQVQLAQ 403
             + I       +IG   +  E +   SG  I V  +        +     S    ++  
Sbjct: 3   IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNG------RIWATCPSRFSEEILI 56

Query: 404 QLIQE 408
           + I++
Sbjct: 57  EAIRK 61

>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 = 35.1 bits (81), Expect = 0.002
 Identities = 7/65 (10%), Positives = 23/65 (35%), Gaps = 7/65 (10%)

Query: 345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQ-VQLAQ 403
           + ++I  +    +IG   + ++ +   +   I V           + ++  +     +A 
Sbjct: 3   KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVA------RNGRIHLECPNEDLEAIAV 56

Query: 404 QLIQE 408
             I+ 
Sbjct: 57  MAIKI 61

>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 = 34.3 bits (79), Expect = 0.004
 Identities = 18/79 (22%), Positives = 27/79 (34%), Gaps = 18/79 (22%)

Query: 84  VPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDA 143
           +   KV  +IGRK  ++K   E T  +I V        +  + +    E           
Sbjct: 7   ISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR------NGRIHLECPNE------DLEAI 54

Query: 144 AVRVFK------RVSGLPE 156
           AV   K        SGL +
Sbjct: 55  AVMAIKIIDEEAYTSGLTK 73

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	466
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.7
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.65
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.62
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.61
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.61
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.6
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.56
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.51
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.5
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.49
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.49
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.48
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.48
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.47
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.47
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.47
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.46
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.45
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.44
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.43
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.39
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.39
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.36
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.35
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.32
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.32
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.3
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.25
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.25
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.24
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.21
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.16
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.06
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.01
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.01
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.0
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.91
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.83
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.66
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.64
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.64
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.63
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.6
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.43
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.22
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.15
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.98
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.73
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.65
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.24
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	95.08
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.17
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.07
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	89.73
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	88.86

>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=99.70  E-value=1.2e-17  Score=126.92  Aligned_cols=70  Identities=33%  Similarity=0.457  Sum_probs=65.9

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 012307          342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMN  411 (466)
Q Consensus       342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~  411 (466)
                      ++|.+|.||.+++|+||||+|.+|++|+++|||+|.|+++.+++++|+|+|+|++++|+.|++||+++|+
T Consensus         1 q~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~is   70 (70)
T d1wvna1           1 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLS   70 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHHHHHHHHHHHHHcC
Confidence            3688999999999999999999999999999999999888777889999999999999999999999874

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=5.5e-17  Score=125.01  Aligned_cols=71  Identities=38%  Similarity=0.533  Sum_probs=67.3

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      +|.+|.||.+++|+||||+|++|++|+++|||+|+|.++.+..++|+|+|+|++++|+.|+.||+++|++.
T Consensus         4 ~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           4 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             EEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            68899999999999999999999999999999999988777788999999999999999999999999863

>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=99.65  E-value=7.4e-17  Score=123.92  Aligned_cols=71  Identities=23%  Similarity=0.343  Sum_probs=66.6

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|.+..+...+|.|+|+|++++|+.|+.+|.++|++.
T Consensus         3 ~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            46889999999999999999999999999999999988777778999999999999999999999999864

>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=99.62  E-value=3.1e-16  Score=119.37  Aligned_cols=67  Identities=34%  Similarity=0.511  Sum_probs=60.6

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCC---CCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESR---GLPDEITVEIKGTSSQVQLAQQLIQEYM  410 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~---~~~~er~V~I~Gt~~~V~~A~~lI~~~i  410 (466)
                      ..+|.||.+++|+||||+|++|++|++.|||+|+|++..   ...++|+|+|+|++++|+.|+.||+++|
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            468999999999999999999999999999999997643   2456899999999999999999999875

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=3.1e-16  Score=121.98  Aligned_cols=73  Identities=27%  Similarity=0.434  Sum_probs=68.6

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCc
Q 012307          342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHK  414 (466)
Q Consensus       342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~  414 (466)
                      .++.+|.||.+++|+|||++|.+|++|++.|||+|.|.++..+.+++.|+|+|++++|+.|+.+|.++|++.+
T Consensus         7 ~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~r   79 (79)
T d1x4na1           7 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGR   79 (79)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             cEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHccC
Confidence            4789999999999999999999999999999999999887777889999999999999999999999998753

>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=99.61  E-value=3.7e-16  Score=118.89  Aligned_cols=69  Identities=23%  Similarity=0.348  Sum_probs=63.7

