Citrus Sinensis ID: 014254

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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-------43
Protein Sequence
MTGSRFNEANLQETIHKPLEVAFQESICRPVETILHETIRRPVDTIPHETIHRPLDTISHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESGPQEILRRPLEVFAPESSHRSSEALSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQDGNWSSSEGQLRCWKRLESRSESS
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHHcccEEEcccccccccEEEEEEccccccccccHHHHHHHHHHHHHHcccccccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHHccEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEcccccccEEEcccccEEEEEEcccccEEEEEccccccccccccEEEEcccHHHHHHHHHHHHHHHHHHcccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEcccEEEEEcccccEHHHHHHHcccEEEEcccccccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccEEEEEEEcccccEEEEcccccEHHHHHHHcccEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEHHHHHcccccccc
Coil and Loop (DISEMBL)
mtgsrfneanlqeTIHKPLEVAFQESICRPVETILHetirrpvdtiphetihrpldtisHETIRRSleavphdtiarpveavPQEILWRSLesgpqeilrrplevfapesshrssealsIETQHRLFGAVSQEILPDLHVDILSQrnsvlttapsssisyvsavrplslesdRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGafisvgatmpecdERLITVtasegpesryspaQKAVVLVFSRLIegtsekgldfssnkgllVNARLVVASNQvgcllgkggtiiSEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVtgrlrdnhfsgtlntartrstssvltetspysrlkdpasfgvhssvavshdfsqppltqdgnwsssegqLRCWKRlesrsess
Flexible Loop (DISEMBL)
mtgsrfneanlqetihkplevafQESICRPVETILhetirrpvdtiphetihrpldtishETIRRSLEavphdtiarpveavpQEILWRSLESGPQEILRRPLEVFAPESSHRSSEALSIETQHRLFGAVSQEILPDLHVDILSQRNSVlttapsssisyvSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTasegpesryspaQKAVVLVFSRLIEGTsekgldfssnKGLLVNARLVVASNQVgcllgkggtiisemrkVTGTSIRIISDQLLKCISENDRvvqisgefskvKDAVYNVtgrlrdnhfsgtlntartrstssvltetspysrlkdPASFGVHSSVAVSHDFsqppltqdgnwsssegqlrcwkrlesrsess
Low Complexity Region (SEG)
MTGSRFNEANLQETIHKPLEVAFQESICRPVETILHETIRRPVDTIPHETIHRPLDTISHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESGPQEILRRPLEVFAPESSHRSSEALSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQDGNWSSSEGQLRCWKRLESRSESS
Disordered region (IsUnstruct)
**************IHKPLEVAFQESICRPVETILHETIRRPVDTIPHETIHRPLDTISHETIRRSLEAVPHDTIARPVEAVPQEILWRSL*******************************QHRLFGAVSQEILPDLHVDILSQRNSVLTT*****ISYVSAVRPL******VATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT************QKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFS*************************************************************************
Disordered Region (DISOPRED)
******************************************************************************************************************************************************************************************SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRL********************ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL*******************************************************************************
Disordered Region (DISEMBL)
MTGSRFNEANLQETIHKPLEVAFQESICRPVETILHETIRRPVDTIPHETIHRPLDTISHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESGPQEILRRPLEVF************SIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNT***************YSRLKDPASFGVHSSVAVSHDFSQPPL**************************
Disordered Region (DISPRO)
*****FNEANLQETIHKPLEVAFQESICRPVETILHETIRRPVDTIPHETIHRPLDTISHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESGPQEILRRPLEVFAPESSHRSSEALSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSS*************************QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKG****SNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQDGNWSS******************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTGSRFNEANLQETIHKPLEVAFQESICRPVETILHETIRRPVDTIPHETIHRPLDTISHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESGPQEILRRPLEVFAPESSHRSSEALSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQDGNWSSSEGQLRCWKRLESRSESS
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	428	2.2.26 [Sep-21-2011]
P58223	606	KH domain-containing prot	no	no	0.355	0.250	0.335	3e-18
Q61990	362	Poly(rC)-binding protein	yes	no	0.478	0.566	0.283	2e-12
Q15366	365	Poly(rC)-binding protein	yes	no	0.478	0.561	0.283	4e-11
P57721	371	Poly(rC)-binding protein	no	no	0.338	0.390	0.298	4e-11
P57722	371	Poly(rC)-binding protein	no	no	0.338	0.390	0.298	6e-11
O19048	356	Poly(rC)-binding protein	no	no	0.348	0.418	0.3	1e-10
P60335	356	Poly(rC)-binding protein	no	no	0.348	0.418	0.3	1e-10
Q15365	356	Poly(rC)-binding protein	no	no	0.348	0.418	0.3	1e-10
Q5E9A3	356	Poly(rC)-binding protein	no	no	0.348	0.418	0.3	1e-10
P57724	403	Poly(rC)-binding protein	no	no	0.331	0.352	0.292	1e-08

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

 Score = 93.2 bits (230), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/176 (33%), Positives = 103/176 (58%), Gaps = 24/176 (13%)

Query: 181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPEC--DERLITVTAS 238
           ++ +E+ F++LC    +  VIGKGG+ I+ ++  +G+ I V  +  +C  DE +I VTA+
Sbjct: 307 SRSEELVFKVLCPLCNIMRVIGKGGSTIKRIREASGSCIEVNDSRTKCGDDECVIIVTAT 366

Query: 239 EGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGT 298
           E P+   S A +AV+L+   + +  +E            V  +L+V+S  +GC++GK G+
Sbjct: 367 ESPDDMKSMAVEAVLLLQEYINDEDAEN-----------VKMQLLVSSKVIGCVIGKSGS 415

Query: 299 IISEMRKVTGTSIRIISDQLLKCISEN--DRVVQISGEFSKVKDAVYNVTGRLRDN 352
           +I+E+RK T  +I         CIS+   D +V++SGE S V+DA+  +  RLR++
Sbjct: 416 VINEIRKRTNANI---------CISKGKKDDLVEVSGEVSSVRDALIQIVLRLRED 462

Arabidopsis thaliana (taxid: 3702)

>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 = 63/222 (28%), Positives = 111/222 (50%), Gaps = 17/222 (7%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+    GP +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLA---GPTNAI 68

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  S    + ++     V  RLVV ++Q G L+GKGG  I E+R+
Sbjct: 69  F---KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRE 125

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRS 365
            TG  +++  D L    +  +R + I+G    + + V  +   + ++   G     R + 
Sbjct: 126 STGAQVQVAGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLESPPKGVTIPYRPKP 182

Query: 366 TSSVLTETSP---YSRLKDPASFGVHS--SVAVSHDFSQPPL 402
           +SS +        YS   D ASF  H+  S+ ++ D   PPL
Sbjct: 183 SSSPVIFAGGQDRYSTGSDSASF-PHTTPSMCLNPDLEGPPL 223

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 = 69.7 bits (169), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 64/226 (28%), Positives = 110/226 (48%), Gaps = 21/226 (9%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+    GP +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLA---GPTNAI 68

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  S    + ++     V  RLVV ++Q G L+GKGG  I E+R+
Sbjct: 69  F---KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRE 125

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVT----GRLRDNHFSGTLNTA 361
            TG  +++  D L    +  +R + I+G    + + V  +       L  +   G     
Sbjct: 126 STGAQVQVAGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLETLSQSPPKGVTIPY 182

Query: 362 RTRSTSSVLTETSP---YSRLKDPASFGVHS--SVAVSHDFSQPPL 402
           R + +SS +        YS   D ASF  H+  S+ ++ D   PPL
Sbjct: 183 RPKPSSSPVIFAGGQDRYSTGSDSASF-PHTTPSMCLNPDLEGPPL 227

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

 Score = 69.7 bits (169), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 49/164 (29%), Positives = 83/164 (50%), Gaps = 19/164 (11%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER++T+T   GP    
Sbjct: 46  LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTIT---GPTD-- 98

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLL----VNARLVVASNQVGCLLGKGGTIIS 301
                A+   F+ +     E  ++  SN        V  RLVV ++Q G L+GKGG+ I 
Sbjct: 99  -----AIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIK 153

Query: 302 EMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345
           E+R+ TG  +++  D L    +  +R V ISG    +   V  +
Sbjct: 154 EIRESTGAQVQVAGDMLP---NSTERAVTISGTPDAIIQCVKQI 194

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 = 68.9 bits (167), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 49/164 (29%), Positives = 83/164 (50%), Gaps = 19/164 (11%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER++T+T   GP    
Sbjct: 46  LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTIT---GPTD-- 98

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLL----VNARLVVASNQVGCLLGKGGTIIS 301
                A+   F+ +     E  ++  SN        V  RLVV ++Q G L+GKGG+ I 
Sbjct: 99  -----AIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIK 153

Query: 302 EMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345
           E+R+ TG  +++  D L    +  +R V ISG    +   V  +
Sbjct: 154 EIRESTGAQVQVAGDMLP---NSTERAVTISGTPDAIIQCVKQI 194

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

Mus musculus (taxid: 10090)

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

 Score = 68.2 bits (165), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 48/160 (30%), Positives = 85/160 (53%), Gaps = 11/160 (6%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+T   GP +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI--SEGNCPERIITLT---GPTNAI 68

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  +    + ++     V  RLVV + Q G L+GKGG  I E+R+
Sbjct: 69  F---KAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRE 125

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345
            TG  +++  D L    +  +R + I+G    V + V  +
Sbjct: 126 STGAQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQI 162

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 = 68.2 bits (165), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 48/160 (30%), Positives = 85/160 (53%), Gaps = 11/160 (6%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+T   GP +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI--SEGNCPERIITLT---GPTNAI 68

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  +    + ++     V  RLVV + Q G L+GKGG  I E+R+
Sbjct: 69  F---KAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRE 125

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345
            TG  +++  D L    +  +R + I+G    V + V  +
Sbjct: 126 STGAQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQI 162

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

Mus musculus (taxid: 10090)

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

 Score = 68.2 bits (165), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 48/160 (30%), Positives = 85/160 (53%), Gaps = 11/160 (6%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+T   GP +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI--SEGNCPERIITLT---GPTNAI 68

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  +    + ++     V  RLVV + Q G L+GKGG  I E+R+
Sbjct: 69  F---KAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRE 125

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345
            TG  +++  D L    +  +R + I+G    V + V  +
Sbjct: 126 STGAQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQI 162

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

Homo sapiens (taxid: 9606)

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

 Score = 68.2 bits (165), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 48/160 (30%), Positives = 85/160 (53%), Gaps = 11/160 (6%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+T   GP +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI--SEGNCPERIITLT---GPTNAI 68

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  +    + ++     V  RLVV + Q G L+GKGG  I E+R+
Sbjct: 69  F---KAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRE 125

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345
            TG  +++  D L    +  +R + I+G    V + V  +
Sbjct: 126 STGAQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQI 162

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

Bos taurus (taxid: 9913)

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

 Score = 61.2 bits (147), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 46/157 (29%), Positives = 80/157 (50%), Gaps = 15/157 (9%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ ++ A I++      C ER+ T+T S       
Sbjct: 18  LTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG--SCPERITTITGST------ 69

Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
           +    AV ++  +L E       +  S     V  RLV+ ++Q G L+GK GT I E+R+
Sbjct: 70  AAVFHAVSMIAFKLDEDLCAAPANGGSVSRPPVTLRLVIPASQCGSLIGKAGTKIKEIRE 129

Query: 306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAV 342
            TG  +++  D L    +  +R V +SG    V DA+
Sbjct: 130 TTGAQVQVAGDLLP---NSTERAVTVSG----VPDAI 159

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	428
225464083	648	PREDICTED: KH domain-containing protein	0.637	0.421	0.660	1e-94
147789223	569	hypothetical protein VITISV_022038 [Viti	0.637	0.479	0.660	4e-94
296088778	585	unnamed protein product [Vitis vinifera]	0.637	0.466	0.660	5e-94
124359392	564	KH, type 1 [Medicago truncatula]	0.591	0.448	0.645	6e-87
357445989	766	Heterogeneous nuclear ribonucleoprotein	0.591	0.330	0.645	1e-86
449438568	658	PREDICTED: KH domain-containing protein	0.621	0.404	0.596	3e-79
224141139	722	predicted protein [Populus trichocarpa]	0.542	0.321	0.676	3e-78
224095794	747	predicted protein [Populus trichocarpa]	0.593	0.340	0.612	5e-77
356557593	710	PREDICTED: KH domain-containing protein	0.572	0.345	0.601	2e-75
356519471	591	PREDICTED: KH domain-containing protein	0.577	0.417	0.594	2e-74

>gi|225464083|ref|XP_002269250.1| PREDICTED: KH domain-containing protein At4g18375-like [Vitis vinifera]

 Score =  352 bits (904), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 183/277 (66%), Positives = 217/277 (78%), Gaps = 4/277 (1%)

Query: 125 RLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQ 184
           R    V Q+ LPD  VD+  QR SVL   PS++ISY S  RPLS+ ++R++TLD +T QQ
Sbjct: 238 RPLEVVPQQSLPDPRVDLFQQRGSVLPPIPSNTISYASGSRPLSINTERISTLDPKTSQQ 297

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESR 244
           EV F+ILCSND+VG VIGKGGTI++ALQ+EAGA ISVGA + ECDERLIT+TASE PESR
Sbjct: 298 EVIFKILCSNDRVGGVIGKGGTIVKALQNEAGASISVGAPVAECDERLITITASENPESR 357

Query: 245 YSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMR 304
           YSPAQ  V+LVF+R IE   EKGLD S +KG  V+ARLVV SNQVGCL+GKGGTIISEMR
Sbjct: 358 YSPAQNGVILVFNRSIEAGIEKGLD-SGSKGSPVSARLVVPSNQVGCLMGKGGTIISEMR 416

Query: 305 KVTGTSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF-SGTLNTAR 362
           K +G  IRII SDQ+ KC SEND+VVQISGEF  V+D +Y++TGRLRDN F S TLN A 
Sbjct: 417 KASGAGIRIIGSDQVPKCASENDQVVQISGEFVNVQDGLYHITGRLRDNLFPSKTLNGAG 476

Query: 363 TRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQ 399
            RS SS + E SPY R++DPASFG+HSSV VS  FS+
Sbjct: 477 IRS-SSAMNEISPYGRVRDPASFGLHSSVGVSPSFSR 512

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147789223|emb|CAN69138.1| hypothetical protein VITISV_022038 [Vitis vinifera]

 Score =  351 bits (900), Expect = 4e-94,   Method: Compositional matrix adjust.
 Identities = 183/277 (66%), Positives = 217/277 (78%), Gaps = 4/277 (1%)

Query: 125 RLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQ 184
           R    V Q+ LPD  VD+  QR SVL   PS++ISY S  RPLS+ ++R++TLD +T QQ
Sbjct: 159 RPLEVVPQQSLPDPRVDLFQQRGSVLPPIPSNTISYASGSRPLSINTERISTLDPKTSQQ 218

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESR 244
           EV F+ILCSND+VG VIGKGGTI++ALQ+EAGA ISVGA + ECDERLIT+TASE PESR
Sbjct: 219 EVIFKILCSNDRVGGVIGKGGTIVKALQNEAGASISVGAPVAECDERLITITASENPESR 278

Query: 245 YSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMR 304
           YSPAQ  V+LVF+R IE   EKGLD S +KG  V+ARLVV SNQVGCL+GKGGTIISEMR
Sbjct: 279 YSPAQNGVILVFNRSIEAGIEKGLD-SGSKGSPVSARLVVPSNQVGCLMGKGGTIISEMR 337

Query: 305 KVTGTSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF-SGTLNTAR 362
           K +G  IRII SDQ+ KC SEND+VVQISGEF  V+D +Y++TGRLRDN F S TLN A 
Sbjct: 338 KASGAGIRIIGSDQVPKCASENDQVVQISGEFVNVQDGLYHITGRLRDNLFPSKTLNGAG 397

Query: 363 TRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQ 399
            RS SS + E SPY R++DPASFG+HSSV VS  FS+
Sbjct: 398 IRS-SSAMNEISPYGRVRDPASFGLHSSVGVSPSFSR 433

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296088778|emb|CBI38228.3| unnamed protein product [Vitis vinifera]

 Score =  351 bits (900), Expect = 5e-94,   Method: Compositional matrix adjust.
 Identities = 183/277 (66%), Positives = 217/277 (78%), Gaps = 4/277 (1%)

Query: 125 RLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQ 184
           R    V Q+ LPD  VD+  QR SVL   PS++ISY S  RPLS+ ++R++TLD +T QQ
Sbjct: 175 RPLEVVPQQSLPDPRVDLFQQRGSVLPPIPSNTISYASGSRPLSINTERISTLDPKTSQQ 234

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESR 244
           EV F+ILCSND+VG VIGKGGTI++ALQ+EAGA ISVGA + ECDERLIT+TASE PESR
Sbjct: 235 EVIFKILCSNDRVGGVIGKGGTIVKALQNEAGASISVGAPVAECDERLITITASENPESR 294

Query: 245 YSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMR 304
           YSPAQ  V+LVF+R IE   EKGLD S +KG  V+ARLVV SNQVGCL+GKGGTIISEMR
Sbjct: 295 YSPAQNGVILVFNRSIEAGIEKGLD-SGSKGSPVSARLVVPSNQVGCLMGKGGTIISEMR 353

Query: 305 KVTGTSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF-SGTLNTAR 362
           K +G  IRII SDQ+ KC SEND+VVQISGEF  V+D +Y++TGRLRDN F S TLN A 
Sbjct: 354 KASGAGIRIIGSDQVPKCASENDQVVQISGEFVNVQDGLYHITGRLRDNLFPSKTLNGAG 413

Query: 363 TRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQ 399
            RS SS + E SPY R++DPASFG+HSSV VS  FS+
Sbjct: 414 IRS-SSAMNEISPYGRVRDPASFGLHSSVGVSPSFSR 449

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|124359392|gb|ABN05856.1| KH, type 1 [Medicago truncatula]

 Score =  327 bits (839), Expect = 6e-87,   Method: Compositional matrix adjust.
 Identities = 164/254 (64%), Positives = 200/254 (78%), Gaps = 1/254 (0%)

Query: 129 AVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSF 188
           AV  E L DLHVD L QR S L+  PSSS SY + V  LS E +RV++L+ +  QQE++F
Sbjct: 72  AVPCETLTDLHVDHLLQRRSALSILPSSSNSYATGVHSLSAEVNRVSSLEPKAHQQEITF 131

Query: 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPA 248
           +I+CSND++G VIGKGG IIRALQSE GA +SVG ++ EC++RLIT+TASE PESRYSPA
Sbjct: 132 KIICSNDRIGGVIGKGGNIIRALQSETGATVSVGPSVAECEDRLITITASESPESRYSPA 191

Query: 249 QKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTG 308
           QKA VLVFSR +E   EKG+D   N G  V A+LVV+SNQVGCLLGKGG I+SEMRK TG
Sbjct: 192 QKATVLVFSRSVEAGIEKGIDSGLNTGSSVTAQLVVSSNQVGCLLGKGGVIVSEMRKATG 251

Query: 309 TSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTS 367
            SIRI+ +D++ KC S+ND+VVQISGEFS V+DA+YN TGRLRDN F GTL +A TRS S
Sbjct: 252 ASIRIVGTDKVSKCASDNDQVVQISGEFSNVQDALYNATGRLRDNLFGGTLKSAGTRSLS 311

Query: 368 SVLTETSPYSRLKD 381
           SV ++TSPY RL+D
Sbjct: 312 SVQSDTSPYGRLRD 325

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357445989|ref|XP_003593272.1| Heterogeneous nuclear ribonucleoprotein K [Medicago truncatula] gi|355482320|gb|AES63523.1| Heterogeneous nuclear ribonucleoprotein K [Medicago truncatula]

 Score =  327 bits (837), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 164/254 (64%), Positives = 200/254 (78%), Gaps = 1/254 (0%)

Query: 129 AVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSF 188
           AV  E L DLHVD L QR S L+  PSSS SY + V  LS E +RV++L+ +  QQE++F
Sbjct: 274 AVPCETLTDLHVDHLLQRRSALSILPSSSNSYATGVHSLSAEVNRVSSLEPKAHQQEITF 333

Query: 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPA 248
           +I+CSND++G VIGKGG IIRALQSE GA +SVG ++ EC++RLIT+TASE PESRYSPA
Sbjct: 334 KIICSNDRIGGVIGKGGNIIRALQSETGATVSVGPSVAECEDRLITITASESPESRYSPA 393

Query: 249 QKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTG 308
           QKA VLVFSR +E   EKG+D   N G  V A+LVV+SNQVGCLLGKGG I+SEMRK TG
Sbjct: 394 QKATVLVFSRSVEAGIEKGIDSGLNTGSSVTAQLVVSSNQVGCLLGKGGVIVSEMRKATG 453

Query: 309 TSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTS 367
            SIRI+ +D++ KC S+ND+VVQISGEFS V+DA+YN TGRLRDN F GTL +A TRS S
Sbjct: 454 ASIRIVGTDKVSKCASDNDQVVQISGEFSNVQDALYNATGRLRDNLFGGTLKSAGTRSLS 513

Query: 368 SVLTETSPYSRLKD 381
           SV ++TSPY RL+D
Sbjct: 514 SVQSDTSPYGRLRD 527

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449438568|ref|XP_004137060.1| PREDICTED: KH domain-containing protein At4g18375-like [Cucumis sativus]

 Score =  301 bits (772), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 161/270 (59%), Positives = 203/270 (75%), Gaps = 4/270 (1%)

Query: 129 AVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSF 188
           AV  E LPDLH+D + QRNSVL   PSSS  + S +  LS+++D +  +D    QQ+V F
Sbjct: 247 AVIHETLPDLHMDHILQRNSVLPILPSSSNIFASGIHSLSIDADMLPPVDTNVAQQDVVF 306

Query: 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPA 248
           +ILC+ND++G VIGKGGTI+RALQ+E+GA +SVG ++  CDERLI++TASE  ESRYSPA
Sbjct: 307 KILCANDRIGGVIGKGGTIVRALQNESGATVSVGPSVTGCDERLISITASENIESRYSPA 366

Query: 249 QKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTG 308
           QKAVVLVFSR ++   EK  + SS+KG  V ARLVV SNQVGC+LGKGG IISE+RKVTG
Sbjct: 367 QKAVVLVFSRSVDVAIEKWQE-SSSKGSPVVARLVVPSNQVGCVLGKGGVIISEIRKVTG 425

Query: 309 TSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRS-- 365
           T+IRII SDQ+  C +E+D +VQISGEFS V+DA+YNVTGRLRDN FS  L+ + TR+  
Sbjct: 426 TNIRIISSDQVPNCAAESDEIVQISGEFSNVQDALYNVTGRLRDNLFSSVLSNSGTRNGG 485

Query: 366 TSSVLTETSPYSRLKDPASFGVHSSVAVSH 395
            +SV  ETSPY R++D A     + V  SH
Sbjct: 486 GTSVYPETSPYGRVRDTAPLVRSTPVGTSH 515

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224141139|ref|XP_002323932.1| predicted protein [Populus trichocarpa] gi|222866934|gb|EEF04065.1| predicted protein [Populus trichocarpa]

 Score =  298 bits (763), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 159/235 (67%), Positives = 179/235 (76%), Gaps = 3/235 (1%)

Query: 150 LTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIR 209
           L T P SSI+Y S V PLSLESDRV T D    QQ V FRILC+ D++G VIGKGG I+R
Sbjct: 265 LPTIPKSSINYASRVHPLSLESDRVVTPDTNIPQQLV-FRILCTTDRIGGVIGKGGNIVR 323

Query: 210 ALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLD 269
           ALQ+E GA ISVG T+ ECDERLITVTASE PESRYS AQK +VLVFSR +E   EKGLD
Sbjct: 324 ALQNETGAAISVGPTVSECDERLITVTASENPESRYSAAQKTIVLVFSRAVESGIEKGLD 383

Query: 270 FSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII-SDQL-LKCISENDR 327
             S++G  V ARLVV+ +QVGCLLGKGGTIISEMRK T TSIRII  DQ   KC+ E D 
Sbjct: 384 PGSSRGSPVTARLVVSPSQVGCLLGKGGTIISEMRKATSTSIRIIVGDQRNPKCVPETDH 443

Query: 328 VVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDP 382
           VV+ISG+F  VKDA+Y+VTGRLRDN FSG L+T   RS SSVL E SPY +L DP
Sbjct: 444 VVEISGDFVNVKDAIYHVTGRLRDNLFSGMLSTPGARSNSSVLAEISPYVKLMDP 498

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224095794|ref|XP_002310483.1| predicted protein [Populus trichocarpa] gi|222853386|gb|EEE90933.1| predicted protein [Populus trichocarpa]

 Score =  294 bits (753), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 163/266 (61%), Positives = 193/266 (72%), Gaps = 12/266 (4%)

Query: 129 AVSQEILPDLHVDILSQRNSVLTT------AP----SSSISYVSAVRPLSLESDRVATLD 178
           AVS+   P++ V+IL Q ++V  T      AP    +SSI Y S     SLES+RV+TLD
Sbjct: 246 AVSRVSFPEVGVEILPQHSAVRPTIAQHSVAPPTVTNSSIDYASGTHLFSLESERVSTLD 305

Query: 179 ARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238
             T QQ+V FRILC+ND+VG VIGKGG I+ ALQ+E GA IS+G  +  CDERLITVTAS
Sbjct: 306 TSTPQQQVVFRILCNNDRVGGVIGKGGNIVTALQNETGATISIGPKVAGCDERLITVTAS 365

Query: 239 EGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGT 298
           E PESRYS AQK VVLVFSR++E   EKGLD  S++G  V+ RLVV+ NQVGCLLGKGGT
Sbjct: 366 ENPESRYSAAQKTVVLVFSRVVESVIEKGLDPGSSEGSPVSVRLVVSPNQVGCLLGKGGT 425

Query: 299 IISEMRKVTGTSIRIIS-DQL-LKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSG 356
           IISEMRK T TSIRII  DQ   KC+ END VV+I G+F  VKD++Y++TGRLRDN FS 
Sbjct: 426 IISEMRKATSTSIRIIGRDQGNPKCVPENDHVVEILGDFLNVKDSIYHITGRLRDNLFSS 485

Query: 357 TLNTARTRSTSSVLTETSPYSRLKDP 382
            L T   RS+SSVL ETSPY R  DP
Sbjct: 486 ILGTPGARSSSSVLAETSPYVRSMDP 511

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356557593|ref|XP_003547100.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  289 bits (740), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 148/246 (60%), Positives = 180/246 (73%), Gaps = 1/246 (0%)

Query: 160 YVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFI 219
           Y + +  L  E +RV++L+ +  +QEV+FRILCSND+VG VIGKGG I+RALQSE GA I
Sbjct: 293 YATRIHSLPTEVNRVSSLEPKALKQEVTFRILCSNDRVGGVIGKGGNIVRALQSETGATI 352

Query: 220 SVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVN 279
           S+G  + EC++RLIT+ ASE PESRYSPAQKA VLVFSR IE   EKGLD   NKG +V 
Sbjct: 353 SIGPAVAECEDRLITIAASENPESRYSPAQKAAVLVFSRSIEVGFEKGLDSGLNKGSIVT 412

Query: 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII-SDQLLKCISENDRVVQISGEFSKV 338
            RLVV S+QVGCL+GKGG I+SEMRK TG +IRII +DQ+ KC S+ND+VVQISGEFS V
Sbjct: 413 VRLVVPSSQVGCLIGKGGVIVSEMRKATGANIRIIGTDQVPKCASDNDQVVQISGEFSSV 472

Query: 339 KDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFS 398
           +DA+YN  GRLRDN F  T N+A TRS SS+  +TSPY R +D    G     A SH  S
Sbjct: 473 QDALYNAMGRLRDNLFVSTQNSAGTRSLSSLRVDTSPYGRQQDVVPLGSQLPPATSHSLS 532

Query: 399 QPPLTQ 404
           +    Q
Sbjct: 533 RHTFAQ 538

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356519471|ref|XP_003528396.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  286 bits (731), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 148/249 (59%), Positives = 187/249 (75%), Gaps = 2/249 (0%)

Query: 129 AVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSF 188
           +V  E L +LH+D   QR+S L+T  + S    S    LS E +RV+ LD +  QQEV+F
Sbjct: 213 SVPLESLTNLHIDRRLQRSSTLSTLSNRSNGNASGAPKLSAEVNRVSALDPKALQQEVTF 272

Query: 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE-GPESRYSP 247
           RI+CSND+VGAVIGKGG+I+RALQ+E+GA IS G ++ EC++RL+T+TASE  PESRYSP
Sbjct: 273 RIICSNDRVGAVIGKGGSIVRALQNESGAIISFGPSLVECEDRLVTITASEQNPESRYSP 332

Query: 248 AQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVT 307
           AQKAVVLVFS+ +E   EKGLD  S K   V A+LVV SNQVGCLLGKGG I+SEMRK T
Sbjct: 333 AQKAVVLVFSKSVEAGVEKGLDMGSKKESYVTAQLVVPSNQVGCLLGKGGAIVSEMRKAT 392

Query: 308 GTSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRST 366
           G +IR+I +D++ KC+S+ND++VQISGEFS V+ A+YN TGRLRDN F  T N+   RS 
Sbjct: 393 GANIRVIGNDKVPKCVSDNDQLVQISGEFSNVQAAIYNATGRLRDNLFVSTQNSGGARSL 452

Query: 367 SSVLTETSP 375
           SSVL+   P
Sbjct: 453 SSVLSGGKP 461

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	428
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.392	0.270	0.440	3.5e-32
TAIR|locus:2066020	632	AT2G22600 "AT2G22600" [Arabido	0.446	0.302	0.405	1.2e-28
TAIR|locus:2161413	644	AT5G46190 "AT5G46190" [Arabido	0.495	0.329	0.347	2.4e-24
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.392	0.306	0.365	1.2e-23
TAIR|locus:2168367	652	RCF3 "AT5G53060" [Arabidopsis	0.579	0.380	0.289	9.6e-21
TAIR|locus:2035807	479	AT1G14170 "AT1G14170" [Arabido	0.640	0.572	0.319	2.6e-20
TAIR|locus:2831364	606	AT4G18375 "AT4G18375" [Arabido	0.380	0.268	0.329	1.9e-16
TAIR|locus:2120755	495	PEP "AT4G26000" [Arabidopsis t	0.378	0.327	0.339	3.6e-15
UNIPROTKB|B4DLC0	301	PCBP2 "Poly(rC)-binding protei	0.478	0.681	0.283	4.8e-14
UNIPROTKB|Q3SYT9	349	PCBP2 "Poly(RC) binding protei	0.478	0.587	0.283	1.3e-13

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

 Score = 358 (131.1 bits), Expect = 3.5e-32, P = 3.5e-32
 Identities = 78/177 (44%), Positives = 117/177 (66%)

Query:   183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPE 242
             ++EV+FR+LC  DKVG++IGKGG ++RALQ+E+GA I V     + +ER+I ++A E  E
Sbjct:   273 EEEVAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISARENLE 332

Query:   243 SRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISE 302
              R+S AQ  V+ V +R++E      + F  +  ++  ARL+V S  +G LLGKGG +ISE
Sbjct:   333 RRHSLAQDGVMRVHNRIVE------IGFEPSAAVV--ARLLVHSPYIGRLLGKGGHLISE 384

Query:   303 MRKVTGTSIRIIS-DQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTL 358
             MR+ TG SIR+ + DQ  K  S++D +VQ+ G    V+DA++ +  RLR+  F G L
Sbjct:   385 MRRATGASIRVFAKDQATKYESQHDEIVQVIGNLKTVQDALFQILCRLREAMFPGRL 441

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 326 (119.8 bits), Expect = 1.2e-28, P = 1.2e-28
 Identities = 81/200 (40%), Positives = 123/200 (61%)

Query:   155 SSSISYVSAVRPLSLESDRVATLDA-RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQS 213
             SSS+S  + +    + S+R    D   + +++V F+I+ ++   G +IGK GTIIRALQ+
Sbjct:   249 SSSLSNATEI----VASNRHLPYDGGNSTERKVVFKIIFTSVVAGGIIGKQGTIIRALQN 304

Query:   214 EAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN 273
             E GA ISVGA +    ER++TV+A E  ESRYS AQ A+ LVF+R +E   EKGL    +
Sbjct:   305 ETGASISVGAPLKVSGERVVTVSARENLESRYSHAQNALALVFARSVEIDVEKGLRPGLH 364

Query:   274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI-ISDQLLKCISENDRVVQIS 332
              G +V  +L+V S+      G G     E    TG  + I + +Q+L+ ISEN+ V++I 
Sbjct:   365 NGAIVKTKLLVPSHFANSFNGNGNR---EAIIATGADVHISVGNQVLEWISENEVVIEIK 421

Query:   333 GEFSKVKDAVYNVTGRLRDN 352
             GE+S V+ A+ +V+ +LR+N
Sbjct:   422 GEYSHVQKALTHVSSKLREN 441

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 299 (110.3 bits), Expect = 2.4e-24, P = 2.4e-24
 Identities = 80/230 (34%), Positives = 129/230 (56%)

Query:   181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDER-LITVTASE 239
             ++ ++++ +++CS+ K+G VIGKGG  I+ ++  +G+ I V  +    D+  +ITVTA+E
Sbjct:   312 SRSEKLAIKVICSSSKIGRVIGKGGLTIKGIRQASGSHIEVNDSRTNHDDDCVITVTATE 371

Query:   240 GPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTI 299
              P+   S A +AV+L+         EK  D   +K   V  +L+V+S  +GC++GK G+I
Sbjct:   372 SPDDLKSMAVEAVLLL--------QEKINDEDEDK---VKMQLLVSSKVIGCIIGKSGSI 420

Query:   300 ISEMRKVTGTSIRIIS-DQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF---- 354
             ISE+RK T   I I   +   KC   ND +V+ISGE S V+DA+  +  RLRD+      
Sbjct:   421 ISEIRKRTKADIHISKGNNTPKCADPNDELVEISGEVSNVRDALIQIVLRLRDDVLRDRE 480

Query:   355 SGTLNTARTRS-TSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLT 403
             +G+ N    RS  ++  + +S  + L  P SF        S DF++ P T
Sbjct:   481 TGSRNQPPARSENNNFFSSSSSNTGLALPQSFMSSVPQVASVDFNRRPET 530

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 292 (107.8 bits), Expect = 1.2e-23, P = 1.2e-23
 Identities = 65/178 (36%), Positives = 104/178 (58%)

Query:   183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITV------T 236
             + +  FR LC   K+G+VIG+GG I++ L+++  + I +G  +P CDER+IT+      T
Sbjct:    47 RDDTVFRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCDERVITIYSPSDET 106

Query:   237 ASEGP-ESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGK 295
              + G  E   SPAQ A+  +  R++   +    + S      V A+L+V S+Q+GC+LG+
Sbjct:   107 NAFGDGEKVLSPAQDALFRIHDRVVADDARS--EDSPEGEKQVTAKLLVPSDQIGCILGR 164

Query:   296 GGTIISEMRKVTGTSIRIISDQLLK-CISENDRVVQISGEFSKVKDAVYNVTGRLRDN 352
             GG I+  +R  TG  IRI+ D+ +  C   +D ++QISGE   VK A+  +  RL +N
Sbjct:   165 GGQIVQNIRSETGAQIRIVKDRNMPLCALNSDELIQISGEVLIVKKALLQIASRLHEN 222

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 270 (100.1 bits), Expect = 9.6e-21, P = 9.6e-21
 Identities = 77/266 (28%), Positives = 135/266 (50%)

Query:   109 ESSHRSSEALS--IETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRP 166
             ES HR          +  R F A   + +P L      Q +         + ++ S    
Sbjct:   251 ESQHRDRSNFQGRSHSPERSFAAAGDDYMPQLR----RQSSDRFPRGNFRNNNFSSRQSN 306

Query:   167 LSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMP 226
              + E+  V  +      +E+ F+ILC  DK+  V+G+   II  LQ+E G  + V   + 
Sbjct:   307 YAEEAPAVP-VGENVYSEELVFQILCPADKIVRVVGESQGIIDLLQNEIGVDVRVSDPVA 365

Query:   227 ECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVAS 286
               DE++IT+++ E P+  + PAQ+A++ + +++I        D   +K  L+  RL+V S
Sbjct:   366 GSDEQIITISSEEAPDDPFFPAQEALLHIQTQII--------DLIPDKDNLITTRLLVPS 417

Query:   287 NQVGCLLGKGGTIISEMRKVTGTSIRIIS-DQLLKCISENDRVVQISGEFSKVKDAVYNV 345
                 CL GK G++ SE+ ++TGTS++I++ +++ +C S ND V+QI+GE    ++A+  +
Sbjct:   418 RDSICLEGKAGSV-SEISRLTGTSVQILAREEIPRCASINDVVIQITGEIRAAREALVEL 476

Query:   346 TGRLRDNHFSGTLNTARTRSTSSVLT 371
             T  LR + F   L+   T   S+  T
Sbjct:   477 TLLLRSHMFK-ELSQKETPPASTSTT 501

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 263 (97.6 bits), Expect = 2.6e-20, P = 2.6e-20
 Identities = 93/291 (31%), Positives = 143/291 (49%)

Query:    70 VPHDTIARPVEAVPQEILWRSLESGPQ-EILRRPLEVFAPESSHRSSEALSIETQHRLFG 128
             VP D I   +    Q I     ++  Q  +++  L   A   SH   E L I  +  +  
Sbjct:   152 VPSDQIGCVIGKGGQVIQNLRNDTNAQIRVIKDHLPACALTLSH--DELLLIIGEPLVVR 209

Query:   129 AVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAV-RPLSLESDR--VATLDARTQQQE 185
                 ++   LH D  S+   +L ++ SSS+    A+    +L S     A        +E
Sbjct:   210 EALYQVASLLH-DNPSRFQHLLLSSSSSSMHQPGAMLMSAALTSSHRNYAVRRDIADARE 268

Query:   186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
                  +C  + VG VIGKGG  I  ++ E GA I V  +  + D+ +I +++ E  E + 
Sbjct:   269 FCVCFICPAENVGGVIGKGGGFINQIRQETGATIRVNTSETDDDDCIIFISSKEFYEDQ- 327

