Citrus Sinensis ID: 020173

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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
Protein Sequence
MAEQGEITVNPTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQQAGAQ
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHHcccEEEcccccccccEEEEEEccccccHHHHHHHHHHHHHHHHHccccccccccccccccccccEEEEEEccccEEccccccccHHHHHHHHccccEEEcccccccccccccccccEEEEEccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccEEEEEEccccccEEEccccHHHHHHHHHcccEEEEEccccccccEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEccccccccccEEEEEccccccccccHHHHHHHHHHHHHHHHccccccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEEccccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEcccccccccEEEEEEccHHHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
maeqgeitvnptvsvvtepeprhdvsgkrrredgeiegsdpkrrAKAQDVLFRIIVpsrqigkvigkeGHRIQKIREETKATIKIADAIARHEERVIIISskdndnvvsDAENALQQIAALILkdddsnseaskVAAGHVAANTIRLLIAGSQagcligmsgqnieklrnssgativilapnqlplcasahesdrvvQISGDVPAVLNALVEIGNqlrenpprqvisispaynysairpaqpfveptsadyvTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKvyggkgeqkhrhiqfgGSAQQVALAKQRVDEYIYSQLIQQAGAQ
Flexible Loop (DISEMBL)
maeqgeitvnptvsvvtepeprhdvsgkrrredgeiegsdpkrrakaqdvlfriivpsrqigkvigkeghriqkireetkaTIKIADAIARHEERVIIISskdndnvvSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGnqlrenpprQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQQAGAQ
Low Complexity Region (SEG)
MAEQGEITVNPTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREEtkatikiadaiaRHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQQAGAQ
Disordered region (IsUnstruct)
************************************************DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL***********VAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLI******
Disordered Region (DISOPRED)
****************************************************RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI*RHEERVIIISSKDNDNVVSDAENALQQIAAL************************RLLIAGSQAGCLIGMSGQNIEK**N******************SAHESDRVVQISGDVPAVLNALVEIGNQLR***********************************FEMLISESLVGGLIGRCGSNISRIRNESGAMIKVY*****QKHRHIQFGGSAQQVALAKQRVDEYI***********
Disordered Region (DISEMBL)
MAEQGEITVNPTVSVV***************************RAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD***********AGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQQAGAQ
Disordered Region (DISPRO)
***********************************************QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN**********VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYS*************ADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLI******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAEQGEITVNPTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQQAGAQ
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	330	2.2.26 [Sep-21-2011]
P57724	403	Poly(rC)-binding protein	yes	no	0.766	0.627	0.268	1e-19
Q0VCU0	403	Poly(rC)-binding protein	yes	no	0.766	0.627	0.265	3e-19
P57723	403	Poly(rC)-binding protein	yes	no	0.766	0.627	0.265	4e-19
P58223	606	KH domain-containing prot	no	no	0.769	0.419	0.242	8e-16
Q5RB68	556	Insulin-like growth facto	no	no	0.727	0.431	0.261	2e-13
Q5SF07	592	Insulin-like growth facto	no	no	0.763	0.425	0.247	3e-13
Q61990	362	Poly(rC)-binding protein	no	no	0.478	0.436	0.290	2e-12
P57721	371	Poly(rC)-binding protein	no	no	0.481	0.428	0.293	3e-12
P57722	371	Poly(rC)-binding protein	no	no	0.481	0.428	0.293	3e-12
Q15366	365	Poly(rC)-binding protein	no	no	0.478	0.432	0.284	5e-11

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

 Score = 97.4 bits (241), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 86/320 (26%), Positives = 151/320 (47%), Gaps = 67/320 (20%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  +++IRE++ A I I++            S  +    ++
Sbjct: 18  LTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG-----------SCPERITTIT 66

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVA--ANTIRLLIAGSQAGCLIGMSGQNIEK 167
            +  A+    ++I    D +  A+    G V+    T+RL+I  SQ G LIG +G  I++
Sbjct: 67  GSTAAVFHAVSMIAFKLDEDLCAAPANGGSVSRPPVTLRLVIPASQCGSLIGKAGTKIKE 126

Query: 168 LRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR-QVI 226
           +R ++GA + + A + LP     + ++R V +SG   A++  + +I   + E+PP+   I
Sbjct: 127 IRETTGAQVQV-AGDLLP-----NSTERAVTVSGVPDAIILCVRQICAVILESPPKGATI 180

Query: 227 SISPAYN-----------------YSAIRPAQ------------PFVEPT-------SAD 250
              P+ +                 Y A+ PA+            PF  P+       S  
Sbjct: 181 PYHPSLSLGTVLLSANQGFSVQGQYGAVTPAEVTKLQQLSGHAVPFASPSVVPGMDPSTQ 240

Query: 251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG---GKGEQKHRHIQFGGSAQQ 307
             + E L+   L+G +IGR GS IS IR  SGA IK+     G GE   RH+   GS   
Sbjct: 241 TSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGE---RHVTITGSPVS 297

Query: 308 VALAKQRVDEYIYSQLIQQA 327
           +ALA     +Y+ +  ++ A
Sbjct: 298 IALA-----QYLITACLETA 312

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.
Mus musculus (taxid: 10090)

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

 Score = 96.3 bits (238), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 85/320 (26%), Positives = 151/320 (47%), Gaps = 67/320 (20%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  +++IRE++ A I I++            S  +    ++
Sbjct: 18  LTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG-----------SCPERITTIT 66

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVA--ANTIRLLIAGSQAGCLIGMSGQNIEK 167
            +  A+    ++I    D +  A+    G+V+    T+RL+I  SQ G LIG +G  I++
Sbjct: 67  GSTAAVFHAVSMIAFKLDEDLCAAPANGGNVSRPPVTLRLVIPASQCGSLIGKAGTKIKE 126

Query: 168 LRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR-QVI 226
           +R ++GA + + A + LP     + ++R V +SG   A++  + +I   + E+PP+   I
Sbjct: 127 IRETTGAQVQV-AGDLLP-----NSTERAVTVSGVPDAIILCVRQICAVILESPPKGATI 180

Query: 227 SISPAYN-----------------YSAIRPAQ------------PFVEPT-------SAD 250
              P+ +                 Y  + PA+            PF  P+       S  
Sbjct: 181 PYHPSLSLGTVLLSTNQGFSVQGQYGTVTPAEVTKLQQLSGHAVPFASPSMVPGLDPSTQ 240

Query: 251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG---GKGEQKHRHIQFGGSAQQ 307
             + E L+   L+G +IGR GS IS IR  SGA IK+     G GE   RH+   GS   
Sbjct: 241 TSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGE---RHVTITGSPVS 297

Query: 308 VALAKQRVDEYIYSQLIQQA 327
           +ALA     +Y+ +  ++ A
Sbjct: 298 IALA-----QYLITACLETA 312

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

Bos taurus (taxid: 9913)

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

 Score = 95.9 bits (237), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 85/320 (26%), Positives = 151/320 (47%), Gaps = 67/320 (20%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  +++IRE++ A I I++            S  +    ++
Sbjct: 18  LTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG-----------SCPERITTIT 66

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVA--ANTIRLLIAGSQAGCLIGMSGQNIEK 167
            +  A+    ++I    D +  A+    G+V+    T+RL+I  SQ G LIG +G  I++
Sbjct: 67  GSTAAVFHAVSMIAFKLDEDLCAAPANGGNVSRPPVTLRLVIPASQCGSLIGKAGTKIKE 126

Query: 168 LRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR-QVI 226
           +R ++GA + + A + LP     + ++R V +SG   A++  + +I   + E+PP+   I
Sbjct: 127 IRETTGAQVQV-AGDLLP-----NSTERAVTVSGVPDAIILCVRQICAVILESPPKGATI 180

Query: 227 SISPAYN-----------------YSAIRPAQ------------PFVEPT-------SAD 250
              P+ +                 Y A+ PA+            PF  P+          
Sbjct: 181 PYHPSLSLGTVLLSANQGFSVQGQYGAVTPAEVTKLQQLSSHAVPFATPSVVPGLDPGTQ 240

Query: 251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG---GKGEQKHRHIQFGGSAQQ 307
             + E L+   L+G +IGR GS IS IR  SGA IK+     G GE   RH+   GS   
Sbjct: 241 TSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGE---RHVTITGSPVS 297

Query: 308 VALAKQRVDEYIYSQLIQQA 327
           +ALA     +Y+ +  ++ A
Sbjct: 298 IALA-----QYLITACLETA 312

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

Homo sapiens (taxid: 9606)

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

 Score = 84.7 bits (208), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 78/322 (24%), Positives = 150/322 (46%), Gaps = 68/322 (21%)

Query: 45  AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIAR--HEERVIIISSK 102
           +++++++F+++ P   I +VIGK G  I++IRE + + I++ D+  +   +E VII+++ 
Sbjct: 307 SRSEELVFKVLCPLCNIMRVIGKGGSTIKRIREASGSCIEVNDSRTKCGDDECVIIVTAT 366

Query: 103 DNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSG 162
           ++     D   ++   A L+L++  ++ +A  V         ++LL++    GC+IG SG
Sbjct: 367 ES----PDDMKSMAVEAVLLLQEYINDEDAENV--------KMQLLVSSKVIGCVIGKSG 414

Query: 163 QNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN-- 220
             I ++R  + A I          C S  + D +V++SG+V +V +AL++I  +LRE+  
Sbjct: 415 SVINEIRKRTNANI----------CISKGKKDDLVEVSGEVSSVRDALIQIVLRLREDVL 464

Query: 221 ----------PPRQ-----------------------VISISPAYNYSAIRPAQPFVEPT 247
                     PP +                       + S S  + Y +  PA   V  +
Sbjct: 465 GDKDSVATRKPPARTDNCSFLSGSSNAGYTLPSFMSSMASTSGFHGYGSF-PAGDNVLGS 523

Query: 248 SADY--------VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHI 299
           +  Y           E+LI    +  ++G+ G N+  IR  SGAMI++   K        
Sbjct: 524 TGPYSYGRLPSSSALEILIPAHAMSKVMGKGGGNLENIRRISGAMIEISASKTSHGDHIA 583

Query: 300 QFGGSAQQVALAKQRVDEYIYS 321
              G+ +Q+  A+  V  ++ S
Sbjct: 584 LLSGTLEQMRCAENLVQAFVMS 605

Arabidopsis thaliana (taxid: 3702)

>sp|Q5RB68|IF2B2_PONAB Insulin-like growth factor 2 mRNA-binding protein 2 OS=Pongo abelii GN=IGF2BP2 PE=2 SV=1

 Score = 77.0 bits (188), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/271 (26%), Positives = 130/271 (47%), Gaps = 31/271 (11%)

Query: 31  REDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI--ADA 88
           RE G   G     +A+  D   RI+VP++ +G +IGKEG  I+ I ++T++ + I   + 
Sbjct: 177 REQGHAPGGT--SQARQIDFPLRILVPTQFVGAIIGKEGLTIKNITKQTQSRVDIHRKEN 234

Query: 89  IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLL 148
               E+ V I ++ +  +       A + I  ++ K+ D    A ++         +++L
Sbjct: 235 SGAAEKPVTIHATPEGTS------EACRMILEIMQKEADETKLAEEIP--------LKIL 280

Query: 149 IAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLN 208
                 G LIG  G+N++K+ + +G  I I +   L    S +  +R + + G V A  +
Sbjct: 281 AHNGLVGRLIGKEGRNLKKIEHETGTKITISSLQDL----SIYNPERTITVKGTVEACAS 336

Query: 209 ALVEIGNQLRENPPRQVISISPAYNY-SAIRPAQ---PFVEPTSADYVTFE---MLISES 261
           A +EI  +LRE     +++++    Y S++ P     PF  P    Y   E   + I   
Sbjct: 337 AEIEIMKKLREAFENDMLAVNTHSGYFSSLYPHHQFGPF--PHHHSYPEQEIVNLFIPTQ 394

Query: 262 LVGGLIGRCGSNISRIRNESGAMIKVYGGKG 292
            VG +IG+ G++I ++   +GA IK+   +G
Sbjct: 395 AVGAIIGKKGAHIKQLARFAGASIKIAPAEG 425

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

Pongo abelii (taxid: 9601)

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

 Score = 76.3 bits (186), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 81/327 (24%), Positives = 139/327 (42%), Gaps = 75/327 (22%)

Query: 16  VTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKI 75
           V+ P P H     R RE G   GS    +A+  D   RI+VP++ +G +IGKEG  I+ I
Sbjct: 160 VSSPSPPH-----RAREQGHGPGSS--SQARQIDFPLRILVPTQFVGAIIGKEGLTIKNI 212

Query: 76  REETKATIKI--ADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEAS 133
            ++T++ + I   +     E+ V I ++ +  +       A + I  ++ K+ D    A 
Sbjct: 213 TKQTQSRVDIHRKENSGAAEKPVTIHATPEGTS------EACRMILEIMQKEADETKLAE 266

Query: 134 KVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHES 193
           +V         +++L      G LIG  G+N++K+ + +G  I I +   L    S +  
Sbjct: 267 EVP--------LKILAHNGFVGRLIGKEGRNLKKIEHETGTKITISSLQDL----SIYNP 314

Query: 194 DRVVQISGDVPAVLNALVEIGNQLRENPPRQVISIS------PAYNYSAI---------- 237
           +R + + G + A  NA +EI  +LRE     +++++      P  N SA+          
Sbjct: 315 ERTITVRGTIEACANAEIEIMKKLREAFENDMLAVNQQANLIPGLNLSALGIFSTGLSVL 374

Query: 238 -RPAQPFVEPTSADYVTF-------------------------------EMLISESLVGG 265
             PA P   P S  Y  F                                + I    VG 
Sbjct: 375 PPPAGPRGVPPSPPYHPFATHSGYFSSLYPHHHFGPFPHHHSYPEQETVSLFIPTQAVGA 434

Query: 266 LIGRCGSNISRIRNESGAMIKVYGGKG 292
           +IG+ G++I ++   +GA IK+   +G
Sbjct: 435 IIGKKGAHIKQLARFAGASIKIAPAEG 461

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

Mus musculus (taxid: 10090)

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

 Score = 73.2 bits (178), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/179 (29%), Positives = 100/179 (55%), Gaps = 21/179 (11%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER+I ++   N     
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTN----- 66

Query: 110 DAENALQQIAALI---LKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIE 166
               A+ +  A+I   L++D S+S  +  AA      T+RL++  SQ G LIG  G  I+
Sbjct: 67  ----AIFKAFAMIIDKLEEDISSSMTNSTAASRPPV-TLRLVVPASQCGSLIGKGGCKIK 121

Query: 167 KLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV 225
           ++R S+GA + + A + LP     + ++R + I+G   +++  + +I   + E+PP+ V
Sbjct: 122 EIRESTGAQVQV-AGDMLP-----NSTERAITIAGIPQSIIECVKQICVVMLESPPKGV 174

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

 Score = 73.2 bits (178), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 51/174 (29%), Positives = 95/174 (54%), Gaps = 15/174 (8%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER++ I+        +
Sbjct: 46  LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISE--GNCPERIVTITGP------T 97

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
           DA      + A   ++D  NS ++  A       T+RL++  SQ G LIG  G  I+++R
Sbjct: 98  DAIFKAFAMIAYKFEEDIINSMSNSPATSKPPV-TLRLVVPASQCGSLIGKGGSKIKEIR 156

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223
            S+GA + + A + LP     + ++R V ISG   A++  + +I   + E+PP+
Sbjct: 157 ESTGAQVQV-AGDMLP-----NSTERAVTISGTPDAIIQCVKQICVVMLESPPK 204

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 = 72.8 bits (177), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 51/174 (29%), Positives = 95/174 (54%), Gaps = 15/174 (8%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER++ I+        +
Sbjct: 46  LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISE--GNCPERIVTITGP------T 97

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
           DA      + A   ++D  NS ++  A       T+RL++  SQ G LIG  G  I+++R
Sbjct: 98  DAIFKAFAMIAYKFEEDIINSMSNSPATSKPPV-TLRLVVPASQCGSLIGKGGSKIKEIR 156

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223
            S+GA + + A + LP     + ++R V ISG   A++  + +I   + E+PP+
Sbjct: 157 ESTGAQVQV-AGDMLP-----NSTERAVTISGTPDAIIQCVKQICVVMLESPPK 204

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

Mus musculus (taxid: 10090)

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

 Score = 68.9 bits (167), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 52/183 (28%), Positives = 100/183 (54%), Gaps = 25/183 (13%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER+I ++   N     
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTN----- 66

Query: 110 DAENALQQIAALI---LKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIE 166
               A+ +  A+I   L++D S+S  +  AA      T+RL++  SQ G LIG  G  I+
Sbjct: 67  ----AIFKAFAMIIDKLEEDISSSMTNSTAASRPPV-TLRLVVPASQCGSLIGKGGCKIK 121

Query: 167 KLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG----NQLRENPP 222
           ++R S+GA + + A + LP     + ++R + I+G   +++  + +I       L ++PP
Sbjct: 122 EIRESTGAQVQV-AGDMLP-----NSTERAITIAGIPQSIIECVKQICVVMLETLSQSPP 175

Query: 223 RQV 225
           + V
Sbjct: 176 KGV 178

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)

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	330
356530005	385	PREDICTED: KH domain-containing protein	0.921	0.789	0.839	1e-145
255541092	363	conserved hypothetical protein [Ricinus	0.987	0.898	0.778	1e-142
359489188	343	PREDICTED: KH domain-containing protein	0.996	0.959	0.759	1e-140
297734587	346	unnamed protein product [Vitis vinifera]	0.996	0.950	0.759	1e-140
147855522	321	hypothetical protein VITISV_031103 [Viti	0.921	0.947	0.697	1e-122
224137186	357	predicted protein [Populus trichocarpa]	0.993	0.918	0.705	1e-122
307136423	331	hypothetical protein [Cucumis melo subsp	0.866	0.864	0.720	1e-111
449445515	276	PREDICTED: poly(rC)-binding protein 2-li	0.693	0.829	0.766	3e-94
357507881	275	Poly(rC)-binding protein [Medicago trunc	0.606	0.727	0.722	8e-75
118482617	159	unknown [Populus trichocarpa]	0.466	0.968	0.767	1e-62

>gi|356530005|ref|XP_003533576.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  521 bits (1342), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 261/311 (83%), Positives = 284/311 (91%), Gaps = 7/311 (2%)

Query: 26  SGKRRREDGEIEG--SDPK----RRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET 79
           SGKRRR+D E  G  S P+    +RAK QDV+FRI+VPSRQIGKVIGKEGHRIQKIRE+T
Sbjct: 73  SGKRRRDD-ENSGTASAPEQSAAKRAKGQDVIFRIVVPSRQIGKVIGKEGHRIQKIREDT 131

Query: 80  KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGH 139
           KATIKIADAIARHEERVIIISSKDND  V+DAE AL+QIA LILK+DDS+ +ASKV AGH
Sbjct: 132 KATIKIADAIARHEERVIIISSKDNDEKVTDAEKALEQIAHLILKEDDSSLDASKVTAGH 191

Query: 140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQI 199
           VAANTIRLLIAGSQAG LIGMSGQNIEKLR+SSGA+I +LAPNQLPLCASAHESDRVVQ+
Sbjct: 192 VAANTIRLLIAGSQAGGLIGMSGQNIEKLRDSSGASITVLAPNQLPLCASAHESDRVVQL 251

Query: 200 SGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLIS 259
           SGDVPAV+ AL EIG QLRENPPRQVISISP YNY+AIRP+QP+++PTS DYVTFEMLIS
Sbjct: 252 SGDVPAVMKALEEIGCQLRENPPRQVISISPTYNYAAIRPSQPYLDPTSVDYVTFEMLIS 311

Query: 260 ESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYI 319
           E++VGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHR IQFGGSAQQVALAKQRVDEYI
Sbjct: 312 ETMVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRQIQFGGSAQQVALAKQRVDEYI 371

Query: 320 YSQLIQQAGAQ 330
           YSQLIQQ G Q
Sbjct: 372 YSQLIQQTGTQ 382

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255541092|ref|XP_002511610.1| conserved hypothetical protein [Ricinus communis] gi|223548790|gb|EEF50279.1| conserved hypothetical protein [Ricinus communis]

 Score =  509 bits (1311), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 260/334 (77%), Positives = 294/334 (88%), Gaps = 8/334 (2%)

Query: 1   MAEQGEITVNPTVSVVTEPEPR-HDVSGKRRREDGEI----EGSDPKRRAKAQDVLFRII 55
           M + G I +N TV  V+ P P  +  + KRRR++ ++    EGS  KR AKAQDV+FRI+
Sbjct: 19  MPQPGGIPMN-TVPPVSFPPPDIYAATAKRRRDEFDVADEPEGSAAKR-AKAQDVIFRIV 76

Query: 56  VPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENAL 115
           VPSRQIGKVIGK G RIQKIREETKATIKIADAIARHEERVIIISSK++D VVSDAENAL
Sbjct: 77  VPSRQIGKVIGKVGCRIQKIREETKATIKIADAIARHEERVIIISSKESDCVVSDAENAL 136

Query: 116 QQIAALILKDDDSNSEASKV-AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGA 174
           ++IA LILK+D+S +E+SKV  AGH+ ANTIRLLIAGSQAG LIG+SGQNIEKLRNSSGA
Sbjct: 137 KKIATLILKEDESPAESSKVVGAGHLGANTIRLLIAGSQAGSLIGVSGQNIEKLRNSSGA 196

Query: 175 TIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNY 234
           TI +LAPNQLPLCASAHESDRVVQISGDVP VL A+ EIG QLRENPP+QVISISP YNY
Sbjct: 197 TITVLAPNQLPLCASAHESDRVVQISGDVPVVLKAVEEIGCQLRENPPKQVISISPTYNY 256

Query: 235 SAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQ 294
           + +RP QP+V+PTSADYVT EM++SE+LVGGLIGRCGSNISRIRNESGAMIKVYGGKGE+
Sbjct: 257 ATVRPTQPYVDPTSADYVTLEMMVSETLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEK 316

Query: 295 KHRHIQFGGSAQQVALAKQRVDEYIYSQLIQQAG 328
           KHRHIQFGG+AQQVALAKQRVDEYIYSQL+QQAG
Sbjct: 317 KHRHIQFGGTAQQVALAKQRVDEYIYSQLVQQAG 350

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489188|ref|XP_002272998.2| PREDICTED: KH domain-containing protein At4g18375-like [Vitis vinifera]

 Score =  503 bits (1296), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 259/341 (75%), Positives = 285/341 (83%), Gaps = 12/341 (3%)

Query: 1   MAEQGEITVNPTVSVVTEPEPRHDVSGKRRRED---------GEI--EGSDPKRRAKAQD 49
           MA++GE+   P +     P P    S KR R+D         GE+  +   PKRRAK QD
Sbjct: 1   MAQEGEVPRTP-IPQSEAPAPSEPTSMKRPRDDDGGVIASATGEVADDHRSPKRRAKNQD 59

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           VLFRI+VPSRQIGKVIGKEG RIQKIREETKATIKIADAIARHEERVIIISSKD++NV+S
Sbjct: 60  VLFRIVVPSRQIGKVIGKEGSRIQKIREETKATIKIADAIARHEERVIIISSKDSENVIS 119

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
           DAENAL Q+A+LILK+DDSN++A KV  GHV AN IRLLIAGSQAGCLIGMSGQNIEKLR
Sbjct: 120 DAENALLQVASLILKEDDSNTDALKVGVGHVVANAIRLLIAGSQAGCLIGMSGQNIEKLR 179

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISIS 229
           NSSGATI IL  NQLPLCASAH+SDR+VQISGDVPAVL AL EIG QLRENPPRQVISIS
Sbjct: 180 NSSGATITILPQNQLPLCASAHDSDRMVQISGDVPAVLKALEEIGCQLRENPPRQVISIS 239

Query: 230 PAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG 289
           P YN +  R +Q +++P SADYVT  M+I E+LVGGLIGRCGSNISRIRNESGAMIKVYG
Sbjct: 240 PIYNPNTNRTSQQYLDPASADYVTLNMMIPETLVGGLIGRCGSNISRIRNESGAMIKVYG 299

Query: 290 GKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQQAGAQ 330
           GKGEQ HR IQFGGSAQQVALAKQRVDEYIYSQL+QQAGAQ
Sbjct: 300 GKGEQNHRQIQFGGSAQQVALAKQRVDEYIYSQLMQQAGAQ 340

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297734587|emb|CBI16638.3| unnamed protein product [Vitis vinifera]

 Score =  503 bits (1296), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 259/341 (75%), Positives = 285/341 (83%), Gaps = 12/341 (3%)

Query: 1   MAEQGEITVNPTVSVVTEPEPRHDVSGKRRRED---------GEI--EGSDPKRRAKAQD 49
           MA++GE+   P +     P P    S KR R+D         GE+  +   PKRRAK QD
Sbjct: 1   MAQEGEVPRTP-IPQSEAPAPSEPTSMKRPRDDDGGVIASATGEVADDHRSPKRRAKNQD 59

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           VLFRI+VPSRQIGKVIGKEG RIQKIREETKATIKIADAIARHEERVIIISSKD++NV+S
Sbjct: 60  VLFRIVVPSRQIGKVIGKEGSRIQKIREETKATIKIADAIARHEERVIIISSKDSENVIS 119

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
           DAENAL Q+A+LILK+DDSN++A KV  GHV AN IRLLIAGSQAGCLIGMSGQNIEKLR
Sbjct: 120 DAENALLQVASLILKEDDSNTDALKVGVGHVVANAIRLLIAGSQAGCLIGMSGQNIEKLR 179

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISIS 229
           NSSGATI IL  NQLPLCASAH+SDR+VQISGDVPAVL AL EIG QLRENPPRQVISIS
Sbjct: 180 NSSGATITILPQNQLPLCASAHDSDRMVQISGDVPAVLKALEEIGCQLRENPPRQVISIS 239

Query: 230 PAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG 289
           P YN +  R +Q +++P SADYVT  M+I E+LVGGLIGRCGSNISRIRNESGAMIKVYG
Sbjct: 240 PIYNPNTNRTSQQYLDPASADYVTLNMMIPETLVGGLIGRCGSNISRIRNESGAMIKVYG 299

Query: 290 GKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQQAGAQ 330
           GKGEQ HR IQFGGSAQQVALAKQRVDEYIYSQL+QQAGAQ
Sbjct: 300 GKGEQNHRQIQFGGSAQQVALAKQRVDEYIYSQLMQQAGAQ 340

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147855522|emb|CAN83854.1| hypothetical protein VITISV_031103 [Vitis vinifera]

 Score =  443 bits (1139), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 240/344 (69%), Positives = 261/344 (75%), Gaps = 40/344 (11%)

Query: 1   MAEQGEITVNPTVSVVTEPEPRHDVSGKRRRED---------GEI--EGSDPKRRAKAQD 49
           MA++ E+   P +     P P    S KR R+D         GE+  +   PKRRAK QD
Sbjct: 1   MAQEAEVPKTP-IPQSEAPAPSESTSMKRPRDDDGGVIASATGEVADDHRSPKRRAKNQD 59

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           VLFRI+VPSRQIGKVIGKEG RIQKIREETKATIKIADAIARHEERVIIISSKD++NV+S
Sbjct: 60  VLFRIVVPSRQIGKVIGKEGSRIQKIREETKATIKIADAIARHEERVIIISSKDSENVIS 119

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
           DAENAL Q A+LILK+DDSN++A KV  GHV AN IRLLIAGSQAGCLIGMSGQNIEKLR
Sbjct: 120 DAENALLQXASLILKEDDSNTDALKVGVGHVVANAIRLLIAGSQAGCLIGMSGQNIEKLR 179

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISIS 229
           NSSGATI IL  NQLPLCASAH+SDR+VQISGDVPAVL AL EIG QLR           
Sbjct: 180 NSSGATITILPQNQLPLCASAHDSDRMVQISGDVPAVLKALEEIGCQLR----------- 228

Query: 230 PAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG 289
                             +ADYVT  M+I E+LVGGLIGRCGSNISRIRNESGAMIKVYG
Sbjct: 229 --------------TTNLAADYVTLNMMIPETLVGGLIGRCGSNISRIRNESGAMIKVYG 274

Query: 290 GKGEQKHRHIQFGGSAQ---QVALAKQRVDEYIYSQLIQQAGAQ 330
           GKGEQ HR IQFGGSAQ   QVALAKQRVDEYIYSQL+QQAGAQ
Sbjct: 275 GKGEQNHRQIQFGGSAQQAYQVALAKQRVDEYIYSQLMQQAGAQ 318

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224137186|ref|XP_002327061.1| predicted protein [Populus trichocarpa] gi|222835376|gb|EEE73811.1| predicted protein [Populus trichocarpa]

 Score =  442 bits (1138), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 239/339 (70%), Positives = 276/339 (81%), Gaps = 11/339 (3%)

Query: 1   MAEQGEITVNPTVSVVTEPEPRH-DVSGKRRREDGEI-EGSDPKRRAKAQDVLFRIIVPS 58
           MA+  E+ +NP+      P+     V+ KRRR+D +  E S  KR+A+A DV+FRI+VPS
Sbjct: 1   MAQPWELQLNPSPPGTELPKLNALPVTAKRRRDDFDGGETSAAKRQARA-DVIFRIVVPS 59

Query: 59  RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118
            +IGKVIGK+GHRIQKIRE+TKATIKIADA+ARHEERVIIISSK+N+N  +DAENALQ+I
Sbjct: 60  GKIGKVIGKQGHRIQKIREDTKATIKIADAVARHEERVIIISSKENENGATDAENALQRI 119

Query: 119 AALILKDDDSNSEASK-------VAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171
           A LIL +DD  S A         V AGHVAANTIRLLIAGSQAG LIGMSGQNI KLRNS
Sbjct: 120 AELILNEDDGGSSAGGGVEIGKLVNAGHVAANTIRLLIAGSQAGSLIGMSGQNIVKLRNS 179

Query: 172 SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPA 231
           SGA I +LAPNQLPLCASA+ESDRVVQISGDVP VL AL EIG QLRENPP+QVISISP+
Sbjct: 180 SGAMITVLAPNQLPLCASAYESDRVVQISGDVPVVLKALEEIGCQLRENPPKQVISISPS 239

Query: 232 YNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK 291
           YNYSA+ P Q +    +ADYVT EM++ E+++GGLIGR GSNISRIR ESGA+IKV+GGK
Sbjct: 240 YNYSAV-PFQQYAPQAAADYVTMEMMVPETMMGGLIGRSGSNISRIRVESGAVIKVHGGK 298

Query: 292 GEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQQAGAQ 330
           G QKHRHIQ  GS+QQVALAKQRVDEYIYSQL+QQAG Q
Sbjct: 299 GAQKHRHIQLAGSSQQVALAKQRVDEYIYSQLVQQAGTQ 337

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307136423|gb|ADN34230.1| hypothetical protein [Cucumis melo subsp. melo]

 Score =  407 bits (1046), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 229/318 (72%), Positives = 252/318 (79%), Gaps = 32/318 (10%)

Query: 20  EPRHDVSGKRRREDGEI----EGSD---PKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRI 72
           EP H V+GKRRRED  I    + SD   PKR+AKA DVLFRI+VPS+QIGKVIGK G RI
Sbjct: 32  EPGHTVTGKRRREDDLIVSNSDASDVSAPKRQAKAHDVLFRIVVPSKQIGKVIGKVGCRI 91

Query: 73  QKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEA 132
           QK+REETKATIKIADA+AR+EERVIIISSKDN+N V+DAE ALQQIAALILK+D S+ E 
Sbjct: 92  QKVREETKATIKIADAVARYEERVIIISSKDNENSVTDAEKALQQIAALILKEDGSSIEE 151

Query: 133 SKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHE 192
            KV  GHVAANTIRLLIAGSQAG LIG SGQNIEKLRNSSGA+I ILAPNQLPLCASAHE
Sbjct: 152 LKVGTGHVAANTIRLLIAGSQAGSLIGASGQNIEKLRNSSGASITILAPNQLPLCASAHE 211

Query: 193 SDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYV 252
           SDRVVQISGD+ AVL AL EIGNQLR+                            + +YV
Sbjct: 212 SDRVVQISGDILAVLKALEEIGNQLRKT-------------------------NLAVNYV 246

Query: 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAK 312
           TFEMLISE+LVGGLIG  G NISRIRNESGA IKV GG+GEQ +R IQFGGSA+QVALAK
Sbjct: 247 TFEMLISETLVGGLIGIGGFNISRIRNESGATIKVCGGRGEQNYRQIQFGGSAEQVALAK 306

Query: 313 QRVDEYIYSQLIQQAGAQ 330
           QRVDEYIYSQ+I+QAG Q
Sbjct: 307 QRVDEYIYSQVIRQAGVQ 324

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449445515|ref|XP_004140518.1| PREDICTED: poly(rC)-binding protein 2-like [Cucumis sativus] gi|449529952|ref|XP_004171961.1| PREDICTED: poly(rC)-binding protein 2-like [Cucumis sativus]

 Score =  351 bits (901), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 181/236 (76%), Positives = 201/236 (85%), Gaps = 7/236 (2%)

Query: 20  EPRHDVSGKRRREDGEI----EGSD---PKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRI 72
           EP H V+GKRRRED  I    + SD   PKR+AKA DVLFRI+VPS+QIGKVIGK G RI
Sbjct: 32  EPGHTVTGKRRREDDLIVSNSDASDISAPKRQAKAHDVLFRIVVPSKQIGKVIGKVGCRI 91

Query: 73  QKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEA 132
           QK+REETKATIKIADA+AR+EERVIIISSKDN+N V+DAE ALQQIAALILK+D S+ E 
Sbjct: 92  QKVREETKATIKIADAVARYEERVIIISSKDNENSVTDAEKALQQIAALILKEDGSSIEE 151

Query: 133 SKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHE 192
            KV  GHVAANTIRLLIAGSQAG LIG SGQNIEKLRNSSGA+I ILAPNQLPLCASAHE
Sbjct: 152 LKVGTGHVAANTIRLLIAGSQAGSLIGASGQNIEKLRNSSGASITILAPNQLPLCASAHE 211

Query: 193 SDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTS 248
           SDRVVQISGD+ AVL AL EIGNQLR NPPRQVIS+SP YNY+ + P Q +++PTS
Sbjct: 212 SDRVVQISGDILAVLKALEEIGNQLRVNPPRQVISVSPTYNYNTMHPPQSYMDPTS 267

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357507881|ref|XP_003624229.1| Poly(rC)-binding protein [Medicago truncatula] gi|355499244|gb|AES80447.1| Poly(rC)-binding protein [Medicago truncatula]

 Score =  286 bits (733), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 151/209 (72%), Positives = 172/209 (82%), Gaps = 9/209 (4%)

Query: 19  PEPRHDV----SGKRRREDGEIEGSDPK-----RRAKAQDVLFRIIVPSRQIGKVIGKEG 69
           P   HD     S KRRR+D ++  +        +RAK QDV+FRI+VPS+QIGKVIGKEG
Sbjct: 60  PYSTHDAGYPSSMKRRRDDEDLGTASSAELSAAKRAKGQDVIFRIVVPSKQIGKVIGKEG 119

Query: 70  HRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN 129
            RIQKIRE T+A IKIADAIARHEERVIIISSKDND +V+DAE AL+QIA LILK+D+S+
Sbjct: 120 CRIQKIREMTRANIKIADAIARHEERVIIISSKDNDEMVTDAEKALEQIANLILKEDNSS 179

Query: 130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCAS 189
            +ASK+ AGHVAANTIRLLIAGSQAG LIGMSGQNIEKLRNSSGA I +LAP+QLPLCAS
Sbjct: 180 FDASKLTAGHVAANTIRLLIAGSQAGGLIGMSGQNIEKLRNSSGAMITVLAPSQLPLCAS 239

Query: 190 AHESDRVVQISGDVPAVLNALVEIGNQLR 218
           AHESDRVVQ+SGDV  V+ AL EIG QLR
Sbjct: 240 AHESDRVVQLSGDVSTVMKALEEIGCQLR 268

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118482617|gb|ABK93228.1| unknown [Populus trichocarpa]

 Score =  246 bits (627), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 119/155 (76%), Positives = 135/155 (87%), Gaps = 1/155 (0%)

Query: 176 IVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYS 235
           I +LAPNQLPLCASA+ESDRVVQISGDVP VL AL EIG QLRENPP+QVISISP+YNYS
Sbjct: 2   ITVLAPNQLPLCASAYESDRVVQISGDVPVVLKALEEIGCQLRENPPKQVISISPSYNYS 61

Query: 236 AIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQK 295
           A+ P Q +    +ADYVT EM++ E+++GGLIGR GSNISRIR ESGA+IKV+GGKG QK
Sbjct: 62  AV-PFQQYAPQAAADYVTMEMMVPETMMGGLIGRSGSNISRIRVESGAVIKVHGGKGAQK 120

Query: 296 HRHIQFGGSAQQVALAKQRVDEYIYSQLIQQAGAQ 330
           HRHIQ  GS+QQVALAKQRVDEYIYSQL+QQAG Q
Sbjct: 121 HRHIQLAGSSQQVALAKQRVDEYIYSQLVQQAGTQ 155

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	330
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.642	0.386	0.333	9.9e-23
TAIR|locus:2084908	577	FLK "AT3G04610" [Arabidopsis t	0.590	0.337	0.282	9e-21
TAIR|locus:2035807	479	AT1G14170 "AT1G14170" [Arabido	0.718	0.494	0.291	5.7e-19
ZFIN|ZDB-GENE-070424-78	350	zgc:162999 "zgc:162999" [Danio	0.472	0.445	0.286	2.4e-18
RGD|1307430	319	Pcbp3 "poly(rC) binding protei	0.472	0.489	0.286	2.9e-18
UNIPROTKB|G3V0E8	318	PCBP2 "Poly(RC) binding protei	0.469	0.487	0.278	8.2e-18
FB|FBgn0262737	557	mub "mushroom-body expressed"	0.503	0.298	0.268	8.2e-18
UNIPROTKB|F1NPL2	319	PCBP3 "Uncharacterized protein	0.469	0.485	0.273	8.5e-18
UNIPROTKB|F1NPL4	326	PCBP3 "Uncharacterized protein	0.469	0.475	0.273	9.9e-18
UNIPROTKB|E2RCF9	331	PCBP2 "Uncharacterized protein	0.469	0.468	0.278	1.1e-17

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

 Score = 270 (100.1 bits), Expect = 9.9e-23, P = 9.9e-23
 Identities = 76/228 (33%), Positives = 115/228 (50%)

Query:    17 TEPEPRHDVSG-KRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKI 75
             + P+  +D +G  +RR  G+   S    R    D +FR + P ++IG VIG+ G  ++++
Sbjct:    19 SRPQSDYDDNGGSKRRYRGDDRDSLVIDR---DDTVFRYLCPVKKIGSVIGRGGDIVKQL 75

Query:    76 REEXXXXXXXXXXXXRHEERVIII-SSKDNDNVVSDAENALQ--QIAALILKD----DDS 128
             R +              +ERVI I S  D  N   D E  L   Q A   + D    DD+
Sbjct:    76 RNDTRSKIRIGEAIPGCDERVITIYSPSDETNAFGDGEKVLSPAQDALFRIHDRVVADDA 135

Query:   129 NSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCA 188
              SE S      V A   +LL+   Q GC++G  GQ ++ +R+ +GA I I+    +PLCA
Sbjct:   136 RSEDSPEGEKQVTA---KLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNMPLCA 192

Query:   189 SAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSA 236
                 SD ++QISG+V  V  AL++I ++L ENP R    +S +  Y A
Sbjct:   193 L--NSDELIQISGEVLIVKKALLQIASRLHENPSRSQNLLSSSGGYPA 238

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 208 (78.3 bits), Expect = 9.0e-21, Sum P(2) = 9.0e-21
 Identities = 57/202 (28%), Positives = 104/202 (51%)

Query:    19 PEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREE 78
             PE    +      ED  + G + +      + +FR++VP++++G +IG++G  I+KI EE
Sbjct:   156 PEHLESLQKSEPEEDATVGGEEKRWPGWPGETVFRMLVPAQKVGSIIGRKGDVIKKIVEE 215

Query:    79 XXXXXXXXXXXXRHEERVIIISSKDN-DNVVSDAENALQQIAALILKDDDSNSEASKVAA 137
                            ER +++S K+  ++ +  + + L ++   I+  D  + EAS+ A 
Sbjct:   216 TRARIKILDGPPGTTERAVMVSGKEEPESSLPPSMDGLLRVHMRIV--DGLDGEASQ-AP 272

Query:   138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVV 197
                  +T RLL+  SQAG LIG  G  ++ ++ +S   + +L    LP+ A   + DRVV
Sbjct:   273 PPSKVST-RLLVPASQAGSLIGKQGGTVKAIQEASACIVRVLGSEDLPVFAL--QDDRVV 329

Query:   198 QISGDVPAVLNALVEIGNQLRE 219
             ++ G+  +V  AL  I + LR+
Sbjct:   330 EVVGEPTSVHRALELIASHLRK 351

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

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

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

 Score = 234 (87.4 bits), Expect = 5.7e-19, P = 5.7e-19
 Identities = 78/268 (29%), Positives = 131/268 (48%)

Query:    47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSK---- 102
             ++D ++R + P ++ G +IGK G   ++IR E              EERV+ + S     
Sbjct:    41 SEDTVYRYLCPVKKTGSIIGKGGEIAKQIRSETKSNMRINEALPGCEERVVTMYSTNEEL 100

Query:   103 ----DNDNVVSDAENALQQIAALILKD---DDSNSEASKVAAGHVAANTIRLLIAGSQAG 155
                 D+  +V  A +AL ++  +++ D   DD   + + +  G     T+R+L+   Q G
Sbjct:   101 NHFGDDGELVCPALDALFKVHDMVVADADQDDGTDDDNDL--GEKQTVTVRMLVPSDQIG 158

Query:   156 CLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGN 215
             C+IG  GQ I+ LRN + A I ++  + LP CA     D ++ I G+   V  AL ++ +
Sbjct:   159 CVIGKGGQVIQNLRNDTNAQIRVIK-DHLPACALTLSHDELLLIIGEPLVVREALYQVAS 217

Query:   216 QLRENPPR-QVISISPAYNYSAIRPAQPFVEP--TS-----------ADYVTFEM--LIS 259
              L +NP R Q + +S + + S  +P    +    TS           AD   F +  +  
Sbjct:   218 LLHDNPSRFQHLLLSSSSS-SMHQPGAMLMSAALTSSHRNYAVRRDIADAREFCVCFICP 276

Query:   260 ESLVGGLIGRCGSNISRIRNESGAMIKV 287
                VGG+IG+ G  I++IR E+GA I+V
Sbjct:   277 AENVGGVIGKGGGFINQIRQETGATIRV 304

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

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

 Score = 172 (65.6 bits), Expect = 2.4e-18, Sum P(2) = 2.4e-18
 Identities = 49/171 (28%), Positives = 88/171 (51%)

Query:    53 RIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNVVSDAE 112
             R+++  +++G +IGK+G  ++K+REE               ER++ I+    D +     
Sbjct:    19 RLLMHGKEVGSIIGKKGETVKKMREESSARINVSEGNC--PERIVTITGP-TDAIFK--- 72

Query:   113 NALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172
              A   IA    ++D  NS ++  A       T+RL++  SQ G LIG  G  I+++R S+
Sbjct:    73 -AFAMIAYKF-EEDIINSMSNSQATSKPPV-TLRLVVPASQCGSLIGKGGSKIKEMREST 129

Query:   173 GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223
             GA + + A + LP     + ++R V ISG   A++  + +I   + E+PP+
Sbjct:   130 GAQVQV-AGDMLP-----NSTERAVTISGTPEAIIQCVKQICVVMLESPPK 174

GO:0003723 "RNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

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

 Score = 171 (65.3 bits), Expect = 2.9e-18, Sum P(2) = 2.9e-18
 Identities = 49/171 (28%), Positives = 88/171 (51%)

Query:    53 RIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNVVSDAE 112
             R+++  +++G +IGK+G  ++K+REE               ER++ I+    D +     
Sbjct:    17 RLLMHGKEVGSIIGKKGETVKKMREESGARINISEGNC--PERIVTITGP-TDAIFK--- 70

Query:   113 NALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172
              A   IA    ++D  NS ++  A       T+RL++  SQ G LIG  G  I+++R S+
Sbjct:    71 -AFAMIAYKF-EEDIINSMSNSPATSKPPV-TLRLVVPASQCGSLIGKGGSKIKEIREST 127

Query:   173 GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223
             GA + + A + LP     + ++R V ISG   A++  + +I   + E+PP+
Sbjct:   128 GAQVQV-AGDMLP-----NSTERAVTISGTPDAIIQCVKQICVVMLESPPK 172

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0005829 "cytosol" evidence=IEA;ISO

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

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|G3V0E8 PCBP2 "Poly(RC) binding protein 2, isoform CRA_f" [Homo sapiens (taxid:9606)]

 Score = 169 (64.5 bits), Expect = 8.2e-18, Sum P(2) = 8.2e-18
 Identities = 49/176 (27%), Positives = 93/176 (52%)

Query:    53 RIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNVVSDAE 112
             R+++  +++G +IGK+G  ++K+REE               ER+I ++   N        
Sbjct:    17 RLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC--PERIITLAGPTN-------- 66

Query:   113 NALQQIAALI---LKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
              A+ +  A+I   L++D S+S  +  AA      T+RL++  SQ G LIG  G  I+++R
Sbjct:    67 -AIFKAFAMIIDKLEEDISSSMTNSTAASRPPV-TLRLVVPASQCGSLIGKGGCKIKEIR 124

Query:   170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV 225
              S+GA + + A + LP     + ++R + I+G   +++  + +I   + E+PP+ V
Sbjct:   125 ESTGAQVQV-AGDMLP-----NSTERAITIAGIPQSIIECVKQICVVMLESPPKGV 174

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 174 (66.3 bits), Expect = 8.2e-18, Sum P(2) = 8.2e-18
 Identities = 50/186 (26%), Positives = 87/186 (46%)

Query:    38 GSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVI 97
             G+  K    +  +  R+I+  +++G +IGK+G  + + REE               ER++
Sbjct:    12 GASIKHEDPSVTLTIRLIMQGKEVGSIIGKKGEIVNRFREESGAKINISDGSC--PERIV 69

Query:    98 IISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCL 157
                       VS   NA+     LI K  +  ++  KV    +    IRL++  SQ G L
Sbjct:    70 ---------TVSGTTNAIFSAFTLITKKFEEFNDVGKVGKTQIP---IRLIVPASQCGSL 117

Query:   158 IGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL 217
             IG SG  I+++R ++G +I + A   LP     + ++R V +SG    +   + +I   +
Sbjct:   118 IGKSGSKIKEIRQTTGCSIQV-ASEMLP-----NSTERAVTLSGSAEQITQCIYQICLVM 171

Query:   218 RENPPR 223
              E+PPR
Sbjct:   172 LESPPR 177

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

GO:0005634 "nucleus" evidence=IC

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

UNIPROTKB|F1NPL2 PCBP3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 173 (66.0 bits), Expect = 8.5e-18, Sum P(2) = 8.5e-18
 Identities = 47/172 (27%), Positives = 89/172 (51%)

Query:    53 RIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNVVSDAE 112
             R+++  +++G +IGK+G  ++K+REE               ER++ I+        +DA 
Sbjct:    17 RLLMHGKEVGSIIGKKGETVKKMREESGARINISEGSC--PERIVTITGP------TDA- 67

Query:   113 NALQQIAALILK-DDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171
                +  + + LK ++D N+  +          T+RL++  SQ G LIG  G  I+++R S
Sbjct:    68 -IFKAFSMIALKFEEDINASMTNSTVTSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRES 126

Query:   172 SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223
             +GA + + A + LP     + ++R V ISG   A++  + +I   + E+PP+
Sbjct:   127 TGAQVQV-AGDMLP-----NSTERAVTISGTPDAIIQCVKQICVVMLESPPK 172

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 173 (66.0 bits), Expect = 9.9e-18, Sum P(2) = 9.9e-18
 Identities = 47/172 (27%), Positives = 89/172 (51%)

Query:    53 RIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNVVSDAE 112
             R+++  +++G +IGK+G  ++K+REE               ER++ I+        +DA 
Sbjct:    17 RLLMHGKEVGSIIGKKGETVKKMREESGARINISEGSC--PERIVTITGP------TDA- 67