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 012307          342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~  412 (466)
                      .++.+|.||.+++|+||||+|.+|++|++.|||+|+|+++.  ..+|+|+|+|++++|++|+.+|.++|++
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 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN--CPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC--CSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCC--CCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            36899999999999999999999999999999999997643  4689999999999999999999999874

>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=99.60  E-value=6.4e-16  Score=118.57  Aligned_cols=69  Identities=25%  Similarity=0.364  Sum_probs=62.2

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG---LPDEITVEIKGTSSQVQLAQQLIQEYMN  411 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~---~~~er~V~I~Gt~~~V~~A~~lI~~~i~  411 (466)
                      .+.+|.||.+++|+||||+|++|++|++.|||+|+|.+..+   ..++|.|+|+|++++|+.|+.||+++|.
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~is   74 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVT   74 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHcC
Confidence            35789999999999999999999999999999999976432   3568999999999999999999999873

>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=99.56  E-value=1.3e-15  Score=118.91  Aligned_cols=71  Identities=24%  Similarity=0.435  Sum_probs=64.9

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCC--CCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 012307          342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESR--GLPDEITVEIKGTSSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~--~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~  412 (466)
                      +++.+|.||.+++|+||||+|++|++|+++|||+|+|.+..  ....+|+|+|+|++++|+.|++||+++|.+
T Consensus         7 ~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           7 NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             cEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            57899999999999999999999999999999999997643  345689999999999999999999999975

>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=99.51  E-value=1.6e-14  Score=118.08  Aligned_cols=74  Identities=31%  Similarity=0.460  Sum_probs=66.4

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC--CCCceEEEEEcCHHHHHHHHHHHHHHHhcCc
Q 012307          341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG--LPDEITVEIKGTSSQVQLAQQLIQEYMNNHK  414 (466)
Q Consensus       341 ~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~--~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~  414 (466)
                      +.++.+|.||.+++|+||||+|.+|++|+++|||+|+|.+..+  ...+|+|+|+|++++|+.|+.+|+++|.+..
T Consensus        13 ~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T d1we8a_          13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhCcH
Confidence            4578899999999999999999999999999999999976533  3468999999999999999999999998654

>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=99.50  E-value=1.2e-14  Score=110.38  Aligned_cols=70  Identities=27%  Similarity=0.534  Sum_probs=63.7

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhh
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  243 (466)
                      ..++++|+||..++|.||||+|++|++|+++|||+|++.+.       ...+|+|+|+|++++|.+|+.+|.++|++
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~-------~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC-------CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            35789999999999999999999999999999999999742       35589999999999999999999999874

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=3.3e-14  Score=109.15  Aligned_cols=73  Identities=23%  Similarity=0.446  Sum_probs=65.7

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ...+.++.||..++|+||||+|++|++|+++|||+|++.+.+  +   +..+|+|+|+|++++|.+|+.+|.++|+++
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--E---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT--S---CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCC--C---CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            346889999999999999999999999999999999996432  2   577999999999999999999999999875

>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=99.49  E-value=2.9e-14  Score=109.16  Aligned_cols=71  Identities=23%  Similarity=0.281  Sum_probs=63.0

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHh
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHL  241 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l  241 (466)
                      ..++|+||..++|.||||+|++|++|+++|||+|+|.+.++.  ..+..+|+|+|+|++++|.+|+.+|.++|
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            457999999999999999999999999999999999865432  22678999999999999999999998875

>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=99.48  E-value=2.9e-14  Score=108.20  Aligned_cols=70  Identities=23%  Similarity=0.414  Sum_probs=61.7

Q ss_pred             EEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHh
Q 012307          170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHL  241 (466)
Q Consensus       170 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l  241 (466)
                      ..+|+||..++|+||||+|++|++|+++|||+|+|.+... + ..+..+|+|+|+|++++|.+|+.+|.++|
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-P-NADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT-T-TSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCC-C-CCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            4689999999999999999999999999999999985432 2 23677899999999999999999998864

>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=99.48  E-value=1.4e-14  Score=112.88  Aligned_cols=75  Identities=25%  Similarity=0.424  Sum_probs=67.6

Q ss_pred             CcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhh
Q 012307          166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  243 (466)
                      +...+.+|+||..++|+||||+|++|++|+++|||+|+|.+.+..+   ...+|.|+|+|++++|.+|+.+|.++|++
T Consensus         5 ~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           5 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS---SCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            4678999999999999999999999999999999999998644333   56789999999999999999999999875

>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=99.47  E-value=2e-14  Score=111.95  Aligned_cols=72  Identities=21%  Similarity=0.264  Sum_probs=64.3

