Citrus Sinensis ID: 005922

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------67
Protein Sequence
MADEPQYSSDGTPSKRKYEDQTTPPSAAARRPTGFSAPDPAVAPTSYNSVPPPADEFQDFQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYPSQPTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSYYGGGYSQPVYTADGNAAPAAQPVQQGGVTKSPQS
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccEEEEEccccHHHHHHHHHHccEEEEcccccccccccccEEEEEccHHHHHHHHHHHHHHHHHHHccccccccccccccccccEEEEEEccccEEEEEEccHHHHHHHHHHHccEEEEEcccccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEcccccccccccccEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEEEEcccHHHHHccccHHHHHHHHHHccEEEEEEccccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
madepqyssdgtpskrkyedqttppsaaarrptgfsapdpavaptsynsvpppadefqDFQAAKRRAEQIAARLCNSvsaeakrprvengsggfdsadkgfssppsdlksipapsaipvsyggyqsmgtskkieipnirvgvIIGKSGETIKYLQLqsgakiqvtrdteadlnsptrsvelmgtpeQIAKAEQLINDVLAeaesggsgivarrltgqagsdhfamkipnnkvglvigkggetIKNMQARTgariqviplhlppgdtstertvqidgtSEQIESAKQLVNEVISenrirnpamaggysqqgyqarpptswgtpgapsmqqpgygyvqpgaypgqtpqynmsqppyggypsqptpggypgnwdqtptqqtsqgsgydyysqqpssqqpqapggsaapadstgysysqppasgynqqgqgyaqdsyggyhapqsgygqaapydqqqgynsaagygnvnntsqeghtpsygaqgdstqapppvqssaamgqqgygtgqqpspntasyppqgatqpsygvpptsqsgygsqvppqsgyagygmpqaqkplanppaygqtqqspgsaggygqpgyshsqpppssyaqpdsgsqrappsnygaatqpgygsaaygappggsqagygqgppsyygggysqpvytadgnaapaaqpvqqggvtkspqs
Flexible Loop (DISEMBL)
madepqyssdgtpskrkyedqttppsaaarrptgFSAPDPAVAPTSYNSVPPPADEFQDFQAAKRRAEQIAARLcnsvsaeakrprvengsggfdsadKGFSSPPSDLKSIPAPSAIPVSYGGYQSMgtskkieipNIRVGVIIGKSGETIKYLQLqsgakiqvtrdteadlnsptrsvelmGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARiqviplhlppgdtsTERTVQIDGTSEQIESAKQLVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYPSQPTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSYYGGGYSQPVYTADGNAAPaaqpvqqggvtkspqs
Low Complexity Region (SEG)
MADEPQYSSDGTPSKRKYEDQTTPPSAAARRPTGFSAPDPAVAPTSYNSVPPPADEFQDFQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYPSQPTPGGYPGNWDqtptqqtsqgsgydyysqqpssqqpqapggsaapadstGYSYSQPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQPDSGSQRAPPSNYGAATqpgygsaaygappggsqagygqgppsyygggysqpVYTADGNaapaaqpvqqggvTKSPQS
Disordered region (IsUnstruct)
***********************************************************************************************************************SYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQ******************************LINDVL********GIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLH*************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
************************************************************************************************************************************IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDT***LNSPTRSVELMGTPEQIAKAEQLI****************************AMKIPNNKVGLVIGKGGETIKNMQARTGARIQ***************TVQIDGTSEQIESAKQLVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMS*******************************************************************************************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
********************************TGFSAPDPAVAPTSYNSVPPPADEFQDFQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYPSQPTPGGYPGNWDQT**************************************SYSQPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSYG***********************************************************VPPQSGYAGYGMPQAQKPLAN************************************************AATQPGYGSAAYGAPPGGSQAGYGQGPPSYYGGGYSQPVYTADGNAAP****************
Disordered Region (DISPRO)
*********************************************SYNSVPPPADEFQDFQAAKRRAEQIAARLCN**************************************************MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAES**************GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYPSQPTPGGYPGNWDQT*T*****GSGY*****************SAAPADSTGYSYSQPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYG******QEGH**********T***********************************TQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSYYGGGYSQP**************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MADEPQYSSDGTPSKRKYEDQTTPPSAAARRPTGFSAPDPAVAPTSYNSVPPPADEFQDFQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYPSQPTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSYYGGGYSQPVYTADGNAAPAAQPVQQGGVTKSPQS
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	669	2.2.26 [Sep-21-2011]
Q8UVD9	769	Far upstream element-bind	yes	no	0.246	0.214	0.339	4e-20
Q3U0V1	748	Far upstream element-bind	yes	no	0.327	0.292	0.282	6e-19
Q99PF5	721	Far upstream element-bind	no	no	0.327	0.303	0.282	9e-19
Q96I24	572	Far upstream element-bind	yes	no	0.316	0.370	0.294	9e-19
Q92945	711	Far upstream element-bind	no	no	0.336	0.316	0.290	1e-18
Q96AE4	644	Far upstream element-bind	no	no	0.340	0.354	0.296	2e-18
Q32PX7	639	Far upstream element-bind	no	no	0.319	0.334	0.291	8e-18
Q91WJ8	651	Far upstream element-bind	no	no	0.319	0.328	0.297	2e-17
Q61990	362	Poly(rC)-binding protein	no	no	0.200	0.370	0.337	8e-11
Q15366	365	Poly(rC)-binding protein	no	no	0.200	0.367	0.337	9e-11

>sp|Q8UVD9|FUBP2_CHICK Far upstream element-binding protein 2 OS=Gallus gallus GN=KHSRP PE=1 SV=1

 Score =  100 bits (249), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 58/171 (33%), Positives = 100/171 (58%), Gaps = 6/171 (3%)

Query: 125 QSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT 184
           +S   +++  +P+  VG+IIG+ GE I  +Q  SG K+Q++ D+      P RSV L G+
Sbjct: 205 RSTTVTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGG---LPERSVSLTGS 261

Query: 185 PEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIK 244
           PE + KA+ +++D+++    G  G       GQ G+    M IP  K GLVIGKGGETIK
Sbjct: 262 PEAVQKAKLMLDDIVSRGRGGPPGQFHDYANGQNGTVQEIM-IPAGKAGLVIGKGGETIK 320

Query: 245 NMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN 295
            +Q R G  +++I +     +T+ ++ ++I G   +++ A ++V +++ E 
Sbjct: 321 QLQERAG--VKMIFIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRER 369

Part of a ternary complex that binds to the downstream control sequence (DCS) of the pre-mRNA. Mediates exon inclusion in transcripts that are subject to tissue-specific alternative splicing. May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly by recruiting degradation machinery to ARE-containing mRNAs. Binds to the dendritic targeting element and may play a role in mRNA trafficking (By similarity). Binds to a 54-nucleotide localization signal (the 'zipcode') found in the 3'-UTR of beta-actin mRNA and may play a role in its localization.
Gallus gallus (taxid: 9031)

>sp|Q3U0V1|FUBP2_MOUSE Far upstream element-binding protein 2 OS=Mus musculus GN=Khsrp PE=1 SV=2

 Score = 96.7 bits (239), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 122/248 (49%), Gaps = 29/248 (11%)

Query: 60  FQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPV 119
           F  A +RA QIAA++    +               ++ D GF      L+    P +  +
Sbjct: 75  FADAVQRARQIAAKIGGDAATTVNN----------NTPDFGFGGQKRQLEDGDQPDSKKL 124

Query: 120 SYGGYQSMGT-------------SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR 166
           +  G  S+G+             +++  +P+  VG+IIG+ GE I  +Q  SG K+Q++ 
Sbjct: 125 ASQG-DSIGSQLGPIHPPPRTSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISP 183

Query: 167 DTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMK 226
           D+      P RSV L G PE + KA+ +++D+++    G  G       G        + 
Sbjct: 184 DSGG---LPERSVSLTGAPESVQKAKMMLDDIVSRGRGGPPGQFHDNANGGQNGTVQEIM 240

Query: 227 IPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQ 286
           IP  K GLVIGKGGETIK +Q R G  +++I +     +T+ ++ ++I G   +++ A +
Sbjct: 241 IPAGKAGLVIGKGGETIKQLQERAG--VKMILIQDGSQNTNVDKPLRIIGDPYKVQQACE 298

Query: 287 LVNEVISE 294
           +V +++ E
Sbjct: 299 MVMDILRE 306

Binds to the dendritic targeting element and may play a role in mRNA trafficking. Part of a ternary complex that binds to the downstream control sequence (DCS) of the pre-mRNA. Mediates exon inclusion in transcripts that are subject to tissue-specific alternative splicing. May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly by recruiting degradation machinery to ARE-containing mRNAs.