Query:   113 NALQQIAALILK-DDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171
                +  + + LK ++D N+  +          T+RL++  SQ G LIG  G  I+++R S
Sbjct:    68 -IFKAFSMIALKFEEDINASMTNSTVTSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRES 126

Query:   172 SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223
             +GA + + A + LP     + ++R V ISG   A++  + +I   + E+PP+
Sbjct:   127 TGAQVQV-AGDMLP-----NSTERAVTISGTPDAIIQCVKQICVVMLESPPK 172

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|E2RCF9 PCBP2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 169 (64.5 bits), Expect = 1.1e-17, Sum P(2) = 1.1e-17
 Identities = 49/176 (27%), Positives = 93/176 (52%)

Query:    53 RIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNVVSDAE 112
             R+++  +++G +IGK+G  ++K+REE               ER+I ++   N        
Sbjct:    17 RLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC--PERIITLAGPTN-------- 66

Query:   113 NALQQIAALI---LKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
              A+ +  A+I   L++D S+S  +  AA      T+RL++  SQ G LIG  G  I+++R
Sbjct:    67 -AIFKAFAMIIDKLEEDISSSMTNSTAASRPPV-TLRLVVPASQCGSLIGKGGCKIKEIR 124

Query:   170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV 225
              S+GA + + A + LP     + ++R + I+G   +++  + +I   + E+PP+ V
Sbjct:   125 ESTGAQVQV-AGDMLP-----NSTERAITIAGIPQSIIECVKQICVVMLESPPKGV 174

GO:0003723 "RNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	330
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	4e-15
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	7e-12
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-10
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-09
pfam00013	59	pfam00013, KH_1, KH domain	1e-08
pfam00013	59	pfam00013, KH_1, KH domain	2e-08
smart00322	68	smart00322, KH, K homology RNA-binding domain	6e-08
smart00322	68	smart00322, KH, K homology RNA-binding domain	7e-08
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	5e-07
pfam13014	42	pfam13014, KH_3, KH domain	8e-07
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	7e-06
pfam00013	59	pfam00013, KH_1, KH domain	8e-06
pfam13014	42	pfam13014, KH_3, KH domain	2e-04
cd02134	61	cd02134, NusA_KH, NusA_K homology RNA-binding doma	3e-04
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	4e-04
smart00322	68	smart00322, KH, K homology RNA-binding domain	5e-04
pfam13014	42	pfam13014, KH_3, KH domain	0.001
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	0.001
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	0.001
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	0.002

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

 Score = 68.7 bits (169), Expect = 4e-15
 Identities = 29/70 (41%), Positives = 41/70 (58%), Gaps = 6/70 (8%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T+RLL+  SQAG +IG  G  I+++R  +GA I +   + LP       ++RVV ISG  
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVS-KSVLPGS-----TERVVTISGKP 54

Query: 204 PAVLNALVEI 213
            AV  AL+ I
Sbjct: 55  SAVQKALLLI 64

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 = 59.8 bits (146), Expect = 7e-12
 Identities = 28/69 (40%), Positives = 40/69 (57%), Gaps = 6/69 (8%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARH-EERVIIISSKDNDNVVSD 110
            R++VPS Q G +IGK G  I++IREET A I+++ ++     ERV+ IS K      S 
Sbjct: 2   LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK-----PSA 56

Query: 111 AENALQQIA 119
            + AL  I 
Sbjct: 57  VQKALLLIL 65

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

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

 Score = 56.0 bits (136), Expect = 1e-10
 Identities = 23/63 (36%), Positives = 35/63 (55%)

Query: 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAK 312
           T  +L+  SLVG +IG+ GS I  IR E+GA IK+       + R +   G+ + V  AK
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60

Query: 313 QRV 315
           + +
Sbjct: 61  ELI 63

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

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

 Score = 53.3 bits (129), Expect = 1e-09
 Identities = 27/67 (40%), Positives = 40/67 (59%), Gaps = 5/67 (7%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
            R++VPS  +G++IGK G  I++IREET A IKI D+ +  EER++ I+           
Sbjct: 2   ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT-----PEAV 56

Query: 112 ENALQQI 118
           E A + I
Sbjct: 57  EKAKELI 63

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

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

 Score = 50.3 bits (121), Expect = 1e-08
 Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 4/63 (6%)

Query: 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAK 312
           T  +LI    VG +IG+ GSNI  IR E+G  I++   + +     +   G+ +QV  AK
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDRDD----TVTISGTPEQVEKAK 56

Query: 313 QRV 315
           + +
Sbjct: 57  ELI 59

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

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 9/67 (13%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
            RI++P  ++G++IGK G  I++IREET   I+I D     ++ V I  + +        
Sbjct: 2   ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD---DRDDTVTISGTPEQ------V 52

Query: 112 ENALQQI 118
           E A + I
Sbjct: 53  EKAKELI 59

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

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

 Score = 48.8 bits (117), Expect = 6e-08
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 7/70 (10%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            +++P+ ++G +IGK G  I+KI EET   I I       EERV+ I+         + E
Sbjct: 6   EVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG--SEERVVEITGPP-----ENVE 58

Query: 113 NALQQIAALI 122
            A + I  ++
Sbjct: 59  KAAELILEIL 68

Length = 68

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

 Score = 48.4 bits (116), Expect = 7e-08
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
           VT E+LI    VG +IG+ GS I +I  E+G  I + G   E++   I   G  + V  A
Sbjct: 3   VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEIT--GPPENVEKA 60

Query: 312 KQRVDEYI 319
            + + E +
Sbjct: 61  AELILEIL 68

Length = 68

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

 Score = 46.0 bits (110), Expect = 5e-07
 Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 7/70 (10%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T R+L+  S  G +IG  G  I+++R  +GA I I               +R+V I+G  
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-------GSEERIVTITGTP 53

Query: 204 PAVLNALVEI 213
            AV  A   I
Sbjct: 54  EAVEKAKELI 63

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

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

 Score = 44.9 bits (107), Expect = 8e-07
 Identities = 17/41 (41%), Positives = 25/41 (60%)

Query: 60  QIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS 100
            +G +IGK G  I++IREET A I+I        ER++ I+
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTIT 41

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

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

 Score = 42.8 bits (102), Expect = 7e-06
 Identities = 16/38 (42%), Positives = 22/38 (57%)

Query: 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG 290
           T  +L+  S  G +IG+ GS I  IR E+GA I+V   
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKS 38

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|215657 pfam00013, KH_1, KH domain

 Score = 42.2 bits (100), Expect = 8e-06
 Identities = 22/70 (31%), Positives = 30/70 (42%), Gaps = 11/70 (15%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T R+LI   + G +IG  G NI+++R  +G  I I             + D  V ISG  
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD-----------DRDDTVTISGTP 49

Query: 204 PAVLNALVEI 213
             V  A   I
Sbjct: 50  EQVEKAKELI 59

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

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

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 15/42 (35%), Positives = 22/42 (52%)

Query: 262 LVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGG 303
           LVG +IG+ G  I  IR E+GA I++   +     R +   G
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42

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

>gnl|CDD|239049 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH)

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

Query: 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI 85
           R++VP  Q+G  IGK G  ++   +     I I
Sbjct: 27 ARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60

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. Length = 61

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

 Score = 41.7 bits (99), Expect = 4e-04
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 10/72 (13%)

Query: 51  LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSD 110
           +  I +   +I  VIG  G  I++I EET A I I D      +  + I++ D +     
Sbjct: 552 IETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEA---- 601

Query: 111 AENALQQIAALI 122
           AE A++ I  + 
Sbjct: 602 AEAAIKMIEGIT 613

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

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

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 9/74 (12%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TI +LI   + G +IG  G  I+K+   +G  I I  P            +RVV+I+G  
Sbjct: 4   TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG---------SEERVVEITGPP 54

Query: 204 PAVLNALVEIGNQL 217
             V  A   I   L
Sbjct: 55  ENVEKAAELILEIL 68

Length = 68

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

 Score = 35.6 bits (83), Expect = 0.001
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 7/49 (14%)

Query: 153 QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG 201
             G +IG  G+ I+++R  +GA I I  P            +R+V I+G
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPE-------PGSGERIVTITG 42

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

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

 Score = 36.7 bits (86), Expect = 0.001
 Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 4/64 (6%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + +P +    +IGK+G  I+KI EET   I+  D  ++ +  + I   K+N   V  A+
Sbjct: 3   EVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDT-ITITGPKEN---VEKAK 58

Query: 113 NALQ 116
             + 
Sbjct: 59  EEIL 62

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

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

 Score = 40.4 bits (96), Expect = 0.001
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 13/73 (17%)

Query: 53  RII---VPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           RI    +P  +I  VIG  G  I++I EET A I I D      +  + I++ D +    
Sbjct: 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDGEA--- 604

Query: 110 DAENALQQIAALI 122
            AE A ++I  + 
Sbjct: 605 -AEAAKERIEGIT 616

Length = 693

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

 Score = 39.9 bits (94), Expect = 0.002
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 10/66 (15%)

Query: 56  VPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENAL 115
           +   +I  VIG  G  I+ I EET   I I D      +  + I++ D ++    A+ A 
Sbjct: 558 IDPDKIRDVIGPGGKTIKAITEETGVKIDIED------DGTVKIAASDGES----AKKAK 607

Query: 116 QQIAAL 121
           ++I A+
Sbjct: 608 ERIEAI 613

Length = 692

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	330
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	100.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	100.0
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.98
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.97
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.92
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.81
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.72
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.72
PRK13763	180	putative RNA-processing protein; Provisional	99.67
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.64
PRK13763	180	putative RNA-processing protein; Provisional	99.6
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.51
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.42
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.41
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.39
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.38
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.33
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.31
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.14
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.12
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.12
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	99.1
PF13014	43	KH_3: KH domain	99.06
COG1094	194	Predicted RNA-binding protein (contains KH domains	99.03
smart00322	69	KH K homology RNA-binding domain.	99.03
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.03
PF13014	43	KH_3: KH domain	99.03
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.86
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.84
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.77
smart00322	69	KH K homology RNA-binding domain.	98.74
KOG2113	394	consensus Predicted RNA binding protein, contains	98.58
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.56
KOG2113	394	consensus Predicted RNA binding protein, contains	98.44
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.42
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.19
PRK08406	140	transcription elongation factor NusA-like protein;	98.02
PRK08406	140	transcription elongation factor NusA-like protein;	97.98
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.83
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.65
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.58
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.58
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.53
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.47
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.42
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	97.38
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.31
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.24
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	97.24
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.22
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.05
KOG2814	345	consensus Transcription coactivator complex, P50 c	97.03
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.96
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.93
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.92
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.84
PRK00106	535	hypothetical protein; Provisional	96.82
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.79
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.77
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.76
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.7
PRK12704	520	phosphodiesterase; Provisional	96.68
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.65
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.5
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.45
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.34
PRK00468	75	hypothetical protein; Provisional	96.14
TIGR01953	341	NusA transcription termination factor NusA. This m	96.12
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.04
PRK02821	77	hypothetical protein; Provisional	95.98
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.78
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.72
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.63
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.61
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.56
PRK01064	78	hypothetical protein; Provisional	95.5
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	95.44
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.44
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.42
PRK12705	508	hypothetical protein; Provisional	95.36
TIGR01953	341	NusA transcription termination factor NusA. This m	95.31
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.16
PRK00468	75	hypothetical protein; Provisional	95.15
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.1
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	95.01
PRK02821	77	hypothetical protein; Provisional	94.98
PRK12704	520	phosphodiesterase; Provisional	94.91
PRK12329	449	nusA transcription elongation factor NusA; Provisi	94.83
PRK00106	535	hypothetical protein; Provisional	94.66
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	94.63
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	94.54
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	94.07
COG1837	76	Predicted RNA-binding protein (contains KH domain)	94.03
PRK01064	78	hypothetical protein; Provisional	93.69
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	93.39
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	93.31
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	92.7
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	91.9
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	91.43
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	91.25
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	91.08
COG5166	657	Uncharacterized conserved protein [Function unknow	90.9
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	90.54
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	90.54
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	90.04
PRK12705	508	hypothetical protein; Provisional	89.99
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	89.89
KOG2874	356	consensus rRNA processing protein [Translation, ri	89.64
KOG2874	356	consensus rRNA processing protein [Translation, ri	89.61
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	88.73
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	88.04
COG5166	657	Uncharacterized conserved protein [Function unknow	87.43
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	87.2
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	87.04
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	86.94
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	86.2
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	85.75
COG1855	604	ATPase (PilT family) [General function prediction	85.68
PRK13764	602	ATPase; Provisional	85.24
PRK13764	602	ATPase; Provisional	84.9
COG1855	604	ATPase (PilT family) [General function prediction	84.59
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	83.14
PRK06418	166	transcription elongation factor NusA-like protein;	82.78
PRK06418	166	transcription elongation factor NusA-like protein;	80.56
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	80.38

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

Probab=100.00  E-value=1e-38  Score=274.27  Aligned_cols=276  Identities=29%  Similarity=0.455  Sum_probs=219.4

Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcce
Q 020173           16 VTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEER   95 (330)
Q Consensus        16 ~~~~~~~~~~~~kr~~~~~~~~~~~~~~~~~~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~er   95 (330)
                      +.++.++.+..+||+.+|+.   ..+.   +...+.++||+.++.+|+||||+|+|||.|+.++++.|+|+++  ++++|
T Consensus        20 ~~~~~e~g~~~gkrp~~d~~---~qa~---k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~per   91 (390)
T KOG2192|consen   20 TFPNTETGGEFGKRPAEDME---EQAF---KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPER   91 (390)
T ss_pred             cCCCCcccccccCCcchhhH---HHHh---hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCce
Confidence            45667777778999999986   2222   3356999999999999999999999999999999999999998  68999


Q ss_pred             EEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCe
Q 020173           96 VIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT  175 (330)
Q Consensus        96 vi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~  175 (330)
                      +|+|+...     +.+-+-++.|.-.+.+..           .....+++||||+.+++|.|||++|+.||+|++++.++
T Consensus        92 i~tisad~-----~ti~~ilk~iip~lee~f-----------~~~~pce~rllihqs~ag~iigrngskikelrekcsar  155 (390)
T KOG2192|consen   92 ILTISADI-----ETIGEILKKIIPTLEEGF-----------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSAR  155 (390)
T ss_pred             eEEEeccH-----HHHHHHHHHHhhhhhhCC-----------CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhh
Confidence            99999874     334444444444443332           12245789999999999999999999999999999999


Q ss_pred             EEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCC-cccCCC-----CCCCCCC-----------
Q 020173          176 IVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV-ISISPA-----YNYSAIR-----------  238 (330)
Q Consensus       176 I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~-~~~~~~-----~~~~~~~-----------  238 (330)
                      ++|...     |+ +++++|+|.+.|.+.+|..+++.|++.|.+.|.++. .+|.|+     |.|..+.           
T Consensus       156 lkift~-----c~-p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pg  229 (390)
T KOG2192|consen  156 LKIFTE-----CC-PHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPG  229 (390)
T ss_pred             hhhhhc-----cC-CCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCC
Confidence            999752     43 479999999999999999999999999999987763 223222     2222210           


Q ss_pred             C---------CCC-----------------C---------------------------CC-------------------C
Q 020173          239 P---------AQP-----------------F---------------------------VE-------------------P  246 (330)
Q Consensus       239 ~---------~~~-----------------~---------------------------~~-------------------~  246 (330)
                      +         +.|                 |                           .+                   +
T Consensus       230 papqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGd  309 (390)
T KOG2192|consen  230 PAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGD  309 (390)
T ss_pred             CCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCC
Confidence            0         000                 0                           00                   0


Q ss_pred             CCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          247 TSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       247 ~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      -.....+.++.||.++-|.|||++|+.|++|++++||.|++..+..++.+|+++|+||.+|++.|++|++.-+..
T Consensus       310 lGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq  384 (390)
T KOG2192|consen  310 LGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ  384 (390)
T ss_pred             CCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence            123457889999999999999999999999999999999999988889999999999999999999999877663

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

Probab=100.00  E-value=2.8e-36  Score=273.49  Aligned_cols=267  Identities=25%  Similarity=0.441  Sum_probs=218.7

Q ss_pred             CCCccccCCCCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC-CCCCcceEEEEecCCCCcchhHHHHHHH
Q 020173           38 GSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQ  116 (330)
Q Consensus        38 ~~~~~~~~~~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervi~I~G~~~~~~~~~~~~A~~  116 (330)
                      .+++..+....+..+|++||..++|.||||.|++||.|.+.|.|+|+|... ..+..|++++|-|++     +.+.+|+.
T Consensus       187 ~~G~~~~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tp-----Eg~s~Ac~  261 (584)
T KOG2193|consen  187 HSGPHHKQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTP-----EGTSKACK  261 (584)
T ss_pred             CCCCcccccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCc-----cchHHHHH
Confidence            356666777889999999999999999999999999999999999999865 457889999999998     56789999


Q ss_pred             HHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcE
Q 020173          117 QIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRV  196 (330)
Q Consensus       117 ~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~  196 (330)
                      +|++++..+.......        ....++++.++..+|++|||.|++||+|+.+||++|.|++-.++..+    +.+|.
T Consensus       262 ~ILeimqkEA~~~k~~--------~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~y----npERT  329 (584)
T KOG2193|consen  262 MILEIMQKEAVDDKVA--------EEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLY----NPERT  329 (584)
T ss_pred             HHHHHHHHhhhccchh--------hhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhccc----Cccce
Confidence            9999998765433221        34578999999999999999999999999999999999986666553    68999


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHhhCCCCCCc------ccCCCCCCCCCCC-------CCCCCCC-------------CCCc
Q 020173          197 VQISGDVPAVLNALVEIGNQLRENPPRQVI------SISPAYNYSAIRP-------AQPFVEP-------------TSAD  250 (330)
Q Consensus       197 v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~------~~~~~~~~~~~~~-------~~~~~~~-------------~~~~  250 (330)
                      |++.|+.++|.+|..+|+++|++....+..      ...|.+|.+..++       ..|+.+|             ....
T Consensus       330 ItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe  409 (584)
T KOG2193|consen  330 ITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPE  409 (584)
T ss_pred             EEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcc
Confidence            999999999999999999999987554421      1223333222211       1111111             1235


Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC-CCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK-GEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~-~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      ....+|.||...+|+|||++|.+||.|.+.+||.|+|.++. ++..+|.|+|+|.+++.-+|+.+|...|.+
T Consensus       410 ~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikE  481 (584)
T KOG2193|consen  410 QEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKE  481 (584)
T ss_pred             hhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhh
Confidence            57789999999999999999999999999999999999875 366799999999999999999999877765

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

Probab=100.00  E-value=1.5e-34  Score=273.88  Aligned_cols=254  Identities=24%  Similarity=0.323  Sum_probs=206.0

Q ss_pred             CCCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhc
Q 020173           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (330)
Q Consensus        46 ~~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~  125 (330)
                      ...-++.+..||...+|+||||+|+.|..|..++||+|++.....+..+|-|.+.|.+     +++..|..++.+++...
T Consensus        50 s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~p-----e~v~~aK~li~evv~r~  124 (600)
T KOG1676|consen   50 SDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSP-----ENVEVAKQLIGEVVSRG  124 (600)
T ss_pred             cccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCc-----ccHHHHHHhhhhhhhcc
Confidence            3356788999999999999999999999999999999998776656789999999998     57788888888876554


Q ss_pred             CCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHH
Q 020173          126 DDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPA  205 (330)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~  205 (330)
                      ......   ...-.....+.+++||...+|+||||+|++||.|++.+||++.+........     ..++.+.|+|+++.
T Consensus       125 ~~~~~~---~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~-----~~~KplritGdp~~  196 (600)
T KOG1676|consen  125 RPPGGF---PDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT-----GADKPLRITGDPDK  196 (600)
T ss_pred             CCCCCc---cccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC-----CCCCceeecCCHHH
Confidence            311110   0011134568999999999999999999999999999999999887654433     36788999999999


Q ss_pred             HHHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeE
Q 020173          206 VLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMI  285 (330)
Q Consensus       206 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I  285 (330)
                      |..|..+|.++|++......-+. ..++.            ......+++|.||++.||.||||+|++||+|+.+||++|
T Consensus       197 ve~a~~lV~dil~e~~~~~~g~~-~~~g~------------~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KI  263 (600)
T KOG1676|consen  197 VEQAKQLVADILREEDDEVPGSG-GHAGV------------RGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKI  263 (600)
T ss_pred             HHHHHHHHHHHHHhcccCCCccc-cccCc------------CccccceeEEeccccceeeEEecCchHHHHHhhccCcee
Confidence            99999999999997432211110 11111            112335899999999999999999999999999999999


Q ss_pred             EEeCCCC-CCceeEEEEEcCHHHHHHHHHHHHHHHHHHHHH
Q 020173          286 KVYGGKG-EQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQ  325 (330)
Q Consensus       286 ~i~~~~~-~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~~~  325 (330)
                      +|.++.+ .+.+|.+.|.|+.++|+.|.+||.++|.+....
T Consensus       264 QfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~  304 (600)
T KOG1676|consen  264 QFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG  304 (600)
T ss_pred             EeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence            9998876 567999999999999999999999999887543

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

Probab=100.00  E-value=2.4e-34  Score=272.41  Aligned_cols=249  Identities=24%  Similarity=0.371  Sum_probs=200.6

Q ss_pred             CCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC-C-CCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhh
Q 020173           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-I-ARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (330)
Q Consensus        47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~-~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~  124 (330)
                      ..+++..|+||++.+|+||||+|++||+|++.+||++.+-.. . ..+..+.+.|+|.+     ..++.|..+++++|.+
T Consensus       136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp-----~~ve~a~~lV~dil~e  210 (600)
T KOG1676|consen  136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDP-----DKVEQAKQLVADILRE  210 (600)
T ss_pred             ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCH-----HHHHHHHHHHHHHHHh
Confidence            456899999999999999999999999999999999987643 2 12267889999987     7889999999999987


Q ss_pred             cCCCCcccc-ccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH
Q 020173          125 DDDSNSEAS-KVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV  203 (330)
Q Consensus       125 ~~~~~~~~~-~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~  203 (330)
                      ++....... ..........+.++-||+..||.||||+|++||+|+.+||++|+|.+ |..|.     +.+|.+.|.|+.
T Consensus       211 ~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkp-Dd~p~-----speR~~~IiG~~  284 (600)
T KOG1676|consen  211 EDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKP-DDDPS-----SPERPAQIIGTV  284 (600)
T ss_pred             cccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeec-CCCCC-----CccceeeeecCH
Confidence            554432221 11111122348999999999999999999999999999999999975 44443     689999999999


Q ss_pred             HHHHHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCC
Q 020173          204 PAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGA  283 (330)
Q Consensus       204 ~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga  283 (330)
                      +.|..|.++|.++|.+.....    ...++.+         .|  .....+.|.||.+.+|.|||++|++||.|..+|||
T Consensus       285 d~ie~Aa~lI~eii~~~~~~~----~~~~~~G---------~P--~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA  349 (600)
T KOG1676|consen  285 DQIEHAAELINEIIAEAEAGA----GGGMGGG---------AP--GLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGA  349 (600)
T ss_pred             HHHHHHHHHHHHHHHHHhccC----CCCcCCC---------Cc--cceeeEEEeccccccccccCCCccchhhhcccCCc
Confidence            999999999999998762211    0001111         11  11138899999999999999999999999999999


Q ss_pred             eEEEeCCC--CCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          284 MIKVYGGK--GEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       284 ~I~i~~~~--~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      ++.++++.  .+..+++|+|+|++.+|+.|++||.+.+..
T Consensus       350 ~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~  389 (600)
T KOG1676|consen  350 RCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGD  389 (600)
T ss_pred             cccccCCCCCCCccceEEEEecCcccchHHHHHHHHHhcc
Confidence            99999872  245799999999999999999999988754

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

Probab=100.00  E-value=2.2e-31  Score=235.16  Aligned_cols=295  Identities=22%  Similarity=0.304  Sum_probs=214.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCccccCCC-CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC---CCCC
Q 020173           17 TEPEPRHDVSGKRRREDGEIEGSDPKRRAKA-QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARH   92 (330)
Q Consensus        17 ~~~~~~~~~~~kr~~~~~~~~~~~~~~~~~~-~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~---~~~~   92 (330)
                      .+.+.+...+.||..+..+............ ..+.++||||+..+|.||||+|++|.+|+++|||+|++++.   .|++
T Consensus         5 ~~~d~~~~~s~kr~~~a~pe~~~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGT   84 (402)
T KOG2191|consen    5 VPIDSDAPDSRKRPLEAPPEPGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGT   84 (402)
T ss_pred             CcccCCCCCCccccccCCCCccccccccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCc
Confidence            3456666778888888766222222222222 34999999999999999999999999999999999999865   6899


Q ss_pred             cceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCccccc--cccCCCcceEEEEEeeccccceecCCCChhHHHHHH
Q 020173           93 EERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASK--VAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRN  170 (330)
Q Consensus        93 ~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~--~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~  170 (330)
                      .||||.|+|+-     +.+...+.-|.++|.+..........  .+...++...+++++|+..+|.||||+|.+||.+++
T Consensus        85 TeRvcli~Gt~-----eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~E  159 (402)
T KOG2191|consen   85 TERVCLIQGTV-----EALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQE  159 (402)
T ss_pred             cceEEEEeccH-----HHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHH
Confidence            99999999984     55666666667766654332111000  111233445799999999999999999999999999


Q ss_pred             HhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCC---cccC----CCCCCCCCCCCCCC
Q 020173          171 SSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV---ISIS----PAYNYSAIRPAQPF  243 (330)
Q Consensus       171 ~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~---~~~~----~~~~~~~~~~~~~~  243 (330)
                      ++||+|+|++......    ...+|++++.|+++++.+|..+|+.+|.++|++..   .+|.    +.-|+++.  ..||
T Consensus       160 qsga~iqisPqkpt~~----sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpvaNsnPt--Gspy  233 (402)
T KOG2191|consen  160 QSGAWIQISPQKPTGI----SLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPVANSNPT--GSPY  233 (402)
T ss_pred             hhCcceEecccCCCCc----cceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCcccccCCC--CCCC
Confidence            9999999995332111    14789999999999999999999999999998763   1111    11122211  1222


Q ss_pred             CCC--CCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC---CCceeEEEEEcCHHHHHHHHHHHHHH
Q 020173          244 VEP--TSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG---EQKHRHIQFGGSAQQVALAKQRVDEY  318 (330)
Q Consensus       244 ~~~--~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~---~~~~r~v~I~Gt~~~v~~A~~~I~~~  318 (330)
                      ...  ..........-++....|..-|.+|.++-.|...+|+.+.++...+   ....+ +.+.|.+-++..|-.+|...
T Consensus       234 a~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~  312 (402)
T KOG2191|consen  234 AYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMAGYGYN-TNILGLGLSILAAEGVLAAK  312 (402)
T ss_pred             CCCCccccccchhhccccccccccccccccccceeeecccccceeeccccccccccccc-ccccchhhhhhhhhhHHHHh
Confidence            221  2233345567789999999999999999999999999999987533   33444 77888888888888877766


Q ss_pred             HHHHH
Q 020173          319 IYSQL  323 (330)
Q Consensus       319 i~~~~  323 (330)
                      ...+.
T Consensus       313 ~~~a~  317 (402)
T KOG2191|consen  313 VASAN  317 (402)
T ss_pred             hcccC
Confidence            55443

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

Probab=99.98  E-value=2.1e-30  Score=248.96  Aligned_cols=265  Identities=30%  Similarity=0.511  Sum_probs=202.1

Q ss_pred             CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCC
Q 020173           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD  127 (330)
Q Consensus        48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~  127 (330)
                      ...++|||++.+.+|.||||+|..|++|+++|.++|+|.+..+++++|+++|+|...+....++.+|+.++.+.+.....
T Consensus        41 ~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~  120 (485)
T KOG2190|consen   41 ETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLE  120 (485)
T ss_pred             CcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccc
Confidence            34559999999999999999999999999999999999999999999999999933322345566677666666554321


Q ss_pred             ----CCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH
Q 020173          128 ----SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV  203 (330)
Q Consensus       128 ----~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~  203 (330)
                          ...+...  ......+++||+||..++|.||||+|+.||+|+++|||+|.+... ++|.|     ++|.|+|.|.+
T Consensus       121 ~d~~~~~d~~~--~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~s-----ter~V~IsG~~  192 (485)
T KOG2190|consen  121 EDDEAAEDNGE--DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPNS-----TERAVTISGEP  192 (485)
T ss_pred             ccccccccCCc--cccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCcc-----cceeEEEcCch
Confidence                1111111  111124789999999999999999999999999999999999764 89985     78889999999


Q ss_pred             HHHHHHHHHHHHHHhhCCCCC------CcccCC----------CCCCCC-----C--------------CCC--------
Q 020173          204 PAVLNALVEIGNQLRENPPRQ------VISISP----------AYNYSA-----I--------------RPA--------  240 (330)
Q Consensus       204 ~~v~~A~~~I~~~i~~~~~~~------~~~~~~----------~~~~~~-----~--------------~~~--------  240 (330)
                      ++|.+|+..|...|.++++..      ...|.|          ++....     .              .+.        
T Consensus       193 ~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g  272 (485)
T KOG2190|consen  193 DAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIG  272 (485)
T ss_pred             HHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeec
Confidence            999999999999999954221      122222          111000     0              000        


Q ss_pred             --------------------CCCCC----------C-----------------------CC-CcceEEEEEEccccccce
Q 020173          241 --------------------QPFVE----------P-----------------------TS-ADYVTFEMLISESLVGGL  266 (330)
Q Consensus       241 --------------------~~~~~----------~-----------------------~~-~~~~~~~v~IP~~~vg~I  266 (330)
                                          .+...          +                       .. ....+.++.||++++|+|
T Consensus       273 ~~~~~i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igci  352 (485)
T KOG2190|consen  273 KGGLVIRALRNETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCI  352 (485)
T ss_pred             CCCccchhhhhhcCCceEeccccCcceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCcccccee
Confidence                                00000          0                       00 233678999999999999


Q ss_pred             ecCCCchHHHHHHHhCCeEEEeCCCC--CCceeEEEEEcCHHHHHHHHHHHHHHHH
Q 020173          267 IGRCGSNISRIRNESGAMIKVYGGKG--EQKHRHIQFGGSAQQVALAKQRVDEYIY  320 (330)
Q Consensus       267 IGk~G~~Ik~i~~~tga~I~i~~~~~--~~~~r~v~I~Gt~~~v~~A~~~I~~~i~  320 (330)
                      |||+|.+|.+|++.|||.|.|.+...  ...++.++|+|+..+...|+.++...+.
T Consensus       353 iGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~  408 (485)
T KOG2190|consen  353 IGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLS  408 (485)
T ss_pred             ecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhcccccc
Confidence            99999999999999999999998766  6789999999999999999999865543

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

Probab=99.97  E-value=7.8e-31  Score=238.13  Aligned_cols=245  Identities=23%  Similarity=0.358  Sum_probs=199.6

Q ss_pred             CCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC---CCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 020173           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (330)
Q Consensus        47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~---~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~  123 (330)
                      ..+++++++..+.++|++|||.|.+||+|+++||++|.|++-   .-.++||.|+|.|+-     +.+..|-.+|...+.
T Consensus       277 ~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsi-----Eac~~AE~eImkKlr  351 (584)
T KOG2193|consen  277 AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSI-----EACVQAEAEIMKKLR  351 (584)
T ss_pred             hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccH-----HHHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999999999874   235689999999974     556666666666665


Q ss_pred             hcCCCCc--------------------c------------ccccc--------cCCCcceEEEEEeeccccceecCCCCh
Q 020173          124 KDDDSNS--------------------E------------ASKVA--------AGHVAANTIRLLIAGSQAGCLIGMSGQ  163 (330)
Q Consensus       124 ~~~~~~~--------------------~------------~~~~~--------~~~~~~~~~~llip~~~~g~iIG~~G~  163 (330)
                      +......                    .            +..+.        ..+.....++++||...+|.|||++|.
T Consensus       352 e~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~  431 (584)
T KOG2193|consen  352 ECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQ  431 (584)
T ss_pred             HHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcch
Confidence            4322100                    0            00000        112345678999999999999999999


Q ss_pred             hHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCC
Q 020173          164 NIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPF  243 (330)
Q Consensus       164 ~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (330)
                      +||.|...+|+.|+|.+.+ .|.     ..+|.|+|+|++++..+|..+|..+|.+...                     
T Consensus       432 hIKql~RfagASiKIappE-~pd-----vseRMViItGppeaqfKAQgrifgKikEenf---------------------  484 (584)
T KOG2193|consen  432 HIKQLSRFAGASIKIAPPE-IPD-----VSERMVIITGPPEAQFKAQGRIFGKIKEENF---------------------  484 (584)
T ss_pred             hHHHHHHhccceeeecCCC-CCC-----cceeEEEecCChHHHHhhhhhhhhhhhhhcc---------------------
Confidence            9999999999999998654 444     5789999999999999999999999988721                     


Q ss_pred             CCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC--CCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          244 VEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG--EQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       244 ~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~--~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      ..|.........+.||...+|+||||||.++++|+..|+|.+.||++..  +.+.-+|.|.|.....+.|+..|.+++..
T Consensus       485 ~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~q  564 (584)
T KOG2193|consen  485 FLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVNQ  564 (584)
T ss_pred             CCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHHH
Confidence            1123455678899999999999999999999999999999999998754  34567889999999999999999999876


Q ss_pred             HH
Q 020173          322 QL  323 (330)
Q Consensus       322 ~~  323 (330)
                      .-
T Consensus       565 vk  566 (584)
T KOG2193|consen  565 VK  566 (584)
T ss_pred             HH
Confidence            54

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

Probab=99.92  E-value=3.8e-24  Score=189.47  Aligned_cols=168  Identities=26%  Similarity=0.375  Sum_probs=139.6

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCC-CCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP-NQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~-~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      ..+.+++|||+..+|.||||+|++|.+|+.++||+|++++. |.+|.     .+||+|.|+|+.+++....+.|+++|++
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPG-----TTeRvcli~Gt~eai~av~efI~dKire  111 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG-----TTERVCLIQGTVEALNAVHEFIADKIRE  111 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCC-----ccceEEEEeccHHHHHHHHHHHHHHHHH
Confidence            34789999999999999999999999999999999999874 44564     7999999999999999999999999999


Q ss_pred             CCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC---CCce
Q 020173          220 NPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG---EQKH  296 (330)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~---~~~~  296 (330)
                      .+......+         -..+|.-   .+....+++.+|+.-+|.||||+|.+||.+++++||+|+|.+.++   .-.+
T Consensus       112 ~p~~~~k~v---------~~~~pqt---~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqe  179 (402)
T KOG2191|consen  112 KPQAVAKPV---------DILQPQT---PDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQE  179 (402)
T ss_pred             hHHhhcCCc---------cccCCCC---ccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCcccee
Confidence            865431100         0011111   112245899999999999999999999999999999999996543   3369


Q ss_pred             eEEEEEcCHHHHHHHHHHHHHHHHHHHHH
Q 020173          297 RHIQFGGSAQQVALAKQRVDEYIYSQLIQ  325 (330)
Q Consensus       297 r~v~I~Gt~~~v~~A~~~I~~~i~~~~~~  325 (330)
                      |+|+++|.+++..+|..+|++.|.++...
T Consensus       180 rvvt~sge~e~~~~A~~~IL~Ki~eDpqs  208 (402)
T KOG2191|consen  180 RVVTVSGEPEQNMKAVSLILQKIQEDPQS  208 (402)
T ss_pred             EEEEecCCHHHHHHHHHHHHHHhhcCCcc
Confidence            99999999999999999999999876544

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

Probab=99.81  E-value=8.5e-19  Score=168.98  Aligned_cols=157  Identities=29%  Similarity=0.446  Sum_probs=132.2

Q ss_pred             eEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEc---------CHHHHHHHHHHH
Q 020173          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG---------DVPAVLNALVEI  213 (330)
Q Consensus       143 ~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G---------~~~~v~~A~~~I  213 (330)
                      .+.|+|++-..+|.|||++|..+++|+.++.++|.+...  .+.|     .+|+++|+|         ..+++.+|..+|
T Consensus        43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~--~~~c-----~eRIiti~g~~~~~~~~~~~~al~ka~~~i  115 (485)
T KOG2190|consen   43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNES--LPGC-----PERIITITGNRVELNLSPATDALFKAFDMI  115 (485)
T ss_pred             ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecC--CCCC-----CcceEEEecccccccCCchHHHHHHHHHHH
Confidence            358999999999999999999999999999999998643  5665     689999999         999999999999


Q ss_pred             HHHHhhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC-C
Q 020173          214 GNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK-G  292 (330)
Q Consensus       214 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~-~  292 (330)
                      ...++++....     .+.+.           .......+++|+||..++|.||||+|+.||+|+++|||+|.+..+. +
T Consensus       116 v~~~~~d~~~~-----~d~~~-----------~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP  179 (485)
T KOG2190|consen  116 VFKLEEDDEAA-----EDNGE-----------DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLP  179 (485)
T ss_pred             hhccccccccc-----ccCCc-----------cccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCC
Confidence            99877442110     01110           1112247899999999999999999999999999999999999873 4


Q ss_pred             CCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          293 EQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       293 ~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      .+++|.|+|+|.++.|..|...|...|.+-
T Consensus       180 ~ster~V~IsG~~~av~~al~~Is~~L~~~  209 (485)
T KOG2190|consen  180 NSTERAVTISGEPDAVKKALVQISSRLLEN  209 (485)
T ss_pred             cccceeEEEcCchHHHHHHHHHHHHHHHhc
Confidence            678999999999999999999999998873

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

Probab=99.72  E-value=3.4e-17  Score=141.63  Aligned_cols=150  Identities=27%  Similarity=0.463  Sum_probs=133.1

Q ss_pred             ceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCC
Q 020173          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (330)
Q Consensus       142 ~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  221 (330)
                      .+++++|+.++.+|.||||+|++||.|+.++++.|++....         ..+|+++|+.+.+.|.+.++.|+..|++.+
T Consensus        47 r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~---------~peri~tisad~~ti~~ilk~iip~lee~f  117 (390)
T KOG2192|consen   47 RVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS---------GPERILTISADIETIGEILKKIIPTLEEGF  117 (390)
T ss_pred             ceeEEEEEecccccceeccccccHHHHhhhccceeeccCCC---------CCceeEEEeccHHHHHHHHHHHhhhhhhCC
Confidence            35899999999999999999999999999999999996432         578999999999999999999999998874


Q ss_pred             CCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC-CCCceeEEE
Q 020173          222 PRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK-GEQKHRHIQ  300 (330)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~-~~~~~r~v~  300 (330)
                      ..                         ......+++|..+++|.|||++|+.||+|++.-.|+++|--.. +++++|+|.
T Consensus       118 ~~-------------------------~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l  172 (390)
T KOG2192|consen  118 QL-------------------------PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVL  172 (390)
T ss_pred             CC-------------------------CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEE
Confidence            32                         1347789999999999999999999999999999999998764 478899999


Q ss_pred             EEcCHHHHHHHHHHHHHHHHHHHHH
Q 020173          301 FGGSAQQVALAKQRVDEYIYSQLIQ  325 (330)
Q Consensus       301 I~Gt~~~v~~A~~~I~~~i~~~~~~  325 (330)
                      |.|.+.+|-.+.+.|.++|.+..++
T Consensus       173 ~~g~~k~v~~~i~~il~~i~e~pik  197 (390)
T KOG2192|consen  173 IGGKPKRVVECIKIILDLISESPIK  197 (390)
T ss_pred             ecCCcchHHHHHHHHHHHhhcCCcC
Confidence            9999999999999999988765443

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.72  E-value=8.7e-17  Score=136.07  Aligned_cols=138  Identities=25%  Similarity=0.400  Sum_probs=108.4

Q ss_pred             EEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEE---EcCHHHHHHHHHHHHHHHhhCCCC
Q 020173          147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQI---SGDVPAVLNALVEIGNQLRENPPR  223 (330)
Q Consensus       147 llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I---~G~~~~v~~A~~~I~~~i~~~~~~  223 (330)
                      +.||...+|.|||++|++|+.|+++||++|.+..            ++..|.|   +++++++.+|..+|..+.....+.
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~------------~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e   69 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS------------ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPE   69 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc------------CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHH
Confidence            5689999999999999999999999999999974            2356777   889999999999999987753211


Q ss_pred             CCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEcc---------ccccceecCCCchHHHHHHHhCCeEEEeCCCCCC
Q 020173          224 QVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISE---------SLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQ  294 (330)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~---------~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~  294 (330)
                      ..+..   +               ...+...-+.|+.         ...|+|||++|++++.|+..|||+|.|+.     
T Consensus        70 ~A~~l---~---------------gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~-----  126 (172)
T TIGR03665        70 KALKL---L---------------DDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG-----  126 (172)
T ss_pred             HHHHh---c---------------CCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC-----
Confidence            00000   0               0112222334444         36899999999999999999999999984     


Q ss_pred             ceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          295 KHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       295 ~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                        ..|.|.|++++++.|+.+|.++|..
T Consensus       127 --~~v~i~G~~~~~~~A~~~i~~li~~  151 (172)
T TIGR03665       127 --KTVGIIGDPEQVQIAREAIEMLIEG  151 (172)
T ss_pred             --CEEEEECCHHHHHHHHHHHHHHHcC
Confidence              5799999999999999999998843

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=99.67  E-value=1.3e-15  Score=129.86  Aligned_cols=141  Identities=26%  Similarity=0.380  Sum_probs=108.6

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEE----cCHHHHHHHHHHHHHHHhh
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS----GDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~----G~~~~v~~A~~~I~~~i~~  219 (330)
                      ...+.||...++.|||++|++|+.|+++||++|.+..            ++..|.|.    ++++++.+|..+|.++...
T Consensus         4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~------------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g   71 (180)
T PRK13763          4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS------------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRG   71 (180)
T ss_pred             eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC------------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence            6788999999999999999999999999999999973            23567784    8999999999999998875


Q ss_pred             CCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEcc---------ccccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173          220 NPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISE---------SLVGGLIGRCGSNISRIRNESGAMIKVYGG  290 (330)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~---------~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~  290 (330)
                      ..+...+..   ++               ..+...-+.|..         ..+|+|||++|++++.|++.|||+|.|.. 
T Consensus        72 f~~e~A~~l---~g---------------d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~-  132 (180)
T PRK13763         72 FSPEKALRL---LD---------------DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG-  132 (180)
T ss_pred             CCHHHHHHH---hC---------------CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-
Confidence            211100000   00               011111111211         36899999999999999999999999984 


Q ss_pred             CCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          291 KGEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       291 ~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                            ..|.|.|++++++.|+..|..++..
T Consensus       133 ------~~v~i~G~~~~~~~A~~~I~~li~g  157 (180)
T PRK13763        133 ------KTVAIIGDPEQVEIAREAIEMLIEG  157 (180)
T ss_pred             ------CEEEEEeCHHHHHHHHHHHHHHHcC
Confidence                  2389999999999999999988743

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.64  E-value=1.3e-15  Score=128.87  Aligned_cols=140  Identities=21%  Similarity=0.289  Sum_probs=104.1

Q ss_pred             EEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEE---ecCCCCcchhHHHHHHHHHHHHHhhcCCCCc
Q 020173           54 IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIII---SSKDNDNVVSDAENALQQIAALILKDDDSNS  130 (330)
Q Consensus        54 i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I---~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~  130 (330)
                      |.||.+.+|.|||++|++|+.|+++|||+|+|.+.     +..|.|   ++++     ..+.+|...|..+.......  
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~-----~~i~kA~~~I~~i~~gf~~e--   69 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDP-----LAVMKAREVVKAIGRGFSPE--   69 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCH-----HHHHHHHHHHHHHHcCCCHH--
Confidence            57899999999999999999999999999999863     345777   3332     67888888888865532211  


Q ss_pred             cccccccCCCcceEEE-EEeec---------cccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEE
Q 020173          131 EASKVAAGHVAANTIR-LLIAG---------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS  200 (330)
Q Consensus       131 ~~~~~~~~~~~~~~~~-llip~---------~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~  200 (330)
                      ++... .+  ..+... +-|+.         ...|+|||++|++++.|++.|||+|.+.              +..|.|.
T Consensus        70 ~A~~l-~g--d~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~--------------~~~v~i~  132 (172)
T TIGR03665        70 KALKL-LD--DDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY--------------GKTVGII  132 (172)
T ss_pred             HHHHh-cC--CcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc--------------CCEEEEE
Confidence            00000 00  011111 22222         3689999999999999999999999984              2579999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCC
Q 020173          201 GDVPAVLNALVEIGNQLRENPP  222 (330)
Q Consensus       201 G~~~~v~~A~~~I~~~i~~~~~  222 (330)
                      |+++++..|...|.+++.+.++
T Consensus       133 G~~~~~~~A~~~i~~li~~~~~  154 (172)
T TIGR03665       133 GDPEQVQIAREAIEMLIEGAPH  154 (172)
T ss_pred             CCHHHHHHHHHHHHHHHcCCCC
Confidence            9999999999999999976643

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=99.60  E-value=1.1e-14  Score=124.21  Aligned_cols=147  Identities=21%  Similarity=0.270  Sum_probs=106.5

Q ss_pred             eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCC
Q 020173           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN  129 (330)
Q Consensus        50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~  129 (330)
                      +...+.||.+.+|.|||++|++|+.|+++|||+|++.+.     +..|.|.... ......+.+|...|..+....... 
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~-~~d~~~i~kA~~~I~ai~~gf~~e-   75 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTD-GEDPLAVLKARDIVKAIGRGFSPE-   75 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCC-CCCHHHHHHHHHHHHHHhcCCCHH-
Confidence            467899999999999999999999999999999999873     3556775111 001367888888888876532211 


Q ss_pred             ccccccccCCCcceEEEE-E----ee-----ccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEE
Q 020173          130 SEASKVAAGHVAANTIRL-L----IA-----GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQI  199 (330)
Q Consensus       130 ~~~~~~~~~~~~~~~~~l-l----ip-----~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I  199 (330)
                       ++... .+  ..+...+ -    .+     ...+|+|||++|++++.|++.|||+|.+..              +.|.|
T Consensus        76 -~A~~l-~g--d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~--------------~~v~i  137 (180)
T PRK13763         76 -KALRL-LD--DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG--------------KTVAI  137 (180)
T ss_pred             -HHHHH-hC--CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC--------------CEEEE
Confidence             00000 00  0011111 0    11     136899999999999999999999999852              34889


Q ss_pred             EcCHHHHHHHHHHHHHHHhhCC
Q 020173          200 SGDVPAVLNALVEIGNQLRENP  221 (330)
Q Consensus       200 ~G~~~~v~~A~~~I~~~i~~~~  221 (330)
                      .|+++++..|...|..+++...
T Consensus       138 ~G~~~~~~~A~~~I~~li~g~~  159 (180)
T PRK13763        138 IGDPEQVEIAREAIEMLIEGAP  159 (180)
T ss_pred             EeCHHHHHHHHHHHHHHHcCCC
Confidence            9999999999999999997653

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.51  E-value=4.6e-14  Score=100.11  Aligned_cols=63  Identities=32%  Similarity=0.475  Sum_probs=58.8

Q ss_pred             EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC-CCceeEEEEEcCHHHHHHHHHHH
Q 020173          253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG-EQKHRHIQFGGSAQQVALAKQRV  315 (330)
Q Consensus       253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~-~~~~r~v~I~Gt~~~v~~A~~~I  315 (330)
                      +++|.||.+++|+|||++|++|++|+++|||+|.+.++.. .+.+|+|+|.|++++++.|+.+|
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence            3689999999999999999999999999999999998765 57799999999999999999987

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

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

Probab=99.42  E-value=1e-12  Score=124.36  Aligned_cols=243  Identities=23%  Similarity=0.317  Sum_probs=173.3

Q ss_pred             CCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcC
Q 020173           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (330)
Q Consensus        47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~  126 (330)
                      ..++.+++.||...+-.++|++|.+|+.|+..++++|.+.+.. -.++++..+.|-+     ..+..|...+..++... 
T Consensus        65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p-----~~v~~a~a~~~~~~~~~-  137 (608)
T KOG2279|consen   65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFP-----VQVCKAKAAIHQILTEN-  137 (608)
T ss_pred             hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCC-----CCCChHHHHHHHHHhcC-
Confidence            3678999999999999999999999999999999999997652 2356666666543     23344444445544332 


Q ss_pred             CCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH
Q 020173          127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV  206 (330)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v  206 (330)
                                    ..+...+-+|...++.|+|++|++++.++..++++|.+....   .|    .-.+...|.|....+
T Consensus       138 --------------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng---r~----g~~~~~~i~~qqk~~  196 (608)
T KOG2279|consen  138 --------------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG---RL----GLSRLIKISGQQKEV  196 (608)
T ss_pred             --------------Ccccccccchhhhcccccccchhhhcchhccccccccccccc---cc----ccccceecccccchH
Confidence                          234567789999999999999999999999999999986432   22    346788899998888


Q ss_pred             HHHHHHHHHHHhhCCC---------------CCCccc------------CC---CCCCCCCCCCCC--------------
Q 020173          207 LNALVEIGNQLRENPP---------------RQVISI------------SP---AYNYSAIRPAQP--------------  242 (330)
Q Consensus       207 ~~A~~~I~~~i~~~~~---------------~~~~~~------------~~---~~~~~~~~~~~~--------------  242 (330)
                      ..|..++.+.+.++-.               +...+.            .+   .+...+..++.+              
T Consensus       197 ~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vs  276 (608)
T KOG2279|consen  197 AAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVS  276 (608)
T ss_pred             HHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEe
Confidence            8999999988866411               110000            00   000000011100              


Q ss_pred             ----------CCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCc---eeEEEEEcCHHHHH
Q 020173          243 ----------FVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQK---HRHIQFGGSAQQVA  309 (330)
Q Consensus       243 ----------~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~---~r~v~I~Gt~~~v~  309 (330)
                                -..+.........|.||..++|.|||+.|+.++.+...|++.+.|.-..-...   -.++.+.|+..-++
T Consensus       277 k~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkqh~~n  356 (608)
T KOG2279|consen  277 KEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQHYEN  356 (608)
T ss_pred             cccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecchhHHHH
Confidence                      00112334456799999999999999999999999999999999986432221   25678999999999


Q ss_pred             HHHHHHHH
Q 020173          310 LAKQRVDE  317 (330)
Q Consensus       310 ~A~~~I~~  317 (330)
                      .|..++..
T Consensus       357 ~vl~ml~~  364 (608)
T KOG2279|consen  357 SVLEMLTV  364 (608)
T ss_pred             HHHhhhhc
Confidence            99988863

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.41  E-value=4.9e-13  Score=93.30  Aligned_cols=60  Identities=35%  Similarity=0.552  Sum_probs=55.6

Q ss_pred             EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHH
Q 020173          253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRV  315 (330)
Q Consensus       253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I  315 (330)
                      |.+|.||.+++|+|||++|++|++|++.|||+|.|+++  + .+..|+|+|++++|+.|+++|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--~-~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--D-ERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHHHHHHHHhhC
Confidence            57899999999999999999999999999999999975  3 566999999999999999886

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

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.39  E-value=5.7e-13  Score=94.50  Aligned_cols=63  Identities=44%  Similarity=0.685  Sum_probs=56.6

Q ss_pred             EEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCC-CCcceEEEEecCCCCcchhHHHHHHHHH
Q 020173           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA-RHEERVIIISSKDNDNVVSDAENALQQI  118 (330)
Q Consensus        51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~-~~~ervi~I~G~~~~~~~~~~~~A~~~i  118 (330)
                      +++|+||.+.+|+|||++|.+|++|+++|||+|++++... +..+|+|+|.|+.     +++.+|+.+|
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKP-----SAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCH-----HHHHHHHHhh
Confidence            3799999999999999999999999999999999998754 6789999999985     7788888776

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.38  E-value=7.6e-13  Score=92.96  Aligned_cols=61  Identities=31%  Similarity=0.388  Sum_probs=56.1

Q ss_pred             EEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHH
Q 020173          254 FEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVD  316 (330)
Q Consensus       254 ~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~  316 (330)
                      .+|.||..++|+|||++|++|++|+++|||+|.+++..  +.++.|+|+|++++|..|+.+|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHhC
Confidence            57899999999999999999999999999999999754  56789999999999999998873

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

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

Probab=99.33  E-value=4.1e-12  Score=89.61  Aligned_cols=62  Identities=35%  Similarity=0.560  Sum_probs=57.8

Q ss_pred             EEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHH
Q 020173          254 FEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRV  315 (330)
Q Consensus       254 ~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I  315 (330)
                      .+|.||..++++|||++|++|++|++.|||+|.|++...+..++.|+|.|+.+++..|+.+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence            57999999999999999999999999999999999866566789999999999999999887

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

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

Probab=99.31  E-value=5.8e-12  Score=87.96  Aligned_cols=59  Identities=22%  Similarity=0.321  Sum_probs=53.9

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVD  316 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~  316 (330)
                      .+..|.||.+++|+|||++|++|++|++.|||+|.+++      ++.|.|+|+ +++++.|+.+|+
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~~~v~~A~~~I~   61 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDKEAAEKAKKMIE   61 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCHHHHHHHHHHhC
Confidence            45689999999999999999999999999999999996      357999999 999999999873

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.14  E-value=1e-10  Score=82.05  Aligned_cols=60  Identities=27%  Similarity=0.362  Sum_probs=54.1

Q ss_pred             EEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHH
Q 020173          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI  213 (330)
Q Consensus       145 ~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I  213 (330)
                      ..+.||..++++|||++|++|++|+++|||+|.++..+         ..++.|+|+|+.++|..|..+|
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            57889999999999999999999999999999997542         3578899999999999999887

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

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

Probab=99.12  E-value=1.4e-10  Score=81.79  Aligned_cols=62  Identities=44%  Similarity=0.665  Sum_probs=53.5

Q ss_pred             EEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHH
Q 020173           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI  118 (330)
Q Consensus        52 ~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i  118 (330)
                      .+|.||.+++++|||++|++|++|+++|||+|.|++......++.|.|.|+.     +++..|..++
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~-----~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTP-----EAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCH-----HHHHHHHHHh
Confidence            6899999999999999999999999999999999986545678999999984     5666666554

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=99.12  E-value=1.4e-10  Score=80.81  Aligned_cols=60  Identities=32%  Similarity=0.445  Sum_probs=53.5

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHH
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI  213 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I  213 (330)
                      |.+|.||..++++|||++|++|++|+++|||+|.++..          .....|+|.|+.++|.+|+++|
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          1234899999999999999876

; 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 ....