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       341 ~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      ..++.+|.||..++++|||++|++|++|+++|||+|+|++... .+++.|+|+|++++|++|+.+|+++++++
T Consensus         8 ~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~-~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           8 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA-PDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC-SCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC-CCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            4578899999999999999999999999999999999976433 34578999999999999999999998864

>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=99.47  E-value=2.8e-14  Score=109.27  Aligned_cols=71  Identities=27%  Similarity=0.442  Sum_probs=64.6

Q ss_pred             ceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhh
Q 012307          168 FCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       168 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  243 (466)
                      ...++|.||.+++|.||||+|++|++|+++|||+|+|...+  +   +..+|+|+|+|++++|.+|+.+|.++|++
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~--~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   72 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD--G---TTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT--T---SCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCC--C---CCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            46799999999999999999999999999999999998543  2   56789999999999999999999999875

>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=99.47  E-value=2.1e-14  Score=111.92  Aligned_cols=71  Identities=18%  Similarity=0.298  Sum_probs=64.7

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       341 ~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      ++++.+|.||..++|+|||++|.+|++|+++|||+|+|++..  ..++.|+|+|++++|++|+.+|++++++.
T Consensus         8 ~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~--~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           8 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD--DPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT--SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC--CCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            457899999999999999999999999999999999996543  46789999999999999999999999864

>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=99.46  E-value=4.2e-14  Score=106.99  Aligned_cols=68  Identities=26%  Similarity=0.378  Sum_probs=61.7

Q ss_pred             eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHh
Q 012307          169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHL  241 (466)
Q Consensus       169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l  241 (466)
                      .+.+|+||..++|+||||+|.+|++|+++|||+|.|.+..  +   +..+|+|+|+|++++|.+|+.+|.++|
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--E---GSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCC--T---TCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCC--C---CCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            5789999999999999999999999999999999996432  2   577899999999999999999998876

>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=99.45  E-value=3.5e-14  Score=107.74  Aligned_cols=66  Identities=18%  Similarity=0.280  Sum_probs=60.1

Q ss_pred             eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 012307          343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYM  410 (466)
Q Consensus       343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i  410 (466)
                      .+.+|.||..++++|||++|++|++|+++|||+|+|+++  ..+++.|+|+|++++|+.|+.+|++++
T Consensus         5 ~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~--~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           5 DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD--SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             EEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC--CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             EEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC--CCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            567899999999999999999999999999999999653  346789999999999999999998864

>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=99.44  E-value=7.2e-14  Score=109.62  Aligned_cols=72  Identities=19%  Similarity=0.291  Sum_probs=64.8

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecC-CCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQES-RGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~-~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      ..+.+|.||..++++|||++|++|++|+++|||+|+|++. .....++.|+|+|+.++|+.|+.+|+++|.+.
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            4678899999999999999999999999999999999654 33466889999999999999999999999864

>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=99.43  E-value=4.3e-14  Score=110.41  Aligned_cols=72  Identities=24%  Similarity=0.313  Sum_probs=63.6

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHhHh-CCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCc
Q 012307          341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTS-GAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHK  414 (466)
Q Consensus       341 ~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~S-GA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~  414 (466)
                      +.++.+|.||..++|+|||++|++|++|++++ +++|++++.  +..++.|+|+|++++|+.|+.+|++++++.+
T Consensus         8 ~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~--~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~~   80 (82)
T d2ctja1           8 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE--GSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   80 (82)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT--TTTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             CcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC--CCCCceEEEeCCHHHHHHHHHHHHHHHhhhh
Confidence            45688999999999999999999999999874 899988543  3467899999999999999999999998754

>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=99.39  E-value=2.2e-13  Score=105.44  Aligned_cols=72  Identities=22%  Similarity=0.282  Sum_probs=65.7

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhh
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  243 (466)
                      ..++.+|.||..++|+|||++|.+|++|+++|||+|.|.+.+  +   +..+|.|+|+|++++|.+|+.+|.++|++
T Consensus         6 ~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~--~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   77 (79)
T d1x4na1           6 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS--G---GLPERSCMLTGTPESVQSAKRLLDQIVEK   77 (79)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC--T---TCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCC--C---CCCceEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            568899999999999999999999999999999999997432  2   57799999999999999999999999875

>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=99.39  E-value=3.1e-13  Score=110.27  Aligned_cols=75  Identities=23%  Similarity=0.302  Sum_probs=66.7

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ..++.+|+||..++|+||||+|.+||+|+++|||+|.|.+.+...   ...+|+|+|+|++++|.+|+.+|.++|++.
T Consensus        13 ~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT---LLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS---SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCC---CCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            568899999999999999999999999999999999997543322   467899999999999999999999999764