Mus musculus (taxid: 10090)

>sp|Q99PF5|FUBP2_RAT Far upstream element-binding protein 2 OS=Rattus norvegicus GN=Khsrp PE=1 SV=1

 Score = 95.9 bits (237), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 122/248 (49%), Gaps = 29/248 (11%)

Query: 60  FQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPV 119
           F  A +RA QIAA++    +               ++ D GF      L+    P +  +
Sbjct: 75  FADAVQRARQIAAKIGGDAATTVNN----------NTPDFGFGGQKRQLEDGDQPDSKKL 124

Query: 120 SYGGYQSMGT-------------SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR 166
           +  G  S+G+             +++  +P+  VG+IIG+ GE I  +Q  SG K+Q++ 
Sbjct: 125 ASQG-DSIGSQLGPIHPPPRTSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISP 183

Query: 167 DTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMK 226
           D+      P RSV L G PE + KA+ +++D+++    G  G       G        + 
Sbjct: 184 DSGG---LPERSVSLTGAPESVQKAKMMLDDIVSRGRGGPPGQFHDNANGGQNGTVQEIM 240

Query: 227 IPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQ 286
           IP  K GLVIGKGGETIK +Q R G  +++I +     +T+ ++ ++I G   +++ A +
Sbjct: 241 IPAGKAGLVIGKGGETIKQLQERAG--VKMILIQDGSQNTNVDKPLRIIGDPYKVQQACE 298

Query: 287 LVNEVISE 294
           +V +++ E
Sbjct: 299 MVMDILRE 306

Part of a ternary complex that binds to the downstream control sequence (DCS) of the pre-mRNA. Mediates exon inclusion in transcripts that are subject to tissue-specific alternative splicing. May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly by recruiting degradation machinery to ARE-containing mRNAs (By similarity). Binds to the dendritic targeting element and may play a role in mRNA trafficking.

Rattus norvegicus (taxid: 10116)

>sp|Q96I24|FUBP3_HUMAN Far upstream element-binding protein 3 OS=Homo sapiens GN=FUBP3 PE=1 SV=2

 Score = 95.9 bits (237), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 125/241 (51%), Gaps = 29/241 (12%)

Query: 60  FQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPV 119
           F  A  R  QIAA++ +S+      P + N +   D +  G+      ++  P    +  
Sbjct: 19  FVDALHRVRQIAAKI-DSI------PHLNNSTPLVDPSVYGYG-----VQKRPLDDGVGN 66

Query: 120 SYGG--YQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTR 177
             G   +Q    +++ ++P+  VG IIG+ GE I  +Q +SG KIQ+  ++      P R
Sbjct: 67  QLGALVHQRTVITEEFKVPDKMVGFIIGRGGEQISRIQAESGCKIQIASESSG---IPER 123

Query: 178 SVELMGTPEQIAKAEQLINDVLAEAESG---GSGIVARRLTGQAGSDHFAMKIPNNKVGL 234
              L GTPE I +A++L+  ++    +G    + I        + S    + IP +KVGL
Sbjct: 124 PCVLTGTPESIEQAKRLLGQIVDRCRNGPGFHNDI-------DSNSTIQEILIPASKVGL 176

Query: 235 VIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294
           VIG+GGETIK +Q RTG  ++++ +   P  T  ++ ++I G + +++ A+++V E+I E
Sbjct: 177 VIGRGGETIKQLQERTG--VKMVMIQDGPLPTGADKPLRITGDAFKVQQAREMVLEIIRE 234

Query: 295 N 295
            
Sbjct: 235 K 235

May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression.

Homo sapiens (taxid: 9606)

>sp|Q92945|FUBP2_HUMAN Far upstream element-binding protein 2 OS=Homo sapiens GN=KHSRP PE=1 SV=4

 Score = 95.5 bits (236), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 119/244 (48%), Gaps = 19/244 (7%)

Query: 60  FQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGG----FDSAD----KGFSSPPSDLKSI 111
           F  A +RA QIAA++    +        + G GG     +  D    K  +S    + S 
Sbjct: 74  FADAVQRARQIAAKIGGDAATTVNNSTPDFGFGGQKRQLEDGDQPESKKLASQGDSISSQ 133

Query: 112 PAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEAD 171
             P   P           +++  +P+  VG+IIG+ GE I  +Q  SG K+Q++ D+   
Sbjct: 134 LGPIHPP------PRTSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGG- 186

Query: 172 LNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNK 231
              P RSV L G PE + KA+ +++D+++    G  G       G        + IP  K
Sbjct: 187 --LPERSVSLTGAPESVQKAKMMLDDIVSRGRGGPPGQFHDNANGGQNGTVQEIMIPAGK 244

Query: 232 VGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEV 291
            GLVIGKGGETIK +Q R G  +++I +     +T+ ++ ++I G   +++ A ++V ++
Sbjct: 245 AGLVIGKGGETIKQLQERAG--VKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDI 302

Query: 292 ISEN 295
           + E 
Sbjct: 303 LRER 306

Binds to the dendritic targeting element and may play a role in mRNA trafficking (By similarity). Part of a ternary complex that binds to the downstream control sequence (DCS) of the pre-mRNA. Mediates exon inclusion in transcripts that are subject to tissue-specific alternative splicing. May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly by recruiting degradation machinery to ARE-containing mRNAs.

Homo sapiens (taxid: 9606)

>sp|Q96AE4|FUBP1_HUMAN Far upstream element-binding protein 1 OS=Homo sapiens GN=FUBP1 PE=1 SV=3

 Score = 94.4 bits (233), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 86/290 (29%), Positives = 140/290 (48%), Gaps = 62/290 (21%)

Query: 46  SYNSVPPPA-----------------DEFQDFQAAKRRAEQIAARLCNSVSAEA------ 82
            Y++VPPP+                 D F+D   A +RA QIAA++              
Sbjct: 3   DYSTVPPPSSGSAGGGGGGGGGGGVNDAFKD---ALQRARQIAAKIGGDAGTSLNSNDYG 59

Query: 83  ----KRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPNI 138
               KRP +E+G    D  D    +P +D      P   P+     +S+ T ++ ++P+ 
Sbjct: 60  YGGQKRP-LEDG----DQPDAKKVAPQNDSFGTQLP---PMHQQQSRSVMT-EEYKVPDG 110

Query: 139 RVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDV 198
            VG IIG+ GE I  +Q +SG KIQ+  D+      P RS  L GTPE +  A++L++ +
Sbjct: 111 MVGFIIGRGGEQISRIQQESGCKIQIAPDSGG---LPERSCMLTGTPESVQSAKRLLDQI 167

Query: 199 LAEAE-----SGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGAR 253
           + +         G G          G+    + IP +K GLVIGKGGETIK +Q R G  
Sbjct: 168 VEKGRPAPGFHHGDG---------PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAG-- 216

Query: 254 IQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE----NRIRN 299
           ++++ +   P +T  ++ ++I G   +++ AK++V E+I +      +RN
Sbjct: 217 VKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQGGFREVRN 266

Regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. May act both as activator and repressor of transcription.

Homo sapiens (taxid: 9606)

>sp|Q32PX7|FUBP1_RAT Far upstream element-binding protein 1 OS=Rattus norvegicus GN=Fubp1 PE=1 SV=1

 Score = 92.8 bits (229), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 125/261 (47%), Gaps = 47/261 (18%)

Query: 60  FQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPV 119
           F+ A +RA QIAA++                    +S D G+      L+    P A  V
Sbjct: 27  FKDALQRARQIAAKIGGDAGTS------------LNSNDYGYGGQKRPLEDGDQPDAKKV 74

Query: 120 -----SYGGY-------QSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRD 167
                S+G         Q    +++ ++P+  VG IIG+ GE I  +Q +SG KIQ+  D
Sbjct: 75  PPQNDSFGAQLPPMHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD 134

Query: 168 TEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE-----SGGSGIVARRLTGQAGSDH 222
           +      P RS  L GTPE +  A++L++ ++ +         G G          G+  
Sbjct: 135 SGG---LPERSCMLTGTPESVQSAKRLLDQIVEKGRPAPGFHHGDG---------PGNAV 182

Query: 223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIE 282
             + IP +K GLVIGKGGETIK +Q R G  ++++ +   P +T  ++ ++I G   +++
Sbjct: 183 QEIMIPASKAGLVIGKGGETIKQLQERAG--VKMVMIQDGPQNTGADKPLRITGDPYKVQ 240

Query: 283 SAKQLVNEVISE----NRIRN 299
            AK++V E+I +      +RN
Sbjct: 241 QAKEMVLELIRDQGGFREVRN 261

Regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. May act both as activator and repressor of transcription.