Query:   246 SPAQKAVVLVFSRLIEGTSEK-GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMR 304
             SPA  A +    RL +  SEK G D +    L ++ RL+V+S+Q+GCL+GKGG +ISEMR
Sbjct:   328 SPAVNAAI----RLQQRCSEKVGKDAND---LAISTRLLVSSSQIGCLIGKGGAVISEMR 380

Query:   305 KVTGTSIRIIS-DQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF 354
              VT  +IRI+  + + K   E++ +VQI+G       A+  V  RLR N F
Sbjct:   381 SVTRANIRILQKEDVPKIAREDEEMVQITGSPDAAMKALTQVILRLRANSF 431

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 232 (86.7 bits), Expect = 1.9e-16, P = 1.9e-16
 Identities = 62/188 (32%), Positives = 108/188 (57%)

Query:   181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPEC--DERLITVTAS 238
             ++ +E+ F++LC    +  VIGKGG+ I+ ++  +G+ I V  +  +C  DE +I VTA+
Sbjct:   307 SRSEELVFKVLCPLCNIMRVIGKGGSTIKRIREASGSCIEVNDSRTKCGDDECVIIVTAT 366

Query:   239 EGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGT 298
             E P+   S A +AV+L+   + +  +E            V  +L+V+S  +GC++GK G+
Sbjct:   367 ESPDDMKSMAVEAVLLLQEYINDEDAEN-----------VKMQLLVSSKVIGCVIGKSGS 415

Query:   299 IISEMRKVTGTSIRIISDQLLKCISEN--DRVVQISGEFSKVKDAVYNVTGRLRDNHFSG 356
             +I+E+RK T  +I         CIS+   D +V++SGE S V+DA+  +  RLR++   G
Sbjct:   416 VINEIRKRTNANI---------CISKGKKDDLVEVSGEVSSVRDALIQIVLRLREDVL-G 465

Query:   357 TLNTARTR 364
               ++  TR
Sbjct:   466 DKDSVATR 473

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 219 (82.2 bits), Expect = 3.6e-15, P = 3.6e-15
 Identities = 56/165 (33%), Positives = 91/165 (55%)

Query:   188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSP 247
             FR++    KVGA+IG+ G  I+ +  E  A I V        +R++ ++  E PE+  SP
Sbjct:    76 FRMIVPVTKVGAIIGRKGDFIKKMCEETRARIKVLDGPVNTPDRIVLISGKEEPEAYMSP 135

Query:   248 AQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNA-RLVVASNQVGCLLGKGGTIISEMRKV 306
             A  AV+ VF R + G  +   D   N G + ++ RL+VAS Q   L+GK G++I  + + 
Sbjct:   136 AMDAVLRVFRR-VSGLPDNDDDDVQNAGSVFSSVRLLVASTQAINLIGKQGSLIKSIVEN 194

Query:   307 TGTSIRIISDQLLKCISEND-RVVQISGEFSKVKDAVYNVTGRLR 350
             +G S+RI+S++     +  D R+V + GE  K+  A+  + G LR
Sbjct:   195 SGASVRILSEEETPFYAAQDERIVDLQGEALKILKALEAIVGHLR 239

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0048367 "shoot system development" evidence=IMP

GO:0048467 "gynoecium development" evidence=IMP

UNIPROTKB|B4DLC0 PCBP2 "Poly(rC)-binding protein 2" [Homo sapiens (taxid:9606)]

 Score = 201 (75.8 bits), Expect = 4.8e-14, P = 4.8e-14
 Identities = 63/222 (28%), Positives = 110/222 (49%)

Query:   186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
             ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER+IT+    GP +  
Sbjct:    14 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLA---GPTNAI 68

Query:   246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
                 KA  ++  +L E  S    + ++     V  RLVV ++Q G L+GKGG  I E+R+
Sbjct:    69 F---KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRE 125

Query:   306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRS 365
              TG  +++  D L    +  +R + I+G    + + V  +   + ++   G     R + 
Sbjct:   126 STGAQVQVAGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLESPPKGVTIPYRPKP 182

Query:   366 TSSVLTETSP---YSRLKDPASFGVHS--SVAVSHDFSQPPL 402
             +SS +        YS   D ASF  H+  S+ ++ D   PPL
Sbjct:   183 SSSPVIFAGGQDRYSTGSDSASFP-HTTPSMCLNPDLEGPPL 223

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|Q3SYT9 PCBP2 "Poly(RC) binding protein 2" [Bos taurus (taxid:9913)]

 Score = 201 (75.8 bits), Expect = 1.3e-13, P = 1.3e-13
 Identities = 63/222 (28%), Positives = 110/222 (49%)

Query:   186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
             ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER+IT+    GP +  
Sbjct:    14 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLA---GPTNAI 68

Query:   246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
                 KA  ++  +L E  S    + ++     V  RLVV ++Q G L+GKGG  I E+R+
Sbjct:    69 F---KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRE 125

Query:   306 VTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRS 365
              TG  +++  D L    +  +R + I+G    + + V  +   + ++   G     R + 
Sbjct:   126 STGAQVQVAGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLESPPKGVTIPYRPKP 182

Query:   366 TSSVLTETSP---YSRLKDPASFGVHS--SVAVSHDFSQPPL 402
             +SS +        YS   D ASF  H+  S+ ++ D   PPL
Sbjct:   183 SSSPVIFAGGQDRYSTGSDSASFP-HTTPSMCLNPDLEGPPL 223

GO:0050687 "negative regulation of defense response to virus" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

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

Your Input: GSVIVG00001893001 SubName- Full=Chromosome undetermined scaffold_123, whole genome shotgun sequence; (817 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	428
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	1e-16
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	2e-14
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-10
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	9e-10
pfam00013	59	pfam00013, KH_1, KH domain	2e-09
pfam13014	42	pfam13014, KH_3, KH domain	1e-07
smart00322	68	smart00322, KH, K homology RNA-binding domain	2e-07
pfam00013	59	pfam00013, KH_1, KH domain	3e-07
pfam13014	42	pfam13014, KH_3, KH domain	3e-07
smart00322	68	smart00322, KH, K homology RNA-binding domain	6e-06
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	3e-05
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	7e-04
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	8e-04

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

 Score = 73.7 bits (182), Expect = 1e-16
 Identities = 27/63 (42%), Positives = 39/63 (61%), Gaps = 3/63 (4%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
           RL+V S+Q G ++GKGG+ I E+R+ TG  IR+    L       +RVV ISG+ S V+ 
Sbjct: 3   RLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGS---TERVVTISGKPSAVQK 59

Query: 341 AVY 343
           A+ 
Sbjct: 60  ALL 62

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 = 67.5 bits (166), Expect = 2e-14
 Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 7/71 (9%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATM-PECDERLITVTASEGPESRY 245
           + R+L  + + G++IGKGG+ I+ ++ E GA I V  ++ P   ER++T++         
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK------P 54

Query: 246 SPAQKAVVLVF 256
           S  QKA++L+ 
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 = 56.4 bits (137), Expect = 1e-10
 Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 4/63 (6%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
           R++V S+ VG ++GKGG+ I E+R+ TG  I+I            +R+V I+G    V+ 
Sbjct: 3   RVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS----GSEERIVTITGTPEAVEK 58

Query: 341 AVY 343
           A  
Sbjct: 59  AKE 61

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 = 54.1 bits (131), Expect = 9e-10
 Identities = 18/53 (33%), Positives = 33/53 (62%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
           + R+L  +  VG +IGKGG+ I+ ++ E GA I +  +    +ER++T+T + 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTP 53

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 = 53.3 bits (129), Expect = 2e-09
 Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 8/62 (12%)

Query: 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVK 339
            R+++  ++VG ++GKGG+ I E+R+ TG  IRI  D+        D  V ISG   +V+
Sbjct: 2   ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR--------DDTVTISGTPEQVE 53

Query: 340 DA 341
            A
Sbjct: 54  KA 55

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

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

 Score = 47.6 bits (114), Expect = 1e-07
 Identities = 18/41 (43%), Positives = 26/41 (63%)

Query: 196 KVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT 236
            VGA+IGKGG  I+ ++ E GA I +    P   ER++T+T
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTIT 41

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

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           V   +++ +++VG ++GKGG+ I ++ + TG  I I            +RVV+I+G    
Sbjct: 3   VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG------SEERVVEITGPPEN 56

Query: 338 VKDAVYNVTGRL 349
           V+ A   +   L
Sbjct: 57  VEKAAELILEIL 68

Length = 68

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

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 4/53 (7%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
           + RIL   DKVG +IGKGG+ I+ ++ E G  I +    P+  +  +T++ + 
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRI----PDDRDDTVTISGTP 49

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

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

 Score = 46.0 bits (110), Expect = 3e-07
 Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 4/46 (8%)

Query: 288 QVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG 333
            VG ++GKGG  I E+R+ TG  I+I            +R+V I+G
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPK----PEPGSGERIVTITG 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|197652 smart00322, KH, K homology RNA-binding domain

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 2/55 (3%)

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
            V+  +L   DKVG +IGKGG+ I+ ++ E G  I +    P  +ER++ +T   
Sbjct: 2   PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--PGSEERVVEITGPP 54

Length = 68

>gnl|CDD|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

 Score = 41.0 bits (97), Expect = 3e-05
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 11/61 (18%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVL 254
           DK+  VIG GG  I+ +  E G  I +       D+  + + AS+        A+KA  +
Sbjct: 11  DKIRDVIGPGGKTIKKIIEETGVKIDIE------DDGTVYIAASDKEA-----AEKAKKM 59

Query: 255 V 255
           +
Sbjct: 60  I 60

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

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

 Score = 41.6 bits (99), Expect = 7e-04
 Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 11/58 (18%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAV 252
           DK+  VIG GG  IR +  E GA I +       D+  + + A++G       A+ A 
Sbjct: 563 DKIRDVIGPGGKTIREITEETGAKIDIE------DDGTVKIAATDGEA-----AEAAK 609

Length = 693

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

 Score = 41.3 bits (98), Expect = 8e-04
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 17/72 (23%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVL 254
           DK+  VIG GG +IR +  E GA I +       D+  + + AS+G E+    A+ A+  
Sbjct: 560 DKIRDVIGPGGKVIREITEETGAKIDIE------DDGTVKIAASDG-EA----AEAAI-- 606

Query: 255 VFSRLIEG-TSE 265
              ++IEG T+E
Sbjct: 607 ---KMIEGITAE 615

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	428
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.96
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.94
KOG1676	600	consensus K-homology type RNA binding proteins [RN	99.92
KOG1676	600	consensus K-homology type RNA binding proteins [RN	99.89
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.88
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.86
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.83
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.83
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.82
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.77
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.64
PRK13763	180	putative RNA-processing protein; Provisional	99.59
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.42
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.31
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.19
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.18
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.13
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.09
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	98.97
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	98.97
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	98.95
PF13014	43	KH_3: KH domain	98.93
PF13014	43	KH_3: KH domain	98.91
smart00322	69	KH K homology RNA-binding domain.	98.9
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.85
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.81
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.69
smart00322	69	KH K homology RNA-binding domain.	98.55
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.24
PRK13763	180	putative RNA-processing protein; Provisional	98.2
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.14
PRK08406	140	transcription elongation factor NusA-like protein;	98.11
KOG2113	394	consensus Predicted RNA binding protein, contains	97.88
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.86
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	97.85
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	97.79
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	97.77
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.68
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.49
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.38
COG0195	190	NusA Transcription elongation factor [Transcriptio	97.36
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.27
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	97.27
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.0
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	96.85
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.7
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	96.59
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	96.52
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.5
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.5
TIGR01953	341	NusA transcription termination factor NusA. This m	96.44
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.42
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.36
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.36
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.32
KOG0119	554	consensus Splicing factor 1/branch point binding p	96.31
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.24
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.21
PRK09202	470	nusA transcription elongation factor NusA; Validat	96.09
PRK00468	75	hypothetical protein; Provisional	95.91
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	95.8
PRK02821	77	hypothetical protein; Provisional	95.65
KOG2814	345	consensus Transcription coactivator complex, P50 c	95.65
KOG2113	394	consensus Predicted RNA binding protein, contains	95.44
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	95.39
KOG2814	345	consensus Transcription coactivator complex, P50 c	95.36
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	95.23
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.18
PRK00468	75	hypothetical protein; Provisional	95.12
PRK12704	520	phosphodiesterase; Provisional	95.1
PRK00106	535	hypothetical protein; Provisional	94.91
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	94.87
PRK01064	78	hypothetical protein; Provisional	94.85
COG5176	269	MSL5 Splicing factor (branch point binding protein	94.77
PRK02821	77	hypothetical protein; Provisional	94.73
COG1837	76	Predicted RNA-binding protein (contains KH domain)	94.31
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	93.94
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	93.78
PRK01064	78	hypothetical protein; Provisional	93.74
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	93.61
COG5176	269	MSL5 Splicing factor (branch point binding protein	93.37
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	92.76
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	92.69
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	92.69
PRK08406	140	transcription elongation factor NusA-like protein;	92.6
PRK12704	520	phosphodiesterase; Provisional	92.6
PRK00106	535	hypothetical protein; Provisional	92.28
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	92.07
PRK06418	166	transcription elongation factor NusA-like protein;	91.7
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	91.66
COG1094	194	Predicted RNA-binding protein (contains KH domains	90.71
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	90.37
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	90.23
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	89.34
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	89.07
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	88.06
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	88.04
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	87.77
PRK12705	508	hypothetical protein; Provisional	87.71
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	87.15
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	86.88
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	85.78
PRK12705	508	hypothetical protein; Provisional	83.79
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	83.52
COG0195	190	NusA Transcription elongation factor [Transcriptio	82.96
COG1855	604	ATPase (PilT family) [General function prediction	82.74
PRK13764	602	ATPase; Provisional	81.94
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	81.89
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	81.83
PRK12328	374	nusA transcription elongation factor NusA; Provisi	81.49
COG1855	604	ATPase (PilT family) [General function prediction	81.41
TIGR01953	341	NusA transcription termination factor NusA. This m	80.87
PRK13764	602	ATPase; Provisional	80.82

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

Probab=99.96  E-value=4.4e-28  Score=238.32  Aligned_cols=186  Identities=26%  Similarity=0.402  Sum_probs=148.0

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc---CCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA---TMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~---~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      .+++|||||+..+|.||||||++|.+||++|||+|++++   ++|+.+||+|.|+|+.+.      .......|.++|.|
T Consensus        38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~ea------i~av~efI~dKire  111 (402)
T KOG2191|consen   38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEA------LNAVHEFIADKIRE  111 (402)
T ss_pred             ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHH------HHHHHHHHHHHHHH
Confidence            499999999999999999999999999999999999986   489999999999998652      22233445566655


Q ss_pred             ccccccc--C--CCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHH
Q 014254          262 GTSEKGL--D--FSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK  337 (428)
Q Consensus       262 ~~~~~g~--~--~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~a  337 (428)
                      .......  +  .....+....++|+||++.+|.||||||.+||.|++++||+|+|+. +.|...+..+|+||++|++++
T Consensus       112 ~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisP-qkpt~~sLqervvt~sge~e~  190 (402)
T KOG2191|consen  112 KPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISP-QKPTGISLQERVVTVSGEPEQ  190 (402)
T ss_pred             hHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecc-cCCCCccceeEEEEecCCHHH
Confidence            4322111  1  0111223356899999999999999999999999999999999983 345556789999999999999


Q ss_pred             HHHHHHHHHHHhhhcCCCCc-cc-------CCCCCCCCCCCCCCCCCCCCCC
Q 014254          338 VKDAVYNVTGRLRDNHFSGT-LN-------TARTRSTSSVLTETSPYSRLKD  381 (428)
Q Consensus       338 V~~A~~lI~~~L~e~~~~~~-~~-------~p~~~~~~~~~~~~spy~~~~~  381 (428)
                      ..+|..+|.++|.++++.+. ++       .|.++++    +.+|||+...+
T Consensus       191 ~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpvaNsn----PtGspya~~~~  238 (402)
T KOG2191|consen  191 NMKAVSLILQKIQEDPQSGSCLNISYANVSGPVANSN----PTGSPYAYQAH  238 (402)
T ss_pred             HHHHHHHHHHHhhcCCcccceeccchhcccCcccccC----CCCCCCCCCCc
Confidence            99999999999999998874 22       4555554    88889887633

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

Probab=99.94  E-value=1.2e-25  Score=236.29  Aligned_cols=169  Identities=37%  Similarity=0.620  Sum_probs=144.6

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhc
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEG  262 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~  262 (428)
                      +...++||||+...+|.||||+|.+||+|+.+|+++|+|.+..+++.||+|+|+|..... ..+++++|+++++++++..
T Consensus        40 ~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~-~~~~~~~al~ka~~~iv~~  118 (485)
T KOG2190|consen   40 DETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL-NLSPATDALFKAFDMIVFK  118 (485)
T ss_pred             CCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-cCCchHHHHHHHHHHHhhc
Confidence            344559999999999999999999999999999999999999999999999999953222 6788999999999988764


Q ss_pred             cc---ccccCCC-CCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHH
Q 014254          263 TS---EKGLDFS-SNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKV  338 (428)
Q Consensus       263 ~~---~~g~~~~-~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV  338 (428)
                      ..   ....+.+ ......++++|+||.+++|+||||+|++||+|++.|||+|++.++++|.   .++|.|+|.|++++|
T Consensus       119 ~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~---ster~V~IsG~~~av  195 (485)
T KOG2190|consen  119 LEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPN---STERAVTISGEPDAV  195 (485)
T ss_pred             ccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCc---ccceeEEEcCchHHH
Confidence            21   1111222 1122368999999999999999999999999999999999999889998   588999999999999


Q ss_pred             HHHHHHHHHHhhhcCCC
Q 014254          339 KDAVYNVTGRLRDNHFS  355 (428)
Q Consensus       339 ~~A~~lI~~~L~e~~~~  355 (428)
                      .+|+..|..+|.+++..
T Consensus       196 ~~al~~Is~~L~~~~~~  212 (485)
T KOG2190|consen  196 KKALVQISSRLLENPPR  212 (485)
T ss_pred             HHHHHHHHHHHHhcCCc
Confidence            99999999999998743

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

Probab=99.92  E-value=7.3e-25  Score=229.38  Aligned_cols=252  Identities=22%  Similarity=0.266  Sum_probs=187.8

Q ss_pred             hhcCccccccCCcCcCCCCCCCCCc--------------cchhhhhcCccccccccccCCCCCcccCC-CCCceecccCC
Q 014254           91 LESGPQEILRRPLEVFAPESSHRSS--------------EALSIETQHRLFGAVSQEILPDLHVDILS-QRNSVLTTAPS  155 (428)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~v~~~~~~~~~~d~~P-gt~~rv~ti~G  155 (428)
                      ||++++-. ++|.+.-+.+-.+.+|              .+|-|+.||--|...+.++.=++...--| ++.+|.|.+.|
T Consensus        27 le~~~~p~-~~~~~~~~l~p~~~~s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G  105 (600)
T KOG1676|consen   27 LEDGPQPF-KGPSEDTDLDPDMDPSDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTG  105 (600)
T ss_pred             ccccCccc-cCCCCccccCcccCCcccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccC
Confidence            34444433 6666655555333333              34468888888888888886554433333 35889999999


Q ss_pred             CcccccccccCCcccccccc--c-hhhhccCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCC--CCCCc
Q 014254          156 SSISYVSAVRPLSLESDRVA--T-LDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATM--PECDE  230 (428)
Q Consensus       156 s~~~~~~a~~~~~~e~~~~~--~-~~~~~~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~--p~s~E  230 (428)
                      ...++..+++.+.....+..  . ........+++.+|+||++++|+||||+|++||+|++.+||++.+-.+.  .....
T Consensus       106 ~pe~v~~aK~li~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~  185 (600)
T KOG1676|consen  106 SPENVEVAKQLIGEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGAD  185 (600)
T ss_pred             CcccHHHHHHhhhhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCC
Confidence            99888888776655433321  1 1112234568999999999999999999999999999999999886542  23367


Q ss_pred             eEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccc---cccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHh
Q 014254          231 RLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE---KGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVT  307 (428)
Q Consensus       231 RvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~---~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~T  307 (428)
                      +.+.|+|.++.      +..|..++++-+.+..-+   .....+.......+.++.||.+.||.||||+|++||+|+.+|
T Consensus       186 KplritGdp~~------ve~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~et  259 (600)
T KOG1676|consen  186 KPLRITGDPDK------VEQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNET  259 (600)
T ss_pred             CceeecCCHHH------HHHHHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhcc
Confidence            88999999775      667777777766643221   112233334455689999999999999999999999999999


Q ss_pred             CCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          308 GTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       308 GA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      |++|+|..|..|.   +.+|.+.|.|+.+.|+.|.++|.++|.+.
T Consensus       260 G~KIQfkpDd~p~---speR~~~IiG~~d~ie~Aa~lI~eii~~~  301 (600)
T KOG1676|consen  260 GAKIQFKPDDDPS---SPERPAQIIGTVDQIEHAAELINEIIAEA  301 (600)
T ss_pred             CceeEeecCCCCC---CccceeeeecCHHHHHHHHHHHHHHHHHH
Confidence            9999999777764   89999999999999999999999999864

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

Probab=99.89  E-value=9.5e-23  Score=213.60  Aligned_cols=238  Identities=18%  Similarity=0.238  Sum_probs=166.2

Q ss_pred             CCCCccchhhhhcCccccccccccCCCC----CcccCCCCCceecccCCCcccccccc---cCCcccccc-ccchhh---
Q 014254          111 SHRSSEALSIETQHRLFGAVSQEILPDL----HVDILSQRNSVLTTAPSSSISYVSAV---RPLSLESDR-VATLDA---  179 (428)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~v~~~~~~~~----~~d~~Pgt~~rv~ti~Gs~~~~~~a~---~~~~~e~~~-~~~~~~---  179 (428)
                      -++...+|-|++||-.+-+||..+.-..    ..+.-++ +..-.-|.|....+..+.   +.++.+... .+....   
T Consensus       145 IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g~~~~~g  223 (600)
T KOG1676|consen  145 IPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-ADKPLRITGDPDKVEQAKQLVADILREEDDEVPGSGGHAG  223 (600)
T ss_pred             cCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-CCCceeecCCHHHHHHHHHHHHHHHHhcccCCCccccccC
Confidence            4677788999999999999999884211    1111121 334445556554444332   222222111 111101   


Q ss_pred             hccCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHH
Q 014254          180 RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSR  258 (428)
Q Consensus       180 ~~~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~  258 (428)
                      .......++++.||.+.||.||||+|++||+|+.+||++|+|-++ .+.+.||.+.|.|+.+.      +..|..+|-+-
T Consensus       224 ~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~------ie~Aa~lI~ei  297 (600)
T KOG1676|consen  224 VRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQ------IEHAAELINEI  297 (600)
T ss_pred             cCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHH------HHHHHHHHHHH
Confidence            112334599999999999999999999999999999999999754 56889999999999875      44454444333


Q ss_pred             hhhccccc--ccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHH
Q 014254          259 LIEGTSEK--GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS  336 (428)
Q Consensus       259 i~e~~~~~--g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~  336 (428)
                      +.+.....  +...+. ........+.||.+.||.||||||++||.|..+|||++.++++  +...+.++++++|.|+..
T Consensus       298 i~~~~~~~~~~~~~G~-P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~--~p~~~~~ektf~IrG~~~  374 (600)
T KOG1676|consen  298 IAEAEAGAGGGMGGGA-PGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ--PPNGNPKEKTFVIRGDKR  374 (600)
T ss_pred             HHHHhccCCCCcCCCC-ccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC--CCCCCccceEEEEecCcc
Confidence            32221111  111111 1122278899999999999999999999999999999999966  444568899999999999


Q ss_pred             HHHHHHHHHHHHhhhcCCCCcc
Q 014254          337 KVKDAVYNVTGRLRDNHFSGTL  358 (428)
Q Consensus       337 aV~~A~~lI~~~L~e~~~~~~~  358 (428)
                      +|..|..||..++.+......+
T Consensus       375 QIdhAk~LIr~kvg~~~~n~~~  396 (600)
T KOG1676|consen  375 QIDHAKQLIRDKVGDIAPNTPY  396 (600)
T ss_pred             cchHHHHHHHHHhcccCCCCCC
Confidence            9999999999999986644333

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

Probab=99.88  E-value=2.4e-23  Score=205.08  Aligned_cols=221  Identities=20%  Similarity=0.267  Sum_probs=175.9

Q ss_pred             hhhhcCcccccccccc-----CCCCCcccCCCCCceecccCCCcccccccccCCccccccccch---------hhhccCC
Q 014254          119 SIETQHRLFGAVSQEI-----LPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATL---------DARTQQQ  184 (428)
Q Consensus       119 ~~~~~~~~~~~v~~~~-----~~~~~~d~~Pgt~~rv~ti~Gs~~~~~~a~~~~~~e~~~~~~~---------~~~~~~~  184 (428)
                      -|++||+.|.++|.++     |+ ++.||||||++|||+|+|+. +...++|.|+.++.++.+.         ++...++
T Consensus        53 IIGKGG~ti~~lqk~tgariklS-ks~dfyPGTTeRvcli~Gt~-eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r  130 (402)
T KOG2191|consen   53 IIGKGGQTIVQLQKETGARIKLS-KSKDFYPGTTERVCLIQGTV-EALNAVHEFIADKIREKPQAVAKPVDILQPQTPDR  130 (402)
T ss_pred             eeccchHHHHHHHhccCcEEEec-cccccCCCccceEEEEeccH-HHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccc
Confidence            6899999999999998     78 99999999999999999999 5566788888887664332         2334556


Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC---CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~---~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      ..++||++|++.+|+||||+|.+||.|++++||.|+|++.   .-+..||+|+++|++++      ..+|+-+|+.++.|
T Consensus       131 ~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~------~~~A~~~IL~Ki~e  204 (402)
T KOG2191|consen  131 IKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQ------NMKAVSLILQKIQE  204 (402)
T ss_pred             cceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHH------HHHHHHHHHHHhhc
Confidence            6789999999999999999999999999999999999953   23678999999999875      78999999999987


Q ss_pred             ccccc-----------c-----cCCC-------CCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc--cC
Q 014254          262 GTSEK-----------G-----LDFS-------SNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII--SD  316 (428)
Q Consensus       262 ~~~~~-----------g-----~~~~-------~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~--~d  316 (428)
                      .....           +     .+.+       ..........+-|+....|..-|.||.++-.+-..+|+.+.++  .+
T Consensus       205 Dpqs~scln~sya~vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~  284 (402)
T KOG2191|consen  205 DPQSGSCLNISYANVSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALN  284 (402)
T ss_pred             CCcccceeccchhcccCcccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccccceeeccccc
Confidence            53210           0     0000       0112334556789999999999999999999999999999888  33


Q ss_pred             CccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254          317 QLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       317 ~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e  351 (428)
                      ..-   +..++ +-+.|-.-++..|-.+|..+...
T Consensus       285 ~m~---g~gy~-~n~~g~~ls~~aa~g~L~~~~~~  315 (402)
T KOG2191|consen  285 TMA---GYGYN-TNILGLGLSILAAEGVLAAKVAS  315 (402)
T ss_pred             ccc---ccccc-ccccchhhhhhhhhhHHHHhhcc
Confidence            222   24444 78889999999998888887754

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

Probab=99.86  E-value=2.4e-21  Score=203.89  Aligned_cols=225  Identities=28%  Similarity=0.458  Sum_probs=168.4

Q ss_pred             hhhhcCccccccccccCCCC-CcccCCCCCceecccCC---------CcccccccccCCccccccccc--hhh--hccCC
Q 014254          119 SIETQHRLFGAVSQEILPDL-HVDILSQRNSVLTTAPS---------SSISYVSAVRPLSLESDRVAT--LDA--RTQQQ  184 (428)
Q Consensus       119 ~~~~~~~~~~~v~~~~~~~~-~~d~~Pgt~~rv~ti~G---------s~~~~~~a~~~~~~e~~~~~~--~~~--~~~~~  184 (428)
                      -|++.|..+...|+++-+.- -.+..|+..+|+.++.|         ..+....+...+......+..  .+.  .....
T Consensus        57 IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~  136 (485)
T KOG2190|consen   57 IIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGP  136 (485)
T ss_pred             EEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcccccccccccCCccccCC
Confidence            57888999999998887633 45558999999999999         554444443333221111111  111  11122


Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcc
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT  263 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~  263 (428)
                      ++++|||||.+++|.||||+|+.||+|+++|||+|+|... .|.+++|.|+|.|.++.      +.+|+..|...+.+..
T Consensus       137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~a------v~~al~~Is~~L~~~~  210 (485)
T KOG2190|consen  137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDA------VKKALVQISSRLLENP  210 (485)
T ss_pred             ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHH------HHHHHHHHHHHHHhcC
Confidence            6899999999999999999999999999999999999876 79999999999999875      5666666666555410


Q ss_pred             ----c---------c-----------cc----------------------------------------------------
Q 014254          264 ----S---------E-----------KG----------------------------------------------------  267 (428)
Q Consensus       264 ----~---------~-----------~g----------------------------------------------------  267 (428)
                          .         .           ..                                                    
T Consensus       211 ~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~  290 (485)
T KOG2190|consen  211 PRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASIS  290 (485)
T ss_pred             CcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceE
Confidence                0         0           00                                                    


Q ss_pred             -----cC-----C--CCCC-------------------------CceeEEEEEeccccccceeCCCCchHHHHHHHhCCe
Q 014254          268 -----LD-----F--SSNK-------------------------GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTS  310 (428)
Q Consensus       268 -----~~-----~--~~~~-------------------------~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~  310 (428)
                           .+     .  ....                         ...++.+|+||++++||||||+|++|.+||+.|||.
T Consensus       291 v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~  370 (485)
T KOG2190|consen  291 VGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGAS  370 (485)
T ss_pred             eccccCcceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCc
Confidence                 00     0  0000                         234789999999999999999999999999999999


Q ss_pred             EEEc-cCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          311 IRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       311 IqI~-~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      |+|. +++..   ..+++.++|+|...+...|++++..++...
T Consensus       371 I~I~~~~~~~---~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~  410 (485)
T KOG2190|consen  371 ISILNKEEVS---GVREALVQITGMLREDLLAQYLIRARLSAP  410 (485)
T ss_pred             eEEccccccC---CcceeEEEecchhHHHHhhhhhcccccccC
Confidence            9999 55442   378999999999999999999998777643

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

Probab=99.83  E-value=1.9e-20  Score=180.52  Aligned_cols=221  Identities=19%  Similarity=0.357  Sum_probs=161.0

Q ss_pred             ccchhhhhcCccccccccccCCCCCcccCCCCCceecccCCCcccccccccCCccccccccchhh-hccCCceEEEEEec
Q 014254          115 SEALSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDA-RTQQQEVSFRILCS  193 (428)
Q Consensus       115 ~~~~~~~~~~~~~~~v~~~~~~~~~~d~~Pgt~~rv~ti~Gs~~~~~~a~~~~~~e~~~~~~~~~-~~~~~evt~rIlVP  193 (428)
                      +.+--+++||+.|.+++-+...-..+ .-..+.+|+|+|+--...++.-...++      +.++. -.....+.+||||.
T Consensus        58 ~agavigkgg~nik~lr~d~na~v~v-pds~~peri~tisad~~ti~~ilk~ii------p~lee~f~~~~pce~rllih  130 (390)
T KOG2192|consen   58 NAGAVIGKGGKNIKALRTDYNASVSV-PDSSGPERILTISADIETIGEILKKII------PTLEEGFQLPSPCELRLLIH  130 (390)
T ss_pred             cccceeccccccHHHHhhhccceeec-cCCCCCceeEEEeccHHHHHHHHHHHh------hhhhhCCCCCCchhhhhhhh
Confidence            34557899999999999886431111 123467899999865543332111111      11111 12334589999999


Q ss_pred             cccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccc-------
Q 014254          194 NDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE-------  265 (428)
Q Consensus       194 ~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~-------  265 (428)
                      .+.+|.|||++|+.||.|++++.|+++|-.. .|++++|||.|.|....      ++..+..|++.+.|..+.       
T Consensus       131 qs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~------v~~~i~~il~~i~e~pikgsa~py~  204 (390)
T KOG2192|consen  131 QSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKR------VVECIKIILDLISESPIKGSAQPYD  204 (390)
T ss_pred             hhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcch------HHHHHHHHHHHhhcCCcCCcCCcCC
Confidence            9999999999999999999999999998754 68999999999998776      556666666655441000       


Q ss_pred             ------------------------------------------------ccc---------C-------------------
Q 014254          266 ------------------------------------------------KGL---------D-------------------  269 (428)
Q Consensus       266 ------------------------------------------------~g~---------~-------------------  269 (428)
                                                                      .+.         +                   
T Consensus       205 p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~Sew  284 (390)
T KOG2192|consen  205 PNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEW  284 (390)
T ss_pred             ccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCcccc
Confidence                                                            000         0                   


Q ss_pred             ----------------------CCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCc
Q 014254          270 ----------------------FSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDR  327 (428)
Q Consensus       270 ----------------------~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eR  327 (428)
                                            .+.-.+...+.++.||.++-|.||||||..|++|++++||.|+|. +.+   .++.||
T Consensus       285 qmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikid-epl---eGsedr  360 (390)
T KOG2192|consen  285 QMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKID-EPL---EGSEDR  360 (390)
T ss_pred             ccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEec-CcC---CCCCce
Confidence                                  000123456889999999999999999999999999999999996 212   247899


Q ss_pred             EEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          328 VVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       328 vVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      +++|+|+.++++.|++++++.++.+
T Consensus       361 IitItGTqdQIqnAQYLlQn~Vkq~  385 (390)
T KOG2192|consen  361 IITITGTQDQIQNAQYLLQNSVKQY  385 (390)
T ss_pred             EEEEeccHHHHhhHHHHHHHHHHhh
Confidence            9999999999999999999999843

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

Probab=99.83  E-value=6.9e-20  Score=176.60  Aligned_cols=156  Identities=28%  Similarity=0.490  Sum_probs=132.6

Q ss_pred             cCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      ....+.++||+.+..+|.||||||++||.|+.+.+|.|+|.+  .+..+|+++|+...+          .+..|+.+++.
T Consensus        44 k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpd--s~~peri~tisad~~----------ti~~ilk~iip  111 (390)
T KOG2192|consen   44 KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPD--SSGPERILTISADIE----------TIGEILKKIIP  111 (390)
T ss_pred             hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccC--CCCCceeEEEeccHH----------HHHHHHHHHhh
Confidence            344589999999999999999999999999999999999987  567899999998654          55666665543


Q ss_pred             cccccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHH
Q 014254          262 GTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA  341 (428)
Q Consensus       262 ~~~~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A  341 (428)
                      .. +.+    ......+.++|+|..+++|.|||++|++||++++++.|+.+|..+   .|..++||+|.|.|.+..|..+
T Consensus       112 ~l-ee~----f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~---c~p~stdrv~l~~g~~k~v~~~  183 (390)
T KOG2192|consen  112 TL-EEG----FQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE---CCPHSTDRVVLIGGKPKRVVEC  183 (390)
T ss_pred             hh-hhC----CCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc---cCCCCcceEEEecCCcchHHHH
Confidence            21 111    123456889999999999999999999999999999999999754   4556999999999999999999


Q ss_pred             HHHHHHHhhhcCCCCc
Q 014254          342 VYNVTGRLRDNHFSGT  357 (428)
Q Consensus       342 ~~lI~~~L~e~~~~~~  357 (428)
                      ++.|++.|.+.+.++.
T Consensus       184 i~~il~~i~e~pikgs  199 (390)
T KOG2192|consen  184 IKIILDLISESPIKGS  199 (390)
T ss_pred             HHHHHHHhhcCCcCCc
Confidence            9999999999998763

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

Probab=99.82  E-value=3.1e-20  Score=187.76  Aligned_cols=160  Identities=26%  Similarity=0.447  Sum_probs=138.1

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhc
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEG  262 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~  262 (428)
                      ..-.+++.||...+|.||||+|.+||+|...+||.|+|..+ .++..+|.|+|+|.++.      ..+|--.||.++.|.
T Consensus       409 e~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppea------qfKAQgrifgKikEe  482 (584)
T KOG2193|consen  409 EQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEA------QFKAQGRIFGKIKEE  482 (584)
T ss_pred             chhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHH------HHhhhhhhhhhhhhh
Confidence            34578899999999999999999999999999999999875 57889999999998774      667888899998876


Q ss_pred             ccccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHH
Q 014254          263 TSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAV  342 (428)
Q Consensus       263 ~~~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~  342 (428)
                      .+     +...+.-.....+-||++.+|+||||||++++|+++.|+|.+.|++|+.|+.  .+.-+|.|+|...+.+.|+
T Consensus       483 nf-----~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdE--nd~vivriiGhfyatq~aQ  555 (584)
T KOG2193|consen  483 NF-----FLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDE--NDQVIVRIIGHFYATQNAQ  555 (584)
T ss_pred             cc-----CCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCc--cceeeeeeechhhcchHHH
Confidence            54     2223456677889999999999999999999999999999999998888762  4445699999999999999


Q ss_pred             HHHHHHhhhcCCCC
Q 014254          343 YNVTGRLRDNHFSG  356 (428)
Q Consensus       343 ~lI~~~L~e~~~~~  356 (428)
                      +.|..++.+....+
T Consensus       556 rki~~iv~qvkq~~  569 (584)
T KOG2193|consen  556 RKIAHIVNQVKQSG  569 (584)
T ss_pred             HHHHHHHHHHHHhh
Confidence            99999999876543

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

Probab=99.77  E-value=1.1e-18  Score=176.73  Aligned_cols=162  Identities=23%  Similarity=0.375  Sum_probs=132.7

Q ss_pred             hccCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHH
Q 014254          180 RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSR  258 (428)
Q Consensus       180 ~~~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~  258 (428)
                      .....+..+|+|||..++|.||||.|++||.|-+.|.|+|.|... ..|..|+.|||.|+++.      +-+|+.+|++-
T Consensus       193 ~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg------~s~Ac~~ILei  266 (584)
T KOG2193|consen  193 KQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG------TSKACKMILEI  266 (584)
T ss_pred             cccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc------hHHHHHHHHHH
Confidence            344567899999999999999999999999999999999999764 46889999999999886      44566665554