>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=99.36  E-value=3.3e-13  Score=107.41  Aligned_cols=70  Identities=17%  Similarity=0.255  Sum_probs=63.6

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      .++.+|.||..++++|||++|.+|++|+++|||+|.|++.  +.+++.|+|+|++++|+.|+.+|++++.+.
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~--~~~~~~v~I~G~~~~V~~A~~~I~~~v~e~   78 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP--ELQSDIIAITGLAANLDRAKAGLLERVKEL   78 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT--TTTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC--CCCcceEEEECCHHHHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999999654  346779999999999999999999999764

>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=99.35  E-value=4.5e-13  Score=104.20  Aligned_cols=73  Identities=18%  Similarity=0.318  Sum_probs=65.0

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhcc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFL  245 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~  245 (466)
                      ...+.++.||..+++.|||++|++|++|+++|||+|+|++.+      ..+.+.|+|+|++++|.+|+++|.+++++++
T Consensus         8 ~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~------~~~~~~v~I~G~~~~V~~A~~~I~~i~~e~~   80 (81)
T d2ctma1           8 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG------APDPNCVTVTGLPENVEEAIDHILNLEEEYL   80 (81)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT------CSCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCcc------CCCCCEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            557789999999999999999999999999999999997533      2345789999999999999999999999874

>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=99.32  E-value=1.8e-13  Score=105.24  Aligned_cols=66  Identities=18%  Similarity=0.272  Sum_probs=58.0

Q ss_pred             ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Q 012307          342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMN  411 (466)
Q Consensus       342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~  411 (466)
                      ..+.+|.||.+++|+|||++|++|++||+.|||+|.+.+.    +++.|+|.| ++++|++|+.||+.+.+
T Consensus         7 ~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~----~~g~v~I~g~~~eav~~A~~~Ie~~~~   73 (78)
T d2cpqa1           7 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGESADAVKKARGFLEFVED   73 (78)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----TTTEEEEEESSHHHHHHHHHHHSCCCC
T ss_pred             CceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC----CCceEEEEECCHHHHHHHHHHHHHhhe
Confidence            4688999999999999999999999999999999998653    346899999 79999999999965443

>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=99.32  E-value=1.2e-12  Score=102.49  Aligned_cols=74  Identities=14%  Similarity=0.271  Sum_probs=65.7

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ...+++|.||..+++.|||++|++|++|+++|||+|.|++.+. +   +..++.|+|+|+.++|.+|+.+|.+++++.
T Consensus         8 ~~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~-~---~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           8 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-G---NQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-C---SSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC-C---CCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            3467899999999999999999999999999999999975432 2   577899999999999999999999998764

>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=99.30  E-value=1.7e-12  Score=101.09  Aligned_cols=64  Identities=17%  Similarity=0.230  Sum_probs=58.5

Q ss_pred             EEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307          346 TMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE  415 (466)
Q Consensus       346 ~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~  415 (466)
                      .+.||.+++|+|||++|++|+.|+++|||+|+|++      +..|+|+|++++|+.|+.+|+..+++...
T Consensus         4 vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~------~g~v~I~G~~e~v~~A~~~I~~i~~ea~~   67 (84)
T d2ba0a3           4 IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ------NGLIWVNGDRRKVSIAEEAIYLIEQEAHT   67 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT------TSEEEEESCHHHHHHHHHHHHHHHHCSCC
T ss_pred             EEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC------CCEEEEEeCHHHHHHHHHHHHHHHHhccc
Confidence            47899999999999999999999999999999953      35899999999999999999999987654

>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=99.25  E-value=2.5e-12  Score=99.89  Aligned_cols=71  Identities=14%  Similarity=0.257  Sum_probs=64.6

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ...+.+|.||..+++.|||++|.+|++|+++|||+|.+++.       +..++.|+|+|+.++|.+|..+|++++.+.
T Consensus         8 ~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-------~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           8 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-------DDPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-------TSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC-------CCCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            55789999999999999999999999999999999999743       456789999999999999999999998764

>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=99.25  E-value=3.4e-12  Score=96.52  Aligned_cols=68  Identities=22%  Similarity=0.346  Sum_probs=61.1

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHh
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHL  241 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l  241 (466)
                      ...+.+|.||..+++.|||++|++|++|+++|||+|+|++.       +.+++.|+|+|++++|.+|+.+|+++.
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~-------~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-------SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC-------CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC-------CCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            45678999999999999999999999999999999999742       456789999999999999999998764