Rattus norvegicus (taxid: 10116)

>sp|Q91WJ8|FUBP1_MOUSE Far upstream element-binding protein 1 OS=Mus musculus GN=Fubp1 PE=1 SV=1

 Score = 91.7 bits (226), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 78/262 (29%), Positives = 124/262 (47%), Gaps = 48/262 (18%)

Query: 60  FQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPV 119
           F+ A +RA QIAA++                    +S D G+      L+    P A  V
Sbjct: 27  FKDALQRARQIAAKIGGDAGTS------------LNSNDYGYGGQKRPLEDGDQPDAKKV 74

Query: 120 -----SYGG-----YQSMGTSKKIE---IPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR 166
                S+G      +Q    S   E   +P+  VG IIG+ GE I  +Q +SG KIQ+  
Sbjct: 75  PPQNDSFGAQLPPMHQQQSRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAP 134

Query: 167 DTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE-----SGGSGIVARRLTGQAGSD 221
           D+      P RS  L GTPE +  A++L++ ++ +         G G          G+ 
Sbjct: 135 DSGG---LPERSCMLTGTPESVQSAKRLLDQIVEKGRPAPGFHHGDG---------PGNA 182

Query: 222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQI 281
              + IP +K GLVIGKGGETIK +Q R G  ++++ +   P +T  ++ ++I G   ++
Sbjct: 183 VQEIMIPASKAGLVIGKGGETIKQLQERAG--VKMVMIQDGPQNTGADKPLRITGDPYKV 240

Query: 282 ESAKQLVNEVISE----NRIRN 299
           + AK++V E+I +      +RN
Sbjct: 241 QQAKEMVLELIRDQGGFREVRN 262

Regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. May act both as activator and repressor of transcription.

Mus musculus (taxid: 10090)

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

 Score = 69.3 bits (168), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 52/154 (33%), Positives = 78/154 (50%), Gaps = 20/154 (12%)

Query: 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL 199
           VG IIGK GE++K ++ +SGA+I ++       N P R + L G    I KA  +I D L
Sbjct: 25  VGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKL 79

Query: 200 AEAESGGSGIVARRLTGQAGSDH----FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQ 255
            E        ++  +T    +        + +P ++ G +IGKGG  IK ++  TGA++Q
Sbjct: 80  EED-------ISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQ 132

Query: 256 VIPLHLPPGDTSTERTVQIDGTSEQ-IESAKQLV 288
           V    LP    STER + I G  +  IE  KQ+ 
Sbjct: 133 VAGDMLP---NSTERAITIAGIPQSIIECVKQIC 163

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

Mus musculus (taxid: 10090)

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

 Score = 69.3 bits (168), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 52/154 (33%), Positives = 78/154 (50%), Gaps = 20/154 (12%)

Query: 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL 199
           VG IIGK GE++K ++ +SGA+I ++       N P R + L G    I KA  +I D L
Sbjct: 25  VGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKL 79

Query: 200 AEAESGGSGIVARRLTGQAGSDH----FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQ 255
            E        ++  +T    +        + +P ++ G +IGKGG  IK ++  TGA++Q
Sbjct: 80  EED-------ISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQ 132

Query: 256 VIPLHLPPGDTSTERTVQIDGTSEQ-IESAKQLV 288
           V    LP    STER + I G  +  IE  KQ+ 
Sbjct: 133 VAGDMLP---NSTERAITIAGIPQSIIECVKQIC 163

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	669
225429462	690	PREDICTED: uncharacterized protein LOC10	0.976	0.946	0.711	0.0
449450341	694	PREDICTED: uncharacterized protein LOC10	0.931	0.897	0.634	0.0
356552330	670	PREDICTED: uncharacterized protein LOC10	0.944	0.943	0.628	0.0
356564071	672	PREDICTED: uncharacterized protein LOC10	0.944	0.940	0.631	0.0
296081618	479	unnamed protein product [Vitis vinifera]	0.686	0.958	0.715	1e-172
357437527	605	Far upstream element-binding protein [Me	0.868	0.960	0.578	1e-168
357465709	605	Far upstream element-binding protein [Me	0.875	0.968	0.550	1e-159
357465707	1145	Far upstream element-binding protein [Me	0.859	0.502	0.548	1e-158
356514579	554	PREDICTED: uncharacterized protein LOC10	0.781	0.944	0.554	1e-151
297825693	634	hypothetical protein ARALYDRAFT_481452 [	0.847	0.894	0.593	1e-140

>gi|225429462|ref|XP_002278761.1| PREDICTED: uncharacterized protein LOC100259454 [Vitis vinifera]

 Score =  795 bits (2052), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 502/706 (71%), Positives = 550/706 (77%), Gaps = 53/706 (7%)

Query: 1   MADEPQYSS--DGTPSKRKYEDQTTPPSAAARRPTGFSAP------DPAVAPTSYNSVPP 52
           MA+E QYSS  D T +KRKYEDQTTP   + RRPTGFSAP      D + AP SYNSVPP
Sbjct: 1   MAEEVQYSSGTDAT-NKRKYEDQTTPSQPSTRRPTGFSAPISTPSPDSSHAPPSYNSVPP 59

Query: 53  PADEFQDFQAAKRRAEQIAARL-CNSVSAEAKRPRVENGSG--GFDSADKGFSSPPSDLK 109
           PADE Q    AK+RA++IAARL  N+ + EAKRPRVENG+G  GFDS DKGFSS PSD+ 
Sbjct: 60  PADEIQ---LAKQRAQEIAARLFSNASNTEAKRPRVENGAGAGGFDSGDKGFSSAPSDVG 116

Query: 110 SIP---APSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR 166
             P    PSAIPVSYG YQ  GTSKKI+IPN RVGVIIGK GETIKYLQLQSGAKIQVTR
Sbjct: 117 QKPMISTPSAIPVSYG-YQ--GTSKKIDIPNGRVGVIIGKGGETIKYLQLQSGAKIQVTR 173

Query: 167 DTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMK 226
           D +AD NSPTR VELMGTP+QIAKAEQLINDVL+EAE+GGSGIV+RRLTGQAGS+ F MK
Sbjct: 174 DMDADPNSPTRLVELMGTPDQIAKAEQLINDVLSEAEAGGSGIVSRRLTGQAGSEQFVMK 233

Query: 227 IPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQ 286
           +PNNKVGL+IGKGGETIKNMQARTGARIQVIPLHLPPGDTS ERTVQIDGTSEQIESAKQ
Sbjct: 234 VPNNKVGLIIGKGGETIKNMQARTGARIQVIPLHLPPGDTSMERTVQIDGTSEQIESAKQ 293

Query: 287 LVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGT-PGAPSMQQPGYGYVQPGAYPGQTP 345
           LVNEVISENRIRNPAMAGGY QQGYQARPP+ WG  PGAP MQQPGY Y QPG+YPG +P
Sbjct: 294 LVNEVISENRIRNPAMAGGYPQQGYQARPPSGWGAPPGAPPMQQPGYSYAQPGSYPGPSP 353

Query: 346 QYNMSQPPYGGYPSQPTPGGYPGNWDQT---PTQQTSQGSGYDYYSQQPSSQQPQAPGGS 402
           QYNMSQP Y GY SQP   G    WDQT   P+QQT+ GSGYDYY QQ + QQ QA GG 
Sbjct: 354 QYNMSQPAYAGY-SQPNATG----WDQTAAPPSQQTTPGSGYDYYGQQQTQQQQQAHGGP 408

Query: 403 AAPADSTGYSYSQPPASGYNQQGQGYAQDSY-GGYH--APQSGYGQAAP---YDQQQGYN 456
           + PAD++GY+Y+QPPASGYNQQGQGY QD Y GGYH  APQ GYGQ  P   YDQQQGYN
Sbjct: 409 SGPADNSGYNYNQPPASGYNQQGQGYPQDGYGGGYHAPAPQPGYGQPQPIPGYDQQQGYN 468