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=99.10  E-value=8.7e-10  Score=112.59  Aligned_cols=229  Identities=21%  Similarity=0.240  Sum_probs=158.9

Q ss_pred             eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCC--cchhHHHHHHHHHHHHHhh---
Q 020173           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDND--NVVSDAENALQQIAALILK---  124 (330)
Q Consensus        50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~--~~~~~~~~A~~~i~~~i~~---  124 (330)
                      +..++.+-...+.++||++|.++..++.++.+.++|++...  ......+.|....  ........++.++..-...   
T Consensus       201 ~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~--~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~  278 (753)
T KOG2208|consen  201 VFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNK--SSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEI  278 (753)
T ss_pred             EEEEeeccccchhhhccccccccccccccceeEEEcccccc--cchhhhhccccccceehhhhhHHHHHHhcChhhhhhh
Confidence            78899999999999999999999999999999999997632  2222233331110  0012233443332221100   


Q ss_pred             ---cCC---C--------------------Ccc------c-----cccc-------------cCCCcceEEEEEeecccc
Q 020173          125 ---DDD---S--------------------NSE------A-----SKVA-------------AGHVAANTIRLLIAGSQA  154 (330)
Q Consensus       125 ---~~~---~--------------------~~~------~-----~~~~-------------~~~~~~~~~~llip~~~~  154 (330)
                         ...   .                    ...      .     ....             ..........+.+....+
T Consensus       279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~  358 (753)
T KOG2208|consen  279 IYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEEL  358 (753)
T ss_pred             hhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhh
Confidence               000   0                    000      0     0000             011233567777888889


Q ss_pred             ceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCCCCC
Q 020173          155 GCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNY  234 (330)
Q Consensus       155 g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~  234 (330)
                      ..++|++|.+|.+|++++.+.+.+....         +++..+.++|...++.+|...+...+.+-+.            
T Consensus       359 ~~v~GK~~~ni~ki~e~~~~~i~~~~~~---------~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n------------  417 (753)
T KOG2208|consen  359 KFVIGKKGANIEKIREESQVKIDLPKQG---------SNNKKVVITGVSANDEKAVEDVEKIIAEILN------------  417 (753)
T ss_pred             hhhcCCCCccHHHHHHhhhhceeccccc---------CCCCCeEEeccccchhHHHHHHHHHHHhhhc------------
Confidence            9999999999999999999999986532         4677899999999999999999999987621            


Q ss_pred             CCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhC-CeEEEeCCCCCCceeEEEEEcCHHHHHHHHH
Q 020173          235 SAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESG-AMIKVYGGKGEQKHRHIQFGGSAQQVALAKQ  313 (330)
Q Consensus       235 ~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tg-a~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~  313 (330)
                                     ......+.||...+..|||.+|..|++|...++ .+|+.+.+  ......+++.|....+..+..
T Consensus       418 ---------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~--~~~~~~~~~~~~~~dv~~~~~  480 (753)
T KOG2208|consen  418 ---------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN--NNSSDMVTIRGISKDVEKSVS  480 (753)
T ss_pred             ---------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC--CcccccceEeccccccchhHH
Confidence                           124567999999999999999999999999999 56666654  444456777787777776555


Q ss_pred             HHHHH
Q 020173          314 RVDEY  318 (330)
Q Consensus       314 ~I~~~  318 (330)
                      +...+
T Consensus       481 ~~~~~  485 (753)
T KOG2208|consen  481 LLKAL  485 (753)
T ss_pred             HHHhh
Confidence            55443

>PF13014 KH_3: KH domain

Probab=99.06  E-value=2.7e-10  Score=73.73  Aligned_cols=42  Identities=36%  Similarity=0.619  Sum_probs=38.0

Q ss_pred             cccceecCCCchHHHHHHHhCCeEEEeC-CCCCCceeEEEEEc
Q 020173          262 LVGGLIGRCGSNISRIRNESGAMIKVYG-GKGEQKHRHIQFGG  303 (330)
Q Consensus       262 ~vg~IIGk~G~~Ik~i~~~tga~I~i~~-~~~~~~~r~v~I~G  303 (330)
                      +||+|||++|++|++|+++|||+|+|++ ...++.++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            5899999999999999999999999998 33467899999998

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

Probab=99.03  E-value=3.3e-09  Score=89.33  Aligned_cols=151  Identities=17%  Similarity=0.204  Sum_probs=108.9

Q ss_pred             ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCC
Q 020173           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS  128 (330)
Q Consensus        49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~  128 (330)
                      .....+.||....+.+||+.|+..+.|++.++++|.++.     .+..+.|..+.........++|...+..+-...+..
T Consensus         7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe   81 (194)
T COG1094           7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPE   81 (194)
T ss_pred             cceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHH
Confidence            455679999999999999999999999999999999986     356677776632112355677777666654433221


Q ss_pred             CccccccccCCCcceEEEE-----Eee------ccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEE
Q 020173          129 NSEASKVAAGHVAANTIRL-----LIA------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVV  197 (330)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~l-----lip------~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v  197 (330)
                      .......     ....+.+     ++.      ....|+|||++|.+.+.|++.|+|.|.+.              +..|
T Consensus        82 ~A~~LL~-----d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~--------------g~tV  142 (194)
T COG1094          82 KALKLLE-----DDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY--------------GKTV  142 (194)
T ss_pred             HHHHHhc-----CCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe--------------CcEE
Confidence            1100000     0001111     111      12459999999999999999999999996              3479


Q ss_pred             EEEcCHHHHHHHHHHHHHHHhhCCCC
Q 020173          198 QISGDVPAVLNALVEIGNQLRENPPR  223 (330)
Q Consensus       198 ~I~G~~~~v~~A~~~I~~~i~~~~~~  223 (330)
                      .|-|..++|..|.+.|..++...++.
T Consensus       143 aiiG~~~~v~iAr~AVemli~G~~h~  168 (194)
T COG1094         143 AIIGGFEQVEIAREAVEMLINGAPHG  168 (194)
T ss_pred             EEecChhhhHHHHHHHHHHHcCCCch
Confidence            99999999999999999999887654

>smart00322 KH K homology RNA-binding domain

Probab=99.03  E-value=1.9e-09  Score=76.36  Aligned_cols=66  Identities=32%  Similarity=0.505  Sum_probs=59.7

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYI  319 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i  319 (330)
                      .+.+|.||..++|.+||++|++|++|++.||++|.++....  ....++|.|+.+++..|..+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHh
Confidence            57789999999999999999999999999999999986432  5688999999999999999998765

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

Probab=99.03  E-value=1.3e-09  Score=76.03  Aligned_cols=57  Identities=26%  Similarity=0.274  Sum_probs=51.7

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHH
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEI  213 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I  213 (330)
                      ...+.||...++.|||++|++|+.|+++|||+|.+..             ++.|.|.|+ .+++..|..+|
T Consensus         3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-------------~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-------------DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-------------CCEEEEEeCCHHHHHHHHHHh
Confidence            5678899999999999999999999999999999852             457999998 99999999886

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

>PF13014 KH_3: KH domain

Probab=99.03  E-value=3.3e-10  Score=73.28  Aligned_cols=42  Identities=43%  Similarity=0.673  Sum_probs=38.2

Q ss_pred             ccceeecccChhhhhhhhccCcEEEEec-CCCCCcceEEEEec
Q 020173           60 QIGKVIGKEGHRIQKIREETKATIKIAD-AIARHEERVIIISS  101 (330)
Q Consensus        60 ~vg~IIGk~G~~Ik~I~~~tg~~I~i~~-~~~~~~ervi~I~G  101 (330)
                      ++|+|||++|.+|++|+++|||+|+|++ ..++..+++|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            5899999999999999999999999998 45577899999987

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

Probab=98.86  E-value=4.9e-08  Score=82.37  Aligned_cols=141  Identities=26%  Similarity=0.377  Sum_probs=106.5

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-----CHHHHHHHHHHHHHHHh
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-----DVPAVLNALVEIGNQLR  218 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G-----~~~~v~~A~~~I~~~i~  218 (330)
                      ...+.||....+.++|+.|+..+.|.+.+++++.+..            .+..|.|..     ++..+++|...|.++-+
T Consensus         9 ~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~------------~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgr   76 (194)
T COG1094           9 SEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS------------KTGSVTIRTTRKTEDPLALLKARDVVKAIGR   76 (194)
T ss_pred             eeeeecCchhheeeecccccchHHHHhhcCeEEEEEC------------CCCeEEEEecCCCCChHHHHHHHHHHHHHhc
Confidence            5678999999999999999999999999999999974            345566643     68999999999988877


Q ss_pred             hCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEE------cc----ccccceecCCCchHHHHHHHhCCeEEEe
Q 020173          219 ENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLI------SE----SLVGGLIGRCGSNISRIRNESGAMIKVY  288 (330)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~I------P~----~~vg~IIGk~G~~Ik~i~~~tga~I~i~  288 (330)
                      ..++...+-...                  +...-..+.|      +.    ..-|+|||++|.+.+.|++.|+|.|.|.
T Consensus        77 GF~pe~A~~LL~------------------d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~  138 (194)
T COG1094          77 GFPPEKALKLLE------------------DDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY  138 (194)
T ss_pred             CCCHHHHHHHhc------------------CCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe
Confidence            654322110000                  0011111111      11    2459999999999999999999999999


Q ss_pred             CCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          289 GGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       289 ~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      .       ..|-|.|.+++++.|+..|.-+|..
T Consensus       139 g-------~tVaiiG~~~~v~iAr~AVemli~G  164 (194)
T COG1094         139 G-------KTVAIIGGFEQVEIAREAVEMLING  164 (194)
T ss_pred             C-------cEEEEecChhhhHHHHHHHHHHHcC
Confidence            6       3699999999999999999877653

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

Probab=98.84  E-value=1.9e-09  Score=102.54  Aligned_cols=146  Identities=29%  Similarity=0.373  Sum_probs=124.8

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  220 (330)
                      ..+..++.++...+-+++|+.|++|+.|+..+++++.+-.++ .       .+++...+.|.+.++..|+..++.++.++
T Consensus        66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~-------g~e~~~~~~~~p~~v~~a~a~~~~~~~~~  137 (608)
T KOG2279|consen   66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-V-------GDERVLLISGFPVQVCKAKAAIHQILTEN  137 (608)
T ss_pred             hheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-C-------CcccchhhccCCCCCChHHHHHHHHHhcC
Confidence            456789999999999999999999999999999999986543 2       35677778889999999999999999876


Q ss_pred             CCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEE
Q 020173          221 PPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQ  300 (330)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~  300 (330)
                      .                             .+...+.+|...+++|+|++|++++.|+..++|+|.+..+...--.+...
T Consensus       138 ~-----------------------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~  188 (608)
T KOG2279|consen  138 T-----------------------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIK  188 (608)
T ss_pred             C-----------------------------cccccccchhhhcccccccchhhhcchhccccccccccccccccccccee
Confidence            2                             35667889999999999999999999999999999999874333467888


Q ss_pred             EEcCHHHHHHHHHHHHHHHHHHH
Q 020173          301 FGGSAQQVALAKQRVDEYIYSQL  323 (330)
Q Consensus       301 I~Gt~~~v~~A~~~I~~~i~~~~  323 (330)
                      |.|...-++.|+.++.+.+++..
T Consensus       189 i~~qqk~~~~a~~~~~~~~~ede  211 (608)
T KOG2279|consen  189 ISGQQKEVAAAKHLILEKVSEDE  211 (608)
T ss_pred             cccccchHHHHHhhhhccccchh
Confidence            89998888899999998877654

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.77  E-value=1.8e-08  Score=103.13  Aligned_cols=218  Identities=21%  Similarity=0.272  Sum_probs=153.3

Q ss_pred             CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCC
Q 020173           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD  127 (330)
Q Consensus        48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~  127 (330)
                      ..+...+.+-..++..++||+|.+|.+|+++++|.|.++..  +..+..+.+.+..     .+..+|...+.....+...
T Consensus       345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~-----~~~~ka~~~v~~~~~ei~n  417 (753)
T KOG2208|consen  345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVS-----ANDEKAVEDVEKIIAEILN  417 (753)
T ss_pred             cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccc-----cchhHHHHHHHHHHHhhhc
Confidence            45778888899999999999999999999999999999984  4566778888875     4556666666666544432


Q ss_pred             CCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhC-CeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH
Q 020173          128 SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSG-ATIVILAPNQLPLCASAHESDRVVQISGDVPAV  206 (330)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sg-a~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v  206 (330)
                      .             .....+++|...+..+||.+|..|..|..+++ ..|.+....         +.....++.|....+
T Consensus       418 ~-------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~---------~~~~~~~~~~~~~dv  475 (753)
T KOG2208|consen  418 S-------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN---------NSSDMVTIRGISKDV  475 (753)
T ss_pred             c-------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC---------cccccceEecccccc
Confidence            1             12567899999999999999999999999999 555543221         233457788877777


Q ss_pred             HHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEE
Q 020173          207 LNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIK  286 (330)
Q Consensus       207 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~  286 (330)
                      ..+...+..+........                       .....+.....|..+.+..+|+.|..+.    ..+....
T Consensus       476 ~~~~~~~~~~~~~a~~~~-----------------------~~~~~~~d~~~~~~~~~~~~g~~~~i~d----~~~~~~i  528 (753)
T KOG2208|consen  476 EKSVSLLKALKADAKNLK-----------------------FRDVVTKDKLLPVKYIGKEIGKNGTIRD----SLGDKSI  528 (753)
T ss_pred             chhHHHHHhhhhhhhcch-----------------------hhhhhhccccchHHhhcccccCceeeec----cCCceee
Confidence            766555555554321100                       0112344566667777777776665544    4455555


Q ss_pred             EeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          287 VYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       287 i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      ++.. .+.++..++|.|..+.|..|...+..++...
T Consensus       529 ~~~~-~~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~  563 (753)
T KOG2208|consen  529 FPPN-EDEDHEKITIEGKLELVLEAPAELKALIEAL  563 (753)
T ss_pred             cccc-cccccceeeecccccchhhhHHHHHhcchhh
Confidence            5542 2345678999999999999999888766543

>smart00322 KH K homology RNA-binding domain

Probab=98.74  E-value=8.6e-08  Score=67.68  Aligned_cols=66  Identities=33%  Similarity=0.462  Sum_probs=58.3

Q ss_pred             eEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 020173          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (330)
Q Consensus       143 ~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  217 (330)
                      .+.++.||...++.+||++|++|++|++.+|++|.+....         .....+.|.|+.+++..|..+|.+.+
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            4789999999999999999999999999999999986421         14578999999999999999998876

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

Probab=98.58  E-value=8.4e-08  Score=85.52  Aligned_cols=154  Identities=17%  Similarity=0.190  Sum_probs=114.6

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  220 (330)
                      ..++..+.+|..+++.++|++|.+||.|+.+|..+|+-+...          .+.++.++|..+.|..|+..|...-+..
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~----------eePiF~vTg~~edv~~aRrei~saaeH~   93 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG----------EEPIFPVTGRHEDVRRARREIPSAAEHF   93 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC----------CCCcceeccCchhHHHHhhcCcccccee
Confidence            456888889999999999999999999999999999876543          4568999999999999999887633321


Q ss_pred             CCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEE
Q 020173          221 PPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQ  300 (330)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~  300 (330)
                      -.   .-+.+.+..+...    +   +...+.+..+.+|...+|.+.|.+|.+|+.+++.++..|.-+-+   ..+-++-
T Consensus        94 ~l---~~~s~s~Sgg~~~----~---s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~---~~~~Vf~  160 (394)
T KOG2113|consen   94 GL---IRASRSFSGGTNG----A---SASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR---CGEPVFC  160 (394)
T ss_pred             ee---eeecccccCCCcc----c---cccCCCceeeeccceeeeeccccccCccchheecccceEeeecc---CCCceEE
Confidence            00   0111111111110    0   11345777889999999999999999999999999999988864   3567899


Q ss_pred             EEcCHHH-HHHHH-HHHHH
Q 020173          301 FGGSAQQ-VALAK-QRVDE  317 (330)
Q Consensus       301 I~Gt~~~-v~~A~-~~I~~  317 (330)
                      ++|.+.+ +++|. ..|..
T Consensus       161 Vtg~~~nC~kra~s~eie~  179 (394)
T KOG2113|consen  161 VTGAPKNCVKRARSCEIEQ  179 (394)
T ss_pred             EecCCcchhhhccccchhh
Confidence            9999998 55555 34443

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

Probab=98.56  E-value=2e-07  Score=73.94  Aligned_cols=60  Identities=22%  Similarity=0.429  Sum_probs=50.3

Q ss_pred             ccccceecCCCchHHHHHHHhCCeEEEeCCCCC-----------------CceeEEEEEcC---HHHHHHHHHHHHHHHH
Q 020173          261 SLVGGLIGRCGSNISRIRNESGAMIKVYGGKGE-----------------QKHRHIQFGGS---AQQVALAKQRVDEYIY  320 (330)
Q Consensus       261 ~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~-----------------~~~r~v~I~Gt---~~~v~~A~~~I~~~i~  320 (330)
                      +++|.|||.+|++||+|+++|||+|.|......                 ...-.|.|++.   .+.++.|..+|..++.
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            478999999999999999999999999975211                 12357889995   5999999999998876

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

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

Probab=98.44  E-value=2.5e-07  Score=82.53  Aligned_cols=151  Identities=21%  Similarity=0.312  Sum_probs=109.1

Q ss_pred             CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhc--
Q 020173           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD--  125 (330)
Q Consensus        48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~--  125 (330)
                      +.++..+.||..+++.|.|++|.+||.|+.+|+++|+-+..   ..+.++.++|..     ++|..|..+|..--.-.  
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~-----edv~~aRrei~saaeH~~l   95 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRH-----EDVRRARREIPSAAEHFGL   95 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCc-----hhHHHHhhcCccccceeee
Confidence            78999999999999999999999999999999999998875   356889999987     56677766665511000  


Q ss_pred             -CCCCcccccc-ccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH
Q 020173          126 -DDSNSEASKV-AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV  203 (330)
Q Consensus       126 -~~~~~~~~~~-~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~  203 (330)
                       .......... .+......+...-+|...+|++.|.+|.+|+.+++.++..|.-.-+          -.+.++.++|-+
T Consensus        96 ~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~----------~~~~Vf~Vtg~~  165 (394)
T KOG2113|consen   96 IRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR----------CGEPVFCVTGAP  165 (394)
T ss_pred             eeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc----------CCCceEEEecCC
Confidence             0000000000 1223445677888899999999999999999999999998876543          245688899988


Q ss_pred             HH-HHHHH-HHHHHH
Q 020173          204 PA-VLNAL-VEIGNQ  216 (330)
Q Consensus       204 ~~-v~~A~-~~I~~~  216 (330)
                      .+ +.+|. ..|+..
T Consensus       166 ~nC~kra~s~eie~t  180 (394)
T KOG2113|consen  166 KNCVKRARSCEIEQT  180 (394)
T ss_pred             cchhhhccccchhhh
Confidence            88 44444 344443

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

Probab=98.42  E-value=6.3e-07  Score=71.04  Aligned_cols=71  Identities=20%  Similarity=0.395  Sum_probs=50.8

Q ss_pred             EEEecC------CccceeecccChhhhhhhhccCcEEEEecCCC---C--------------CcceEEEEecCCCCcchh
Q 020173           53 RIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADAIA---R--------------HEERVIIISSKDNDNVVS  109 (330)
Q Consensus        53 ~i~vP~------~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~---~--------------~~ervi~I~G~~~~~~~~  109 (330)
                      +|.||.      +++|.|||++|.+||+|+++|||+|.|...-.   +              ...--|.|++....  .+
T Consensus         3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~--~e   80 (120)
T cd02395           3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPP--EE   80 (120)
T ss_pred             EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcH--HH
Confidence            566776      57899999999999999999999999986410   0              01134777776410  15


Q ss_pred             HHHHHHHHHHHHHhhc
Q 020173          110 DAENALQQIAALILKD  125 (330)
Q Consensus       110 ~~~~A~~~i~~~i~~~  125 (330)
                      .+.+|+.+|..++...
T Consensus        81 ~~~~A~~~I~~ll~~~   96 (120)
T cd02395          81 ALAKAVEAIEELLKPA   96 (120)
T ss_pred             HHHHHHHHHHHHhccC
Confidence            6778888888877543

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.19  E-value=9.7e-06  Score=81.86  Aligned_cols=63  Identities=21%  Similarity=0.352  Sum_probs=57.7

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIY  320 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~  320 (330)
                      ....|.||.+.+|.|||.||.+||.|.++||++|.|.+      +..|.|.+. .+.+++|+.+|..++.
T Consensus       578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~  641 (719)
T TIGR02696       578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIAN  641 (719)
T ss_pred             eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence            67789999999999999999999999999999999995      367999885 8999999999998876

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.02  E-value=2.5e-05  Score=63.69  Aligned_cols=103  Identities=18%  Similarity=0.305  Sum_probs=71.0

Q ss_pred             eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCC
Q 020173           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN  129 (330)
Q Consensus        50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~  129 (330)
                      -.+.++|+...+|+.||++|++|+.|++..|-+|.+-.-.             +         ++...+...+....-..
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s-------------~---------d~~~fI~n~l~Pa~V~~   89 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS-------------D---------DPEEFIKNIFAPAAVRS   89 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcC-------------C---------CHHHHHHHHcCCCEEEE
Confidence            5678889999999999999999999999999888876521             1         12222333322111000


Q ss_pred             ccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEE
Q 020173          130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI  178 (330)
Q Consensus       130 ~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i  178 (330)
                      .   ... .........+.|+....|.+||++|++++.++.-++-.+.+
T Consensus        90 v---~I~-~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di  134 (140)
T PRK08406         90 V---TIK-KKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             E---EEE-ecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence            0   000 00112356778999999999999999999999999877765

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.98  E-value=1.9e-05  Score=64.44  Aligned_cols=103  Identities=20%  Similarity=0.269  Sum_probs=74.0

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCC
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR  223 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~  223 (330)
                      .+.++|+...+|..||++|++|+.|++..|-+|.+-.-          +++              +..+|...+.-....
T Consensus        33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~----------s~d--------------~~~fI~n~l~Pa~V~   88 (140)
T PRK08406         33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY----------SDD--------------PEEFIKNIFAPAAVR   88 (140)
T ss_pred             EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc----------CCC--------------HHHHHHHHcCCCEEE
Confidence            68889999999999999999999999999988888632          121              233444444321110


Q ss_pred             CCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEe
Q 020173          224 QVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVY  288 (330)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~  288 (330)
                      ...     ..             .........+.|+.+..|..|||+|++++.++..++-.+.|.
T Consensus        89 ~v~-----I~-------------~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         89 SVT-----IK-------------KKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             EEE-----EE-------------ecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            000     00             011235667889999999999999999999999999988775

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.83  E-value=6.2e-05  Score=76.98  Aligned_cols=63  Identities=19%  Similarity=0.265  Sum_probs=55.6

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIY  320 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~  320 (330)
                      ....+.||.+.+|.|||++|++||.|.++|||+|.|.+      +..|.|.+. .+.++.|+++|..+..
T Consensus       551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~~~~~~a~~~I~~~~~  614 (684)
T TIGR03591       551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEAAEAAIKMIEGITA  614 (684)
T ss_pred             eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcHHHHHHHHHHHHhhhc
Confidence            67789999999999999999999999999999999985      356777774 8899999999987754

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=97.65  E-value=0.00039  Score=66.20  Aligned_cols=72  Identities=24%  Similarity=0.350  Sum_probs=56.3

Q ss_pred             ceEEEEEEcc------ccccceecCCCchHHHHHHHhCCeEEEeCCC---------------C-CCceeEEEEEc-CHHH
Q 020173          251 YVTFEMLISE------SLVGGLIGRCGSNISRIRNESGAMIKVYGGK---------------G-EQKHRHIQFGG-SAQQ  307 (330)
Q Consensus       251 ~~~~~v~IP~------~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~---------------~-~~~~r~v~I~G-t~~~  307 (330)
                      ..+.+|.||-      +|+|.|||..|.|.|+|+++|||+|.|-...               . ..++=-+.|++ |.+.
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            3556677765      4899999999999999999999999998621               0 11223466777 5999


Q ss_pred             HHHHHHHHHHHHHHH
Q 020173          308 VALAKQRVDEYIYSQ  322 (330)
Q Consensus       308 v~~A~~~I~~~i~~~  322 (330)
                      |++|..+|+.+|.++
T Consensus       217 i~~Ai~vienli~~a  231 (554)
T KOG0119|consen  217 IKKAIAVIENLIQSA  231 (554)
T ss_pred             HHHHHHHHHHHHHhh
Confidence            999999999999863

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.58  E-value=0.00038  Score=56.69  Aligned_cols=103  Identities=18%  Similarity=0.266  Sum_probs=68.8

Q ss_pred             EEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCc
Q 020173           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS  130 (330)
Q Consensus        51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~  130 (330)
                      .+-+.|....+|+.||++|++|+.|++..|=+|.+-.-.           ...        .   .-+...+....-.  
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys-----------~D~--------~---~fI~N~l~PA~V~--   89 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYS-----------ENL--------E---EFVANKLAPAEVK--   89 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcC-----------CCH--------H---HHHHHcCCCceEE--
Confidence            677889999999999999999999998889888876521           110        0   1111111100000  


Q ss_pred             cccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEe
Q 020173          131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVIL  179 (330)
Q Consensus       131 ~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~  179 (330)
                       .-.. ....+.....+.|+....+..||++|.+++..+.-++-++.+.
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 0001223677889999999999999999999999988777653

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.58  E-value=0.0004  Score=70.44  Aligned_cols=94  Identities=24%  Similarity=0.309  Sum_probs=70.9

Q ss_pred             hhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 020173          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (330)
Q Consensus       108 ~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~  187 (330)
                      +..+.+++..|.+.+.+..... ..    ....-+....+.||....+.|||++|.+||.|.++||++|.+.        
T Consensus       548 L~~A~~g~~~Il~~m~~al~~p-~~----~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~--------  614 (719)
T TIGR02696       548 LKQARDARLAILDVMAEAIDTP-DE----MSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE--------  614 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCc-cc----cccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe--------
Confidence            4455666667777665543322 11    1112244678899999999999999999999999999999995        


Q ss_pred             cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhh
Q 020173          188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  219 (330)
                           ++..|.|.+ +.+.+.+|+.+|..++..
T Consensus       615 -----d~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       615 -----DDGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             -----cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence                 345788877 688999999999999885

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.53  E-value=0.00021  Score=73.96  Aligned_cols=63  Identities=16%  Similarity=0.247  Sum_probs=56.5

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCe-EEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAM-IKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIY  320 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~-I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~  320 (330)
                      ....+.||.+.+|.|||.||.+||.|.++||+. |.+.+      +-.|.|.+. .+.++.|+.+|.++..
T Consensus       685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~~~i~~A~~~I~~l~~  749 (891)
T PLN00207        685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDLSSLEKSKAIISSLTM  749 (891)
T ss_pred             eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            677899999999999999999999999999999 88885      367888885 9999999999998864

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.47  E-value=0.0005  Score=56.01  Aligned_cols=103  Identities=17%  Similarity=0.287  Sum_probs=71.4

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCC
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR  223 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~  223 (330)
                      .+-++|....+|..||++|++|+.|++..|-+|.+-.                  .+.++..      +|...+.-....
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------------------YSENLEE------FVANKLAPAEVK   89 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE------------------cCCCHHH------HHHHcCCCceEE
Confidence            6778899999999999999999999998888887753                  2222222      222222110000


Q ss_pred             CCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEe
Q 020173          224 QVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVY  288 (330)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~  288 (330)
                         .....               .........+.||.+..+..|||+|++++.....++-++.|.
T Consensus        90 ---~V~i~---------------~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        90 ---NVTVS---------------EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             ---EEEEE---------------cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence               00000               001235677889999999999999999999999999888775

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.

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

Probab=97.42  E-value=0.00031  Score=65.88  Aligned_cols=72  Identities=24%  Similarity=0.275  Sum_probs=60.4

Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHHHH
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQ  325 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~~~  325 (330)
                      ....-|.|-+++||.+||++|++|+.|+..|+++|+|.+.   ..+-.|+|.|.-+--.+|+..|...+..+-..
T Consensus        46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~m~~kaka~id~~~~k~e~y  117 (629)
T KOG0336|consen   46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINHMRKKAKASIDRGQDKDERY  117 (629)
T ss_pred             CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHHHHHHHHhhHhhhhhhhhhc
Confidence            4566788999999999999999999999999999999973   45678999999888888888887766554433

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

Probab=97.38  E-value=0.00015  Score=64.15  Aligned_cols=41  Identities=24%  Similarity=0.589  Sum_probs=36.9

Q ss_pred             CCceEEEEEecCC------ccceeecccChhhhhhhhccCcEEEEec
Q 020173           47 AQDVLFRIIVPSR------QIGKVIGKEGHRIQKIREETKATIKIAD   87 (330)
Q Consensus        47 ~~~~~~~i~vP~~------~vg~IIGk~G~~Ik~I~~~tg~~I~i~~   87 (330)
                      .-.++.+|+||.+      +||.|+|++|.++|+|+++|||+|.|.-
T Consensus        89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG  135 (259)
T KOG1588|consen   89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG  135 (259)
T ss_pred             ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence            3457889999985      8999999999999999999999999973

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

Probab=97.31  E-value=0.0017  Score=61.93  Aligned_cols=78  Identities=21%  Similarity=0.262  Sum_probs=56.5

Q ss_pred             ceEEEEEeec------cccceecCCCChhHHHHHHHhCCeEEEeCCCCCC---------cccCCCCCCcEEEEEcC-HHH
Q 020173          142 ANTIRLLIAG------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP---------LCASAHESDRVVQISGD-VPA  205 (330)
Q Consensus       142 ~~~~~llip~------~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p---------~~~~~~~~~r~v~I~G~-~~~  205 (330)
                      ..+.+++||.      .++|+|||..|.|.|+|+++|||+|.|-.+..+.         .......++=-+.|+++ .+.
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            3567888885      5789999999999999999999999997522111         11110122234677774 788


Q ss_pred             HHHHHHHHHHHHhh
Q 020173          206 VLNALVEIGNQLRE  219 (330)
Q Consensus       206 v~~A~~~I~~~i~~  219 (330)
                      |.+|++.|..+|.+
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            88899999999986

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

Probab=97.24  E-value=0.00047  Score=64.67  Aligned_cols=56  Identities=27%  Similarity=0.446  Sum_probs=48.9

Q ss_pred             CCCCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCC
Q 020173           45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD  103 (330)
Q Consensus        45 ~~~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~  103 (330)
                      +...++.+++.|-+++||.+||++|++|+.|+..|+++|+|-..   ..+-.++|-|..
T Consensus        42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~   97 (629)
T KOG0336|consen   42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGIN   97 (629)
T ss_pred             cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechH
Confidence            34578999999999999999999999999999999999999875   456678888863

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=97.24  E-value=0.023  Score=49.64  Aligned_cols=129  Identities=15%  Similarity=0.117  Sum_probs=97.7

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCC
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR  223 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~  223 (330)
                      .+.+.++....-++...+|..++.|....|++|.+..            ....+.|+|+...+..+...|...+...   
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~------------~~~~i~I~g~k~~~~~i~~~i~~~l~~i---   91 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR------------SENRIRITGTKSTAEYIEASINEILSNI---   91 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec------------CCcEEEEEccHHHHHHHHHHHHHHHhhc---
Confidence            4566667888889999999999999888999999974            3568999999999999998888888754   


Q ss_pred             CCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceec----CCCchHHHHHHHhCCeEEEeCCCCCCceeEE
Q 020173          224 QVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIG----RCGSNISRIRNESGAMIKVYGGKGEQKHRHI  299 (330)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIG----k~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v  299 (330)
                                                  .+..|.++.-.--.--+    .....++.|++.|++.|...++     ...+
T Consensus        92 ----------------------------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~-----~~~~  138 (210)
T PF14611_consen   92 ----------------------------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD-----GNKL  138 (210)
T ss_pred             ----------------------------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC-----CCeE
Confidence                                        55566666443211111    2357899999999999998863     2234


Q ss_pred             EEE-----cCHHHHHHHHHHHHHHHH
Q 020173          300 QFG-----GSAQQVALAKQRVDEYIY  320 (330)
Q Consensus       300 ~I~-----Gt~~~v~~A~~~I~~~i~  320 (330)
                      .|+     -....++.|++++.-.+.
T Consensus       139 ~i~~~~~~~~~~~~~~a~RlL~~a~~  164 (210)
T PF14611_consen  139 KISWLASPENEKRADRAKRLLLWALD  164 (210)
T ss_pred             EEEEEeeccccchHHHHHHHHHHhcc
Confidence            444     468899999999987664

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

Probab=97.22  E-value=0.00092  Score=66.60  Aligned_cols=65  Identities=20%  Similarity=0.308  Sum_probs=57.2

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~~~  322 (330)
                      ....+.|+.+.++.+||++|.+|++|.++||++|.+.++      -.|.|.++ .+.++.|+..|..+..+.
T Consensus       552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd------Gtv~i~~s~~~~~~~ak~~I~~i~~e~  617 (692)
T COG1185         552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD------GTVKIAASDGESAKKAKERIEAITREV  617 (692)
T ss_pred             ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC------CcEEEEecchHHHHHHHHHHHHHHhhc
Confidence            567899999999999999999999999999999999942      45899897 588999999999887553

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.05  E-value=0.0023  Score=65.65  Aligned_cols=94  Identities=22%  Similarity=0.192  Sum_probs=64.9

Q ss_pred             hHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCccc
Q 020173          109 SDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCA  188 (330)
Q Consensus       109 ~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~  188 (330)
                      ..+.++...|.+.+.+........    ....-+....+.||...++.|||++|++||.|.++|||+|.|..        
T Consensus       521 ~~a~~~~~~I~~~m~~~l~~~~~~----~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d--------  588 (684)
T TIGR03591       521 EQAKEGRLHILGEMNKVISEPRAE----LSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED--------  588 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhcc----ccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec--------
Confidence            344555566666554432211100    01112346788899999999999999999999999999999952        


Q ss_pred             CCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhh
Q 020173          189 SAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       189 ~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  219 (330)
                           +..|.|.+ ....+.+|...|..+...
T Consensus       589 -----dG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       589 -----DGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             -----CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence                 34566665 678888898888877653

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).

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

Probab=97.03  E-value=0.00061  Score=62.02  Aligned_cols=71  Identities=34%  Similarity=0.391  Sum_probs=57.5

Q ss_pred             ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhc
Q 020173           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (330)
Q Consensus        49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~  125 (330)
                      +....+++++.+.|.|||++|.+.++|+++|+|+|.+|.+  ++....++|.|-.    ...|..|..+|..+|...
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~~----~~~V~~a~~Ri~~~ids~  126 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGIS----RNCVIQALERIAKLIDSD  126 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeehh----HHHHHHHHHHHHHHHHhh
Confidence            4667889999999999999999999999999999999987  3344456666643    467888888888887543

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

Probab=96.96  E-value=0.0053  Score=54.46  Aligned_cols=42  Identities=26%  Similarity=0.514  Sum_probs=37.0

Q ss_pred             CcceEEEEEEccc------cccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173          249 ADYVTFEMLISES------LVGGLIGRCGSNISRIRNESGAMIKVYGG  290 (330)
Q Consensus       249 ~~~~~~~v~IP~~------~vg~IIGk~G~~Ik~i~~~tga~I~i~~~  290 (330)
                      ....+.+|.||-.      +||+|+|.+|.++|+|+++|||+|.|-..
T Consensus        89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr  136 (259)
T KOG1588|consen   89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR  136 (259)
T ss_pred             ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence            3457788888865      99999999999999999999999999864

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

Probab=96.93  E-value=0.0013  Score=59.90  Aligned_cols=72  Identities=24%  Similarity=0.265  Sum_probs=59.7

Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHH
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQL  323 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~  323 (330)
                      .+...+.++..+.|.|||++|.+.+.|+++|+++|.+|.+.+. .+.++.+.++-++|..|...|.-+|.+.-
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 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTN-KEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCC-cceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            4667789999999999999999999999999999999986422 23344445579999999999998887764

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

Probab=96.92  E-value=0.00093  Score=46.38  Aligned_cols=37  Identities=30%  Similarity=0.504  Sum_probs=34.2

Q ss_pred             ceEEEEEecCCccceeecccChhhhhhhhccCcEEEE
Q 020173           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI   85 (330)
Q Consensus        49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i   85 (330)
                      .....+.||.+..|..|||+|.+|+.+++.+|-+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            4678999999999999999999999999999988876

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.