>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=99.24  E-value=5.7e-12  Score=99.69  Aligned_cols=68  Identities=21%  Similarity=0.323  Sum_probs=61.2

Q ss_pred             cceEEEEEeccCcccceeccccchHHHHHhH-hCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307          341 TQITQTMQIPISYAEDIIGVGGTSIENIRRT-SGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       341 ~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~-SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~  413 (466)
                      +.+|.+|.||..++++|||++|++|++|+++ +|++|.+++     ++..|+|+|++++|+.|+.+|++++.+-
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~-----~~~~v~i~G~~~~ve~Ak~~I~~iv~el   87 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC-----CCceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            3478999999999999999999999999999 489999964     3468999999999999999999998763

>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=99.21  E-value=4.9e-12  Score=98.45  Aligned_cols=71  Identities=24%  Similarity=0.368  Sum_probs=63.2

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHH-hCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQEN-SGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~-sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      +..+.+|.||..++|+||||+|++|++|+++ ++++|.++..       +..++.|+|+|++++|.+|+.+|++++++.
T Consensus         8 ~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~-------~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           8 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-------TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC-------CCCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            5678999999999999999999999999987 5899988632       456789999999999999999999998864

>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=99.16  E-value=1.3e-11  Score=97.95  Aligned_cols=71  Identities=18%  Similarity=0.316  Sum_probs=64.4

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ..++..|.||..+++.|||++|.+|++|+++|||+|.|++.       +..++.|+|+|+.++|.+|+.+|++++.+.
T Consensus         8 ~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-------~~~~~~v~I~G~~~~V~~A~~~I~~~v~e~   78 (91)
T d2ctka1           8 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-------ELQSDIIAITGLAANLDRAKAGLLERVKEL   78 (91)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT-------TTTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC-------CCCcceEEEECCHHHHHHHHHHHHHHHHHH
Confidence            35789999999999999999999999999999999999743       455779999999999999999999999864

>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=99.06  E-value=2.3e-11  Score=93.32  Aligned_cols=64  Identities=25%  Similarity=0.199  Sum_probs=56.8

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHH
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVG  239 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~  239 (466)
                      ...+.+|.||.+++|+|||++|++|++|+++|||+|.+..         ..++.|+|.| ++++|.+|+.+|..
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~---------~~~g~v~I~g~~~eav~~A~~~Ie~   70 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD---------EDTGTFRIYGESADAVKKARGFLEF   70 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE---------TTTTEEEEEESSHHHHHHHHHHHSC
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEec---------CCCceEEEEECCHHHHHHHHHHHHH
Confidence            4578899999999999999999999999999999999862         3357899999 69999999999954

>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=99.01  E-value=4.4e-11  Score=92.74  Aligned_cols=63  Identities=17%  Similarity=0.228  Sum_probs=52.3

Q ss_pred             EEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEE-----EcCHHHHHHHHHHHHHHHhc
Q 012307          345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEI-----KGTSSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I-----~Gt~~~V~~A~~lI~~~i~~  412 (466)
                      .+|.||.+++|.|||++|++|++|+++|||+|+|+++.+     .|.+     .|.+.++++|+.+|.++-..
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g-----~v~i~~~~~~~~~~a~~~a~~iI~aI~rG   72 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENS-----MVIVEPEAEGIPPVNLMKAAEVVKAISLG   72 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTT-----EEEEEESSTTSCHHHHHHHHHHHHHHHHT
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCC-----eEEEecCCccccHHHHHHHHHHHHHHhCC
Confidence            358999999999999999999999999999999975433     4444     45678899999999886543

>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=99.01  E-value=2.8e-10  Score=89.71  Aligned_cols=68  Identities=21%  Similarity=0.337  Sum_probs=61.3

Q ss_pred             cceEEEEEeccCcceeeecCCchhHHHHHHHh-CCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENS-GASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      ...+..+.||..+++.|||++|++|++|++++ +++|.++.          .+..|+|+|++++|.+|+.+|.+++.+.
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~----------~~~~v~i~G~~~~ve~Ak~~I~~iv~el   87 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC----------CCceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            56899999999999999999999999999995 89999852          3568999999999999999999998764

>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=99.00  E-value=1.6e-10  Score=89.71  Aligned_cols=63  Identities=22%  Similarity=0.263  Sum_probs=56.7

Q ss_pred             EEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307          171 VRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       171 ~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  244 (466)
                      .-+.||.+.+|.|||++|++|++|+++|||+|.|..           +..|+|.|++++|.+|+.+|..++++.
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            457899999999999999999999999999999952           357999999999999999998888764