Query: 457 SAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQ 516
           SA GYGNV N +QEGHT SYGAQG++ QAPP VQ S A+GQQGY T QQPSP+ ASYPPQ
Sbjct: 469 SATGYGNVANPTQEGHTTSYGAQGETGQAPPSVQPS-AIGQQGYNT-QQPSPSPASYPPQ 526

Query: 517 GATQPSYGVPPTSQSGYGSQVPPQSGY-AGYGMPQAQKPLANPPAYGQTQQSPGSAGGYG 575
           G+ QP+YG+PPTSQ+G+GSQ P QSGY   YG PQAQK  ANPP YGQTQQSP + GGY 
Sbjct: 527 GSNQPAYGMPPTSQTGFGSQPPAQSGYTTNYGPPQAQKAPANPPVYGQTQQSPSAQGGYA 586

Query: 576 -----QPGYSHSQPPP--SSYAQPDSGSQRAPPSNYG-AATQPGYGSAAYGAPPGGSQAG 627
                QPGY HSQ PP  S YAQ DS SQRA PS+YG AA QPGYG  +  + P  +QAG
Sbjct: 587 QPAPVQPGYPHSQQPPAQSGYAQTDSSSQRAAPSSYGTAAGQPGYGGPSAYSAPTVTQAG 646

Query: 628 YGQGPPSYYGGGYSQ---PVYTADGNAAPAAQPVQQGGVTK-SPQS 669
           YGQ PP     G      P+Y AD  A P +QP QQ GV K SPQS
Sbjct: 647 YGQQPPYSGSYGGGYSQPPMYAAD--ATPTSQPAQQSGVAKTSPQS 690

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449450341|ref|XP_004142921.1| PREDICTED: uncharacterized protein LOC101216803 [Cucumis sativus] gi|449494409|ref|XP_004159539.1| PREDICTED: uncharacterized LOC101216803 [Cucumis sativus]

 Score =  691 bits (1782), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 446/703 (63%), Positives = 499/703 (70%), Gaps = 80/703 (11%)

Query: 1   MADEPQYSS--DGTPSKRKYEDQTTPPSAAARRPTGFSAPDPAVAPTS-----YNSVPPP 53
           MADE QYSS  D   +KRKY+DQ  P     RRPTGFS P    +P+S     YN+VPPP
Sbjct: 1   MADEAQYSSATDTPSNKRKYDDQPPP-----RRPTGFSGP--ITSPSSDSAPSYNNVPPP 53

Query: 54  ADEFQDFQAAKRRAEQIAARLCNS-----------VSAEAKRPRVENGSGGFDSADKGFS 102
            DE Q    AK+RA++IA+RL  S           V A+ KRPRVENG GG+DS DKGFS
Sbjct: 54  MDEIQ---LAKQRAQEIASRLIISSGGVGAGAGPGVGADVKRPRVENG-GGYDSYDKGFS 109

Query: 103 SPPSDLK---SIPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSG 159
           S P DLK   S  APSAIP+SYG     G+SKKIEIPN RVGVIIGK GETIKYLQLQSG
Sbjct: 110 SGP-DLKPHMSNSAPSAIPISYG---FQGSSKKIEIPNGRVGVIIGKGGETIKYLQLQSG 165

Query: 160 AKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAG 219
           AKIQVTRD +AD NS TR VELMGTP+QIAKAEQLINDVL+EAESGGSGIV+RRLTG +G
Sbjct: 166 AKIQVTRDMDADPNSTTRMVELMGTPDQIAKAEQLINDVLSEAESGGSGIVSRRLTGPSG 225

Query: 220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSE 279
           S+ F MKIPNNKVGLVIGKGGETIK+MQARTGARIQVIPLHLPPGDTSTERT+QIDG+SE
Sbjct: 226 SEQFVMKIPNNKVGLVIGKGGETIKSMQARTGARIQVIPLHLPPGDTSTERTLQIDGSSE 285

Query: 280 QIESAKQLVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGA 339
           QIESAKQLVNEVISENR RN  M+GGY+QQGYQARPP+SWG PGAP MQQP YGY Q G 
Sbjct: 286 QIESAKQLVNEVISENRARNSGMSGGYNQQGYQARPPSSWGPPGAPPMQQPNYGYGQQGG 345

Query: 340 YPGQTPQYNMSQPPYGGYPSQPTPGGYPGNWDQT---PTQQTSQGSGYDYYSQQPSSQQP 396
           Y   + QYN+SQPPY GY SQP  GGY  NWDQ+   P Q  +QGSGYDYY QQ   QQ 
Sbjct: 346 YSAPSSQYNISQPPYQGY-SQPASGGYASNWDQSTVPPNQPATQGSGYDYYGQQAPQQQQ 404

Query: 397 QAPGGSAAPADSTGYSYSQPPASGYNQQGQGYAQDSYGG-YHAPQSGYGQAAPYDQQQGY 455
            A GG  A  D++GYSY QPPA+ YNQ  QGY+QD YGG YHAPQSGYGQ   YD QQGY
Sbjct: 405 TA-GGPGATGDNSGYSYGQPPATTYNQ--QGYSQDGYGGNYHAPQSGYGQPPTYD-QQGY 460

Query: 456 NSAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQ-SSAAMGQQGYGTGQQPSPNTASYP 514
           +S   YGNV N +Q+G   SYG+QGDS+Q  PP     +++ QQGY   QQPSPN  SY 
Sbjct: 461 SSTTNYGNVANATQDGLN-SYGSQGDSSQTVPPAAPQPSSVSQQGYSANQQPSPNPGSY- 518

Query: 515 PQGATQPSYGVPPTSQSGYGSQVPPQSGYAG-----------YGMPQAQK-PLANPPAYG 562
                      PP SQSGYG   P Q+GY             YG PQ QK P  NPPAYG
Sbjct: 519 -----------PPPSQSGYGMTAPSQTGYGNQPAAQAAYGAAYGAPQTQKQPPTNPPAYG 567

Query: 563 QTQQSPGSAGGYGQP-----GYSHSQPPPSSYAQPDSGSQRAPPSNYG-AATQPGYGSAA 616
           Q+ QSP +A GYGQP     GYS +QPP S Y QPDS SQRAPPS+YG AA QPG+    
Sbjct: 568 QSTQSPSTASGYGQPAGLPSGYSSTQPPASGYTQPDSASQRAPPSSYGTAAAQPGFAPPP 627

Query: 617 YGAPPGGSQAGYGQGPPSY---YGGGYSQPVYTADGNAAPAAQ 656
           YG  P  +Q+ YGQ PP Y   YG GY QP Y+++GNA  A +
Sbjct: 628 YGGAPPTNQSAYGQAPPPYGGSYGAGYPQPHYSSEGNAGGATR 670

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552330|ref|XP_003544521.1| PREDICTED: uncharacterized protein LOC100813135 [Glycine max]

 Score =  680 bits (1754), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 444/707 (62%), Positives = 499/707 (70%), Gaps = 75/707 (10%)

Query: 1   MADEPQYSS--DGTPS----KRKYEDQTTPPSAAARRPTGFSAPDPAVAPT--SYNSVPP 52
           MADE QYS+  D  P+    KRKY D          RPTGFS    +VAP   SYNSVPP
Sbjct: 1   MADESQYSANPDSIPTPPSLKRKYNDD---------RPTGFSDGPDSVAPPPPSYNSVPP 51

Query: 53  PADEFQDFQAAKRRAEQIAARLCNSV--SAEAKRPRVENGSGGFDSADKGFSSPPSDLKS 110
           P+    DF+ AK+RA+++AARL +        KRP+ +N    FDS D      P  + S
Sbjct: 52  PSSAASDFELAKQRAQEVAARLLSGAPPLDPTKRPKHDNNGSSFDSIDVN----PYSVPS 107

Query: 111 IPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEA 170
           I +PSA+  S+   Q  G SKKI+IPN RVGVIIGK GETIKYLQLQSGAKIQVTRD +A
Sbjct: 108 I-SPSAVSYSH---QVGGASKKIDIPNGRVGVIIGKGGETIKYLQLQSGAKIQVTRDMDA 163