Q ss_pred             hhhcccccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc--cCCccccCCCCCcEEEEEeCHH
Q 014254          259 LIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII--SDQLLKCISENDRVVQISGEFS  336 (428)
Q Consensus       259 i~e~~~~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~--~d~~P~~~~s~eRvVtItGt~~  336 (428)
                      +-.+..+..      -...+.++++..+++||++|||.|.+||+|.++||++|.|.  .| +..  .+.+|.+++.|+.+
T Consensus       267 mqkEA~~~k------~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqe-ls~--ynpERTItVkGsiE  337 (584)
T KOG2193|consen  267 MQKEAVDDK------VAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQE-LSL--YNPERTITVKGSIE  337 (584)
T ss_pred             HHHhhhccc------hhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhh-hcc--cCccceEEecccHH
Confidence            433221111      12456778999999999999999999999999999999999  33 222  35799999999999


Q ss_pred             HHHHHHHHHHHHhhhcCCCC
Q 014254          337 KVKDAVYNVTGRLRDNHFSG  356 (428)
Q Consensus       337 aV~~A~~lI~~~L~e~~~~~  356 (428)
                      +|..|..+|+.+|+++.-.+
T Consensus       338 ac~~AE~eImkKlre~yEnD  357 (584)
T KOG2193|consen  338 ACVQAEAEIMKKLRECYEND  357 (584)
T ss_pred             HHHHHHHHHHHHHHHHHhhh
Confidence            99999999999999887554

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.64  E-value=7.8e-16  Score=142.50  Aligned_cols=142  Identities=19%  Similarity=0.257  Sum_probs=100.8

Q ss_pred             EEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEee---CCCCCCcCccHHHHHHHHHHHHhhhccccc
Q 014254          190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT---ASEGPESRYSPAQKAVVLVFSRLIEGTSEK  266 (428)
Q Consensus       190 IlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtIt---Gs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~  266 (428)
                      |.||.+.+|.|||+||++||.|+++|||+|++.+     ++..|.|.   ++++      .+++|...+..-.....++.
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~------~i~kA~~~I~~i~~gf~~e~   70 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPL------AVMKAREVVKAIGRGFSPEK   70 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHH------HHHHHHHHHHHHHcCCCHHH
Confidence            5689999999999999999999999999999984     33568883   3322      25555544443222101110


Q ss_pred             ccCCCCCCCceeEEE-EEecc---------ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHH
Q 014254          267 GLDFSSNKGLLVNAR-LVVAS---------NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS  336 (428)
Q Consensus       267 g~~~~~~~~~~vt~~-L~VP~---------s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~  336 (428)
                      ..  .. .+..+..+ +-|+.         ..+|+|||++|++++.|++.|||+|.|.           +..|.|+|+++
T Consensus        71 A~--~l-~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~-----------~~~v~i~G~~~  136 (172)
T TIGR03665        71 AL--KL-LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY-----------GKTVGIIGDPE  136 (172)
T ss_pred             HH--Hh-cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc-----------CCEEEEECCHH
Confidence            00  00 01112222 23333         3689999999999999999999999995           25699999999


Q ss_pred             HHHHHHHHHHHHhhhcCCCC
Q 014254          337 KVKDAVYNVTGRLRDNHFSG  356 (428)
Q Consensus       337 aV~~A~~lI~~~L~e~~~~~  356 (428)
                      +++.|..+|..+|.+.....
T Consensus       137 ~~~~A~~~i~~li~~~~~~~  156 (172)
T TIGR03665       137 QVQIAREAIEMLIEGAPHGT  156 (172)
T ss_pred             HHHHHHHHHHHHHcCCCChh
Confidence            99999999999997765443

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=99.59  E-value=9.3e-15  Score=136.27  Aligned_cols=145  Identities=17%  Similarity=0.217  Sum_probs=101.4

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEee----CCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT----ASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtIt----Gs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      +...+.||.+.+|.|||++|++||.|+++|||+|++.+     ++..|.|.    ++++      .+.+|...+..-...
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~-----~~g~V~I~~~~~~d~~------~i~kA~~~I~ai~~g   71 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS-----ETGEVIIEPTDGEDPL------AVLKARDIVKAIGRG   71 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC-----CCCeEEEEeCCCCCHH------HHHHHHHHHHHHhcC
Confidence            45678999999999999999999999999999999984     34677785    3322      245555444432221


Q ss_pred             cccccccCCCCCCCceeEEEE-Eec---------cccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEE
Q 014254          262 GTSEKGLDFSSNKGLLVNARL-VVA---------SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI  331 (428)
Q Consensus       262 ~~~~~g~~~~~~~~~~vt~~L-~VP---------~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtI  331 (428)
                      ..++....  . .+..+..++ .|.         ...+|+|||++|++++.|++.|||+|.|..           ..|.|
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 FSPEKALR--L-LDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG-----------KTVAI  137 (180)
T ss_pred             CCHHHHHH--H-hCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-----------CEEEE
Confidence            01110000  0 011112221 111         136899999999999999999999999952           34999


Q ss_pred             EeCHHHHHHHHHHHHHHhhhcCCC
Q 014254          332 SGEFSKVKDAVYNVTGRLRDNHFS  355 (428)
Q Consensus       332 tGt~~aV~~A~~lI~~~L~e~~~~  355 (428)
                      .|+++++..|...|..+++.....
T Consensus       138 ~G~~~~~~~A~~~I~~li~g~~~~  161 (180)
T PRK13763        138 IGDPEQVEIAREAIEMLIEGAPHG  161 (180)
T ss_pred             EeCHHHHHHHHHHHHHHHcCCCcH
Confidence            999999999999999999766543

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.42  E-value=4.6e-13  Score=104.61  Aligned_cols=65  Identities=42%  Similarity=0.647  Sum_probs=58.1

Q ss_pred             EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHH
Q 014254          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVT  346 (428)
Q Consensus       279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~  346 (428)
                      +.+|+||.+.+|+||||+|++|++|++.|||+|++.++..+   ...+|+|+|+|++++++.|+.+|.
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLP---GSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCC---CCCceEEEEEeCHHHHHHHHHhhC
Confidence            36899999999999999999999999999999999844332   368999999999999999999873

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

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.31  E-value=2.1e-12  Score=100.86  Aligned_cols=63  Identities=33%  Similarity=0.665  Sum_probs=55.4

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCC-CCCceEEEeeCCCCCCcCccHHHHHHHHH
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMP-ECDERLITVTASEGPESRYSPAQKAVVLV  255 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p-~s~ERvVtItGs~e~~~~~s~a~~Ai~~I  255 (428)
                      ++||+||.+.+|.||||+|++|++|+++|||+|++.+... +.++|+|+|+|+.++      +.+|+.+|
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSA------VQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHH------HHHHHHhh
Confidence            4799999999999999999999999999999999987643 788999999998765      66776654

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.19  E-value=2.2e-11  Score=93.15  Aligned_cols=60  Identities=35%  Similarity=0.528  Sum_probs=54.1

Q ss_pred             EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHH
Q 014254          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV  345 (428)
Q Consensus       279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI  345 (428)
                      |.+|.||.+++|+|||++|++|++|++.|||+|+|+++       ..+..|+|+|++++|+.|+.+|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-------~~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-------DERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-------TEEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-------CCcEEEEEEeCHHHHHHHHhhC
Confidence            57899999999999999999999999999999999743       1345899999999999999886

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.18  E-value=4.3e-11  Score=92.09  Aligned_cols=60  Identities=20%  Similarity=0.333  Sum_probs=54.5

Q ss_pred             EEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHH
Q 014254          280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV  345 (428)
Q Consensus       280 ~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI  345 (428)
                      .++.||.+++|+|||++|++|++|+++|||+|.|+...      +.++.|+|+|+.++|..|..+|
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~------~~~~~v~I~G~~~~v~~A~~~i   61 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG------SKSDTITITGPKENVEKAKEEI   61 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC------CCCCEEEEEcCHHHHHHHHHHh
Confidence            57899999999999999999999999999999998432      4678999999999999999887

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

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

Probab=99.13  E-value=1.7e-10  Score=89.39  Aligned_cols=58  Identities=21%  Similarity=0.313  Sum_probs=52.6

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHH
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNV  345 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI  345 (428)
                      ....+.||.+++|+||||||++|++|+++|||+|.|.+          ++.|+|+|+ .++++.|..+|
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            35678999999999999999999999999999999962          457999999 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.

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

Probab=99.09  E-value=3.4e-10  Score=86.68  Aligned_cols=62  Identities=35%  Similarity=0.578  Sum_probs=55.3

Q ss_pred             EEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHH
Q 014254          280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV  345 (428)
Q Consensus       280 ~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI  345 (428)
                      .++.||.+++|+|||++|++|++|++.|||+|.|.....    ...++.|+|.|+.+++..|+.+|
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            578999999999999999999999999999999983211    35789999999999999999886

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=98.97  E-value=3.3e-10  Score=86.56  Aligned_cols=52  Identities=27%  Similarity=0.500  Sum_probs=46.0

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCC
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP  241 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~  241 (428)
                      |.+|.||.+.+|+||||+|++|++|+++|||+|+|++.  + .+..|+|+|+.+.
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--~-~~~~v~I~G~~~~   52 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--D-ERDIVTISGSPEQ   52 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHHH
Confidence            57899999999999999999999999999999999865  3 4559999996553

; 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=98.97  E-value=1.1e-09  Score=83.80  Aligned_cols=54  Identities=33%  Similarity=0.606  Sum_probs=48.6

Q ss_pred             EEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCC
Q 014254          188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP  241 (428)
Q Consensus       188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~  241 (428)
                      .+|.||...+|.|||++|++|++|+++|||+|.|.+...+..++.|.|.|+.++
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~   55 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEA   55 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHH
Confidence            579999999999999999999999999999999987555678999999998553

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.

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=98.95  E-value=6e-10  Score=85.72  Aligned_cols=52  Identities=23%  Similarity=0.254  Sum_probs=46.7

Q ss_pred             EEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCC
Q 014254          188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP  241 (428)
Q Consensus       188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~  241 (428)
                      .+|.||.+.+|.|||++|++|++|+++|||+|.+++..  ..++.|+|+|+.++
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~   53 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKEN   53 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHH
Confidence            57899999999999999999999999999999998743  67899999998653

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.

>PF13014 KH_3: KH domain

Probab=98.93  E-value=1.5e-09  Score=78.05  Aligned_cols=42  Identities=40%  Similarity=0.743  Sum_probs=39.0

Q ss_pred             cccceeccCchHHHHHHHHhCCcEEEcc-CCCCCCceEEEeeC
Q 014254          196 KVGAVIGKGGTIIRALQSEAGAFISVGA-TMPECDERLITVTA  237 (428)
Q Consensus       196 ~vG~IIGKgG~tIK~IqeeTGA~I~Is~-~~p~s~ERvVtItG  237 (428)
                      ++|.||||+|++|++|+++|||+|+|++ ..++..+|+|+|+|
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            4799999999999999999999999998 56788999999998

>PF13014 KH_3: KH domain

Probab=98.91  E-value=2.1e-09  Score=77.39  Aligned_cols=43  Identities=44%  Similarity=0.737  Sum_probs=38.0

Q ss_pred             cccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe
Q 014254          288 QVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG  333 (428)
Q Consensus       288 ~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG  333 (428)
                      ++|+||||+|++|++|+++|||+|+|+++..+   ..+++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~---~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEP---GSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCC---CCCceEEEEEC
Confidence            58999999999999999999999999963333   37899999998

>smart00322 KH K homology RNA-binding domain

Probab=98.90  E-value=9.9e-09  Score=77.84  Aligned_cols=66  Identities=32%  Similarity=0.553  Sum_probs=59.0

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHh
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL  349 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L  349 (428)
                      .+.++.||...+|++||++|++|++|++.||++|.+....      .....|+|.|+.+++..|..+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~------~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG------SEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            5678999999999999999999999999999999997321      25788999999999999999998876

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

Probab=98.85  E-value=4.6e-09  Score=81.43  Aligned_cols=47  Identities=28%  Similarity=0.413  Sum_probs=42.5

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS  238 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs  238 (428)
                      ....|.||.+.+|.||||||++||+|+++|||+|.|++      ++.|.|+|+
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~   48 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAAS   48 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeC
Confidence            35668999999999999999999999999999999974      467999996

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.

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

Probab=98.81  E-value=4.8e-08  Score=91.76  Aligned_cols=148  Identities=20%  Similarity=0.262  Sum_probs=102.0

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccc
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE  265 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~  265 (428)
                      ..+.+.||.+.+|.+||+.|++.+.|.+.+++++.+.     +.+..|+|.......+ ....++|...+..-  .    
T Consensus         8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~D-p~~~~ka~d~VkAI--g----   75 (194)
T COG1094           8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTED-PLALLKARDVVKAI--G----   75 (194)
T ss_pred             ceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCC-hHHHHHHHHHHHHH--h----
Confidence            3566899999999999999999999999999999997     5678888987632111 11233333222111  0    


Q ss_pred             cccCCCCC---CCceeEEE------EEecc-----ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEE
Q 014254          266 KGLDFSSN---KGLLVNAR------LVVAS-----NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI  331 (428)
Q Consensus       266 ~g~~~~~~---~~~~vt~~------L~VP~-----s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtI  331 (428)
                      .|+++..+   -...+.+.      +.-++     ...|+|||++|.+-+-|++.|||+|.|.           +..|-|
T Consensus        76 rGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~-----------g~tVai  144 (194)
T COG1094          76 RGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY-----------GKTVAI  144 (194)
T ss_pred             cCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe-----------CcEEEE
Confidence            01110000   00011111      11111     2459999999999999999999999996           346999


Q ss_pred             EeCHHHHHHHHHHHHHHhhhcCCCC
Q 014254          332 SGEFSKVKDAVYNVTGRLRDNHFSG  356 (428)
Q Consensus       332 tGt~~aV~~A~~lI~~~L~e~~~~~  356 (428)
                      .|.+++|+.|...|..+|...+...
T Consensus       145 iG~~~~v~iAr~AVemli~G~~h~~  169 (194)
T COG1094         145 IGGFEQVEIAREAVEMLINGAPHGK  169 (194)
T ss_pred             ecChhhhHHHHHHHHHHHcCCCchh
Confidence            9999999999999999998776544

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

Probab=98.69  E-value=1.4e-08  Score=106.89  Aligned_cols=147  Identities=23%  Similarity=0.387  Sum_probs=116.5

Q ss_pred             cCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      ..+++.++++|+...+-++|||+|++||.|++.++++|.+.+.. -.++++-++.|.+.+   ++++.   ..++.++.+
T Consensus        64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~---v~~a~---a~~~~~~~~  136 (608)
T KOG2279|consen   64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQ---VCKAK---AAIHQILTE  136 (608)
T ss_pred             chhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCC---CChHH---HHHHHHHhc
Confidence            34678899999999999999999999999999999999997532 245677777776554   33333   334444433


Q ss_pred             cccccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHH
Q 014254          262 GTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA  341 (428)
Q Consensus       262 ~~~~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A  341 (428)
                                   ...+...+-+|...+++|+|++|.++.+|+..++|+|.+..+.    .....+...|.|....+..|
T Consensus       137 -------------~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng----r~g~~~~~~i~~qqk~~~~a  199 (608)
T KOG2279|consen  137 -------------NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG----RLGLSRLIKISGQQKEVAAA  199 (608)
T ss_pred             -------------CCcccccccchhhhcccccccchhhhcchhccccccccccccc----ccccccceecccccchHHHH
Confidence                         3456778899999999999999999999999999999997331    12457788888888888899


Q ss_pred             HHHHHHHhhhc
Q 014254          342 VYNVTGRLRDN  352 (428)
Q Consensus       342 ~~lI~~~L~e~  352 (428)
                      ..++.+++.++
T Consensus       200 ~~~~~~~~~ed  210 (608)
T KOG2279|consen  200 KHLILEKVSED  210 (608)
T ss_pred             Hhhhhccccch
Confidence            99999988754

>smart00322 KH K homology RNA-binding domain

Probab=98.55  E-value=2.6e-07  Score=69.95  Aligned_cols=54  Identities=33%  Similarity=0.645  Sum_probs=46.9

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG  240 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e  240 (428)
                      .++.+|.||...+|.+||++|++|+.|++.||++|.+...  .....+|.|.|..+
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~--~~~~~~v~i~g~~~   55 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED--GSEERVVEITGPPE   55 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC--CCCccEEEEEcCHH
Confidence            3578899999999999999999999999999999999752  22678899999854

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.24  E-value=1.2e-06  Score=81.31  Aligned_cols=61  Identities=28%  Similarity=0.367  Sum_probs=54.5

Q ss_pred             EEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEE---EeCHHHHHHHHHHHHHHhhh
Q 014254          282 LVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI---SGEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       282 L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtI---tGt~~aV~~A~~lI~~~L~e  351 (428)
                      +.||.+.+|.|||+||++|++|++.|||+|++..         .+..|.|   +++++++.+|..+|..+...
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~---------~~g~V~I~~~t~d~~~i~kA~~~I~~i~~g   65 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS---------ETGEVKIEEEDEDPLAVMKAREVVKAIGRG   65 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc---------CCceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence            5789999999999999999999999999999962         2356888   89999999999999997774

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

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.20  E-value=2.8e-06  Score=79.46  Aligned_cols=65  Identities=25%  Similarity=0.270  Sum_probs=57.6

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEE----eCHHHHHHHHHHHHHHhhh
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS----GEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtIt----Gt~~aV~~A~~lI~~~L~e  351 (428)
                      ....+.||.+.+|.|||++|++|+.|++.|||+|++..         .+..|.|.    ++++++.+|+.+|..++..
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~---------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g   71 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS---------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRG   71 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC---------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence            35688999999999999999999999999999999962         23678885    8999999999999998874

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

Probab=98.14  E-value=6.3e-06  Score=72.49  Aligned_cols=67  Identities=27%  Similarity=0.318  Sum_probs=51.5

Q ss_pred             ccccceeCCCCchHHHHHHHhCCeEEEccCCc------------cccCC-CCCcEEEEEeCH---HHHHHHHHHHHHHhh
Q 014254          287 NQVGCLLGKGGTIISEMRKVTGTSIRIISDQL------------LKCIS-ENDRVVQISGEF---SKVKDAVYNVTGRLR  350 (428)
Q Consensus       287 s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~------------P~~~~-s~eRvVtItGt~---~aV~~A~~lI~~~L~  350 (428)
                      +++|.|||++|++||+|+++|||+|.|.++..            |.... ...-.|.|++..   +++++|..+|..++.
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            57899999999999999999999999984310            11011 122459999965   899999999999998


Q ss_pred             hcC
Q 014254          351 DNH  353 (428)
Q Consensus       351 e~~  353 (428)
                      +..
T Consensus        95 ~~~   97 (120)
T cd02395          95 PAI   97 (120)
T ss_pred             cCC
Confidence            443

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

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.11  E-value=1e-05  Score=72.89  Aligned_cols=104  Identities=20%  Similarity=0.300  Sum_probs=70.8

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccc
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE  265 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~  265 (428)
                      -.+.|+|+...+|..||++|++|+.|++..|-+|.|-.           -  +.+       ..+-+..++.   .....
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve-----------~--s~d-------~~~fI~n~l~---Pa~V~   88 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE-----------Y--SDD-------PEEFIKNIFA---PAAVR   88 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE-----------c--CCC-------HHHHHHHHcC---CCEEE
Confidence            35668999999999999999999999999998887743           1  112       1111111111   11000


Q ss_pred             cccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          266 KGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       266 ~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      . ..- ........+.+.|+.+..|..|||+|++|+.++..+|-++.|.
T Consensus        89 ~-v~I-~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         89 S-VTI-KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             E-EEE-EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            0 000 0012234667889999999999999999999999999888773

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

Probab=97.88  E-value=6.7e-06  Score=81.99  Aligned_cols=142  Identities=21%  Similarity=0.279  Sum_probs=99.0

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHH-----
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSR-----  258 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~-----  258 (428)
                      +.++..+-+|...++.|.|++|.+||.|+.+|...|+-+   ....+-++.++|..+.      +..|-..+...     
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tP---sr~eePiF~vTg~~ed------v~~aRrei~saaeH~~   94 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTP---SRGEEPIFPVTGRHED------VRRARREIPSAAEHFG   94 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccC---CCCCCCcceeccCchh------HHHHhhcCccccceee
Confidence            568888899999999999999999999999999999865   2345578889998775      22222222110     


Q ss_pred             -hhhcccccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc-cCCccccCCCCCcEEEEEeCHH
Q 014254          259 -LIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII-SDQLLKCISENDRVVQISGEFS  336 (428)
Q Consensus       259 -i~e~~~~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~-~d~~P~~~~s~eRvVtItGt~~  336 (428)
                       +.......+.-.+.......+...-+|...+|.|.|..|.+|+.|++.+...|.-+ .+        .+-++.++|-+.
T Consensus        95 l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~--------~~~Vf~Vtg~~~  166 (394)
T KOG2113|consen   95 LIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC--------GEPVFCVTGAPK  166 (394)
T ss_pred             eeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC--------CCceEEEecCCc
Confidence             00000000001111123445667889999999999999999999999999999887 32        456677888777


Q ss_pred             H-HHHHH
Q 014254          337 K-VKDAV  342 (428)
Q Consensus       337 a-V~~A~  342 (428)
                      + +++|.
T Consensus       167 nC~kra~  173 (394)
T KOG2113|consen  167 NCVKRAR  173 (394)
T ss_pred             chhhhcc
Confidence            7 44444

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.86  E-value=6.3e-05  Score=83.27  Aligned_cols=92  Identities=16%  Similarity=0.207  Sum_probs=69.4

Q ss_pred             HHHHHHHHHHHHhhhcccccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCC
Q 014254          247 PAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISEND  326 (428)
Q Consensus       247 ~a~~Ai~~I~~~i~e~~~~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~e  326 (428)
                      .+.++...|++.+.+..... .  ....-......+.||.+.+|.|||+||++|++|+++|||+|.|.          .+
T Consensus       550 ~A~~g~~~Il~~m~~al~~p-~--~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~----------d~  616 (719)
T TIGR02696       550 QARDARLAILDVMAEAIDTP-D--EMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE----------DD  616 (719)
T ss_pred             HHHHHHHHHHHHHHHHHhCc-c--ccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe----------cC
Confidence            45556666665544322211 1  11233456778999999999999999999999999999999995          35


Q ss_pred             cEEEEEeC-HHHHHHHHHHHHHHhhh
Q 014254          327 RVVQISGE-FSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       327 RvVtItGt-~~aV~~A~~lI~~~L~e  351 (428)
                      ..|.|.+. .+++++|+.+|..++..
T Consensus       617 G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       617 GTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            67999995 88999999999999884

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.

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

Probab=97.85  E-value=4e-05  Score=67.40  Aligned_cols=36  Identities=28%  Similarity=0.537  Sum_probs=31.1

Q ss_pred             EEEecc------ccccceeccCchHHHHHHHHhCCcEEEccC
Q 014254          189 RILCSN------DKVGAVIGKGGTIIRALQSEAGAFISVGAT  224 (428)
Q Consensus       189 rIlVP~------~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~  224 (428)
                      |+.||.      +.+|.|||++|++||+|+++|||+|.|...
T Consensus         3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~   44 (120)
T cd02395           3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGK   44 (120)
T ss_pred             EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecC
Confidence            455665      478999999999999999999999999763

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.

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=97.79  E-value=6.5e-05  Score=84.16  Aligned_cols=140  Identities=16%  Similarity=0.258  Sum_probs=104.4

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccc
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE  265 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~  265 (428)
                      +...+-+-......|+||+|.+|.+|+++++|.|.+..  .+.++..+.++|...+   +..+.+.+..++..+..    
T Consensus       347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~~~---~~ka~~~v~~~~~ei~n----  417 (753)
T KOG2208|consen  347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVSAN---DEKAVEDVEKIIAEILN----  417 (753)
T ss_pred             eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccccc---hhHHHHHHHHHHHhhhc----
Confidence            56667778889999999999999999999999999986  5677888999997665   22333334333333321    


Q ss_pred             cccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhC-CeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHH
Q 014254          266 KGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTG-TSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYN  344 (428)
Q Consensus       266 ~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TG-A~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~l  344 (428)
                                ......+.||...+..+||.+|..|++|...+| ..|+...+.      .....+++.|....+..+..+
T Consensus       418 ----------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~------~~~~~~~~~~~~~dv~~~~~~  481 (753)
T KOG2208|consen  418 ----------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN------NSSDMVTIRGISKDVEKSVSL  481 (753)
T ss_pred             ----------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC------cccccceEeccccccchhHHH
Confidence                      134557899999999999999999999999999 666665321      334557888887777766666


Q ss_pred             HHHHhh
Q 014254          345 VTGRLR  350 (428)
Q Consensus       345 I~~~L~  350 (428)
                      +..+..
T Consensus       482 ~~~~~~  487 (753)
T KOG2208|consen  482 LKALKA  487 (753)
T ss_pred             HHhhhh
Confidence            655554

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

Probab=97.77  E-value=5.4e-05  Score=80.41  Aligned_cols=167  Identities=19%  Similarity=0.235  Sum_probs=113.0

Q ss_pred             cCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      .+..+...+-+|...++.|+|++|.+++.|+.-++|+|.+....-..-.+...|.|....+      ..|-.++.+++.+
T Consensus       136 ~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~------~~a~~~~~~~~~e  209 (608)
T KOG2279|consen  136 ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEV------AAAKHLILEKVSE  209 (608)
T ss_pred             cCCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchH------HHHHhhhhccccc
Confidence            3456777888999999999999999999999999999999876445567888888865431      1111112222111


Q ss_pred             c----------------------cc-----------------------ccccCC-----C--------------------
Q 014254          262 G----------------------TS-----------------------EKGLDF-----S--------------------  271 (428)
Q Consensus       262 ~----------------------~~-----------------------~~g~~~-----~--------------------  271 (428)
                      .                      .+                       ..+.+.     +                    
T Consensus       210 deelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~  289 (608)
T KOG2279|consen  210 DEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSF  289 (608)
T ss_pred             hhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCcccccc
Confidence            0                      00                       000000     0                    


Q ss_pred             CCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccC-CCCCcEEEEEeCHHHHHHHHHHHHHHhh
Q 014254          272 SNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCI-SENDRVVQISGEFSKVKDAVYNVTGRLR  350 (428)
Q Consensus       272 ~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~-~s~eRvVtItGt~~aV~~A~~lI~~~L~  350 (428)
                      ........-++.||..++|.+||+.|+.++.+...+++.+.|...  |-.. ...-.++.+.|+..-+..|..|+..+.-
T Consensus       290 ~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~--pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~p  367 (608)
T KOG2279|consen  290 QKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQ--PYTSRVLQLQICVNEGKQHYENSVLEMLTVHVP  367 (608)
T ss_pred             ccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEec--cccchhhhhhhheecchhHHHHHHHhhhhccCC
Confidence            001122345789999999999999999999999999999999722  2200 0112457899999999999999996555


Q ss_pred             hcCCCC
Q 014254          351 DNHFSG  356 (428)
Q Consensus       351 e~~~~~  356 (428)
                      +..|..
T Consensus       368 ~~~f~e  373 (608)
T KOG2279|consen  368 DIVFAE  373 (608)
T ss_pred             cccccc
Confidence            444443

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.68  E-value=8.3e-05  Score=67.22  Aligned_cols=103  Identities=22%  Similarity=0.284  Sum_probs=69.7

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhccccc
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK  266 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~  266 (428)
                      .+-|+|....+|..||++|++|+.|++..|-+|.|-.           -+  .+.          ...+.+.+...... 
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe-----------ys--~D~----------~~fI~N~l~PA~V~-   89 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE-----------YS--ENL----------EEFVANKLAPAEVK-   89 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE-----------cC--CCH----------HHHHHHcCCCceEE-
Confidence            5668999999999999999999999988888887743           11  111          00111111110000 


Q ss_pred             ccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          267 GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       267 g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      .... ...+......+.||.+..|..|||+|++++...+.+|-++.|.
T Consensus        90 ~V~i-~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        90 NVTV-SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             EEEE-EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            0000 0012335678899999999999999999999999999888773

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.49  E-value=0.00033  Score=77.94  Aligned_cols=66  Identities=21%  Similarity=0.358  Sum_probs=56.5

Q ss_pred             ceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhh
Q 014254          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e  351 (428)
                      ......+.||.+.+|.|||+||++||+|+++|||+|.|.          .+-.|.|.+. ...+.+|..+|..+..+
T Consensus       549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~----------ddG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE----------DDGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe----------cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            355678899999999999999999999999999999995          2456888875 77889999999988764

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

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

Probab=97.38  E-value=0.00074  Score=71.22  Aligned_cols=76  Identities=21%  Similarity=0.318  Sum_probs=57.9

Q ss_pred             eeEEEEEecc------ccccceeCCCCchHHHHHHHhCCeEEEcc-----CCc------cccCCCCCc-EEEEEeC-HHH
Q 014254          277 LVNARLVVAS------NQVGCLLGKGGTIISEMRKVTGTSIRIIS-----DQL------LKCISENDR-VVQISGE-FSK  337 (428)
Q Consensus       277 ~vt~~L~VP~------s~VG~IIGKgG~~IkeIre~TGA~IqI~~-----d~~------P~~~~s~eR-vVtItGt-~~a  337 (428)
                      .++.+|.||-      ++||.|||..|.+.|+|+++|||+|.|-+     |..      .......+. -+.|+++ .+.
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            5667788875      58999999999999999999999999983     111      111112233 3888886 778


Q ss_pred             HHHHHHHHHHHhhhc
Q 014254          338 VKDAVYNVTGRLRDN  352 (428)
Q Consensus       338 V~~A~~lI~~~L~e~  352 (428)
                      |++|+.+|..+|.+.
T Consensus       217 i~~Ai~vienli~~a  231 (554)
T KOG0119|consen  217 IKKAIAVIENLIQSA  231 (554)
T ss_pred             HHHHHHHHHHHHHhh
Confidence            999999999999963

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=97.36  E-value=0.00078  Score=63.78  Aligned_cols=101  Identities=28%  Similarity=0.325  Sum_probs=67.4

Q ss_pred             EEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccc
Q 014254          188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKG  267 (428)
Q Consensus       188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g  267 (428)
                      +-+.+-.+.+|..|||+|++|+.|+++.|-+|.|-.             -++++       ..-+..++.-..-....  
T Consensus        78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe-------------~s~d~-------~~fI~nal~Pa~v~~V~--  135 (190)
T COG0195          78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE-------------WSEDP-------AEFIKNALAPAEVLSVN--  135 (190)
T ss_pred             EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEE-------------eCCCH-------HHHHHHhcCcceEeEEE--
Confidence            334555678999999999999999999997676632             22332       11111111100000000  


Q ss_pred             cCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          268 LDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       268 ~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      ..  . .+.. ...+.||.++.+..|||+|.+++-+.+.||-++.|.
T Consensus       136 ~~--~-~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~  178 (190)
T COG0195         136 IK--E-DDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE  178 (190)
T ss_pred             EE--e-CCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence            00  0 0111 678899999999999999999999999999999996

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

Probab=97.27  E-value=0.00057  Score=71.12  Aligned_cols=71  Identities=25%  Similarity=0.289  Sum_probs=55.3

Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHH---HHHhh
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV---TGRLR  350 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI---~~~L~  350 (428)
                      ........+.|.+++||.|||+||++|+.||..|+++|+|.+.       ..+-.|+|-|...--.+|...|   ..+..
T Consensus        43 g~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~-------~~e~kv~ifg~~~m~~kaka~id~~~~k~e  115 (629)
T KOG0336|consen   43 GGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC-------DLEVKVTIFGINHMRKKAKASIDRGQDKDE  115 (629)
T ss_pred             CCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc-------CceeEEEEechHHHHHHHHhhHhhhhhhhh
Confidence            3455667788999999999999999999999999999999843       3467899999966555554444   44444


Q ss_pred             h
Q 014254          351 D  351 (428)
Q Consensus       351 e  351 (428)
                      +
T Consensus       116 ~  116 (629)
T KOG0336|consen  116 R  116 (629)
T ss_pred             h
Confidence            4

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=97.27  E-value=0.00067  Score=76.18  Aligned_cols=164  Identities=18%  Similarity=0.179  Sum_probs=108.1

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCc-CccHHHHHHHHHHH----
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPES-RYSPAQKAVVLVFS----  257 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~-~~s~a~~Ai~~I~~----  257 (428)
                      ..-+..++.+-...++.+||+||.+++.+++++.+.|+|....  .......|.|..+... ...-.+.++.++-.    
T Consensus       198 ~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn--~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~  275 (753)
T KOG2208|consen  198 ERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSN--KSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDY  275 (753)
T ss_pred             ceeEEEEeeccccchhhhccccccccccccccceeEEEccccc--ccchhhhhccccccceehhhhhHHHHHHhcChhhh
Confidence            3447888999999999999999999999999999999998531  1111122222211100 00001111111100    


Q ss_pred             -----H----------------hhhc---------ccccccC----CC-----------------CCCCceeEEEEEecc
Q 014254          258 -----R----------------LIEG---------TSEKGLD----FS-----------------SNKGLLVNARLVVAS  286 (428)
Q Consensus       258 -----~----------------i~e~---------~~~~g~~----~~-----------------~~~~~~vt~~L~VP~  286 (428)
                           +                +...         .+....+    .+                 .-....+.+.+.|-.
T Consensus       276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~  355 (753)
T KOG2208|consen  276 DEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFP  355 (753)
T ss_pred             hhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecH
Confidence                 0                0000         0000000    00                 002344678889999


Q ss_pred             ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcCC
Q 014254          287 NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF  354 (428)
Q Consensus       287 s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~~  354 (428)
                      ..+..++||+|.+|.+|++.+++.|.+...      ++++..|.++|...++.+|...+...+.+-+.
T Consensus       356 ~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n  417 (753)
T KOG2208|consen  356 EELKFVIGKKGANIEKIREESQVKIDLPKQ------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN  417 (753)
T ss_pred             HhhhhhcCCCCccHHHHHHhhhhceecccc------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc
Confidence            999999999999999999999999999742      26788899999999999999999988887665

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.00  E-value=0.0015  Score=74.17  Aligned_cols=67  Identities=18%  Similarity=0.260  Sum_probs=57.8

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHhCCe-EEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhh
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTS-IRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~-IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e  351 (428)
                      -......+.||.+.+|.|||.||++|++|.++||++ |.+.          .+-.|.|.+. .+++++|+.+|.++..+
T Consensus       682 ~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~----------ddg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        682 YAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ----------DDGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             cCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC----------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            345677899999999999999999999999999999 8884          2456889885 88999999999998764

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=96.85  E-value=0.0019  Score=71.82  Aligned_cols=50  Identities=32%  Similarity=0.519  Sum_probs=43.8

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG  240 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e  240 (428)
                      .....+.||.+++|.|||+||.+||.|+++||++|.|.+      +..|.|.+...
T Consensus       577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~  626 (719)
T TIGR02696       577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADG  626 (719)
T ss_pred             CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCH
Confidence            356778999999999999999999999999999999974      57799998643

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.

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

Probab=96.70  E-value=0.0027  Score=49.20  Aligned_cols=36  Identities=31%  Similarity=0.541  Sum_probs=33.7

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEE
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV  221 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~I  221 (428)
                      ..+.+.|+.+.+|.+|||+|.+|+.+++.+|-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            678899999999999999999999999999988876

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.