>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=98.91  E-value=2.8e-11  Score=90.54  Aligned_cols=62  Identities=16%  Similarity=0.149  Sum_probs=47.9

Q ss_pred             EEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcC
Q 012307          346 TMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGT-SSQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       346 ~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt-~~~V~~A~~lI~~~i~~~  413 (466)
                      -|.||.+++|+||||+|++|+.|+++|||+|.|.+      +..|+|.|. .+.++.|+.+|+.+.++.
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            37899999999999999999999999999999953      347999996 678999999998766653

>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=98.83  E-value=4.2e-09  Score=81.56  Aligned_cols=63  Identities=11%  Similarity=0.113  Sum_probs=55.9

Q ss_pred             EEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcCc
Q 012307          346 TMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGT-SSQVQLAQQLIQEYMNNHK  414 (466)
Q Consensus       346 ~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt-~~~V~~A~~lI~~~i~~~~  414 (466)
                      .+.||.+++|.|||++|++|+.|+++|||+|.|.++      -.|.|.|. .+.+..|+.+|+.+.++..
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~------G~V~I~g~~~~~~~~A~~~I~~I~~ea~   67 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN------GRIHLECPNEDLEAIAVMAIKIIDEEAY   67 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETT------TEEEEECSCHHHHHHHHHHHHHHHHCSC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCC------cEEEEEeCCHHHHHHHHHHHHHHHHhch
Confidence            478999999999999999999999999999999642      37999995 7889999999998877654

>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=98.66  E-value=1.1e-08  Score=78.90  Aligned_cols=66  Identities=20%  Similarity=0.231  Sum_probs=54.6

Q ss_pred             EEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEE-----ecCHHHHHHHHHHHHHHhhhcc
Q 012307          171 VRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEM-----QGEAAKVLKALEAVVGHLRKFL  245 (466)
Q Consensus       171 ~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I-----~G~~~~V~~A~~~I~~~l~~~~  245 (466)
                      +.+.||.+.+|.|||++|++||+|+++|||+|+|..+          +..|.+     .|.+.++.+|.++|.++.+.|.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d----------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~rGf~   74 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE----------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFP   74 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT----------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCC
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC----------CCeEEEecCCccccHHHHHHHHHHHHHHhCCCC
Confidence            4689999999999999999999999999999999632          223333     4578999999999999887764


Q ss_pred             c
Q 012307          246 V  246 (466)
Q Consensus       246 ~  246 (466)
                      .
T Consensus        75 P   75 (84)
T d1tuaa1          75 P   75 (84)
T ss_dssp             H
T ss_pred             h
Confidence            3

>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=98.64  E-value=1.1e-08  Score=81.80  Aligned_cols=53  Identities=28%  Similarity=0.365  Sum_probs=48.3

Q ss_pred             cccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 012307          353 YAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNN  412 (466)
Q Consensus       353 ~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~  412 (466)
                      ..|+|||++|.+|+.|++.|||.|.|++       ..|.|.|++++++.|+.+|..++..
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            4799999999999999999999999943       3688899999999999999999975

>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=98.64  E-value=2.2e-09  Score=80.03  Aligned_cols=57  Identities=12%  Similarity=0.137  Sum_probs=40.0

Q ss_pred             EEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCC-CCCCCCCChhHHHHHH
Q 012307           81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGK-EEPEAPVSPAMDAAVR  146 (466)
Q Consensus        81 rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~-~e~~~~v~~A~~ai~~  146 (466)
                      -|.||.+++|.||||+|++||+|+++|||+|+|.+.      ..|+|.|. .+.   +..|+++|..
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~------g~v~I~g~~~~~---v~~A~~~I~~   61 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN------GRIWATCPSRFS---EEILIEAIRK   61 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT------SEEEC-----CT---TCCTHHHHTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC------CEEEEEeCCHHH---HHHHHHHHHH
Confidence            367899999999999999999999999999999643      35899996 444   4456666544

>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=98.63  E-value=2e-09  Score=75.67  Aligned_cols=48  Identities=33%  Similarity=0.582  Sum_probs=16.2

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCC
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE  132 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e  132 (466)
                      ..+|.||.+++|.|||++|++||+|+++|||+|++.+      +..|.|.|...
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d------dg~v~I~a~~~   51 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADG   51 (54)
T ss_dssp             CC---------------------CHHHHSCCCC--------------CCCCBSS
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC------CeEEEEEecCc
Confidence            3568899999999999999999999999999999964      46799988754

>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=1.7e-09  Score=76.12  Aligned_cols=45  Identities=29%  Similarity=0.480  Sum_probs=14.1