Query: 171 DLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNN 230
           D NS TR+VELMG+P+ IA AE+LIN+VLAEAE+GGSGI+ARR+ GQAGSD +  KIPNN
Sbjct: 164 DPNSATRTVELMGSPDAIATAEKLINEVLAEAETGGSGIIARRVAGQAGSDEYVSKIPNN 223

Query: 231 KVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNE 290
           KVGLVIGKGGETIKNMQA TGARIQVIPLHLPPGDTSTERT++I+GT EQIESAKQ+VN+
Sbjct: 224 KVGLVIGKGGETIKNMQASTGARIQVIPLHLPPGDTSTERTLKIEGTPEQIESAKQMVNQ 283

Query: 291 VIS-ENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNM 349
           VIS ENR RNPAM+GGYSQQGYQARPPTSWG P AP MQQ GYGYVQPGAY G  PQYNM
Sbjct: 284 VISGENRHRNPAMSGGYSQQGYQARPPTSWGPPAAP-MQQSGYGYVQPGAYSG-PPQYNM 341

Query: 350 SQPPYGGYPSQPTPGGYPGNWDQ-TPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADS 408
            Q  Y GYP Q + G    NWDQ T  QQ S  +GYDYYSQQ            A  +D 
Sbjct: 342 PQQQYAGYPPQSSGGYSATNWDQSTAPQQQSTHAGYDYYSQQQQQN-------PAPSSDG 394

Query: 409 TGYSYSQPPASGYNQQGQGYAQDSYGGYHA-PQSGYGQAAPYDQQQGYNSAAGYGNVNNT 467
           T Y+YSQPP+SGYNQ GQGYAQD YGGYHA PQ GYGQ   YDQQQGY+SA  YG  +N 
Sbjct: 395 TAYNYSQPPSSGYNQPGQGYAQDGYGGYHAPPQLGYGQPPSYDQQQGYSSAPSYG--SNP 452

Query: 468 SQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPP 527
           +QEGHT +YG+QGDSTQAPP     A    QGYGT QQPSPN A+YPPQ   QP YGVPP
Sbjct: 453 AQEGHTANYGSQGDSTQAPP-----AQPPSQGYGTSQQPSPNAANYPPQ--AQPGYGVPP 505

Query: 528 TSQ-SGYGSQVPPQSGY-AGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGY------ 579
           TSQ + YGSQ P QSGY +GYG PQ QKP   PP YGQ+ QSP +AGGYGQ G+      
Sbjct: 506 TSQPAAYGSQPPAQSGYGSGYGPPQTQKPSGTPPVYGQS-QSPNTAGGYGQSGHLQSGYP 564

Query: 580 SHSQPPPSSYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSY---- 635
               PP   YAQP+SGSQ+APPS YG A QPGYG  +YG  P G Q GYGQ PPSY    
Sbjct: 565 PSQPPPSGGYAQPESGSQKAPPSGYGGAVQPGYGPPSYGGVPAGGQPGYGQAPPSYSNSS 624

Query: 636 YG-GGYSQ-PVYTADGNA----------APAAQPVQQGGVTK-SPQS 669
           YG GGY+Q PVY++DGNA          AP AQ VQQ  V K SPQS
Sbjct: 625 YGAGGYAQPPVYSSDGNAGGTTRGTYDGAP-AQAVQQASVAKTSPQS 670

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356564071|ref|XP_003550280.1| PREDICTED: uncharacterized protein LOC100782717 [Glycine max]

 Score =  669 bits (1726), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 446/706 (63%), Positives = 503/706 (71%), Gaps = 74/706 (10%)

Query: 1   MADEPQYSS--DGTPS----KRKYEDQTTPPSAAARRPTGFS--APDPAVAPTSYNSVPP 52
           MADE QYS+  D TP+    KRKY D          RPTGFS      A  P SYN+VPP
Sbjct: 1   MADESQYSANPDSTPTPPSLKRKYNDD--------HRPTGFSDGPDPAAPPPPSYNNVPP 52

Query: 53  PADEFQDFQAAKRRAEQIAARLCNSVSAE--AKRPRVENGSGGFDSAD-KGFSSPPSDLK 109
           P+    DF+ AK+RA+++AARL +  +     KRP+ +N    FDS D KG    P  + 
Sbjct: 53  PSSAASDFELAKQRAQEVAARLLSGAAPLDPTKRPKHDNNGSSFDSIDVKG----PYSVP 108

Query: 110 SIPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTE 169
           SI +PSA+  SY   Q  G SKKI+IPN RVGVIIGK GETIKYLQLQSGAKIQVTRD +
Sbjct: 109 SI-SPSAVSYSY---QGGGASKKIDIPNGRVGVIIGKGGETIKYLQLQSGAKIQVTRDMD 164

Query: 170 ADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPN 229
           AD NS TR+VELMG+P+ IA AE+LIN+VLAEAE+GGSGIVARR+ GQAGSD +  KIPN
Sbjct: 165 ADPNSATRTVELMGSPDAIATAEKLINEVLAEAETGGSGIVARRVAGQAGSDEYVSKIPN 224

Query: 230 NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVN 289
           NKVGLVIGKGGETIKNMQA TGARIQVIPLHLPPGDTSTERT++I+GT EQIESAKQ+VN
Sbjct: 225 NKVGLVIGKGGETIKNMQASTGARIQVIPLHLPPGDTSTERTLKIEGTPEQIESAKQMVN 284

Query: 290 EVIS-ENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYN 348
           +VIS ENR RNP+M+GGYSQQGYQARPPTSWG P AP MQQ GYGYVQPGAY G  PQYN
Sbjct: 285 QVISGENRQRNPSMSGGYSQQGYQARPPTSWGPPAAP-MQQSGYGYVQPGAYSG-PPQYN 342

Query: 349 MSQPPYGGYPSQPTPGGYPGNWDQ-TPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPAD 407
           + Q PY GYP Q + G    NWDQ T  QQ S  +GYDYYSQQ   Q P      A P+D
Sbjct: 343 VPQQPYAGYPPQSSGGYSAANWDQSTAPQQQSAHAGYDYYSQQQQQQNP------APPSD 396

Query: 408 STGYSYSQPPASGYNQQGQGYAQDSYGGYHA-PQSGYGQAAPYDQQQGYNSAAGYGNVNN 466
            T Y+YSQPP+SGY+Q GQGYAQD YGGYHA PQSGYGQ   YDQQQGY+SAA YG  +N
Sbjct: 397 GTAYNYSQPPSSGYSQPGQGYAQDGYGGYHAPPQSGYGQPPSYDQQQGYSSAASYG--SN 454

Query: 467 TSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVP 526
            + EGHT +YG+QGDSTQAPP     A    QGYGTGQQPSPN A+Y PQ   QP YGVP
Sbjct: 455 PAPEGHTANYGSQGDSTQAPP-----AQPPSQGYGTGQQPSPNAANYAPQ--AQPGYGVP 507

Query: 527 PTSQ-SGYGSQVPPQSGY-AGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGY----- 579
           PTSQ + YGSQ P QSGY +GYG PQ QKP   PP YGQ+ QSP +AGGYGQ G+     
Sbjct: 508 PTSQPATYGSQPPAQSGYGSGYGPPQTQKPSGTPPVYGQS-QSPNTAGGYGQSGHLQSGY 566

Query: 580 -SHSQPPPSSYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSY--- 635
                PP   YAQP+SGSQ+APPS YG A QPGYG  +YG  P G Q GYGQ PPSY   
Sbjct: 567 PPSQPPPSGGYAQPESGSQKAPPSGYGGAVQPGYGPPSYGGAPAGGQPGYGQAPPSYSNS 626

Query: 636 -YG-GGYSQ-PVYTADGNA----------APAAQPVQQGGVTKSPQ 668
            YG  GY+Q PVY++DGN           AP AQPVQQ   T SPQ
Sbjct: 627 SYGAAGYAQPPVYSSDGNVGGTTRGAYDGAP-AQPVQQAAKT-SPQ 670

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296081618|emb|CBI20623.3| unnamed protein product [Vitis vinifera]

 Score =  613 bits (1581), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 365/510 (71%), Positives = 401/510 (78%), Gaps = 51/510 (10%)

Query: 1   MADEPQYSS--DGTPSKRKYEDQTTPPSAAARRPTGFSAP------DPAVAPTSYNSVPP 52
           MA+E QYSS  D T +KRKYEDQTTP   + RRPTGFSAP      D + AP SYNSVPP
Sbjct: 1   MAEEVQYSSGTDAT-NKRKYEDQTTPSQPSTRRPTGFSAPISTPSPDSSHAPPSYNSVPP 59