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

Probab=96.59  E-value=0.0014  Score=68.40  Aligned_cols=57  Identities=23%  Similarity=0.297  Sum_probs=49.1

Q ss_pred             ccCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254          181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG  240 (428)
Q Consensus       181 ~~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e  240 (428)
                      ....++.+.|.|-+..||.|||+||++||.||..|+++|+|.+   ...+-.|+|-|...
T Consensus        42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~---~~~e~kv~ifg~~~   98 (629)
T KOG0336|consen   42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIK---CDLEVKVTIFGINH   98 (629)
T ss_pred             cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEec---cCceeEEEEechHH
Confidence            4567788899999999999999999999999999999999974   34567799999643

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=96.52  E-value=0.0032  Score=70.21  Aligned_cols=49  Identities=33%  Similarity=0.508  Sum_probs=42.3

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCC
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE  239 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~  239 (428)
                      .....+.||.+++|.|||+||++||.|+++|||+|.|.+      +-.|.|.+..
T Consensus       550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~  598 (684)
T TIGR03591       550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASD  598 (684)
T ss_pred             CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECc
Confidence            456778999999999999999999999999999999974      4567787753

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=96.50  E-value=0.0077  Score=66.20  Aligned_cols=73  Identities=19%  Similarity=0.291  Sum_probs=61.1

Q ss_pred             eeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCH-HHHHHHHHHHHHHhhhcCCC
Q 014254          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEF-SKVKDAVYNVTGRLRDNHFS  355 (428)
Q Consensus       277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~-~aV~~A~~lI~~~L~e~~~~  355 (428)
                      .....+.|+.+.++-+||+||++|++|.++|||+|.|.          .+-.|.|.++. +.+.+|+..|.++.++.-..
T Consensus       551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg  620 (692)
T COG1185         551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE----------DDGTVKIAASDGESAKKAKERIEAITREVEVG  620 (692)
T ss_pred             CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec----------CCCcEEEEecchHHHHHHHHHHHHHHhhcccc
Confidence            34567889999999999999999999999999999995          24469999985 78899999999999776554


Q ss_pred             Cccc
Q 014254          356 GTLN  359 (428)
Q Consensus       356 ~~~~  359 (428)
                      ..|.
T Consensus       621 ~iy~  624 (692)
T COG1185         621 EVYE  624 (692)
T ss_pred             cEEE
Confidence            4443

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

Probab=96.50  E-value=0.004  Score=48.21  Aligned_cols=36  Identities=39%  Similarity=0.611  Sum_probs=33.9

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEE
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI  313 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI  313 (428)
                      ....+.|+.+.+|.+|||+|.+|+.+++.+|-+|.+
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            578899999999999999999999999999998876

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

>TIGR01953 NusA transcription termination factor NusA

Probab=96.44  E-value=0.0011  Score=68.04  Aligned_cols=94  Identities=28%  Similarity=0.393  Sum_probs=62.7

Q ss_pred             ccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCC
Q 014254          195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN  273 (428)
Q Consensus       195 ~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~  273 (428)
                      +-+|..||++|++|+.|.++. |=+|.|-.             =+.++          ...+...+....... ..- . 
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~-------------~s~d~----------~~fi~nal~Pa~v~~-v~i-~-  296 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIE-------------YSDDP----------AEFIANALSPAKVIS-VEV-L-  296 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhcCCceEEE-EEE-E-
Confidence            469999999999999999998 66666632             12221          001111111100000 000 0 


Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      ......+.+.||.++.+..|||+|.+++-..+.||.+|.|.
T Consensus       297 ~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~  337 (341)
T TIGR01953       297 DEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVK  337 (341)
T ss_pred             cCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEE
Confidence            01224688999999999999999999999999999999996

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=96.42  E-value=0.0024  Score=66.06  Aligned_cols=93  Identities=25%  Similarity=0.293  Sum_probs=62.8

Q ss_pred             ccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCC
Q 014254          195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN  273 (428)
Q Consensus       195 ~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~  273 (428)
                      +-+|..||++|.+|+.|.++. |=+|.|-.             =+.++          ...+...+....... ...   
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~-------------~s~D~----------~~fI~Nal~Pa~V~~-V~i---  303 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIE-------------YSNVP----------EIFIARALAPAIISS-VKI---  303 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhCCCceeeE-EEE---
Confidence            469999999999999999998 66666632             12221          011111111100000 000   


Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      ......+.+.||.++.+..|||+|.+++-..+.||.+|.|.
T Consensus       304 ~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~  344 (374)
T PRK12328        304 EEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN  344 (374)
T ss_pred             cCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence            01224678899999999999999999999999999999998

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

Probab=96.36  E-value=0.0037  Score=61.55  Aligned_cols=39  Identities=23%  Similarity=0.457  Sum_probs=35.1

Q ss_pred             CceEEEEEeccc------cccceeccCchHHHHHHHHhCCcEEEc
Q 014254          184 QEVSFRILCSND------KVGAVIGKGGTIIRALQSEAGAFISVG  222 (428)
Q Consensus       184 ~evt~rIlVP~~------~vG~IIGKgG~tIK~IqeeTGA~I~Is  222 (428)
                      -.++.||+||..      .||.|+|..|.++|+|+++|||+|.|-
T Consensus        90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir  134 (259)
T KOG1588|consen   90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR  134 (259)
T ss_pred             eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence            357888999975      799999999999999999999999885

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.36  E-value=0.0013  Score=68.04  Aligned_cols=94  Identities=28%  Similarity=0.328  Sum_probs=63.1

Q ss_pred             ccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCC
Q 014254          195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN  273 (428)
Q Consensus       195 ~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~  273 (428)
                      +-+|..||++|.+|+.|.++. |-+|.|-..             +.++          ...+...+....... ..- . 
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~-------------s~d~----------~~fi~nal~Pa~v~~-v~i-~-  298 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDW-------------SEDP----------AEFVANALSPAKVVS-VEV-D-  298 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEc-------------CCCH----------HHHHHHhCCCceEEE-EEE-E-
Confidence            469999999999999999998 777766421             2221          011111111100000 000 0 


Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      ......+.+.||.++.+..|||+|.+++--.+.||.+|.|.
T Consensus       299 ~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~  339 (362)
T PRK12327        299 DEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIK  339 (362)
T ss_pred             cCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEE
Confidence            01224678999999999999999999999999999999997

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.32  E-value=0.0069  Score=67.69  Aligned_cols=65  Identities=22%  Similarity=0.337  Sum_probs=54.8

Q ss_pred             eeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhh
Q 014254          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e  351 (428)
                      .....+.||.+.++.+||.||.+|++|.++||++|.+.          .+-.|.|.+. ..++.+|..+|..+..+
T Consensus       553 p~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        553 PRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE----------DDGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             chheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence            34456778999999999999999999999999988874          2456888884 88899999999988865

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

Probab=96.31  E-value=0.0063  Score=64.40  Aligned_cols=39  Identities=26%  Similarity=0.435  Sum_probs=34.4

Q ss_pred             ceEEEEEecc------ccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254          185 EVSFRILCSN------DKVGAVIGKGGTIIRALQSEAGAFISVGA  223 (428)
Q Consensus       185 evt~rIlVP~------~~vG~IIGKgG~tIK~IqeeTGA~I~Is~  223 (428)
                      .++-|+.||.      +.||+|||..|.|.|+|+++|||+|.|-.
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRG  181 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRG  181 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEec
Confidence            5677788886      47999999999999999999999999954

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.24  E-value=0.011  Score=62.41  Aligned_cols=94  Identities=28%  Similarity=0.337  Sum_probs=62.3

Q ss_pred             ccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCC
Q 014254          195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN  273 (428)
Q Consensus       195 ~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~  273 (428)
                      +-+|..||++|.+|+.|.++. |=+|.|-.             =+.++          ...+...+.......- .- . 
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~-------------ys~Dp----------~~fI~NaLsPA~V~~V-~i-~-  330 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIR-------------WSPDP----------ATYIANALSPARVDEV-RL-V-  330 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhcCCceeeEE-EE-E-
Confidence            459999999999999999998 66666632             12221          0111111111000000 00 0 


Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      ......+.+.||.++.+..|||+|.+++--.+.||.+|.|.
T Consensus       331 ~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~  371 (449)
T PRK12329        331 DPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK  371 (449)
T ss_pred             cCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence            01123578999999999999999999999999999999996

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.21  E-value=0.011  Score=57.57  Aligned_cols=67  Identities=22%  Similarity=0.314  Sum_probs=57.5

Q ss_pred             EEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhhcCCCC
Q 014254          280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRDNHFSG  356 (428)
Q Consensus       280 ~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e~~~~~  356 (428)
                      ..+.||.++++.+||++|.+|+.|.+.++++|.+-          .+-.|.|.|. .+++.+|..+|...-++++.++
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~~~  214 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG----------QNGRIWIKGPDEEDEEIAIEAIKKIEREAHTSG  214 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhhccC
Confidence            56889999999999999999999999999999983          3457999997 5588999999998887777654

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=96.09  E-value=0.0025  Score=68.12  Aligned_cols=93  Identities=28%  Similarity=0.383  Sum_probs=62.8

Q ss_pred             ccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCC
Q 014254          195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN  273 (428)
Q Consensus       195 ~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~  273 (428)
                      +-+|..||++|++|+.|.++. |=+|.|-.             =+.++          ...+...+.......-.   . 
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~-------------~s~d~----------~~fi~nal~pa~v~~v~---~-  297 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDIIL-------------WSDDP----------AQFIINALSPAEVSSVV---V-  297 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhCCCCEEEEEE---E-
Confidence            359999999999999999998 66666632             12221          11111111110000000   0 


Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      ......+.+.||.++.+..|||+|.+++-..+.||.+|.|.
T Consensus       298 ~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~  338 (470)
T PRK09202        298 DEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIM  338 (470)
T ss_pred             eCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEE
Confidence            01123778999999999999999999999999999999998

>PRK00468 hypothetical protein; Provisional

Probab=95.91  E-value=0.0086  Score=48.62  Aligned_cols=35  Identities=29%  Similarity=0.508  Sum_probs=30.7

Q ss_pred             cCCceEEEEEeccccccceeccCchHHHHHHHHhC
Q 014254          182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAG  216 (428)
Q Consensus       182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTG  216 (428)
                      .++.+.+++.|..+.+|.||||+|.+|+.|+.--.
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~   60 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK   60 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence            44568999999999999999999999999998643

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

Probab=95.80  E-value=0.046  Score=53.99  Aligned_cols=77  Identities=19%  Similarity=0.245  Sum_probs=54.2

Q ss_pred             CCceeEEEEEeccc------cccceeCCCCchHHHHHHHhCCeEEEcc-----C--------CccccCCCCCc---EEEE
Q 014254          274 KGLLVNARLVVASN------QVGCLLGKGGTIISEMRKVTGTSIRIIS-----D--------QLLKCISENDR---VVQI  331 (428)
Q Consensus       274 ~~~~vt~~L~VP~s------~VG~IIGKgG~~IkeIre~TGA~IqI~~-----d--------~~P~~~~s~eR---vVtI  331 (428)
                      ...+.+.++.||-.      +||+|||..|.++|+++++|||+|-|-+     |        ..|+.+..++-   .|+.
T Consensus        88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~  167 (259)
T KOG1588|consen   88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIET  167 (259)
T ss_pred             CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEE
Confidence            34567788888865      8999999999999999999999999982     1        12222223332   3666


Q ss_pred             EeCHHHH----HHHHHHHHHHhh
Q 014254          332 SGEFSKV----KDAVYNVTGRLR  350 (428)
Q Consensus       332 tGt~~aV----~~A~~lI~~~L~  350 (428)
                      .+++.-+    ..|+..|...|.
T Consensus       168 ~~p~~ea~~rl~~AleeI~klL~  190 (259)
T KOG1588|consen  168 EAPPAEAYARLAYALEEIKKLLV  190 (259)
T ss_pred             eCCHHHHHHHHHHHHHHHHHhcC
Confidence            6665544    457777777776

>PRK02821 hypothetical protein; Provisional

Probab=95.65  E-value=0.011  Score=48.20  Aligned_cols=36  Identities=28%  Similarity=0.523  Sum_probs=31.2

Q ss_pred             cCCceEEEEEeccccccceeccCchHHHHHHHHhCC
Q 014254          182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGA  217 (428)
Q Consensus       182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA  217 (428)
                      .+..+.+.|.|..+.+|.||||+|.+|+.|+.--.+
T Consensus        27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            345578999999999999999999999999987554

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

Probab=95.65  E-value=0.016  Score=58.92  Aligned_cols=71  Identities=21%  Similarity=0.298  Sum_probs=58.1

Q ss_pred             eeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe-CHHHHHHHHHHHHHHhhhcC
Q 014254          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG-t~~aV~~A~~lI~~~L~e~~  353 (428)
                      .....+.|+++..|.|||+.|.+-++|+++|+++|.+++   |+   ++...++|+| ..++|..|...|...|.+.-
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 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR---PN---TNKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC---CC---CCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            345678999999999999999999999999999999983   22   3445566655 58889999999999887654

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

Probab=95.44  E-value=0.011  Score=59.69  Aligned_cols=65  Identities=23%  Similarity=0.381  Sum_probs=57.5

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc-cCCccccCCCCCcEEEEEeCHHHHHHHHHHHHH
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTG  347 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~-~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~  347 (428)
                      ...++..+.||..+++-|.|++|++||.++.+|..+|+-+ +..        +-++.++|..+.|..|...|..
T Consensus        23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e--------ePiF~vTg~~edv~~aRrei~s   88 (394)
T KOG2113|consen   23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE--------EPIFPVTGRHEDVRRARREIPS   88 (394)
T ss_pred             CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC--------CCcceeccCchhHHHHhhcCcc
Confidence            3678889999999999999999999999999999999998 432        3469999999999999988866

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=95.39  E-value=0.66  Score=43.94  Aligned_cols=131  Identities=16%  Similarity=0.153  Sum_probs=85.6

Q ss_pred             EEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhccccccc
Q 014254          189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGL  268 (428)
Q Consensus       189 rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~  268 (428)
                      .+.++....-++...+|..++.|-...||+|.+.     ..+..|.|+|++.       ..+.+...+..+..       
T Consensus        29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~-----~~~~~i~I~g~k~-------~~~~i~~~i~~~l~-------   89 (210)
T PF14611_consen   29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVS-----RSENRIRITGTKS-------TAEYIEASINEILS-------   89 (210)
T ss_pred             EEEecchheeeeecCCchHHHHHHHhcCceEEEe-----cCCcEEEEEccHH-------HHHHHHHHHHHHHh-------
Confidence            3444577788899999999999988899999997     3667899999865       33344443443332       


Q ss_pred             CCCCCCCceeEEEEEecccccccee----CCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe-----CHHHHH
Q 014254          269 DFSSNKGLLVNARLVVASNQVGCLL----GKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-----EFSKVK  339 (428)
Q Consensus       269 ~~~~~~~~~vt~~L~VP~s~VG~II----GKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG-----t~~aV~  339 (428)
                             ...+..+-++.-.--..-    -.....+++|++.|++.|...++         +..+.|++     ....+.
T Consensus        90 -------~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~---------~~~~~i~~~~~~~~~~~~~  153 (210)
T PF14611_consen   90 -------NIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD---------GNKLKISWLASPENEKRAD  153 (210)
T ss_pred             -------hcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC---------CCeEEEEEEeeccccchHH
Confidence                   122333333322111111    11356799999999999999732         33355554     577888


Q ss_pred             HHHHHHHHHhhhcCC
Q 014254          340 DAVYNVTGRLRDNHF  354 (428)
Q Consensus       340 ~A~~lI~~~L~e~~~  354 (428)
                      .|..++.-.+..++.
T Consensus       154 ~a~RlL~~a~~~~~~  168 (210)
T PF14611_consen  154 RAKRLLLWALDYNPH  168 (210)
T ss_pred             HHHHHHHHhccCCcc
Confidence            999999888854443

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

Probab=95.36  E-value=0.019  Score=58.33  Aligned_cols=52  Identities=25%  Similarity=0.362  Sum_probs=43.6

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS  238 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs  238 (428)
                      ....-+++++..+|.|||+.|.+-|+|+++|+++|.++.  |+.....|+|+|-
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~--p~~n~~~i~i~~~  107 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR--PNTNKEEIKIIGI  107 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC--CCCCcceEEEeeh
Confidence            355668999999999999999999999999999999986  5555556667664

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=95.23  E-value=0.047  Score=59.12  Aligned_cols=64  Identities=19%  Similarity=0.296  Sum_probs=50.2

Q ss_pred             EEEEEecc-ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe-CHHHHHHHHHHHHHHhhh
Q 014254          279 NARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       279 t~~L~VP~-s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG-t~~aV~~A~~lI~~~L~e  351 (428)
                      ...+.+|+ ++-|+||||.|.+|+-+...||+.|.|.  .       +...|+|+| +|---+.|...+..+|.|
T Consensus       205 ~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid--d-------tp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       205 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--D-------TPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             eeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc--C-------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            34567887 5669999999999999999999999995  2       334688888 566666777777777764

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

Probab=95.18  E-value=0.022  Score=46.41  Aligned_cols=33  Identities=27%  Similarity=0.535  Sum_probs=30.0

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHh
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEA  215 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeT  215 (428)
                      +..+.++|-+..+.+|.||||+|.+|+.|+.--
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            567889999999999999999999999999863

>PRK00468 hypothetical protein; Provisional

Probab=95.12  E-value=0.024  Score=46.06  Aligned_cols=33  Identities=33%  Similarity=0.454  Sum_probs=29.0

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHh
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVT  307 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~T  307 (428)
                      +..+..++.+..+.+|+||||+|.+|+.||..-
T Consensus        27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            455788999999999999999999999998643

>PRK12704 phosphodiesterase; Provisional

Probab=95.10  E-value=0.056  Score=58.61  Aligned_cols=65  Identities=18%  Similarity=0.285  Sum_probs=49.8

Q ss_pred             EEEEEecc-ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe-CHHHHHHHHHHHHHHhhhc
Q 014254          279 NARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       279 t~~L~VP~-s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG-t~~aV~~A~~lI~~~L~e~  352 (428)
                      ...+.+|+ ++-|+||||.|.+|+-+...||+.|.|.  .       +...|.|+| ++---+.|...+...+.+.
T Consensus       211 ~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid--d-------tp~~v~ls~~~~~rre~a~~~l~~l~~dg  277 (520)
T PRK12704        211 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--D-------TPEAVILSGFDPIRREIARLALEKLVQDG  277 (520)
T ss_pred             eeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc--C-------CCCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence            33466787 5679999999999999999999999995  2       345688999 5655556777776666654

>PRK00106 hypothetical protein; Provisional

Probab=94.91  E-value=0.071  Score=57.94  Aligned_cols=64  Identities=22%  Similarity=0.345  Sum_probs=50.6

Q ss_pred             EEEEEecc-ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe-CHHHHHHHHHHHHHHhhh
Q 014254          279 NARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       279 t~~L~VP~-s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG-t~~aV~~A~~lI~~~L~e  351 (428)
                      ...+.+|+ ++-|+||||.|.+|+-+...||+.+.|.  .       +...|+|+| +|---+.|...+..+|.|
T Consensus       226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliid--d-------tp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID--D-------TPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc--C-------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            34567887 5679999999999999999999999995  2       345688998 576667777777777664

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=94.87  E-value=0.027  Score=64.20  Aligned_cols=50  Identities=22%  Similarity=0.393  Sum_probs=43.4

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCc-EEEccCCCCCCceEEEeeCCCC
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAF-ISVGATMPECDERLITVTASEG  240 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~-I~Is~~~p~s~ERvVtItGs~e  240 (428)
                      .....|.||.+++|.|||.||.+||.|+++||++ |.+.+      +-.|.|.+...
T Consensus       684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~  734 (891)
T PLN00207        684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDL  734 (891)
T ss_pred             CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCH
Confidence            4667789999999999999999999999999999 98863      56788888643

>PRK01064 hypothetical protein; Provisional

Probab=94.85  E-value=0.029  Score=45.92  Aligned_cols=35  Identities=20%  Similarity=0.467  Sum_probs=30.9

Q ss_pred             cCCceEEEEEeccccccceeccCchHHHHHHHHhC
Q 014254          182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAG  216 (428)
Q Consensus       182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTG  216 (428)
                      .+..+.+++.|.....|.+|||+|.+|+.|+.-.+
T Consensus        26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~   60 (78)
T PRK01064         26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV   60 (78)
T ss_pred             CCCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence            35668999999999999999999999999998643

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

Probab=94.77  E-value=0.074  Score=51.06  Aligned_cols=40  Identities=23%  Similarity=0.437  Sum_probs=34.4

Q ss_pred             CceeEEEEEec------cccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          275 GLLVNARLVVA------SNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       275 ~~~vt~~L~VP------~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      ...++-++.||      .++||.|||..|.++|++++.|+|+|.|-
T Consensus       145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIR  190 (269)
T COG5176         145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIR  190 (269)
T ss_pred             cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEe
Confidence            44556667776      46899999999999999999999999997

>PRK02821 hypothetical protein; Provisional

Probab=94.73  E-value=0.032  Score=45.59  Aligned_cols=33  Identities=21%  Similarity=0.416  Sum_probs=28.8

Q ss_pred             ceeEEEEEeccccccceeCCCCchHHHHHHHhC
Q 014254          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTG  308 (428)
Q Consensus       276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TG  308 (428)
                      ......|.+..+.+|+||||+|.+|+.||..-.
T Consensus        29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             CcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            446789999999999999999999999997543

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

Probab=94.31  E-value=0.05  Score=44.33  Aligned_cols=32  Identities=31%  Similarity=0.493  Sum_probs=29.0

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHH
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKV  306 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~  306 (428)
                      ......+|.+..+.+|.||||+|.+|+.||-.
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            56778999999999999999999999999864

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=93.94  E-value=0.088  Score=51.34  Aligned_cols=47  Identities=32%  Similarity=0.386  Sum_probs=40.1

Q ss_pred             EEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254          188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG  240 (428)
Q Consensus       188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e  240 (428)
                      +.+.||...++.+||++|.+|+.|.+++++.|.+..      +-.|.|.|...
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~  193 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDE  193 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCH
Confidence            447889999999999999999999999999999963      35588888644

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

Probab=93.78  E-value=0.051  Score=62.68  Aligned_cols=70  Identities=17%  Similarity=0.150  Sum_probs=58.2

Q ss_pred             EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e  351 (428)
                      .-++-+|-....+|||+||.+|+.++..|||.|.+.+-+ |.  .-.||.+.+.|.++.++.|...|.-.|.|
T Consensus      1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq-~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ-PD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC-Cc--cchhhhcccCCCChhhhhhhccccceeec
Confidence            346778888899999999999999999999999997311 21  14689999999999999998888776654

>PRK01064 hypothetical protein; Provisional

Probab=93.74  E-value=0.068  Score=43.75  Aligned_cols=33  Identities=27%  Similarity=0.438  Sum_probs=29.3

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHh
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVT  307 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~T  307 (428)
                      ...+..++.|..+..|.+|||+|++|+.||...
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            466788999999999999999999999999753

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

Probab=93.61  E-value=0.082  Score=58.43  Aligned_cols=48  Identities=35%  Similarity=0.575  Sum_probs=41.6

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG  240 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e  240 (428)
                      ...+.|+.++++-+||+||.+|+.|.++|||+|.|.      ++-.|.|.++..
T Consensus       553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie------ddGtv~i~~s~~  600 (692)
T COG1185         553 IETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE------DDGTVKIAASDG  600 (692)
T ss_pred             eEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec------CCCcEEEEecch
Confidence            456789999999999999999999999999999996      345588888754

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

Probab=93.37  E-value=0.076  Score=50.97  Aligned_cols=39  Identities=23%  Similarity=0.360  Sum_probs=33.8

Q ss_pred             ceEEEEEecc------ccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254          185 EVSFRILCSN------DKVGAVIGKGGTIIRALQSEAGAFISVGA  223 (428)
Q Consensus       185 evt~rIlVP~------~~vG~IIGKgG~tIK~IqeeTGA~I~Is~  223 (428)
                      .++-++.||.      ..||+|||..|.|.|+|++.|+|+|-|-.
T Consensus       147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG  191 (269)
T COG5176         147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG  191 (269)
T ss_pred             cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence            4566778875      47999999999999999999999999964

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=92.76  E-value=0.069  Score=42.39  Aligned_cols=36  Identities=25%  Similarity=0.344  Sum_probs=30.2

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCc
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAF  218 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~  218 (428)
                      .....+.+-|..+..|.||||.|.+++.||.-.+.-
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~   61 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAA   61 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHHHH
Confidence            345677788899999999999999999999876543

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

Probab=92.69  E-value=0.068  Score=51.04  Aligned_cols=62  Identities=26%  Similarity=0.345  Sum_probs=53.5

Q ss_pred             cccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcCCCCcc
Q 014254          286 SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTL  358 (428)
Q Consensus       286 ~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~~~~~~  358 (428)
                      +..+|+|+||+|++--.|.+.|.++|.+.           +..|.|-|..++++.|...|+..|-.++....|
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVla-----------d~kIHiLG~~~niriAR~avcsLIlGsppgkVy  238 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA-----------DSKIHILGAFQNIRIARDAVCSLILGSPPGKVY  238 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEec-----------CceEEEeecchhhHHHHHhhHhhhccCCchhHH
Confidence            45689999999999999999999999985           456999999999999999999999877654433

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=92.69  E-value=0.22  Score=54.02  Aligned_cols=48  Identities=21%  Similarity=0.322  Sum_probs=39.0

Q ss_pred             eEEEEEecc-ccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254          186 VSFRILCSN-DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS  238 (428)
Q Consensus       186 vt~rIlVP~-~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs  238 (428)
                      ++--+-+|+ +.-|.||||.|.|||.|+.-||+.|-|.+     +-..|+|+|.
T Consensus       204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~f  252 (514)
T TIGR03319       204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGF  252 (514)
T ss_pred             eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC-----CCCeEEecCC
Confidence            344478887 57899999999999999999999999975     2334668873

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=92.60  E-value=0.15  Score=46.07  Aligned_cols=37  Identities=24%  Similarity=0.496  Sum_probs=34.3

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      -.+.++|+...+|..||++|++|+.|++..|-+|.+.
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            3677899999999999999999999999999999997

>PRK12704 phosphodiesterase; Provisional

Probab=92.60  E-value=0.15  Score=55.40  Aligned_cols=48  Identities=21%  Similarity=0.322  Sum_probs=39.3

Q ss_pred             eEEEEEecc-ccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254          186 VSFRILCSN-DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS  238 (428)
Q Consensus       186 vt~rIlVP~-~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs  238 (428)
                      ++--+-+|+ +.-|.||||.|.|||.|+.-||+.|-|.+     +..+|+|+|.
T Consensus       210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~~  258 (520)
T PRK12704        210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGF  258 (520)
T ss_pred             ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC-----CCCeEEEecC
Confidence            334477887 57899999999999999999999999975     3345778885

>PRK00106 hypothetical protein; Provisional

Probab=92.28  E-value=0.28  Score=53.47  Aligned_cols=48  Identities=19%  Similarity=0.340  Sum_probs=39.2

Q ss_pred             eEEEEEecc-ccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254          186 VSFRILCSN-DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS  238 (428)
Q Consensus       186 vt~rIlVP~-~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs  238 (428)
                      ++--+-+|+ +.-|.||||.|.|||.|+.-||+.|-|.+     +...|+|+|.
T Consensus       225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-----tp~~v~lS~f  273 (535)
T PRK00106        225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD-----TPEVVVLSGF  273 (535)
T ss_pred             eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC-----CCCeEEEeCC
Confidence            444488888 57899999999999999999999999975     2334668874

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=92.07  E-value=0.13  Score=57.73  Aligned_cols=49  Identities=33%  Similarity=0.523  Sum_probs=39.9

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG  240 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e  240 (428)
                      ....+.||.++++.+||+||.+||.|+++||++|.+.+      +-.|.|.+...
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~  602 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDG  602 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccH
Confidence            34456779999999999999999999999999988853      45578887543

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=91.70  E-value=0.83  Score=42.60  Aligned_cols=101  Identities=23%  Similarity=0.244  Sum_probs=60.0

Q ss_pred             EEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccc
Q 014254          188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKG  267 (428)
Q Consensus       188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g  267 (428)
                      +-|+|-... |.-|||+|.+||++++..|-+|.+-.             .+.+.           ..++..++....-.+
T Consensus        63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE-------------~s~d~-----------~~fl~Nl~~PA~V~g  117 (166)
T PRK06418         63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE-------------KTNDI-----------KKLAVQLLSPARVLG  117 (166)
T ss_pred             EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE-------------cCCCH-----------HHHHHhcCCCcEEEE
Confidence            446777777 99999999999999999999998843             22221           111111111000000


Q ss_pred             cCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEE
Q 014254          268 LDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI  313 (428)
Q Consensus       268 ~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI  313 (428)
                      .......++....++.|+...-..+=.|-..-=.-+++.||..+.|
T Consensus       118 V~i~~~~dG~~~~kV~Vd~~Dk~~l~~k~e~~~~v~~kltgk~v~~  163 (166)
T PRK06418        118 VNTVWLPDGTVQYVIRVSRRDRRRLPAKPELLESILSKITGTEVKI  163 (166)
T ss_pred             EEEEEeCCCcEEEEEEECHHHhhcccccHHHHHHHHHHHHCCcEEE
Confidence            0000011234555677887777776666665555667788888776

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

Probab=91.66  E-value=0.27  Score=37.15  Aligned_cols=35  Identities=34%  Similarity=0.495  Sum_probs=28.8

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcE
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFI  219 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I  219 (428)
                      ...+.+.+.....|.+|||+|.+++.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            35566777766799999999999999999988554

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.

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

Probab=90.71  E-value=0.79  Score=43.68  Aligned_cols=68  Identities=21%  Similarity=0.218  Sum_probs=55.4

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-----HHHHHHHHHHHHHHhhhc
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-----FSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-----~~aV~~A~~lI~~~L~e~  352 (428)
                      ....+.||...+|.+||+.|.+-+.|.+.+|+++.+.         +.+..|+|..+     |.++.+|...|..+=+..
T Consensus         8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD---------~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF   78 (194)
T COG1094           8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID---------SKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGF   78 (194)
T ss_pred             ceeeeecCchhheeeecccccchHHHHhhcCeEEEEE---------CCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCC
Confidence            3456899999999999999999999999999999996         34556777654     778899999888766554


Q ss_pred             CC
Q 014254          353 HF  354 (428)
Q Consensus       353 ~~  354 (428)
                      ++
T Consensus        79 ~p   80 (194)
T COG1094          79 PP   80 (194)
T ss_pred             CH
Confidence            43

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

Probab=90.37  E-value=0.19  Score=40.09  Aligned_cols=35  Identities=37%  Similarity=0.547  Sum_probs=28.0

Q ss_pred             EEEEecccc-----ccceeccCchHHHHHHHHh-CCcEEEc
Q 014254          188 FRILCSNDK-----VGAVIGKGGTIIRALQSEA-GAFISVG  222 (428)
Q Consensus       188 ~rIlVP~~~-----vG~IIGKgG~tIK~IqeeT-GA~I~Is  222 (428)
                      .++.|-...     +|..||++|.+||.|.++. |-+|.|-
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV   45 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV   45 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence            456666666     9999999999999999999 8888874

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

Probab=90.23  E-value=0.48  Score=35.72  Aligned_cols=35  Identities=29%  Similarity=0.434  Sum_probs=28.2

Q ss_pred             eeEEEEEeccccccceeCCCCchHHHHHHHhCCeE
Q 014254          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSI  311 (428)
Q Consensus       277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~I  311 (428)
                      .....+.+.....|.+|||+|++|+.++..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            35556667666789999999999999999988544

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=89.34  E-value=0.38  Score=38.35  Aligned_cols=36  Identities=28%  Similarity=0.548  Sum_probs=30.0

Q ss_pred             EEEEEecccc-----ccceeCCCCchHHHHHHHh-CCeEEEc
Q 014254          279 NARLVVASNQ-----VGCLLGKGGTIISEMRKVT-GTSIRII  314 (428)
Q Consensus       279 t~~L~VP~s~-----VG~IIGKgG~~IkeIre~T-GA~IqI~  314 (428)
                      .+.+.|-+..     +|..||++|.+|+.|.++. |-+|.+.
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV   45 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV   45 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence            3567777777     9999999999999999999 9999997

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=89.07  E-value=0.22  Score=39.78  Aligned_cols=35  Identities=26%  Similarity=0.370  Sum_probs=29.7

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEE
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFIS  220 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~  220 (428)
                      ....+.+..+..|.|||++|++|+.|.+..+-.+.
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            35568889999999999999999999998766553

; 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=88.06  E-value=1.2  Score=48.48  Aligned_cols=69  Identities=19%  Similarity=0.279  Sum_probs=57.0

Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhhc
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e~  352 (428)
                      +...+...+.|+.+....+||.+|...|+|..+||+.-++.           +..++|.-. +.+..+|+..|..++.+.
T Consensus       593 ~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-----------e~t~~i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  593 EYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-----------EGTFSIFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             ccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec-----------CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence            34567788999999999999999999999999999655552           455777774 788899999999998864


Q ss_pred             C
Q 014254          353 H  353 (428)
Q Consensus       353 ~  353 (428)
                      -
T Consensus       662 ~  662 (760)
T KOG1067|consen  662 Q  662 (760)
T ss_pred             c
Confidence            3

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=88.04  E-value=0.68  Score=42.00  Aligned_cols=36  Identities=31%  Similarity=0.637  Sum_probs=33.7

Q ss_pred             EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      .+-++|....+|..||++|++|+.|++..|-+|.+.
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            667899999999999999999999999999999997

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.

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=87.77  E-value=0.28  Score=38.90  Aligned_cols=33  Identities=15%  Similarity=0.253  Sum_probs=27.9

Q ss_pred             ceeEEEEEeccccccceeCCCCchHHHHHHHhC
Q 014254          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTG  308 (428)
Q Consensus       276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TG  308 (428)
                      ......+.+..+..|.||||.|++++.||-..+
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            344677888999999999999999999997654

>PRK12705 hypothetical protein; Provisional

Probab=87.71  E-value=1.1  Score=48.49  Aligned_cols=63  Identities=22%  Similarity=0.228  Sum_probs=44.3

Q ss_pred             EEEEecc-ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhh
Q 014254          280 ARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       280 ~~L~VP~-s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e  351 (428)
                      ..+.+|+ ++-|+||||.|.+|+.+...||+.|.|.  ..|       +.|+|++- +.--+.|...+..+|.+
T Consensus       200 s~v~lp~demkGriIGreGrNir~~E~~tGvdliid--dtp-------~~V~ls~fdp~rreia~~~l~~Li~d  264 (508)
T PRK12705        200 SVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID--DTP-------EAVVISSFNPIRREIARLTLEKLLAD  264 (508)
T ss_pred             eeeecCChHhhccccCccchhHHHHHHhhCCceEec--CCc-------cchhhcccCccchHHHHHHHHHHHhc
Confidence            3456776 4669999999999999999999999995  333       34666663 44445555555555544

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=87.15  E-value=0.3  Score=39.03  Aligned_cols=34  Identities=24%  Similarity=0.424  Sum_probs=28.8

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeE
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSI  311 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~I  311 (428)
                      ....+.+..++.|.|||++|++|++|+...+..+
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l   58 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL   58 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence            3567889999999999999999999987765544

; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=86.88  E-value=0.63  Score=37.43  Aligned_cols=35  Identities=31%  Similarity=0.461  Sum_probs=27.9

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCcEEE
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV  221 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~I  221 (428)
                      .+.+-+..+..|.+|||.|++++.||--++.-++-
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~   59 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR   59 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence            34556667889999999999999999987765543

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.

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

Probab=85.78  E-value=0.33  Score=56.44  Aligned_cols=57  Identities=19%  Similarity=0.120  Sum_probs=49.3

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCC
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGP  241 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~  241 (428)
                      ...-++-+|...+.+|||+||.+|..++.-|||-|.|.+. ..+..||.+++.|.++.
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            3456788999999999999999999999999999999874 34568999999998763

>PRK12705 hypothetical protein; Provisional

Probab=83.79  E-value=0.8  Score=49.68  Aligned_cols=47  Identities=17%  Similarity=0.291  Sum_probs=36.9

Q ss_pred             EEEEEecc-ccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254          187 SFRILCSN-DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS  238 (428)
Q Consensus       187 t~rIlVP~-~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs  238 (428)
                      +--+-+|+ +.-|.||||.|.+||.++..||+.|-|.+     ....|+|++.
T Consensus       199 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-----tp~~V~ls~f  246 (508)
T PRK12705        199 VSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD-----TPEAVVISSF  246 (508)
T ss_pred             eeeeecCChHhhccccCccchhHHHHHHhhCCceEecC-----Cccchhhccc
Confidence            33367776 57899999999999999999999999975     2233566663

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=83.52  E-value=7.2  Score=36.88  Aligned_cols=63  Identities=16%  Similarity=0.261  Sum_probs=52.5

Q ss_pred             EEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254          280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       280 ~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e  351 (428)
                      +.+.++....-.++..+|..+++|....||+|.+..         .+..+.|+|+...+..+...|.+.+..
T Consensus        28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~---------~~~~i~I~g~k~~~~~i~~~i~~~l~~   90 (210)
T PF14611_consen   28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR---------SENRIRITGTKSTAEYIEASINEILSN   90 (210)
T ss_pred             eEEEecchheeeeecCCchHHHHHHHhcCceEEEec---------CCcEEEEEccHHHHHHHHHHHHHHHhh
Confidence            345556778889999999999999888899999973         356799999999999988888888764

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=82.96  E-value=1.2  Score=42.42  Aligned_cols=37  Identities=24%  Similarity=0.364  Sum_probs=34.7

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA  223 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~  223 (428)
                      .+.+.||.+..+..|||+|.+++.+.+-||-++.|..
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            7778999999999999999999999999999999864

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

Probab=82.74  E-value=0.9  Score=48.70  Aligned_cols=36  Identities=28%  Similarity=0.432  Sum_probs=33.3

Q ss_pred             EEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254          188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA  223 (428)
Q Consensus       188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~  223 (428)
                      ..+.||...++.+|||+|.+|++|+++.|-+|.|-.
T Consensus       488 avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~  523 (604)
T COG1855         488 AVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP  523 (604)
T ss_pred             EEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence            457899999999999999999999999999999965

>PRK13764 ATPase; Provisional

Probab=81.94  E-value=1.6  Score=48.34  Aligned_cols=37  Identities=27%  Similarity=0.439  Sum_probs=34.8

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      -.+.+.||...++.+|||||++|++|.+..|.+|.|-
T Consensus       481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~  517 (602)
T PRK13764        481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVR  517 (602)
T ss_pred             CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEE
Confidence            3567899999999999999999999999999999998

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

Probab=81.89  E-value=1.6  Score=35.90  Aligned_cols=35  Identities=23%  Similarity=0.298  Sum_probs=29.2

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCcEEE
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV  221 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~I  221 (428)
                      .+++.|-...-|.|||++|+.|++|+++-.....+
T Consensus        31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~   65 (81)
T cd02413          31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF   65 (81)
T ss_pred             eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence            46778888899999999999999999987655544

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.

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=81.83  E-value=1.6  Score=35.14  Aligned_cols=33  Identities=15%  Similarity=0.476  Sum_probs=26.2

Q ss_pred             EEEEEeccccccceeCCCCchHHHHHHHhCCeE
Q 014254          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSI  311 (428)
Q Consensus       279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~I  311 (428)
                      .+.+.|..+..|.+|||.|++++.||-.+..-+
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~   57 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL   57 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence            355667778899999999999999997665433

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.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=81.49  E-value=1.6  Score=45.70  Aligned_cols=39  Identities=26%  Similarity=0.243  Sum_probs=35.7

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA  223 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~  223 (428)
                      ...+.+.||.+..+..|||+|.+++...+-||.+|.|-.
T Consensus       307 ~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s  345 (374)
T PRK12328        307 EKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE  345 (374)
T ss_pred             CcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence            356788999999999999999999999999999999953

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

Probab=81.41  E-value=1.1  Score=48.10  Aligned_cols=36  Identities=31%  Similarity=0.458  Sum_probs=34.0

Q ss_pred             EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      ...+.||...++.+|||+|.+|++|.+..|-+|.+.
T Consensus       487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~  522 (604)
T COG1855         487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVK  522 (604)
T ss_pred             eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEE
Confidence            467899999999999999999999999999999997

>TIGR01953 NusA transcription termination factor NusA

Probab=80.87  E-value=1.7  Score=44.94  Aligned_cols=37  Identities=30%  Similarity=0.429  Sum_probs=34.8

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEc
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG  222 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is  222 (428)
                      ..+.+.||.+..+..|||+|.+++....-||.+|.|-
T Consensus       301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~  337 (341)
T TIGR01953       301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVK  337 (341)
T ss_pred             cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEE
Confidence            5678999999999999999999999999999999985

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.