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.84  E-value=0.0029  Score=56.42  Aligned_cols=66  Identities=21%  Similarity=0.220  Sum_probs=56.5

Q ss_pred             EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHHHHHH
Q 020173          253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIYSQLI  324 (330)
Q Consensus       253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~~~~~  324 (330)
                      -+.+.||..+++.+||++|.+|+.|.+.+++.|.+..      +-.|-|+|+ .+.++.|+.+|..+-++.++
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~  212 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDEEDEEIAIEAIKKIEREAHT  212 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence            3678999999999999999999999999999999985      356888886 77999999999877665543

>PRK00106 hypothetical protein; Provisional

Probab=96.82  E-value=0.0067  Score=60.04  Aligned_cols=67  Identities=16%  Similarity=0.335  Sum_probs=55.7

Q ss_pred             cceEEEEEEccc-cccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEc-CHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISES-LVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGG-SAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       250 ~~~~~~v~IP~~-~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~G-t~~~v~~A~~~I~~~i~~  321 (330)
                      ..+...|.+|++ +-|+|||+-|.+|+.+...||+.|-|.+     +...|+|+| .|---+.|+.-+..+|.+
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-----tp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD-----TPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC-----CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            446678899996 5599999999999999999999999995     234678999 588888888888777764

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.79  E-value=0.0067  Score=60.17  Aligned_cols=67  Identities=16%  Similarity=0.320  Sum_probs=55.3

Q ss_pred             cceEEEEEEccc-cccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEc-CHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISES-LVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGG-SAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       250 ~~~~~~v~IP~~-~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~G-t~~~v~~A~~~I~~~i~~  321 (330)
                      ..+...|.+|++ +-|+|||+.|.+|+.+...||+.|-|.+     +...|+|+| .|---+.|+.-+..+|.+
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC-----CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            346677899996 5599999999999999999999999995     234677998 488888888888777754

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.77  E-value=0.0051  Score=52.69  Aligned_cols=101  Identities=20%  Similarity=0.248  Sum_probs=68.4

Q ss_pred             EEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCC
Q 020173          146 RLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV  225 (330)
Q Consensus       146 ~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~  225 (330)
                      -+.+-...+|..||++|++++.|+++.|-+|.+-.-          ++        ++      ...|...+.  |- ..
T Consensus        79 ~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~----------s~--------d~------~~fI~nal~--Pa-~v  131 (190)
T COG0195          79 SNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW----------SE--------DP------AEFIKNALA--PA-EV  131 (190)
T ss_pred             EeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe----------CC--------CH------HHHHHHhcC--cc-eE
Confidence            334445678999999999999999999977776532          11        11      123333332  10 00


Q ss_pred             cccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeC
Q 020173          226 ISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG  289 (330)
Q Consensus       226 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~  289 (330)
                      .++...+                .......+.||++..+..||++|.+++-..+.||-++.|..
T Consensus       132 ~~V~~~~----------------~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         132 LSVNIKE----------------DDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             eEEEEEe----------------CCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            0110000                01126788899999999999999999999999999999985

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.76  E-value=0.0025  Score=65.53  Aligned_cols=63  Identities=21%  Similarity=0.336  Sum_probs=54.1

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIY  320 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~  320 (330)
                      ....+.||.+.++.+||.||.+||.|.++||+.|.+.+      +-.|.|.+. .+.++.|+++|..+..
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~~~~~~a~~~I~~~~~  617 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDGEAAEAAKERIEGITA  617 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccHHHHHHHHHHHHHhcc
Confidence            45567789999999999999999999999999888863      356888885 8999999999988764

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.70  E-value=0.0065  Score=52.04  Aligned_cols=102  Identities=22%  Similarity=0.319  Sum_probs=67.3

Q ss_pred             EEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCcc
Q 020173           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSE  131 (330)
Q Consensus        52 ~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~  131 (330)
                      +-+.+-...+|..||++|.+|+.|.++.|=+|+|-.-             +++.  ..-+.+|+.       .   ....
T Consensus        78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-------------s~d~--~~fI~nal~-------P---a~v~  132 (190)
T COG0195          78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-------------SEDP--AEFIKNALA-------P---AEVL  132 (190)
T ss_pred             EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-------------CCCH--HHHHHHhcC-------c---ceEe
Confidence            3444445678999999999999999999977776542             1110  112222221       0   0000


Q ss_pred             ccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeC
Q 020173          132 ASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (330)
Q Consensus       132 ~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~  180 (330)
                      .-.. ... ......+.||....+..||++|.+++...+-||-++.|..
T Consensus       133 ~V~~-~~~-d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         133 SVNI-KED-DGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEE-EeC-CCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            0000 000 1116788899999999999999999999999999999864

>PRK12704 phosphodiesterase; Provisional

Probab=96.68  E-value=0.0093  Score=59.26  Aligned_cols=67  Identities=15%  Similarity=0.311  Sum_probs=53.5

Q ss_pred             cceEEEEEEccc-cccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEc-CHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISES-LVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGG-SAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       250 ~~~~~~v~IP~~-~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~G-t~~~v~~A~~~I~~~i~~  321 (330)
                      ..+...|.+|++ +-|+|||+.|.+||.+...||+.|-|.+     +...|.|+| .|-.-+.|+.-+..++.+
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC-----CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence            346667889996 5599999999999999999999999995     235678999 477767777777666543

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

Probab=96.65  E-value=0.0032  Score=43.65  Aligned_cols=36  Identities=19%  Similarity=0.351  Sum_probs=33.8

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEE
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV  287 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i  287 (330)
                      ....+.||.+..|..|||+|.+|+.++..+|-+|.+
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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.50  E-value=0.0073  Score=62.87  Aligned_cols=95  Identities=17%  Similarity=0.216  Sum_probs=67.5

Q ss_pred             hhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCe-EEEeCCCCCCc
Q 020173          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT-IVILAPNQLPL  186 (330)
Q Consensus       108 ~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~-I~i~~~~~~p~  186 (330)
                      +..+.+|+..|.+.+.+........    ....-.....+-||...++.|||.+|.+||.|.++||+. |.+.       
T Consensus       654 L~~A~~g~~~Il~~M~~~i~~pr~~----~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-------  722 (891)
T PLN00207        654 LLQAKDGRKHILAEMSKCSPPPSKR----LSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-------  722 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhh----hcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-------
Confidence            3444555566666665543221110    111223467889999999999999999999999999999 8773       


Q ss_pred             ccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhh
Q 020173          187 CASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       187 ~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  219 (330)
                            ++-.|.|.+ +.+.+.+|+.+|..++.+
T Consensus       723 ------ddg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        723 ------DDGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             ------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence                  345677777 688999999999888864

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

Probab=96.45  E-value=0.0046  Score=52.67  Aligned_cols=43  Identities=21%  Similarity=0.458  Sum_probs=37.3

Q ss_pred             CCCceEEEEEecC------CccceeecccChhhhhhhhccCcEEEEecC
Q 020173           46 KAQDVLFRIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADA   88 (330)
Q Consensus        46 ~~~~~~~~i~vP~------~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (330)
                      ....++-++.||.      +++|+|||+.|.++|+|+..|+|+|-|.-.
T Consensus       144 rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         144 RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             CcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            3456777888886      689999999999999999999999999754

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

Probab=96.34  E-value=0.012  Score=58.87  Aligned_cols=96  Identities=20%  Similarity=0.204  Sum_probs=70.5

Q ss_pred             hhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 020173          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (330)
Q Consensus       108 ~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~  187 (330)
                      +..+..|...|+..+.+........    ..........+-|+.....-+||++|.+|++|.+++|++|.+.        
T Consensus       521 L~QAk~aRlhIL~~M~~ai~~pr~e----ls~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie--------  588 (692)
T COG1185         521 LEQAKGARLHILIVMNEAISEPRKE----LSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE--------  588 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhh----hhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec--------
Confidence            4556677777877776544322100    0111233667889999999999999999999999999999995        


Q ss_pred             cCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhhC
Q 020173          188 ASAHESDRVVQISGD-VPAVLNALVEIGNQLREN  220 (330)
Q Consensus       188 ~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~~~  220 (330)
                           ++..|.|.++ .+.+.+|+..|..+.++-
T Consensus       589 -----ddGtv~i~~s~~~~~~~ak~~I~~i~~e~  617 (692)
T COG1185         589 -----DDGTVKIAASDGESAKKAKERIEAITREV  617 (692)
T ss_pred             -----CCCcEEEEecchHHHHHHHHHHHHHHhhc
Confidence                 3456888876 588888999999998764

>PRK00468 hypothetical protein; Provisional

Probab=96.14  E-value=0.0051  Score=44.47  Aligned_cols=34  Identities=35%  Similarity=0.587  Sum_probs=29.6

Q ss_pred             CCCceEEEEEecCCccceeecccChhhhhhhhcc
Q 020173           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET   79 (330)
Q Consensus        46 ~~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~t   79 (330)
                      .++.+.+++.+..+..|.||||+|.+++.||.--
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            3456889999999999999999999999998643

>TIGR01953 NusA transcription termination factor NusA

Probab=96.12  E-value=0.02  Score=53.78  Aligned_cols=95  Identities=23%  Similarity=0.319  Sum_probs=63.3

Q ss_pred             CccceeecccChhhhhhhhcc-CcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCcccccccc
Q 020173           59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (330)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~  137 (330)
                      +-+|+.||++|.+|+.|.++. |=+|+|-.-.   +        .+    ..-+.+|+.-       ..     -..+.-
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s---~--------d~----~~fi~nal~P-------a~-----v~~v~i  295 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYS---D--------DP----AEFIANALSP-------AK-----VISVEV  295 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcC---C--------CH----HHHHHHhcCC-------ce-----EEEEEE
Confidence            459999999999999999998 7778775421   0        00    0111111110       00     000000


Q ss_pred             CCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeC
Q 020173          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (330)
Q Consensus       138 ~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~  180 (330)
                      .........+.||..+.+..||++|.|++-...-||.+|.|..
T Consensus       296 ~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       296 LDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             EcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            0001136889999999999999999999999999999999975

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=96.04  E-value=0.017  Score=54.49  Aligned_cols=96  Identities=21%  Similarity=0.194  Sum_probs=64.2

Q ss_pred             CccceeecccChhhhhhhhcc-CcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCcccccccc
Q 020173           59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (330)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~  137 (330)
                      +-+|+.||++|.+|+.|.++. |=+|+|-.-.             ++         -..-|...+....     -..+..
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s-------------~D---------~~~fI~Nal~Pa~-----V~~V~i  303 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYS-------------NV---------PEIFIARALAPAI-----ISSVKI  303 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhCCCce-----eeEEEE
Confidence            458999999999999999988 7777775421             10         0001111111000     000000


Q ss_pred             CCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCC
Q 020173          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN  182 (330)
Q Consensus       138 ~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~  182 (330)
                      . .......+.||..+.+..||++|.+++-...-+|.+|.|..-+
T Consensus       304 ~-~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~  347 (374)
T PRK12328        304 E-EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG  347 (374)
T ss_pred             c-CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence            0 1123678899999999999999999999999999999998644

>PRK02821 hypothetical protein; Provisional

Probab=95.98  E-value=0.0064  Score=44.12  Aligned_cols=35  Identities=26%  Similarity=0.438  Sum_probs=30.1

Q ss_pred             CCceEEEEEecCCccceeecccChhhhhhhhccCc
Q 020173           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKA   81 (330)
Q Consensus        47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~   81 (330)
                      .+.+.+++.+..+..|.||||+|.+++.||.--.+
T Consensus        28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            45578999999999999999999999999965543

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.78  E-value=0.028  Score=53.10  Aligned_cols=96  Identities=23%  Similarity=0.302  Sum_probs=64.0

Q ss_pred             CccceeecccChhhhhhhhcc-CcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCcccccccc
Q 020173           59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (330)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~  137 (330)
                      +-+|+.||++|.+|+.|.++. |=+|+|-.-.             +         +-...|...+....     -..+.-
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s-------------~---------d~~~fi~nal~Pa~-----v~~v~i  297 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWS-------------E---------DPAEFVANALSPAK-----VVSVEV  297 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcC-------------C---------CHHHHHHHhCCCce-----EEEEEE
Confidence            459999999999999999888 7888875421             1         00011111111000     000000


Q ss_pred             CCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCC
Q 020173          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (330)
Q Consensus       138 ~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~  181 (330)
                      .........+.||..+.+..||++|.|++-...-+|.+|.|...
T Consensus       298 ~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        298 DDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             EcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            00112368899999999999999999999999999999999754

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.72  E-value=0.024  Score=53.40  Aligned_cols=95  Identities=17%  Similarity=0.168  Sum_probs=65.0

Q ss_pred             ccceecCCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCC
Q 020173          153 QAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPA  231 (330)
Q Consensus       153 ~~g~iIG~~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~  231 (330)
                      -+|..||.+|++|+.|.++. |-+|.+-.-          +++.              ..+|...|.-.   ...++.  
T Consensus       252 PvGacIG~~G~rI~~I~~eL~gEkIDvI~~----------s~D~--------------~~fI~Nal~Pa---~V~~V~--  302 (374)
T PRK12328        252 PIGATVGVKGVRINAVSKELNGENIDCIEY----------SNVP--------------EIFIARALAPA---IISSVK--  302 (374)
T ss_pred             hHHhhcCCCcchHHHHHHHhCCCeEEEEEc----------CCCH--------------HHHHHHhCCCc---eeeEEE--
Confidence            47999999999999998887 777877642          1221              11222222100   000000  


Q ss_pred             CCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC
Q 020173          232 YNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK  291 (330)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~  291 (330)
                                     -........+.||.+..+.-|||+|++++-....||.+|.|..-.
T Consensus       303 ---------------i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~  347 (374)
T PRK12328        303 ---------------IEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG  347 (374)
T ss_pred             ---------------EcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence                           001235678999999999999999999999999999999998653

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.63  E-value=0.025  Score=58.30  Aligned_cols=95  Identities=21%  Similarity=0.202  Sum_probs=66.1

Q ss_pred             hhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 020173          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (330)
Q Consensus       108 ~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~  187 (330)
                      +..+.+++..|.+.+.+.........    .........+.|+...++.+||.+|.+||.|.+++|+.|.+.        
T Consensus       523 l~~a~~g~~~I~~~M~~aI~~~r~~~----~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~--------  590 (693)
T PRK11824        523 LEQAKEGRLHILGKMNEAISEPRAEL----SPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE--------  590 (693)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCChhhh----cccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC--------
Confidence            34556666777777765433221111    011123456667889999999999999999999999988763        


Q ss_pred             cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhh
Q 020173          188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  219 (330)
                           ++..|.|.+ ..+.+.+|...|..+..+
T Consensus       591 -----d~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        591 -----DDGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             -----CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence                 345677777 688888899988887754

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

Probab=95.61  E-value=0.026  Score=48.18  Aligned_cols=40  Identities=28%  Similarity=0.402  Sum_probs=33.9

Q ss_pred             eEEEEEee------ccccceecCCCChhHHHHHHHhCCeEEEeCCC
Q 020173          143 NTIRLLIA------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPN  182 (330)
Q Consensus       143 ~~~~llip------~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~  182 (330)
                      ++-+++||      ..++|+|||+.|+++|+|++.|+|+|.|-...
T Consensus       148 ~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g  193 (269)
T COG5176         148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG  193 (269)
T ss_pred             ccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence            45677777      45799999999999999999999999996543

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.56  E-value=0.031  Score=54.74  Aligned_cols=92  Identities=24%  Similarity=0.379  Sum_probs=63.2

Q ss_pred             ccceeecccChhhhhhhhcc-CcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHH--HHHHHhhcCCCCccccccc
Q 020173           60 QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQ--IAALILKDDDSNSEASKVA  136 (330)
Q Consensus        60 ~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~--i~~~i~~~~~~~~~~~~~~  136 (330)
                      -+|+.||++|.+|+.|.++. |=+|+|-.-.   ++.            ..-+.+|+.-  +..++.+.           
T Consensus       246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s---~d~------------~~fi~nal~pa~v~~v~~~~-----------  299 (470)
T PRK09202        246 PVGACVGMRGSRIQAISNELGGEKIDIILWS---DDP------------AQFIINALSPAEVSSVVVDE-----------  299 (470)
T ss_pred             hhHccCCCCCchHHHHHHHhCCCeEEEEEcC---CCH------------HHHHHHhCCCCEEEEEEEeC-----------
Confidence            48999999999999999988 7788875421   100            0111111100  00000000           


Q ss_pred             cCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCC
Q 020173          137 AGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (330)
Q Consensus       137 ~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~  181 (330)
                          ......+.||..+.+..||++|.|++..+.-+|.+|.|...
T Consensus       300 ----~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        300 ----DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             ----CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence                11278899999999999999999999999999999999753

>PRK01064 hypothetical protein; Provisional

Probab=95.50  E-value=0.015  Score=42.33  Aligned_cols=33  Identities=36%  Similarity=0.708  Sum_probs=29.4

Q ss_pred             CCceEEEEEecCCccceeecccChhhhhhhhcc
Q 020173           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET   79 (330)
Q Consensus        47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~t   79 (330)
                      ...+.+++.|.....|.+|||+|.+|+.|+.-.
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            456889999999999999999999999999643

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

Probab=95.44  E-value=0.032  Score=54.53  Aligned_cols=69  Identities=25%  Similarity=0.228  Sum_probs=56.8

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEc-CHHHHHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGG-SAQQVALAKQRVDEYIYSQLIQ  325 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~G-t~~~v~~A~~~I~~~i~~~~~~  325 (330)
                      ......+.++++....+||.+|.+.|.|..+||+.-.+.       +..++|.. ++...+.|+.+|..++-...++
T Consensus       595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-------e~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~  664 (760)
T KOG1067|consen  595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-------EGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQ  664 (760)
T ss_pred             CceeeEEeecchhhheeecCccceeeeEeeeccceeeec-------CceEEEEecCHHHHHHHHHHHHHHhcCcccc
Confidence            346778999999999999999999999999999655554       35688877 5999999999999887664443

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.44  E-value=0.031  Score=53.63  Aligned_cols=95  Identities=23%  Similarity=0.277  Sum_probs=62.7

Q ss_pred             CccceeecccChhhhhhhhcc-CcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCcccccccc
Q 020173           59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (330)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~  137 (330)
                      +-+|+.||++|.+|+.|.++. |=+|+|-.-.             ++         -...|...+....     -..+.-
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys-------------~D---------p~~fI~NaLsPA~-----V~~V~i  329 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS-------------PD---------PATYIANALSPAR-----VDEVRL  329 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhcCCce-----eeEEEE
Confidence            459999999999999999998 7777775421             10         0001111110000     000000


Q ss_pred             CCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeC
Q 020173          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA  180 (330)
Q Consensus       138 ~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~  180 (330)
                      .........+.||..+.++.||++|.|++-...-||.+|.|..
T Consensus       330 ~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        330 VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            0001135789999999999999999999999999999999864

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

Probab=95.42  E-value=0.016  Score=41.85  Aligned_cols=32  Identities=41%  Similarity=0.637  Sum_probs=28.6

Q ss_pred             CCceEEEEEecCCccceeecccChhhhhhhhc
Q 020173           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREE   78 (330)
Q Consensus        47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~   78 (330)
                      ...+.+++-+.....|.||||+|.+|+.|+.-
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            45678999999999999999999999999854

>PRK12705 hypothetical protein; Provisional

Probab=95.36  E-value=0.045  Score=53.97  Aligned_cols=66  Identities=17%  Similarity=0.262  Sum_probs=48.7

Q ss_pred             cceEEEEEEccccc-cceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLV-GGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIY  320 (330)
Q Consensus       250 ~~~~~~v~IP~~~v-g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~  320 (330)
                      ......+.+|++-. |+|||+-|.+|+.+...||+.|.|.+.     ...|+|++- |.--+.|...+..+|.
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt-----p~~V~ls~fdp~rreia~~~l~~Li~  263 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT-----PEAVVISSFNPIRREIARLTLEKLLA  263 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC-----ccchhhcccCccchHHHHHHHHHHHh
Confidence            34666788998755 999999999999999999999999963     234666664 5555555555555543

>TIGR01953 NusA transcription termination factor NusA

Probab=95.31  E-value=0.05  Score=51.10  Aligned_cols=94  Identities=24%  Similarity=0.312  Sum_probs=63.9

Q ss_pred             ccceecCCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCC
Q 020173          153 QAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPA  231 (330)
Q Consensus       153 ~~g~iIG~~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~  231 (330)
                      -+|..||.+|++|+.|.++. |-+|.+-.-          +++.              ..+|...|.-...   .++   
T Consensus       244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~----------s~d~--------------~~fi~nal~Pa~v---~~v---  293 (341)
T TIGR01953       244 PVGACVGPKGSRIQAISKELNGEKIDIIEY----------SDDP--------------AEFIANALSPAKV---ISV---  293 (341)
T ss_pred             cceeeECCCCchHHHHHHHhCCCeEEEEEc----------CCCH--------------HHHHHHhcCCceE---EEE---
Confidence            37999999999999999887 777777642          2221              1122222210000   000   


Q ss_pred             CCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeC
Q 020173          232 YNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG  289 (330)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~  289 (330)
                                 ..  .........+.||.+..+.-|||+|.+++-....||.+|.|..
T Consensus       294 -----------~i--~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       294 -----------EV--LDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             -----------EE--EcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence                       00  0012257889999999999999999999999999999999975

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.16  E-value=0.043  Score=53.74  Aligned_cols=103  Identities=20%  Similarity=0.304  Sum_probs=68.8

Q ss_pred             EEEEEeecc-----ccceecCCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 020173          144 TIRLLIAGS-----QAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (330)
Q Consensus       144 ~~~llip~~-----~~g~iIG~~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  217 (330)
                      ..++.|-+.     -+|..||.+|++|+.|.++. |-+|.+..-          +++.              ..+|...|
T Consensus       232 RaKvAV~s~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~----------s~d~--------------~~fi~nal  287 (470)
T PRK09202        232 RAKIAVKSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILW----------SDDP--------------AQFIINAL  287 (470)
T ss_pred             eeEEEEEcCCCCCChhHccCCCCCchHHHHHHHhCCCeEEEEEc----------CCCH--------------HHHHHHhC
Confidence            345555432     37999999999999999887 777777642          2221              11222222


Q ss_pred             hhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173          218 RENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG  290 (330)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~  290 (330)
                      .-....   .+.                 -........+.||.+..+.-|||+|++++-....||.+|.|...
T Consensus       288 ~pa~v~---~v~-----------------~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        288 SPAEVS---SVV-----------------VDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             CCCEEE---EEE-----------------EeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            110000   000                 00112578899999999999999999999999999999999863

>PRK00468 hypothetical protein; Provisional

Probab=95.15  E-value=0.027  Score=40.70  Aligned_cols=32  Identities=25%  Similarity=0.380  Sum_probs=28.2

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHh
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNES  281 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~t  281 (330)
                      ....+++.+.++-+|+||||+|.+|+.|+.--
T Consensus        28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            34778899999999999999999999998764

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.10  E-value=0.06  Score=50.95  Aligned_cols=95  Identities=19%  Similarity=0.262  Sum_probs=64.7

Q ss_pred             ccceecCCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCC
Q 020173          153 QAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPA  231 (330)
Q Consensus       153 ~~g~iIG~~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~  231 (330)
                      -+|..||++|++|+.|.++. |-+|.+-.-          +++.              ..+|...|.-...   .++   
T Consensus       246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~----------s~d~--------------~~fi~nal~Pa~v---~~v---  295 (362)
T PRK12327        246 AKGACVGPKGQRVQNIVSELKGEKIDIIDW----------SEDP--------------AEFVANALSPAKV---VSV---  295 (362)
T ss_pred             chheeECCCChhHHHHHHHhCCCeEEEEEc----------CCCH--------------HHHHHHhCCCceE---EEE---
Confidence            47999999999999998887 777777642          2221              1122222210000   000   


Q ss_pred             CCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173          232 YNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG  290 (330)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~  290 (330)
                                   .-.........+.||.+..+.-|||+|.+++-....||.+|.|...
T Consensus       296 -------------~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        296 -------------EVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             -------------EEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence                         0000123568899999999999999999999999999999999864

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=95.01  E-value=0.061  Score=47.94  Aligned_cols=65  Identities=22%  Similarity=0.227  Sum_probs=53.2

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhhCC
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLRENP  221 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~~~~  221 (330)
                      -+.+-||...++.+||++|.+|+.|.+.+++.|.+-             .+..|.|.+. .+++.+|..+|..+-++..
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-------------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~  211 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-------------QNGRIWIKGPDEEDEEIAIEAIKKIEREAH  211 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-------------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence            356889999999999999999999999999999883             3456888886 5578888888877776653

>PRK02821 hypothetical protein; Provisional

Probab=94.98  E-value=0.031  Score=40.59  Aligned_cols=33  Identities=27%  Similarity=0.383  Sum_probs=28.9

Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCC
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGA  283 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga  283 (330)
                      ...+.+.+.++-+|+||||+|.+|+.|+.--.+
T Consensus        30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             cEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            367899999999999999999999999887543

>PRK12704 phosphodiesterase; Provisional

Probab=94.91  E-value=0.048  Score=54.24  Aligned_cols=51  Identities=25%  Similarity=0.484  Sum_probs=42.2

Q ss_pred             CceEEEEEecC-CccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCC
Q 020173           48 QDVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD  103 (330)
Q Consensus        48 ~~~~~~i~vP~-~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~  103 (330)
                      ...+-.+.+|+ +.-|.||||.|.||+.++.-||+.|-|++.    + .+|+++|-+
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt----p-~~v~ls~~~  259 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----P-EAVILSGFD  259 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC----C-CeEEEecCC
Confidence            34566778898 569999999999999999999999999874    3 457788853

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=94.83  E-value=0.065  Score=51.47  Aligned_cols=103  Identities=18%  Similarity=0.260  Sum_probs=67.7

Q ss_pred             EEEEEeecc-----ccceecCCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 020173          144 TIRLLIAGS-----QAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (330)
Q Consensus       144 ~~~llip~~-----~~g~iIG~~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  217 (330)
                      ..++.|-+.     -+|..||.+|++|+.|.++. |-+|.+..-          +++.              ..+|...|
T Consensus       264 RtKVAV~S~d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~y----------s~Dp--------------~~fI~NaL  319 (449)
T PRK12329        264 RTKIAVDTLERDVDPVGACIGARGSRIQAVVNELRGEKIDVIRW----------SPDP--------------ATYIANAL  319 (449)
T ss_pred             eeEEEEEcCCCCCChhhccCCCCcchHHHHHHHhCCCeEEEEEc----------CCCH--------------HHHHHHhc
Confidence            445555432     37999999999999999887 777777542          1221              11222222


Q ss_pred             hhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeC
Q 020173          218 RENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG  289 (330)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~  289 (330)
                      .-....   ++.              .  .........+.||.+..+.-|||+|.+++-....||.+|.|..
T Consensus       320 sPA~V~---~V~--------------i--~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        320 SPARVD---EVR--------------L--VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             CCceee---EEE--------------E--EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            100000   000              0  0012245789999999999999999999999999999999985

>PRK00106 hypothetical protein; Provisional

Probab=94.66  E-value=0.11  Score=51.50  Aligned_cols=64  Identities=23%  Similarity=0.375  Sum_probs=48.9

Q ss_pred             EEEEEeec-cccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhh
Q 020173          144 TIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       144 ~~~llip~-~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  219 (330)
                      ...+.+|+ .+-|+|||+.|.||+.|+.-||+.+-|..            +...|+|+| +|---.-|...+..++.+
T Consensus       226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd------------tp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD------------TPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC------------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            45667787 57799999999999999999999999852            334677888 565555566666666654

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=94.63  E-value=0.11  Score=51.68  Aligned_cols=64  Identities=22%  Similarity=0.332  Sum_probs=48.3

Q ss_pred             EEEEEeec-cccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhh
Q 020173          144 TIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       144 ~~~llip~-~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  219 (330)
                      ...+.+|+ .+-|+|||+.|.||+.|+..||+.+-|..            +...|+|+| +|---.-|...+..++.+
T Consensus       205 ~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd------------tp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       205 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD------------TPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             eeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC------------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            45667777 57799999999999999999999999852            334677888 455555566666666654

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=94.54  E-value=1.9  Score=37.47  Aligned_cols=130  Identities=15%  Similarity=0.119  Sum_probs=83.2

Q ss_pred             EEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCccc
Q 020173           53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEA  132 (330)
Q Consensus        53 ~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~  132 (330)
                      .+.++....-++...+|..++.|-...||+|.+..     ++..+.|+|++     ..+..+...|.+.+..-       
T Consensus        29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k-----~~~~~i~~~i~~~l~~i-------   91 (210)
T PF14611_consen   29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTK-----STAEYIEASINEILSNI-------   91 (210)
T ss_pred             EEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccH-----HHHHHHHHHHHHHHhhc-------
Confidence            34445778889999999999999888899999986     35679999986     23333333344433211       


Q ss_pred             cccccCCCcceEEEEEeeccccceec-C---CCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEE-----cCH
Q 020173          133 SKVAAGHVAANTIRLLIAGSQAGCLI-G---MSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS-----GDV  203 (330)
Q Consensus       133 ~~~~~~~~~~~~~~llip~~~~g~iI-G---~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~-----G~~  203 (330)
                                .+..+-++.-....-. +   .....++.|++.|++.+.....            +..+.|.     -..
T Consensus        92 ----------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~------------~~~~~i~~~~~~~~~  149 (210)
T PF14611_consen   92 ----------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD------------GNKLKISWLASPENE  149 (210)
T ss_pred             ----------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC------------CCeEEEEEEeecccc
Confidence                      1333333322111111 1   1345689999999999997642            2234443     467


Q ss_pred             HHHHHHHHHHHHHHhhCC
Q 020173          204 PAVLNALVEIGNQLRENP  221 (330)
Q Consensus       204 ~~v~~A~~~I~~~i~~~~  221 (330)
                      ..+..|..++...+...+
T Consensus       150 ~~~~~a~RlL~~a~~~~~  167 (210)
T PF14611_consen  150 KRADRAKRLLLWALDYNP  167 (210)
T ss_pred             chHHHHHHHHHHhccCCc
Confidence            788888988888885443

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

Probab=94.07  E-value=0.0093  Score=62.41  Aligned_cols=72  Identities=19%  Similarity=0.117  Sum_probs=61.6

Q ss_pred             EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCC-CCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHHH
Q 020173          253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG-KGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLI  324 (330)
Q Consensus       253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~-~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~~  324 (330)
                      .-++.+|-....+|||++|.+|+.++..||+.|.+.+- .+...+|.+.+.|.++.+..|-..|.-.|.+..+
T Consensus      1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpdv 1413 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPDV 1413 (2131)
T ss_pred             ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeecCCc
Confidence            45788999999999999999999999999999999983 3345699999999999999999888877765443

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

Probab=94.03  E-value=0.069  Score=38.53  Aligned_cols=32  Identities=31%  Similarity=0.456  Sum_probs=28.2

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHHh
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS  172 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~s  172 (330)
                      ....+++.+.....|.+||++|.+|+.|+.--
T Consensus        28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             CeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            45578999999999999999999999999753

>PRK01064 hypothetical protein; Provisional

Probab=93.69  E-value=0.088  Score=38.33  Aligned_cols=32  Identities=25%  Similarity=0.515  Sum_probs=28.2

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHh
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNES  281 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~t  281 (330)
                      ....+++.+..+-.|.+|||+|.+|+.|+.-.
T Consensus        28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            44778899999999999999999999998753

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

Probab=93.39  E-value=0.23  Score=42.35  Aligned_cols=155  Identities=17%  Similarity=0.150  Sum_probs=92.2

Q ss_pred             eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCC
Q 020173           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN  129 (330)
Q Consensus        50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~  129 (330)
                      -+-++.||.....-+=-.==..-.-|-+..+.+|.+.-.     .|-+.+.-..+.....+.+++..-+..++...+...
T Consensus        74 e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK-----~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~D  148 (252)
T KOG3273|consen   74 ETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLK-----ARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDD  148 (252)
T ss_pred             ceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecc-----cceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchh
Confidence            345677777655332100001112255677777777643     244444433333234666777777777766554322


Q ss_pred             ccc------cccc-cCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC
Q 020173          130 SEA------SKVA-AGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD  202 (330)
Q Consensus       130 ~~~------~~~~-~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~  202 (330)
                      .-.      .... ..-....+++=.=-+..+|+|+|++|.+--.|++.|-++|.+.              +..|.|-|.
T Consensus       149 AiALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla--------------d~kIHiLG~  214 (252)
T KOG3273|consen  149 AIALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA--------------DSKIHILGA  214 (252)
T ss_pred             HHHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec--------------CceEEEeec
Confidence            100      0000 0000001111111245679999999999889999999999884              347999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCC
Q 020173          203 VPAVLNALVEIGNQLRENPPR  223 (330)
Q Consensus       203 ~~~v~~A~~~I~~~i~~~~~~  223 (330)
                      .+++.-|+..|+.+|-.+|+.
T Consensus       215 ~~niriAR~avcsLIlGsppg  235 (252)
T KOG3273|consen  215 FQNIRIARDAVCSLILGSPPG  235 (252)
T ss_pred             chhhHHHHHhhHhhhccCCch
Confidence            999999999999999888654

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=93.31  E-value=0.036  Score=39.77  Aligned_cols=35  Identities=17%  Similarity=0.352  Sum_probs=29.5

Q ss_pred             CCceEEEEEecCCccceeecccChhhhhhhhccCc
Q 020173           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKA   81 (330)
Q Consensus        47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~   81 (330)
                      .+...+.+.+..+..|.+|||+|.+++.||.-.+.
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            35667888889999999999999999999966553

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

Probab=92.70  E-value=0.15  Score=35.31  Aligned_cols=35  Identities=29%  Similarity=0.462  Sum_probs=28.3

Q ss_pred             ceEEEEEecCCccceeecccChhhhhhhhccCcEE
Q 020173           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATI   83 (330)
Q Consensus        49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I   83 (330)
                      .....+.+.....|.+||++|.+++.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            45556666666799999999999999999988544

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.

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=91.90  E-value=0.09  Score=37.67  Aligned_cols=33  Identities=24%  Similarity=0.275  Sum_probs=28.7

Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCC
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGA  283 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga  283 (330)
                      ...+.+.+..+..|.+|||+|.+++.|+.-.+.
T Consensus        28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             ceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            467888899999999999999999999876654

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

Probab=91.43  E-value=0.22  Score=35.41  Aligned_cols=38  Identities=32%  Similarity=0.392  Sum_probs=30.1

Q ss_pred             EEEEEEcccc-----ccceecCCCchHHHHHHHh-CCeEEEeCC
Q 020173          253 TFEMLISESL-----VGGLIGRCGSNISRIRNES-GAMIKVYGG  290 (330)
Q Consensus       253 ~~~v~IP~~~-----vg~IIGk~G~~Ik~i~~~t-ga~I~i~~~  290 (330)
                      ...+.|-...     +|..||.+|++|+.|.++. |-+|.+-..
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            4566777776     8999999999999999999 889988764

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

Probab=91.25  E-value=0.14  Score=43.51  Aligned_cols=122  Identities=16%  Similarity=0.130  Sum_probs=80.5

Q ss_pred             HHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCCCCCC
Q 020173          168 LRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPT  247 (330)
Q Consensus       168 I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (330)
                      |-+..+.+|.++-+...       -+-|...-+-++.+++++...|.+.+...+..+.+...        +         
T Consensus        99 ive~lklqiRmNlK~r~-------VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DAiALl--------r---------  154 (252)
T KOG3273|consen   99 IVEHLKLQIRMNLKARS-------VELRTCKDTEDPSALQKGADFVRAFILGFDIDDAIALL--------R---------  154 (252)
T ss_pred             HHHhhhheeEeecccce-------eEeecCCCCCChHHHHHHHHHHHHHHhCCcchhHHHHH--------h---------
Confidence            56777877877643110       11222333456889999999998888765432211000        0         


Q ss_pred             CCcceEEEEEE----------ccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHH
Q 020173          248 SADYVTFEMLI----------SESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDE  317 (330)
Q Consensus       248 ~~~~~~~~v~I----------P~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~  317 (330)
                      ....+...|.|          -...+|+|+|++|.+--.|++.|.++|.+.+       ..|.|-|+.+++..|+..|-.
T Consensus       155 lddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~niriAR~avcs  227 (252)
T KOG3273|consen  155 LDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQNIRIARDAVCS  227 (252)
T ss_pred             hhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchhhHHHHHhhHh
Confidence            00011112222          2347899999999999999999999999985       358999999999999998877


Q ss_pred             HHH
Q 020173          318 YIY  320 (330)
Q Consensus       318 ~i~  320 (330)
                      +|.
T Consensus       228 LIl  230 (252)
T KOG3273|consen  228 LIL  230 (252)
T ss_pred             hhc
Confidence            764

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

Probab=91.08  E-value=0.69  Score=45.59  Aligned_cols=95  Identities=20%  Similarity=0.199  Sum_probs=67.3

Q ss_pred             hhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 020173          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (330)
Q Consensus       108 ~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~  187 (330)
                      +.++.+|...|++.+.+......    ............+-++.+....+||++|...|+|..+||+.-.+         
T Consensus       566 l~~a~~ar~~Il~~m~k~i~~Pr----~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v---------  632 (760)
T KOG1067|consen  566 LQKAREARLQILDIMEKNINSPR----GSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV---------  632 (760)
T ss_pred             HHhhhHHHHHHHHHHHhhcCCcc----cCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee---------
Confidence            34556666777877765543221    11222344577888999999999999999999999999953333         


Q ss_pred             cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhhC
Q 020173          188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~~  220 (330)
                           ++..+.|-. +.....+|++.|..++...
T Consensus       633 -----De~t~~i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  633 -----DEGTFSIFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             -----cCceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence                 345677666 5778888999998888764

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=90.90  E-value=0.49  Score=45.99  Aligned_cols=154  Identities=14%  Similarity=0.157  Sum_probs=108.0

Q ss_pred             eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCC
Q 020173           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN  129 (330)
Q Consensus        50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~  129 (330)
                      ..+.+.||.+.+..|||.||..|.+++...++.|.+....    ++     |       .+          . + .+   
T Consensus       449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~----~~-----~-------qs----------~-~-~d---  497 (657)
T COG5166         449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFY----KF-----G-------QS----------Q-W-HD---  497 (657)
T ss_pred             hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhh----hc-----c-------hh----------h-h-hc---
Confidence            3567889999999999999999999999999888886531    00     1       00          0 0 00   


Q ss_pred             ccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHh----CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHH
Q 020173          130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS----GATIVILAPNQLPLCASAHESDRVVQISGDVPA  205 (330)
Q Consensus       130 ~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~s----ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~  205 (330)
                                    .+-+-.|.+-.+.|+|++.-.+..+++.+    ...|.+..           ..-+++++-|-.+.
T Consensus       498 --------------NV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~-----------~~~sI~~v~~~~~~  552 (657)
T COG5166         498 --------------NVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCP-----------QSTSIFTVDIYSDE  552 (657)
T ss_pred             --------------ceEEECCccCccchhcccccHHHHHhhhcccccccceEEcC-----------CceEEEEEcccccH
Confidence                          24566788888999999988887787665    34555542           24568999998877


Q ss_pred             HHHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceec---CCCchHHHHHHHhC
Q 020173          206 VLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIG---RCGSNISRIRNESG  282 (330)
Q Consensus       206 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIG---k~G~~Ik~i~~~tg  282 (330)
                      +.+... -...+.+.                              .....+.+|.+.++..+|   -.|++|..+.....
T Consensus       553 I~rv~k-ne~v~~~~------------------------------p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~  601 (657)
T COG5166         553 IERVIK-NETVLLEF------------------------------PAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYN  601 (657)
T ss_pred             HHHHhh-ccceEEec------------------------------ccccccccchhhhhccCCcccccccchhhhhhhhh
Confidence            665443 22222222                              133457889999999999   78999999988888


Q ss_pred             CeEEEeCC
Q 020173          283 AMIKVYGG  290 (330)
Q Consensus       283 a~I~i~~~  290 (330)
                      -.|...-.
T Consensus       602 ~~ie~~~t  609 (657)
T COG5166         602 SYIEFSTT  609 (657)
T ss_pred             ccceeecC
Confidence            88877754

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

Probab=90.54  E-value=1.3  Score=36.05  Aligned_cols=90  Identities=26%  Similarity=0.229  Sum_probs=60.4

Q ss_pred             CCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH---HHHHHHHHHHHhhCCCCCCcccCCCCCCC
Q 020173          159 GMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV---LNALVEIGNQLRENPPRQVISISPAYNYS  235 (330)
Q Consensus       159 G~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v---~~A~~~I~~~i~~~~~~~~~~~~~~~~~~  235 (330)
                      -.+|.-|++|...---+|.+-                     .+++..   ..|.+.|.+++-++-.-      .++.  
T Consensus        22 ~~~~dli~~lAk~lrKRIvvR---------------------~dps~l~~~e~A~~~I~~ivP~ea~i------~di~--   72 (145)
T cd02410          22 AEDGDLVKDLAKDLRKRIVIR---------------------PDPSVLKPPEEAIKIILEIVPEEAGI------TDIY--   72 (145)
T ss_pred             hcccHHHHHHHHHHhceEEEc---------------------CChhhcCCHHHHHHHHHHhCCCccCc------eeeE--
Confidence            344667788877766666653                     222222   35788888877443100      0111  


Q ss_pred             CCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173          236 AIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG  290 (330)
Q Consensus       236 ~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~  290 (330)
                                   ....+-++.|-...-|.+||++|.++++|...||-.-.+-+.
T Consensus        73 -------------Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          73 -------------FDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             -------------ecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence                         122456788888999999999999999999999988888764

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

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

Probab=90.54  E-value=0.17  Score=35.95  Aligned_cols=36  Identities=36%  Similarity=0.624  Sum_probs=28.8

Q ss_pred             EEEEecCCc-----cceeecccChhhhhhhhcc-CcEEEEec
Q 020173           52 FRIIVPSRQ-----IGKVIGKEGHRIQKIREET-KATIKIAD   87 (330)
Q Consensus        52 ~~i~vP~~~-----vg~IIGk~G~~Ik~I~~~t-g~~I~i~~   87 (330)
                      .++.|-+..     +|..||++|.+|+.|.++. |-+|+|-.
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            456666766     9999999999999999999 88888754

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

Probab=90.04  E-value=0.1  Score=55.02  Aligned_cols=71  Identities=20%  Similarity=0.153  Sum_probs=55.0

Q ss_pred             ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC-CCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhh
Q 020173           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (330)
Q Consensus        49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~  124 (330)
                      ....++.+|.....++||++|.+|..++.-||+.|.+.+- ..+..||.+.+.|.+     ....-|...|.-.+.+
T Consensus      1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p-----~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRP-----PSQRVATSPIGLPIID 1410 (2131)
T ss_pred             ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCC-----hhhhhhhccccceeec
Confidence            3456788999999999999999999999999999999873 345678999999987     3344454444444433

>PRK12705 hypothetical protein; Provisional

Probab=89.99  E-value=0.38  Score=47.56  Aligned_cols=41  Identities=27%  Similarity=0.436  Sum_probs=35.3

Q ss_pred             CceEEEEEecC-CccceeecccChhhhhhhhccCcEEEEecC
Q 020173           48 QDVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADA   88 (330)
Q Consensus        48 ~~~~~~i~vP~-~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (330)
                      ...+--+.+|+ +.-|.||||.|.||+.++..||+.|-|++.
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt  237 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT  237 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence            34556677788 569999999999999999999999999874

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

Probab=89.89  E-value=0.58  Score=32.27  Aligned_cols=34  Identities=18%  Similarity=0.392  Sum_probs=27.2

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeE
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMI  285 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I  285 (330)
                      ....+.+.....|.+||++|++++.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            4555666665689999999999999999988554

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.

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

Probab=89.64  E-value=0.74  Score=41.34  Aligned_cols=51  Identities=16%  Similarity=0.249  Sum_probs=45.3

Q ss_pred             ceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          155 GCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       155 g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      -++||++|++++.|+--|.|.|-+.              ...|.+.|....+.++...+.+++..
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVq--------------G~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQ--------------GNTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEee--------------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence            5699999999999999999999884              24799999999999999999998875

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

Probab=89.61  E-value=0.71  Score=41.44  Aligned_cols=51  Identities=20%  Similarity=0.283  Sum_probs=44.9

Q ss_pred             cceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          264 GGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       264 g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      -++||.+|++++.|+-.|.|.|-|..       .+|.+.|....+..+.+.+.+-+.+
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeC-------cEEEeecCcchHHHHHHHHHHHHhc
Confidence            47999999999999999999999995       3688999999999999988876543

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=88.73  E-value=0.43  Score=34.56  Aligned_cols=34  Identities=18%  Similarity=0.407  Sum_probs=26.9

Q ss_pred             EEEEEecCCccceeecccChhhhhhhhccCcEEE
Q 020173           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIK   84 (330)
Q Consensus        51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~   84 (330)
                      .+.+.+.....|.+|||+|.++..||--++.-++
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            3556667788999999999999999977664444

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.

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=88.04  E-value=0.58  Score=33.87  Aligned_cols=36  Identities=25%  Similarity=0.350  Sum_probs=28.8

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEE
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV  287 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i  287 (330)
                      ....+.|..+..|.+||++|+++..||--+..-++-
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~   59 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR   59 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence            345677788889999999999999998877654443

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.

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=87.43  E-value=1.7  Score=42.38  Aligned_cols=127  Identities=13%  Similarity=0.046  Sum_probs=81.7

Q ss_pred             eecCCCChhHHHHHHHhCCeE--EEeCCCCCCcccCCCCCCcEEE-EEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCCC
Q 020173          156 CLIGMSGQNIEKLRNSSGATI--VILAPNQLPLCASAHESDRVVQ-ISGDVPAVLNALVEIGNQLRENPPRQVISISPAY  232 (330)
Q Consensus       156 ~iIG~~G~~Ik~I~~~sga~I--~i~~~~~~p~~~~~~~~~r~v~-I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~  232 (330)
                      +|-|++.-++..|.+...|-+  .+...          ...++.+ +.|..-...++...+.+    .            
T Consensus       393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~----------~gs~~~~~~~g~~~~F~k~~~~~~~----E------------  446 (657)
T COG5166         393 FLRGKKNGKATRIMKGVSCSELSSIVSS----------TGSIVETNGIGEKMSFSKKLSIPPT----E------------  446 (657)
T ss_pred             HhccccCcchhhhhhhcccceeeEEEec----------CCcEEEEeccCcchhhHHHhcCCcc----c------------
Confidence            677877777999999888874  44332          1223333 45665555544433211    1            


Q ss_pred             CCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC--CCceeE-EEEEcC---HH
Q 020173          233 NYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG--EQKHRH-IQFGGS---AQ  306 (330)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~--~~~~r~-v~I~Gt---~~  306 (330)
                                       -.....|.||...|..|||.||..|++.+...++.|++.....  .+..+. |.|.-+   .+
T Consensus       447 -----------------Fpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~  509 (657)
T COG5166         447 -----------------FPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQD  509 (657)
T ss_pred             -----------------CchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCcc
Confidence                             1244679999999999999999999999999999999886432  333333 666654   33


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 020173          307 QVALAKQRVDEYIYSQLIQ  325 (330)
Q Consensus       307 ~v~~A~~~I~~~i~~~~~~  325 (330)
                      ++-.++.-+.+++.+++.-
T Consensus       510 ni~~~KNd~~~~V~~~c~f  528 (657)
T COG5166         510 NISGKKNDKLDKVKQQCRF  528 (657)
T ss_pred             chhcccccHHHHHhhhccc
Confidence            4444555566666655533

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=87.20  E-value=0.39  Score=34.74  Aligned_cols=34  Identities=35%  Similarity=0.461  Sum_probs=28.6

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeE
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMI  285 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I  285 (330)
                      ....+.+....-|.+||++|++|++|....+-.+
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            4567888999999999999999999987765544

; 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 ....

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

Probab=87.04  E-value=1.9  Score=38.09  Aligned_cols=46  Identities=22%  Similarity=0.480  Sum_probs=38.0

Q ss_pred             EEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCC
Q 020173           53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDN  104 (330)
Q Consensus        53 ~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~  104 (330)
                      -+.||...+.++||++|+.++.|.+.|+|.|-+-..      -.|-|.+..+
T Consensus       149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~  194 (239)
T COG1097         149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENE  194 (239)
T ss_pred             EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCc
Confidence            467899999999999999999999999999999652      3366666553

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

Probab=86.94  E-value=1.8  Score=38.21  Aligned_cols=38  Identities=26%  Similarity=0.297  Sum_probs=34.9

Q ss_pred             EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173          253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG  290 (330)
Q Consensus       253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~  290 (330)
                      -.-+.||+..+.++||++|+.++-|.+.|+|+|.+-.+
T Consensus       147 G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N  184 (239)
T COG1097         147 GQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN  184 (239)
T ss_pred             CEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC
Confidence            35688999999999999999999999999999999965

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

Probab=86.20  E-value=0.64  Score=34.13  Aligned_cols=36  Identities=19%  Similarity=0.423  Sum_probs=30.5

Q ss_pred             EEEEEecCCccceeecccChhhhhhhhccCcEEEEe
Q 020173           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA   86 (330)
Q Consensus        51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~   86 (330)
                      ..++.|....-|.|||++|++|++|+++-.-...+.
T Consensus        31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~   66 (81)
T cd02413          31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP   66 (81)
T ss_pred             eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence            478888999999999999999999998876665553

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.