Query: 53  PADEFQDFQAAKRRAEQIAARL-CNSVSAEAKRPRVENGSG--GFDSADKGFSSPPSDLK 109
           PADE Q    AK+RA++IAARL  N+ + EAKRPRVENG+G  GFDS DKGFSS PSD+ 
Sbjct: 60  PADEIQ---LAKQRAQEIAARLFSNASNTEAKRPRVENGAGAGGFDSGDKGFSSAPSDVG 116

Query: 110 ---SIPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR 166
               I  PSAIPVSYG YQ  GTSKKI+IPN RVGVIIGK GETIKYLQLQSGAKIQVTR
Sbjct: 117 QKPMISTPSAIPVSYG-YQ--GTSKKIDIPNGRVGVIIGKGGETIKYLQLQSGAKIQVTR 173

Query: 167 DTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMK 226
           D +AD NSPTR VELMGTP+QIAKAEQLINDVL+EAE+GGSGIV+RRLTGQAGS+ F MK
Sbjct: 174 DMDADPNSPTRLVELMGTPDQIAKAEQLINDVLSEAEAGGSGIVSRRLTGQAGSEQFVMK 233

Query: 227 IPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQ 286
           +PNNKVGL+IGKGGETIKNMQARTGARIQVIPLHLPPGDTS ERTVQIDGTSEQIESAKQ
Sbjct: 234 VPNNKVGLIIGKGGETIKNMQARTGARIQVIPLHLPPGDTSMERTVQIDGTSEQIESAKQ 293

Query: 287 LVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGT-PGAPSMQQPGYGYVQPGAYPGQTP 345
           LVNEVISENRIRNPAMAGGY QQGYQARPP+ WG  PGAP MQQPGY Y QPG+YPG +P
Sbjct: 294 LVNEVISENRIRNPAMAGGYPQQGYQARPPSGWGAPPGAPPMQQPGYSYAQPGSYPGPSP 353

Query: 346 QYNMSQPPYGGYPSQPTPGGYPGNWDQT---PTQQTSQGSGYDYYSQQPSSQQPQAPGGS 402
           QYNMSQP Y GY SQP   G    WDQT   P+QQT+ GSGYDYY QQ + QQ QA GG 
Sbjct: 354 QYNMSQPAYAGY-SQPNATG----WDQTAAPPSQQTTPGSGYDYYGQQQTQQQQQAHGGP 408

Query: 403 AAPADSTGYSYSQPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYG 462
           + PAD++GY+Y+QPPASGYNQ                     Q   YDQQQGYNSA GYG
Sbjct: 409 SGPADNSGYNYNQPPASGYNQ---------------------QGQGYDQQQGYNSATGYG 447

Query: 463 NVNNTSQEGHTPSYGAQGDSTQAPPPVQSS 492
           NV N +QEGHT SYGAQG++ QAPP + +S
Sbjct: 448 NVANPTQEGHTTSYGAQGETGQAPPSLSTS 477

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357437527|ref|XP_003589039.1| Far upstream element-binding protein [Medicago truncatula] gi|355478087|gb|AES59290.1| Far upstream element-binding protein [Medicago truncatula]

 Score =  599 bits (1544), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 401/693 (57%), Positives = 455/693 (65%), Gaps = 112/693 (16%)

Query: 1   MADEPQYSSDGTPSKRKYEDQTTPPSAAARRPTGFSAPDPAVAPTSYNSVPPPADEFQDF 60
           MADE QY S     KRKY++Q  P S    R TGFS   P   P SYN+VPPPA    DF
Sbjct: 1   MADESQYDSTPPSLKRKYDEQPPPHS----RTTGFSDGPP---PPSYNNVPPPATA--DF 51

Query: 61  QAAKRRAEQIAARLCNSVSA---EAKRPRVENGSGG-FDSADKGFSSPPSDLKSIPAPSA 116
           +  K+RA+Q+AARL +  +A     KR + +NG    +DS         SDLKS     A
Sbjct: 52  ELIKQRAQQVAARLLSGAAAPSDVVKRTKFDNGPPSPYDS---------SDLKSQ---YA 99

Query: 117 IPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPT 176
            P+S   Y   G+SKKIEIPN RVGVIIGK GETIKYLQLQSGAKIQVTRD +AD NSP 
Sbjct: 100 APMSIPSYSHQGSSKKIEIPNGRVGVIIGKGGETIKYLQLQSGAKIQVTRDMDADPNSPN 159

Query: 177 RSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVI 236
           R VEL GT + IA AE+LI +VLAEAESGG+G+V RR+TGQ G+D F+MKIPNNKVGL+I
Sbjct: 160 RLVELTGTSDAIATAEKLIKEVLAEAESGGNGLVTRRMTGQGGADEFSMKIPNNKVGLII 219

Query: 237 GKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVIS-EN 295
           GKGGETIK+MQA TGARIQVIPLHLPPGDTSTERT++I+GTSEQIESAKQLV+ ++S EN
Sbjct: 220 GKGGETIKSMQATTGARIQVIPLHLPPGDTSTERTLKIEGTSEQIESAKQLVDSILSGEN 279

Query: 296 RIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYG 355
           R+RNP+M+GGYSQQGYQARPP+SW  P A   QQPGYGY QPGAYPG TPQYN+ Q  Y 
Sbjct: 280 RLRNPSMSGGYSQQGYQARPPSSWAPPAA--SQQPGYGYAQPGAYPGPTPQYNVPQQAYA 337

Query: 356 GYPSQPTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQ 415
           GYP   + GGY  NWDQ+    T+Q S YDYY+QQP   Q     G A PAD T Y+YSQ
Sbjct: 338 GYPPH-SAGGYSTNWDQSTA--TTQQSTYDYYNQQPQQPQNPG--GPAPPADGTAYNYSQ 392

Query: 416 PPASGYNQQGQGYAQDSYGGYHA-PQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTP 474
           PP++GYNQ GQGY+QD YG Y   PQSGY Q   YDQQQGY SA          QEG T 
Sbjct: 393 PPSAGYNQPGQGYSQDGYGAYQQPPQSGYAQPTSYDQQQGYGSA----------QEGQTT 442

Query: 475 S-YGA--QGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPTSQS 531
           + YG+  QGD+TQ  PPVQ S    QQGYG+ QQPSPN A YPPQGA QPSYGVPPTSQ+
Sbjct: 443 TNYGSQGQGDATQV-PPVQPS----QQGYGSSQQPSPNAAKYPPQGAAQPSYGVPPTSQT 497

Query: 532 GYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQ 591
            YGSQ   QS   GYG PQ QKP   PPAYGQ+ QSP +AGGYG        P PS Y+Q
Sbjct: 498 AYGSQPQTQS---GYGPPQTQKPSGTPPAYGQS-QSPNAAGGYG-------HPLPSGYSQ 546

Query: 592 PDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSY----YGGGYSQ-PVYT 646
           P                                  GYGQ P SY    YG GY Q P Y+
Sbjct: 547 P----------------------------------GYGQAPQSYNSGSYGAGYPQAPAYS 572

Query: 647 ADGNAA----------PAAQPVQQGGVTKSPQS 669
           ADGNA+            AQ  QQ  V KSPQS
Sbjct: 573 ADGNASGNARGGSYDGAPAQGAQQASVAKSPQS 605

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357465709|ref|XP_003603139.1| Far upstream element-binding protein [Medicago truncatula] gi|355492187|gb|AES73390.1| Far upstream element-binding protein [Medicago truncatula]

 Score =  567 bits (1462), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 379/688 (55%), Positives = 452/688 (65%), Gaps = 102/688 (14%)

Query: 1   MADEPQYSSDGTPSKRKYEDQTTPPSAAARRPTGFSAPDPAVAPTSYNSVPPPADEFQDF 60
           MA+E QY++     KRKY+DQ                             P   D   + 
Sbjct: 1   MAEEAQYAT----LKRKYDDQ-----------------------------PTATDIELEV 27

Query: 61  QAAKRRAEQIAARLCNS-----VSAEAKRPRVENGS--GGFDSADKGFSSPPSDLKSIPA 113
             AK+RA+++AARL +      +S + KR + +NG+   GFDS D         LK  P 
Sbjct: 28  ANAKQRAQEVAARLLSVTGAPPLSYDPKRTKSDNGAPQSGFDSYD---------LK--PQ 76