Q ss_pred             EEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcC
Q 012307          345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGT  395 (466)
Q Consensus       345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt  395 (466)
                      .+|.||.+++|.|||++|.+||.|+++|||+|+|.+      +..|+|.|.
T Consensus         5 ~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d------dg~v~I~a~   49 (54)
T d1e3ha4           5 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAA   49 (54)
T ss_dssp             C---------------------CHHHHSCCCC--------------CCCCB
T ss_pred             EEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC------CeEEEEEec
Confidence            468999999999999999999999999999999963      467888775

>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=98.43  E-value=1.3e-07  Score=72.95  Aligned_cols=62  Identities=13%  Similarity=0.153  Sum_probs=53.9

Q ss_pred             EEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecC-HHHHHHHHHHHHHHhhhc
Q 012307          172 RLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGE-AAKVLKALEAVVGHLRKF  244 (466)
Q Consensus       172 ~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I~~~l~~~  244 (466)
                      -+.||.+.++.|||++|++|+.|+++|||+|.|..           +-.|.|.|. .+.+..|+.+|..+.++.
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            47799999999999999999999999999999952           236899995 888999999998876653

>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=98.22  E-value=4.6e-07  Score=72.25  Aligned_cols=53  Identities=21%  Similarity=0.238  Sum_probs=46.6

Q ss_pred             cceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhh
Q 012307          179 QAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK  243 (466)
Q Consensus       179 ~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  243 (466)
                      +.|+|||++|.+|+.|++.|||+|.|.            +..|.|.|.++++..|+.+|..++.+
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~------------d~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVG------------EYEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEEC------------SSEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEe------------CCeEEEEECchhHHHHHHHHHHHHcC
Confidence            368999999999999999999999994            12467789999999999999998875

>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=98.15  E-value=2.4e-06  Score=70.16  Aligned_cols=71  Identities=17%  Similarity=0.373  Sum_probs=56.9

Q ss_pred             ceEEEEEeccC------cccceeccccchHHHHHhHhCCeEEEecC----------CC------CCCceEEEEEcC-HHH
Q 012307          342 QITQTMQIPIS------YAEDIIGVGGTSIENIRRTSGAIITVQES----------RG------LPDEITVEIKGT-SSQ  398 (466)
Q Consensus       342 ~~t~~i~IP~~------~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~----------~~------~~~er~V~I~Gt-~~~  398 (466)
                      +++.+|.||.+      ++|.|||.+|+++|+|+++|||+|.|-..          .+      ...+-.|.|++. ++.
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            46788999976      58999999999999999999999999431          00      122456778884 679


Q ss_pred             HHHHHHHHHHHHhc
Q 012307          399 VQLAQQLIQEYMNN  412 (466)
Q Consensus       399 V~~A~~lI~~~i~~  412 (466)
                      ++.|..+|+++|..
T Consensus        82 ~~~A~~~i~~ll~~   95 (122)
T d1k1ga_          82 VKKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999974

>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=97.98  E-value=1.1e-05  Score=66.24  Aligned_cols=76  Identities=18%  Similarity=0.298  Sum_probs=57.5

Q ss_pred             eEEEEEeccCc------ceeeecCCchhHHHHHHHhCCeEEEecCCCC----------CCCC-CCCceEEEEec-CHHHH
Q 012307          169 CSVRLLVPSTQ------AINLIGKQGSLIKSIQENSGASVRVLSADEA----------PFYV-TEDERIVEMQG-EAAKV  230 (466)
Q Consensus       169 ~~~~llVP~~~------vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~----------p~~~-~~~er~v~I~G-~~~~V  230 (466)
                      .+.+++||.+.      +|.|||.+|.++|+|+++|||+|.|..+...          +... ....=-|.|++ +.+.+
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            56788999764      8999999999999999999999999864321          0011 12233466777 57799


Q ss_pred             HHHHHHHHHHhhhc
Q 012307          231 LKALEAVVGHLRKF  244 (466)
Q Consensus       231 ~~A~~~I~~~l~~~  244 (466)
                      .+|+.+|..+|...
T Consensus        83 ~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          83 KKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999998754

>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=97.73  E-value=2.2e-05  Score=65.11  Aligned_cols=71  Identities=15%  Similarity=0.353  Sum_probs=54.9