>PRK13764 ATPase; Provisional

Probab=80.82  E-value=1.3  Score=49.11  Aligned_cols=38  Identities=26%  Similarity=0.419  Sum_probs=34.6

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA  223 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~  223 (428)
                      -...+.||...++.+|||+|.+|++|+++.|..|.|-.
T Consensus       481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~  518 (602)
T PRK13764        481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP  518 (602)
T ss_pred             CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence            34558999999999999999999999999999999965

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	428
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		9e-11
3krm_A	163	Imp1 Kh34 Length = 163		3e-06

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 46/148 (31%), Positives = 81/148 (54%), Gaps = 11/148 (7%)
Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+    GP +  
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLA---GPTNAI 59
Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
               KA  ++  +L E  S    + ++     V  RLVV ++Q G L+GKGG  I E+R+
Sbjct: 60  F---KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRE 116
Query: 306 VTGTSIRIISDQLLKCISENDRVVQISG 333
            TG  +++  D L    +  +R + I+G
Sbjct: 117 STGAQVQVAGDMLP---NSTERAITIAG 141

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 40/149 (26%), Positives = 72/149 (48%), Gaps = 16/149 (10%)
Query: 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA-TMPECDERLITVTASEGPESRYSP 247
           ++      VGA+IGK G  I+ L   A A I +     P+   R++ +T    PE+++  
Sbjct: 6   QVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGP--PEAQF-- 61
Query: 248 AQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVT 307
             KA   ++ +L E        F   + + +   + V ++  G ++GKGG  ++E++ +T
Sbjct: 62  --KAQGRIYGKLKEENF-----FGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLT 114
Query: 308 GTSIRIISDQLLKCISENDRV-VQISGEF 335
              + +  DQ      END+V V+I G F
Sbjct: 115 AAEVVVPRDQ---TPDENDQVIVKIIGHF 140

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	428
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-41
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-10
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-08
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-38
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-09
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-08
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-37
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	4e-08
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-07
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-36
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	1e-09
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-09
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	4e-32
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	7e-10
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-08
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-13
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	3e-13
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-12
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	3e-10
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	2e-12
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	3e-10
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	3e-11
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-09
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	4e-11
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	7e-11
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	7e-11
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	7e-11
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	1e-10
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-10
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-10
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	2e-10
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	1e-09
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-10
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-08
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	4e-10
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	7e-10
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-09
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	5e-08
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	1e-09
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-08
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-08
1we8_A	104	Tudor and KH domain containing protein; structural	2e-08
1we8_A	104	Tudor and KH domain containing protein; structural	1e-06
1tua_A	191	Hypothetical protein APE0754; structural genomics,	1e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	3e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-05
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	1e-04
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	3e-04
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	3e-04
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	3e-04
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	4e-04
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	6e-04

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

 Score =  143 bits (362), Expect = 2e-41
 Identities = 44/170 (25%), Positives = 84/170 (49%), Gaps = 11/170 (6%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP 241
           +   ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER+IT+      
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPT-- 56

Query: 242 ESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIIS 301
               +   KA  ++  +L E  S    + ++     V  RLVV ++Q G L+GKGG  I 
Sbjct: 57  ----NAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIK 112

Query: 302 EMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351
           E+R+ TG  +++  D      +  +R + I+G    + + V  +   + +
Sbjct: 113 EIRESTGAQVQVAGDM---LPNSTERAITIAGIPQSIIECVKQICVVMLE 159

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

 Score = 57.5 bits (139), Expect = 3e-10
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 7/85 (8%)

Query: 178 DARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV-GATMPECDERLITVT 236
                +  V+ R++    + G++IGKGG  I+ ++   GA + V G  +P   ER IT+ 
Sbjct: 81  STAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIA 140

Query: 237 ASEGPESRYSPAQKAVVLVFSRLIE 261
               P+S      + V  +   ++E
Sbjct: 141 GI--PQS----IIECVKQICVVMLE 159

>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 = 51.3 bits (123), Expect = 5e-08
 Identities = 21/100 (21%), Positives = 44/100 (44%), Gaps = 6/100 (6%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           +  RL++   +VG ++GK G  + +MR+ +G  I I         +  +R++ ++G  + 
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG------NCPERIITLAGPTNA 58

Query: 338 VKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYS 377
           +  A   +  +L ++  S   N+         L    P S
Sbjct: 59  IFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPAS 98

>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 =  136 bits (343), Expect = 2e-38
 Identities = 36/175 (20%), Positives = 76/175 (43%), Gaps = 8/175 (4%)

Query: 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV---GATMPECDERLITVTASEG 240
            +   ++L  +   G++IGKGG  I  LQ E GA I +       P   ER+  +  +  
Sbjct: 4   SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIE 63

Query: 241 PESRYSPAQKAVVLVFSRLI---EGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGG 297
             +         +    + +   E  S      + N       +++V ++  G ++GKGG
Sbjct: 64  ALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGG 123

Query: 298 TIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN 352
             +  + + +G  +++        I+  +RVV +SGE  + + AV  +  +++++
Sbjct: 124 ATVKAIMEQSGAWVQLSQKP--DGINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176

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

 Score = 56.4 bits (136), Expect = 1e-09
 Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 8/86 (9%)

Query: 178 DARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV--GATMPECDERLITV 235
                 +    +I+  N   G +IGKGG  ++A+  ++GA++ +           R++TV
Sbjct: 96  TTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTV 155

Query: 236 TASEGPESRYSPAQKAVVLVFSRLIE 261
           +    PE      +KAV L+  ++ E
Sbjct: 156 SGE--PEQ----NRKAVELIIQKIQE 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 = 52.9 bits (127), Expect = 2e-08
 Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
           ++++ S   G ++GKGG  I +++K TG +I++   +     +  +RV  I G    +  
Sbjct: 9   KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTT-ERVCLIQGTIEALNA 67

Query: 341 AVYNVTGRLRDNH 353
               +  ++R+  
Sbjct: 68  VHGFIAEKIREMP 80

>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 =  132 bits (334), Expect = 2e-37
 Identities = 36/169 (21%), Positives = 70/169 (41%), Gaps = 14/169 (8%)

Query: 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG-ATMPECDERLITVTASEGPE 242
           ++   ++      VGA+IGK G  I+ L   A A I +     P+   R++ +T      
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPP--- 57

Query: 243 SRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISE 302
                  KA   ++ +L E        F   + + +   + V ++  G ++GKGG  ++E
Sbjct: 58  ---EAQFKAQGRIYGKLKEEN-----FFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNE 109

Query: 303 MRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351
           ++ +T   + +  DQ       +  +V+I G F   + A   +   L  
Sbjct: 110 LQNLTAAEVVVPRDQTPD--ENDQVIVKIIGHFYASQMAQRKIRDILAQ 156

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

 Score = 51.7 bits (124), Expect = 4e-08
 Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
           ++ + +  VG ++GK G  I ++ +    SI+I   +         R+V I+G       
Sbjct: 6   QVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDS---KVRMVIITGPPEAQFK 62

Query: 341 AVYNVTGRLRDNHFSG 356
           A   + G+L++ +F G
Sbjct: 63  AQGRIYGKLKEENFFG 78

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

 Score = 49.4 bits (118), Expect = 3e-07
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 8/83 (9%)

Query: 181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPEC--DERLITVTAS 238
            ++ ++   I       G VIGKGG  +  LQ+   A + V         D+ ++ +   
Sbjct: 80  KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGH 139

Query: 239 EGPESRYSPAQKAVVLVFSRLIE 261
               +    +Q A   +   L +
Sbjct: 140 --FYA----SQMAQRKIRDILAQ 156

>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 =  130 bits (329), Expect = 2e-36
 Identities = 31/174 (17%), Positives = 60/174 (34%), Gaps = 10/174 (5%)

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESR 244
                +      VG VIG+ G +I+ +Q++AG  I          ER+  +T        
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 245 YSPAQKAVVLVFSRLIEGT---------SEKGLDFSSNKGLLVNARLVVASNQVGCLLGK 295
            +     ++        G            +G       G L     +V + + G ++GK
Sbjct: 62  AAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGK 121

Query: 296 GGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL 349
           GG  I  + + +G  I  +          N ++  I G   ++  A   +  ++
Sbjct: 122 GGETIKSISQQSGARIE-LQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

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

 Score = 56.4 bits (136), Expect = 1e-09
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 4/72 (5%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + +    VG ++G+ G +I +++   G  I+   D      +  +R+ QI+G   + + 
Sbjct: 6   DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG----TTPERIAQITGPPDRAQH 61

Query: 341 AVYNVTGRLRDN 352
           A   +T  LR  
Sbjct: 62  AAEIITDLLRSV 73

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

 Score = 54.5 bits (131), Expect = 4e-09
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 9/81 (11%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPEC---DERLITVTAS 238
                 F  +    K G +IGKGG  I+++  ++GA I +    P     + +L T+  +
Sbjct: 100 PGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGT 159

Query: 239 EGPESRYSPAQKAVVLVFSRL 259
             P+        A  L+  ++
Sbjct: 160 --PQQ----IDYARQLIEEKI 174

>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 =  118 bits (298), Expect = 4e-32
 Identities = 33/167 (19%), Positives = 67/167 (40%), Gaps = 11/167 (6%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV--GATMPECDERLITVTASEGPESR 244
              I+    K G VIGKGG  I+ LQ  AG  + +    +     ++ + +    G   +
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRII---GDPYK 59

Query: 245 YSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMR 304
              A + V+ +     +G      ++ S  G      + V  + VG ++G+ G +I +++
Sbjct: 60  VQQACEMVMDILRERDQGGFGDRNEYGSRIG--GGIDVPVPRHSVGVVIGRSGEMIKKIQ 117

Query: 305 KVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351
              G  I+   D      +  +++  I G   + + A   +   L+ 
Sbjct: 118 NDAGVRIQFKQDDG----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 = 56.7 bits (137), Expect = 7e-10
 Identities = 12/59 (20%), Positives = 24/59 (40%)

Query: 178 DARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT 236
           +    +      +      VG VIG+ G +I+ +Q++AG  I          E++  + 
Sbjct: 83  NEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM 141

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

 Score = 52.1 bits (125), Expect = 3e-08
 Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            +++ + + G ++GKGG  I ++++  G  + +I D      +  D+ ++I G+  KV+ 
Sbjct: 5   EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN--TNVDKPLRIIGDPYKVQQ 62

Query: 341 AVYNVTGRLRDNH 353
           A   V   LR+  
Sbjct: 63  ACEMVMDILRERD 75

>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 = 64.2 bits (157), Expect = 2e-13
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 8/80 (10%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP 241
           +   ++ R+L    +VG++IGK G  ++ ++ E+GA I++      C ER+IT+      
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGP--T 56

Query: 242 ESRYSPAQKAVVLVFSRLIE 261
            +      KA  ++  +L E
Sbjct: 57  NA----IFKAFAMIIDKLEE 72

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

 Score = 63.4 bits (155), Expect = 3e-13
 Identities = 17/75 (22%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           +  RL++   +VG ++GK G  + +MR+ +G  I  IS+      +  +R++ ++G  + 
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARIN-ISEG-----NCPERIITLAGPTNA 58

Query: 338 VKDAVYNVTGRLRDN 352
           +  A   +  +L ++
Sbjct: 59  IFKAFAMIIDKLEED 73

>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 = 61.5 bits (150), Expect = 2e-12
 Identities = 19/81 (23%), Positives = 41/81 (50%), Gaps = 6/81 (7%)

Query: 181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240
                ++ ++    D  G++IGKGG  I+ ++ E+GA I +   +   ++R+IT+T +  
Sbjct: 2   AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-- 59

Query: 241 PESRYSPAQKAVVLVFSRLIE 261
            +      Q A  L+ + + +
Sbjct: 60  QDQ----IQNAQYLLQNSVKQ 76

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

 Score = 55.4 bits (134), Expect = 3e-10
 Identities = 18/78 (23%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE 334
           G ++  ++ +  +  G ++GKGG  I ++R  +G SI+I            DR++ I+G 
Sbjct: 4   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE----GSEDRIITITGT 59

Query: 335 FSKVKDAVYNVTGRLRDN 352
             ++++A Y +   ++  
Sbjct: 60  QDQIQNAQYLLQNSVKQY 77

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

 Score = 61.6 bits (150), Expect = 2e-12
 Identities = 19/81 (23%), Positives = 42/81 (51%), Gaps = 6/81 (7%)

Query: 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPES 243
             ++ ++    D  G++IGKGG  I+ ++ E+GA I +   +   ++R+IT+T +   + 
Sbjct: 12  PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT--QDQ 69

Query: 244 RYSPAQKAVVLVFSRLIEGTS 264
                Q A  L+ + + + + 
Sbjct: 70  ----IQNAQYLLQNSVKQYSG 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 = 55.8 bits (135), Expect = 3e-10
 Identities = 18/83 (21%), Positives = 41/83 (49%), Gaps = 4/83 (4%)

Query: 270 FSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVV 329
           +    G ++  ++ +  +  G ++GKGG  I ++R  +G SI+I            DR++
Sbjct: 6   YGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE----GSEDRII 61

Query: 330 QISGEFSKVKDAVYNVTGRLRDN 352
            I+G   ++++A Y +   ++  
Sbjct: 62  TITGTQDQIQNAQYLLQNSVKQY 84

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

 Score = 58.1 bits (141), Expect = 3e-11
 Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 6/80 (7%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP 241
           + Q  S  +   ND +G +IG+ G  I  ++  +GA I +   +    +R +T+T S   
Sbjct: 1   KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGS--A 58

Query: 242 ESRYSPAQKAVVLVFSRLIE 261
            S       A  L+  RL  
Sbjct: 59  AS----ISLAQYLINVRLSS 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 = 53.8 bits (130), Expect = 1e-09
 Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG 333
           K    +  L + ++ +GC++G+ G  I+E+R+++G  I+I +          DR V I+G
Sbjct: 1   KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPV----EGSTDRQVTITG 56

Query: 334 EFSKVKDAVYNVTGRLRD 351
             + +  A Y +  RL  
Sbjct: 57  SAASISLAQYLINVRLSS 74

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

 Score = 58.1 bits (141), Expect = 4e-11
 Identities = 22/86 (25%), Positives = 34/86 (39%), Gaps = 8/86 (9%)

Query: 178 DARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV--GATMPECDERLITV 235
           +A   Q      I+    K G VIGKGG  I+ LQ  AG  + +    +     ++ + +
Sbjct: 6   NANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRI 65

Query: 236 TASEGPESRYSPAQKAVVLVFSRLIE 261
                P       Q+A  +V   L E
Sbjct: 66  IGD--PYK----VQQACEMVMDILRE 85

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

 Score = 57.4 bits (139), Expect = 7e-11
 Identities = 18/71 (25%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            +++ + + G ++GKGG  I ++++  G  + +I D      +  D+ ++I G+  KV+ 
Sbjct: 17  EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN--TNVDKPLRIIGDPYKVQQ 74

Query: 341 AVYNVTGRLRD 351
           A   V   LR+
Sbjct: 75  ACEMVMDILRE 85

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

 Score = 59.3 bits (143), Expect = 7e-11
 Identities = 29/155 (18%), Positives = 50/155 (32%), Gaps = 31/155 (20%)

Query: 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPA 248
           + +   D +G  IG  G  I+  +         G T  + DE   T              
Sbjct: 7   QFIVREDLMGLAIGTHGANIQQARKVP------GVTAIDLDEDTCTFH------------ 48

Query: 249 QKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTG 308
                      I G  +  +  + +        + V  N VG ++GK G +I E+   +G
Sbjct: 49  -----------IYGEDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSG 97

Query: 309 -TSIRIISDQLLKCISENDRV-VQISGEFSKVKDA 341
              +RI ++       E   V     G    + +A
Sbjct: 98  VVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANA 132

>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 = 57.3 bits (139), Expect = 7e-11
 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPES 243
            + +  +   N+ +G +IG+ G  I  ++  +GA I +   +     R +T+T S    S
Sbjct: 4   SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS--AAS 61

Query: 244 RYSPAQKAVVLVFSRLIE 261
                  A  L+ +RL  
Sbjct: 62  ----ISLAQYLINARLSS 75

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

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 4/79 (5%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
               L + +N +GC++G+ G  I+E+R+++G  I+I +         + R V I+G  + 
Sbjct: 6   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV----EGSSGRQVTITGSAAS 61

Query: 338 VKDAVYNVTGRLRDNHFSG 356
           +  A Y +  RL      G
Sbjct: 62  ISLAQYLINARLSSEKGMG 80

>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 = 56.1 bits (136), Expect = 1e-10
 Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 9/80 (11%)

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV---GATMPECDERLITVTASEGP 241
           +    +    + VGA++GKGG  +   Q   GA I +   G  +P    R +T+T S  P
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS--P 59

Query: 242 ESRYSPAQKAVVLVFSRLIE 261
            +     Q A  L+  R+  
Sbjct: 60  AA----TQAAQYLISQRVTY 75

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

 Score = 55.4 bits (134), Expect = 2e-10
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + V  N VG +LGKGG  + E +++TG  I+ IS +        +R V I+G  +  + 
Sbjct: 6   EMAVPENLVGAILGKGGKTLVEYQELTGARIQ-ISKKGEFLPGTRNRRVTITGSPAATQA 64

Query: 341 AVYNVTGRLRD 351
           A Y ++ R+  
Sbjct: 65  AQYLISQRVTY 75

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

 Score = 56.7 bits (137), Expect = 2e-10
 Identities = 18/71 (25%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            +++ +++ G ++GKGG  I ++++  G  + +I D      +  D+ ++I+G+  KV+ 
Sbjct: 18  EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG--PQNTGADKPLRITGDPYKVQQ 75

Query: 341 AVYNVTGRLRD 351
           A   V   +RD
Sbjct: 76  AKEMVLELIRD 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 = 54.3 bits (131), Expect = 1e-09
 Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 8/82 (9%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG--ATMPECDERLITVTASE 239
                   I+    K G VIGKGG  I+ LQ  AG  + +          ++ + +T   
Sbjct: 11  GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGD- 69

Query: 240 GPESRYSPAQKAVVLVFSRLIE 261
            P       Q+A  +V   + +
Sbjct: 70  -PYK----VQQAKEMVLELIRD 86

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

 Score = 55.9 bits (135), Expect = 4e-10
 Identities = 12/52 (23%), Positives = 22/52 (42%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238
              +      VG VIG+ G +I+ +Q++AG  I          E++  +   
Sbjct: 12  GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGP 63

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

 Score = 50.2 bits (120), Expect = 4e-08
 Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 4/63 (6%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + V  + VG ++G+ G +I +++   G  I+   D      +  +++  I G   + + 
Sbjct: 14  DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD----GTGPEKIAHIMGPPDRCEH 69

Query: 341 AVY 343
           A  
Sbjct: 70  AAR 72

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

 Score = 55.0 bits (133), Expect = 4e-10
 Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 9/80 (11%)

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV---GATMPECDERLITVTASEGP 241
           +    I    + VGA++GKGG  +   Q   GA I +   G  +P    R +T+T S  P
Sbjct: 2   KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS--P 59

Query: 242 ESRYSPAQKAVVLVFSRLIE 261
            +     Q A  L+  R+  
Sbjct: 60  AA----TQAAQYLISQRVTY 75

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

 Score = 54.7 bits (132), Expect = 7e-10
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + V  N VG +LGKGG  + E +++TG  I+ IS +        +R V I+G  +  + 
Sbjct: 6   EIAVPENLVGAILGKGGKTLVEYQELTGARIQ-ISKKGEFLPGTRNRRVTITGSPAATQA 64

Query: 341 AVYNVTGRLRDNH 353
           A Y ++ R+    
Sbjct: 65  AQYLISQRVTYEQ 77

>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 = 54.0 bits (130), Expect = 1e-09
 Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 6/85 (7%)

Query: 180 RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
           + Q+  ++      +  VG +IG+GG  I  +Q E+G  I +        ER   +T + 
Sbjct: 9   QQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT- 67

Query: 240 GPESRYSPAQKAVVLVFSRLIEGTS 264
            PES     Q A  L+   + +G S
Sbjct: 68  -PES----VQSAKRLLDQIVEKGRS 87

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

 Score = 49.3 bits (118), Expect = 5e-08
 Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 4/66 (6%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           +     V    VG ++G+GG  IS +++ +G  I+I  D         +R   ++G    
Sbjct: 15  MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS----GGLPERSCMLTGTPES 70

Query: 338 VKDAVY 343
           V+ A  
Sbjct: 71  VQSAKR 76

>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 = 57.0 bits (137), Expect = 1e-09
 Identities = 24/181 (13%), Positives = 67/181 (37%), Gaps = 26/181 (14%)

Query: 170 ESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECD 229
           + + V   D   +  +    +    D++  +IGK G   + ++      I++     + +
Sbjct: 18  DGEIVEDEDEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITI-----DSE 72

Query: 230 ERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK---------GLDFSSNKGLLVNA 280
              + +T+++  E   +   KA  +V +     + E+          L+  +   +++  
Sbjct: 73  TGEVWITSTKETEDPLA-VWKARDIVLAIGRGFSPERAFRLLNEGEYLEIINLTDIIIGN 131

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
                    G ++G+ G     + +++G S+ +             + V I G   +++ 
Sbjct: 132 EKNALPRVRGRIIGRKGRTRQIIEEMSGASVSV-----------YGKTVAIIGNPIQIEI 180

Query: 341 A 341
           A
Sbjct: 181 A 181

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

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 14/72 (19%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
              + +++ G ++G+GG  +  + + TG  +  IS QL      N ++  I G   ++  
Sbjct: 10  TFSIPTHKCGLVIGRGGENVKAINQQTGAFVE-ISRQLPPNGDPNFKLFIIRGSPQQIDH 68

Query: 341 AVYNVTGRLRDN 352
           A   +  ++   
Sbjct: 69  AKQLIEEKIEGP 80

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

 Score = 51.4 bits (123), Expect = 2e-08
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 9/83 (10%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECD---ERLITVTAS 238
                         K G VIG+GG  ++A+  + GAF+ +   +P       +L  +  S
Sbjct: 3   MAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGS 62

Query: 239 EGPESRYSPAQKAVVLVFSRLIE 261
             P+        A  L+  ++  
Sbjct: 63  --PQQ----IDHAKQLIEEKIEG 79

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

 Score = 51.4 bits (123), Expect = 2e-08
 Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG--ATMPECDERLITVTAS 238
           T+   V  ++      VG +IG+GG  IR++   +GA I+    +       RLI ++ +
Sbjct: 10  TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGT 69

Query: 239 EGPESRYSPAQKAVVLVFSRLIE 261
              +        A  L+  ++ E
Sbjct: 70  --QKE----VAAAKHLILEKVSE 86

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

 Score = 46.0 bits (109), Expect = 1e-06
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
           +L V    VG ++G+GG  I  + K +G  I    +   +      R+++ISG   +V  
Sbjct: 18  QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES--EGTLLLSRLIKISGTQKEVAA 75

Query: 341 AVY 343
           A +
Sbjct: 76  AKH 78

>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 = 47.7 bits (113), Expect = 1e-06
 Identities = 29/160 (18%), Positives = 56/160 (35%), Gaps = 19/160 (11%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYS 246
              +    +++GAVIG  G +   +    G  I+V                      + +
Sbjct: 5   RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAA 64

Query: 247 PAQKAVVLVFS-----RLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIIS 301
              KA+ L F      RL+E   ++ L     K ++ +          G ++G+GG    
Sbjct: 65  EVVKAISLGFPPEKAFRLLEE--DQILVVVDLKQVVGD-SQNHLKRIKGRIIGEGGRARR 121

Query: 302 EMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341
            + ++T T I +            +  V I G++ +   A
Sbjct: 122 TIEEMTDTYINV-----------GEYEVAIIGDYERAMAA 150

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

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 180 RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
              Q + S  +    +    VIGK G  ++ L+ +    I +    P+     I +T ++
Sbjct: 11  ARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSNQIKITGTK 68

>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 = 42.4 bits (100), Expect = 2e-05
 Identities = 11/66 (16%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
            +A + +       ++GK G  + ++   T T I+I          +    ++I+G    
Sbjct: 17  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP------DDPSNQIKITGTKEG 70

Query: 338 VKDAVY 343
           ++ A +
Sbjct: 71  IEKARH 76

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 41.5 bits (96), Expect = 1e-04
 Identities = 8/40 (20%), Positives = 19/40 (47%), Gaps = 14/40 (35%)

Query: 84  QEILWRSLESGPQEILRRPLEVFAPESSHRSSEALSIETQ 123
           Q +  + L++         L+++A +    S+ AL+I+  
Sbjct: 20  QAL--KKLQAS--------LKLYADD----SAPALAIKAT 45

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 42.1 bits (100), Expect = 3e-04
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 11/58 (18%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAV 252
           DK+  VIGKGG++IRAL  E G  I +       D+  + + A++G +     A+ A+
Sbjct: 569 DKIKDVIGKGGSVIRALTEETGTTIEIE------DDGTVKIAATDGEK-----AKHAI 615

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

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 6/65 (9%)

Query: 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS 336
           +    + +       L+GK G  I+ ++     S+RI  D       E   +++I G+  
Sbjct: 4   MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS------EKSNLIRIEGDPQ 57

Query: 337 KVKDA 341
            V+ A
Sbjct: 58  GVQQA 62

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Length = 757

 Score = 41.8 bits (99), Expect = 3e-04
 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 11/58 (18%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAV 252
           DK+G VIG    +I  +Q + GA I++       D+  I + A++GP      A+ A 
Sbjct: 607 DKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAADGPA-----AEAAR 653

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Length = 630

 Score = 41.7 bits (99), Expect = 4e-04
 Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 6/46 (13%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240
            K    +G GG  ++ LQ+E G  IS        DE   +V A   
Sbjct: 576 SKRAKFVGPGGYNLKKLQAETGVTISQV------DEETFSVFAPTP 615

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 41.3 bits (98), Expect = 6e-04
 Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 6/46 (13%)

Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240
           DK+  VIG GG +IR + +  GA + +       D+ ++ V+AS+G
Sbjct: 579 DKIREVIGSGGKVIREIVATTGAKVDIN------DDGVVKVSASDG 618

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	428
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.95
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.95
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.94
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.93
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.93
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.78
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.7
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.67
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.56
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.53
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.53
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.52
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.52
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.51
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.48
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.47
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.46
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.44
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.44
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.44
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.43
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.43
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.42
1we8_A	104	Tudor and KH domain containing protein; structural	99.4
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.39
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.39
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.39
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.36
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.34
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.33
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.33
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.32
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.29
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.29
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.28
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.27
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.27
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.26
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.26
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.26
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.23
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.23
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.22
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.21
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.2
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.19
1we8_A	104	Tudor and KH domain containing protein; structural	99.17
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.11
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.08
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.05
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.04
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	98.97
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.92
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	98.9
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.85
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	98.72
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.69
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	98.68
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.52
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	98.5
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.45
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.44
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.18
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.15
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.06
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.01
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	97.95
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	97.94
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.93
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.75
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.52
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.27
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.09
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	96.98
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.23
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.23
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	95.82
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.03
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	94.65
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	94.17
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	90.07
2cxc_A	144	NUSA; transcription termination, RNA binding prote	89.26
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	84.87
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	81.23

>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=99.95  E-value=1.3e-27  Score=215.43  Aligned_cols=156  Identities=23%  Similarity=0.401  Sum_probs=131.2

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcc
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT  263 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~  263 (428)
                      +-+++|+||.+.+|.||||+|++||+|+++|||+|+|.+. .+++.+|+|+|+|+.+.      +.+|..+++..+.+..
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~------v~~A~~~I~~~~~e~~   75 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEA------QFKAQGRIYGKLKEEN   75 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHH------HHHHHHHHHHHHHHTT
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHH------HHHHHHHHHHHHhccc
Confidence            3578999999999999999999999999999999999875 57889999999997654      6677777777665542


Q ss_pred             cccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHH
Q 014254          264 SEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVY  343 (428)
Q Consensus       264 ~~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~  343 (428)
                      .     +........+.+|.||.+++|+||||||++|++|++.|||+|+|+++..|.  ...++.|+|+|++++|++|+.
T Consensus        76 ~-----~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~--~~~~~~v~I~G~~~~v~~A~~  148 (163)
T 3krm_A           76 F-----FGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPD--ENDQVIVKIIGHFYASQMAQR  148 (163)
T ss_dssp             S-----SCSSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCC--TTSEEEEEEEECHHHHHHHHH
T ss_pred             c-----cccccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCC--CCCceEEEEEeCHHHHHHHHH
Confidence            1     112234567889999999999999999999999999999999999766665  234458999999999999999


Q ss_pred             HHHHHhhhcC
Q 014254          344 NVTGRLRDNH  353 (428)
Q Consensus       344 lI~~~L~e~~  353 (428)
                      +|.++|++.-
T Consensus       149 ~I~~~i~~~~  158 (163)
T 3krm_A          149 KIRDILAQVK  158 (163)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHHH
Confidence            9999998654

>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=99.95  E-value=8.5e-28  Score=216.02  Aligned_cols=157  Identities=29%  Similarity=0.518  Sum_probs=130.1

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcc
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT  263 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~  263 (428)
                      ..++++|+||.+.+|.||||+|++||+|+++|||+|+|++.  ++.+|+|+|+|+.++      +.+|..++.+.+.+..
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~~------v~~A~~~I~~~i~e~~   74 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNA------IFKAFAMIIDKLEEDI   74 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHHH------HHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHHH------HHHHHHHHHHHHHhhc
Confidence            46899999999999999999999999999999999999873  678999999997543      6667776766655432


Q ss_pred             cccccC-CCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHH
Q 014254          264 SEKGLD-FSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAV  342 (428)
Q Consensus       264 ~~~g~~-~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~  342 (428)
                      . .... ........++.++.||.+++|+||||||++|++|++.|||+|+|.++..|.   ++++.|+|+|++++|++|+
T Consensus        75 ~-~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~---~~~~~v~I~G~~~~v~~A~  150 (160)
T 2jzx_A           75 S-SSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN---STERAITIAGIPQSIIECV  150 (160)
T ss_dssp             T-SCCCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTT---CCEEEEEEEECHHHHHHHH
T ss_pred             c-ccCCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCC---CCceEEEEEcCHHHHHHHH
Confidence            1 1111 011123468899999999999999999999999999999999998666665   6899999999999999999


Q ss_pred             HHHHHHhhhc
Q 014254          343 YNVTGRLRDN  352 (428)
Q Consensus       343 ~lI~~~L~e~  352 (428)
                      .+|.+++.|+
T Consensus       151 ~~I~~~i~e~  160 (160)
T 2jzx_A          151 KQICVVMLET  160 (160)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHHHhcC
Confidence            9999998763

>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=99.94  E-value=1.6e-27  Score=218.00  Aligned_cols=163  Identities=21%  Similarity=0.382  Sum_probs=129.4

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC---CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHh
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSRL  259 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~---~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i  259 (428)
                      ..+++++|+||.+.+|.||||+|++||+|+++|||+|+|++.   .+++.+|+|+|+|+.++      +.+|..++.+.+
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            456899999999999999999999999999999999999863   46889999999998653      566666666655


Q ss_pred             hhccccccc-------C--CCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEE
Q 014254          260 IEGTSEKGL-------D--FSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQ  330 (428)
Q Consensus       260 ~e~~~~~g~-------~--~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVt  330 (428)
                      .+.......       +  .........+.+|.||.+++|+||||+|++|++|++.|||+|+|.++.  .+...+++.|+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~--~~~~~~~~~v~  154 (178)
T 2anr_A           77 REMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKP--DGINLQNRVVT  154 (178)
T ss_dssp             TCCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC------CCEEEEE
T ss_pred             hccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCC--CCCCCCceEEE
Confidence            442110000       0  001123457889999999999999999999999999999999998432  22346789999


Q ss_pred             EEeCHHHHHHHHHHHHHHhhhcC
Q 014254          331 ISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       331 ItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      |+|++++|++|+.+|.++|+++|
T Consensus       155 I~G~~~~v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          155 VSGEPEQNRKAVELIIQKIQEDP  177 (178)
T ss_dssp             EESSHHHHHHHHHHHHHHHHSCC
T ss_pred             EEcCHHHHHHHHHHHHHHHHhCC
Confidence            99999999999999999999876

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

Probab=99.93  E-value=4.9e-26  Score=207.61  Aligned_cols=158  Identities=22%  Similarity=0.347  Sum_probs=123.7

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhccc
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTS  264 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~  264 (428)
                      ..+++|+||.+.+|.||||+|++||+|+++|||+|+|.+..+++.+|+|+|+|+.++      +.+|..+|.+.+.+...
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~------v~~A~~~I~~~~~~~~~   75 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDR------AQHAAEIITDLLRSVQA   75 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHH------HHHHHHHHHHHHHHHC-
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHH------HHHHHHHHHHHHHhccc
Confidence            467899999999999999999999999999999999987666788999999998653      55666666554443210


Q ss_pred             cc-c--------c-----CCC-CCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEE
Q 014254          265 EK-G--------L-----DFS-SNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVV  329 (428)
Q Consensus       265 ~~-g--------~-----~~~-~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvV  329 (428)
                      .. +        .     .+. .......+.+|.||.+++|+||||+|++|++|++.|||+|+|.++. +.+..++++.|
T Consensus        76 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~-~~~~~~~~~~v  154 (174)
T 1j4w_A           76 GNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP-PPNADPNMKLF  154 (174)
T ss_dssp             ----------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCC-TTTSCTTEEEE
T ss_pred             CCCCCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCC-CCCCCCCceEE
Confidence            00 0        0     000 0012346889999999999999999999999999999999998543 33445778999


Q ss_pred             EEEeCHHHHHHHHHHHHHHh
Q 014254          330 QISGEFSKVKDAVYNVTGRL  349 (428)
Q Consensus       330 tItGt~~aV~~A~~lI~~~L  349 (428)
                      +|+|++++|+.|+++|.++|
T Consensus       155 ~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          155 TIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             EEECCHHHHHHHHHHHHHHC
T ss_pred             EEECCHHHHHHHHHHHHHhC
Confidence            99999999999999999875

>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=1.4e-25  Score=201.74  Aligned_cols=155  Identities=21%  Similarity=0.327  Sum_probs=123.7

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC--CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcc
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT--MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT  263 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~--~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~  263 (428)
                      ++++|+||.+.+|.||||+|++||+|+++|||+|+|.+.  .++..+|+|+|+|+.+.      +.+|...+.+.+.+..
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------VQQACEMVMDILRERD   75 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHH------HHHHHHHHHHHTTCSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHH------HHHHHHHHHHHHHhcc
Confidence            678999999999999999999999999999999999754  35678999999997553      6667777766654422


Q ss_pred             cccccCCCC--CCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHH
Q 014254          264 SEKGLDFSS--NKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA  341 (428)
Q Consensus       264 ~~~g~~~~~--~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A  341 (428)
                      . .+.....  ......+.+|.||.+++|+||||+|++|++|++.|||+|+|.++. +   ...++.|+|+|++++|+.|
T Consensus        76 ~-~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~-~---~~~~~~v~I~G~~~~v~~A  150 (164)
T 2jvz_A           76 Q-GGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-G---TGPEKIAHIMGPPDRCEHA  150 (164)
T ss_dssp             S-CCCSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC-T---TSSEEEEEEESCHHHHHHH
T ss_pred             C-CCCCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC-C---CCCcEEEEEEcCHHHHHHH
Confidence            1 1111100  011134578999999999999999999999999999999998431 2   2568999999999999999


Q ss_pred             HHHHHHHhhh
Q 014254          342 VYNVTGRLRD  351 (428)
Q Consensus       342 ~~lI~~~L~e  351 (428)
                      +.+|.++|++
T Consensus       151 ~~~I~~~i~~  160 (164)
T 2jvz_A          151 ARIINDLLQS  160 (164)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhh
Confidence            9999999875

>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=99.78  E-value=5.4e-19  Score=157.63  Aligned_cols=137  Identities=20%  Similarity=0.252  Sum_probs=99.7

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhccc
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTS  264 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~  264 (428)
                      .++.+|+||++.+|++|||+|++|++|++++|  |.+.... ...++.+...++++          ++..+.. +.+.  
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~-~~~~~~i~~~~~p~----------~v~~~~~-~l~~--   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLD-EDTCTFHIYGEDQD----------AVKKARS-FLEF--   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEE-TTTTEEEEEESSHH----------HHHHHHH-HHCE--
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccC-CCchheeeccCCHH----------HHHHHHH-hhhc--
Confidence            46889999999999999999999999999999  5553321 22344443333332          1222211 2110  


Q ss_pred             ccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCC-eEEEccCCccccCCCCCc--EEEEEeCHHHHHHH
Q 014254          265 EKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGT-SIRIISDQLLKCISENDR--VVQISGEFSKVKDA  341 (428)
Q Consensus       265 ~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA-~IqI~~d~~P~~~~s~eR--vVtItGt~~aV~~A  341 (428)
                                   ...++.||.+++|++|||+|++|+.|++.||| +|+|..+..+.. ..+++  .|+|+|++++|+.|
T Consensus        67 -------------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~-~~~~~~~~vtI~G~~~~v~~A  132 (144)
T 2qnd_A           67 -------------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV-PQEEGMVPFVFVGTKDSIANA  132 (144)
T ss_dssp             -------------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC-CCCTTEEEEEEEEEHHHHHHH
T ss_pred             -------------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc-cccCCeeEEEEEeCHHHHHHH
Confidence                         13789999999999999999999999999997 999993321111 12344  48999999999999


Q ss_pred             HHHHHHHhhh
Q 014254          342 VYNVTGRLRD  351 (428)
Q Consensus       342 ~~lI~~~L~e  351 (428)
                      +.+|.++|++
T Consensus       133 k~li~~~l~~  142 (144)
T 2qnd_A          133 TVLLDYHLNY  142 (144)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHHh
Confidence            9999999864

>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=1.6e-17  Score=157.85  Aligned_cols=154  Identities=14%  Similarity=0.195  Sum_probs=110.4

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhccc
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTS  264 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~  264 (428)
                      ....++.||.+.+|.|||++|++|+.|+++|||+|.|..     +++.|+|.|+.... ....+++|...|.+......+
T Consensus        33 P~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~-----~~g~V~I~~~~~t~-d~~~i~kA~~~I~~i~rg~~~  106 (219)
T 2e3u_A           33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS-----ETGEVWITSTKETE-DPLAVWKARDIVLAIGRGFSP  106 (219)
T ss_dssp             CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT-----TTCEEEEEECTTCC-SHHHHHHHHHHHHHHHTTCCH
T ss_pred             CEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc-----CCCEEEEecCCCCC-CHHHHHHHHHHHHHHhccCCc
Confidence            346689999999999999999999999999999999972     46789999865211 112366666666553321111