Query: 114 PSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLN 173
            S    SYG      +SKKIEIPN RVGV+IGK GETIKYLQ+QSGAKIQVTRD +AD N
Sbjct: 77  YSQQGGSYG------SSKKIEIPNGRVGVLIGKGGETIKYLQMQSGAKIQVTRDMDADPN 130

Query: 174 SPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVG 233
           S TR VELMGTP+ ++ AE+LIN+VLAEAE+G S    RR+  Q+G D F M+IPNNKVG
Sbjct: 131 SQTRMVELMGTPDAVSSAEKLINEVLAEAEAGASVGGTRRMVAQSGGDEFVMQIPNNKVG 190

Query: 234 LVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVIS 293
           L+IGKGGETIK MQA TGARIQVIPLH PPGDTSTERT++IDGT +QIESAKQLVN++++
Sbjct: 191 LIIGKGGETIKGMQASTGARIQVIPLHPPPGDTSTERTLKIDGTPDQIESAKQLVNQILT 250

Query: 294 -ENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQP 352
            ENR+RN   +GGY+QQGYQ+RPP+SW  P AP +QQ GYGY QPG+Y G +PQYN  QP
Sbjct: 251 GENRLRNSGNSGGYTQQGYQSRPPSSWAPPAAP-VQQAGYGYGQPGSYSGPSPQYNTPQP 309

Query: 353 PYGGYPSQPTPGGYPGNWDQTPT---QQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADST 409
           PY GYP Q  PGGY  NWDQ+     QQ++  SGYDYY+QQP  QQ     G + PAD +
Sbjct: 310 PYTGYPPQ-QPGGYSANWDQSTAPSHQQSTHASGYDYYNQQPQQQQNPG--GPSQPADGS 366

Query: 410 GYSYSQPPASGYNQQGQGYAQDSYGGYHA-PQSGYGQAAPYDQQQGYNSAAGYGNVNNTS 468
            YSYSQPP+SGY+Q GQGY Q+SYG Y+A  QSGYGQ   YDQQQGY SA  YG+ +N +
Sbjct: 367 AYSYSQPPSSGYSQPGQGYGQESYGAYNAQQQSGYGQPQTYDQQQGYGSAPSYGSGSNPT 426

Query: 469 QEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPT 528
           QEGHT +YG+Q D++Q   P      + QQGY T QQ +P           QP Y V PT
Sbjct: 427 QEGHTSNYGSQADTSQTSQPT----TVAQQGYATNQQGTP-----------QPGYAVAPT 471

Query: 529 SQSGYGSQVPPQSGY-AGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPS 587
           SQ+ YGSQ  PQSGY  GYG P +QKP ANPP YGQ+ QSP +A GYGQ  Y  SQ PPS
Sbjct: 472 SQATYGSQ--PQSGYGTGYGAPPSQKPSANPPVYGQS-QSPSTAAGYGQSAYPSSQAPPS 528

Query: 588 SYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSY----YGGGYSQ- 642
            YAQP+ G+QRAP        QPGYG  +YGAP GG Q  YGQ P SY    YG GY+Q 
Sbjct: 529 GYAQPELGTQRAP-------VQPGYGPQSYGAPQGG-QPSYGQTPASYGNSSYGAGYAQA 580

Query: 643 PVYTADGNAAPAAQPVQQGGVTK-SPQS 669
           P Y +DG     AQ V QGGV K SP+S
Sbjct: 581 PAYASDGA---TAQAVPQGGVAKVSPKS 605

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357465707|ref|XP_003603138.1| Far upstream element-binding protein [Medicago truncatula] gi|355492186|gb|AES73389.1| Far upstream element-binding protein [Medicago truncatula]

 Score =  565 bits (1456), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 369/673 (54%), Positives = 442/673 (65%), Gaps = 98/673 (14%)

Query: 1   MADEPQYSSDGTPSKRKYEDQTTPPSAAARRPTGFSAPDPAVAPTSYNSVPPPADEFQDF 60
           MA+E QY++     KRKY+DQ                             P   D   + 
Sbjct: 1   MAEEAQYAT----LKRKYDDQ-----------------------------PTATDIELEV 27

Query: 61  QAAKRRAEQIAARLCNS-----VSAEAKRPRVENGS--GGFDSADKGFSSPPSDLKSIPA 113
             AK+RA+++AARL +      +S + KR + +NG+   GFDS D         LK  P 
Sbjct: 28  ANAKQRAQEVAARLLSVTGAPPLSYDPKRTKSDNGAPHSGFDSYD---------LK--PQ 76

Query: 114 PSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLN 173
            S      GG  S G+SKKIEIPN RVGV+IGK GETIKYLQ+QSGAKIQVTRD +AD N
Sbjct: 77  YS----QQGG--SYGSSKKIEIPNGRVGVLIGKGGETIKYLQMQSGAKIQVTRDMDADPN 130

Query: 174 SPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVG 233
           S TR VELMGTP+ ++ AE+LIN+VLAEAE+G SG   RR+  Q+G D F M+IPNNKVG
Sbjct: 131 SQTRMVELMGTPDAVSSAEKLINEVLAEAEAGASGGGTRRMVAQSGGDEFVMQIPNNKVG 190

Query: 234 LVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVIS 293
           L+IGKGGETIK+MQA TGARIQVIPLH PPGDTSTERT++IDGT +QIESAKQLVN++++
Sbjct: 191 LIIGKGGETIKSMQASTGARIQVIPLHPPPGDTSTERTLKIDGTPDQIESAKQLVNQILT 250

Query: 294 -ENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQP 352
            ENR+RN   +GGY+QQGYQ+RPP+S   P    +QQ GYGY QPG+Y G +PQYNM QP
Sbjct: 251 GENRLRNSGNSGGYTQQGYQSRPPSS-WAPPPAPVQQAGYGYGQPGSYSGPSPQYNMPQP 309

Query: 353 PYGGYPSQPTPGGYPGNWDQTPT---QQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADST 409
           PY GYP Q  PGGY  NWDQ+     QQ++  SGYDYY+QQP  QQ         PAD +
Sbjct: 310 PYAGYPPQQ-PGGYSANWDQSTAPSHQQSTHASGYDYYNQQPQQQQNPGG--PPQPADGS 366

Query: 410 GYSYSQPPASGYNQQGQGYAQDSYGGYHA-PQSGYGQAAPYDQQQGYNSAAGYGNVNNTS 468
           GYSYSQPP+SGY+Q GQGY Q+SYG Y+A  QSGYGQ   YDQQQGY SA  YG+ +N +
Sbjct: 367 GYSYSQPPSSGYSQPGQGYGQESYGAYNAQQQSGYGQPQTYDQQQGYGSAPSYGSGSNPT 426

Query: 469 QEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPT 528
           QEGHT +YG+Q D++Q   P      + QQGY T Q  +P           QP Y V PT
Sbjct: 427 QEGHTSNYGSQADTSQTSQP----TTVAQQGYATNQPETP-----------QPGYAVAPT 471

Query: 529 SQSGYGSQVPPQSGYA-GYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPS 587
           +Q+ YGSQ  PQSGY   YG P +QKP ANPP YGQ+ QSP +AGGYG   Y  SQ PPS
Sbjct: 472 TQAAYGSQ--PQSGYGPSYGAPPSQKPSANPPVYGQS-QSPSTAGGYGHSAYPSSQAPPS 528

Query: 588 SYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSY----YGGGYSQ- 642
            YAQP+ G+QRAP        QPGYG  +YGAP GG Q GYGQ PPSY    YGG Y+Q 
Sbjct: 529 GYAQPELGTQRAP-------VQPGYGPQSYGAPQGG-QPGYGQTPPSYGNSSYGGSYAQA 580

Query: 643 PVYTADGNAAPAA 655
           P Y +DG  A A 
Sbjct: 581 PAYASDGATAQAV 593

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356514579|ref|XP_003525983.1| PREDICTED: uncharacterized protein LOC100797476 [Glycine max]

 Score =  541 bits (1395), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 369/666 (55%), Positives = 417/666 (62%), Gaps = 143/666 (21%)