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=85.75  E-value=0.61  Score=33.70  Aligned_cols=33  Identities=36%  Similarity=0.595  Sum_probs=27.9

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeE
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATI  176 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I  176 (330)
                      ...+.+...+.+.+||++|++|++|.....-.+
T Consensus        26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l   58 (78)
T PF07650_consen   26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKEL   58 (78)
T ss_dssp             EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence            578889999999999999999999887755443

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

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

Probab=85.68  E-value=0.4  Score=46.30  Aligned_cols=39  Identities=33%  Similarity=0.454  Sum_probs=34.9

Q ss_pred             eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC
Q 020173           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (330)
Q Consensus        50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (330)
                      -...+.||.++.+.+|||+|.+|++|++..|-+|.|-..
T Consensus       486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~  524 (604)
T COG1855         486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL  524 (604)
T ss_pred             CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence            345678899999999999999999999999999999764

>PRK13764 ATPase; Provisional

Probab=85.24  E-value=0.48  Score=47.95  Aligned_cols=41  Identities=37%  Similarity=0.528  Sum_probs=36.2

Q ss_pred             CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC
Q 020173           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (330)
Q Consensus        48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (330)
                      .+-..-+.||.+.++.+|||+|.+|++|++..|..|+|...
T Consensus       479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~  519 (602)
T PRK13764        479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL  519 (602)
T ss_pred             cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence            34455788899999999999999999999999999999764

>PRK13764 ATPase; Provisional

Probab=84.90  E-value=6.8  Score=39.81  Aligned_cols=43  Identities=21%  Similarity=0.358  Sum_probs=38.3

Q ss_pred             eEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCC
Q 020173          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP  185 (330)
Q Consensus       143 ~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p  185 (330)
                      ....+.||...++.+|||+|.+|++|+++.|..|.+...+..+
T Consensus       481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~  523 (602)
T PRK13764        481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP  523 (602)
T ss_pred             CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence            3678999999999999999999999999999999998765443

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

Probab=84.59  E-value=2.5  Score=41.09  Aligned_cols=39  Identities=15%  Similarity=0.238  Sum_probs=35.9

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCC
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN  182 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~  182 (330)
                      ...+.+|..+.+.+||++|.+|++|+++.|.+|.+...+
T Consensus       487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e  525 (604)
T COG1855         487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE  525 (604)
T ss_pred             eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence            678899999999999999999999999999999997643

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

Probab=83.14  E-value=5.7  Score=32.41  Aligned_cols=92  Identities=14%  Similarity=0.313  Sum_probs=62.3

Q ss_pred             ccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEE
Q 020173           67 KEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIR  146 (330)
Q Consensus        67 k~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~  146 (330)
                      .+|.-|++|-++..-+|.|....   +     +        +..-.+|.+.|.+++-++..-..-.+       ...+-+
T Consensus        23 ~~~dli~~lAk~lrKRIvvR~dp---s-----~--------l~~~e~A~~~I~~ivP~ea~i~di~F-------d~~tGE   79 (145)
T cd02410          23 EDGDLVKDLAKDLRKRIVIRPDP---S-----V--------LKPPEEAIKIILEIVPEEAGITDIYF-------DDDTGE   79 (145)
T ss_pred             cccHHHHHHHHHHhceEEEcCCh---h-----h--------cCCHHHHHHHHHHhCCCccCceeeEe-------cCCCcE
Confidence            45778888888888888886431   0     0        11225788888887643322111111       112457


Q ss_pred             EEeeccccceecCCCChhHHHHHHHhCCeEEEeCC
Q 020173          147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (330)
Q Consensus       147 llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~  181 (330)
                      +.|-...-|++||++|.++++|..++|-.-.+...
T Consensus        80 V~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          80 VIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             EEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence            78888889999999999999999999988887653

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=82.78  E-value=1.2  Score=37.35  Aligned_cols=38  Identities=21%  Similarity=0.352  Sum_probs=32.2

Q ss_pred             ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEec
Q 020173           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD   87 (330)
Q Consensus        49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~   87 (330)
                      +-.+-++|-... |.-|||+|.+++++++..|-+|.+-.
T Consensus        60 ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE   97 (166)
T PRK06418         60 DDLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE   97 (166)
T ss_pred             CCEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence            445566777777 99999999999999999998888865

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=80.56  E-value=2.6  Score=35.37  Aligned_cols=39  Identities=15%  Similarity=0.191  Sum_probs=33.2

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK  291 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~  291 (330)
                      ...-|.|.... |.-||++|++++.+++..|-+|.+-...
T Consensus        61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s   99 (166)
T PRK06418         61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEKT   99 (166)
T ss_pred             CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEcC
Confidence            45567777777 9999999999999999999999998653

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

Probab=80.38  E-value=1.4  Score=32.58  Aligned_cols=28  Identities=29%  Similarity=0.484  Sum_probs=23.6

Q ss_pred             EEEEecCCccceeecccChhhhhhhhcc
Q 020173           52 FRIIVPSRQIGKVIGKEGHRIQKIREET   79 (330)
Q Consensus        52 ~~i~vP~~~vg~IIGk~G~~Ik~I~~~t   79 (330)
                      .++.|....-|.+||++|.+|++|++..
T Consensus        40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l   67 (85)
T cd02411          40 TQITIYAERPGMVIGRGGKNIRELTEIL   67 (85)
T ss_pred             EEEEEEECCCCceECCCchhHHHHHHHH
Confidence            5666667899999999999999988664

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	330
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		4e-10
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		5e-06
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		7e-06
1wvn_A	82	Crsytal Structure Of Domain 3 Of Human Alpha Polyc		8e-05
3vke_A	76	Contribution Of The First K-Homology Domain Of Poly		2e-04
2p2r_A	76	Crystal Structure Of The Third Kh Domain Of Human P		3e-04
1ztg_A	74	Human Alpha Polyc Binding Protein Kh1 Length = 74		4e-04
2axy_A	73	Crystal Structure Of Kh1 Domain Of Human Poly(C)-Bi		4e-04

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 45/146 (30%), Positives = 73/146 (50%), Gaps = 25/146 (17%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL+ G + G +IG  G++++K+R  SGA I I         +  +  +R++ ++G  
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINI---------SEGNCPERIITLAGPT 56
Query: 204 PAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLV 263
            A+  A   I ++L E+     IS S   + +A RP            VT  +++  S  
Sbjct: 57  NAIFKAFAMIIDKLEED-----ISSSMTNSTAASRPP-----------VTLRLVVPASQC 100
Query: 264 GGLIGRCGSNISRIRNESGAMIKVYG 289
           G LIG+ G  I  IR  +GA ++V G
Sbjct: 101 GSLIGKGGCKIKEIRESTGAQVQVAG 126

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 44/144 (30%), Positives = 74/144 (51%), Gaps = 13/144 (9%)
Query: 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP 204
           +++LI    AG +IG  GQ I +L+  +GATI +              ++RV  I G + 
Sbjct: 8   LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDF----YPGTTERVCLIQGTIE 63
Query: 205 AVLNAL-VEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLV 263
           A LNA+   I  ++RE  P+ V    P    S ++P Q  V P  A+ V  ++++  S  
Sbjct: 64  A-LNAVHGFIAEKIREX-PQNVAKTEPV---SILQP-QTTVNPDRANQV--KIIVPNSTA 115
Query: 264 GGLIGRCGSNISRIRNESGAMIKV 287
           G +IG+ G+ +  I  +SGA +++
Sbjct: 116 GLIIGKGGATVKAIXEQSGAWVQL 139

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 44/144 (30%), Positives = 74/144 (51%), Gaps = 13/144 (9%)
Query: 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP 204
           +++LI    AG +IG  GQ I +L+  +GATI +              ++RV  I G + 
Sbjct: 8   LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDF----YPGTTERVCLIQGTIE 63
Query: 205 AVLNAL-VEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLV 263
           A LNA+   I  ++RE  P+ V    P    S ++P Q  V P  A+ V  ++++  S  
Sbjct: 64  A-LNAVHGFIAEKIREM-PQNVAKTEPV---SILQP-QTTVNPDRANQV--KIIVPNSTA 115
Query: 264 GGLIGRCGSNISRIRNESGAMIKV 287
           G +IG+ G+ +  I  +SGA +++
Sbjct: 116 GLIIGKGGATVKAIMEQSGAWVQL 139

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 40/71 (56%)
Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
            T E+ I  +L+G +IGR G+NI+ IR  SGA IK+         R +   GSA  ++LA
Sbjct: 6   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLA 65
Query: 312 KQRVDEYIYSQ 322
           +  ++  + S+
Sbjct: 66  QYLINARLSSE 76

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL+ G + G +IG  G++++++R  SGA I I         +  +  +R++ ++G  
Sbjct: 4   TIRLLMHGKEVGSIIGKKGESVKRIREESGARINI---------SEGNSPERIITLTGPT 54
Query: 204 PAVLNALVEIGNQLREN 220
            A+  A   I ++L E+
Sbjct: 55  NAIFKAFAMIIDKLEED 71

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 249 ADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQV 308
           A   + E+ I   L+G +IGR G+ I+ IR  SGA IK+         R +   GSA  +
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASI 61
Query: 309 ALAKQRVDEYIYSQ 322
           +LA+  ++  + S+
Sbjct: 62  SLAQYLINVRLSSE 75

>pdb|1ZTG|A Chain A, Human Alpha Polyc Binding Protein Kh1 Length = 74

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL+ G + G +IG  G++++++R  SGA I I   N    C      +R++ ++G  
Sbjct: 4   TIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN----CP-----ERIITLTGPT 54
Query: 204 PAVLNALVEIGNQLREN 220
            A+  A   I ++L E+
Sbjct: 55  NAIFKAFAMIIDKLEED 71

>pdb|2AXY|A Chain A, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding Protein-2 With C-Rich Strand Of Human Telomeric Dna Length = 73

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 9/77 (11%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL  G + G +IG  G++++K R  SGA I I   N    C      +R++ ++G  
Sbjct: 6   TIRLLXHGKEVGSIIGKKGESVKKXREESGARINISEGN----CP-----ERIITLAGPT 56
Query: 204 PAVLNALVEIGNQLREN 220
            A+  A   I ++L E+
Sbjct: 57  NAIFKAFAXIIDKLEED 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	330
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-33
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-23
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-08
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	9e-08
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-32
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	4e-23
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-09
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-08
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-28
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-27
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-08
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-28
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-24
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-08
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	8e-08
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	9e-28
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-25
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-09
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-14
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	3e-10
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	7e-09
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	3e-14
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-10
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	8e-09
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	4e-14
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	3e-09
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	5e-08
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-13
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	4e-11
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-10
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	3e-13
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	7e-08
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	7e-05
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	3e-13
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	9e-10
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-07
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-12
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	5e-08
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	2e-06
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	7e-11
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	5e-08
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	6e-07
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	3e-10
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	3e-08
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-07
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	1e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	2e-08
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	5e-08
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-09
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	8e-07
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-06
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-09
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-07
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-08
1we8_A	104	Tudor and KH domain containing protein; structural	3e-08
1we8_A	104	Tudor and KH domain containing protein; structural	1e-07
1we8_A	104	Tudor and KH domain containing protein; structural	3e-05
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	3e-08
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	1e-05
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	3e-07
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	1e-04
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	4e-07
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	2e-05
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	6e-04
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	3e-06
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	4e-05
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	3e-06
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	8e-04
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	1e-05
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	6e-05
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	9e-05
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	1e-04
1tua_A	191	Hypothetical protein APE0754; structural genomics,	2e-04
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	2e-04
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	3e-04
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	3e-04
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	3e-04
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	6e-04

>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 =  121 bits (305), Expect = 1e-33
 Identities = 43/180 (23%), Positives = 84/180 (46%), Gaps = 10/180 (5%)

Query: 47  AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA---DAIARHEERVIIISSKD 103
                 ++++PS   G +IGK G  I ++++ET ATIK++   D      ERV +I    
Sbjct: 3   GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI 62

Query: 104 N--DNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMS 161
              + V       ++++   + K +  +    +       AN +++++  S AG +IG  
Sbjct: 63  EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKG 122

Query: 162 GQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP 221
           G  ++ +   SGA + +   +Q P   +     RVV +SG+      A+  I  +++E+P
Sbjct: 123 GATVKAIMEQSGAWVQL---SQKPDGINLQN--RVVTVSGEPEQNRKAVELIIQKIQEDP 177

>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 = 94.9 bits (236), Expect = 1e-23
 Identities = 39/178 (21%), Positives = 74/178 (41%), Gaps = 13/178 (7%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
            +++LI    AG +IG  GQ I +L+  +GATI +              ++RV  I G +
Sbjct: 7   FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFY----PGTTERVCLIQGTI 62

Query: 204 PAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLV 263
            A+      I  ++RE P     +         +   QP            ++++  S  
Sbjct: 63  EALNAVHGFIAEKIREMPQNVAKT-------EPVSILQPQTTVNPDRANQVKIIVPNSTA 115

Query: 264 GGLIGRCGSNISRIRNESGAMIKVYGGK--GEQKHRHIQFGGSAQQVALAKQRVDEYI 319
           G +IG+ G+ +  I  +SGA +++         ++R +   G  +Q   A + + + I
Sbjct: 116 GLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKI 173

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

 Score = 52.5 bits (126), Expect = 2e-08
 Identities = 19/105 (18%), Positives = 43/105 (40%), Gaps = 7/105 (6%)

Query: 24  DVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATI 83
           ++     + +              +    +IIVP+   G +IGK G  ++ I E++ A +
Sbjct: 78  EMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWV 137

Query: 84  KIA--DAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126
           +++        + RV+ +S  + +        A++ I   I +D 
Sbjct: 138 QLSQKPDGINLQNRVVTVSG-EPEQN----RKAVELIIQKIQEDP 177

>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 = 50.6 bits (121), Expect = 9e-08
 Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 3/71 (4%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQK---HRHIQFGGSAQQV 308
              ++LI     G +IG+ G  I +++ E+GA IK+   K        R     G+ + +
Sbjct: 6   YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEAL 65

Query: 309 ALAKQRVDEYI 319
                 + E I
Sbjct: 66  NAVHGFIAEKI 76

>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 =  116 bits (293), Expect = 3e-32
 Identities = 46/174 (26%), Positives = 90/174 (51%), Gaps = 15/174 (8%)

Query: 46  KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDND 105
           K   +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER+I ++     
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC--PERIITLAGP--- 55

Query: 106 NVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNI 165
              +    A   I   + +D  S+   S  A+      T+RL++  SQ G LIG  G  I
Sbjct: 56  --TNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPV--TLRLVVPASQCGSLIGKGGCKI 111

Query: 166 EKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219
           +++R S+GA + + A + LP     + ++R + I+G   +++  + +I   + E
Sbjct: 112 KEIRESTGAQVQV-AGDMLP-----NSTERAITIAGIPQSIIECVKQICVVMLE 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 = 92.9 bits (231), Expect = 4e-23
 Identities = 44/177 (24%), Positives = 76/177 (42%), Gaps = 26/177 (14%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL+ G + G +IG  G++++K+R  SGA I I         +  +  +R++ ++G  
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINI---------SEGNCPERIITLAGPT 56

Query: 204 PAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLV 263
            A+  A   I ++L E+                   +       S   VT  +++  S  
Sbjct: 57  NAIFKAFAMIIDKLEEDIS----------------SSMTNSTAASRPPVTLRLVVPASQC 100

Query: 264 GGLIGRCGSNISRIRNESGAMIKVYGGKGEQKH-RHIQFGGSAQQVALAKQRVDEYI 319
           G LIG+ G  I  IR  +GA ++V G        R I   G  Q +    +++   +
Sbjct: 101 GSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVM 157

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

 Score = 53.2 bits (128), Expect = 7e-09
 Identities = 27/93 (29%), Positives = 46/93 (49%), Gaps = 6/93 (6%)

Query: 32  EDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA-DAIA 90
           E+           A    V  R++VP+ Q G +IGK G +I++IRE T A +++A D + 
Sbjct: 71  EEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLP 130

Query: 91  RHEERVIIISSKDNDNVVSDAENALQQIAALIL 123
              ER I I+     ++       ++QI  ++L
Sbjct: 131 NSTERAITIAG-IPQSI----IECVKQICVVML 158

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

 Score = 51.7 bits (124), Expect = 3e-08
 Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
           +T  +L+    VG +IG+ G ++ ++R ESGA I +   +G    R I   G    +  A
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLAGPTNAIFKA 62

Query: 312 KQRVDEYI 319
              + + +
Sbjct: 63  FAMIIDKL 70

>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 =  107 bits (269), Expect = 2e-28
 Identities = 33/179 (18%), Positives = 61/179 (34%), Gaps = 22/179 (12%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
             + +P   +G VIG+ G  I+KI+ +    I+         ER+  I+          A
Sbjct: 5   IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP-----PDRA 59

Query: 112 ENALQQIAALILKDDDSNSEASKVAA-------------GHVAANTIRLLIAGSQAGCLI 158
           ++A + I  L+      N                               ++   + G +I
Sbjct: 60  QHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLII 119

Query: 159 GMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL 217
           G  G+ I+ +   SGA I +      P  A    + ++  I G    +  A   I  ++
Sbjct: 120 GKGGETIKSISQQSGARIEL--QRNPPPNAD--PNMKLFTIRGTPQQIDYARQLIEEKI 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 =  104 bits (261), Expect = 2e-27
 Identities = 39/180 (21%), Positives = 69/180 (38%), Gaps = 11/180 (6%)

Query: 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
           + I + I     G +IG +G+ I+K++N +G  I     +           +R+ QI+G 
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-------GTTPERIAQITGP 55

Query: 203 VPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESL 262
                +A   I + LR           P       R    +          F  ++    
Sbjct: 56  PDRAQHAAEIITDLLRSVQAGNPGGPGPGGRGRG-RGQGNWNMGPPGGLQEFNFIVPTGK 114

Query: 263 VGGLIGRCGSNISRIRNESGAMIKVYGGK---GEQKHRHIQFGGSAQQVALAKQRVDEYI 319
            G +IG+ G  I  I  +SGA I++        +   +     G+ QQ+  A+Q ++E I
Sbjct: 115 TGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

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

 Score = 51.4 bits (123), Expect = 3e-08
 Identities = 18/112 (16%), Positives = 37/112 (33%), Gaps = 8/112 (7%)

Query: 14  SVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQ 73
            ++   +  +                +           F  IVP+ + G +IGK G  I+
Sbjct: 68  DLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIK 127

Query: 74  KIREETKATIKIADAIARHE---ERVIIISSKDNDNVVSDAENALQQIAALI 122
            I +++ A I++      +     ++  I       +    + A Q I   I
Sbjct: 128 SISQQSGARIELQRNPPPNADPNMKLFTIRG-TPQQI----DYARQLIEEKI 174

>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 =  106 bits (267), Expect = 2e-28
 Identities = 36/178 (20%), Positives = 77/178 (43%), Gaps = 18/178 (10%)

Query: 48  QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARH-EERVIIISSKDNDN 106
           +  + ++ +P++ +G +IGK+G  I+++     A+IKIA       + R++II+      
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPE-- 58

Query: 107 VVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIE 166
                  A  +I   + +++    +               + +  S AG +IG  G+ + 
Sbjct: 59  ---AQFKAQGRIYGKLKEENFFGPKEE-------VKLETHIRVPASAAGRVIGKGGKTVN 108

Query: 167 KLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQ 224
           +L+N + A +V+   +Q P          +V+I G   A   A  +I + L +   + 
Sbjct: 109 ELQNLTAAEVVV-PRDQTP----DENDQVIVKIIGHFYASQMAQRKIRDILAQVKQQH 161

>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 = 95.6 bits (238), Expect = 3e-24
 Identities = 34/178 (19%), Positives = 70/178 (39%), Gaps = 29/178 (16%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
            +++ I     G +IG  GQ+I++L   + A+I I  P       +     R+V I+G  
Sbjct: 4   MVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPE------TPDSKVRMVIITGPP 57

Query: 204 PAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLV 263
            A   A   I  +L+E                     + F  P     +   + +  S  
Sbjct: 58  EAQFKAQGRIYGKLKE---------------------ENFFGPKEEVKLETHIRVPASAA 96

Query: 264 GGLIGRCGSNISRIRNESGAMIKVYGGK--GEQKHRHIQFGGSAQQVALAKQRVDEYI 319
           G +IG+ G  ++ ++N + A + V   +   E     ++  G      +A++++ + +
Sbjct: 97  GRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDIL 154

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

 Score = 51.7 bits (124), Expect = 3e-08
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVY-GGKGEQKHRHIQFGGSAQQVAL 310
              ++ I    VG +IG+ G +I ++   + A IK+      + K R +   G  +    
Sbjct: 3   EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFK 62

Query: 311 AKQRVDEYIYSQ 322
           A+ R+   +  +
Sbjct: 63  AQGRIYGKLKEE 74

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

 Score = 50.1 bits (120), Expect = 8e-08
 Identities = 16/97 (16%), Positives = 40/97 (41%), Gaps = 5/97 (5%)

Query: 36  IEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA-DAIARHEE 94
           ++  +     +   +   I VP+   G+VIGK G  + +++  T A + +  D      +
Sbjct: 71  LKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDEND 130

Query: 95  RVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSE 131
           +VI+             + A ++I  ++ +    + +
Sbjct: 131 QVIVKIIGHFYAS----QMAQRKIRDILAQVKQQHQK 163

>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 =  105 bits (263), Expect = 9e-28
 Identities = 34/178 (19%), Positives = 68/178 (38%), Gaps = 20/178 (11%)

Query: 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG 201
                ++I   +AG +IG  G+ I++L+  +G  ++++              D+ ++I G
Sbjct: 1   GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTN-----VDKPLRIIG 55

Query: 202 DVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISES 261
           D   V  A   + + LRE                         E  S      ++ +   
Sbjct: 56  DPYKVQQACEMVMDILRERDQG---------------GFGDRNEYGSRIGGGIDVPVPRH 100

Query: 262 LVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYI 319
            VG +IGR G  I +I+N++G  I+     G    +     G   +   A + +++ +
Sbjct: 101 SVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL 158

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

 Score = 99.1 bits (247), Expect = 2e-25
 Identities = 30/170 (17%), Positives = 67/170 (39%), Gaps = 15/170 (8%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IARHEERVIIISSKDNDNVVS 109
             I++P+ + G VIGK G  I++++E     + +        + ++ + I          
Sbjct: 4   QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGD-----PY 58

Query: 110 DAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169
             + A + +  ++ ++ D      +   G      I + +     G +IG SG+ I+K++
Sbjct: 59  KVQQACEMVMDIL-RERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQ 117

Query: 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219
           N +G  I     +           +++  I G      +A   I + L+ 
Sbjct: 118 NDAGVRIQFKQDD-------GTGPEKIAHIMGPPDRCEHAARIINDLLQS 160

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

 Score = 54.8 bits (132), Expect = 2e-09
 Identities = 18/89 (20%), Positives = 30/89 (33%), Gaps = 4/89 (4%)

Query: 31  REDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA 90
           RE  +    D             + VP   +G VIG+ G  I+KI+ +    I+      
Sbjct: 72  RERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG 131

Query: 91  RHEERVIIIS-SKDNDNVVSDAENALQQI 118
              E++  I    D       A   +  +
Sbjct: 132 TGPEKIAHIMGPPDR---CEHAARIINDL 157

>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 = 67.3 bits (165), Expect = 1e-14
 Identities = 21/72 (29%), Positives = 36/72 (50%)

Query: 248 SADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQ 307
               +T ++ I + L G +IG+ G  I +IR+ESGA IK+       + R I   G+  Q
Sbjct: 10  GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ 69

Query: 308 VALAKQRVDEYI 319
           +  A+  +   +
Sbjct: 70  IQNAQYLLQNSV 81

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

 Score = 55.4 bits (134), Expect = 3e-10
 Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 4/73 (5%)

Query: 47  AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS-SKDND 105
              +  ++ +P    G +IGK G RI++IR E+ A+IKI + +   E+R+I I+ ++D  
Sbjct: 11  GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ- 69

Query: 106 NVVSDAENALQQI 118
             + +A+  LQ  
Sbjct: 70  --IQNAQYLLQNS 80

>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 = 51.6 bits (124), Expect = 7e-09
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 7/81 (8%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T ++ I    AG +IG  GQ I+++R+ SGA+I I  P            DR++ I+G  
Sbjct: 15  TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-------LEGSEDRIITITGTQ 67

Query: 204 PAVLNALVEIGNQLRENPPRQ 224
             + NA   + N +++   + 
Sbjct: 68  DQIQNAQYLLQNSVKQYSGKF 88

>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 = 66.2 bits (162), Expect = 3e-14
 Identities = 21/73 (28%), Positives = 36/73 (49%)

Query: 247 TSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQ 306
                +T ++ I + L G +IG+ G  I +IR+ESGA IK+       + R I   G+  
Sbjct: 2   AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD 61

Query: 307 QVALAKQRVDEYI 319
           Q+  A+  +   +
Sbjct: 62  QIQNAQYLLQNSV 74

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

 Score = 55.4 bits (134), Expect = 2e-10
 Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 7/79 (8%)

Query: 45  AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS-SKD 103
           A    +  ++ +P    G +IGK G RI++IR E+ A+IKI + +   E+R+I I+ ++D
Sbjct: 2   AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD 61

Query: 104 NDNVVSDAENALQQIAALI 122
                   +NA   +   +
Sbjct: 62  Q------IQNAQYLLQNSV 74

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

 Score = 51.1 bits (123), Expect = 8e-09
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 7/81 (8%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T ++ I    AG +IG  GQ I+++R+ SGA+I I  P            DR++ I+G  
Sbjct: 8   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-------LEGSEDRIITITGTQ 60

Query: 204 PAVLNALVEIGNQLRENPPRQ 224
             + NA   + N +++   + 
Sbjct: 61  DQIQNAQYLLQNSVKQYSGKF 81

>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 = 65.8 bits (161), Expect = 4e-14
 Identities = 25/71 (35%), Positives = 40/71 (56%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
            T E+ I  +L+G +IGR G+NI+ IR  SGA IK+         R +   GSA  ++LA
Sbjct: 6   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLA 65

Query: 312 KQRVDEYIYSQ 322
           +  ++  + S+
Sbjct: 66  QYLINARLSSE 76

>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 = 52.3 bits (126), Expect = 3e-09
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 7/74 (9%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS-SKDNDNVVSDA 111
            + +P+  IG +IG++G  I +IR+ + A IKIA+ +     R + I+ S  +       
Sbjct: 9   ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS------I 62

Query: 112 ENALQQIAALILKD 125
             A   I A +  +
Sbjct: 63  SLAQYLINARLSSE 76

>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 = 48.8 bits (117), Expect = 5e-08
 Identities = 25/76 (32%), Positives = 33/76 (43%), Gaps = 7/76 (9%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T  L I  +  GC+IG  G NI ++R  SGA I I  P           S R V I+G  
Sbjct: 7   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-------VEGSSGRQVTITGSA 59

Query: 204 PAVLNALVEIGNQLRE 219
            ++  A   I  +L  
Sbjct: 60  ASISLAQYLINARLSS 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 = 1e-13
 Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 9/77 (11%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL+ G + G +IG  G++++K+R  SGA I I         +  +  +R++ ++G  
Sbjct: 6   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINI---------SEGNCPERIITLAGPT 56

Query: 204 PAVLNALVEIGNQLREN 220
            A+  A   I ++L E+
Sbjct: 57  NAIFKAFAMIIDKLEED 73

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

 Score = 57.3 bits (139), Expect = 4e-11
 Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 7/80 (8%)

Query: 46  KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDND 105
           K   +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER+I ++     
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC--PERIITLAGP--- 55

Query: 106 NVVSDAENALQQIAALILKD 125
              +    A   I   + +D
Sbjct: 56  --TNAIFKAFAMIIDKLEED 73

>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 = 55.4 bits (134), Expect = 2e-10
 Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
           +T  +L+    VG +IG+ G ++ ++R ESGA I +   +G    R I   G    +  A
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINIS--EGNCPERIITLAGPTNAIFKA 62

Query: 312 KQRVDEYI 319
              + + +
Sbjct: 63  FAMIIDKL 70

>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 = 63.6 bits (155), Expect = 3e-13
 Identities = 23/74 (31%), Positives = 37/74 (50%)

Query: 246 PTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSA 305
                 +T E  + + +VG +IGR G  ISRI+ ESG  I++    G    R     G+ 
Sbjct: 9   QQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTP 68

Query: 306 QQVALAKQRVDEYI 319
           + V  AK+ +D+ +
Sbjct: 69  ESVQSAKRLLDQIV 82

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

 Score = 48.6 bits (116), Expect = 7e-08
 Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS-SKDNDNVVSDA 111
              VP   +G +IG+ G +I +I++E+   I+IA       ER  +++ + ++   V  A
Sbjct: 18  EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPES---VQSA 74

Query: 112 ENALQQI 118
           +  L QI
Sbjct: 75  KRLLDQI 81

>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 = 40.1 bits (94), Expect = 7e-05
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 7/76 (9%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T    +     G +IG  G+ I +++  SG  I I          S    +R   ++G  
Sbjct: 16  TEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD-------SGGLPERSCMLTGTP 68

Query: 204 PAVLNALVEIGNQLRE 219
            +V +A   +   + +
Sbjct: 69  ESVQSAKRLLDQIVEK 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 = 63.1 bits (154), Expect = 3e-13
 Identities = 23/71 (32%), Positives = 38/71 (53%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
            + E+ I   L+G +IGR G+ I+ IR  SGA IK+         R +   GSA  ++LA
Sbjct: 5   TSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLA 64

Query: 312 KQRVDEYIYSQ 322
           +  ++  + S+
Sbjct: 65  QYLINVRLSSE 75

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

 Score = 53.5 bits (129), Expect = 9e-10
 Identities = 19/55 (34%), Positives = 34/55 (61%)

Query: 46  KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS 100
           KAQ     + +P+  IG +IG++G +I +IR+ + A IKIA+ +    +R + I+
Sbjct: 1   KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTIT 55

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

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 23/76 (30%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           +  L I     GC+IG  G  I ++R  SGA I I  P           +DR V I+G  
Sbjct: 6   SHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP-------VEGSTDRQVTITGSA 58

Query: 204 PAVLNALVEIGNQLRE 219
            ++  A   I  +L  
Sbjct: 59  ASISLAQYLINVRLSS 74

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

 Score = 61.0 bits (148), Expect = 4e-12
 Identities = 14/67 (20%), Positives = 30/67 (44%)

Query: 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAK 312
             ++ +    VG +IGR G  I +I+N++G  I+     G    +     G   +   A 
Sbjct: 12  GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAA 71

Query: 313 QRVDEYI 319
           + +++ +
Sbjct: 72  RIINDLL 78

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

 Score = 49.4 bits (118), Expect = 5e-08
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 5/78 (6%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + VP   +G VIG+ G  I+KI+ +    I+         E++  I    +       E
Sbjct: 14  DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRC-----E 68

Query: 113 NALQQIAALILKDDDSNS 130
           +A + I  L+        
Sbjct: 69  HAARIINDLLQSLRSGPP 86

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

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 18/89 (20%), Positives = 34/89 (38%), Gaps = 7/89 (7%)

Query: 135 VAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESD 194
           +A G      I + +     G +IG SG+ I+K++N +G  I     +           +
Sbjct: 3   MATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-------GTGPE 55

Query: 195 RVVQISGDVPAVLNALVEIGNQLRENPPR 223
           ++  I G      +A   I + L+     
Sbjct: 56  KIAHIMGPPDRCEHAARIINDLLQSLRSG 84

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

 Score = 57.0 bits (138), Expect = 7e-11
 Identities = 15/80 (18%), Positives = 35/80 (43%), Gaps = 3/80 (3%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV---YGGKGEQKHRHIQFGGSAQQV 308
              E+ + E+LVG ++G+ G  +   +  +GA I++          ++R +   GS    
Sbjct: 3   ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62

Query: 309 ALAKQRVDEYIYSQLIQQAG 328
             A+  + + +  +   +A 
Sbjct: 63  QAAQYLISQRVTYEQGVRAS 82

>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 = 48.9 bits (117), Expect = 5e-08
 Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 4/82 (4%)

Query: 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
             + + +  +  G ++G  G+ + + +  +GA I I    +          +R V I+G 
Sbjct: 3   ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGT----RNRRVTITGS 58

Query: 203 VPAVLNALVEIGNQLRENPPRQ 224
             A   A   I  ++      +
Sbjct: 59  PAATQAAQYLISQRVTYEQGVR 80

>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 = 45.8 bits (109), Expect = 6e-07
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA---DAIARHEERVIIIS 100
             I VP   +G ++GK G  + + +E T A I+I+   + +     R + I+
Sbjct: 5   VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTIT 56

>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 = 55.0 bits (133), Expect = 3e-10
 Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV---YGGKGEQKHRHIQFGGSAQQV 308
              EM + E+LVG ++G+ G  +   +  +GA I++          ++R +   GS    
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62

Query: 309 ALAKQRVDEYIYSQ 322
             A+  + + +  +
Sbjct: 63  QAAQYLISQRVTYE 76

>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 = 49.2 bits (118), Expect = 3e-08
 Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 4/77 (5%)

Query: 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
             + + +  +  G ++G  G+ + + +  +GA I I    +          +R V I+G 
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGT----RNRRVTITGS 58

Query: 203 VPAVLNALVEIGNQLRE 219
             A   A   I  ++  
Sbjct: 59  PAATQAAQYLISQRVTY 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 = 46.9 bits (112), Expect = 2e-07
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 3/52 (5%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHE---ERVIIIS 100
             + VP   +G ++GK G  + + +E T A I+I+           R + I+
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTIT 56

>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 = 54.0 bits (130), Expect = 1e-09
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVY--GGKGEQKHRHIQFGGSAQQVA 309
              E++I  S  G +IG+ G  I +++  +G  + +   G +     + ++  G   +V 
Sbjct: 15  AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQ 74

Query: 310 LAKQRVDEYIYSQ 322
            AK+ V E I  Q
Sbjct: 75  QAKEMVLELIRDQ 87

>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 = 50.1 bits (120), Expect = 2e-08
 Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
              ++I  S+AG +IG  G+ I++L+  +G  +V++             +D+ ++I+GD 
Sbjct: 16  VQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN-----TGADKPLRITGDP 70

Query: 204 PAVLNALVEIGNQLRENPPR 223
             V  A   +   +R+    
Sbjct: 71  YKVQQAKEMVLELIRDQGSG 90

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

 Score = 49.3 bits (118), Expect = 5e-08
 Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 7/82 (8%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA--DAIARHEERVIIISSKDNDNVVSD 110
            I++P+ + G VIGK G  I++++E     + +          ++ + I+  D   V   
Sbjct: 18  EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG-DPYKV--- 73

Query: 111 AENALQQIAALILKDDDSNSEA 132
            + A + +  LI       S  
Sbjct: 74  -QQAKEMVLELIRDQGSGPSSG 94

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

 Score = 54.1 bits (130), Expect = 1e-09
 Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV---YGGKGEQKHRHIQFGGSAQQVA 309
                I     G +IGR G N+  I  ++GA +++       G+   +     GS QQ+ 
Sbjct: 8   EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQID 67

Query: 310 LAKQRVDEYIYSQLIQQA 327
            AKQ ++E I   L    
Sbjct: 68  HAKQLIEEKIEGPLCPVG 85

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

 Score = 46.0 bits (109), Expect = 8e-07
 Identities = 16/100 (16%), Positives = 34/100 (34%), Gaps = 4/100 (4%)

Query: 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
             +   I   + G +IG  G+N++ +   +GA + I       L  +   + ++  I G 
Sbjct: 7   GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEI----SRQLPPNGDPNFKLFIIRGS 62

Query: 203 VPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQP 242
              + +A   I  ++                   + P  P
Sbjct: 63  PQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAGPMGPFNP 102

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

 Score = 44.9 bits (106), Expect = 2e-06
 Identities = 12/52 (23%), Positives = 27/52 (51%), Gaps = 3/52 (5%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHE---ERVIIIS 100
               +P+ + G VIG+ G  ++ I ++T A ++I+  +  +     ++ II 
Sbjct: 9   MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR 60

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

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 2/70 (2%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVY--GGKGEQKHRHIQFGGSAQQVA 309
              E++I     G +IG+ G  I +++  +G  + +   G +     + ++  G   +V 
Sbjct: 14  TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQ 73

Query: 310 LAKQRVDEYI 319
            A + V + +
Sbjct: 74  QACEMVMDIL 83

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 5/84 (5%)

Query: 136 AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDR 195
           A G        ++I   +AG +IG  G+ I++L+  +G  ++++              D+
Sbjct: 7   ANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN-----TNVDK 61

Query: 196 VVQISGDVPAVLNALVEIGNQLRE 219
            ++I GD   V  A   + + LRE
Sbjct: 62  PLRIIGDPYKVQQACEMVMDILRE 85

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

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 14/72 (19%), Positives = 34/72 (47%), Gaps = 7/72 (9%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA--DAIARHEERVIIISSKDNDNVVSD 110
            I++P+ + G VIGK G  I++++E     + +    +   + ++ + I   D   V   
Sbjct: 17  EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIG-DPYKV--- 72

Query: 111 AENALQQIAALI 122
            + A + +  ++
Sbjct: 73  -QQACEMVMDIL 83

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 54.5 bits (130), Expect = 3e-08
 Identities = 52/350 (14%), Positives = 102/350 (29%), Gaps = 115/350 (32%)

Query: 27  GKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA 86
                 +  +E          Q +L++I                RI  I+ E +  +K  
Sbjct: 190 KNCNSPETVLE--------MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK 241

Query: 87  DAIARHEERVIIISSKDNDNVVSDAE--NALQ---QIAALILKDDDSNSEA-SKVAAGHV 140
                +E  ++++      NV  +A+  NA     +I  L+       ++  S     H+
Sbjct: 242 ----PYENCLLVL-----LNV-QNAKAWNAFNLSCKI--LLTTRFKQVTDFLSAATTTHI 289

Query: 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS 200
           + +   +            ++   ++ L        +   P  LP      E   V+  +
Sbjct: 290 SLDHHSM-----------TLTPDEVKSLL----LKYLDCRPQDLP-----RE---VLTTN 326

Query: 201 GDVPAVLNALVEIGNQLRENPPR-------------QVISIS-----PA-----YNYSAI 237
              P  L ++  I   +R+                  +I  S     PA     ++  ++
Sbjct: 327 ---PRRL-SI--IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380

Query: 238 RPAQPFVE----PTSADYVTFEML-------ISESLVGGLIGRCGSNISRIRNESGAMIK 286
                F      PT        ++           +V  L     S + +   ES   I 
Sbjct: 381 -----FPPSAHIPTI----LLSLIWFDVIKSDVMVVVNKLHKY--SLVEKQPKES--TIS 427

Query: 287 VYG------GKGEQK---HRHI----QFGGSAQQVALAKQRVDEYIYSQL 323
           +         K E +   HR I        +     L    +D+Y YS +
Sbjct: 428 IPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHI 477

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

 Score = 49.8 bits (119), Expect = 3e-08
 Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVY--GGKGEQKHRHIQFGGSAQQVA 309
           V  ++ + +  VG +IGR G  I  I   SGA I             R I+  G+ ++VA
Sbjct: 15  VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVA 74

Query: 310 LAKQRVDEYI 319
            AK  + E +
Sbjct: 75  AAKHLILEKV 84

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

 Score = 48.3 bits (115), Expect = 1e-07
 Identities = 22/103 (21%), Positives = 39/103 (37%), Gaps = 7/103 (6%)

Query: 38  GSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IARHEER 95
                   +   V  ++ VP R +G++IG+ G  I+ I + + A I             R
Sbjct: 3   SGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSR 62

Query: 96  VIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAG 138
           +I IS      V      A   I   + +D++     +  A+G
Sbjct: 63  LIKISG-TQKEV----AAAKHLILEKVSEDEELRKRIAHSASG 100

>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 = 41.3 bits (97), Expect = 3e-05
 Identities = 23/104 (22%), Positives = 40/104 (38%), Gaps = 6/104 (5%)

Query: 130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCAS 189
           S  S            +L +     G +IG  G+ I  +  +SGA I     ++      
Sbjct: 2   SSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE-----G 56

Query: 190 AHESDRVVQISGDVPAVLNALVEIGNQLRENP-PRQVISISPAY 232
                R+++ISG    V  A   I  ++ E+   R+ I+ S + 
Sbjct: 57  TLLLSRLIKISGTQKEVAAAKHLILEKVSEDEELRKRIAHSASG 100

>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 = 50.8 bits (121), Expect = 3e-08
 Identities = 29/167 (17%), Positives = 52/167 (31%), Gaps = 31/167 (18%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
           + IV    +G  IG  G  IQ+ R+    T    D     +     I  +          
Sbjct: 7   QFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLD----EDTCTFHIYGE---------- 52

Query: 113 NALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172
                           + +A K A   +      + +  +  G +IG +G+ I+++ + S
Sbjct: 53  ----------------DQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKS 96

Query: 173 GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219
           G   V +                 V   G   ++ NA V +   L  
Sbjct: 97  GVVRVRIEAENEKNVPQEEGMVPFV-FVGTKDSIANATVLLDYHLNY 142

>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 = 43.8 bits (103), Expect = 1e-05
 Identities = 33/185 (17%), Positives = 63/185 (34%), Gaps = 52/185 (28%)

Query: 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS 200
           +    + ++     G  IG  G NI++ R   G T + L            E      I 
Sbjct: 2   SRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDL-----------DEDTCTFHIY 50

Query: 201 GDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISE 260
           G+                              +  A++ A+ F+E     +    + +  
Sbjct: 51  GE------------------------------DQDAVKKARSFLE-----FAEDVIQVPR 75

Query: 261 SLVGGLIGRCGSNISRIRNESGA-MIKVYGGKG-----EQKHRHIQFGGSAQQVALAKQR 314
           +LVG +IG+ G  I  I ++SG   +++          E+      F G+   +A A   
Sbjct: 76  NLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVL 135

Query: 315 VDEYI 319
           +D ++
Sbjct: 136 LDYHL 140

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 46.5 bits (110), Expect = 3e-07
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 3/74 (4%)

Query: 246 PTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSA 305
            +S    T ++ +   +VG ++G  G+ I RI+  +   I      G  K       G  
Sbjct: 4   GSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVT---PGRDKEPVFAVTGMP 60

Query: 306 QQVALAKQRVDEYI 319
           + V  A++ ++ +I
Sbjct: 61  ENVDRAREEIEAHI 74

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 8/69 (11%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + VP R +G V+G +G  I++I++ T   I       R +E V  ++    +NV    + 
Sbjct: 14  VRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPG---RDKEPVFAVTG-MPENV----DR 65

Query: 114 ALQQIAALI 122
           A ++I A I
Sbjct: 66  AREEIEAHI 74

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

 Score = 45.8 bits (109), Expect = 4e-07
 Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 2/69 (2%)

Query: 249 ADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQV 308
                 E+ I       LIG+ G+NI+RI+++    +++      +K   I+  G  Q V
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI--PPDSEKSNLIRIEGDPQGV 59

Query: 309 ALAKQRVDE 317
             AK+ + E
Sbjct: 60  QQAKRELLE 68

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

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 4/74 (5%)

Query: 47  AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDN 106
            +     I +  +    +IGK G  I +I+++ K +++I    +     + I        
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-SEKSNLIRIEGDPQG-- 58

Query: 107 VVSDAENALQQIAA 120
            V  A+  L ++A+
Sbjct: 59  -VQQAKRELLELAS 71

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

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 11/77 (14%), Positives = 34/77 (44%), Gaps = 3/77 (3%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
            +  + I +     +IG+ G  +  +  ++   I++   + +     I+  G+ + +  A
Sbjct: 17  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSNQIKITGTKEGIEKA 74

Query: 312 KQRVDEYIYSQLIQQAG 328
           +  V   I ++  +++G
Sbjct: 75  RHEVLL-ISAEQDKRSG 90

>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 = 43.6 bits (103), Expect = 4e-06
 Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + +P      VIGK G ++Q +  +T   I+I         ++ I  +K+        E
Sbjct: 20  TVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-DDPSNQIKITGTKEG------IE 72

Query: 113 NALQQIAALILKDDDSNSEAS 133
            A  ++  +  + D  +  +S
Sbjct: 73  KARHEVLLISAEQDKRSGPSS 93

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

 Score = 37.4 bits (87), Expect = 6e-04
 Identities = 15/92 (16%), Positives = 33/92 (35%), Gaps = 9/92 (9%)

Query: 128 SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187
           S+  +  + A      +  + I       +IG +G+ ++ L   +   I I  P+     
Sbjct: 2   SSGSSGDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD----- 56

Query: 188 ASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219
               +    ++I+G    +  A  E+     E
Sbjct: 57  ----DPSNQIKITGTKEGIEKARHEVLLISAE 84

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 44.4 bits (105), Expect = 3e-06
 Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 1/69 (1%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV-YGGKGEQKHRHIQFGGSAQQVAL 310
               + +       +IGR G+ I++IR E    I+      G Q    I   G  +    
Sbjct: 17  FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEA 76

Query: 311 AKQRVDEYI 319
           A+  +   +
Sbjct: 77  ARDAILRIV 85

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 41.0 bits (96), Expect = 4e-05
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + V  +   K+IG++G  I +IR E    I+  D    ++ +  I  +    N     E 
Sbjct: 21  VTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNT----EA 76

Query: 114 ALQQIAALILKDDDSNSEAS 133
           A   I  ++ + +  +  +S
Sbjct: 77  ARDAILRIVGELEQMSGPSS 96

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 44.4 bits (105), Expect = 3e-06
 Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 2/68 (2%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
           VT E+ +   L   +IG+ GS I ++ +E    I V     E +   I   G A  +  A
Sbjct: 17  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAITGLAANLDRA 74

Query: 312 KQRVDEYI 319
           K  + E +
Sbjct: 75  KAGLLERV 82

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 37.5 bits (87), Expect = 8e-04
 Identities = 17/92 (18%), Positives = 34/92 (36%), Gaps = 9/92 (9%)

Query: 128 SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187
           S+  + K A   +   TI + +       +IG  G  I K+ +     I + AP      
Sbjct: 2   SSGSSGKEALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE----- 56

Query: 188 ASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219
                   ++ I+G    +  A   +  +++E
Sbjct: 57  ----LQSDIIAITGLAANLDRAKAGLLERVKE 84

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 3/72 (4%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + +  R   ++IG  G  I+KI +E K  I+   + A     V +    +N   V +A +
Sbjct: 21  VPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPEN---VEEAID 77

Query: 114 ALQQIAALILKD 125
            +  +    L D
Sbjct: 78  HILNLEEEYLAD 89

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 40.1 bits (94), Expect = 6e-05
 Identities = 12/69 (17%), Positives = 24/69 (34%), Gaps = 1/69 (1%)

Query: 249 ADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQV 308
              V+ ++ +   +   +IG  G  I +I +E    I+     G      +   G  + V
Sbjct: 14  EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-PQSGAPDPNCVTVTGLPENV 72

Query: 309 ALAKQRVDE 317
             A   +  
Sbjct: 73  EEAIDHILN 81

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

 Score = 43.3 bits (103), Expect = 9e-05
 Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 10/69 (14%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + VP  +  K +G  G+ ++K++ ET  TI   D      E    + +            
Sbjct: 571 VQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD------EETFSVFAPTPSA----MHE 620

Query: 114 ALQQIAALI 122
           A   I  + 
Sbjct: 621 ARDFITEIC 629

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

 Score = 42.9 bits (102), Expect = 1e-04
 Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 10/69 (14%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           I +P+ +I +VIG  G  I++I   T A + I D      + V+ +S+ D        + 
Sbjct: 574 INIPTDKIREVIGSGGKVIREIVATTGAKVDIND------DGVVKVSASDGAK----IKA 623

Query: 114 ALQQIAALI 122
           A+  I ++ 
Sbjct: 624 AIDWIKSIT 632

>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 = 40.8 bits (95), Expect = 2e-04
 Identities = 28/187 (14%), Positives = 55/187 (29%), Gaps = 35/187 (18%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
             + V   ++G VIG  G    +I   T   I +       E  ++I+  +       + 
Sbjct: 6   IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVD-----TENSMVIVEPEAEGIPPVNL 60

Query: 112 ENALQQIAAL-----------ILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGM 160
             A + + A+           +L++D              + N ++ +      G +IG 
Sbjct: 61  MKAAEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIK-----GRIIGE 115

Query: 161 SGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220
            G+    +   +   I +               +  V I GD    + A   I       
Sbjct: 116 GGRARRTIEEMTDTYINV--------------GEYEVAIIGDYERAMAAKQAIEMLAEGR 161

Query: 221 PPRQVIS 227
               V  
Sbjct: 162 MHSTVYR 168

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

 Score = 41.7 bits (99), Expect = 2e-04
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 10/69 (14%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           I +   +I  VIGK G  I+ + EET  TI+I D      +  + I++ D +     A++
Sbjct: 564 IKINPDKIKDVIGKGGSVIRALTEETGTTIEIED------DGTVKIAATDGEK----AKH 613

Query: 114 ALQQIAALI 122
           A+++I  + 
Sbjct: 614 AIRRIEEIT 622

>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 = 39.9 bits (92), Expect = 3e-04
 Identities = 11/51 (21%), Positives = 20/51 (39%), Gaps = 24/51 (47%)

Query: 163 QNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV-LNALVE 212
           Q ++KL+ S    + + A +      SA             PA+ + A +E
Sbjct: 20  QALKKLQAS----LKLYADD------SA-------------PALAIKATME 47

>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 = 41.4 bits (98), Expect = 3e-04
 Identities = 24/73 (32%), Positives = 34/73 (46%), Gaps = 13/73 (17%)

Query: 53  RII---VPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           RII   +P  +IG+VIG +   I +I+E+T A I I D      +  I I + D      
Sbjct: 598 RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADGPA--- 648

Query: 110 DAENALQQIAALI 122
            AE A   I  + 
Sbjct: 649 -AEAARATINGIA 660

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 249 ADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQV 308
           A+    E+ I   L   LIG  G  I  I  E G  + ++          +   G +  V
Sbjct: 14  ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGG-VHIHFPVEGSGSDTVVIRGPSSDV 72

Query: 309 ALAKQRVDE 317
             AK+++  
Sbjct: 73  EKAKKQLLH 81

>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 = 39.3 bits (91), Expect = 6e-04
 Identities = 38/217 (17%), Positives = 72/217 (33%), Gaps = 33/217 (15%)

Query: 22  RHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKA 81
           +     +   +DGEI   + +     +   + + +P  +I  +IGK+G   ++I + TK 
Sbjct: 7   KLMKKFENVNKDGEIVEDEDEWEEFFKQEEY-VKIPKDRIAVLIGKKGQTKKEIEKRTKT 65

Query: 82  TIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI----------LKDDDSNSE 131
            I I       E   + I+S            A   + A+           L ++    E
Sbjct: 66  KITID-----SETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPERAFRLLNEGEYLE 120

Query: 132 ASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAH 191
              +    +      L       G +IG  G+  + +   SGA++ +             
Sbjct: 121 IINLTDIIIGNEKNALPRV---RGRIIGRKGRTRQIIEEMSGASVSV------------- 164

Query: 192 ESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISI 228
              + V I G+   +  A   I    R +P   V   
Sbjct: 165 -YGKTVAIIGNPIQIEIAKTAIEKLARGSPHGSVYRY 200

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	330
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.95
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.95
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.94
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.94
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.94
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.93
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.93
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.93
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.92
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.92
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.92
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.82
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.77
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.72
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.69
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.64
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.64
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.63
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.62
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.62
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.6
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.6
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.59
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.58
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.56
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.56
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.54
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.53
1we8_A	104	Tudor and KH domain containing protein; structural	99.51
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.51
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.51
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.49
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.48
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.48
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.48
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.47
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.46
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.45
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.44
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.44
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.42
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.41
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.41
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.39
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.38
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.37
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.36
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.35
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.35
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.35
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.32
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.3
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.3
1we8_A	104	Tudor and KH domain containing protein; structural	99.27
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.21
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.21
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.2
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.09
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.08
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.06
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.96
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.82
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.77
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.75
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.65
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.52
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.27
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.26
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.16
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	98.11
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.68
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.64
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.56
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.48
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.47
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.78
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	96.01
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.96
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.68
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.57
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.36
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	95.24
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	94.42
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	93.94
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	92.42
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	91.96

>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=8e-27  Score=195.58  Aligned_cols=156  Identities=22%  Similarity=0.340  Sum_probs=132.4

Q ss_pred             eEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCC
Q 020173          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPP  222 (330)
Q Consensus       143 ~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~  222 (330)
                      .+++|+||...+|.|||++|++|++|+++|||+|.+... ..|.     +.+|+|+|+|+++++.+|+.+|.+++.+...
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~-~~~~-----~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~   76 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPP-ETPD-----SKVRMVIITGPPEAQFKAQGRIYGKLKEENF   76 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCC-SSTT-----CSEEEEEEEECHHHHHHHHHHHHHHHHHTTS
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCC-CCCC-----CCceEEEEEcCHHHHHHHHHHHHHHHhcccc
Confidence            478999999999999999999999999999999999753 2333     5789999999999999999999999987621