Q ss_pred             ccccCCCCCCCceeEEEEEec-----------cccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe
Q 014254          265 EKGLDFSSNKGLLVNARLVVA-----------SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG  333 (428)
Q Consensus       265 ~~g~~~~~~~~~~vt~~L~VP-----------~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG  333 (428)
                      +.+...-  .+......+.|+           ...+|+||||+|++|+.|++.|||+|.|.           ++.|+|.|
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            1110000  011111123333           23689999999999999999999999995           35699999


Q ss_pred             CHHHHHHHHHHHHHHhhhcCCCCc
Q 014254          334 EFSKVKDAVYNVTGRLRDNHFSGT  357 (428)
Q Consensus       334 t~~aV~~A~~lI~~~L~e~~~~~~  357 (428)
                      ++++++.|..+|.++|.+.+++..
T Consensus       174 ~~~~i~~A~~~i~~li~g~~~~~v  197 (219)
T 2e3u_A          174 NPIQIEIAKTAIEKLARGSPHGSV  197 (219)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             CHHHHHHHHHHHHHHHcCCCcHHH
Confidence            999999999999999987765543

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

Probab=99.67  E-value=1.6e-16  Score=161.32  Aligned_cols=162  Identities=14%  Similarity=0.155  Sum_probs=115.1

Q ss_pred             CCceEEEEEeccccccceeccCc--hHHHHHHHHhCCcEEEccCC-----CCCCceEEEeeCCCCCCcCccHHHHHHHHH
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGG--TIIRALQSEAGAFISVGATM-----PECDERLITVTASEGPESRYSPAQKAVVLV  255 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG--~tIK~IqeeTGA~I~Is~~~-----p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I  255 (428)
                      ...+++++.||...++.||||||  ++|++|+++|||+|+|++..     +......|+|+|..++      +.+|-.++
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~en------VE~AR~~I  100 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGD------VDRARMLM  100 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHH------HHHHHHHH
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHH------HHHHHHHH
Confidence            45699999999999999999999  99999999999999998743     1234578999998765      33333222


Q ss_pred             HH---------------------Hhhhc--c------c---cc--c--cC---------------------------CCC
Q 014254          256 FS---------------------RLIEG--T------S---EK--G--LD---------------------------FSS  272 (428)
Q Consensus       256 ~~---------------------~i~e~--~------~---~~--g--~~---------------------------~~~  272 (428)
                      .+                     ..+..  .      +   ..  +  .+                           ...
T Consensus       101 ~~l~Pl~i~~elp~~~i~~~~l~~~I~qq~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~~nv~~akeA~~~Ll~~l~~~e~  180 (376)
T 3n89_A          101 RRNCHFTVFMALSKMKMPLHELQAHVRQNPIQNVEMSFVDAPEKNGIVTTYLRITAREKNQHELIEAAKRLNEILFRESP  180 (376)
T ss_dssp             HHSCEEEEEEECTTCSSCHHHHHHHHHHCCCTTCEEEEEEEC-----CEEEEEEEEEGGGHHHHHHHHHHHHHHHCC--C
T ss_pred             HhcCCceEEEEccccccCcchhhhhhccceeCceEEEeCCcccccCCCCCEEEEEcChhhHHHHHHHHHHHHHHHHhhhc
Confidence            21                     01110  0      0   00  0  00                           000


Q ss_pred             CCCceeEEEEEeccccccceeCCCC--chHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhh
Q 014254          273 NKGLLVNARLVVASNQVGCLLGKGG--TIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLR  350 (428)
Q Consensus       273 ~~~~~vt~~L~VP~s~VG~IIGKgG--~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~  350 (428)
                      .....++..+.|+..++..||||+|  ..|++|+++|||+|++++...+.....+...|+|+|+.++|.+|..+|.++|=
T Consensus       181 ~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lLP  260 (376)
T 3n89_A          181 APENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLLP  260 (376)
T ss_dssp             CCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTSE
T ss_pred             ccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhCC
Confidence            1134688999999999999999999  56799999999999999432222111345689999999999999999999885

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

Probab=99.56  E-value=5.9e-15  Score=137.50  Aligned_cols=148  Identities=18%  Similarity=0.237  Sum_probs=105.8

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhccccc
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK  266 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~  266 (428)
                      .++++||.+.+|.|||++|++++.|++.+|++|++.     ..++.|+|..+.... ....+++|...|..-...-.++.
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id-----~~~~~V~i~t~~~t~-dp~~i~KA~dlI~ai~rgf~~e~   78 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVD-----TENSMVIVEPEAEGI-PPVNLMKAAEVVKAISLGFPPEK   78 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEE-----TTTTEEEEEESSTTS-CHHHHHHHHHHHHHHHHTCCHHH
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEE-----cCCCeEEEEeCCCCC-CHHHHHHHHHHHHHHHcCCCHHH
Confidence            368999999999999999999999999999999997     457888888432211 12236666655543222111111


Q ss_pred             ccCCCCCCCceeEEEEEec----------cccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHH
Q 014254          267 GLDFSSNKGLLVNARLVVA----------SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS  336 (428)
Q Consensus       267 g~~~~~~~~~~vt~~L~VP----------~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~  336 (428)
                      .... . .+..+...+.++          ...+|+||||+|.+|+.|+..|||+|.|.           +..|.|.|+++
T Consensus        79 A~~L-l-~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~-----------~~~v~i~G~~~  145 (191)
T 1tua_A           79 AFRL-L-EEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG-----------EYEVAIIGDYE  145 (191)
T ss_dssp             HGGG-G-STTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC-----------SSEEEEEEEHH
T ss_pred             hhhc-c-cCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc-----------CCEEEEEeChH
Confidence            0000 0 112222223344          23689999999999999999999999995           23799999999


Q ss_pred             HHHHHHHHHHHHhhhcC
Q 014254          337 KVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       337 aV~~A~~lI~~~L~e~~  353 (428)
                      +++.|...|..+|...+
T Consensus       146 ~i~~Ar~~i~~li~g~~  162 (191)
T 1tua_A          146 RAMAAKQAIEMLAEGRM  162 (191)
T ss_dssp             HHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHcCCC
Confidence            99999999999997544

>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=99.53  E-value=9.3e-15  Score=115.74  Aligned_cols=71  Identities=23%  Similarity=0.495  Sum_probs=64.5

Q ss_pred             ceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      ..++.+|+||.+.+|+||||||++|++|++.|||+|+|.++      +..+|.|+|+|+++++.+|+.+|.++|+++
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~------~~~er~v~I~G~~~~v~~A~~~I~~~l~ed   73 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG------NCPERIITLAGPTNAIFKAFAMIIDKLEED   73 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS------CCSEEEEEEEECHHHHHHHHHHHHHHHHC-
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC------CCCcEEEEEEeCHHHHHHHHHHHHHHHhcC
Confidence            45789999999999999999999999999999999999843      256899999999999999999999999864

>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=99.53  E-value=1.5e-14  Score=114.72  Aligned_cols=71  Identities=31%  Similarity=0.485  Sum_probs=63.5

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccC--CccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISD--QLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d--~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e  351 (428)
                      .+.++.||.+++|+||||||++|++|++.|||+|+|.++  ..|   ++.++.|+|+|++++++.|+.+|.+++.+
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 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP---GTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCST---TCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCC---CCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999943  233   36789999999999999999999999865

>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=99.52  E-value=3.2e-14  Score=114.91  Aligned_cols=74  Identities=26%  Similarity=0.581  Sum_probs=66.4

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      +..++.+|.||.+++|+||||+|++|++|++.|||+|+|.++ .|   +++++.|+|+|++++|++|+.+|.+++.+.
T Consensus         4 g~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~-~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            4 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-LE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT-TS---CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC-CC---CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            456889999999999999999999999999999999999732 23   367899999999999999999999999864

>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=99.52  E-value=2.1e-14  Score=115.91  Aligned_cols=74  Identities=28%  Similarity=0.578  Sum_probs=65.6

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      +..++.+|.||.+++|+||||||++|++|++.|||+|+|.++ .   .++.++.|+|+|+++++++|+.+|.+++.+.
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~-~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-V---EGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC-C---TTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC-C---CCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            456789999999999999999999999999999999999842 2   2478999999999999999999999999876

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

Probab=99.51  E-value=1.8e-14  Score=114.54  Aligned_cols=73  Identities=27%  Similarity=0.559  Sum_probs=65.7

Q ss_pred             ceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      ..++.+|.||.+++|+||||||++|++|++.|||+|+|.+. .|   ++.++.|+|+|+++++++|+.+|.+++.+.
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~-~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP-VE---GSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC-CT---TCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC-CC---CCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            46788999999999999999999999999999999999842 23   478999999999999999999999998753

>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=99.48  E-value=3.7e-14  Score=115.66  Aligned_cols=73  Identities=30%  Similarity=0.474  Sum_probs=65.3

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccC--CccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcC
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISD--QLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d--~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      .+.+|.||.+++|+||||||++|++|++.|||+|+|.++  ..|+   +.++.|+|+|++++++.|+.+|.++|.+..
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g---~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   77 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG---TRNRRVTITGSPAATQAAQYLISQRVTYEQ   77 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTT---SCEEEEEEESSHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCC---CCceEEEEEcCHHHHHHHHHHHHHHHhccc
Confidence            578999999999999999999999999999999999943  2343   678999999999999999999999998643

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

Probab=99.47  E-value=8e-14  Score=118.26  Aligned_cols=74  Identities=15%  Similarity=0.286  Sum_probs=65.5

Q ss_pred             EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcC
Q 014254          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      +.+|.||.+++|+||||+|++|++|+++|||+|+|.++..+. .+.+++.|+|+|++++|++|+.+|.++|.+..
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 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPN-GDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTT-CCTTEEEEEEESCHHHHHHHHHHHHHHSCSCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCC-CCCCceEEEEECCHHHHHHHHHHHHHHHhccc
Confidence            679999999999999999999999999999999998543332 23578999999999999999999999998654

>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=99.46  E-value=7.2e-14  Score=114.62  Aligned_cols=75  Identities=25%  Similarity=0.569  Sum_probs=67.3

Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      ....++.+|.||.+++|+||||+|++|++|+++|||+|+|.++ .|   +++++.|+|+|++++|++|+.+|.+++.+.
T Consensus        10 ~~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~-~~---~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-LE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC-CS---SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC-CC---CCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            3567899999999999999999999999999999999999732 23   367899999999999999999999999874

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

Probab=99.44  E-value=2.6e-13  Score=110.31  Aligned_cols=74  Identities=24%  Similarity=0.396  Sum_probs=65.1

Q ss_pred             ceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e  351 (428)
                      .....+|.||.+.+|+||||||++|++|+++|||+|.|..+..+  ..+.+|.|+|+|+++++++|+.+|.+++++
T Consensus        12 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~--~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           12 NGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ--NTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCS--STTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCC--CCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            45678999999999999999999999999999999999854332  236789999999999999999999998864

>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=99.44  E-value=1.2e-14  Score=132.43  Aligned_cols=139  Identities=16%  Similarity=0.250  Sum_probs=100.9

Q ss_pred             chhhhhcCccccccccccCC----CCCcccCCCCCceecccCCCcccccccccCCccccccccc-------------hhh
Q 014254          117 ALSIETQHRLFGAVSQEILP----DLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVAT-------------LDA  179 (428)
Q Consensus       117 ~~~~~~~~~~~~~v~~~~~~----~~~~d~~Pgt~~rv~ti~Gs~~~~~~a~~~~~~e~~~~~~-------------~~~  179 (428)
                      +.-|+.||..+..++++|..    +...+++|+..+|+++|.|...++..+...+.......+.             ...
T Consensus        18 g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~   97 (178)
T 2anr_A           18 GSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTT   97 (178)
T ss_dssp             HHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCCCC---------------
T ss_pred             eeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhccCCccccCCcccccCCccC
Confidence            34689999999999999842    1345789999999999999876666554332211111100             000


Q ss_pred             hccCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC--CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHH
Q 014254          180 RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT--MPECDERLITVTASEGPESRYSPAQKAVVLVFS  257 (428)
Q Consensus       180 ~~~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~--~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~  257 (428)
                      ...+...+++|+||.+.+|.||||+|++||+|+++|||+|+|.+.  .++..+|+|+|+|+.++      +.+|..++.+
T Consensus        98 ~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~------v~~A~~~I~~  171 (178)
T 2anr_A           98 VNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQ------NRKAVELIIQ  171 (178)
T ss_dssp             --CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEEEEEEESSHHH------HHHHHHHHHH
T ss_pred             CCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEcCHHH------HHHHHHHHHH
Confidence            112345789999999999999999999999999999999999864  24567899999998654      6777777777


Q ss_pred             Hhhh
Q 014254          258 RLIE  261 (428)
Q Consensus       258 ~i~e  261 (428)
                      .+.+
T Consensus       172 ~i~e  175 (178)
T 2anr_A          172 KIQE  175 (178)
T ss_dssp             HHHS
T ss_pred             HHHh
Confidence            6654

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

Probab=99.44  E-value=2e-13  Score=112.66  Aligned_cols=75  Identities=21%  Similarity=0.351  Sum_probs=67.2

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcC
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      ...++.+|.||.+++|+||||+|++|++|+++|||+|+|.++. +   +..++.|+|+|++++|++|+.+|.++|.+..
T Consensus        12 ~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~-~---g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~   86 (92)
T 1x4n_A           12 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS-G---GLPERSCMLTGTPESVQSAKRLLDQIVEKGR   86 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC-T---TCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC-C---CCCccEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            4568899999999999999999999999999999999998432 2   3578999999999999999999999998754

>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=99.43  E-value=1.2e-13  Score=112.39  Aligned_cols=70  Identities=20%  Similarity=0.280  Sum_probs=62.8

Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhh
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLR  350 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~  350 (428)
                      .....+.+|.||.+++|+||||+|++||+|+++|||+|+|++.       .+++.|+|+|+++++++|+++|.+++.
T Consensus         6 ~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~-------~~~~~v~ItG~~e~v~~A~~~I~~~i~   75 (83)
T 2dgr_A            6 SGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR-------DKEPVFAVTGMPENVDRAREEIEAHIT   75 (83)
T ss_dssp             SCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS-------SSCCEEEEEECTTTHHHHHHHHHHHHH
T ss_pred             CCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC-------CCCCeEEEEcCHHHHHHHHHHHHHHHh
Confidence            3456789999999999999999999999999999999999832       236899999999999999999999875

>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=8.7e-14  Score=110.15  Aligned_cols=70  Identities=30%  Similarity=0.596  Sum_probs=61.0

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      ..++++|+||++.+|.||||||++||+|+++|||+|+|++.  ++++|+|+|+|+.+.      +.+|..++...+.+
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--NCPERIITLAGPTNA------IFKAFAMIIDKLEE   72 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHH------HHHHHHHHHHHHHC
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC--CCCcEEEEEEeCHHH------HHHHHHHHHHHHhc
Confidence            46899999999999999999999999999999999999974  678999999998654      67777777776643

>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=99.42  E-value=2.3e-13  Score=112.72  Aligned_cols=77  Identities=23%  Similarity=0.394  Sum_probs=67.5

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcC
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      ...++.+|.||.+++|+||||+|++|++|+++|||+|+|.++..+.  ...+|.|+|+|++++|++|+.+|.++|.+.-
T Consensus        12 p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~--~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   88 (94)
T 1x4m_A           12 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN--TGADKPLRITGDPYKVQQAKEMVLELIRDQG   88 (94)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS--SCSCEEEEEEECTTTHHHHHHHHHHHHCCCS
T ss_pred             CCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCC--CCCceEEEEEeCHHHHHHHHHHHHHHHhccC
Confidence            4668899999999999999999999999999999999998543321  2478999999999999999999999997643

>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=99.40  E-value=4.9e-13  Score=112.72  Aligned_cols=78  Identities=23%  Similarity=0.330  Sum_probs=67.4

Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcC
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      .....+.+|.||.+++|+||||||++|++|+++|||+|+|.++..+  ..+.++.|+|+|+.+++++|+.+|.+++.+.+
T Consensus        11 ~~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~--~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T 1we8_A           11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG--TLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC--SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCC--CCCCcceEEEEcCHHHHHHHHHHHHHHHhhCh
Confidence            3456789999999999999999999999999999999999843211  12468999999999999999999999998765

>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=99.39  E-value=4.7e-13  Score=108.03  Aligned_cols=72  Identities=26%  Similarity=0.500  Sum_probs=61.9

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      ..++++|+||.+.+|.||||+|++||+|+++|||+|+|.+..++.++|+|+|+|+.++      +.+|..++...+.+
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~------v~~A~~~I~~~i~~   76 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ------IQNAQYLLQNSVKQ   76 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHH------HHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHH------HHHHHHHHHHHHHh
Confidence            4588999999999999999999999999999999999998777889999999998653      66666666665543

>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=2.2e-13  Score=108.27  Aligned_cols=71  Identities=28%  Similarity=0.437  Sum_probs=62.1

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhh
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLI  260 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~  260 (428)
                      ..++++|+||.+.+|.||||||++||+|+++|||+|+|.+..+++.+|.|+|+|+.++      +.+|..++.+.+.
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~------v~~A~~~I~~~i~   73 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAAS------ISLAQYLINVRLS   73 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHH------HHHHHHHHHHHHT
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHH------HHHHHHHHHHHHH
Confidence            3578999999999999999999999999999999999998778889999999998653      6677777766554

>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=99.39  E-value=3e-13  Score=109.12  Aligned_cols=72  Identities=24%  Similarity=0.406  Sum_probs=62.3

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      ..++++|+||.+.+|.||||||++||+|+++|||+|+|.+..++..+|.|+|+|+.++      +.+|..++.+.+.+
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~------v~~A~~~I~~~i~~   75 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS------ISLAQYLINARLSS   75 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHH------HHHHHHHHHHHTC-
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHH------HHHHHHHHHHHHHh
Confidence            4688999999999999999999999999999999999998777889999999998653      66777777766543

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

Probab=99.36  E-value=8.5e-13  Score=112.00  Aligned_cols=72  Identities=18%  Similarity=0.356  Sum_probs=63.9

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcC
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|.++. +   .+.+|.|+|+|++++|++|+.+|.+++.+..
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~-~---~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~   82 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-G---TGPEKIAHIMGPPDRCEHAARIINDLLQSLR   82 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC-S---SSSEEEEEEESSHHHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC-C---CCceeEEEEEeCHHHHHHHHHHHHHHHhccc
Confidence            3679999999999999999999999999999999998432 2   2568999999999999999999999998754

>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=99.34  E-value=1.9e-12  Score=108.05  Aligned_cols=72  Identities=13%  Similarity=0.179  Sum_probs=64.2

Q ss_pred             eeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e  351 (428)
                      ..+..|.||.+++|.||||||++|++|+++|||+|+|+.+..|.   ..++.|+|+|+.+++.+|+.+|..++.+
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~---~~~~~V~I~G~~e~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGN---QPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCS---SCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCC---CCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            46889999999999999999999999999999999998543332   4788999999999999999999998864

>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=99.33  E-value=6.6e-13  Score=108.85  Aligned_cols=73  Identities=26%  Similarity=0.489  Sum_probs=62.9

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      ...++++|+||.+.+|.||||+|++||+|+++|||+|+|.+..+++++|+|+|+|+.++      +.+|..+|.+.+.+
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~------v~~A~~~I~~~i~e   83 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ------IQNAQYLLQNSVKQ   83 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHH------HHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHH------HHHHHHHHHHHHHh
Confidence            45689999999999999999999999999999999999998777889999999998654      66677666665543

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

Probab=99.33  E-value=2.1e-12  Score=101.65  Aligned_cols=68  Identities=21%  Similarity=0.300  Sum_probs=60.6

Q ss_pred             ceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHh
Q 014254          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL  349 (428)
Q Consensus       276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L  349 (428)
                      ...+..|.||.+++|.|||+||++|++|+++|||+|+|+.+.      ..++.|+|+|+.+++++|+.+|.+++
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g------~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC------CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            346789999999999999999999999999999999998432      35689999999999999999998864

>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=99.32  E-value=1.2e-12  Score=103.64  Aligned_cols=68  Identities=29%  Similarity=0.466  Sum_probs=58.0

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC---CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHh
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSRL  259 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~---~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i  259 (428)
                      .+++|+||.+.+|.||||||++||+|+++|||+|+|.+.   .++..+|.|+|+|+.++      +.+|..++.+.+
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~------v~~A~~~I~~~i   73 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA------TQAAQYLISQRV   73 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHH------HHHHHHHHHHHC
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHH------HHHHHHHHHHHH
Confidence            578999999999999999999999999999999999864   46778999999998553      666666666544

>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=99.29  E-value=3.4e-12  Score=105.72  Aligned_cols=73  Identities=16%  Similarity=0.246  Sum_probs=64.7

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcC
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      ...++.+|.||.+++|.|||+||++|++|+++|||+|+|+...      ..++.|+|+|+++++.+|..+|..++.+..
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~------~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~   86 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD------DPSNQIKITGTKEGIEKARHEVLLISAEQD   86 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT------SSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC------CCCCeEEEEECHHHHHHHHHHHHHHhhccc
Confidence            4568899999999999999999999999999999999998321      235789999999999999999999998654

>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=99.29  E-value=2.2e-12  Score=106.41  Aligned_cols=72  Identities=24%  Similarity=0.289  Sum_probs=61.3

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      ..++++|+||.+.+|.||||+|++||+|+++|||+|+|.+..++..+|.|+|+|+.++      +.+|..+|.+.+.+
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~------v~~A~~~I~~~i~~   84 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPES------VQSAKRLLDQIVEK   84 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHH------HHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHH------HHHHHHHHHHHHHh
Confidence            4588999999999999999999999999999999999998766788999999998653      66666666655443

>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=99.28  E-value=1.7e-13  Score=122.56  Aligned_cols=138  Identities=17%  Similarity=0.285  Sum_probs=97.8

Q ss_pred             chhhhhcCccccccccccCCCCCcccCCCCCceecccCCCcccccccccCCccccccc--cchh--hhccCCceEEEEEe
Q 014254          117 ALSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRV--ATLD--ARTQQQEVSFRILC  192 (428)
Q Consensus       117 ~~~~~~~~~~~~~v~~~~~~~~~~d~~Pgt~~rv~ti~Gs~~~~~~a~~~~~~e~~~~--~~~~--~~~~~~evt~rIlV  192 (428)
                      ++-|+.||..+..++.++......+- ++..+|+++|.|...++..+...+.....+.  .+..  .......++++|+|
T Consensus        17 g~iIGkgG~~Ik~i~~~tg~~I~i~~-~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~~~~~~~~~~~~~~~~~~i~v   95 (160)
T 2jzx_A           17 GSIIGKKGESVKKMREESGARINISE-GNCPERIITLAGPTNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVV   95 (160)
T ss_dssp             HHHHCGGGHHHHHHHHHHCSEEEEEC-CTTTEEEEEEEEEHHHHHHHHHHHHHHHHHHHTSCCCSSSCCCCCSEEEEEEE
T ss_pred             eeeECCCcHHHHHHHHHHCCEEEEcC-CCCCceEEEEEeCHHHHHHHHHHHHHHHHhhccccCCCCccCCCCCEEEEEEE
Confidence            44689999999999999854222211 2466899999998766655544332211110  0000  01123358999999


Q ss_pred             ccccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          193 SNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       193 P~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      |.+.+|.||||+|++||+|+++|||+|+|.+. .++++++.|+|+|+.++      +.+|..++.+.+.|
T Consensus        96 p~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G~~~~------v~~A~~~I~~~i~e  159 (160)
T 2jzx_A           96 PASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQS------IIECVKQICVVMLE  159 (160)
T ss_dssp             EHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEECHHH------HHHHHHHHHHHHHH
T ss_pred             ChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEEEcCHHH------HHHHHHHHHHHHhc
Confidence            99999999999999999999999999999863 57788999999997654      66677666665543

>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=99.27  E-value=6.6e-12  Score=103.93  Aligned_cols=73  Identities=26%  Similarity=0.369  Sum_probs=61.4

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCC--CCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhh
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMP--ECDERLITVTASEGPESRYSPAQKAVVLVFSRLI  260 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p--~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~  260 (428)
                      ...++++|+||.+++|.||||+|++||+|+++|||+|+|.+...  ..++|+|+|+|+.+.      +.+|..+|...+.
T Consensus        12 p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~------v~~A~~~I~~~i~   85 (94)
T 1x4m_A           12 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYK------VQQAKEMVLELIR   85 (94)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTT------HHHHHHHHHHHHC
T ss_pred             CCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHH------HHHHHHHHHHHHh
Confidence            45689999999999999999999999999999999999987532  457999999998775      6777777776654


Q ss_pred             h
Q 014254          261 E  261 (428)
Q Consensus       261 e  261 (428)
                      +
T Consensus        86 ~   86 (94)
T 1x4m_A           86 D   86 (94)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.27  E-value=7e-12  Score=104.27  Aligned_cols=76  Identities=13%  Similarity=0.182  Sum_probs=66.8

Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcC
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      ....++..+.||.+++|.|||+||++|++|+++|||+|+|+.+.     ..+++.|+|+|++++|++|+.+|..++.+..
T Consensus        13 l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g-----~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~   87 (95)
T 2ctm_A           13 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-----APDPNCVTVTGLPENVEEAIDHILNLEEEYL   87 (95)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-----CSCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             hcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC-----CCCCcEEEEEcCHHHHHHHHHHHHHHHHHHH
Confidence            35678899999999999999999999999999999999998431     1357899999999999999999999998766


Q ss_pred             C
Q 014254          354 F  354 (428)
Q Consensus       354 ~  354 (428)
                      .
T Consensus        88 ~   88 (95)
T 2ctm_A           88 A   88 (95)
T ss_dssp             T
T ss_pred             H
Confidence            4

>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=99.26  E-value=3e-12  Score=104.32  Aligned_cols=70  Identities=30%  Similarity=0.444  Sum_probs=59.2

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC---CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~---~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      .+++|+||.+.+|.||||||++||+|+++|||+|+|.+.   .+++.+|.|+|+|+.++      +.+|..+|...+.+
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~------v~~A~~~I~~~i~~   75 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA------TQAAQYLISQRVTY   75 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHH------HHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHH------HHHHHHHHHHHHhc
Confidence            578899999999999999999999999999999999864   46788999999998653      66666666665543

>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=99.26  E-value=7.2e-12  Score=112.33  Aligned_cols=73  Identities=22%  Similarity=0.390  Sum_probs=66.6

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcC
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      .+++|+||.+.+|.||||+|++|++|++.|||+|+|..+..|+   +.+|.|+|+|+++++.+|+.+|.+++.+..
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~---~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~   75 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPD---SKVRMVIITGPPEAQFKAQGRIYGKLKEEN   75 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTT---CSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCC---CCceEEEEEcCHHHHHHHHHHHHHHHhccc
Confidence            4789999999999999999999999999999999998554444   789999999999999999999999998774

>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=99.26  E-value=5.4e-13  Score=121.19  Aligned_cols=135  Identities=14%  Similarity=0.185  Sum_probs=93.1

Q ss_pred             chhhhhcCccccccccccCCCCCcc-cCCCCCceecccCCCcccccccccCCccccccccc--h----------------
Q 014254          117 ALSIETQHRLFGAVSQEILPDLHVD-ILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVAT--L----------------  177 (428)
Q Consensus       117 ~~~~~~~~~~~~~v~~~~~~~~~~d-~~Pgt~~rv~ti~Gs~~~~~~a~~~~~~e~~~~~~--~----------------  177 (428)
                      ++-|+.||..|..++.++......+ ..++..+|+++|.|...++..|...+.........  .                
T Consensus        15 g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~~~~~p~~~~~~~~~~~   94 (174)
T 1j4w_A           15 GIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGN   94 (174)
T ss_dssp             HHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred             eeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcccCCCCCCCCCCCCCCCCCCc
Confidence            3468999999999999986433222 24678889999999976666554333211100000  0                


Q ss_pred             -hhhccCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCC---CCCCceEEEeeCCCCCCcCccHHHHHHH
Q 014254          178 -DARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATM---PECDERLITVTASEGPESRYSPAQKAVV  253 (428)
Q Consensus       178 -~~~~~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~---p~s~ERvVtItGs~e~~~~~s~a~~Ai~  253 (428)
                       ........++++|+||.+.+|.||||+|++||+|+++|||+|+|.+..   .+..+|+|+|+|+.++      +.+|..
T Consensus        95 ~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~------v~~A~~  168 (174)
T 1j4w_A           95 WNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQ------IDYARQ  168 (174)
T ss_dssp             ---------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHH------HHHHHH
T ss_pred             cccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHH------HHHHHH
Confidence             000112346889999999999999999999999999999999998642   2467899999997653      556665


Q ss_pred             HHHH
Q 014254          254 LVFS  257 (428)
Q Consensus       254 ~I~~  257 (428)
                      +|.+
T Consensus       169 ~I~~  172 (174)
T 1j4w_A          169 LIEE  172 (174)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5544

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

Probab=99.23  E-value=7.3e-12  Score=106.22  Aligned_cols=70  Identities=20%  Similarity=0.333  Sum_probs=58.4

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      .+++|+||.+++|.||||+|++||+|+++|||+|+|.+..++..+|+|+|+|+.++      +.+|..+|.+.+.+
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~------v~~A~~~I~~ii~~   80 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDR------CEHAARIINDLLQS   80 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHH------HHHHHHHHHHHHHH
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHH------HHHHHHHHHHHHhc
Confidence            36789999999999999999999999999999999987666778999999998653      55666666555443

>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=99.23  E-value=8.9e-12  Score=101.29  Aligned_cols=68  Identities=18%  Similarity=0.279  Sum_probs=58.0

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHh
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRL  259 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i  259 (428)
                      ...++++|.||.+.+|+||||+|++||+|+++|||+|+|++.   .++++|+|+|+.+.      +.+|..+|...+
T Consensus         7 ~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~---~~~~~v~ItG~~e~------v~~A~~~I~~~i   74 (83)
T 2dgr_A            7 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR---DKEPVFAVTGMPEN------VDRAREEIEAHI   74 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS---SSCCEEEEEECTTT------HHHHHHHHHHHH
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC---CCCCeEEEEcCHHH------HHHHHHHHHHHH
Confidence            356889999999999999999999999999999999999742   34799999999876      667777776643

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

Probab=99.22  E-value=1.3e-11  Score=100.21  Aligned_cols=68  Identities=25%  Similarity=0.327  Sum_probs=56.2

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCC--CCCCceEEEeeCCCCCCcCccHHHHHHHHHHH
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATM--PECDERLITVTASEGPESRYSPAQKAVVLVFS  257 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~--p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~  257 (428)
                      ...+.+|.||.+++|.||||+|++||+|+++|||+|+|.+..  +...+|.|+|+|+++.      +.+|..+|..
T Consensus        12 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~------v~~A~~~I~~   81 (85)
T 2opv_A           12 NGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYK------VQQACEMVMD   81 (85)
T ss_dssp             SSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHH------HHHHHHHHHH
T ss_pred             CCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHH------HHHHHHHHHH
Confidence            457889999999999999999999999999999999998752  3678999999996543      5555555544

>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=99.21  E-value=2.4e-11  Score=108.61  Aligned_cols=74  Identities=24%  Similarity=0.429  Sum_probs=65.2

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcC
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      ++.+|+||.+++|+||||+|++|++|++.|||+|++..+. + +.+..+|.|+|+|++++|.+|+.+|.+++.+..
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 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG-S-QNTNVDKPLRIIGDPYKVQQACEMVMDILRERD   75 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCT-T-SSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCC-C-CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhcc
Confidence            4679999999999999999999999999999999998432 1 123678999999999999999999999998765

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

Probab=99.20  E-value=1.1e-11  Score=105.14  Aligned_cols=69  Identities=22%  Similarity=0.427  Sum_probs=58.0

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCC---CCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATM---PECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~---p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      +++|+||.+++|.||||+|++||+|+++|||+|+|.+..   .+..+|+|+|+|+.++      +.+|..+|.+.+.+
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~------v~~A~~~I~~~i~e   79 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQ------IDHAKQLIEEKIEG   79 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHH------HHHHHHHHHHHSCS
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHH------HHHHHHHHHHHHhc
Confidence            678999999999999999999999999999999998752   3457899999997664      66777777766544

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

Probab=99.19  E-value=2e-11  Score=103.07  Aligned_cols=71  Identities=15%  Similarity=0.236  Sum_probs=62.7

Q ss_pred             ceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      ...+..|.||.+++|.|||+||++|++|+++|||+|+|+.+.      ...+.|+|+|+.+++++|+.+|..++.+.
T Consensus        15 ap~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g------~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   85 (104)
T 2ctk_A           15 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE------LQSDIIAITGLAANLDRAKAGLLERVKEL   85 (104)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT------TTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC------CCcceEEEEcCHHHHHHHHHHHHHHHhhH
Confidence            357889999999999999999999999999999999998431      23468999999999999999999988754

>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=99.17  E-value=2.1e-11  Score=102.68  Aligned_cols=71  Identities=24%  Similarity=0.384  Sum_probs=57.9

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCC--CCceEEEeeCCCCCCcCccHHHHHHHHHHHHhh
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPE--CDERLITVTASEGPESRYSPAQKAVVLVFSRLI  260 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~--s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~  260 (428)
                      ..++++|+||.+.+|.||||||++||+|+++|||+|+|.+...+  .++|.|+|+|+.+.      +.+|..+|...+.
T Consensus        13 ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~------v~~A~~~I~~~i~   85 (104)
T 1we8_A           13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE------VAAAKHLILEKVS   85 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHH------HHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHH------HHHHHHHHHHHHh
Confidence            35789999999999999999999999999999999999875333  36899999998663      5566666655443

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

Probab=99.11  E-value=7.3e-11  Score=92.81  Aligned_cols=64  Identities=16%  Similarity=0.149  Sum_probs=53.1

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHH
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVF  256 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~  256 (428)
                      ..+..|.||.+.+|.||||||++|++|+++|||+|+|++  .+..+|.|+|+|..+.      +.+|..++.
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~--~g~~~~~V~I~G~~~~------v~~A~~~I~   67 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPP--DSEKSNLIRIEGDPQG------VQQAKRELL   67 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCC--CCSSSEEEEEEESSHH------HHHHHHHHH
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECC--CCCcccEEEEEcCHHH------HHHHHHHHH
Confidence            467889999999999999999999999999999999986  3447799999998542      455554443

>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=99.08  E-value=1.1e-10  Score=97.29  Aligned_cols=57  Identities=18%  Similarity=0.233  Sum_probs=50.1

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCC-CCCCceEEEeeCCCC
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATM-PECDERLITVTASEG  240 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~-p~s~ERvVtItGs~e  240 (428)
                      ..+++.|.||.+.+|.||||||++|++|+++|||+|+|++.. ++..+|.|+|+|..+
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e   72 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK   72 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHH
Confidence            357899999999999999999999999999999999998742 344789999999854

>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=99.05  E-value=1e-10  Score=96.82  Aligned_cols=69  Identities=20%  Similarity=0.221  Sum_probs=55.8

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHh
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRL  259 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i  259 (428)
                      +..++.+|.||.+.+|.||||||++||+|+++|||+|+|++.  +..++.|+|+|+.+.      +.+|..+|...+
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~--~~~~~~V~I~G~~e~------v~~A~~~I~~i~   82 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP--DDPSNQIKITGTKEG------IEKARHEVLLIS   82 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT--TSSCCEEEEEECHHH------HHHHHHHHHHHH
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCC--CCCCCeEEEEECHHH------HHHHHHHHHHHh
Confidence            446899999999999999999999999999999999999752  334689999998543      555665555443

>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=99.04  E-value=2.1e-10  Score=95.42  Aligned_cols=73  Identities=16%  Similarity=0.251  Sum_probs=64.6

Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHh-CCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVT-GTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~T-GA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      ..+.++..|.||.++++.|||+||++|++|+++| ||+|.|+.+.      +..+.|+|.|+..+|++|+.+|.+++.+.
T Consensus        13 ~~~~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           13 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG------SGSDTVVIRGPSSDVEKAKKQLLHLAEEK   86 (95)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT------TTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             HhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC------CCcceEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            3566788999999999999999999999999999 9999998431      45678999999999999999999998764

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

Probab=98.97  E-value=1.1e-09  Score=92.21  Aligned_cols=68  Identities=15%  Similarity=0.241  Sum_probs=60.9

Q ss_pred             eeEEEEEeccccccceeCCCCchHHHHHHH-hCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcC
Q 014254          277 LVNARLVVASNQVGCLLGKGGTIISEMRKV-TGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~-TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      .++..|.||..+++.|||++|++|++|+++ ++++|.|++         .++.|+|+|++++|.+|..+|..++++..
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~---------~~~~ItI~G~~~~V~~a~~~I~~~v~el~   94 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE---------GEDKITLEGPTEDVSVAQEQIEGMVKDLI   94 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS---------SSCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC---------CCCEEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            378999999999999999999999999997 599999973         35689999999999999999999987643

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

Probab=98.92  E-value=7.9e-10  Score=91.83  Aligned_cols=68  Identities=22%  Similarity=0.220  Sum_probs=54.5

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHH
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFS  257 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~  257 (428)
                      ...++..|.||.+.+|.|||+||++||+|+++|||+|+|++. ....+|.|+|+|..++      +.+|..++..
T Consensus        14 ~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~-g~~~~~~V~I~G~~e~------v~~A~~~I~~   81 (95)
T 2ctm_A           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQS-GAPDPNCVTVTGLPEN------VEEAIDHILN   81 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCT-TCSCTTEEEEESCHHH------HHHHHHHHHH
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCC-CCCCCcEEEEEcCHHH------HHHHHHHHHH
Confidence            446889999999999999999999999999999999999763 1235789999998543      4455544444

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

Probab=98.90  E-value=7.5e-10  Score=93.41  Aligned_cols=65  Identities=25%  Similarity=0.267  Sum_probs=52.9