Q ss_pred             eEEEEEecc------CcccceeccccchHHHHHhHhCCeEEEecCC------------------CCCCceEEEEEcCH--
Q 012307          343 ITQTMQIPI------SYAEDIIGVGGTSIENIRRTSGAIITVQESR------------------GLPDEITVEIKGTS--  396 (466)
Q Consensus       343 ~t~~i~IP~------~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~------------------~~~~er~V~I~Gt~--  396 (466)
                      ++.+|.||.      +++|.|||.+|.++|+|+++|||+|.|-...                  +..++-.|.|++..  
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            456778874      4789999999999999999999999995421                  01245678888853  


Q ss_pred             ----HHHHHHHHHHHHHHhcC
Q 012307          397 ----SQVQLAQQLIQEYMNNH  413 (466)
Q Consensus       397 ----~~V~~A~~lI~~~i~~~  413 (466)
                          ..++.|..+|+.+|...
T Consensus        82 ~~a~~kl~~A~~~I~~lL~p~  102 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLVPA  102 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHHHHHHHHHHcCCC
Confidence                35889999999999653

>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=97.65  E-value=1.7e-05  Score=65.74  Aligned_cols=38  Identities=32%  Similarity=0.398  Sum_probs=34.5

Q ss_pred             eEEEEEeccc------ccceeeecCChhHHHHHHHhCceEEEeC
Q 012307           78 CVFRMIVPVL------KVGSIIGRKGELIKKTCEDTRARIKVLD  115 (466)
Q Consensus        78 ~~~rllvp~~------~vG~IIGk~G~~Ik~I~~etga~I~v~~  115 (466)
                      +.-||+||.+      ++|.|||.+|.++|+|+++|||+|.|.-
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrG   45 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRG   45 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEES
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEe
Confidence            5678999975      6999999999999999999999999984

>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=95.24  E-value=0.0054  Score=43.98  Aligned_cols=40  Identities=23%  Similarity=0.338  Sum_probs=36.2

Q ss_pred             ceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC
Q 012307           77 HCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG  116 (466)
Q Consensus        77 ~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~  116 (466)
                      .-.+.++||.+..+..|||+|.|||-..+-||.+|.|...
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            3478899999999999999999999999999999999754

>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=95.08  E-value=0.0065  Score=43.67  Aligned_cols=37  Identities=22%  Similarity=0.331  Sum_probs=34.8

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCceEEEeC
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLD  115 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~  115 (466)
                      .+.+.||.+..+..|||+|.|||-..+-||.+|.|..
T Consensus        28 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          28 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            6788999999999999999999999999999999964

>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=94.17  E-value=0.013  Score=41.96  Aligned_cols=37  Identities=19%  Similarity=0.293  Sum_probs=34.3

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE  380 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~  380 (466)
                      ...+.||.+..+..|||+|.||+-..+.||.+|.|..
T Consensus        28 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          28 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            4678999999999999999999999999999999964

>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=94.07  E-value=0.013  Score=41.83  Aligned_cols=37  Identities=19%  Similarity=0.191  Sum_probs=34.3

Q ss_pred             EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307          344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE  380 (466)
Q Consensus       344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~  380 (466)
                      ...+.||.+.....|||+|.||+-..+.||.+|.|..
T Consensus        27 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          27 AARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            5678999999999999999999999999999999964

>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=89.73  E-value=0.21  Score=37.15  Aligned_cols=60  Identities=8%  Similarity=0.090  Sum_probs=47.2

Q ss_pred             EEEeccCcccceeccccc-hHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Q 012307          346 TMQIPISYAEDIIGVGGT-SIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMN  411 (466)
Q Consensus       346 ~i~IP~~~~G~IIGkgG~-~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~  411 (466)
                      -+.|+..++.++||++++ -++.|.+.+++.|.|-.+      -.|=|.| +.+..-.+...|.++-+
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~N------GrIWi~~~~~~~~i~i~~aI~~~e~   65 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLN------GKIWVKCEELSNTLACYRTIMECCQ   65 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETT------TEEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecC------cEEEEECCCHHHHHHHHHHHHHHHH
Confidence            367999999999999998 799999999999999642      2688888 46666666666655443

>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=88.86  E-value=0.067  Score=40.53  Aligned_cols=33  Identities=18%  Similarity=0.363  Sum_probs=27.8

Q ss_pred             EEEEEecccccceeeecCChhHHHHHHHhCceE
Q 012307           79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARI  111 (466)
Q Consensus        79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I  111 (466)
                      .+++.|....-|.||||+|+.|++|+++-.-++
T Consensus        36 ~i~I~I~tarPGivIGrkG~~I~~L~~~l~k~~   68 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGEKGRRIRELTAVVQKRF   68 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCCCceeeccCchhHHHHHHHHHHHH
Confidence            467889999999999999999999997755443