Q ss_pred             CCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC--CCceeEEE
Q 020173          223 RQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG--EQKHRHIQ  300 (330)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~--~~~~r~v~  300 (330)
                      ..                     |......+.+|.||.+++|+|||++|++|++|++.|||+|.|+++..  ..+++.|+
T Consensus        77 ~~---------------------~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v~  135 (163)
T 3krm_A           77 FG---------------------PKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVK  135 (163)
T ss_dssp             SC---------------------SSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEEE
T ss_pred             cc---------------------cccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEEE
Confidence            10                     11223467899999999999999999999999999999999987542  23456899


Q ss_pred             EEcCHHHHHHHHHHHHHHHHHHHHH
Q 020173          301 FGGSAQQVALAKQRVDEYIYSQLIQ  325 (330)
Q Consensus       301 I~Gt~~~v~~A~~~I~~~i~~~~~~  325 (330)
                      |+|++++|+.|+.+|.++|.+...+
T Consensus       136 I~G~~~~v~~A~~~I~~~i~~~~~~  160 (163)
T 3krm_A          136 IIGHFYASQMAQRKIRDILAQVKQQ  160 (163)
T ss_dssp             EEECHHHHHHHHHHHHHHHHHHTC-
T ss_pred             EEeCHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999876543

>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=99.95  E-value=1.3e-26  Score=194.52  Aligned_cols=160  Identities=21%  Similarity=0.346  Sum_probs=131.9

Q ss_pred             eEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCC
Q 020173          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPP  222 (330)
Q Consensus       143 ~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~  222 (330)
                      .+.+|+||...+|.|||++|++|++|+++|||+|.+.+....+.     ..+|.|+|+|++++|.+|+.+|.+++.+...
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~-----~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~   76 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNT-----NVDKPLRIIGDPYKVQQACEMVMDILRERDQ   76 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSS-----SSCEEEEEEECHHHHHHHHHHHHHHTTCSSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCC-----CCceEEEEEcCHHHHHHHHHHHHHHHHhccC
Confidence            47899999999999999999999999999999999975432222     5689999999999999999999999987632


Q ss_pred             CCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEE
Q 020173          223 RQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFG  302 (330)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~  302 (330)
                      ..   +.+         ...|.+.   ...+.+|.||.+++|+|||++|++|++|++.|||+|.|++..+.+.++.|+|+
T Consensus        77 ~~---~~~---------~~~~~~~---~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~  141 (164)
T 2jvz_A           77 GG---FGD---------RNEYGSR---IGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM  141 (164)
T ss_dssp             CC---CSS---------CSSCTTS---CSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEE
T ss_pred             CC---CCC---------ccccCCC---CCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEE
Confidence            21   000         0011110   12457899999999999999999999999999999999986655668999999


Q ss_pred             cCHHHHHHHHHHHHHHHHHH
Q 020173          303 GSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       303 Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      |++++++.|+.+|.++|.+.
T Consensus       142 G~~~~v~~A~~~I~~~i~~~  161 (164)
T 2jvz_A          142 GPPDRCEHAARIINDLLQSL  161 (164)
T ss_dssp             SCHHHHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHHhhh
Confidence            99999999999999998764

>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=1.5e-26  Score=196.76  Aligned_cols=169  Identities=24%  Similarity=0.359  Sum_probs=133.2

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCC-CCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN-QLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~-~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      ..++++|+||...+|.|||++|++|++|+++|||+|++.... ..|.     ..+|+|+|+|+.+++.+|..+|.+++.+
T Consensus         4 ~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~-----~~er~v~I~G~~~~v~~A~~~I~~~~~~   78 (178)
T 2anr_A            4 SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPG-----TTERVCLIQGTIEALNAVHGFIAEKIRE   78 (178)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTT-----SSEEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCC-----CCCceEEEEeCHHHHHHHHHHHHHHHhc
Confidence            457899999999999999999999999999999999997543 2343     5789999999999999999999999988


Q ss_pred             CCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC--CCcee
Q 020173          220 NPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG--EQKHR  297 (330)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~--~~~~r  297 (330)
                      .+.....+       ......+|..........+.+|.||.+++|+|||++|++|++|++.|||+|.|++...  .+.++
T Consensus        79 ~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~  151 (178)
T 2anr_A           79 MPQNVAKT-------EPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNR  151 (178)
T ss_dssp             CCCC------------------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEE
T ss_pred             cCCccccC-------CcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCCCce
Confidence            75432100       0000001111111234578899999999999999999999999999999999997532  34689


Q ss_pred             EEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          298 HIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       298 ~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      .|+|+|++++|+.|+.+|.++|.+
T Consensus       152 ~v~I~G~~~~v~~A~~~I~~~i~e  175 (178)
T 2anr_A          152 VVTVSGEPEQNRKAVELIIQKIQE  175 (178)
T ss_dssp             EEEEESSHHHHHHHHHHHHHHHHS
T ss_pred             EEEEEcCHHHHHHHHHHHHHHHHh
Confidence            999999999999999999998864

>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=9.3e-27  Score=197.98  Aligned_cols=165  Identities=25%  Similarity=0.387  Sum_probs=133.7

Q ss_pred             CCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC---CCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 020173           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (330)
Q Consensus        47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~---~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~  123 (330)
                      .++++++|+||.+.+|.||||+|++|++|+++|||+|+|++.   .++.++|+|+|+|+.     +++.+|..+|.+++.
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~-----~~v~~A~~~I~~~~~   77 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI-----EALNAVHGFIAEKIR   77 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECH-----HHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCH-----HHHHHHHHHHHHHHh
Confidence            468999999999999999999999999999999999999864   356789999999985     678899999999886


Q ss_pred             hcCCCCccc-------cccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcE
Q 020173          124 KDDDSNSEA-------SKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRV  196 (330)
Q Consensus       124 ~~~~~~~~~-------~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~  196 (330)
                      +........       ...........+.+|+||..++|+|||++|++|++|++.|||+|.+.+....+.     ..++.
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~-----~~~~~  152 (178)
T 2anr_A           78 EMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGIN-----LQNRV  152 (178)
T ss_dssp             CCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC---------CCEEE
T ss_pred             ccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCC-----CCceE
Confidence            543221100       000011123468999999999999999999999999999999999976533232     57899


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHhhCC
Q 020173          197 VQISGDVPAVLNALVEIGNQLRENP  221 (330)
Q Consensus       197 v~I~G~~~~v~~A~~~I~~~i~~~~  221 (330)
                      |+|+|++++|.+|+.+|.+++.++|
T Consensus       153 v~I~G~~~~v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          153 VTVSGEPEQNRKAVELIIQKIQEDP  177 (178)
T ss_dssp             EEEESSHHHHHHHHHHHHHHHHSCC
T ss_pred             EEEEcCHHHHHHHHHHHHHHHHhCC
Confidence            9999999999999999999999885

>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=99.94  E-value=5.1e-26  Score=190.09  Aligned_cols=155  Identities=29%  Similarity=0.497  Sum_probs=130.5

Q ss_pred             ceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCC
Q 020173          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (330)
Q Consensus       142 ~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  221 (330)
                      ..+++|+||...+|.|||++|++|++|+++|||+|++...+         ..+|.|+|.|+.+++.+|+.+|.+++.+..
T Consensus         4 ~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~~---------~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   74 (160)
T 2jzx_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN---------CPERIITLAGPTNAIFKAFAMIIDKLEEDI   74 (160)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECCT---------TTEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCCC---------CCceEEEEEeCHHHHHHHHHHHHHHHHhhc
Confidence            46899999999999999999999999999999999997531         468999999999999999999999997752


Q ss_pred             CCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC-CCCceeEEE
Q 020173          222 PRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK-GEQKHRHIQ  300 (330)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~-~~~~~r~v~  300 (330)
                      ...   ....+             .......+.+|.||.+++|+|||++|++|++|++.|||+|.|+++. +.+.++.|+
T Consensus        75 ~~~---~~~~~-------------~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~  138 (160)
T 2jzx_A           75 SSS---MTNST-------------AASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAIT  138 (160)
T ss_dssp             TSC---CCSSS-------------CCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEE
T ss_pred             ccc---CCCCc-------------cCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEE
Confidence            210   00000             0112347899999999999999999999999999999999998642 356789999


Q ss_pred             EEcCHHHHHHHHHHHHHHHHH
Q 020173          301 FGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       301 I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      |+|++++|+.|+.+|.+++.+
T Consensus       139 I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          139 IAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             EEECHHHHHHHHHHHHHHHHH
T ss_pred             EEcCHHHHHHHHHHHHHHHhc
Confidence            999999999999999998865

>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=1.1e-25  Score=190.65  Aligned_cols=169  Identities=23%  Similarity=0.332  Sum_probs=126.4

Q ss_pred             eEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCC
Q 020173          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPP  222 (330)
Q Consensus       143 ~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~  222 (330)
                      .+++|+||...+|.|||++|++|++|+++|||+|+|...+  +.     ..+|+|+|+|+.++|.+|+.+|.+++.+...
T Consensus         3 ~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~--~~-----~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~   75 (174)
T 1j4w_A            3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD--GT-----TPERIAQITGPPDRAQHAAEIITDLLRSVQA   75 (174)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT--TS-----CSEEEEEEEECHHHHHHHHHHHHHHHHHHC-
T ss_pred             eEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCC--CC-----CCccEEEEEeCHHHHHHHHHHHHHHHHhccc
Confidence            4789999999999999999999999999999999997532  22     4689999999999999999999999987532


Q ss_pred             CCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC---CCceeEE
Q 020173          223 RQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG---EQKHRHI  299 (330)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~---~~~~r~v  299 (330)
                      ...-+..+.-. ...+....|.........+.+|.||.+++|+|||++|++|++|++.|||+|+|++..+   ++.++.|
T Consensus        76 ~~~~~~~p~~~-~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v  154 (174)
T 1j4w_A           76 GNPGGPGPGGR-GRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLF  154 (174)
T ss_dssp             -----------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEE
T ss_pred             CCCCCCCCCCC-CCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEE
Confidence            11000000000 0000000110000123468899999999999999999999999999999999997532   3568999


Q ss_pred             EEEcCHHHHHHHHHHHHHHH
Q 020173          300 QFGGSAQQVALAKQRVDEYI  319 (330)
Q Consensus       300 ~I~Gt~~~v~~A~~~I~~~i  319 (330)
                      +|+|++++++.|+.+|.++|
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            99999999999999999864

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

Probab=99.93  E-value=1.5e-25  Score=187.90  Aligned_cols=155  Identities=23%  Similarity=0.363  Sum_probs=130.9

Q ss_pred             ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC-CCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCC
Q 020173           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD  127 (330)
Q Consensus        49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~  127 (330)
                      .-+++|+||.+.+|.||||+|++|++|+++|||+|+|++. .++..+|+|+|+|+.     +.+.+|..+|.+.+.+...
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~-----e~v~~A~~~I~~~~~e~~~   76 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPP-----EAQFKAQGRIYGKLKEENF   76 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECH-----HHHHHHHHHHHHHHHHTTS
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCH-----HHHHHHHHHHHHHHhcccc
Confidence            3578999999999999999999999999999999999986 567889999999975     7889999999998876532


Q ss_pred             CCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHH
Q 020173          128 SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVL  207 (330)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~  207 (330)
                      ...       ......+.+|+||..++|+|||++|++|++|++.|||+|.+.. +..|..    .+++.|+|+|++++|.
T Consensus        77 ~~~-------~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~-~~~~~~----~~~~~v~I~G~~~~v~  144 (163)
T 3krm_A           77 FGP-------KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR-DQTPDE----NDQVIVKIIGHFYASQ  144 (163)
T ss_dssp             SCS-------SCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCT-TCCCCT----TSEEEEEEEECHHHHH
T ss_pred             ccc-------ccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECC-CCCCCC----CCceEEEEEeCHHHHH
Confidence            111       1123457899999999999999999999999999999999964 444541    3445899999999999


Q ss_pred             HHHHHHHHHHhhC
Q 020173          208 NALVEIGNQLREN  220 (330)
Q Consensus       208 ~A~~~I~~~i~~~  220 (330)
                      +|+.+|.+++.+.
T Consensus       145 ~A~~~I~~~i~~~  157 (163)
T 3krm_A          145 MAQRKIRDILAQV  157 (163)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999999875

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

Probab=99.93  E-value=1.1e-25  Score=188.14  Aligned_cols=159  Identities=27%  Similarity=0.492  Sum_probs=131.8

Q ss_pred             CCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcC
Q 020173           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (330)
Q Consensus        47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~  126 (330)
                      +..++++|+||.+.+|.||||+|++|++|+++|||+|+|++.  ++++|+|+|.|+.     +++.+|..+|.+.+.+..
T Consensus         2 ~~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~-----~~v~~A~~~I~~~i~e~~   74 (160)
T 2jzx_A            2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPT-----NAIFKAFAMIIDKLEEDI   74 (160)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEH-----HHHHHHHHHHHHHHHHHH
T ss_pred             CccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCH-----HHHHHHHHHHHHHHHhhc
Confidence            356899999999999999999999999999999999999986  5678999999984     688899999988876542


Q ss_pred             CCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH
Q 020173          127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV  206 (330)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v  206 (330)
                      .... ... ........+.+++||..++|+|||++|++|++|++.|||+|.+.. +..|.     ..++.|+|+|+++++
T Consensus        75 ~~~~-~~~-~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~-~~~~~-----~~~~~v~I~G~~~~v  146 (160)
T 2jzx_A           75 SSSM-TNS-TAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG-DMLPN-----STERAITIAGIPQSI  146 (160)
T ss_dssp             TSCC-CSS-SCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCC-CCSTT-----CCEEEEEEEECHHHH
T ss_pred             cccC-CCC-ccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECC-CCCCC-----CCceEEEEEcCHHHH
Confidence            2110 000 011123568999999999999999999999999999999999964 34443     578999999999999


Q ss_pred             HHHHHHHHHHHhhC
Q 020173          207 LNALVEIGNQLREN  220 (330)
Q Consensus       207 ~~A~~~I~~~i~~~  220 (330)
                      .+|+.+|.+++.++
T Consensus       147 ~~A~~~I~~~i~e~  160 (160)
T 2jzx_A          147 IECVKQICVVMLET  160 (160)
T ss_dssp             HHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhcC
Confidence            99999999998763

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

Probab=99.92  E-value=2.6e-25  Score=206.05  Aligned_cols=221  Identities=11%  Similarity=0.105  Sum_probs=156.9

Q ss_pred             CCCceEEEEEecCCccceeecccC--hhhhhhhhccCcEEEEecCCC-----CCcceEEEEecCCCCcchhHHHHHHHHH
Q 020173           46 KAQDVLFRIIVPSRQIGKVIGKEG--HRIQKIREETKATIKIADAIA-----RHEERVIIISSKDNDNVVSDAENALQQI  118 (330)
Q Consensus        46 ~~~~~~~~i~vP~~~vg~IIGk~G--~~Ik~I~~~tg~~I~i~~~~~-----~~~ervi~I~G~~~~~~~~~~~~A~~~i  118 (330)
                      +.+.+++++.||..++++||||+|  ++|++|+++|||+|+|++..+     ......|+|+|..     +++++|..+|
T Consensus        26 ~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~-----enVE~AR~~I  100 (376)
T 3n89_A           26 NPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYF-----GDVDRARMLM  100 (376)
T ss_dssp             CTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEH-----HHHHHHHHHH
T ss_pred             cCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCH-----HHHHHHHHHH
Confidence            467899999999999999999999  999999999999999998641     1234689999986     7888888888


Q ss_pred             HHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEE
Q 020173          119 AALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQ  198 (330)
Q Consensus       119 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~  198 (330)
                      .+.+                   ...+.+.+|...+..  ..-+..|.+ ++.++++|.+........     .....|+
T Consensus       101 ~~l~-------------------Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~~-----~~sd~V~  153 (376)
T 3n89_A          101 RRNC-------------------HFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKNG-----IVTTYLR  153 (376)
T ss_dssp             HHSC-------------------EEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC----------CEEEEE
T ss_pred             HhcC-------------------CceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCcccccC-----CCCCEEE
Confidence            8742                   123444455432221  111223444 567999999865321100     1245799


Q ss_pred             EEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCC--chHHH
Q 020173          199 ISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCG--SNISR  276 (330)
Q Consensus       199 I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G--~~Ik~  276 (330)
                      |+|...++.+|.+.+..++.......                     ......++..|.|+..+|..|||++|  ..|++
T Consensus       154 IrG~~~nv~~akeA~~~Ll~~l~~~e---------------------~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~Ikk  212 (376)
T 3n89_A          154 ITAREKNQHELIEAAKRLNEILFRES---------------------PAPENNFTLHFTLSTYYVDQVLGSSSTAQLMPV  212 (376)
T ss_dssp             EEEEGGGHHHHHHHHHHHHHHHCC-----------------------CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHH
T ss_pred             EEcChhhHHHHHHHHHHHHHHHHhhh---------------------cccccceEEEEEeCHHHHHHhhcCCCcchHHHH
Confidence            99998766665555444443321100                     01124588999999999999999999  66799


Q ss_pred             HHHHhCCeEEEeCCCCC----CceeEEEEEcCHHHHHHHHHHHHHHH
Q 020173          277 IRNESGAMIKVYGGKGE----QKHRHIQFGGSAQQVALAKQRVDEYI  319 (330)
Q Consensus       277 i~~~tga~I~i~~~~~~----~~~r~v~I~Gt~~~v~~A~~~I~~~i  319 (330)
                      |+++|||+|.+|+..+.    .....|+|+|+.++|..|+++|.++|
T Consensus       213 Ir~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lL  259 (376)
T 3n89_A          213 IERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLL  259 (376)
T ss_dssp             HHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTS
T ss_pred             HHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhC
Confidence            99999999999975331    23578999999999999999998864

>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=99.92  E-value=1.5e-24  Score=181.75  Aligned_cols=157  Identities=19%  Similarity=0.327  Sum_probs=127.9

Q ss_pred             eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCC--CCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCC
Q 020173           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI--ARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD  127 (330)
Q Consensus        50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~--~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~  127 (330)
                      ++++|+||.+.+|+|||++|++|++|+++|||+|+|.+..  ++.++|+|+|+|+.     +++.+|+.+|.+++.+...
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~-----~~v~~A~~~I~~ii~e~~~   76 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDP-----YKVQQACEMVMDILRERDQ   76 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECH-----HHHHHHHHHHHHHTTCSSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCH-----HHHHHHHHHHHHHHHhccC
Confidence            5789999999999999999999999999999999997542  45678999999975     7889999999998765542


Q ss_pred             CCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHH
Q 020173          128 SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVL  207 (330)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~  207 (330)
                      ..... ....+.....+.+|+||..++|+|||++|++|++|+++|||+|.+.+.+  +.     +.++.|+|+|+++++.
T Consensus        77 ~~~~~-~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~--~~-----~~~~~v~I~G~~~~v~  148 (164)
T 2jvz_A           77 GGFGD-RNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--GT-----GPEKIAHIMGPPDRCE  148 (164)
T ss_dssp             CCCSS-CSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC--TT-----SSEEEEEEESCHHHHH
T ss_pred             CCCCC-ccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC--CC-----CCcEEEEEEcCHHHHH
Confidence            21100 0011111234688999999999999999999999999999999997543  11     4579999999999999


Q ss_pred             HHHHHHHHHHhh
Q 020173          208 NALVEIGNQLRE  219 (330)
Q Consensus       208 ~A~~~I~~~i~~  219 (330)
                      +|+.+|.+++.+
T Consensus       149 ~A~~~I~~~i~~  160 (164)
T 2jvz_A          149 HAARIINDLLQS  160 (164)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhh
Confidence            999999999875

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

Probab=99.92  E-value=1.1e-24  Score=184.55  Aligned_cols=160  Identities=21%  Similarity=0.331  Sum_probs=126.2

Q ss_pred             ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCC
Q 020173           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS  128 (330)
Q Consensus        49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~  128 (330)
                      ..+++|+||.+.+|.||||+|++|++|+++|||+|+|++..++.++|+|.|.|+.     +++.+|+.+|.+++.+....
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~-----~~v~~A~~~I~~~~~~~~~~   76 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPP-----DRAQHAAEIITDLLRSVQAG   76 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECH-----HHHHHHHHHHHHHHHHHC--
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCH-----HHHHHHHHHHHHHHHhcccC
Confidence            4678999999999999999999999999999999999876556789999999985     67889999998887654321


Q ss_pred             Ccccc------------ccc-cCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCc
Q 020173          129 NSEAS------------KVA-AGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDR  195 (330)
Q Consensus       129 ~~~~~------------~~~-~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r  195 (330)
                      .....            ... .......+.+|+||..++|+|||++|++|++|++.|||+|.|.... .+ +.  .+.++
T Consensus        77 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~-~~-~~--~~~~~  152 (174)
T 1j4w_A           77 NPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP-PP-NA--DPNMK  152 (174)
T ss_dssp             ---------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCC-TT-TS--CTTEE
T ss_pred             CCCCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCC-CC-CC--CCCce
Confidence            10000            000 0001245889999999999999999999999999999999997532 12 11  25679


Q ss_pred             EEEEEcCHHHHHHHHHHHHHHH
Q 020173          196 VVQISGDVPAVLNALVEIGNQL  217 (330)
Q Consensus       196 ~v~I~G~~~~v~~A~~~I~~~i  217 (330)
                      .|+|+|+++++.+|+.+|.++|
T Consensus       153 ~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          153 LFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             EEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEECCHHHHHHHHHHHHHhC
Confidence            9999999999999999998864

>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=99.82  E-value=6.3e-20  Score=149.94  Aligned_cols=134  Identities=22%  Similarity=0.277  Sum_probs=106.7

Q ss_pred             ceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCC
Q 020173          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (330)
Q Consensus       142 ~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  221 (330)
                      .++.+|+||...+|.+||++|++|+.|++++|+++.....          ..+..+...++++.|.+|..++    . . 
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~~----------~~~~~i~~~~~p~~v~~~~~~l----~-~-   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE----------DTCTFHIYGEDQDAVKKARSFL----E-F-   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEET----------TTTEEEEEESSHHHHHHHHHHH----C-E-
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccCC----------CchheeeccCCHHHHHHHHHhh----h-c-
Confidence            3578999999999999999999999999999954433321          2345555566799998886532    1 1 


Q ss_pred             CCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCC-eEEEeCCCCCC---ce-
Q 020173          222 PRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGA-MIKVYGGKGEQ---KH-  296 (330)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga-~I~i~~~~~~~---~~-  296 (330)
                                                    ...++.||.+++|.+|||+|++|+.+++.||+ +|+|+...+..   ++ 
T Consensus        67 ------------------------------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~  116 (144)
T 2qnd_A           67 ------------------------------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEG  116 (144)
T ss_dssp             ------------------------------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTT
T ss_pred             ------------------------------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCC
Confidence                                          23789999999999999999999999999997 99999753321   22 


Q ss_pred             -eEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          297 -RHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       297 -r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                       +.|+|+|++++|+.|+.+|+++|.+
T Consensus       117 ~~~vtI~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A          117 MVPFVFVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             EEEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred             eeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence             4699999999999999999998854

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

Probab=99.77  E-value=2.5e-18  Score=140.43  Aligned_cols=137  Identities=20%  Similarity=0.247  Sum_probs=101.9

Q ss_pred             ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCC
Q 020173           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS  128 (330)
Q Consensus        49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~  128 (330)
                      .++.+|+||.+.+|++||++|++|++|++++|+.|...+   ..++.++...+++     ..+.+    +..++ ..   
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~---~~~~~~i~~~~~p-----~~v~~----~~~~l-~~---   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLD---EDTCTFHIYGEDQ-----DAVKK----ARSFL-EF---   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEE---TTTTEEEEEESSH-----HHHHH----HHHHH-CE---
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccC---CCchheeeccCCH-----HHHHH----HHHhh-hc---
Confidence            578899999999999999999999999999994443333   2344544444443     23333    22222 11   


Q ss_pred             CccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCC-eEEEeCCCCCCcccCCCCCCc--EEEEEcCHHH
Q 020173          129 NSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGA-TIVILAPNQLPLCASAHESDR--VVQISGDVPA  205 (330)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga-~I~i~~~~~~p~~~~~~~~~r--~v~I~G~~~~  205 (330)
                                    ...++.||..++|++|||+|++|+.+++.||+ +|.|...+....    ..+++  .|+|+|+.++
T Consensus        67 --------------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~----~~~~~~~~vtI~G~~~~  128 (144)
T 2qnd_A           67 --------------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV----PQEEGMVPFVFVGTKDS  128 (144)
T ss_dssp             --------------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC----CCCTTEEEEEEEEEHHH
T ss_pred             --------------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc----cccCCeeEEEEEeCHHH
Confidence                          13789999999999999999999999999997 899986432211    02343  5899999999


Q ss_pred             HHHHHHHHHHHHhh
Q 020173          206 VLNALVEIGNQLRE  219 (330)
Q Consensus       206 v~~A~~~I~~~i~~  219 (330)
                      |.+|..+|..+|.+
T Consensus       129 v~~Ak~li~~~l~~  142 (144)
T 2qnd_A          129 IANATVLLDYHLNY  142 (144)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999875

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

Probab=99.72  E-value=3.3e-17  Score=142.22  Aligned_cols=142  Identities=22%  Similarity=0.287  Sum_probs=111.1

Q ss_pred             eEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-----HHHHHHHHHHHHHHH
Q 020173          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-----VPAVLNALVEIGNQL  217 (330)
Q Consensus       143 ~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-----~~~v~~A~~~I~~~i  217 (330)
                      ....+.||...++.|||++|++|+.|+++||++|.+..            .++.|+|.|+     ++++.+|..+|.++.
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~------------~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~  101 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS------------ETGEVWITSTKETEDPLAVWKARDIVLAIG  101 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT------------TTCEEEEEECTTCCSHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc------------CCCEEEEecCCCCCCHHHHHHHHHHHHHHh
Confidence            46799999999999999999999999999999999963            3567888875     699999999999988


Q ss_pred             hhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEcc-----------ccccceecCCCchHHHHHHHhCCeEE
Q 020173          218 RENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISE-----------SLVGGLIGRCGSNISRIRNESGAMIK  286 (330)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~-----------~~vg~IIGk~G~~Ik~i~~~tga~I~  286 (330)
                      +...+......               .   ........+.|+.           ..+|+|||++|++|+.|++.|||+|.
T Consensus       102 rg~~~e~g~~l---------------l---~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~  163 (219)
T 2e3u_A          102 RGFSPERAFRL---------------L---NEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVS  163 (219)
T ss_dssp             TTCCHHHHGGG---------------G---STTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEE
T ss_pred             ccCCcccccee---------------c---cCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEE
Confidence            54321100000               0   0011222233332           26899999999999999999999999


Q ss_pred             EeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          287 VYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       287 i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      |..       +.|+|.|++++++.|+.+|.++|..
T Consensus       164 v~~-------~~v~i~G~~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          164 VYG-------KTVAIIGNPIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             EET-------TEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             ECC-------eEEEEEeCHHHHHHHHHHHHHHHcC
Confidence            984       4699999999999999999999843

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

Probab=99.69  E-value=1.8e-17  Score=143.78  Aligned_cols=150  Identities=20%  Similarity=0.208  Sum_probs=111.6

Q ss_pred             eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCC
Q 020173           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN  129 (330)
Q Consensus        50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~  129 (330)
                      -..++.||.+.+|.|||++|++|+.|+++|||+|+|+.     .++.+.|.++........+.+|...|..++.......
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~-----~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg~~~e~  108 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS-----ETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPER  108 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT-----TTCEEEEEECTTCCSHHHHHHHHHHHHHHHTTCCHHH
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc-----CCCEEEEecCCCCCCHHHHHHHHHHHHHHhccCCccc
Confidence            45699999999999999999999999999999999984     2466888886532223678899999988763221100


Q ss_pred             ccccccccCCCcceEEEEEee-----------ccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEE
Q 020173          130 SEASKVAAGHVAANTIRLLIA-----------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQ  198 (330)
Q Consensus       130 ~~~~~~~~~~~~~~~~~llip-----------~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~  198 (330)
                      ......    .....-.+-++           ....|+|||++|++|+.|++.|||+|.+.              ++.|.
T Consensus       109 g~~ll~----dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~--------------~~~v~  170 (219)
T 2e3u_A          109 AFRLLN----EGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY--------------GKTVA  170 (219)
T ss_dssp             HGGGGS----TTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE--------------TTEEE
T ss_pred             cceecc----CCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC--------------CeEEE
Confidence            000000    00111112222           23689999999999999999999999995              35799


Q ss_pred             EEcCHHHHHHHHHHHHHHHhhCCC
Q 020173          199 ISGDVPAVLNALVEIGNQLRENPP  222 (330)
Q Consensus       199 I~G~~~~v~~A~~~I~~~i~~~~~  222 (330)
                      |.|+.+++..|..+|++++.+.++
T Consensus       171 i~G~~~~i~~A~~~i~~li~g~~~  194 (219)
T 2e3u_A          171 IIGNPIQIEIAKTAIEKLARGSPH  194 (219)
T ss_dssp             EEECHHHHHHHHHHHHHHHTTCCH
T ss_pred             EEeCHHHHHHHHHHHHHHHcCCCc
Confidence            999999999999999999977654

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

Probab=99.64  E-value=8.9e-16  Score=113.10  Aligned_cols=73  Identities=29%  Similarity=0.428  Sum_probs=67.4

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      ...+.+|.||.+++|.|||++|++|++|+++|||+|+|++..+++.+|.|+|+|++++++.|+.+|.+++.+.
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            4588999999999999999999999999999999999998656678899999999999999999999998753

>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=99.64  E-value=7.8e-16  Score=130.34  Aligned_cols=141  Identities=16%  Similarity=0.238  Sum_probs=114.2

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEE-----cCHHHHHHHHHHHHHHHh
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS-----GDVPAVLNALVEIGNQLR  218 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~-----G~~~~v~~A~~~I~~~i~  218 (330)
                      ..+++||...+|.|||++|++++.|++.+|++|.+..            .++.++|.     |++.++.+|..+|.++.+
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~------------~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~r   72 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT------------ENSMVIVEPEAEGIPPVNLMKAAEVVKAISL   72 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET------------TTTEEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc------------CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHc
Confidence            4689999999999999999999999999999999963            46778888     999999999999999887


Q ss_pred             hCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEcc----------ccccceecCCCchHHHHHHHhCCeEEEe
Q 020173          219 ENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISE----------SLVGGLIGRCGSNISRIRNESGAMIKVY  288 (330)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~----------~~vg~IIGk~G~~Ik~i~~~tga~I~i~  288 (330)
                      ..++.+.....                  .+......|.|+.          ...|+|||++|.+|+.|+..|||+|.|.
T Consensus        73 gf~~e~A~~Ll------------------~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~  134 (191)
T 1tua_A           73 GFPPEKAFRLL------------------EEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG  134 (191)
T ss_dssp             TCCHHHHGGGG------------------STTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC
T ss_pred             CCCHHHhhhcc------------------cCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc
Confidence            65322110000                  0122333444542          3579999999999999999999999998


Q ss_pred             CCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          289 GGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       289 ~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      .       ..|.|.|++++++.|+..|..+|..
T Consensus       135 ~-------~~v~i~G~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          135 E-------YEVAIIGDYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             S-------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             C-------CEEEEEeChHHHHHHHHHHHHHHcC
Confidence            4       3799999999999999999998864

>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=99.63  E-value=1.7e-15  Score=114.03  Aligned_cols=73  Identities=32%  Similarity=0.471  Sum_probs=67.8

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      ...+.+|.||.+++|.|||++|++|++|+++|||+|+|+++.++..+|.|+|+|++++|+.|+.+|.++|.+.
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~   85 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            4588999999999999999999999999999999999998765677999999999999999999999998764

>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=99.62  E-value=6.2e-16  Score=113.96  Aligned_cols=74  Identities=34%  Similarity=0.502  Sum_probs=66.6

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQL  323 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~  323 (330)
                      ...+.+|.||.+++|.|||++|++|++|++.|||+|+|++..+++.+|.|+|+|++++++.|+.+|.+++.+..
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   77 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSEK   77 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC---
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhhh
Confidence            45889999999999999999999999999999999999986566789999999999999999999999987763

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

Probab=99.62  E-value=5.5e-16  Score=112.59  Aligned_cols=71  Identities=32%  Similarity=0.501  Sum_probs=66.2

Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      ..+.+|.||.+++|.|||++|++|++|++.|||+|+|++..+++.+|.|+|+|++++++.|+.+|.+++.+
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   74 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSS   74 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            47889999999999999999999999999999999999866677899999999999999999999998753

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

Probab=99.60  E-value=1.5e-15  Score=113.66  Aligned_cols=74  Identities=28%  Similarity=0.425  Sum_probs=68.2

Q ss_pred             CcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          249 ADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       249 ~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      ....+.+|.||.+++|.|||++|++|++|+++|||+|+|++...++.+|.|+|+|++++++.|+.+|.+++.+.
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            45688999999999999999999999999999999999998656678999999999999999999999998764

>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=99.60  E-value=1.4e-15  Score=109.44  Aligned_cols=69  Identities=26%  Similarity=0.442  Sum_probs=64.5

Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      ..+++|.||.+++|.|||++|++|++|+++|||+|+|+++  +..+|.|+|+|++++++.|+.+|.++|.+
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC--CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            4789999999999999999999999999999999999975  46789999999999999999999998864

>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=99.59  E-value=3.9e-15  Score=110.96  Aligned_cols=79  Identities=19%  Similarity=0.322  Sum_probs=68.8

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC---CCCceeEEEEEcCHHHHHHHHHHHHHHHHHHHHH-hh
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK---GEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQ-QA  327 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~---~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~~~-~~  327 (330)
                      .+.+|.||.+++|.|||++|++|++|++.|||+|+|+++.   +++.+|.|+|+|++++++.|+.+|.++|.+...+ .+
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~r~~   82 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQGVRAS   82 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccccccc
Confidence            5789999999999999999999999999999999999753   3567899999999999999999999998875444 44


Q ss_pred             cCC
Q 020173          328 GAQ  330 (330)
Q Consensus       328 ~~~  330 (330)
                      +.|
T Consensus        83 ~~~   85 (87)
T 1ec6_A           83 NPQ   85 (87)
T ss_dssp             SCC
T ss_pred             ccc
Confidence            443

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

Probab=99.58  E-value=3.1e-15  Score=108.64  Aligned_cols=70  Identities=21%  Similarity=0.379  Sum_probs=63.2

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC---CCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK---GEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~---~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      .+.+|.||.+++|.|||++|++|++|++.|||+|+|+++.   +++.+|.|+|+|++++++.|+.+|.+++.+
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            6789999999999999999999999999999999999753   345689999999999999999999988643

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

Probab=99.56  E-value=6.9e-15  Score=113.27  Aligned_cols=73  Identities=21%  Similarity=0.344  Sum_probs=66.2

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLI  324 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~~  324 (330)
                      .+.+|.||.+++|.|||++|++||+|+++|+|+|+|+++...+.+|.|+|+|+++++++|+.+|.+++.+..+
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~~   83 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRS   83 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC-
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhcccc
Confidence            5789999999999999999999999999999999999766566799999999999999999999999987644

>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=99.56  E-value=2.9e-15  Score=110.12  Aligned_cols=69  Identities=22%  Similarity=0.344  Sum_probs=62.4

Q ss_pred             CcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHH
Q 020173          249 ADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIY  320 (330)
Q Consensus       249 ~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~  320 (330)
                      ....+.+|.||.+++|.|||++|++||+|+++|||+|+|++..   +++.|+|+|++++++.|+++|.+++.
T Consensus         7 ~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~---~~~~v~ItG~~e~v~~A~~~I~~~i~   75 (83)
T 2dgr_A            7 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD---KEPVFAVTGMPENVDRAREEIEAHIT   75 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS---SCCEEEEEECTTTHHHHHHHHHHHHH
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC---CCCeEEEEcCHHHHHHHHHHHHHHHh
Confidence            3568899999999999999999999999999999999999632   36889999999999999999999754

>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=99.54  E-value=1.6e-14  Score=122.29  Aligned_cols=147  Identities=18%  Similarity=0.209  Sum_probs=110.4

Q ss_pred             EEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCc
Q 020173           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS  130 (330)
Q Consensus        51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~  130 (330)
                      .++++||.+.+|.|||++|++++.|++.+|++|+++.     .++.+.|..+........+++|...|..+.......  
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--   77 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPE--   77 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET-----TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCHH--
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc-----CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCHH--
Confidence            3699999999999999999999999999999999975     356778874433333477889998888776543211  


Q ss_pred             cccccccCCCcceEEEEEee----------ccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEE
Q 020173          131 EASKVAAGHVAANTIRLLIA----------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS  200 (330)
Q Consensus       131 ~~~~~~~~~~~~~~~~llip----------~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~  200 (330)
                      ++...-.  +....-.+-++          ....|+|||++|.+++.|+..|||+|.|.              ++.+.|.
T Consensus        78 ~A~~Ll~--Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~--------------~~~v~i~  141 (191)
T 1tua_A           78 KAFRLLE--EDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG--------------EYEVAII  141 (191)
T ss_dssp             HHGGGGS--TTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC--------------SSEEEEE
T ss_pred             Hhhhccc--CcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc--------------CCEEEEE
Confidence            1111000  01111122233          23579999999999999999999999994              3479999


Q ss_pred             cCHHHHHHHHHHHHHHHhhC
Q 020173          201 GDVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       201 G~~~~v~~A~~~I~~~i~~~  220 (330)
                      |+.+++..|...|.+++...
T Consensus       142 G~~~~i~~Ar~~i~~li~g~  161 (191)
T 1tua_A          142 GDYERAMAAKQAIEMLAEGR  161 (191)
T ss_dssp             EEHHHHHHHHHHHHHHHTTC
T ss_pred             eChHHHHHHHHHHHHHHcCC
Confidence            99999999999999999754

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

Probab=99.53  E-value=3.4e-14  Score=105.29  Aligned_cols=70  Identities=17%  Similarity=0.281  Sum_probs=64.0

Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC--CCceeEEEEEcCHHHHHHHHHHHHHHHH
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG--EQKHRHIQFGGSAQQVALAKQRVDEYIY  320 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~--~~~~r~v~I~Gt~~~v~~A~~~I~~~i~  320 (330)
                      ..+..|.||.+++|.|||++|++||+|+++|||+|.|+++..  .+.+|.|+|+|++++++.|+.+|.+++.
T Consensus        13 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~   84 (85)
T 2opv_A           13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILR   84 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhc
Confidence            477899999999999999999999999999999999998643  4568999999999999999999999874

>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=99.51  E-value=6.6e-14  Score=107.74  Aligned_cols=74  Identities=28%  Similarity=0.326  Sum_probs=66.0

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCC--CceeEEEEEcCHHHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGE--QKHRHIQFGGSAQQVALAKQRVDEYIYSQL  323 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~--~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~  323 (330)
                      ...+.+|.||.+++|.|||++|++|++|+++|||+|+|++....  +.++.|+|+|++++++.|+.+|.+++.+..
T Consensus        13 ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T 1we8_A           13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhCh
Confidence            34788999999999999999999999999999999999975433  358999999999999999999999986543

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

Probab=99.51  E-value=3.2e-14  Score=109.99  Aligned_cols=69  Identities=28%  Similarity=0.415  Sum_probs=62.9

Q ss_pred             EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC---CCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG---EQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~---~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      +.+|.||.+++|.|||++|++||+|+++|||+|+|.++.+   +..+|.|+|+|++++|+.|+.+|.++|.+
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 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEG   79 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCS
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhc
Confidence            6789999999999999999999999999999999997642   34689999999999999999999998754

>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=99.51  E-value=2.5e-14  Score=108.06  Aligned_cols=73  Identities=23%  Similarity=0.346  Sum_probs=65.9

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC--CCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG--EQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~--~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      ...+.+|.||.+++|.|||++|++||+|+++|||+|+|+++..  ...+|.|+|+|++++++.|+.+|.+++.+.
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           13 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            4588999999999999999999999999999999999997643  346899999999999999999999998653

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

Probab=99.49  E-value=1.9e-14  Score=104.35  Aligned_cols=72  Identities=26%  Similarity=0.437  Sum_probs=65.7

Q ss_pred             CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhh
Q 020173           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (330)
Q Consensus        48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~  124 (330)
                      ..++++|+||.+.+|.|||++|++|++|+++|||+|+|++..++..+|+|.|.|+.     +++..|..+|.+++.+
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~-----~~v~~A~~~I~~~i~~   74 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSA-----ASISLAQYLINVRLSS   74 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECH-----HHHHHHHHHHHHHHTT
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCH-----HHHHHHHHHHHHHHHc
Confidence            46889999999999999999999999999999999999987677889999999985     7889999999998754

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

Probab=99.48  E-value=3.9e-14  Score=101.21  Aligned_cols=67  Identities=27%  Similarity=0.390  Sum_probs=61.1

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEY  318 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~  318 (330)
                      ...+..|.||.+++|.|||++|++|++|+++|||+|+|+++.  ..+|.|+|+|++++++.|+.+|.++
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g--~~~~~V~I~G~~~~v~~A~~~I~~i   69 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS--EKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC--SSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC--CcccEEEEEcCHHHHHHHHHHHHHH
Confidence            357889999999999999999999999999999999999753  3568999999999999999999875

>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=99.48  E-value=6.3e-14  Score=103.13  Aligned_cols=73  Identities=29%  Similarity=0.505  Sum_probs=65.9

Q ss_pred             CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhc
Q 020173           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (330)
Q Consensus        48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~  125 (330)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|++..++..+|+|+|+|+.     +++..|..+|.+++.+.
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~-----~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ-----DQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECH-----HHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCH-----HHHHHHHHHHHHHHHhc
Confidence            46899999999999999999999999999999999999987677789999999975     78889999999887653

>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=99.48  E-value=3.7e-14  Score=104.41  Aligned_cols=74  Identities=26%  Similarity=0.424  Sum_probs=65.5

Q ss_pred             CCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhc
Q 020173           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (330)
Q Consensus        47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~  125 (330)
                      ...++++|+||.+.+|.||||+|++|++|+++|||+|+|++..++..+|.|+|+|++     +++.+|..+|.+++.+.
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 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSA-----ASISLAQYLINARLSSE   76 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECH-----HHHHHHHHHHHHHTC--
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCH-----HHHHHHHHHHHHHHHhh
Confidence            356889999999999999999999999999999999999987667789999999986     68889999999987544

>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=99.47  E-value=8.4e-14  Score=100.05  Aligned_cols=70  Identities=36%  Similarity=0.629  Sum_probs=63.6

Q ss_pred             ceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       142 ~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  220 (330)
                      ...++|+||...+|.|||++|++|++|+++|||+|++.+.+         .++|+|+|.|+++++.+|+.+|.++|.++
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~---------~~er~v~I~G~~~~v~~A~~~I~~~l~ed   73 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN---------CPERIITLAGPTNAIFKAFAMIIDKLEED   73 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC---------CSEEEEEEEECHHHHHHHHHHHHHHHHC-
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecCC---------CCcEEEEEEeCHHHHHHHHHHHHHHHhcC
Confidence            46899999999999999999999999999999999997531         46899999999999999999999999863

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

Probab=99.46  E-value=1.5e-13  Score=104.22  Aligned_cols=72  Identities=18%  Similarity=0.247  Sum_probs=64.6

Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC-CCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG-EQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~-~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      .++..|.||..++|.|||++|++|++|+++|||+|+|+++.. ...+|.|+|+|+.++++.|+.+|..++...
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~   88 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGEL   88 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999999997543 235789999999999999999999987654

>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=99.45  E-value=8.8e-14  Score=104.99  Aligned_cols=74  Identities=14%  Similarity=0.166  Sum_probs=65.8

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQ  325 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~~~  325 (330)
                      ...+..|.||.+++|.|||++|++|++|+++|||+|+|++..  ..++.|+|+|++++++.|+.+|.+++.+....
T Consensus        15 ~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~--~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~~~   88 (94)
T 2cte_A           15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD--DPSNQIKITGTKEGIEKARHEVLLISAEQDKR   88 (94)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT--SSCCEEEEEECHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC--CCCCeEEEEECHHHHHHHHHHHHHHhhccccc
Confidence            458899999999999999999999999999999999999642  23578999999999999999999998876543

>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=1.7e-13  Score=103.04  Aligned_cols=74  Identities=22%  Similarity=0.366  Sum_probs=66.6

Q ss_pred             CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcC
Q 020173           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (330)
Q Consensus        48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~  126 (330)
                      ..++++|+||.+++|+||||+|++|++|+++|||+|+|++..++..+|+|+|.|+.     +++.+|..+|.+++.+..
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~-----e~v~~A~~~I~~~i~~~~   86 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTP-----ESVQSAKRLLDQIVEKGR   86 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECH-----HHHHHHHHHHHHHHHHTT
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCH-----HHHHHHHHHHHHHHHhcc
Confidence            56899999999999999999999999999999999999987666789999999985     788999999999886653

>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=99.44  E-value=1.9e-13  Score=103.21  Aligned_cols=75  Identities=16%  Similarity=0.178  Sum_probs=66.2

Q ss_pred             CcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHHH
Q 020173          249 ADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLI  324 (330)
Q Consensus       249 ~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~~  324 (330)
                      ....+..|.||.+++|.|||++|++|++|+++|||+|+|+++. ....+.|+|+|++++|+.|+.+|.+++.+...
T Consensus        14 ~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g-~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~~   88 (95)
T 2ctm_A           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-APDPNCVTVTGLPENVEEAIDHILNLEEEYLA   88 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-CSCTTEEEEESCHHHHHHHHHHHHHHHHHHHT
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC-CCCCcEEEEEcCHHHHHHHHHHHHHHHHHHHH
Confidence            4568899999999999999999999999999999999998642 23468999999999999999999998876543

>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=99.42  E-value=1.1e-13  Score=103.50  Aligned_cols=73  Identities=29%  Similarity=0.505  Sum_probs=66.2

Q ss_pred             CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhc
Q 020173           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD  125 (330)
Q Consensus        48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~  125 (330)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|++..++..+|+|+|+|+.     +++.+|..+|.+++.+.
T Consensus        12 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~-----e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           12 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ-----DQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEH-----HHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCH-----HHHHHHHHHHHHHHHhh
Confidence            47899999999999999999999999999999999999987677789999999985     78889999999887654

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

Probab=99.41  E-value=5.3e-13  Score=96.69  Aligned_cols=72  Identities=22%  Similarity=0.376  Sum_probs=63.1

Q ss_pred             eEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCC-CCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ-LPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       143 ~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~-~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      .+.+|+||...+|.|||++|++|++|++.|||+|.+.+.+. .|.     +.++.|+|+|+++++.+|..+|.+++.+
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 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG-----TRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTT-----CCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCC-----CceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            47899999999999999999999999999999999986432 232     5789999999999999999999998764

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

Probab=99.41  E-value=9.9e-15  Score=111.61  Aligned_cols=68  Identities=16%  Similarity=0.299  Sum_probs=61.5

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHH-hCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNE-SGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLI  324 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~-tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~~  324 (330)
                      .+.+|.||..+|+.|||++|++|++|+++ ++++|.||+     .++.|+|.|++++|+.|+.+|.+++.+..-
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-----~~~~ItI~G~~~~V~~a~~~I~~~v~el~~   95 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTEDVSVAQEQIEGMVKDLIN   95 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-----CCCEEEEECCHHHHHHHHHHHHHHHHHHHh
Confidence            78899999999999999999999999996 599999996     356899999999999999999998876443

>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=99.39  E-value=6.8e-13  Score=100.10  Aligned_cols=75  Identities=19%  Similarity=0.356  Sum_probs=65.4

Q ss_pred             CCCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCC--CCcceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 020173           46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA--RHEERVIIISSKDNDNVVSDAENALQQIAALIL  123 (330)
Q Consensus        46 ~~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~--~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~  123 (330)
                      .+..++++|+||.+.+|+||||+|++|++|+++|||+|+|.+...  ...+|+|+|+|+.     +.+..|+.+|.+++.
T Consensus        11 ~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~-----~~v~~A~~~I~~~i~   85 (94)
T 1x4m_A           11 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDP-----YKVQQAKEMVLELIR   85 (94)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECT-----TTHHHHHHHHHHHHC
T ss_pred             CCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCH-----HHHHHHHHHHHHHHh
Confidence            457899999999999999999999999999999999999987632  3468999999976     578899999999886