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHH
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFS  257 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~  257 (428)
                      .++..|.||.+.+|.|||+||++||+|+++|||+|+|++.  +...+.|+|+|..+.      +.+|..+|..
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~--g~~~~~V~I~G~~e~------v~~A~~~I~~   80 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP--ELQSDIIAITGLAAN------LDRAKAGLLE   80 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT--TTTCCEEEEEECHHH------HHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCC--CCCcceEEEEcCHHH------HHHHHHHHHH
Confidence            3788899999999999999999999999999999999863  335579999998543      4555554444

>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=98.85  E-value=2.2e-09  Score=88.73  Aligned_cols=70  Identities=23%  Similarity=0.246  Sum_probs=60.2

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHhCCe-EEEccCCccccCCCCCcEEEEEe-CHHHHHHHHHHHHHHhhhc
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTS-IRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~-IqI~~d~~P~~~~s~eRvVtItG-t~~aV~~A~~lI~~~L~e~  352 (428)
                      ...+...+.||.+.+|.+||+||++|++|++.|||+ |.|..         .+..|+|.| +.+++++|+.+|...-...
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e---------ddG~V~I~g~~~ea~~~A~~~I~~ie~~~   82 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE---------DTGTFRIYGESADAVKKARGFLEFVEDFI   82 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET---------TTTEEEEEESSHHHHHHHHHHHSCCCCCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc---------CCCEEEEEECCHHHHHHHHHHHHhhheEE
Confidence            456788999999999999999999999999999998 99952         357899999 7999999999987755443


Q ss_pred             C
Q 014254          353 H  353 (428)
Q Consensus       353 ~  353 (428)
                      .
T Consensus        83 ~   83 (91)
T 2cpq_A           83 Q   83 (91)
T ss_dssp             C
T ss_pred             e
Confidence            3

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

Probab=98.72  E-value=1.7e-08  Score=84.95  Aligned_cols=74  Identities=12%  Similarity=0.106  Sum_probs=58.3

Q ss_pred             ccCCCcccccccccCCccccccccchhhhccCCceEEEEEeccccccceeccCchHHHHHHHH-hCCcEEEccCCCCCCc
Q 014254          152 TAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSE-AGAFISVGATMPECDE  230 (428)
Q Consensus       152 ti~Gs~~~~~~a~~~~~~e~~~~~~~~~~~~~~evt~rIlVP~~~vG~IIGKgG~tIK~Iqee-TGA~I~Is~~~p~s~E  230 (428)
                      .+.|..+++..+...+.....           ..++.+|.||...++.||||+|++||+|+++ +++.|+|++     .+
T Consensus         4 ~i~G~~~~V~~A~~~i~~~~~-----------~~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-----~~   67 (102)
T 2ctf_A            4 GSSGEPEKLGQALTEVYAKAN-----------SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GE   67 (102)
T ss_dssp             CCCCCCCCCCCSCCCCCCCCC-----------CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SS
T ss_pred             ccCcCHHHHHHHHHHHHHHhc-----------CeEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-----CC
Confidence            456776666666655543221           2378999999999999999999999999998 599999975     56


Q ss_pred             eEEEeeCCCCC
Q 014254          231 RLITVTASEGP  241 (428)
Q Consensus       231 RvVtItGs~e~  241 (428)
                      +.|+|.|+++.
T Consensus        68 ~~ItI~G~~~~   78 (102)
T 2ctf_A           68 DKITLEGPTED   78 (102)
T ss_dssp             CEEEEEECHHH
T ss_pred             CEEEEECCHHH
Confidence            89999998664

>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=98.69  E-value=1e-08  Score=85.27  Aligned_cols=68  Identities=15%  Similarity=0.250  Sum_probs=54.9

Q ss_pred             cCCceEEEEEeccccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHH
Q 014254          182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFS  257 (428)
Q Consensus       182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~  257 (428)
                      ....++..|.||.++++.|||+||++||+|+++| ||+|.|++  .+...+.|+|+|+...      +.+|..++..
T Consensus        13 ~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~--~g~~~~~V~I~G~~~~------v~~A~~~I~~   81 (95)
T 2ctj_A           13 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV--EGSGSDTVVIRGPSSD------VEKAKKQLLH   81 (95)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCC--TTTTCCEEEEESCHHH------HHHHHHHHHH
T ss_pred             HhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCC--CCCCcceEEEEcCHHH------HHHHHHHHHH
Confidence            3456788899999999999999999999999999 99999986  4456778999997542      4445444444

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

Probab=98.68  E-value=2.3e-08  Score=101.63  Aligned_cols=75  Identities=16%  Similarity=0.139  Sum_probs=63.2

Q ss_pred             CCceeEEEEEeccccccceeCCCC--chHHHHHHHhCCeEEEccCCcc-ccCCCCCcEEEEEeCHHHHHHHHHHHHHH
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGG--TIISEMRKVTGTSIRIISDQLL-KCISENDRVVQISGEFSKVKDAVYNVTGR  348 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG--~~IkeIre~TGA~IqI~~d~~P-~~~~s~eRvVtItGt~~aV~~A~~lI~~~  348 (428)
                      ..+.+|.++.||..+++.||||||  ++|++|+++|||+|+|+....+ .........|+|+|.+++|++|..+|.+.
T Consensus        26 ~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l  103 (376)
T 3n89_A           26 NPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRN  103 (376)
T ss_dssp             CTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHS
T ss_pred             cCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhc
Confidence            467899999999999999999999  9999999999999999833210 11124567899999999999999999884

>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=98.52  E-value=2.3e-07  Score=81.40  Aligned_cols=77  Identities=18%  Similarity=0.282  Sum_probs=61.5

Q ss_pred             ceeEEEEEeccc------cccceeCCCCchHHHHHHHhCCeEEEccCC-cc-----------ccCCCCCcEEEEEeC-HH
Q 014254          276 LLVNARLVVASN------QVGCLLGKGGTIISEMRKVTGTSIRIISDQ-LL-----------KCISENDRVVQISGE-FS  336 (428)
Q Consensus       276 ~~vt~~L~VP~s------~VG~IIGKgG~~IkeIre~TGA~IqI~~d~-~P-----------~~~~s~eRvVtItGt-~~  336 (428)
                      ..++.+|.||.+      ++|.|||++|++||+|+++|||+|.|.+.. ..           ......+-.|.|+++ .+
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            467889999988      899999999999999999999999997311 00           001123557999995 88


Q ss_pred             HHHHHHHHHHHHhhhc
Q 014254          337 KVKDAVYNVTGRLRDN  352 (428)
Q Consensus       337 aV~~A~~lI~~~L~e~  352 (428)
                      ++++|+.+|..+|.+.
T Consensus        85 ~~~~A~~~I~~ll~~~  100 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQG  100 (131)
T ss_dssp             HHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhcc
Confidence            9999999999999763

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

Probab=98.50  E-value=6.5e-08  Score=85.86  Aligned_cols=66  Identities=24%  Similarity=0.329  Sum_probs=52.1

Q ss_pred             EEEEeccccccceeccCchHHHHHHHHhCC-cEEEccCCC---CCCc--eEEEeeCCCCCCcCccHHHHHHHHHHHHh
Q 014254          188 FRILCSNDKVGAVIGKGGTIIRALQSEAGA-FISVGATMP---ECDE--RLITVTASEGPESRYSPAQKAVVLVFSRL  259 (428)
Q Consensus       188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA-~I~Is~~~p---~s~E--RvVtItGs~e~~~~~s~a~~Ai~~I~~~i  259 (428)
                      .++.||.+.+|++|||+|++||.|++.||| +|+|.....   ..++  +.|+|+|+.++      +++|..++...+
T Consensus        69 ~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~------v~~Ak~li~~~l  140 (144)
T 2qnd_A           69 DVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDS------IANATVLLDYHL  140 (144)
T ss_dssp             EEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHH------HHHHHHHHHHHH
T ss_pred             EEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHH------HHHHHHHHHHHH
Confidence            789999999999999999999999999997 899975321   1223  35899998775      666766665554

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

Probab=98.45  E-value=6.4e-07  Score=77.40  Aligned_cols=76  Identities=14%  Similarity=0.064  Sum_probs=58.3

Q ss_pred             ceeEEEEEeccc-------cccceeCCCCchHHHHHHHhCCeEEEccCCc------cccCCCCCcEEEEEeC-HHHHHHH
Q 014254          276 LLVNARLVVASN-------QVGCLLGKGGTIISEMRKVTGTSIRIISDQL------LKCISENDRVVQISGE-FSKVKDA  341 (428)
Q Consensus       276 ~~vt~~L~VP~s-------~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~------P~~~~s~eRvVtItGt-~~aV~~A  341 (428)
                      ..++.+|.||-+       ++|.|||++|++||+|+++|||+|.|.+...      .......+-.|.|++. .+++++|
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            457778888865       7899999999999999999999999972210      0000113346888875 9999999


Q ss_pred             HHHHHHHhhh
Q 014254          342 VYNVTGRLRD  351 (428)
Q Consensus       342 ~~lI~~~L~e  351 (428)
                      +.+|.++|.+
T Consensus        90 ~~~Ie~Ll~~   99 (119)
T 2yqr_A           90 KKLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHhhc
Confidence            9999999874

>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=98.44  E-value=3.7e-08  Score=81.34  Aligned_cols=52  Identities=17%  Similarity=0.270  Sum_probs=46.1

Q ss_pred             cCCceEEEEEeccccccceeccCchHHHHHHHHhCCc-EEEccCCCCCCceEEEeeCC
Q 014254          182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAF-ISVGATMPECDERLITVTAS  238 (428)
Q Consensus       182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~-I~Is~~~p~s~ERvVtItGs  238 (428)
                      ....+...|.||.+++|.|||+||++||+|+++||++ |.|.+     ++..|+|.|.
T Consensus        11 ~~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e-----ddG~V~I~g~   63 (91)
T 2cpq_A           11 LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-----DTGTFRIYGE   63 (91)
T ss_dssp             SSCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-----TTTEEEEEES
T ss_pred             ccCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc-----CCCEEEEEEC
Confidence            3445888899999999999999999999999999998 99973     4588999995

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.18  E-value=1.1e-06  Score=77.82  Aligned_cols=74  Identities=27%  Similarity=0.277  Sum_probs=55.5

Q ss_pred             eEEEEEecccc------ccceeCCCCchHHHHHHHhCCeEEEccCCc-------------cccCCC-CCcEEEEEeC-HH
Q 014254          278 VNARLVVASNQ------VGCLLGKGGTIISEMRKVTGTSIRIISDQL-------------LKCISE-NDRVVQISGE-FS  336 (428)
Q Consensus       278 vt~~L~VP~s~------VG~IIGKgG~~IkeIre~TGA~IqI~~d~~-------------P~~~~s-~eRvVtItGt-~~  336 (428)
                      ++.+|.||-+.      +|.|||++|.++|+|+++|||+|.|-+...             |+.... .+--|.|++. ++
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            46788888655      899999999999999999999999984321             110011 2236889995 43


Q ss_pred             -----HHHHHHHHHHHHhhh
Q 014254          337 -----KVKDAVYNVTGRLRD  351 (428)
Q Consensus       337 -----aV~~A~~lI~~~L~e  351 (428)
                           .+++|+.+|..+|..
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p  101 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVP  101 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSC
T ss_pred             hhHHHHHHHHHHHHHHHCCC
Confidence                 789999999998863

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

Probab=98.15  E-value=1.7e-06  Score=82.08  Aligned_cols=65  Identities=26%  Similarity=0.195  Sum_probs=57.6

Q ss_pred             eeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-----HHHHHHHHHHHHHHhh
Q 014254          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-----FSKVKDAVYNVTGRLR  350 (428)
Q Consensus       277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-----~~aV~~A~~lI~~~L~  350 (428)
                      .....+.||.+.+|.|||+||++|+.|++.|||+|+|..         .+..|+|.|+     ++++++|..+|..+++
T Consensus        33 P~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~---------~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~r  102 (219)
T 2e3u_A           33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS---------ETGEVWITSTKETEDPLAVWKARDIVLAIGR  102 (219)
T ss_dssp             CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT---------TTCEEEEEECTTCCSHHHHHHHHHHHHHHHT
T ss_pred             CEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc---------CCCEEEEecCCCCCCHHHHHHHHHHHHHHhc
Confidence            346689999999999999999999999999999999962         3567899886     6999999999999885

>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=98.06  E-value=4.7e-06  Score=73.03  Aligned_cols=40  Identities=28%  Similarity=0.469  Sum_probs=36.7

Q ss_pred             CceEEEEEeccc------cccceeccCchHHHHHHHHhCCcEEEcc
Q 014254          184 QEVSFRILCSND------KVGAVIGKGGTIIRALQSEAGAFISVGA  223 (428)
Q Consensus       184 ~evt~rIlVP~~------~vG~IIGKgG~tIK~IqeeTGA~I~Is~  223 (428)
                      ..++.+|.||.+      .+|.|||++|.+||+|+++|||+|.|..
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~Irg   50 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRG   50 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEE
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecC
Confidence            357889999987      8999999999999999999999999975

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

Probab=98.01  E-value=6.9e-06  Score=76.35  Aligned_cols=65  Identities=18%  Similarity=0.213  Sum_probs=58.8

Q ss_pred             EEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEE-----eCHHHHHHHHHHHHHHhhhcC
Q 014254          280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS-----GEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       280 ~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtIt-----Gt~~aV~~A~~lI~~~L~e~~  353 (428)
                      .++.||.+.+|.|||++|++++.|++.+|++|++.         ..++.|+|.     |++.++.+|..+|....+...
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            58999999999999999999999999999999995         346788999     999999999999988777544

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=97.95  E-value=6e-06  Score=73.18  Aligned_cols=38  Identities=24%  Similarity=0.444  Sum_probs=34.4

Q ss_pred             eEEEEEecccc------ccceeccCchHHHHHHHHhCCcEEEcc
Q 014254          186 VSFRILCSNDK------VGAVIGKGGTIIRALQSEAGAFISVGA  223 (428)
Q Consensus       186 vt~rIlVP~~~------vG~IIGKgG~tIK~IqeeTGA~I~Is~  223 (428)
                      ++-||.||.+.      +|.|||++|.++|+|+++|||+|.|..
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrG   45 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRG   45 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEES
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEec
Confidence            56788999765      999999999999999999999999975

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

Probab=97.94  E-value=1.2e-05  Score=69.35  Aligned_cols=39  Identities=21%  Similarity=0.260  Sum_probs=34.6

Q ss_pred             ceEEEEEeccc-------cccceeccCchHHHHHHHHhCCcEEEcc
Q 014254          185 EVSFRILCSND-------KVGAVIGKGGTIIRALQSEAGAFISVGA  223 (428)
Q Consensus       185 evt~rIlVP~~-------~vG~IIGKgG~tIK~IqeeTGA~I~Is~  223 (428)
                      .++-||.||.+       .+|.|||++|.+||+|+++|||+|.|..
T Consensus        11 ~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G   56 (119)
T 2yqr_A           11 YVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRG   56 (119)
T ss_dssp             CEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEES
T ss_pred             EEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEec
Confidence            46778888864       7999999999999999999999999963

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.93  E-value=1.1e-05  Score=87.17  Aligned_cols=64  Identities=17%  Similarity=0.202  Sum_probs=54.6

Q ss_pred             ceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHh
Q 014254          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRL  349 (428)
Q Consensus       276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L  349 (428)
                      ......+.||.+.+|.|||+||++|++|+++|||+|.|.          ++-.|.|.|+ .+++++|+.+|..++
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            455778999999999999999999999999999999995          2467999997 678899999887654

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.75  E-value=1.8e-05  Score=70.38  Aligned_cols=104  Identities=22%  Similarity=0.315  Sum_probs=73.0

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccc
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE  265 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~  265 (428)
                      -.+.|+|+...+|..||++|++|+.|+++.|-+|.|-.             =+.++          ...+.+.+......
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~-------------~s~d~----------~~fI~naLsPA~V~   92 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVE-------------YSSDL----------ERIVKNLFPGVKIE   92 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEE-------------CCSSH----------HHHHHHHSTTSCEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEE-------------cCCCH----------HHHHHHhcCCceEE
Confidence            46778999999999999999999999999999998843             12221          11111111110000


Q ss_pred             cccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          266 KGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       266 ~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                       ...... .+......+.||.++.+..|||+|.+++-..+.||.+|.|.
T Consensus        93 -~V~i~~-~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           93 -SINVRE-RNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             -EEEEEE-ETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             -EEEEee-cCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence             000000 02345778999999999999999999999999999988874

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

Probab=97.52  E-value=0.00019  Score=63.14  Aligned_cols=67  Identities=21%  Similarity=0.152  Sum_probs=57.7

Q ss_pred             EEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254          280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       280 ~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e  351 (428)
                      .-+.|.+..++.|+|++|+.|++|+..|+|.|++..- .    .++.--|+|.|++..-+.|..+|.....-
T Consensus        58 lVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~-~----s~g~tEVtIfG~~~~Q~rak~MI~sLA~~  124 (140)
T 3v69_A           58 KRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVW-G----PERRAEIWIFGPPPFRRDVDRMLTDLAHY  124 (140)
T ss_dssp             EEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECC-C----TTSCEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEehhhhhcccCCCcCccchHHhhcceeEEEecc-C----CCCcEEEEEECCHHHHHHHHHHHHHHHHH
Confidence            5678999999999999999999999999999999722 1    13566799999999999999999887653

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.27  E-value=0.00012  Score=80.19  Aligned_cols=72  Identities=21%  Similarity=0.353  Sum_probs=12.2

Q ss_pred             eeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhhcCCC
Q 014254          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRDNHFS  355 (428)
Q Consensus       277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e~~~~  355 (428)
                      .....+.||.+.+|.|||+||++|++|+++||++|.|.          .+-.|.|.+. .+++++|+.+|..++.+....
T Consensus       569 p~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~----------ddG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG  638 (726)
T 4aid_A          569 PKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN----------DDGVVKVSASDGAKIKAAIDWIKSITDEAEVG  638 (726)
T ss_dssp             CC-----------------------------------------------------CCSCHHHHHHHHHC-----------
T ss_pred             CeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE----------CCceEEEEeCCHHHHHHHHHHHHHHhhhhcCC
Confidence            44567899999999999999999999999999999995          2455788886 788899999999988765544


Q ss_pred             Ccc
Q 014254          356 GTL  358 (428)
Q Consensus       356 ~~~  358 (428)
                      ..|
T Consensus       639 ~v~  641 (726)
T 4aid_A          639 KIY  641 (726)
T ss_dssp             ---
T ss_pred             cEE
Confidence            444

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.09  E-value=0.00021  Score=77.20  Aligned_cols=49  Identities=29%  Similarity=0.328  Sum_probs=43.4

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCC
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE  239 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~  239 (428)
                      .....|.||.+++|.|||+||++||.|+++|||+|.|.+      +-.|.|.|..
T Consensus       566 p~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d------~G~V~I~~~~  614 (630)
T 3u1k_A          566 PVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD------EETFSVFAPT  614 (630)
T ss_dssp             CEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS------SSEEEEEESS
T ss_pred             CeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC------CcEEEEEeCC
Confidence            456779999999999999999999999999999999963      4679999853

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

Probab=96.98  E-value=0.00099  Score=58.56  Aligned_cols=53  Identities=21%  Similarity=0.184  Sum_probs=45.4

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG  240 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e  240 (428)
                      .+.|.+.+..++.|||++|+.|+.|+..|++.|+|..-.+ +.+--|+|.|+..
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s-~g~tEVtIfG~~~  109 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP-ERRAEIWIFGPPP  109 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT-TSCEEEEEESCHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC-CCcEEEEEECCHH
Confidence            3446899999999999999999999999999999986544 3567799999865

>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=96.23  E-value=0.005  Score=62.32  Aligned_cols=94  Identities=27%  Similarity=0.303  Sum_probs=64.8

Q ss_pred             ccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCC
Q 014254          195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN  273 (428)
Q Consensus       195 ~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~  273 (428)
                      +-+|..||++|++|+.|.++. |-+|.|-.             =+.++          ...+.+.+....... ... . 
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~-------------~s~dp----------~~fi~nalsPA~V~~-V~~-~-  302 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIID-------------YDDDP----------ARFVANALSPAKVVS-VSV-I-  302 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEE-------------CCSSH----------HHHHHHHTTTSCCSE-EEE-E-
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhcCCcceeE-EEE-E-
Confidence            569999999999999999998 77777642             22222          111222221111000 000 0 


Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      ......+.+.||.++.+..|||+|.+++-..+.||.+|.|.
T Consensus       303 ~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~  343 (366)
T 1k0r_A          303 DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIR  343 (366)
T ss_dssp             ETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEE
T ss_pred             cCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeee
Confidence            01234688999999999999999999999999999999997

>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=96.23  E-value=0.0049  Score=59.37  Aligned_cols=94  Identities=24%  Similarity=0.259  Sum_probs=62.9

Q ss_pred             ccccceeccCchHHHHH-HHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCC
Q 014254          195 DKVGAVIGKGGTIIRAL-QSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN  273 (428)
Q Consensus       195 ~~vG~IIGKgG~tIK~I-qeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~  273 (428)
                      +-+|..||++|++|+.| ++-.|-+|.|-.             =+.++          ...+...+.......-. . . 
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~-------------~s~dp----------~~fi~nalsPA~V~~V~-i-~-  179 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIID-------------YDDDP----------ARFVANALSPAKVVSVS-V-I-  179 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEE-------------CCSSH----------HHHHHHHTTTSCCSEEE-E-E-
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEE-------------ecCCH----------HHHHHhccCCcceEEEE-E-E-
Confidence            46999999999999999 565777777643             22222          11122222111100000 0 0 


Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      ......+.+.||.++.+.-|||+|.+++--.+.||.+|.|.
T Consensus       180 ~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~  220 (251)
T 2asb_A          180 DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIR  220 (251)
T ss_dssp             ETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             cCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecce
Confidence            01124688999999999999999999999999999999997

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=95.82  E-value=0.0015  Score=71.62  Aligned_cols=49  Identities=31%  Similarity=0.519  Sum_probs=3.4

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCC
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE  239 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~  239 (428)
                      .....|.||.+++|.|||+||.+||.|+++||++|.|.+      +-.|.|.+..
T Consensus       569 p~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d------dG~v~I~~~~  617 (726)
T 4aid_A          569 PKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND------DGVVKVSASD  617 (726)
T ss_dssp             CC-------------------------------------------------CCSC
T ss_pred             CeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC------CceEEEEeCC
Confidence            345678999999999999999999999999999999963      4567888853

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=95.03  E-value=0.0068  Score=66.44  Aligned_cols=67  Identities=24%  Similarity=0.378  Sum_probs=0.0

Q ss_pred             eeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhhcC
Q 014254          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e~~  353 (428)
                      .....+.||.+.+|.+||+||++|+.|.+.||+.|.|.          .+..|.|.+. ...+++|..+|...+.+..
T Consensus       559 p~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~----------~dg~v~I~~~~~~~~~~a~~~i~~i~~~~~  626 (723)
T 3cdi_A          559 PRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIE----------DDGTVKIAATDGEKAKHAIRRIEEITAEIE  626 (723)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             ceEEEEEECHHHhcccccccceeeeeeehhhCceEEec----------CCccEEEecCCHHHHHHHHHHHHHHhhhhh
Confidence            44567889999999999999999999999999999884          2455777775 5677888888777665443

>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=94.65  E-value=0.046  Score=54.88  Aligned_cols=94  Identities=32%  Similarity=0.382  Sum_probs=63.3

Q ss_pred             ccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCC
Q 014254          195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN  273 (428)
Q Consensus       195 ~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~  273 (428)
                      +-+|+.||.+|.+|+.+.++. |-+|.|-             .=+.++          ...+...+.......- .  ..
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii-------------~~s~d~----------~~fi~nal~Pa~v~~v-~--~~  298 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVL-------------KWSDDP----------KQLIANALAPATVIEV-E--IL  298 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEE-------------ECCSSH----------HHHHHHHTCSSCCSEE-E--EE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEE-------------ecCCCH----------HHHHHHhcCccEEEEE-E--EE
Confidence            469999999999999999997 5555553             223332          1112222211100000 0  00


Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      ......+.+.||.++.+.-|||+|.+++--.+.||.+|.|.
T Consensus       299 d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~  339 (344)
T 1hh2_P          299 DKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIK  339 (344)
T ss_dssp             ETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             cCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEecee
Confidence            01234688999999999999999999999999999999996

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=94.17  E-value=0.0043  Score=68.32  Aligned_cols=62  Identities=18%  Similarity=0.299  Sum_probs=21.1

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHh
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRL  349 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L  349 (428)
                      ....+.||.+.+|.+||+||++|++|++.||+.|.|.          .+..|.|++. ..+.++|...|..+.
T Consensus       598 ~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~----------~dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          598 RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE----------DDGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             BCCCC------------------CTTCCCCCSCC------------------CCCBSSHHHHCC---------
T ss_pred             eeEEEEEChHHeehcccccceeeehhhHhhCCEEEec----------CCceEEEecCCHHHHHHHHHHHHHhc
Confidence            3446789999999999999999999999999999984          2456777776 566667776776654

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=90.07  E-value=0.056  Score=59.22  Aligned_cols=48  Identities=35%  Similarity=0.597  Sum_probs=0.0

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCC
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE  239 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~  239 (428)
                      ....+.||.++++.|||+||.+|+.|.++||+.|.|.+      +..|.|.+..
T Consensus       560 ~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~------dg~v~I~~~~  607 (723)
T 3cdi_A          560 RIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED------DGTVKIAATD  607 (723)
T ss_dssp             ------------------------------------------------------
T ss_pred             eEEEEEECHHHhcccccccceeeeeeehhhCceEEecC------CccEEEecCC
Confidence            45667899999999999999999999999999998863      4567787753

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=89.26  E-value=0.22  Score=44.07  Aligned_cols=37  Identities=24%  Similarity=0.571  Sum_probs=34.7

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      -.+.++|+...+|+.||++|++|+.|+++.|-+|.|.
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV   72 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVV   72 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEE
Confidence            3678999999999999999999999999999999998

>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=84.87  E-value=0.068  Score=58.85  Aligned_cols=46  Identities=28%  Similarity=0.452  Sum_probs=16.6

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS  238 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs  238 (428)
                      ...|.||.+++|.+||++|.+||.|+++||+.|.|.+      +..|.|++.
T Consensus       599 ~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~------dG~v~Is~~  644 (757)
T 1e3p_A          599 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAA  644 (757)
T ss_dssp             CCCC------------------CTTCCCCCSCC--------------CCCBS
T ss_pred             eEEEEEChHHeehcccccceeeehhhHhhCCEEEecC------CceEEEecC
Confidence            3457899999999999999999999999999999863      456778775

>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=81.23  E-value=0.92  Score=43.56  Aligned_cols=38  Identities=21%  Similarity=0.262  Sum_probs=35.2

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA  223 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~  223 (428)
                      ....+.||.+..++.|||+|.+|+.-.+-||.+|.|..
T Consensus       184 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~  221 (251)
T 2asb_A          184 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG  221 (251)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             cEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceE
Confidence            46789999999999999999999999999999999853

---

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	428
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	4e-13
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-11
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-11
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-08
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	5e-11
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	9e-10
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	6e-11
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	7e-08
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	6e-11
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-08
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	1e-10
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	4e-10
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	3e-10
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	2e-06
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-09
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	6e-09
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	6e-09
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	3e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	3e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	2e-04
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-07
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-06
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	3e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	9e-05
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-06
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	5e-05
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	8e-04
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	3e-05
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	4e-04
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	6e-05
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	0.002
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
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	4e-04
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.003

>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 = 61.7 bits (150), Expect = 4e-13
 Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           +  RL++   +VG ++GK G  + +MR+ +G  I I            +R++ ++G  + 
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN------CPERIITLAGPTNA 57

Query: 338 VKDAVYNVTGRLRD 351
           +  A   +  +L +
Sbjct: 58  IFKAFAMIIDKLEE 71

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.7 bits (137), Expect = 3e-11
 Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 8/76 (10%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ R+L    +VG++IGK G  ++ ++ E+GA I++  +   C ER+IT+       +  
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLAGP--TNA-- 57

Query: 246 SPAQKAVVLVFSRLIE 261
               KA  ++  +L E
Sbjct: 58  --IFKAFAMIIDKLEE 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 = 57.5 bits (139), Expect = 1e-11
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + V  N VG +LGKGG  + E +++TG  I+I            +R V I+G  +  + 
Sbjct: 6   EMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKG-EFLPGTRNRRVTITGSPAATQA 64

Query: 341 AVYNVTGRL 349
           A Y ++ R+
Sbjct: 65  AQYLISQRV 73

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (118), Expect = 1e-08
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 9/75 (12%)

Query: 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV---GATMPECDERLITVTASEGPESR 244
             +    + VGA++GKGG  +   Q   GA I +   G  +P    R +T+T S  P + 
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS--PAA- 61

Query: 245 YSPAQKAVVLVFSRL 259
               Q A  L+  R+
Sbjct: 62  ---TQAAQYLISQRV 73

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.4 bits (136), Expect = 5e-11
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 180 RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
           + Q+  ++      +  VG +IG+GG  I  +Q E+G  I +        ER   +T + 
Sbjct: 2   QQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT- 60

Query: 240 GPESRYSPAQKAVVLVFSRLIEG 262
            PES     Q A  L+   + +G
Sbjct: 61  -PES----VQSAKRLLDQIVEKG 78

>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 = 52.9 bits (127), Expect = 9e-10
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           +     V    VG ++G+GG  IS +++ +G  I+I  D         +R   ++G    
Sbjct: 8   MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD----SGGLPERSCMLTGTPES 63

Query: 338 VKDAVYNVTGRLRDN 352
           V+ A   +   +   
Sbjct: 64  VQSAKRLLDQIVEKG 78

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.1 bits (135), Expect = 6e-11
 Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
               +++ +++ G ++GKGG  I ++++  G  + +I D      +  D+ ++I+G+  K
Sbjct: 8   AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG--PQNTGADKPLRITGDPYK 65

Query: 338 VKDAVYNVTGRLRD 351
           V+ A   V   +RD
Sbjct: 66  VQQAKEMVLELIRD 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 = 47.6 bits (113), Expect = 7e-08
 Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 4/78 (5%)

Query: 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPES 243
                 I+    K G VIGKGG  I+ LQ  AG  + +    P+       +  +  P  
Sbjct: 6   GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYK 65

Query: 244 RYSPAQKAVVLVFSRLIE 261
                Q+A  +V   + +
Sbjct: 66  ----VQQAKEMVLELIRD 79

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.7 bits (134), Expect = 6e-11
 Identities = 13/63 (20%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
             +V + + G ++GKGG  I  + + +G  I +  +        N ++  I G   ++  
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP-PPNADPNMKLFTIRGTPQQIDY 62

Query: 341 AVY 343
           A  
Sbjct: 63  ARQ 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 = 48.7 bits (116), Expect = 2e-08
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 9/75 (12%)

Query: 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV---GATMPECDERLITVTASEGPESR 244
           F  +    K G +IGKGG  I+++  ++GA I +        + + +L T+  +  P+  
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGT--PQQ- 59

Query: 245 YSPAQKAVVLVFSRL 259
                 A  L+  ++
Sbjct: 60  ---IDYARQLIEEKI 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 = 55.2 bits (133), Expect = 1e-10
 Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESR 244
           + +  +   N+ +G +IG+ G  I  ++  +GA I +   +     R +T+T S    S 
Sbjct: 1   QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS--AAS- 57

Query: 245 YSPAQKAVVLVFSRL 259
                 A  L+ +RL
Sbjct: 58  ---ISLAQYLINARL 69

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.3 bits (128), Expect = 4e-10
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
               L + +N +GC++G+ G  I+E+R+++G  I+I +         + R V I+G  + 
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP----VEGSSGRQVTITGSAAS 57

Query: 338 VKDAVYNVTGRL 349
           +  A Y +  RL
Sbjct: 58  ISLAQYLINARL 69

>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 = 54.6 bits (131), Expect = 3e-10
 Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           V  +L V    VG ++G+GG  I  + K +G  I    +   +      R+++ISG   +
Sbjct: 15  VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES--EGTLLLSRLIKISGTQKE 72

Query: 338 VKDAVYNVTGRLRDN 352
           V  A + +  ++ ++
Sbjct: 73  VAAAKHLILEKVSED 87

>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 = 44.2 bits (104), Expect = 2e-06
 Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV--GATMPECDERLITVTAS 238
           T+   V  ++      VG +IG+GG  IR++   +GA I+    +       RLI ++ +
Sbjct: 10  TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGT 69

Query: 239 EGPESRYSPAQKAVVLVFSRLIE 261
              +        A  L+  ++ E
Sbjct: 70  --QKE----VAAAKHLILEKVSE 86

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.8 bits (124), Expect = 2e-09
 Identities = 18/76 (23%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE 334
           G ++  ++ +  +  G ++GKGG  I ++R  +G SI+I            DR++ I+G 
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP----LEGSEDRIITITGT 56

Query: 335 FSKVKDAVYNVTGRLR 350
             ++++A Y +   ++
Sbjct: 57  QDQIQNAQYLLQNSVK 72

>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 = 50.3 bits (120), Expect = 6e-09
 Identities = 19/76 (25%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           ++ ++    D  G++IGKGG  I+ ++ E+GA I +   +   ++R+IT+T +   +   
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT--QDQ-- 59

Query: 246 SPAQKAVVLVFSRLIE 261
              Q A  L+ + + +
Sbjct: 60  --IQNAQYLLQNSVKQ 73

>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 = 50.3 bits (120), Expect = 6e-09
 Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 4/71 (5%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + +    VG ++G+ G +I +++   G  I+   D      +  +R+ QI+G   + + 
Sbjct: 6   DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD----DGTTPERIAQITGPPDRAQH 61

Query: 341 AVYNVTGRLRD 351
           A   +T  LR 
Sbjct: 62  AAEIITDLLRS 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 = 48.3 bits (115), Expect = 3e-08
 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 6/73 (8%)

Query: 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYS 246
              +      VG VIG+ G +I+ +Q++AG  I          ER+  +T    P+    
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP--PDR--- 58

Query: 247 PAQKAVVLVFSRL 259
            AQ A  ++   L
Sbjct: 59  -AQHAAEIITDLL 70

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 47.7 bits (114), Expect = 3e-08
 Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 6/58 (10%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPES 243
               +    DK+G VIG    +I  +Q + GA I++       D+  I + A++GP +
Sbjct: 3   RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAADGPAA 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 = 36.9 bits (86), Expect = 2e-04
 Identities = 10/53 (18%), Positives = 25/53 (47%), Gaps = 10/53 (18%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG 333
            + +  +++G ++G    +I+++++ TG  I I          E+D  + I  
Sbjct: 6   TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITI----------EDDGTIYIGA 48

>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 = 46.2 bits (110), Expect = 2e-07
 Identities = 11/66 (16%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
            +A + +       ++GK G  + ++   T T I+I          +    ++I+G    
Sbjct: 10  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP------DDPSNQIKITGTKEG 63

Query: 338 VKDAVY 343
           ++ A +
Sbjct: 64  IEKARH 69

>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 = 43.2 bits (102), Expect = 2e-06
 Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
           Q + S  +    +    VIGK G  ++ L+ +    I +    P+     I +T ++
Sbjct: 7   QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKITGTK 61

>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 = 46.0 bits (109), Expect = 3e-07
 Identities = 11/74 (14%), Positives = 30/74 (40%), Gaps = 6/74 (8%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           V   + V  +    ++G+ G+ I +M      +I + +            ++ I+G  + 
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP------ELQSDIIAITGLAAN 63

Query: 338 VKDAVYNVTGRLRD 351
           +  A   +  R+++
Sbjct: 64  LDRAKAGLLERVKE 77

>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 = 39.0 bits (91), Expect = 9e-05
 Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
           V+  +    D    VIG+ G+ IR +  E    I V    P  + +   +  +    +  
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV----PAPELQSDIIAITGLAAN-- 63

Query: 246 SPAQKAVVLVFSRLIEGTSEK 266
               +A   +  R+ E  +E+
Sbjct: 64  --LDRAKAGLLERVKELQAEQ 82

>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 = 43.7 bits (103), Expect = 1e-06
 Identities = 9/71 (12%), Positives = 27/71 (38%), Gaps = 3/71 (4%)

Query: 281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKD 340
            + V       ++G+ G +I+++R     +I+          ++    + I+G     + 
Sbjct: 13  SVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDK---DDGNQPQDQITITGYEKNTEA 69

Query: 341 AVYNVTGRLRD 351
           A   +   + +
Sbjct: 70  ARDAILRIVGE 80

>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 = 39.4 bits (92), Expect = 5e-05
 Identities = 10/59 (16%), Positives = 19/59 (32%), Gaps = 1/59 (1%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG-ATMPECDERLITVTASE 239
             +     +         +IG+ G +I  ++ E    I           +  IT+T  E
Sbjct: 6   ALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYE 64

>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 = 14/66 (21%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS 336
           +    + +       L+GK G  I+ ++     S+RI  D       E   +++I G+  
Sbjct: 4   MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS------EKSNLIRIEGDPQ 57

Query: 337 KVKDAV 342
            V+ A 
Sbjct: 58  GVQQAK 63

>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 = 35.5 bits (82), Expect = 8e-04
 Identities = 8/53 (15%), Positives = 16/53 (30%), Gaps = 2/53 (3%)

Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238
               I   +     +IGK G  I  ++ +    + +          LI +   
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPP--DSEKSNLIRIEGD 55

>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 = 39.8 bits (93), Expect = 3e-05
 Identities = 9/32 (28%), Positives = 16/32 (50%)

Query: 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISV 221
           +    +++GAVIG  G +   +    G  I+V
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVITV 38

>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 = 37.1 bits (86), Expect = 4e-04
 Identities = 9/43 (20%), Positives = 22/43 (51%)

Query: 284 VASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISEND 326
           V   ++G ++G  G + +E+ + TGT I + ++  +  +    
Sbjct: 9   VKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEA 51

>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 = 39.0 bits (91), Expect = 6e-05
 Identities = 10/65 (15%), Positives = 24/65 (36%), Gaps = 5/65 (7%)

Query: 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337
           V+  + +       ++G  G  I ++       IR          + +   V ++G    
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-----APDPNCVTVTGLPEN 64