Q ss_pred             hc
Q 020173          124 KD  125 (330)
Q Consensus       124 ~~  125 (330)
                      +.
T Consensus        86 ~~   87 (94)
T 1x4m_A           86 DQ   87 (94)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>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=99.38  E-value=8.4e-13  Score=101.31  Aligned_cols=71  Identities=25%  Similarity=0.203  Sum_probs=64.0

Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHH
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQL  323 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~  323 (330)
                      ..+..|.||.+++|.|||++|++|++|+++|||+|+|+++..  ..+.|+|+|++++++.|+.+|.+++.+..
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~--~~~~V~I~G~~e~v~~A~~~I~~i~~e~e   86 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL--QSDIIAITGLAANLDRAKAGLLERVKELQ   86 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT--TCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCC--CcceEEEEcCHHHHHHHHHHHHHHHhhHH
Confidence            378899999999999999999999999999999999997533  45699999999999999999999987654

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

Probab=99.37  E-value=2.2e-12  Score=95.44  Aligned_cols=74  Identities=24%  Similarity=0.433  Sum_probs=64.1

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      .....+|.||...+|.|||++|++|++|+++|||+|.+......+.     +.+|.|+|+|+++++.+|+.+|.+++.+
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 NGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNT-----NVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSST-----TSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCC-----CCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            3457899999999999999999999999999999999976322222     5789999999999999999999998853

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

Probab=99.36  E-value=1.5e-12  Score=120.71  Aligned_cols=144  Identities=8%  Similarity=0.011  Sum_probs=102.5

Q ss_pred             CcceEEEEEeeccccceecCCCC--hhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 020173          140 VAANTIRLLIAGSQAGCLIGMSG--QNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (330)
Q Consensus       140 ~~~~~~~llip~~~~g~iIG~~G--~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  217 (330)
                      ...+++.+.||..+|+.|||++|  ++|++|+++|||+|+|+..+. +.. .+......|+|+|.+++|.+|+.+|.+++
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~-~~~-~~~~ks~~VtItG~~enVE~AR~~I~~l~  104 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSV-GGT-TPDPFAQQVTITGYFGDVDRARMLMRRNC  104 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCC-CSS-SCCTTTTEEEEEEEHHHHHHHHHHHHHSC
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcc-ccc-CCcCCCCeEEEEcCHHHHHHHHHHHHhcC
Confidence            45679999999999999999999  999999999999999975430 000 00123468999999999999999998743


Q ss_pred             hhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC--CCc
Q 020173          218 RENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG--EQK  295 (330)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~--~~~  295 (330)
                                                       ..+..+.+|...++.  ...+..|.+ ++.++++|.++....  +..
T Consensus       105 ---------------------------------Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~~~~  148 (376)
T 3n89_A          105 ---------------------------------HFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKNGIV  148 (376)
T ss_dssp             ---------------------------------EEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC-----C
T ss_pred             ---------------------------------CceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCcccccCCC
Confidence                                             255667777644332  111234444 567899999875422  113


Q ss_pred             eeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          296 HRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       296 ~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      ...|+|+|...+++.|++.+.+++..
T Consensus       149 sd~V~IrG~~~nv~~akeA~~~Ll~~  174 (376)
T 3n89_A          149 TTYLRITAREKNQHELIEAAKRLNEI  174 (376)
T ss_dssp             EEEEEEEEEGGGHHHHHHHHHHHHHH
T ss_pred             CCEEEEEcChhhHHHHHHHHHHHHHH
Confidence            67899999998888777666555543

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

Probab=99.35  E-value=6.4e-13  Score=102.23  Aligned_cols=72  Identities=24%  Similarity=0.338  Sum_probs=63.4

Q ss_pred             eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcC
Q 020173           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD  126 (330)
Q Consensus        50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~  126 (330)
                      .+++|+||.+.+++||||+|++|++|+++|+|+|+|++.....++|+|+|+|+.     +++.+|..+|.+++.+..
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 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPP-----DRCEHAARIINDLLQSLR   82 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSH-----HHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCH-----HHHHHHHHHHHHHHhccc
Confidence            468999999999999999999999999999999999876556678999999985     678899999999886654

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

Probab=99.35  E-value=1.6e-12  Score=96.67  Aligned_cols=73  Identities=22%  Similarity=0.375  Sum_probs=64.5

Q ss_pred             eEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCC-CCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173          143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ-LPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       143 ~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~-~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  220 (330)
                      .+.+|+||...+|.|||++|++|++|++.|||+|.|...+. .|.     +.++.|+|+|+++++.+|..+|.+++.+.
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g-----~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG-----TRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTT-----SCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCC-----CCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            37899999999999999999999999999999999976432 232     57899999999999999999999999764

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.35  E-value=8.4e-13  Score=96.92  Aligned_cols=70  Identities=20%  Similarity=0.281  Sum_probs=63.0

Q ss_pred             CcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       140 ~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      ....+.+|.||..++|+|||++|++||+|+++|||+|++++.          .++++++|+|+++++.+|+.+|.+++..
T Consensus         7 ~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~----------~~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            7 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR----------DKEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS----------SSCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC----------CCCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            345789999999999999999999999999999999999753          2468999999999999999999998764

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

Probab=99.32  E-value=1.7e-12  Score=92.58  Aligned_cols=67  Identities=19%  Similarity=0.355  Sum_probs=58.5

Q ss_pred             CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHH
Q 020173           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL  121 (330)
Q Consensus        48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~  121 (330)
                      ...+..|.||.+++|.|||++|++|++|+++|||+|+|++.  +..++.|+|.|+.     +.+.+|..+|..+
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~--g~~~~~V~I~G~~-----~~v~~A~~~I~~i   69 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD--SEKSNLIRIEGDP-----QGVQQAKRELLEL   69 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC--CSSSEEEEEEESS-----HHHHHHHHHHHHT
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCC--CCcccEEEEEcCH-----HHHHHHHHHHHHH
Confidence            34678999999999999999999999999999999999885  4467899999985     5778888887764

>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=99.30  E-value=3.2e-12  Score=96.28  Aligned_cols=72  Identities=24%  Similarity=0.267  Sum_probs=64.7

Q ss_pred             CcceEEEEEEccccccceecCCCchHHHHHHHh-CCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          249 ADYVTFEMLISESLVGGLIGRCGSNISRIRNES-GAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       249 ~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      .+..+..|.||.++++.|||++|++|++|+++| ||+|+|+++  ++..+.|+|.|+..++++|+.+|++++.+.
T Consensus        14 ~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~--g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~   86 (95)
T 2ctj_A           14 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE--GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   86 (95)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT--TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC--CCCcceEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            456788999999999999999999999999999 999999974  345678999999999999999999998753

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

Probab=99.30  E-value=6.6e-12  Score=96.93  Aligned_cols=74  Identities=19%  Similarity=0.272  Sum_probs=64.3

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCC
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP  221 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  221 (330)
                      +.+|+||..+++.|||++|++|++|+++|||+|+|.... .+..   ...++.|+|+|+.++|.+|+.+|.+++.+..
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 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQL-PPNG---DPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCC-CTTC---CTTEEEEEEESCHHHHHHHHHHHHHHSCSCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCcc-CCCC---CCCceEEEEECCHHHHHHHHHHHHHHHhccc
Confidence            789999999999999999999999999999999997532 2211   1467999999999999999999999998763

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

Probab=99.27  E-value=1.4e-11  Score=94.58  Aligned_cols=76  Identities=24%  Similarity=0.271  Sum_probs=65.4

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  220 (330)
                      ...+.+|+||...+|.|||++|++|++|+++|||+|.|.......     ...++.|+|+|+.+++.+|+.+|.+++.+.
T Consensus        13 ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~-----~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT-----LLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS-----SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCC-----CCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            346889999999999999999999999999999999997542111     135899999999999999999999999775


Q ss_pred             C
Q 020173          221 P  221 (330)
Q Consensus       221 ~  221 (330)
                      +
T Consensus        88 ~   88 (104)
T 1we8_A           88 E   88 (104)
T ss_dssp             H
T ss_pred             h
Confidence            3

>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=99.21  E-value=2.1e-11  Score=91.82  Aligned_cols=71  Identities=18%  Similarity=0.295  Sum_probs=63.3

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  220 (330)
                      ..++..|.||...+|.|||++|++|++|+++|||+|.|+..+         ..++.|+|+|+.+++.+|+.+|..++.+.
T Consensus        15 ~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~---------~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD---------DPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT---------SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC---------CCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            346899999999999999999999999999999999997532         23578999999999999999999999775

>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=99.21  E-value=4.5e-11  Score=90.50  Aligned_cols=72  Identities=15%  Similarity=0.134  Sum_probs=63.0

Q ss_pred             ceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       142 ~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      ..+..|.||..+++.|||++|++|++|+++|||+|.|++... +.     ..++.|+|+|+.+++.+|+.+|..++.+
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 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-GN-----QPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-CS-----SCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC-CC-----CCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            358999999999999999999999999999999999975321 21     3578999999999999999999998865

>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=99.20  E-value=5.3e-11  Score=89.69  Aligned_cols=73  Identities=18%  Similarity=0.148  Sum_probs=64.0

Q ss_pred             CcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       140 ~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      ...++..+.||..+++.|||++|++|++|+++|||+|+|+....        ..++.|+|+|.++++.+|+.+|..++.+
T Consensus        14 ~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~--------~~~~~V~I~G~~e~v~~A~~~I~~i~~e   85 (95)
T 2ctm_A           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA--------PDPNCVTVTGLPENVEEAIDHILNLEEE   85 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC--------SCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC--------CCCcEEEEEcCHHHHHHHHHHHHHHHHH
Confidence            34568999999999999999999999999999999999965321        2467899999999999999999999876


Q ss_pred             C
Q 020173          220 N  220 (330)
Q Consensus       220 ~  220 (330)
                      .
T Consensus        86 ~   86 (95)
T 2ctm_A           86 Y   86 (95)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.09  E-value=1.8e-10  Score=88.28  Aligned_cols=69  Identities=20%  Similarity=0.280  Sum_probs=61.3

Q ss_pred             ceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       142 ~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      .....|.||...++.|||++|++|++|+++|||+|.|+..+         ...+.|+|+|..+++.+|+.+|..++.+
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g---------~~~~~V~I~G~~e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE---------LQSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT---------TTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC---------CCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            35889999999999999999999999999999999997532         2345899999999999999999999865

>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=99.08  E-value=5.5e-11  Score=89.49  Aligned_cols=76  Identities=22%  Similarity=0.321  Sum_probs=64.8

Q ss_pred             cCCCCceEEEEEecCCccceeecccChhhhhhhhcc-CcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHH
Q 020173           44 RAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (330)
Q Consensus        44 ~~~~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i  122 (330)
                      +..++.++..|.||.++++.|||++|.+|++|+++| ||+|+|++.  +...+.|+|.|++     ..+.+|..+|..++
T Consensus        11 ~e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~--g~~~~~V~I~G~~-----~~v~~A~~~I~~iv   83 (95)
T 2ctj_A           11 KDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE--GSGSDTVVIRGPS-----SDVEKAKKQLLHLA   83 (95)
T ss_dssp             CCCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT--TTTCCEEEEESCH-----HHHHHHHHHHHHHH
T ss_pred             HHHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC--CCCcceEEEEcCH-----HHHHHHHHHHHHHH
Confidence            345678899999999999999999999999999999 999999875  4456789999986     57788888888887


Q ss_pred             hhcC
Q 020173          123 LKDD  126 (330)
Q Consensus       123 ~~~~  126 (330)
                      .+..
T Consensus        84 ~e~e   87 (95)
T 2ctj_A           84 EEKQ   87 (95)
T ss_dssp             HHHS
T ss_pred             hhhh
Confidence            5543

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

Probab=99.06  E-value=5.1e-10  Score=85.35  Aligned_cols=66  Identities=24%  Similarity=0.368  Sum_probs=57.1

Q ss_pred             ceEEEEEecCCccceeecccChhhhhhhhc-cCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhh
Q 020173           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREE-TKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (330)
Q Consensus        49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~-tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~  124 (330)
                      -++.+|.||..++++|||++|++|++|+++ ++++|+|++     .++.|+|.|+.     +.+.+|..+|..++.+
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-----~~~~ItI~G~~-----~~V~~a~~~I~~~v~e   92 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPT-----EDVSVAQEQIEGMVKD   92 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECH-----HHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-----CCCEEEEECCH-----HHHHHHHHHHHHHHHH
Confidence            378999999999999999999999999996 599999997     35789999986     6778888887776644

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.96  E-value=9.4e-10  Score=81.34  Aligned_cols=64  Identities=28%  Similarity=0.344  Sum_probs=57.4

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCe-EEEeCCCCCCceeEEEEEc-CHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAM-IKVYGGKGEQKHRHIQFGG-SAQQVALAKQRVDEY  318 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~-I~i~~~~~~~~~r~v~I~G-t~~~v~~A~~~I~~~  318 (330)
                      ..+...|.||.+++|.+||++|++|++|++.||++ |.|.+     ++..|+|.| +.+++++|+.+|..+
T Consensus        13 ~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e-----ddG~V~I~g~~~ea~~~A~~~I~~i   78 (91)
T 2cpq_A           13 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-----DTGTFRIYGESADAVKKARGFLEFV   78 (91)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             CceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc-----CCCEEEEEECCHHHHHHHHHHHHhh
Confidence            45888999999999999999999999999999998 99984     247899999 799999999998643

>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=98.82  E-value=1.5e-09  Score=80.29  Aligned_cols=54  Identities=22%  Similarity=0.322  Sum_probs=47.6

Q ss_pred             CCCCceEEEEEecCCccceeecccChhhhhhhhccCcE-EEEecCCCCCcceEEEEecCC
Q 020173           45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKAT-IKIADAIARHEERVIIISSKD  103 (330)
Q Consensus        45 ~~~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~-I~i~~~~~~~~ervi~I~G~~  103 (330)
                      .....+...|.||.+.+|.+||++|++|++|+++|||+ |.|.+     ++..|.|.|.+
T Consensus        10 ~~~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e-----ddG~V~I~g~~   64 (91)
T 2cpq_A           10 QLAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-----DTGTFRIYGES   64 (91)
T ss_dssp             SSSCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-----TTTEEEEEESS
T ss_pred             hccCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc-----CCCEEEEEECC
Confidence            44567899999999999999999999999999999998 99975     34789999965

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

Probab=98.77  E-value=3.7e-08  Score=76.77  Aligned_cols=74  Identities=18%  Similarity=0.205  Sum_probs=58.9

Q ss_pred             cceEEEEEEccc-------cccceecCCCchHHHHHHHhCCeEEEeCCCC----------CCceeEEEEEc-CHHHHHHH
Q 020173          250 DYVTFEMLISES-------LVGGLIGRCGSNISRIRNESGAMIKVYGGKG----------EQKHRHIQFGG-SAQQVALA  311 (330)
Q Consensus       250 ~~~~~~v~IP~~-------~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~----------~~~~r~v~I~G-t~~~v~~A  311 (330)
                      ...+.+|.||-+       ++|.|||++|.+||+|+++|||+|.|.....          ..++-.|.|++ +++++++|
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            346778887765       7899999999999999999999999973311          11344677876 59999999


Q ss_pred             HHHHHHHHHHHH
Q 020173          312 KQRVDEYIYSQL  323 (330)
Q Consensus       312 ~~~I~~~i~~~~  323 (330)
                      +.+|.++|....
T Consensus        90 ~~~Ie~Ll~~v~  101 (119)
T 2yqr_A           90 KKLCENLLQTVH  101 (119)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHhhchH
Confidence            999999987643

>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=98.75  E-value=2.3e-08  Score=79.49  Aligned_cols=72  Identities=24%  Similarity=0.357  Sum_probs=60.6

Q ss_pred             cceEEEEEEccc------cccceecCCCchHHHHHHHhCCeEEEeCCCC----------------CCceeEEEEEcC-HH
Q 020173          250 DYVTFEMLISES------LVGGLIGRCGSNISRIRNESGAMIKVYGGKG----------------EQKHRHIQFGGS-AQ  306 (330)
Q Consensus       250 ~~~~~~v~IP~~------~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~----------------~~~~r~v~I~Gt-~~  306 (330)
                      ...+.+|.||.+      ++|.|||++|.+||+|+++|||+|.|.....                ...+-.|.|++. .+
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            357889999988      8999999999999999999999999986311                123567889995 99


Q ss_pred             HHHHHHHHHHHHHHH
Q 020173          307 QVALAKQRVDEYIYS  321 (330)
Q Consensus       307 ~v~~A~~~I~~~i~~  321 (330)
                      .++.|+.+|..+|..
T Consensus        85 ~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999854

>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=98.65  E-value=4.5e-08  Score=77.80  Aligned_cols=73  Identities=21%  Similarity=0.412  Sum_probs=58.3

Q ss_pred             CceEEEEEecCC------ccceeecccChhhhhhhhccCcEEEEecCC----------------CCCcceEEEEecCCCC
Q 020173           48 QDVLFRIIVPSR------QIGKVIGKEGHRIQKIREETKATIKIADAI----------------ARHEERVIIISSKDND  105 (330)
Q Consensus        48 ~~~~~~i~vP~~------~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~----------------~~~~ervi~I~G~~~~  105 (330)
                      ..++.+|.||.+      ++|.|||++|.+||+|+++|||+|.|...-                ....+--|.|++..  
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~--   82 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANT--   82 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESS--
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECC--
Confidence            468899999998      788999999999999999999999997521                01123457788864  


Q ss_pred             cchhHHHHHHHHHHHHHhh
Q 020173          106 NVVSDAENALQQIAALILK  124 (330)
Q Consensus       106 ~~~~~~~~A~~~i~~~i~~  124 (330)
                        -+.+.+|+.+|..++..
T Consensus        83 --~e~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           83 --MENVKKAVEQIRNILKQ   99 (131)
T ss_dssp             --HHHHHHHHHHHHHHHTT
T ss_pred             --HHHHHHHHHHHHHHHhc
Confidence              36788999999998865

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

Probab=98.52  E-value=1.3e-07  Score=73.64  Aligned_cols=72  Identities=22%  Similarity=0.124  Sum_probs=54.2

Q ss_pred             ceEEEEEecCC-------ccceeecccChhhhhhhhccCcEEEEecCCC----------CCcceEEEEecCCCCcchhHH
Q 020173           49 DVLFRIIVPSR-------QIGKVIGKEGHRIQKIREETKATIKIADAIA----------RHEERVIIISSKDNDNVVSDA  111 (330)
Q Consensus        49 ~~~~~i~vP~~-------~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~----------~~~ervi~I~G~~~~~~~~~~  111 (330)
                      .+..+|.||.+       ++|.|||++|.+||+|+++|||+|.|...-.          ...+--|.|.+.+    .+.+
T Consensus        11 ~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~----~e~i   86 (119)
T 2yqr_A           11 YVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPK----PEGL   86 (119)
T ss_dssp             CEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESS----HHHH
T ss_pred             EEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCC----HHHH
Confidence            46778988875       6899999999999999999999999973210          0122357777654    2677


Q ss_pred             HHHHHHHHHHHhh
Q 020173          112 ENALQQIAALILK  124 (330)
Q Consensus       112 ~~A~~~i~~~i~~  124 (330)
                      .+|+.+|..++..
T Consensus        87 ~~A~~~Ie~Ll~~   99 (119)
T 2yqr_A           87 AAAKKLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhc
Confidence            8888888887754

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.27  E-value=9.3e-07  Score=70.62  Aligned_cols=75  Identities=19%  Similarity=0.401  Sum_probs=53.5

Q ss_pred             eEEEEEecCCc------cceeecccChhhhhhhhccCcEEEEecCCC-----------C------Ccc-eEEEEecCCCC
Q 020173           50 VLFRIIVPSRQ------IGKVIGKEGHRIQKIREETKATIKIADAIA-----------R------HEE-RVIIISSKDND  105 (330)
Q Consensus        50 ~~~~i~vP~~~------vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~-----------~------~~e-rvi~I~G~~~~  105 (330)
                      ++.+|.||.+.      +|.|||++|.++|+|+++|||+|.|...-.           +      ..+ --|.|++.+..
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            56789999754      899999999999999999999999985310           0      011 14668875432


Q ss_pred             c-chhHHHHHHHHHHHHHhh
Q 020173          106 N-VVSDAENALQQIAALILK  124 (330)
Q Consensus       106 ~-~~~~~~~A~~~i~~~i~~  124 (330)
                      . -...+.+|+..|..++..
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            1 112577888888887754

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.26  E-value=9e-07  Score=70.69  Aligned_cols=69  Identities=19%  Similarity=0.319  Sum_probs=53.5

Q ss_pred             eEEEEEEccc------cccceecCCCchHHHHHHHhCCeEEEeCCCCC------------------CceeEEEEEcC-H-
Q 020173          252 VTFEMLISES------LVGGLIGRCGSNISRIRNESGAMIKVYGGKGE------------------QKHRHIQFGGS-A-  305 (330)
Q Consensus       252 ~~~~v~IP~~------~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~------------------~~~r~v~I~Gt-~-  305 (330)
                      .+.+|.||.+      ++|.|||++|.++|+|+++|||+|.|-...+.                  ...--|.|++. + 
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            3557777754      59999999999999999999999999964321                  11236888884 3 


Q ss_pred             ----HHHHHHHHHHHHHHH
Q 020173          306 ----QQVALAKQRVDEYIY  320 (330)
Q Consensus       306 ----~~v~~A~~~I~~~i~  320 (330)
                          ..++.|+.+|..+|.
T Consensus        82 ~~~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             hhHHHHHHHHHHHHHHHCC
Confidence                379999999998875

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

Probab=98.16  E-value=2.5e-06  Score=84.62  Aligned_cols=62  Identities=16%  Similarity=0.221  Sum_probs=54.7

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYI  319 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i  319 (330)
                      ....|.||.+.+|.|||+||++||.|+++|||+|.|.+      +..|.|.|+ .+.+++|+.+|.+++
T Consensus       567 ~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d------~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          567 VVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD------EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS------SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             eEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC------CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            67889999999999999999999999999999999984      357999997 789999999998764

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

Probab=98.11  E-value=1.4e-05  Score=62.63  Aligned_cols=70  Identities=11%  Similarity=0.098  Sum_probs=61.8

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      ....|.|...+++.|+|++|+.|++|+..|++.|++..-. .++.-.|+|.|++..-..|+.+|..+..-.
T Consensus        56 dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~-s~g~tEVtIfG~~~~Q~rak~MI~sLA~~h  125 (140)
T 3v69_A           56 DPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWG-PERRAEIWIFGPPPFRRDVDRMLTDLAHYC  125 (140)
T ss_dssp             SCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC-TTSCEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC-CCCcEEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            4567899999999999999999999999999999999863 346788999999999999999998876544

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

Probab=97.68  E-value=5.8e-05  Score=74.92  Aligned_cols=93  Identities=17%  Similarity=0.178  Sum_probs=66.3

Q ss_pred             hhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 020173          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (330)
Q Consensus       108 ~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~  187 (330)
                      +..+.+++..|.+.+.+........    ....-.....+-||...++.|||++|++||.|+++|||+|.|.        
T Consensus       536 L~~A~~g~~~I~~~m~~al~~~~~~----~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~--------  603 (630)
T 3u1k_A          536 IQQASVAKKEILQIMNKTISKPRAS----RKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV--------  603 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSCCSS----CCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC--------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhh----hcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc--------
Confidence            3455666666777665543322110    1111234678899999999999999999999999999999985        


Q ss_pred             cCCCCCCcEEEEEcC-HHHHHHHHHHHHHHH
Q 020173          188 ASAHESDRVVQISGD-VPAVLNALVEIGNQL  217 (330)
Q Consensus       188 ~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i  217 (330)
                           ++..|.|.|. .+.+.+|+.+|..++
T Consensus       604 -----d~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          604 -----DEETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             -----SSSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             -----CCcEEEEEeCCHHHHHHHHHHHHHHh
Confidence                 3457888886 678889998886654

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

Probab=97.64  E-value=3.7e-05  Score=77.19  Aligned_cols=65  Identities=15%  Similarity=0.207  Sum_probs=12.1

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~~~  322 (330)
                      ....+.||.+.+|.|||+||.+||.|.++||++|.|.+      +..|.|.++ .+.++.|+.+|..++...
T Consensus       570 ~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d------dG~v~I~~~~~~~~~~A~~~i~~i~~~~  635 (726)
T 4aid_A          570 KIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND------DGVVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             C-------------------------------------------------CCSCHHHHHHHHHC--------
T ss_pred             eEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC------CceEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence            45679999999999999999999999999999999984      256888776 899999999998887543

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

Probab=97.56  E-value=0.00028  Score=55.28  Aligned_cols=68  Identities=16%  Similarity=0.121  Sum_probs=59.5

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      .+.+.+....++.|+|++|+.|+.|+..|++.|++..-+.        +..-.|+|.|++..-.+|..+|.++..-
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s--------~g~tEVtIfG~~~~Q~rak~MI~sLA~~  124 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP--------ERRAEIWIFGPPPFRRDVDRMLTDLAHY  124 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT--------TSCEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC--------CCcEEEEEECCHHHHHHHHHHHHHHHHH
Confidence            5788999999999999999999999999999999986431        2356799999999999999999988754

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.48  E-value=0.0001  Score=59.18  Aligned_cols=103  Identities=25%  Similarity=0.314  Sum_probs=74.6

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCC
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR  223 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~  223 (330)
                      .+.++|+...+|..||++|++|+.|.++.|-+|.+-.-          +++        +      ..+|...|.-.   
T Consensus        37 r~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~----------s~d--------~------~~fI~naLsPA---   89 (144)
T 2cxc_A           37 RLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEY----------SSD--------L------ERIVKNLFPGV---   89 (144)
T ss_dssp             EEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEEC----------CSS--------H------HHHHHHHSTTS---
T ss_pred             EEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEc----------CCC--------H------HHHHHHhcCCc---
Confidence            78999999999999999999999999999999988643          222        1      22333333210   


Q ss_pred             CCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEe
Q 020173          224 QVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVY  288 (330)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~  288 (330)
                      ...++...+               .+......+.||.+..+..|||+|++++-....||.+|.|.
T Consensus        90 ~V~~V~i~~---------------~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           90 KIESINVRE---------------RNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             CEEEEEEEE---------------ETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             eEEEEEEee---------------cCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            000000000               01346778999999999999999999999999999988776

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.47  E-value=6.1e-05  Score=60.44  Aligned_cols=104  Identities=17%  Similarity=0.282  Sum_probs=72.5

Q ss_pred             eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCC
Q 020173           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN  129 (330)
Q Consensus        50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~  129 (330)
                      -.+.+.|+...+|+.||++|++|+.|+++.|-+|+|-.-.             +         +-...+...+....   
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s-------------~---------d~~~fI~naLsPA~---   90 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYS-------------S---------DLERIVKNLFPGVK---   90 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECC-------------S---------SHHHHHHHHSTTSC---
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcC-------------C---------CHHHHHHHhcCCce---
Confidence            5678999999999999999999999999999999986531             1         01111222221110   


Q ss_pred             ccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEe
Q 020173          130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVIL  179 (330)
Q Consensus       130 ~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~  179 (330)
                      -..-.. ....+.....+.||..+.+..||++|.+++-...-+|.++.|.
T Consensus        91 V~~V~i-~~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           91 IESINV-RERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             EEEEEE-EEETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             EEEEEE-eecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            000000 0001234788999999999999999999999999999877764

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

Probab=96.78  E-value=0.00083  Score=67.51  Aligned_cols=96  Identities=23%  Similarity=0.272  Sum_probs=25.1

Q ss_pred             hhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 020173          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (330)
Q Consensus       108 ~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~  187 (330)
                      +..+.+++..|.+.+.+........    .....+....+-||....+.|||++|.+||.|.++||++|.+.        
T Consensus       539 L~~A~~g~~~I~~~m~~al~~~r~~----~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~--------  606 (726)
T 4aid_A          539 LAQAKEGRAHILGEMNKAMDAPRAD----VGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN--------  606 (726)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSSCCSS----CCSSCCC--------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhh----hcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE--------
Confidence            4555666677777765544322110    1111233568889999999999999999999999999999985        


Q ss_pred             cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhhC
Q 020173          188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~~  220 (330)
                           ++..|.|.+ +.+...+|+..|..++.+.
T Consensus       607 -----ddG~v~I~~~~~~~~~~A~~~i~~i~~~~  635 (726)
T 4aid_A          607 -----DDGVVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             ------------CCSCHHHHHHHHHC--------
T ss_pred             -----CCceEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence                 234567766 4888888999988887643

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

Probab=96.01  E-value=0.0023  Score=64.53  Aligned_cols=63  Identities=19%  Similarity=0.358  Sum_probs=0.0

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIY  320 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~  320 (330)
                      ....+.||.+.++.+||++|.+|+.|.++||+.|.|..      +..|.|++. .+.++.|..+|..++.
T Consensus       560 ~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~------dg~v~I~~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          560 RIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED------DGTVKIAATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             ----------------------------------------------------------------------
T ss_pred             eEEEEEECHHHhcccccccceeeeeeehhhCceEEecC------CccEEEecCCHHHHHHHHHHHHHHhh
Confidence            55678999999999999999999999999999998884      356777765 6777888887776653

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=95.96  E-value=0.0094  Score=51.93  Aligned_cols=97  Identities=24%  Similarity=0.270  Sum_probs=65.5

Q ss_pred             CccceeecccChhhhhh-hhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCcccccccc
Q 020173           59 RQIGKVIGKEGHRIQKI-REETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (330)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I-~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~  137 (330)
                      +-+|+.||++|++|+.| ++-.|=+|+|-.-.             +         +...-|...+....-..-   ..  
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s-------------~---------dp~~fi~nalsPA~V~~V---~i--  178 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD-------------D---------DPARFVANALSPAKVVSV---SV--  178 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC-------------S---------SHHHHHHHHTTTSCCSEE---EE--
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEec-------------C---------CHHHHHHhccCCcceEEE---EE--
Confidence            44899999999999999 67778888886531             1         011112222211110000   00  


Q ss_pred             CCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCC
Q 020173          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN  182 (330)
Q Consensus       138 ~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~  182 (330)
                      .........+.||..+.+..||++|.|++.-..-||.+|.|....
T Consensus       179 ~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  223 (251)
T 2asb_A          179 IDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  223 (251)
T ss_dssp             EETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             EcCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHH
Confidence            000123789999999999999999999999999999999997643

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=95.68  E-value=0.013  Score=54.03  Aligned_cols=97  Identities=23%  Similarity=0.290  Sum_probs=66.7

Q ss_pred             CccceeecccChhhhhhhhcc-CcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCcccccccc
Q 020173           59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (330)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~  137 (330)
                      +-+|+.||++|.+|+.|.++. |=+|+|-.-             ++         +-...|...+....-..-.  ..  
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~-------------s~---------dp~~fi~nalsPA~V~~V~--~~--  302 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDY-------------DD---------DPARFVANALSPAKVVSVS--VI--  302 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEEC-------------CS---------SHHHHHHHHTTTSCCSEEE--EE--
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEc-------------CC---------CHHHHHHHhcCCcceeEEE--EE--
Confidence            458999999999999999999 888887653             11         0111222222111100000  00  


Q ss_pred             CCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCC
Q 020173          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN  182 (330)
Q Consensus       138 ~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~  182 (330)
                       ........+.||..+.+..||++|.+++-...-||.+|.|....
T Consensus       303 -~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  346 (366)
T 1k0r_A          303 -DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  346 (366)
T ss_dssp             -ETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESS
T ss_pred             -cCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHH
Confidence             01123789999999999999999999999999999999997643

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=95.57  E-value=0.015  Score=50.57  Aligned_cols=105  Identities=20%  Similarity=0.275  Sum_probs=71.6

Q ss_pred             EEEEEeec-----cccceecCCCChhHHHH-HHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 020173          144 TIRLLIAG-----SQAGCLIGMSGQNIEKL-RNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (330)
Q Consensus       144 ~~~llip~-----~~~g~iIG~~G~~Ik~I-~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  217 (330)
                      ..++.|-+     .-+|..||++|++|+.| ++..|-+|.|-.-          +++              ...+|...|
T Consensus       113 R~KiAV~s~d~~iDpvGacIG~~G~rI~~i~~eL~gekIDIi~~----------s~d--------------p~~fi~nal  168 (251)
T 2asb_A          113 RSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDY----------DDD--------------PARFVANAL  168 (251)
T ss_dssp             EEEEEEEESSTTCCHHHHHHCGGGHHHHHHHHHTTTCEEEEEEC----------CSS--------------HHHHHHHHT
T ss_pred             eeEEEEEcCCCCCCHHHHHhCCCchHHHHHHHHhCCCeEEEEEe----------cCC--------------HHHHHHhcc
Confidence            34555554     23799999999999999 7888999988743          233              122333333


Q ss_pred             hhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC
Q 020173          218 RENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK  291 (330)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~  291 (330)
                      .-.....   +.              .  .........+.||.+..+.-|||+|++++--...||.+|.|....
T Consensus       169 sPA~V~~---V~--------------i--~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  223 (251)
T 2asb_A          169 SPAKVVS---VS--------------V--IDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  223 (251)
T ss_dssp             TTSCCSE---EE--------------E--EETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             CCcceEE---EE--------------E--EcCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHH
Confidence            2111000   00              0  001225688999999999999999999999999999999998643

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=95.36  E-value=0.028  Score=51.74  Aligned_cols=104  Identities=18%  Similarity=0.244  Sum_probs=72.5

Q ss_pred             EEEEEeec-----cccceecCCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 020173          144 TIRLLIAG-----SQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (330)
Q Consensus       144 ~~~llip~-----~~~g~iIG~~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  217 (330)
                      ..++.|-+     .-+|..||++|++|+.|.++. |-+|.|-.-          +++        +      ..+|...+
T Consensus       236 RaKIAV~s~d~~iDpvGacIG~~G~rI~~i~~eL~gekIDIi~~----------s~d--------p------~~fi~nal  291 (366)
T 1k0r_A          236 RSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDY----------DDD--------P------ARFVANAL  291 (366)
T ss_dssp             EEEEEEEESSTTCCHHHHHHCGGGHHHHHHHHHTTTCEEEEEEC----------CSS--------H------HHHHHHHT
T ss_pred             eEEEEEEeCCCCCCCcccccCCcchHHHHHHHHhCCCeEEEEEc----------CCC--------H------HHHHHHhc
Confidence            45666655     357999999999999999998 888888642          223        1      22333333


Q ss_pred             hhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173          218 RENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG  290 (330)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~  290 (330)
                      .-.....   +.                -.........+.||.+..+..|||+|++++-....||.+|.|...
T Consensus       292 sPA~V~~---V~----------------~~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          292 SPAKVVS---VS----------------VIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             TTSCCSE---EE----------------EEETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             CCcceeE---EE----------------EEcCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            2111000   00                000123578899999999999999999999999999999999864

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

Probab=95.24  E-value=0.0021  Score=64.99  Aligned_cols=61  Identities=20%  Similarity=0.336  Sum_probs=21.2

Q ss_pred             EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHH
Q 020173          253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYI  319 (330)
Q Consensus       253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i  319 (330)
                      ...|.||.+.+|.+||++|.+||.|.++||+.|.|..      +..|.|++. ....+.|+..|..+.
T Consensus       599 ~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          599 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CCCC------------------CTTCCCCCSCC--------------CCCBSSHHHHCC---------
T ss_pred             eEEEEEChHHeehcccccceeeehhhHhhCCEEEecC------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            3468899999999999999999999999999999884      356788775 677777877776654

>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=94.42  E-value=0.047  Score=49.98  Aligned_cols=96  Identities=26%  Similarity=0.287  Sum_probs=64.9

Q ss_pred             CccceeecccChhhhhhhhcc-CcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCcccccccc
Q 020173           59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA  137 (330)
Q Consensus        59 ~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~  137 (330)
                      +-+|+.||.+|.+|+.|..+. |=+|+|-.-             ++         +-...|...|....-..     +.-
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~-------------s~---------d~~~fi~nal~Pa~v~~-----v~~  297 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKW-------------SD---------DPKQLIANALAPATVIE-----VEI  297 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEEC-------------CS---------SHHHHHHHHTCSSCCSE-----EEE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEec-------------CC---------CHHHHHHHhcCccEEEE-----EEE
Confidence            358999999999999999998 777777543             11         11112222221110000     000


Q ss_pred             CCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCC
Q 020173          138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (330)
Q Consensus       138 ~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~  181 (330)
                      .........+.||..+.+..||++|.|++.-..-||.+|.|...
T Consensus       298 ~d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          298 LDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             EETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EcCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            00112378999999999999999999999999999999998753

>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=93.94  E-value=0.089  Score=48.12  Aligned_cols=103  Identities=18%  Similarity=0.249  Sum_probs=69.2

Q ss_pred             EEEEEeecc-----ccceecCCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 020173          144 TIRLLIAGS-----QAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (330)
Q Consensus       144 ~~~llip~~-----~~g~iIG~~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  217 (330)
                      ..++.|-+.     -+|..||.+|.+|+.+.++. |-+|.+-.-          +++        +      ..+|...|
T Consensus       232 R~KiAV~s~d~~iDpvGacvg~~G~ri~~i~~el~ge~Idii~~----------s~d--------~------~~fi~nal  287 (344)
T 1hh2_P          232 RTKVAVASNDPNVDPIGACIGEGGSRIAAILKELKGEKLDVLKW----------SDD--------P------KQLIANAL  287 (344)
T ss_dssp             EEEEEEEESSTTSCHHHHHHCTTSTTHHHHHHHTTTCEEEEEEC----------CSS--------H------HHHHHHHT
T ss_pred             ccceeEEccCCCccccceeeccCCcEeHHHHHHhCCCeeeEEec----------CCC--------H------HHHHHHhc
Confidence            345555432     47999999999999999887 777777642          222        1      22333333


Q ss_pred             hhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeC
Q 020173          218 RENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG  289 (330)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~  289 (330)
                      .-....   ++.              .  .........+.||.+..+.-|||+|++++--...||.+|.|..
T Consensus       288 ~Pa~v~---~v~--------------~--~d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          288 APATVI---EVE--------------I--LDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             CSSCCS---EEE--------------E--EETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CccEEE---EEE--------------E--EcCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            211000   000              0  0012357889999999999999999999999999999999874

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

Probab=92.42  E-value=0.013  Score=59.33  Aligned_cols=46  Identities=37%  Similarity=0.630  Sum_probs=16.7

Q ss_pred             EEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCC
Q 020173           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD  103 (330)
Q Consensus        52 ~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~  103 (330)
                      ..|.||.+..|.+||++|.+|+.|.++||+.|+|.+      +..+.|++.+
T Consensus       600 ~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~------dG~v~Is~~~  645 (757)
T 1e3p_A          600 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAAD  645 (757)
T ss_dssp             CCC------------------CTTCCCCCSCC--------------CCCBSS
T ss_pred             EEEEEChHHeehcccccceeeehhhHhhCCEEEecC------CceEEEecCC
Confidence            356789999999999999999999999999999974      3557777764

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

Probab=91.96  E-value=0.061  Score=54.22  Aligned_cols=94  Identities=21%  Similarity=0.240  Sum_probs=10.8

Q ss_pred             hhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 020173          108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC  187 (330)
Q Consensus       108 ~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~  187 (330)
                      +..+.+++..|.+.+.+.........    ...-+....+-||....+.+||++|.+|+.|.+++|+.|.+.        
T Consensus       529 l~~A~~~~~~I~~~m~~al~~~~~~~----~~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~--------  596 (723)
T 3cdi_A          529 LNQAKGARLHILGVMEQAINAPRGDI----SEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIE--------  596 (723)
T ss_dssp             HHHHHHHHHHHHHHHHHHCC------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHhhhcchhc----cccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEec--------
Confidence            34455566666666655432211100    011223567788999999999999999999999999999874        


Q ss_pred             cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHh
Q 020173          188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLR  218 (330)
Q Consensus       188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~  218 (330)
                           ++..+.|.+ +...+.+|...|..++.
T Consensus       597 -----~dg~v~I~~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          597 -----DDGTVKIAATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             --------------------------------
T ss_pred             -----CCccEEEecCCHHHHHHHHHHHHHHhh
Confidence                 234566655 45666677776666553

---

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	330
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	7e-11
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-08
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	3e-07
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	7e-11
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-08
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-07
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-10
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-10
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-08
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	5e-10
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	4e-08
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-07
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	1e-09
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	1e-07
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	2e-06
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-09
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-07
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	4e-06
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	7e-09
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	4e-08
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	7e-08
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-08
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	2e-07
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	9e-06
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-08
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	3e-08
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	6e-07
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	3e-08
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	9e-07
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	8e-05
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	5e-08
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	8e-08
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	9e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	5e-05
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	1e-07
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	3e-07
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	0.002
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-07
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-06
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-07
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	6e-07
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-04
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	1e-06
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	0.001
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	3e-05
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	6e-05
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	4e-05
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	0.001
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	2e-04
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.002
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	3e-04
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	4e-04
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	0.002
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	0.001

>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 = 55.6 bits (134), Expect = 7e-11
 Identities = 23/68 (33%), Positives = 37/68 (54%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
           +T E  + + +VG +IGR G  ISRI+ ESG  I++    G    R     G+ + V  A
Sbjct: 8   MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSA 67

Query: 312 KQRVDEYI 319
           K+ +D+ +
Sbjct: 68  KRLLDQIV 75

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.0 bits (117), Expect = 1e-08
 Identities = 15/70 (21%), Positives = 33/70 (47%), Gaps = 5/70 (7%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
              VP   +G +IG+ G +I +I++E+   I+IA       ER  +++           +
Sbjct: 11  EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT-----PESVQ 65

Query: 113 NALQQIAALI 122
           +A + +  ++
Sbjct: 66  SAKRLLDQIV 75

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.2 bits (107), Expect = 3e-07
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 7/77 (9%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T    +     G +IG  G+ I +++  SG  I I   +           +R   ++G  
Sbjct: 9   TEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS-------GGLPERSCMLTGTP 61

Query: 204 PAVLNALVEIGNQLREN 220
            +V +A   +   + + 
Sbjct: 62  ESVQSAKRLLDQIVEKG 78

>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 = 7e-11
 Identities = 24/68 (35%), Positives = 38/68 (55%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
            T E+ I  +L+G +IGR G+NI+ IR  SGA IK+         R +   GSA  ++LA
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLA 61

Query: 312 KQRVDEYI 319
           +  ++  +
Sbjct: 62  QYLINARL 69

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.3 bits (115), Expect = 2e-08
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + +P+  IG +IG++G  I +IR+ + A IKIA+ +     R + I+        +   
Sbjct: 5   ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS-----AASIS 59

Query: 113 NALQQIAALI 122
            A   I A +
Sbjct: 60  LAQYLINARL 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 = 45.6 bits (108), Expect = 2e-07
 Identities = 25/74 (33%), Positives = 33/74 (44%), Gaps = 7/74 (9%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T  L I  +  GC+IG  G NI ++R  SGA I I  P           S R V I+G  
Sbjct: 3   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV-------EGSSGRQVTITGSA 55

Query: 204 PAVLNALVEIGNQL 217
            ++  A   I  +L
Sbjct: 56  ASISLAQYLINARL 69

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.4 bits (131), Expect = 2e-10
 Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
           +T  +L+    VG +IG+ G ++ ++R ESGA I +   +G    R I   G    +  A
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINIS--EGNCPERIITLAGPTNAIFKA 61

Query: 312 KQRVDEYI 319
              + + +
Sbjct: 62  FAMIIDKL 69

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (130), Expect = 2e-10
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 9/76 (11%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TIRLL+ G + G +IG  G++++K+R  SGA I I   N           +R++ ++G  
Sbjct: 5   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN---------CPERIITLAGPT 55

Query: 204 PAVLNALVEIGNQLRE 219
            A+  A   I ++L E
Sbjct: 56  NAIFKAFAMIIDKLEE 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 = 48.6 bits (116), Expect = 2e-08
 Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 7/73 (9%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVS 109
           +  R+++  +++G +IGK+G  ++K+REE+ A I I++      ER+I ++        +
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGP-----TN 56

Query: 110 DAENALQQIAALI 122
               A   I   +
Sbjct: 57  AIFKAFAMIIDKL 69

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.0 bits (127), Expect = 5e-10
 Identities = 21/71 (29%), Positives = 36/71 (50%)

Query: 249 ADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQV 308
              +T ++ I + L G +IG+ G  I +IR+ESGA IK+       + R I   G+  Q+
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQI 60

Query: 309 ALAKQRVDEYI 319
             A+  +   +
Sbjct: 61  QNAQYLLQNSV 71

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.6 bits (113), Expect = 4e-08
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
           ++ +P    G +IGK G RI++IR E+ A+IKI + +   E+R+I I+           +
Sbjct: 7   QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-----QDQIQ 61

Query: 113 NALQQIAALI 122
           NA   +   +
Sbjct: 62  NAQYLLQNSV 71

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (109), Expect = 1e-07
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 7/76 (9%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           T ++ I    AG +IG  GQ I+++R+ SGA+I I  P            DR++ I+G  
Sbjct: 5   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL-------EGSEDRIITITGTQ 57

Query: 204 PAVLNALVEIGNQLRE 219
             + NA   + N +++
Sbjct: 58  DQIQNAQYLLQNSVKQ 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 = 52.2 bits (125), Expect = 1e-09
 Identities = 17/67 (25%), Positives = 30/67 (44%)

Query: 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAK 312
             ++ I    VG +IGR G  I +I+N++G  I+     G    R  Q  G   +   A 
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAA 63

Query: 313 QRVDEYI 319
           + + + +
Sbjct: 64  EIITDLL 70

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.4 bits (110), Expect = 1e-07
 Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 5/71 (7%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
             + +P   +G VIG+ G  I+KI+ +    I+         ER+  I+          A
Sbjct: 5   IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP-----PDRA 59

Query: 112 ENALQQIAALI 122
           ++A + I  L+
Sbjct: 60  QHAAEIITDLL 70

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.9 bits (101), Expect = 2e-06
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
           + I + I     G +IG +G+ I+K++N +G  I     +           +R+ QI+G 
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-------GTTPERIAQITGP 55

Query: 203 VPAVLNALVEIGNQLRE 219
                +A   I + LR 
Sbjct: 56  PDRAQHAAEIITDLLRS 72

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.4 bits (123), Expect = 2e-09
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV---YGGKGEQKHRHIQFGGSAQQVA 309
            F  ++     G +IG+ G  I  I  +SGA I++        +   +     G+ QQ+ 
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQID 61

Query: 310 LAKQRVDEYI 319
            A+Q ++E I
Sbjct: 62  YARQLIEEKI 71

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.4 bits (110), Expect = 1e-07
 Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 4/70 (5%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
               ++   + G +IG  G+ I+ +   SGA I +          +A  + ++  I G  
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP----PPNADPNMKLFTIRGTP 57

Query: 204 PAVLNALVEI 213
             +  A   I
Sbjct: 58  QQIDYARQLI 67

>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 = 41.8 bits (98), Expect = 4e-06
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 8/74 (10%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA---DAIARHEERVIIISSKDNDNVV 108
           F  IVP+ + G +IGK G  I+ I +++ A I++       A    ++  I         
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGT-----P 57

Query: 109 SDAENALQQIAALI 122
              + A Q I   I
Sbjct: 58  QQIDYARQLIEEKI 71

>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 = 50.4 bits (120), Expect = 7e-09
 Identities = 21/96 (21%), Positives = 39/96 (40%), Gaps = 7/96 (7%)

Query: 45  AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI--ARHEERVIIISSK 102
            +   V  ++ VP R +G++IG+ G  I+ I + + A I             R+I IS  
Sbjct: 10  TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGT 69

Query: 103 DNDNVVSDAENALQQIAALILKDDDSNSEASKVAAG 138
                  +   A   I   + +D++     +  A+G
Sbjct: 70  -----QKEVAAAKHLILEKVSEDEELRKRIAHSASG 100

>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 = 48.4 bits (115), Expect = 4e-08
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 5/81 (6%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
             +L +     G +IG  G+ I  +  +SGA I     ++           R+++ISG  
Sbjct: 16  FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE-----GTLLLSRLIKISGTQ 70

Query: 204 PAVLNALVEIGNQLRENPPRQ 224
             V  A   I  ++ E+   +
Sbjct: 71  KEVAAAKHLILEKVSEDEELR 91

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.7 bits (113), Expect = 7e-08
 Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVY--GGKGEQKHRHIQFGGSAQQVA 309
           V  ++ + +  VG +IGR G  I  I   SGA I             R I+  G+ ++VA
Sbjct: 15  VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVA 74

Query: 310 LAKQRVDEYI 319
            AK  + E +
Sbjct: 75  AAKHLILEKV 84

>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 = 49.2 bits (117), Expect = 1e-08
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVY--GGKGEQKHRHIQFGGSAQQVA 309
              E++I  S  G +IG+ G  I +++  +G  + +   G +     + ++  G   +V 
Sbjct: 8   AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQ 67

Query: 310 LAKQRVDEYIYSQ 322
            AK+ V E I  Q
Sbjct: 68  QAKEMVLELIRDQ 80

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.1 bits (109), Expect = 2e-07
 Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
              ++I  S+AG +IG  G+ I++L+  +G  +V++             +D+ ++I+GD 
Sbjct: 9   VQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN-----TGADKPLRITGDP 63

Query: 204 PAVLNALVEIGNQLRE 219
             V  A   +   +R+
Sbjct: 64  YKVQQAKEMVLELIRD 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 = 41.1 bits (96), Expect = 9e-06
 Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 7/77 (9%)

Query: 48  QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IARHEERVIIISSKDND 105
            + +  I++P+ + G VIGK G  I++++E     + +          ++ + I+     
Sbjct: 6   GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGD--- 62

Query: 106 NVVSDAENALQQIAALI 122
                 + A + +  LI
Sbjct: 63  --PYKVQQAKEMVLELI 77

>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 = 49.1 bits (117), Expect = 1e-08
 Identities = 15/70 (21%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG---EQKHRHIQFGGSAQQVA 309
             EM + E+LVG ++G+ G  +   +  +GA I++          ++R +   GS     
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 310 LAKQRVDEYI 319
            A+  + + +
Sbjct: 64  AAQYLISQRV 73

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.9 bits (114), Expect = 3e-08
 Identities = 14/75 (18%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
             + + +  +  G ++G  G+ + + +  +GA I I    +          +R V I+G 
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGT----RNRRVTITGS 58

Query: 203 VPAVLNALVEIGNQL 217
             A   A   I  ++
Sbjct: 59  PAATQAAQYLISQRV 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 = 44.0 bits (104), Expect = 6e-07
 Identities = 15/74 (20%), Positives = 32/74 (43%), Gaps = 8/74 (10%)

Query: 52  FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA---DAIARHEERVIIISSKDNDNVV 108
             + VP   +G ++GK G  + + +E T A I+I+   + +     R + I+        
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS-----P 59

Query: 109 SDAENALQQIAALI 122
           +  + A   I+  +
Sbjct: 60  AATQAAQYLISQRV 73

>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 = 48.3 bits (115), Expect = 3e-08
 Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 1/69 (1%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG-GKGEQKHRHIQFGGSAQQVAL 310
               + +       +IGR G+ I++IR E    I+      G Q    I   G  +    
Sbjct: 10  FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEA 69

Query: 311 AKQRVDEYI 319
           A+  +   +
Sbjct: 70  ARDAILRIV 78

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.1 bits (104), Expect = 9e-07
 Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 4/70 (5%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + V  +   K+IG++G  I +IR E    I+  D    ++ +  I  +    N     E
Sbjct: 13  SVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNT----E 68

Query: 113 NALQQIAALI 122
            A   I  ++
Sbjct: 69  AARDAILRIV 78

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (90), Expect = 8e-05
 Identities = 11/76 (14%), Positives = 23/76 (30%), Gaps = 6/76 (7%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
            + + +       +IG  G  I ++R      I     +        ++    + I+G  
Sbjct: 11  KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKD------DGNQPQDQITITGYE 64

Query: 204 PAVLNALVEIGNQLRE 219
                A   I   + E
Sbjct: 65  KNTEAARDAILRIVGE 80

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 46.6 bits (111), Expect = 5e-08
 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 6/56 (10%)

Query: 50  VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDND 105
            +  + +P  +IG+VIG +   I +I+E+T A I I D      +  I I + D  
Sbjct: 3   RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADGP 52

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (112), Expect = 8e-08
 Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 2/68 (2%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
           VT E+ +   L   +IG+ GS I ++ +E    I V     E +   I   G A  +  A
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAITGLAANLDRA 67

Query: 312 KQRVDEYI 319
           K  + E +
Sbjct: 68  KAGLLERV 75

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (105), Expect = 9e-07
 Identities = 14/70 (20%), Positives = 29/70 (41%), Gaps = 7/70 (10%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + VP      VIG++G  I+K+ +E +  I +       +  +I I+     N+    +
Sbjct: 13  EVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA--PELQSDIIAITG-LAANL----D 65

Query: 113 NALQQIAALI 122
            A   +   +
Sbjct: 66  RAKAGLLERV 75

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (92), Expect = 5e-05
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 9/76 (11%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           TI + +       +IG  G  I K+ +     I + AP              ++ I+G  
Sbjct: 11  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE---------LQSDIIAITGLA 61

Query: 204 PAVLNALVEIGNQLRE 219
             +  A   +  +++E
Sbjct: 62  ANLDRAKAGLLERVKE 77

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (110), Expect = 1e-07
 Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 4/68 (5%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            I +  +    +IGK G  I +I+++ K +++I          + I         V  A+
Sbjct: 8   EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-EKSNLIRIEGDPQG---VQQAK 63

Query: 113 NALQQIAA 120
             L ++A+
Sbjct: 64  RELLELAS 71

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (107), Expect = 3e-07
 Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 2/66 (3%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
              E+ I       LIG+ G+NI+RI+++    +++      +K   I+  G  Q V  A
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI--PPDSEKSNLIRIEGDPQGVQQA 62

Query: 312 KQRVDE 317
           K+ + E
Sbjct: 63  KRELLE 68

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 9/70 (12%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
            + + I       LIG SG NI ++++    ++ I             E   +++I GD 
Sbjct: 6   YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI---------PPDSEKSNLIRIEGDP 56

Query: 204 PAVLNALVEI 213
             V  A  E+
Sbjct: 57  QGVQQAKREL 66

>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 = 46.0 bits (109), Expect = 2e-07
 Identities = 12/69 (17%), Positives = 24/69 (34%), Gaps = 1/69 (1%)

Query: 249 ADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQV 308
              V+ ++ +   +   +IG  G  I +I +E    I+     G      +   G  + V
Sbjct: 7   EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-PQSGAPDPNCVTVTGLPENV 65

Query: 309 ALAKQRVDE 317
             A   +  
Sbjct: 66  EEAIDHILN 74

>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 = 43.3 bits (102), Expect = 2e-06
 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 6/70 (8%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + +  R   ++IG  G  I+KI +E K  I+   + A     V +    +N       E
Sbjct: 13  DVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPEN------VE 66

Query: 113 NALQQIAALI 122
            A+  I  L 
Sbjct: 67  EAIDHILNLE 76

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (107), Expect = 3e-07
 Identities = 9/68 (13%), Positives = 27/68 (39%), Gaps = 2/68 (2%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
            +  + I +     +IG+ G  +  +  ++   I++   + +     I+  G+ + +  A
Sbjct: 10  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSNQIKITGTKEGIEKA 67

Query: 312 KQRVDEYI 319
           +  V    
Sbjct: 68  RHEVLLIS 75

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (105), Expect = 6e-07
 Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 4/68 (5%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAE 112
            + +P      VIGK G ++Q +  +T   I+I         ++ I  +K+    +  A 
Sbjct: 13  TVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-DDPSNQIKITGTKEG---IEKAR 68

Query: 113 NALQQIAA 120
           + +  I+A
Sbjct: 69  HEVLLISA 76

>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 = 37.8 bits (88), Expect = 1e-04
 Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 9/80 (11%)

Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
           +  + I       +IG +G+ ++ L   +   I I  P+         +    ++I+G  
Sbjct: 11  SATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD---------DPSNQIKITGTK 61

Query: 204 PAVLNALVEIGNQLRENPPR 223
             +  A  E+     E   R
Sbjct: 62  EGIEKARHEVLLISAEQDKR 81

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.7 bits (103), Expect = 1e-06
 Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 249 ADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQV 308
           A+    E+ I   L   LIG  G  I  I  E G  + ++          +   G +  V
Sbjct: 7   ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGG-VHIHFPVEGSGSDTVVIRGPSSDV 65

Query: 309 ALAKQRVDE 317
             AK+++  
Sbjct: 66  EKAKKQLLH 74

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 8/71 (11%)

Query: 53  RIIVPSRQIGKVIGKEGHRIQKIREE-TKATIKIADAIARHEERVIIISSKDNDNVVSDA 111
            + +P++    +IG +G  I+ I EE     I             ++I    + +V    
Sbjct: 13  EVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV--EGSGSDTVVIRG-PSSDV---- 65

Query: 112 ENALQQIAALI 122
           E A +Q+  L 
Sbjct: 66  EKAKKQLLHLA 76

>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 = 39.7 bits (93), Expect = 3e-05
 Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 8/67 (11%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + +   ++ +VIGK+G  I+ ++ E    I +          + +   +     VS AE 
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-----NGLIWVNGDRRK---VSIAEE 56

Query: 114 ALQQIAA 120
           A+  I  
Sbjct: 57  AIYLIEQ 63

>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 = 39.0 bits (91), Expect = 6e-05
 Identities = 14/62 (22%), Positives = 31/62 (50%), Gaps = 6/62 (9%)

Query: 256 MLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRV 315
           + I+ + V  +IG+ GS I  +++E    I V       ++  I   G  ++V++A++ +
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVV------GQNGLIWVNGDRRKVSIAEEAI 58

Query: 316 DE 317
             
Sbjct: 59  YL 60

>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 = 39.4 bits (92), Expect = 4e-05
 Identities = 13/68 (19%), Positives = 26/68 (38%), Gaps = 5/68 (7%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + V   ++G VIG  G    +I   T   I +       E  ++I+  +       +   
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGIPPVNLMK 61

Query: 114 ALQQIAAL 121
           A + + A+
Sbjct: 62  AAEVVKAI 69

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 11/63 (17%), Positives = 20/63 (31%)

Query: 255 EMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQR 314
            + +    +G +IG  G   + I   +G +I V              G     +  A + 
Sbjct: 6   YVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEV 65

Query: 315 VDE 317
           V  
Sbjct: 66  VKA 68

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 37.0 bits (86), Expect = 2e-04
 Identities = 10/67 (14%), Positives = 26/67 (38%), Gaps = 7/67 (10%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           I +   ++ +VIGK     + +  ++  +I +A+         I  +     +       
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN------NGRIWATCPSRFS-EEILIE 57

Query: 114 ALQQIAA 120
           A+++I  
Sbjct: 58  AIRKIEN 64

>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 = 0.002
 Identities = 11/62 (17%), Positives = 21/62 (33%), Gaps = 5/62 (8%)

Query: 256 MLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRV 315
           + I    V  +IG+  S    + ++SG  I V         R      S     +  + +
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFV-----ANNGRIWATCPSRFSEEILIEAI 59

Query: 316 DE 317
            +
Sbjct: 60  RK 61

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.4 bits (87), Expect = 3e-04
 Identities = 14/58 (24%), Positives = 21/58 (36%), Gaps = 6/58 (10%)

Query: 58  SRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENAL 115
            R  G++IG+ G   + I E T   I + +        V II   +       A   L
Sbjct: 21  KRIKGRIIGEGGRARRTIEEMTDTYINVGE------YEVAIIGDYERAMAAKQAIEML 72

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (84), Expect = 4e-04
 Identities = 13/69 (18%), Positives = 22/69 (31%), Gaps = 8/69 (11%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
            +V    +G  IG  G  IQ+ R+    T          +     I  +  D V    + 
Sbjct: 12  FVVREDLMGLAIGTHGSNIQQARKVPGVTAI----ELDEDTGTFRIYGESADAV----KK 63

Query: 114 ALQQIAALI 122
           A   +  + 
Sbjct: 64  ARGFLEFVE 72

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.5 bits (79), Expect = 0.002
 Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 3/66 (4%)

Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
              E ++ E L+G  IG  GSNI + R   G                  +G SA  V  A
Sbjct: 8   FHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRI---YGESADAVKKA 64

Query: 312 KQRVDE 317
           +  ++ 
Sbjct: 65  RGFLEF 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 = 35.1 bits (81), Expect = 0.001
 Identities = 12/67 (17%), Positives = 30/67 (44%), Gaps = 7/67 (10%)

Query: 54  IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAEN 113
           + +   ++ +VIG++   ++ + E+T+  I +A          I +   + D   + A  
Sbjct: 5   VEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR------NGRIHLECPNEDL-EAIAVM 57

Query: 114 ALQQIAA 120
           A++ I  
Sbjct: 58  AIKIIDE 64

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	330
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.69
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.69
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.69
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.66
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.63
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.62
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.62
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.58
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.58
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.54
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.53
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.53
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.53
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.53
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.52
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.52
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.5
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.5
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.48
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.48
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.48
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.44
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.43
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.41
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.35
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.33
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.32
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.3
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.3
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.29
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.24
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.11
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.1
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.08
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.07
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.0
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.88
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.85
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.66
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.62
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.62
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.6
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.58
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.34
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.22
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.06
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.88
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.87
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	95.53
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.37
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.89
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.73
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	91.0
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	85.61
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	82.4

>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=99.69  E-value=5.3e-17  Score=115.93  Aligned_cols=72  Identities=29%  Similarity=0.437  Sum_probs=67.7

Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      ..+.+|.||.+++|+|||++|++|++|+++|||+|+|+++.+.+.+|.|+|+|++++|+.|+.+|.++|.+.
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            478899999999999999999999999999999999998777788999999999999999999999998764

>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=99.69  E-value=2.3e-17  Score=116.02  Aligned_cols=68  Identities=35%  Similarity=0.553  Sum_probs=64.5

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYI  319 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i  319 (330)
                      .+.+|.||.+++|+|||++|.+|++|++.|||+|.|++..+++.+|.|+|+|++++|+.|+.+|.+.|
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            67899999999999999999999999999999999998777788999999999999999999999876

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=2.9e-17  Score=116.96  Aligned_cols=71  Identities=25%  Similarity=0.382  Sum_probs=67.3

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      .+++|.||.+++|+|||++|++|++|++.|||+|+|++..+++.+|.|+|+|++++|+.|+.+|.++|.+.
T Consensus         3 ~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            67899999999999999999999999999999999998877778999999999999999999999999874

>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=99.66  E-value=9.8e-17  Score=113.18  Aligned_cols=67  Identities=27%  Similarity=0.483  Sum_probs=60.8

Q ss_pred             EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC---CCceeEEEEEcCHHHHHHHHHHHHHHH
Q 020173          253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG---EQKHRHIQFGGSAQQVALAKQRVDEYI  319 (330)
Q Consensus       253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~---~~~~r~v~I~Gt~~~v~~A~~~I~~~i  319 (330)
                      .++|.||.+++|+|||++|++|++|++.|||+|+|+++..   ++.+|.|+|+|++++|+.|+.+|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            4689999999999999999999999999999999987543   456899999999999999999999864

>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=99.63  E-value=3.4e-16  Score=111.27  Aligned_cols=68  Identities=22%  Similarity=0.413  Sum_probs=62.1

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC---CCceeEEEEEcCHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG---EQKHRHIQFGGSAQQVALAKQRVDEYI  319 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~---~~~~r~v~I~Gt~~~v~~A~~~I~~~i  319 (330)
                      ..++|.||.+++|+|||++|++|++|++.|||+|+|+++.+   ++.+|.|+|+|++++|+.|+.+|.++|
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            56789999999999999999999999999999999987543   456899999999999999999999875

>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=99.62  E-value=4.8e-16  Score=111.99  Aligned_cols=72  Identities=32%  Similarity=0.482  Sum_probs=67.9

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      ...+.+|.||..++|+|||++|.+|++|++.|||+|.|++...++.+|.|+|+|++++|+.|+.+|.++|.+
T Consensus         6 ~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   77 (79)
T d1x4na1           6 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEK   77 (79)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            458899999999999999999999999999999999999877778899999999999999999999999875

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=2.7e-16  Score=110.80  Aligned_cols=68  Identities=26%  Similarity=0.447  Sum_probs=63.2

Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHH
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIY  320 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~  320 (330)
                      ..+++|.||.+++|+|||++|++|++|++.|||+|+++++  ...+|+|+|+|++++|..|+.+|.++|.
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l~   70 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLE   70 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC--CCCcceEEEEECHHHHHHHHHHHHHHhc
Confidence            3789999999999999999999999999999999999874  4558999999999999999999999885

>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=99.58  E-value=1.3e-15  Score=110.21  Aligned_cols=72  Identities=22%  Similarity=0.348  Sum_probs=65.2

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC--CCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK--GEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~--~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      ...+.+|.||..++|+|||++|++|++|+++|||+|.|+++.  ..+.+|.|+|+|++++|+.|+.+|.++|.+
T Consensus         6 ~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           6 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             ccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            458999999999999999999999999999999999998653  245689999999999999999999998854

>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=99.58  E-value=5.6e-15  Score=111.95  Aligned_cols=75  Identities=28%  Similarity=0.301  Sum_probs=67.0

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC--CCceeEEEEEcCHHHHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG--EQKHRHIQFGGSAQQVALAKQRVDEYIYSQLI  324 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~--~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~~  324 (330)
                      ...+.+|.||..++|+|||++|.+|++|++.|||+|+|++..+  ...+|+|+|+|++++|+.|+.+|.++|.+...
T Consensus        13 ~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~   89 (104)
T d1we8a_          13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEE   89 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhCcHH
Confidence            4578899999999999999999999999999999999987543  44689999999999999999999999976553

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=4.2e-15  Score=107.39  Aligned_cols=72  Identities=14%  Similarity=0.184  Sum_probs=65.9

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQL  323 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~  323 (330)
                      ...+.+|.||..++|+|||++|++|++|++.|||+|+|++.  ++.++.|+|+|++++|+.|+.+|.+++.+..
T Consensus         8 ~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~--~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~~   79 (81)
T d2ctea1           8 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP--DDPSNQIKITGTKEGIEKARHEVLLISAEQD   79 (81)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT--TSSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC--CCCCCEEEEEeCHHHHHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999999999999999864  4567899999999999999999999988754

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=5.6e-15  Score=105.18  Aligned_cols=72  Identities=29%  Similarity=0.525  Sum_probs=65.5

Q ss_pred             CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhh
Q 020173           48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (330)
Q Consensus        48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~  124 (330)
                      ..++.+|.||.+++|+|||++|++|++|+++|||+|+|++..++..+|+|+|+|+.     +++.+|..+|.+++.+
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~-----~~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ-----DQIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECH-----HHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCH-----HHHHHHHHHHHHHHHh
Confidence            35789999999999999999999999999999999999988778889999999986     7889999999888754

>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=99.53  E-value=8.8e-15  Score=106.46  Aligned_cols=71  Identities=20%  Similarity=0.289  Sum_probs=64.7

Q ss_pred             eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC-CCCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK-GEQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~-~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      ++..|.||..++++|||++|++|++|++.|||+|+|++.. .+..++.|+|+|++++|+.|+.+|.+++.+.
T Consensus        10 ~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1          10 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            6789999999999999999999999999999999998653 3566889999999999999999999998764

>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=99.53  E-value=3.1e-15  Score=104.92  Aligned_cols=69  Identities=28%  Similarity=0.448  Sum_probs=63.0

Q ss_pred             ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHH
Q 020173           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI  122 (330)
Q Consensus        49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i  122 (330)
                      +.+.+|+||.+++|+|||++|.+|++|+++|||+|.|++..++.++|+|+|+|+.     +++.+|..+|.+.|
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 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSA-----ASISLAQYLINARL   69 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECH-----HHHHHHHHHHHHHT
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCH-----HHHHHHHHHHHHHc
Confidence            3688999999999999999999999999999999999988778889999999986     78889998888765

>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=99.53  E-value=7.8e-15  Score=105.93  Aligned_cols=73  Identities=16%  Similarity=0.188  Sum_probs=64.8

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQL  323 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~  323 (330)
                      ...+..|.||..++|+|||++|++|++|++.|||+|+|++... ...+.|+|+|++++|++|+++|++++.+..
T Consensus         8 ~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~-~~~~~v~I~G~~~~V~~A~~~I~~i~~e~~   80 (81)
T d2ctma1           8 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA-PDPNCVTVTGLPENVEEAIDHILNLEEEYL   80 (81)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC-SCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC-CCCCEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            4577899999999999999999999999999999999997533 335689999999999999999999988753

>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=99.52  E-value=9.1e-15  Score=102.82  Aligned_cols=69  Identities=36%  Similarity=0.628  Sum_probs=63.0

Q ss_pred             ceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       142 ~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      .++++|+||..++|+|||++|++|++|++.|||+|++++..         .++|+|+|+|++++|.+|..+|.++|++
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~---------~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN---------CPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC---------CSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCC---------CCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            46899999999999999999999999999999999997531         4689999999999999999999999875

>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=99.52  E-value=3.5e-15  Score=105.96  Aligned_cols=71  Identities=24%  Similarity=0.409  Sum_probs=64.6

Q ss_pred             ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhh
Q 020173           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (330)
Q Consensus        49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~  124 (330)
                      ...++|.||.+++|+|||++|++|++|+++|||+|+|++..++.++|+|+|+|+.     +++..|..+|.+++..
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 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPP-----DRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECH-----HHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCH-----HHHHHHHHHHHHHHHh
Confidence            5789999999999999999999999999999999999988777889999999986     7888999999888753

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=9.8e-15  Score=102.63  Aligned_cols=68  Identities=26%  Similarity=0.381  Sum_probs=61.5

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYI  319 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i  319 (330)
                      ...+.+|.||..++++|||++|++|++|+++|||+|.|+++  .+.++.|+|+|++++|+.|+.+|+++.
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            35778999999999999999999999999999999999864  455689999999999999999998763

>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=99.50  E-value=1.6e-14  Score=104.24  Aligned_cols=75  Identities=24%  Similarity=0.429  Sum_probs=66.7

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  220 (330)
                      ...+.+|+||..++|+|||++|++|++|+++|||+|.|.+.+..+.     +.+|.|+|+|++++|.+|..+|.++|++.
T Consensus         6 ~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~-----~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   80 (81)
T d1x4ma1           6 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNT-----GADKPLRITGDPYKVQQAKEMVLELIRDQ   80 (81)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSS-----CSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             ccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCC-----CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            5678999999999999999999999999999999999976443333     57899999999999999999999999763

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=3.5e-14  Score=100.65  Aligned_cols=70  Identities=20%  Similarity=0.343  Sum_probs=62.1

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  217 (330)
                      .++++||+.++|.|||++|++|++|+++|||+|++.+.+....    ...+|.|+|+|++++|.+|..+|.++|
T Consensus         4 ~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~----~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           4 LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP----GTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCST----TCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCC----CCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            6799999999999999999999999999999999976543322    257899999999999999999998875

>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=1.6e-14  Score=103.75  Aligned_cols=73  Identities=22%  Similarity=0.369  Sum_probs=66.8

Q ss_pred             CCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhh
Q 020173           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK  124 (330)
Q Consensus        47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~  124 (330)
                      ...++.+|+||.+++|+|||++|.+|++|+++|||+|.|++..++..+++|+|+|+.     +++..|..+|.+++.+
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~-----~~v~~A~~~I~~~i~e   77 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTP-----ESVQSAKRLLDQIVEK   77 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECH-----HHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCH-----HHHHHHHHHHHHHHHc
Confidence            356899999999999999999999999999999999999988777889999999986     7889999999988764

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=4.5e-14  Score=99.21  Aligned_cols=70  Identities=20%  Similarity=0.360  Sum_probs=60.8

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  217 (330)
                      +.+|+||+.++|+|||++|++|++|++.|||+|+++.... +..   ...+|.|+|+|++++|.+|..+|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~-~~~---~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPP-PNA---DPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT-TTS---CTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCC-CCC---CCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            5789999999999999999999999999999999976432 221   257899999999999999999998864

>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=99.48  E-value=2.1e-14  Score=103.96  Aligned_cols=71  Identities=23%  Similarity=0.261  Sum_probs=63.5

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHH-hCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNE-SGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~-tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      +..+.+|.||..+||+|||++|++|++|+++ ++++|++++.  ++.++.|+|+|++++|+.|+.+|++++.+.
T Consensus         8 ~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~--~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           8 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE--GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT--TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC--CCCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            4578899999999999999999999999977 5999999864  456789999999999999999999998764

>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=99.44  E-value=4.2e-15  Score=109.38  Aligned_cols=69  Identities=17%  Similarity=0.372  Sum_probs=62.3

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHH-hCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNE-SGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQL  323 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~-tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~  323 (330)
                      ...+..|.||..+|+.|||++|++|++|+++ ++++|.++++     +..|+|+|++++|+.|+.+|++++.+..
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~-----~~~v~i~G~~~~ve~Ak~~I~~iv~el~   88 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG-----EDKITLEGPTEDVSVAQEQIEGMVKDLI   88 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS-----SCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC-----CceEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            4589999999999999999999999999998 5899999853     4679999999999999999999987754

>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=99.43  E-value=1.3e-13  Score=101.64  Aligned_cols=70  Identities=27%  Similarity=0.238  Sum_probs=63.9

Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      ..+..|.||..+||+|||++|.+|++|++.|||+|.|++.  ++.++.|+|+|++++|+.|+.+|.+++.+.
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~--~~~~~~v~I~G~~~~V~~A~~~I~~~v~e~   78 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP--ELQSDIIAITGLAANLDRAKAGLLERVKEL   78 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT--TTTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC--CCCcceEEEECCHHHHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999999875  445678999999999999999999988754

>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=99.41  E-value=3.1e-13  Score=102.14  Aligned_cols=75  Identities=25%  Similarity=0.303  Sum_probs=65.7

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  220 (330)
                      ..++.+|+||..++++|||++|.+|++|+++|||+|.|.+.+....     ..+|+|+|+|++++|.+|..+|.+++.+.
T Consensus        13 ~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~-----~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTL-----LLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSS-----SSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCC-----CCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            3567899999999999999999999999999999999976543221     46799999999999999999999999764

>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=99.35  E-value=1.2e-12  Score=94.84  Aligned_cols=72  Identities=15%  Similarity=0.134  Sum_probs=63.5

Q ss_pred             ceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       142 ~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      ..++.+.||..++++|||++|++|++|+++|||+|.|++.+. +.     ..++.|+|+|+.++|.+|..+|.+++.+
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 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-GN-----QPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-CS-----SCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC-CC-----CCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            357899999999999999999999999999999999975432 21     4678999999999999999999999875

>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=99.34  E-value=1.6e-12  Score=93.48  Aligned_cols=72  Identities=18%  Similarity=0.159  Sum_probs=63.1

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  220 (330)
                      ..++..+.||..+++.|||++|++|++|+++|||+|.|+..+.        ...+.|+|+|++++|.+|..+|.+++++.
T Consensus         8 ~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~--------~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           8 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA--------PDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC--------SCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC--------CCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            4457899999999999999999999999999999999975421        23568999999999999999999998864

>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=99.33  E-value=1e-12  Score=94.58  Aligned_cols=71  Identities=18%  Similarity=0.295  Sum_probs=63.6

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  220 (330)
                      ...+..+.||..++++|||++|++|++|+++|||+|.++..+         +.++.|+|+|+.++|.+|..+|.+++.+.
T Consensus         8 ~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~---------~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           8 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD---------DPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT---------SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC---------CCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            346889999999999999999999999999999999996532         45678999999999999999999999764

>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=99.32  E-value=7.9e-13  Score=95.34  Aligned_cols=63  Identities=22%  Similarity=0.220  Sum_probs=57.2

Q ss_pred             EEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173          254 FEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQ  322 (330)
Q Consensus       254 ~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~  322 (330)
                      ..+.||++++|.|||++|++|++|+++|||+|.|++      ++.|+|+|++++++.|+.+|+.++.+.
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~------~g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ------NGLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT------TSEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC------CCEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            358899999999999999999999999999999985      257999999999999999998887654

>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=99.30  E-value=1.6e-12  Score=90.98  Aligned_cols=67  Identities=24%  Similarity=0.342  Sum_probs=59.9

Q ss_pred             ceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 020173          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL  217 (330)
Q Consensus       142 ~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  217 (330)
                      ....++.||..++++|||++|++|++|+++|||+|.|++.+         ++++.|+|+|++++|.+|..+|++++
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~---------~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS---------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC---------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCC---------CCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999999999999996532         46788999999999999999998764

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=7.7e-13  Score=94.10  Aligned_cols=65  Identities=26%  Similarity=0.293  Sum_probs=57.6

Q ss_pred             cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEc-CHHHHHHHHHHHHHH
Q 020173          250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGG-SAQQVALAKQRVDEY  318 (330)
Q Consensus       250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~G-t~~~v~~A~~~I~~~  318 (330)
                      ..++.+|.||.+++|.|||++|++|++|++.|||+|.+.++    +++.|+|.| ++++|++|+.+|+.+
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~----~~g~v~I~g~~~eav~~A~~~Ie~~   71 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGESADAVKKARGFLEFV   71 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC----CCceEEEEECCHHHHHHHHHHHHHh
Confidence            45788999999999999999999999999999999998753    346799999 699999999999643

>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=99.29  E-value=2.6e-12  Score=92.62  Aligned_cols=71  Identities=20%  Similarity=0.250  Sum_probs=62.4

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHH-hCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNS-SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~-sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      +..+..|.||..++++|||++|++|++|+++ ++++|.++..+         ..++.|+|+|++++|.+|..+|..++++
T Consensus         8 ~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~---------~~~~~v~I~G~~~~v~~A~~~I~~~v~e   78 (82)
T d2ctja1           8 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG---------SGSDTVVIRGPSSDVEKAKKQLLHLAEE   78 (82)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT---------TTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCC---------CCCceEEEeCCHHHHHHHHHHHHHHHhh
Confidence            3458899999999999999999999999987 58999886432         4678999999999999999999999987


Q ss_pred             C
Q 020173          220 N  220 (330)
Q Consensus       220 ~  220 (330)
                      .
T Consensus        79 ~   79 (82)
T d2ctja1          79 K   79 (82)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.24  E-value=6.2e-12  Score=92.43  Aligned_cols=69  Identities=20%  Similarity=0.280  Sum_probs=62.5

Q ss_pred             ceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       142 ~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      .++..+.||..+++.|||++|++|++|+++|||+|.|+..+         +.++.|+|+|+.++|.+|..+|..++.+
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~---------~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE---------LQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT---------TTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCC---------CCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999999999996542         4567899999999999999999999875

>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=99.11  E-value=1e-10  Score=85.41  Aligned_cols=67  Identities=16%  Similarity=0.230  Sum_probs=60.2

Q ss_pred             cceEEEEEeeccccceecCCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173          141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE  219 (330)
Q Consensus       141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  219 (330)
                      ...+..+.||..+|++|||++|++|++|++++ +++|.++.            .+..|+|+|++++|.+|..+|.+++.+
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~------------~~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE------------GEDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS------------SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC------------CCceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            45689999999999999999999999999995 79999853            356899999999999999999999875

>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=99.10  E-value=9.8e-11  Score=84.14  Aligned_cols=63  Identities=22%  Similarity=0.195  Sum_probs=57.4

Q ss_pred             EEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173          145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       145 ~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  220 (330)
                      .-+.||...++.|||++|++|++|+++|||+|.+.             .+..|+|.|+++++.+|..+|..++++.
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~-------------~~g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVG-------------QNGLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEEC-------------TTSEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEEC-------------CCCEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            35789999999999999999999999999999995             2457999999999999999999998875

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.08  E-value=2e-11  Score=87.59  Aligned_cols=66  Identities=17%  Similarity=0.138  Sum_probs=52.5

Q ss_pred             EEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHH
Q 020173          254 FEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYI  319 (330)
Q Consensus       254 ~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i  319 (330)
                      +.+.||.+.+|.|||++|++||+|++.|||+|+|+.+......+.....|.+.++++|+.+|.++.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g~v~i~~~~~~~~~~a~~~a~~iI~aI~   70 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAIS   70 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTTEEEEEESSTTSCHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCCeEEEecCCccccHHHHHHHHHHHHHHh
Confidence            468999999999999999999999999999999985422111222334567999999999998764

>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=99.07  E-value=4.2e-11  Score=84.91  Aligned_cols=64  Identities=20%  Similarity=0.228  Sum_probs=52.5

Q ss_pred             CCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHH
Q 020173           47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI  118 (330)
Q Consensus        47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i  118 (330)
                      ...++.+|.||.+++|+|||+||++|++|+++|||+|.+.+.    .++.+.|.|.+    -+.+.+|..+|
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~----~~g~v~I~g~~----~eav~~A~~~I   68 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGES----ADAVKKARGFL   68 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----TTTEEEEEESS----HHHHHHHHHHH
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC----CCceEEEEECC----HHHHHHHHHHH
Confidence            456788999999999999999999999999999999999864    45779999953    14555655555

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.00  E-value=2e-12  Score=89.61  Aligned_cols=63  Identities=16%  Similarity=0.069  Sum_probs=48.9

Q ss_pred             EEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHHHHH
Q 020173          255 EMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIYSQL  323 (330)
Q Consensus       255 ~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~~~~  323 (330)
                      .+.||.+++|.|||++|++||+|+++|||+|.|.++      ..|+|+|. .++++.|+.+|..+..+++
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 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN------GRIWATCPSRFSEEILIEAIRKIENESH   67 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT------SEEEC-----CTTCCTHHHHTTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC------CEEEEEeCCHHHHHHHHHHHHHHHHhhc
Confidence            478999999999999999999999999999999742      36999996 7899999999987766544

>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=98.88  E-value=8.2e-10  Score=79.21  Aligned_cols=63  Identities=19%  Similarity=0.115  Sum_probs=55.6

Q ss_pred             EEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHHHHH
Q 020173          255 EMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIYSQL  323 (330)
Q Consensus       255 ~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~~~~  323 (330)
                      .+.||.+.+|.|||++|++|+.|++.|||+|.|.++      ..|.|.|. .+.+..|+.+|..+..++.
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~------G~V~I~g~~~~~~~~A~~~I~~I~~ea~   67 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN------GRIHLECPNEDLEAIAVMAIKIIDEEAY   67 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETT------TEEEEECSCHHHHHHHHHHHHHHHHCSC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCC------cEEEEEeCCHHHHHHHHHHHHHHHHhch
Confidence            578999999999999999999999999999999853      36999995 8999999999988766543

>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=98.85  E-value=1.5e-09  Score=77.56  Aligned_cols=65  Identities=18%  Similarity=0.313  Sum_probs=46.3

Q ss_pred             EEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHH
Q 020173           52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL  121 (330)
Q Consensus        52 ~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~  121 (330)
                      +.+.||.+.+|.|||++|++|++|+++|||+|+|++.     ...+.+.+......-..+++|...|.++
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d-----~g~v~i~~~~~~~~~~a~~~a~~iI~aI   69 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE-----NSMVIVEPEAEGIPPVNLMKAAEVVKAI   69 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT-----TTEEEEEESSTTSCHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC-----CCeEEEecCCccccHHHHHHHHHHHHHH
Confidence            3588999999999999999999999999999999753     2445555543221123444555555554

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.66  E-value=7.4e-10  Score=72.01  Aligned_cols=47  Identities=36%  Similarity=0.637  Sum_probs=15.4

Q ss_pred             EEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCC
Q 020173           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD  103 (330)
Q Consensus        51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~  103 (330)
                      ..+|.||.+.+|.|||+||.+||+|+++|||+|++.+      +..|.|.|.+
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d------dg~v~I~a~~   50 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAAD   50 (54)
T ss_dssp             CC---------------------CHHHHSCCCC--------------CCCCBS
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC------CeEEEEEecC
Confidence            3478899999999999999999999999999999975      4678888865

>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=98.62  E-value=1.2e-09  Score=70.95  Aligned_cols=46  Identities=24%  Similarity=0.396  Sum_probs=14.5

Q ss_pred             EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC
Q 020173          253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS  304 (330)
Q Consensus       253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt  304 (330)
                      ...|.||.+.+|.|||++|++||.|+++|||+|.+.+      +..|+|+|.
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d------dg~v~I~a~   49 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAA   49 (54)
T ss_dssp             CC---------------------CHHHHSCCCC--------------CCCCB
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC------CeEEEEEec
Confidence            3468999999999999999999999999999999984      467888775

>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=98.62  E-value=1e-09  Score=75.68  Aligned_cols=62  Identities=16%  Similarity=0.102  Sum_probs=47.1

Q ss_pred             EEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhhC
Q 020173          146 RLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLREN  220 (330)
Q Consensus       146 ~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~~~  220 (330)
                      -+.||...++.|||++|++|+.|+++|||+|.+.             .+..|+|.|. .+.+.+|..+|..+.++.
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~-------------~~g~v~I~g~~~~~v~~A~~~I~~i~~ea   66 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVA-------------NNGRIWATCPSRFSEEILIEAIRKIENES   66 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEEC-------------TTSEEEC-----CTTCCTHHHHTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEc-------------CCCEEEEEeCCHHHHHHHHHHHHHHHHhh
Confidence            4679999999999999999999999999999994             2346999995 678999999997766554

>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=98.60  E-value=1.9e-08  Score=74.43  Aligned_cols=53  Identities=21%  Similarity=0.273  Sum_probs=47.0

Q ss_pred             cccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173          262 LVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYS  321 (330)
Q Consensus       262 ~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~  321 (330)
                      +.|+|||++|.+|+.|++.|||.|.|..       ..|.|.|++++++.|+.+|..++..
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d-------~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS-------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeC-------CeEEEEECchhHHHHHHHHHHHHcC
Confidence            4699999999999999999999999974       2477889999999999999988753

>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=98.58  E-value=8.1e-08  Score=68.56  Aligned_cols=62  Identities=13%  Similarity=0.101  Sum_probs=54.5

Q ss_pred             EEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhhC
Q 020173          146 RLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLREN  220 (330)
Q Consensus       146 ~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~~~  220 (330)
                      -+-||...++.|||++|++|+.|+++|||+|.|..             +..|.|.|. .+.+..|..+|..+.++.
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d-------------~G~V~I~g~~~~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-------------NGRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET-------------TTEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC-------------CcEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            46799999999999999999999999999999952             347999995 888899999998887765

>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=98.34  E-value=2.7e-07  Score=68.02  Aligned_cols=53  Identities=21%  Similarity=0.242  Sum_probs=46.9

Q ss_pred             cceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173          154 AGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN  220 (330)
Q Consensus       154 ~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  220 (330)
                      .|.|||++|.+|+.|++.|||.|.|.              +..+.+.|+++++..|..+|..++.+.
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~--------------d~~v~iig~~e~i~~A~~~Ie~li~~~   76 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVG--------------EYEVAIIGDYERAMAAKQAIEMLAEGR   76 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEEC--------------SSEEEEEEEHHHHHHHHHHHHHHHTTC
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEe--------------CCeEEEEECchhHHHHHHHHHHHHcCC
Confidence            48999999999999999999999994              225777899999999999999999754

>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=98.22  E-value=2e-06  Score=65.35  Aligned_cols=69  Identities=25%  Similarity=0.380  Sum_probs=55.4

Q ss_pred             eEEEEEEccc------cccceecCCCchHHHHHHHhCCeEEEeCCCC----------------CCceeEEEEEcC-HHHH
Q 020173          252 VTFEMLISES------LVGGLIGRCGSNISRIRNESGAMIKVYGGKG----------------EQKHRHIQFGGS-AQQV  308 (330)
Q Consensus       252 ~~~~v~IP~~------~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~----------------~~~~r~v~I~Gt-~~~v  308 (330)
                      .+.+|.||-+      ++|.|||.+|.++|+|+++|||+|.|-...+                ....=-|.|++. ++.+
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~   82 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENV   82 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHH
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhH
Confidence            5667888875      6899999999999999999999999964211                112335778885 8899


Q ss_pred             HHHHHHHHHHHH
Q 020173          309 ALAKQRVDEYIY  320 (330)
Q Consensus       309 ~~A~~~I~~~i~  320 (330)
                      +.|..+|.++|.
T Consensus        83 ~~A~~~i~~ll~   94 (122)
T d1k1ga_          83 KKAVEQIRNILK   94 (122)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHH
Confidence            999999999984

>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=98.06  E-value=3.6e-06  Score=63.91  Aligned_cols=73  Identities=21%  Similarity=0.435  Sum_probs=54.1

Q ss_pred             ceEEEEEecCC------ccceeecccChhhhhhhhccCcEEEEecC---------C------CCCcce-EEEEecCCCCc
Q 020173           49 DVLFRIIVPSR------QIGKVIGKEGHRIQKIREETKATIKIADA---------I------ARHEER-VIIISSKDNDN  106 (330)
Q Consensus        49 ~~~~~i~vP~~------~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~---------~------~~~~er-vi~I~G~~~~~  106 (330)
                      .++.+|+||.+      ++|.|||++|.++|+|+++|||+|.|.-.         .      +...+. =|.|++..   
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~---   78 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANT---   78 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESS---
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCC---
Confidence            46789999986      49999999999999999999999999631         0      011222 25566654   


Q ss_pred             chhHHHHHHHHHHHHHhhc
Q 020173          107 VVSDAENALQQIAALILKD  125 (330)
Q Consensus       107 ~~~~~~~A~~~i~~~i~~~  125 (330)
                       ...+..|+..|..++...
T Consensus        79 -~~~~~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          79 -MENVKKAVEQIRNILKQG   96 (122)
T ss_dssp             -HHHHHHHHHHHHHHHTTT
T ss_pred             -hhhHHHHHHHHHHHHHhc
Confidence             357788888888888543

>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=97.88  E-value=7.3e-06  Score=62.93  Aligned_cols=75  Identities=19%  Similarity=0.379  Sum_probs=51.7

Q ss_pred             eEEEEEecC------CccceeecccChhhhhhhhccCcEEEEecCC-----------C------CCcce-EEEEecCCCC
Q 020173           50 VLFRIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADAI-----------A------RHEER-VIIISSKDND  105 (330)
Q Consensus        50 ~~~~i~vP~------~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~-----------~------~~~er-vi~I~G~~~~  105 (330)
                      +..+|+||.      +++|.|||++|.++|+|+++|||+|.|.-.-           .      ...+. =|.|++....
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            567899996      4799999999999999999999999997420           0      01122 2566665422


Q ss_pred             c-chhHHHHHHHHHHHHHhh
Q 020173          106 N-VVSDAENALQQIAALILK  124 (330)
Q Consensus       106 ~-~~~~~~~A~~~i~~~i~~  124 (330)
                      . ....+..|+..|..++..
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            1 112466778888887754

>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=97.87  E-value=1.1e-05  Score=61.80  Aligned_cols=67  Identities=18%  Similarity=0.311  Sum_probs=51.4

Q ss_pred             EEEEEEcc------ccccceecCCCchHHHHHHHhCCeEEEeCCCC------------------CCceeEEEEEcCH---
Q 020173          253 TFEMLISE------SLVGGLIGRCGSNISRIRNESGAMIKVYGGKG------------------EQKHRHIQFGGSA---  305 (330)
Q Consensus       253 ~~~v~IP~------~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~------------------~~~~r~v~I~Gt~---  305 (330)
                      +.+|.||.      +++|.|||.+|.++|+|+++|||+|.|-....                  ....=-|.|++..   
T Consensus         3 ~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~~   82 (134)
T d2bl5a1           3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQN   82 (134)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCH
T ss_pred             ceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcHH
Confidence            45677774      48899999999999999999999999986431                  0123457777752   


Q ss_pred             ---HHHHHHHHHHHHHH
Q 020173          306 ---QQVALAKQRVDEYI  319 (330)
Q Consensus       306 ---~~v~~A~~~I~~~i  319 (330)
                         ..++.|..+|..+|
T Consensus        83 ~a~~kl~~A~~~I~~lL   99 (134)
T d2bl5a1          83 RAELKLKRAVEEVKKLL   99 (134)
T ss_dssp             HHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHc
Confidence               35888999998887

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=95.53  E-value=0.0024  Score=42.48  Aligned_cols=38  Identities=29%  Similarity=0.374  Sum_probs=35.2

Q ss_pred             eEEEEEecCCccceeecccChhhhhhhhccCcEEEEec
Q 020173           50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD   87 (330)
Q Consensus        50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~   87 (330)
                      -...+.||.+..+..|||+|.|++-..+-||.+|+|.+
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            35788999999999999999999999999999999975

>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=95.37  E-value=0.0026  Score=42.14  Aligned_cols=40  Identities=30%  Similarity=0.359  Sum_probs=36.1

Q ss_pred             ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC
Q 020173           49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA   88 (330)
Q Consensus        49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~   88 (330)
                      .-.+.+.||.+..+..|||+|.|++-..+-||.+|+|-..
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            3467889999999999999999999999999999998653

>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=94.89  E-value=0.01  Score=39.12  Aligned_cols=40  Identities=18%  Similarity=0.213  Sum_probs=36.5

Q ss_pred             ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173          251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG  290 (330)
Q Consensus       251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~  290 (330)
                      .....+.+|.+....-|||+|.+++-..+.||.+|.|..+
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            3578899999999999999999999999999999999853

>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=94.73  E-value=0.015  Score=38.39  Aligned_cols=38  Identities=29%  Similarity=0.310  Sum_probs=35.3

Q ss_pred             EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCC
Q 020173          144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP  181 (330)
Q Consensus       144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~  181 (330)
                      ...+.||..+.+..||++|.+++-...-+|.+|.|...
T Consensus        28 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~   65 (68)
T d1hh2p3          28 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI   65 (68)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEc
Confidence            68899999999999999999999999999999999753

>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=91.00  E-value=0.13  Score=35.31  Aligned_cols=59  Identities=5%  Similarity=-0.057  Sum_probs=47.4

Q ss_pred             EEEEEccccccceecCCCc-hHHHHHHHhCCeEEEeCCCCCCceeEEEEEc-CHHHHHHHHHHHHHH
Q 020173          254 FEMLISESLVGGLIGRCGS-NISRIRNESGAMIKVYGGKGEQKHRHIQFGG-SAQQVALAKQRVDEY  318 (330)
Q Consensus       254 ~~v~IP~~~vg~IIGk~G~-~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~G-t~~~v~~A~~~I~~~  318 (330)
                      +-+.||..++..++|++++ .++.|.+.+++.|.|-.+      ..|=|.| +.+..-.+...|...
T Consensus         3 ~v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~N------GrIWi~~~~~~~~i~i~~aI~~~   63 (85)
T d2ja9a2           3 MIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLN------GKIWVKCEELSNTLACYRTIMEC   63 (85)
T ss_dssp             EEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETT------TEEEEECSSHHHHHHHHHHHHHH
T ss_pred             EEEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecC------cEEEEECCCHHHHHHHHHHHHHH
Confidence            3578999999999999998 899999999999999964      4577888 467766666656443

>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=85.61  E-value=0.087  Score=36.80  Aligned_cols=32  Identities=22%  Similarity=0.436  Sum_probs=26.9

Q ss_pred             EEEEEecCCccceeecccChhhhhhhhccCcE
Q 020173           51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKAT   82 (330)
Q Consensus        51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~   82 (330)
                      .++|.|....-|.|||++|+.|++|+++-.-.
T Consensus        36 ~i~I~I~tarPGivIGrkG~~I~~L~~~l~k~   67 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGEKGRRIRELTAVVQKR   67 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCCCceeeccCchhHHHHHHHHHHH
Confidence            36788899999999999999999998665433

>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=82.40  E-value=1  Score=30.58  Aligned_cols=62  Identities=11%  Similarity=0.017  Sum_probs=46.9

Q ss_pred             EEEeeccccceecCCCCh-hHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhhC
Q 020173          146 RLLIAGSQAGCLIGMSGQ-NIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLREN  220 (330)
Q Consensus       146 ~llip~~~~g~iIG~~G~-~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~~~  220 (330)
                      -+-|+-.++..++|++++ -++.|.+.+++.|.+=             .+..|-|.|. .+....+...|...-++.
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG-------------~NGrIWi~~~~~~~~i~i~~aI~~~e~~~   67 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIG-------------LNGKIWVKCEELSNTLACYRTIMECCQKN   67 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEE-------------TTTEEEEECSSHHHHHHHHHHHHHHHHHC
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEe-------------cCcEEEEECCCHHHHHHHHHHHHHHHHhC
Confidence            456788889999999998 6899999999999984             3446888884 666666666665554443