Query: 338 VKDAV 342
           V++A+
Sbjct: 65  VEEAI 69

>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 = 34.4 bits (79), Expect = 0.002
 Identities = 11/59 (18%), Positives = 18/59 (30%)

Query: 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240
            +Q VS  +   +     +IG  G  IR +  E    I    +       +      E 
Sbjct: 6   LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPEN 64

>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 = 16/50 (32%), Positives = 23/50 (46%), Gaps = 6/50 (12%)

Query: 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
           +  +  +V  VIGK G++I+ L+SE    I VG         LI V    
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVVG------QNGLIWVNGDR 48

>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 = 12/74 (16%), Positives = 30/74 (40%), Gaps = 10/74 (13%)

Query: 284 VASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVY 343
           +   +V  ++GK G++I  ++      I +            + ++ ++G+  KV  A  
Sbjct: 7   INPARVPRVIGKKGSMIKLLKSELDVQIVV----------GQNGLIWVNGDRRKVSIAEE 56

Query: 344 NVTGRLRDNHFSGT 357
            +    ++ H  G 
Sbjct: 57  AIYLIEQEAHTEGL 70

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.0 bits (86), Expect = 4e-04
 Identities = 9/33 (27%), Positives = 17/33 (51%)

Query: 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG 222
           +  S  KV  VIG+  ++++ L+ +    I V 
Sbjct: 5   VEISPAKVPRVIGRKMSMLKTLEEKTECKIFVA 37

>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 = 33.9 bits (78), Expect = 0.003
 Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 6/49 (12%)

Query: 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238
           I     KV  VIGK  ++   L S++G  I V       +   I  T  
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVA------NNGRIWATCP 47

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	428
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.59
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.59
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.57
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.56
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.55
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.54
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.53
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.48
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.48
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.46
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.46
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.43
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.42
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.39
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.39
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.38
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.37
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.37
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.37
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.32
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.31
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.31
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.29
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.22
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.19
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.18
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.16
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.13
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.1
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.04
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.02
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.97
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.97
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.79
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.77
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.76
d2cpqa1	78	Fragile X mental retardation syndrome related prot	98.71
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.7
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.68
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.57
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.55
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.46
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.44
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.4
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.32
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.15
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.64
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	97.59
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.36
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.13
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.02
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.79
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.57
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.19
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	83.81
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	81.54
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	80.09

>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=99.59  E-value=8.8e-16  Score=119.08  Aligned_cols=70  Identities=19%  Similarity=0.380  Sum_probs=62.2

Q ss_pred             EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHh
Q 014254          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL  349 (428)
Q Consensus       279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L  349 (428)
                      ..+|.||.+++|+||||+|++|++|++.|||+|+|+++..+. ..+++|.|+|+|++++|++|+.+|.++|
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 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPN-ADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTT-SCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCC-CCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            468999999999999999999999999999999998544333 3467899999999999999999999875

>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=99.59  E-value=1.6e-15  Score=118.37  Aligned_cols=73  Identities=25%  Similarity=0.559  Sum_probs=65.6

Q ss_pred             ceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      ..++.++.||.+++|+||||+|++|++|+++|||+|+|..+ .+   .+++++|+|+|++++|..|+.+|.++|+++
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~-~~---~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-LE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT-TS---CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccC-CC---CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            45788999999999999999999999999999999999732 22   367899999999999999999999999874

>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=99.57  E-value=2e-15  Score=117.90  Aligned_cols=71  Identities=30%  Similarity=0.476  Sum_probs=62.1

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHh
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL  349 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L  349 (428)
                      ..++|.||.+++|+||||+|++|++|++.|||+|+|.++..+ ..++++|.|+|+|++++|+.|+.+|.++|
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            357899999999999999999999999999999999843221 12367999999999999999999999987

>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=99.56  E-value=1.6e-15  Score=117.62  Aligned_cols=70  Identities=23%  Similarity=0.490  Sum_probs=63.9

Q ss_pred             ceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e  351 (428)
                      .+++.+|+||.+++|+||||+|++|++|++.|||+|+|+++.      ..+|+|+|+|++++|.+|+.+|.++|+|
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~------~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN------CPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC------CSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCC------CCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            357899999999999999999999999999999999998432      4589999999999999999999999975

>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=99.55  E-value=3.1e-15  Score=118.79  Aligned_cols=75  Identities=24%  Similarity=0.395  Sum_probs=66.6

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e  351 (428)
                      ...++.+|.||.+++|+||||+|++|++|++.|||+|+|+++.  .+..+.+|.|+|+|++++|.+|..+|.++|+|
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 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG--PQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSC--CCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCC--CCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999999999999998432  12236789999999999999999999999976

>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=99.54  E-value=4e-15  Score=115.13  Aligned_cols=68  Identities=29%  Similarity=0.608  Sum_probs=61.6

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHh
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL  349 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L  349 (428)
                      .+.+|.||.+++|+||||+|++|++|++.|||+|+|.+. .+   ++++|.|+|+|++++|+.|+.+|.++|
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 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-VE---GSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC-CT---TCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCC-CC---CCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            578999999999999999999999999999999999732 22   367899999999999999999999987

>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=99.53  E-value=4.5e-15  Score=115.71  Aligned_cols=71  Identities=23%  Similarity=0.383  Sum_probs=63.7

Q ss_pred             eeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e  351 (428)
                      ..+++|.||.+++|+||||+|++|++|+++|||+|+|..+. +   ...+|.|+|+|++++|++|+.+|.++|++
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            45789999999999999999999999999999999998331 2   25789999999999999999999999875

>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=99.48  E-value=3.3e-14  Score=117.83  Aligned_cols=78  Identities=23%  Similarity=0.330  Sum_probs=67.9

Q ss_pred             CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcC
Q 014254          274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      ....++.+|.||.+++|+||||+|.+|++|++.|||+|+|+++..+  ....+|+|+|+|++++|.+|+.+|.++|.+..
T Consensus        11 ~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T d1we8a_          11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG--TLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC--SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC--CCCCccEEEEEeCHHHHHHHHHHHHHHHhCcH
Confidence            4567889999999999999999999999999999999999843222  23568999999999999999999999998653

>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=99.48  E-value=2.6e-14  Score=112.68  Aligned_cols=74  Identities=22%  Similarity=0.343  Sum_probs=66.6

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      ...++.+|.||.+++|+|||++|.+|++|++.|||+|+|++. .+   +++++.|+|+|++++|+.|..+|.++|.++
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~-~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD-SG---GLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSC-CT---TCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCC-CC---CCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            467899999999999999999999999999999999999842 12   367899999999999999999999999864

>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=2.2e-14  Score=110.93  Aligned_cols=69  Identities=25%  Similarity=0.431  Sum_probs=61.9

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHh
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRL  259 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i  259 (428)
                      +++.+|+||++.+|.||||+|++|++|+++|||+|+|++..+++++|+|+|+|++++      +.+|..++.+++
T Consensus         1 q~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~------v~~A~~~I~~~i   69 (70)
T d1wvna1           1 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS------ISLAQYLINARL   69 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHH------HHHHHHHHHHHT
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHH------HHHHHHHHHHHc
Confidence            368899999999999999999999999999999999998888899999999998765      777877777654

>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=99.46  E-value=1.8e-14  Score=111.62  Aligned_cols=69  Identities=29%  Similarity=0.585  Sum_probs=60.1

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhh
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLI  260 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~  260 (428)
                      ..++++|+||++.+|.||||+|++|++|+++|||+|+|++  ++.++|+|+|+|++++      +.+|..++.+.+.
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~--~~~~er~v~I~G~~~~------v~~A~~~I~~~l~   70 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTNA------IFKAFAMIIDKLE   70 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECS--SCCSEEEEEEEECHHH------HHHHHHHHHHHHH
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcC--CCCCcceEEEEECHHH------HHHHHHHHHHHhc
Confidence            3589999999999999999999999999999999999987  4677999999998765      6677777776553

>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=99.43  E-value=8.5e-14  Score=108.41  Aligned_cols=71  Identities=27%  Similarity=0.508  Sum_probs=62.3

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      .++.+|.||++.+|.||||+|++|++|+++|||+|+|.+..+++++|+|+|+|+.++      +.+|..++.+.+.+
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~------v~~A~~~I~~~i~e   73 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ------IQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHH------HHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHH------HHHHHHHHHHHHHh
Confidence            478899999999999999999999999999999999998878889999999998764      66777777666543

>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=99.42  E-value=1.6e-13  Score=109.36  Aligned_cols=72  Identities=13%  Similarity=0.180  Sum_probs=64.4

Q ss_pred             eeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254          277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e  351 (428)
                      .+++++.||..++|+|||++|++|++|++.|||+|+|++...+   ..+++.|+|+|+.++|..|..+|.+.+.+
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~---~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG---NQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTC---SSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCC---CCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            4678999999999999999999999999999999999844333   36788999999999999999999999875

>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=99.39  E-value=1.1e-13  Score=107.77  Aligned_cols=69  Identities=26%  Similarity=0.364  Sum_probs=59.9

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHh
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRL  259 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i  259 (428)
                      ..+++|.||++.+|.||||+|++||+|+++|||+|+|.+..++..+|+|+|+|+.++      +.+|..++.+.+
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~------v~~A~~~I~~~i   70 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDR------AQHAAEIITDLL   70 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHH------HHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHH------HHHHHHHHHHHH
Confidence            368999999999999999999999999999999999998777889999999998764      666666665544

>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=99.39  E-value=1.3e-13  Score=106.58  Aligned_cols=66  Identities=24%  Similarity=0.451  Sum_probs=56.2

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC---CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHH
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSR  258 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~---~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~  258 (428)
                      +++|+||++.+|.||||+|++||+|+++|||+|+|++.   .++..+|+|+|+|++++      +.+|..++.++
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~------v~~A~~~I~e~   70 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQ------IDYARQLIEEK   70 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHH------HHHHHHHHHHH
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHH------HHHHHHHHHhh
Confidence            46889999999999999999999999999999999753   34678899999998764      66777766654

>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=99.38  E-value=3e-13  Score=107.18  Aligned_cols=72  Identities=17%  Similarity=0.246  Sum_probs=64.9

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      ...++.++.||..++|+|||++|++|++|++.|||+|+|+..      ++.++.|+|+|+.++|.+|..+|.+++.+.
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~------~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP------DDPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT------TSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC------CCCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            456789999999999999999999999999999999999833      246788999999999999999999998864

>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=99.37  E-value=2.7e-13  Score=107.46  Aligned_cols=74  Identities=14%  Similarity=0.197  Sum_probs=65.1

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcC
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~  353 (428)
                      ...++.++.||..++|+|||++|++|++|++.|||+|+|+.+..     .+++.|+|+|++++|++|..+|.+++++++
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~-----~~~~~v~I~G~~~~V~~A~~~I~~i~~e~~   80 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA-----PDPNCVTVTGLPENVEEAIDHILNLEEEYL   80 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC-----SCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC-----CCCCEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            45677899999999999999999999999999999999984321     245789999999999999999999998864

>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=99.37  E-value=4e-13  Score=106.34  Aligned_cols=73  Identities=25%  Similarity=0.342  Sum_probs=62.8

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC--CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhh
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT--MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLI  260 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~--~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~  260 (428)
                      ...++.+|+||.+.+|.||||+|++||+|+++|||+|+|.+.  .++..+|+|+|+|+++.      +.+|..+|.+.+.
T Consensus         5 ~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~------v~~A~~~I~~~i~   78 (81)
T d1x4ma1           5 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYK------VQQAKEMVLELIR   78 (81)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTT------HHHHHHHHHHHHC
T ss_pred             CccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHH------HHHHHHHHHHHHH
Confidence            457899999999999999999999999999999999999864  45667999999999886      6777777776654


Q ss_pred             h
Q 014254          261 E  261 (428)
Q Consensus       261 e  261 (428)
                      +
T Consensus        79 e   79 (81)
T d1x4ma1          79 D   79 (81)
T ss_dssp             C
T ss_pred             h
Confidence            3

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=2.1e-13  Score=106.21  Aligned_cols=68  Identities=29%  Similarity=0.466  Sum_probs=58.4

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC---CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHh
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSRL  259 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~---~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i  259 (428)
                      ..++|+||++.+|.||||+|++||+|+++|||+|+|.+.   .++..+|+|+|+|+.++      +.+|..++.+++
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 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA------TQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHH------HHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHH------HHHHHHHHHHHc
Confidence            357899999999999999999999999999999999763   45778999999998764      677777776654

>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=99.32  E-value=6e-13  Score=104.69  Aligned_cols=72  Identities=24%  Similarity=0.290  Sum_probs=63.0

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhh
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLI  260 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~  260 (428)
                      ...++.+|.||.+.+|.|||++|.+|++|+++|||+|+|++..+++.+|+|+|+|+.++      +.+|..++.+.+.
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~------v~~A~~~I~~~i~   76 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPES------VQSAKRLLDQIVE   76 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHH------HHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHH------HHHHHHHHHHHHH
Confidence            34688999999999999999999999999999999999998878889999999998765      6677777666554

>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=99.31  E-value=7.2e-13  Score=105.02  Aligned_cols=72  Identities=17%  Similarity=0.267  Sum_probs=63.6

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHH-hCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKV-TGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~-TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      .+.++.+|.||..++|+||||+|++|++|++. +|++|+++..      ++.++.|+|+|++++|++|..+|.+++++.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~------~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT------TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC------CCCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            45678899999999999999999999999977 5999999732      256789999999999999999999999864

>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=99.31  E-value=1.2e-12  Score=101.15  Aligned_cols=68  Identities=22%  Similarity=0.309  Sum_probs=60.7

Q ss_pred             ceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHh
Q 014254          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL  349 (428)
Q Consensus       276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L  349 (428)
                      ...+++|.||..++|.|||++|++|++|+++|||+|+|+++      +++++.|+|+|++++|++|..+|.++.
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            34678999999999999999999999999999999999843      246788999999999999999998864

>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=99.29  E-value=1.6e-12  Score=105.03  Aligned_cols=70  Identities=16%  Similarity=0.246  Sum_probs=63.6

Q ss_pred             ceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254          276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD  351 (428)
Q Consensus       276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e  351 (428)
                      ..++..+.||.+++|+|||++|++|++|++.|||+|.|+..      ++.++.|+|+|+.++|++|..+|.+++.+
T Consensus         8 ~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~------~~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           8 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP------ELQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT------TTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC------CCCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            46889999999999999999999999999999999999832      25677999999999999999999999875

>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=99.22  E-value=4.4e-12  Score=104.81  Aligned_cols=72  Identities=25%  Similarity=0.389  Sum_probs=60.2

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCC--CCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATM--PECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE  261 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~--p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e  261 (428)
                      ..++.+|+||...+|.||||+|.+||+|+++|||+|+|.+..  ....+|+|+|+|++++      +.+|..+|.+.+.+
T Consensus        13 ~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~------v~~A~~~I~~~i~e   86 (104)
T d1we8a_          13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE------VAAAKHLILEKVSE   86 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHH------HHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHH------HHHHHHHHHHHHhC
Confidence            458899999999999999999999999999999999997643  3456899999998775      66777777666643

>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=99.19  E-value=1.1e-11  Score=99.13  Aligned_cols=65  Identities=17%  Similarity=0.237  Sum_probs=58.8

Q ss_pred             EEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcCCC
Q 014254          281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFS  355 (428)
Q Consensus       281 ~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~~~  355 (428)
                      -+.||.+.+|.||||||++|++|++.|||+|+|.          .+..|+|+|++++++.|+.+|..++++....
T Consensus         4 vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~----------~~g~v~I~G~~e~v~~A~~~I~~i~~ea~~~   68 (84)
T d2ba0a3           4 IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVG----------QNGLIWVNGDRRKVSIAEEAIYLIEQEAHTE   68 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEEC----------TTSEEEEESCHHHHHHHHHHHHHHHHCSCCS
T ss_pred             EEEEChhhcceeeCCcHHHHHHHHHHHCCEEEEC----------CCCEEEEEeCHHHHHHHHHHHHHHHHhcccC
Confidence            5789999999999999999999999999999995          2457999999999999999999998876644

>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=99.18  E-value=7.6e-12  Score=98.71  Aligned_cols=66  Identities=24%  Similarity=0.293  Sum_probs=57.9

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe-CHHHHHHHHHHHHHH
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGR  348 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG-t~~aV~~A~~lI~~~  348 (428)
                      ...++.++.||.+++|+|||+||++|++|++.|||+|.+..        ..++.|+|.| ++++|++|+.+|..+
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~--------~~~g~v~I~g~~~eav~~A~~~Ie~~   71 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD--------EDTGTFRIYGESADAVKKARGFLEFV   71 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE--------TTTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEec--------CCCceEEEEECCHHHHHHHHHHHHHh
Confidence            35678899999999999999999999999999999999863        2457899999 699999999999543

>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=99.16  E-value=1.4e-11  Score=97.88  Aligned_cols=70  Identities=16%  Similarity=0.198  Sum_probs=57.9

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHh
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSRL  259 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i  259 (428)
                      ..++++|.||...+|.||||+|++|++|+++|||+|+|++. .++..+++|+|+|+.++      +..|..++...+
T Consensus         8 ~~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~------v~~A~~~I~~~i   78 (84)
T d2ctla1           8 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKN------TEAARDAILRIV   78 (84)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHH------HHHHHHHHHHHH
T ss_pred             ccEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHH------HHHHHHHHHHHH
Confidence            45788999999999999999999999999999999999764 45678899999998764      555555555433

>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=99.13  E-value=5.9e-11  Score=95.76  Aligned_cols=69  Identities=14%  Similarity=0.239  Sum_probs=61.8

Q ss_pred             CceeEEEEEeccccccceeCCCCchHHHHHHH-hCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKV-TGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~-TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      .+.++..+.||..+++.|||+||++|++|+++ +|++|.++.         .+..|+|+|++++|+.|..+|.+++.+.
T Consensus        18 ~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~---------~~~~v~i~G~~~~ve~Ak~~I~~iv~el   87 (90)
T d2ctfa1          18 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE---------GEDKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS---------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC---------CCceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            45689999999999999999999999999999 589999973         3467999999999999999999998763

>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=99.10  E-value=2.4e-11  Score=95.99  Aligned_cols=69  Identities=22%  Similarity=0.257  Sum_probs=58.4

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHh
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRL  259 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i  259 (428)
                      +..++..|.||...+|.|||++|.+|++|+++|||+|+|++  ++..++.|+|+|+.++      +.+|..++.+.+
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~--~~~~~~~v~I~G~~~~------v~~A~~~I~~iv   75 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKITGTKEG------IEKARHEVLLIS   75 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCC--TTSSCCEEEEEECHHH------HHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECC--CCCCCCEEEEEeCHHH------HHHHHHHHHHHH
Confidence            34578999999999999999999999999999999999975  4677899999998775      566666665544

>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=99.04  E-value=1e-10  Score=90.11  Aligned_cols=65  Identities=15%  Similarity=0.154  Sum_probs=54.6

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHH
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVF  256 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~  256 (428)
                      .....+|.||...+|.|||++|++|++|+++|||+|+|++  ++.+++.|+|+|++++      +.+|..++.
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~--~~~~~~~v~I~G~~~~------v~~A~~~I~   67 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPP--DSEKSNLIRIEGDPQG------VQQAKRELL   67 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCC--CCSSSEEEEEEESSHH------HHHHHHHHH
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCC--CCCCCCEEEEECCHHH------HHHHHHHHH
Confidence            3467889999999999999999999999999999999975  4567899999998764      455555444

>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=99.02  E-value=7.5e-11  Score=93.10  Aligned_cols=70  Identities=14%  Similarity=0.222  Sum_probs=57.0

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHH-hCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhh
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSE-AGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLI  260 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~Iqee-TGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~  260 (428)
                      ...++..|.||...+|.||||+|++|++|+++ ++++|++++  .+..+++|+|+|++++      +.+|..++...+.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~--~~~~~~~v~I~G~~~~------v~~A~~~I~~~v~   77 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV--EGSGSDTVVIRGPSSD------VEKAKKQLLHLAE   77 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCC--TTTTCCEEEEESCHHH------HHHHHHHHHHHHH
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeC--CCCCCceEEEeCCHHH------HHHHHHHHHHHHh
Confidence            34578899999999999999999999999988 589998875  5667899999998775      5566666655443

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.97  E-value=1.5e-10  Score=93.14  Aligned_cols=67  Identities=27%  Similarity=0.328  Sum_probs=56.6

Q ss_pred             ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHh
Q 014254          185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRL  259 (428)
Q Consensus       185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i  259 (428)
                      .++..|.||...+|.|||++|.+|++|+++|||+|.|++  .+..+++|+|+|+.++      +.+|..++...+
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~--~~~~~~~v~I~G~~~~------V~~A~~~I~~~v   75 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA--PELQSDIIAITGLAAN------LDRAKAGLLERV   75 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCC--TTTTCCEEEEEECHHH------HHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECC--CCCCcceEEEECCHHH------HHHHHHHHHHHH
Confidence            478999999999999999999999999999999999975  4667789999998764      556666655544

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.97  E-value=2e-10  Score=90.49  Aligned_cols=69  Identities=22%  Similarity=0.197  Sum_probs=55.1

Q ss_pred             CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHH
Q 014254          183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSR  258 (428)
Q Consensus       183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~  258 (428)
                      +..++..+.||...+|.|||++|++|++|+++|||+|+|++.. ..+.+.|+|+|++++      +.+|..++.+.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-~~~~~~v~I~G~~~~------V~~A~~~I~~i   75 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPEN------VEEAIDHILNL   75 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-CSCTTEEEEESCHHH------HHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCcc-CCCCCEEEEeCCHHH------HHHHHHHHHHH
Confidence            3456788999999999999999999999999999999997632 234578999998775      55565555543

>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=98.79  E-value=1.7e-10  Score=88.78  Aligned_cols=63  Identities=11%  Similarity=0.131  Sum_probs=48.4

Q ss_pred             EEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhhcC
Q 014254          281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRDNH  353 (428)
Q Consensus       281 ~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e~~  353 (428)
                      -+.||.+.+|.||||+|++|++|+++|||+|.|..          +..|+|+|. .+++..|..+|..+.++..
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~----------~g~v~I~g~~~~~v~~A~~~I~~i~~ea~   67 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN----------NGRIWATCPSRFSEEILIEAIRKIENESH   67 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT----------TSEEEC-----CTTCCTHHHHTTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC----------CCEEEEEeCCHHHHHHHHHHHHHHHHhhc
Confidence            47899999999999999999999999999999952          346999996 7789999999987766543

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.77  E-value=4.6e-09  Score=83.61  Aligned_cols=64  Identities=19%  Similarity=0.239  Sum_probs=52.8

Q ss_pred             EEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEE-----eCHHHHHHHHHHHHHHhhhc
Q 014254          280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS-----GEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       280 ~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtIt-----Gt~~aV~~A~~lI~~~L~e~  352 (428)
                      +.+.||.+.+|.||||||++|++|++.|||+|+|..+         +..|.+.     |.+.++++|..+|.++-+..
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d---------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~rGf   73 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE---------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGF   73 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT---------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTC
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC---------CCeEEEecCCccccHHHHHHHHHHHHHHhCCC
Confidence            3589999999999999999999999999999999633         2345554     56888999999998876643

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.76  E-value=2.2e-09  Score=85.41  Aligned_cols=56  Identities=30%  Similarity=0.398  Sum_probs=46.4

Q ss_pred             EEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHH
Q 014254          189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVF  256 (428)
Q Consensus       189 rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~  256 (428)
                      -+.||.+.+|.||||+|++|++|+++|||+|+|.+      +..|+|+|+.++      +.+|..+|.
T Consensus         4 vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~------~g~v~I~G~~e~------v~~A~~~I~   59 (84)
T d2ba0a3           4 IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ------NGLIWVNGDRRK------VSIAEEAIY   59 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT------TSEEEEESCHHH------HHHHHHHHH
T ss_pred             EEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC------CCEEEEEeCHHH------HHHHHHHHH
Confidence            37899999999999999999999999999999963      457999998654      455555543

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.71  E-value=1.4e-09  Score=85.42  Aligned_cols=51  Identities=16%  Similarity=0.168  Sum_probs=45.0

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS  238 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs  238 (428)
                      ..++-+|.||.+.+|.|||+||++||+|+++|||+|.+.+    .+++.|+|.|.
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~----~~~g~v~I~g~   56 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD----EDTGTFRIYGE   56 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE----TTTTEEEEEES
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEec----CCCceEEEEEC
Confidence            3467789999999999999999999999999999999875    35578999995

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.70  E-value=9.4e-09  Score=82.52  Aligned_cols=53  Identities=15%  Similarity=0.126  Sum_probs=47.0

Q ss_pred             CceEEEEEeccccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCC
Q 014254          184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGP  241 (428)
Q Consensus       184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~  241 (428)
                      ..++..+.||...++.|||+||++|++|++++ |++|.+++     ++..|+|+|+++.
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~-----~~~~v~i~G~~~~   72 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTED   72 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC-----CCceEEEeCCHHH
Confidence            45899999999999999999999999999995 89999973     4678999998764

>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=98.68  E-value=1.8e-08  Score=80.64  Aligned_cols=66  Identities=12%  Similarity=0.119  Sum_probs=57.0

Q ss_pred             EEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhhcCCCC
Q 014254          281 RLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRDNHFSG  356 (428)
Q Consensus       281 ~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e~~~~~  356 (428)
                      -+.||.+.+|.|||+||++|+.|++.|||+|.|..          +-.|.|.|. .+.+..|..+|..+.++...++
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d----------~G~V~I~g~~~~~~~~A~~~I~~I~~ea~v~g   70 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR----------NGRIHLECPNEDLEAIAVMAIKIIDEEAYTSG   70 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET----------TTEEEEECSCHHHHHHHHHHHHHHHHCSCCTT
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC----------CcEEEEEeCCHHHHHHHHHHHHHHHHhchhcc
Confidence            47899999999999999999999999999999952          346999995 7888999999999877665443

>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=98.57  E-value=2.6e-09  Score=78.30  Aligned_cols=48  Identities=31%  Similarity=0.532  Sum_probs=15.9

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG  240 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e  240 (428)
                      ...|.||.+++|.|||+||.+||.|+++|||+|.+.      ++..|+|.|...
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~------ddg~v~I~a~~~   51 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAADG   51 (54)
T ss_dssp             CC---------------------CHHHHSCCCC--------------CCCCBSS
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEe------CCeEEEEEecCc
Confidence            456899999999999999999999999999999996      467899998643

>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=98.55  E-value=3.5e-08  Score=78.37  Aligned_cols=45  Identities=22%  Similarity=0.489  Sum_probs=38.5

Q ss_pred             EEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254          189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS  238 (428)
Q Consensus       189 rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs  238 (428)
                      .+.||.+.+|.||||||++||+|+++|||+|+|..     ++..|.+.+.
T Consensus         6 ~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~-----d~g~v~i~~~   50 (84)
T d1tuaa1           6 YVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPE   50 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET-----TTTEEEEEES
T ss_pred             EEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEc-----CCCeEEEecC
Confidence            47899999999999999999999999999999963     3345666654

>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=98.46  E-value=7.1e-08  Score=79.51  Aligned_cols=54  Identities=20%  Similarity=0.318  Sum_probs=48.1

Q ss_pred             cccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254          288 QVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN  352 (428)
Q Consensus       288 ~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~  352 (428)
                      ..|+|||+||++|+.|++.|||+|.|.           +..|.|.|+++++..|..+|..++.+.
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~-----------d~~v~iig~~e~i~~A~~~Ie~li~~~   76 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVG-----------EYEVAIIGDYERAMAAKQAIEMLAEGR   76 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEEC-----------SSEEEEEEEHHHHHHHHHHHHHHHTTC
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEe-----------CCeEEEEECchhHHHHHHHHHHHHcCC
Confidence            469999999999999999999999995           224888999999999999999999754

>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=98.44  E-value=6.2e-09  Score=76.22  Aligned_cols=46  Identities=20%  Similarity=0.408  Sum_probs=14.3

Q ss_pred             EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC
Q 014254          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE  334 (428)
Q Consensus       279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt  334 (428)
                      ...|.||.+.+|.|||+||++||+|+++|||+|.|.          +|..|+|.|.
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~----------ddg~v~I~a~   49 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE----------DDGTIYIGAA   49 (54)
T ss_dssp             CC---------------------CHHHHSCCCC------------------CCCCB
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEe----------CCeEEEEEec
Confidence            346889999999999999999999999999999995          3456777775

>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=98.40  E-value=1.5e-08  Score=77.67  Aligned_cols=43  Identities=33%  Similarity=0.298  Sum_probs=33.4

Q ss_pred             EEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254          190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS  238 (428)
Q Consensus       190 IlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs  238 (428)
                      +.||.+.+|.||||+|++||+|+++|||+|.|.+      +..|+|+|.
T Consensus         5 i~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~------~g~v~I~g~   47 (69)
T d2je6i3           5 IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN------NGRIWATCP   47 (69)
T ss_dssp             EECCGGGHHHHHCGGGHHHHHHHTTC---CEECT------TSEEEC---
T ss_pred             EEEChhhccceECCchhHHHHHHHHHCCEEEEcC------CCEEEEEeC
Confidence            6899999999999999999999999999999963      346899996

>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=98.32  E-value=3.8e-07  Score=72.72  Aligned_cols=45  Identities=22%  Similarity=0.294  Sum_probs=39.9

Q ss_pred             EEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254          190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG  240 (428)
Q Consensus       190 IlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e  240 (428)
                      +.||.+.+|.|||+||++||.|+++|||+|.|.+      +-.|.|.|...
T Consensus         5 i~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d------~G~V~I~g~~~   49 (87)
T d2z0sa2           5 VEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR------NGRIHLECPNE   49 (87)
T ss_dssp             EECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET------TTEEEEECSCH
T ss_pred             EEEChhhcceeECCCCcHHHHHHHHHCCEEEECC------CcEEEEEeCCH
Confidence            6899999999999999999999999999999974      23689999643

>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=3.5e-06  Score=71.02  Aligned_cols=77  Identities=19%  Similarity=0.324  Sum_probs=58.5

Q ss_pred             eeEEEEEecccc------ccceeCCCCchHHHHHHHhCCeEEEcc-CC----------ccccCCCCCc-EEEEEeC-HHH
Q 014254          277 LVNARLVVASNQ------VGCLLGKGGTIISEMRKVTGTSIRIIS-DQ----------LLKCISENDR-VVQISGE-FSK  337 (428)
Q Consensus       277 ~vt~~L~VP~s~------VG~IIGKgG~~IkeIre~TGA~IqI~~-d~----------~P~~~~s~eR-vVtItGt-~~a  337 (428)
                      .++.+|.||-+.      +|.|||.+|.++|+|+++|||+|.|-+ ..          .+.....++. -|.|+++ ++.
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            457789999764      899999999999999999999999972 11          0111112233 4889997 778


Q ss_pred             HHHHHHHHHHHhhhcC
Q 014254          338 VKDAVYNVTGRLRDNH  353 (428)
Q Consensus       338 V~~A~~lI~~~L~e~~  353 (428)
                      +..|..+|...|...+
T Consensus        82 ~~~A~~~i~~ll~~~~   97 (122)
T d1k1ga_          82 VKKAVEQIRNILKQGI   97 (122)
T ss_dssp             HHHHHHHHHHHHTTTT
T ss_pred             HHHHHHHHHHHHHhcC
Confidence            9999999999997543

>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=97.64  E-value=2.1e-05  Score=67.07  Aligned_cols=74  Identities=28%  Similarity=0.255  Sum_probs=54.0

Q ss_pred             eEEEEEecc------ccccceeCCCCchHHHHHHHhCCeEEEccCCc-------------cccCCCCC-cEEEEEeCH--
Q 014254          278 VNARLVVAS------NQVGCLLGKGGTIISEMRKVTGTSIRIISDQL-------------LKCISEND-RVVQISGEF--  335 (428)
Q Consensus       278 vt~~L~VP~------s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~-------------P~~~~s~e-RvVtItGt~--  335 (428)
                      ++.+|.||-      +++|.|||.+|.++|+|+++|||+|.|-+...             +.....++ =-|.|+++.  
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            456788885      47899999999999999999999999983210             11111223 348888862  


Q ss_pred             ----HHHHHHHHHHHHHhhh
Q 014254          336 ----SKVKDAVYNVTGRLRD  351 (428)
Q Consensus       336 ----~aV~~A~~lI~~~L~e  351 (428)
                          ..+.+|+.+|...|..
T Consensus        82 ~~a~~kl~~A~~~I~~lL~p  101 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLVP  101 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHHHHHHHHcCC
Confidence                3578899999998853

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.59  E-value=1.6e-05  Score=65.09  Aligned_cols=38  Identities=24%  Similarity=0.486  Sum_probs=31.5

Q ss_pred             cccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254          196 KVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG  240 (428)
Q Consensus       196 ~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e  240 (428)
                      ..|.||||||.+||.|++.|||+|.|.+       ..|.|.|+.+
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d-------~~v~iig~~e   60 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGDYE   60 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS-------SEEEEEEEHH
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeC-------CeEEEEECch
Confidence            3799999999999999999999999963       2366677654

>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=97.36  E-value=4.5e-05  Score=64.01  Aligned_cols=37  Identities=30%  Similarity=0.539  Sum_probs=33.9

Q ss_pred             eEEEEEecccc------ccceeccCchHHHHHHHHhCCcEEEc
Q 014254          186 VSFRILCSNDK------VGAVIGKGGTIIRALQSEAGAFISVG  222 (428)
Q Consensus       186 vt~rIlVP~~~------vG~IIGKgG~tIK~IqeeTGA~I~Is  222 (428)
                      ++-+|+||.+.      +|.|||.+|+++|+|+++|||+|.|-
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~Ir   45 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIR   45 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEE
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEE
Confidence            57789999864      99999999999999999999999995

>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=97.13  E-value=8.1e-05  Score=63.35  Aligned_cols=38  Identities=24%  Similarity=0.405  Sum_probs=33.4

Q ss_pred             eEEEEEeccc------cccceeccCchHHHHHHHHhCCcEEEcc
Q 014254          186 VSFRILCSND------KVGAVIGKGGTIIRALQSEAGAFISVGA  223 (428)
Q Consensus       186 vt~rIlVP~~------~vG~IIGKgG~tIK~IqeeTGA~I~Is~  223 (428)
                      ++-||+||.+      .+|.|||.+|.++|+|+++|||+|.|-.
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            4568888854      6899999999999999999999999953

>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=95.02  E-value=0.0072  Score=45.09  Aligned_cols=39  Identities=33%  Similarity=0.378  Sum_probs=35.9

Q ss_pred             eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccC
Q 014254          278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISD  316 (428)
Q Consensus       278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d  316 (428)
                      ..+.+.||.++.+..|||+|.+++-..+.||.+|.|..+
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            467889999999999999999999999999999999844

>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=94.79  E-value=0.0093  Score=44.46  Aligned_cols=38  Identities=21%  Similarity=0.262  Sum_probs=34.8

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA  223 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~  223 (428)
                      ..+.+.||.+..+..|||+|.++|-..+-||.+|.|-.
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            46778999999999999999999999999999999853

>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=94.57  E-value=0.012  Score=44.02  Aligned_cols=38  Identities=26%  Similarity=0.360  Sum_probs=34.8

Q ss_pred             eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254          186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA  223 (428)
Q Consensus       186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~  223 (428)
                      -.+.+.||.+..+..|||+|.+||-..+-||.+|.|..
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            35778999999999999999999999999999999853

>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=94.19  E-value=0.014  Score=43.60  Aligned_cols=36  Identities=36%  Similarity=0.477  Sum_probs=34.4

Q ss_pred             EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254          279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII  314 (428)
Q Consensus       279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~  314 (428)
                      .+.+.||.++.+..|||+|.+++-..+.||.+|.|.
T Consensus        28 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~   63 (68)
T d1hh2p3          28 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIK   63 (68)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             EEEEEECcccccccccCCcchHHHHHHHHCCEEeeE
Confidence            578999999999999999999999999999999996

>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=83.81  E-value=0.2  Score=39.07  Aligned_cols=31  Identities=23%  Similarity=0.326  Sum_probs=26.5

Q ss_pred             EEEEEeccccccceeccCchHHHHHHHHhCC
Q 014254          187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGA  217 (428)
Q Consensus       187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA  217 (428)
                      .++|.|-...-|.||||+|+.|++|+++-.-
T Consensus        36 ~i~I~I~tarPGivIGrkG~~I~~L~~~l~k   66 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGEKGRRIRELTAVVQK   66 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHHHHH
T ss_pred             eEEEEEEeCCCceeeccCchhHHHHHHHHHH
Confidence            4667888889999999999999999887543

>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=81.54  E-value=0.71  Score=35.25  Aligned_cols=58  Identities=14%  Similarity=0.032  Sum_probs=44.3

Q ss_pred             EEEeccccccceeCCCCc-hHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHH
Q 014254          281 RLVVASNQVGCLLGKGGT-IISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGR  348 (428)
Q Consensus       281 ~L~VP~s~VG~IIGKgG~-~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~  348 (428)
                      -+.|+..++..+||++++ .++.|.+.+++.|-|=          .+-.|=|.|. .+..-.+...|...
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG----------~NGrIWi~~~~~~~~i~i~~aI~~~   63 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIG----------LNGKIWVKCEELSNTLACYRTIMEC   63 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEE----------TTTEEEEECSSHHHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEe----------cCcEEEEECCCHHHHHHHHHHHHHH
Confidence            356888999999999998 8999999999999993          3556889995 55555444444443

>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: GTPase Era C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.09  E-value=0.31  Score=39.26  Aligned_cols=31  Identities=29%  Similarity=0.410  Sum_probs=25.4

Q ss_pred             ceEEEEEecc-ccccceeccCchHHHHHHHHh
Q 014254          185 EVSFRILCSN-DKVGAVIGKGGTIIRALQSEA  215 (428)
Q Consensus       185 evt~rIlVP~-~~vG~IIGKgG~tIK~IqeeT  215 (428)
                      .+...|.|+. ++.+.||||+|++||+|...+
T Consensus        48 ~I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~a   79 (113)
T d1egaa2          48 DINGLILVEREGQKKMVIGNKGAKIKTIGIEA   79 (113)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             EEEEEEEECCcchhhhhhcccchHHHHHHHHH
Confidence            4677789986 568999999999999887654