Query: 1   MADEPQYSS--DGTPSKRKYEDQTTPPSAAARRPTGFSAPDPAVAPTSYNSVPPPADEFQ 58
           MA+E QYSS  D  P KRKYEDQ          P+G                        
Sbjct: 1   MAEEAQYSSGPDSAPLKRKYEDQ----------PSG------------------------ 26

Query: 59  DFQAAKRRAEQIAARLCNSV---SAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPS 115
             + AK+RA+++AARL N+      +AKRP+ +    GFDS          DLK + + S
Sbjct: 27  -IELAKQRAQEVAARLLNAAPPPPLDAKRPKPDT---GFDSL---------DLKPLYSAS 73

Query: 116 AIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSP 175
             PVSYG     G+SKKI+IPN RVGVIIGK GETIKYLQLQSGAKIQ+TRD +AD NS 
Sbjct: 74  PPPVSYG---HQGSSKKIDIPNGRVGVIIGKGGETIKYLQLQSGAKIQITRDIDADPNSS 130

Query: 176 TRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLV 235
           TR+VELMGTPE I+ AE+LIN+VLAEAESGGSGIV RR TGQAGSD F MKIPNNKVGL+
Sbjct: 131 TRTVELMGTPEAISSAEKLINEVLAEAESGGSGIVTRRFTGQAGSDEFVMKIPNNKVGLI 190

Query: 236 IGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVIS-E 294
           IGKGGETIKNMQA TGARIQVIPLHLPPGDTSTERT++IDGT EQIESAKQLV +VIS E
Sbjct: 191 IGKGGETIKNMQASTGARIQVIPLHLPPGDTSTERTLKIDGTPEQIESAKQLVYQVISGE 250

Query: 295 NRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPY 354
           NR+RNPAM+GGY QQGYQ+RPP++W  P AP+ QQPGYGYVQPGAY G +PQYNM Q PY
Sbjct: 251 NRVRNPAMSGGYPQQGYQSRPPSNWAPP-APT-QQPGYGYVQPGAYSGPSPQYNMPQQPY 308

Query: 355 GGYPSQPTPGGYPGNWDQT---PTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGY 411
            GYP Q  P GY  NWDQ+   P QQ++ G GY         QQPQ PGG A PAD + Y
Sbjct: 309 AGYPPQ-QPDGYSTNWDQSTAPPHQQSTHGGGYY--YYSQQPQQPQNPGGPAPPADGSAY 365

Query: 412 SYSQPPASGYNQQG-QGYAQDSYGGYHA-PQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQ 469
           +YSQPP+SGYNQ   QGYAQDSY  Y+A  QSGYGQ   YDQQQ      GYG+ +N +Q
Sbjct: 366 NYSQPPSSGYNQSAQQGYAQDSYNAYNAQSQSGYGQPPTYDQQQ------GYGSESNPAQ 419

Query: 470 EGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPTS 529
           EGHT +Y  QGDS QA  P      + QQGY T Q PS NTA+YPPQG  QP YGVPPTS
Sbjct: 420 EGHTANYAVQGDSAQA--PSAQPITVAQQGYPTNQLPSSNTANYPPQGTPQPGYGVPPTS 477

Query: 530 QSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSY 589
           Q+ YG+Q  P  GY                            GG  QPGY          
Sbjct: 478 QAAYGNQSQP--GY----------------------------GGAVQPGYG--------- 498

Query: 590 AQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSY----YGGGYSQ-PV 644
                      P  YGA              P G Q GYGQ  PSY    YG GY+Q P 
Sbjct: 499 -----------PQTYGA--------------PQGGQPGYGQALPSYSNSSYGAGYTQTPA 533

Query: 645 YTADGN 650
           YT DGN
Sbjct: 534 YTGDGN 539

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297825693|ref|XP_002880729.1| hypothetical protein ARALYDRAFT_481452 [Arabidopsis lyrata subsp. lyrata] gi|297326568|gb|EFH56988.1| hypothetical protein ARALYDRAFT_481452 [Arabidopsis lyrata subsp. lyrata]

 Score =  506 bits (1302), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 381/642 (59%), Positives = 443/642 (69%), Gaps = 75/642 (11%)

Query: 1   MADEPQYSSDGTPSKRKYEDQTTPPSAAARRPTGFSA-------PDPAVA----PTSYNS 49
           MADE QYSSD   +KRKYE+QT PP  + RRPTGFS+       PD   +    P+SYNS
Sbjct: 1   MADESQYSSDTYSNKRKYEEQTAPP-PSTRRPTGFSSGPIPSASPDLTASAVPPPSSYNS 59

Query: 50  VPPPADEFQDFQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSAD-KGFSSPPSDL 108
           VPPP DE Q    AK++A++IAARL NS  A+AKRPRVENG+  +D  D KGFSS PS+ 
Sbjct: 60  VPPPMDEIQ---IAKQKAQEIAARLLNS--ADAKRPRVENGAS-YDYGDNKGFSSYPSEG 113

Query: 109 KSIPA--PSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR 166
           K +    PS+IPVSYG +Q  GT+KKI+IPN+RVGVIIGK GETIKYLQLQSGAKIQVTR
Sbjct: 114 KQMSGTPPSSIPVSYGSFQ--GTTKKIDIPNMRVGVIIGKGGETIKYLQLQSGAKIQVTR 171

Query: 167 DTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG---IVARRLTGQAGSDHF 223
           D +AD N+ TR+V+L GTP+QI+KAEQLI DVL EAE+G +       RR+ GQAG+D F
Sbjct: 172 DMDADPNATTRTVDLTGTPDQISKAEQLITDVLQEAEAGNTAGSGGGGRRMGGQAGADQF 231

Query: 224 AMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIES 283
            MKIPNNKVGL+IGKGGETIK+MQA+TGARIQVIPLHLPPGD + ERT+QIDG +EQIE 
Sbjct: 232 VMKIPNNKVGLIIGKGGETIKSMQAKTGARIQVIPLHLPPGDPTPERTLQIDGITEQIEH 291

Query: 284 AKQLVNEVIS-ENRIRNPAM-AGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYP 341
           AKQLVNE+IS ENR+RN AM  G   Q GYQARPP+SW  PGAP  Q    GY+QPGAYP
Sbjct: 292 AKQLVNEIISGENRMRNSAMGGGYPQQGGYQARPPSSWAPPGAPPAQPGYGGYMQPGAYP 351

Query: 342 GQTPQYNMSQPPYGGYPSQPTPGGYPGNWDQT---PTQQTSQGSGYDYYSQQPSSQQPQA 398
           G  PQY  S  PYG YP Q T GGY   WDQ+   P+QQ++ G  YDYY QQ  SQQP +
Sbjct: 352 G-PPQYGQS--PYGSYPQQ-TSGGYSSTWDQSSVPPSQQSAHGE-YDYYGQQ-QSQQPSS 405

Query: 399 PGGSAAPADSTGYSYSQPPASGYNQQGQGYAQDSYGGYHAP-QSGYGQAAPYDQQQGYNS 457
            G SA P D+TGY+Y Q  ASGY Q GQGY QD YG Y+A  QSGYGQAA YDQQ     
Sbjct: 406 GGSSAPPTDTTGYNYYQ-HASGYGQAGQGYQQDGYGAYNASQQSGYGQAAGYDQQ----- 459

Query: 458 AAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYG-TGQQPSPNTASYPPQ 516
             GYG+  N SQE          D++QA PP  SSA  GQ GYG TGQQP       P Q
Sbjct: 460 -GGYGSTTNPSQE---------EDTSQAAPP--SSAQSGQAGYGTTGQQP-------PAQ 500

Query: 517 GAT-QPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYG 575
           G+T Q  YG  PTSQ+GY SQ PP +  +GYG P          AYGQ+QQSPG+ G YG
Sbjct: 501 GSTSQAGYGAAPTSQAGYSSQ-PPAAYSSGYGAPPPSSKPP---AYGQSQQSPGAPGSYG 556

Query: 576 -QPGYSHSQPPPSSYAQPDS-GSQRAPPS--NYGAATQPGYG 613
            Q GY  +QP  S Y QP + G  +AP +  +YG  TQP  G
Sbjct: 557 SQSGY--AQPAASGYGQPPAYGYGQAPQAYGSYGGYTQPAAG 596

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	669
TAIR|locus:2043530	632	AT2G25970 "AT2G25970" [Arabido	0.850	0.900	0.543	2.7e-148
TAIR|locus:2140513	725	AT4G10070 "AT4G10070" [Arabido	0.360	0.332	0.480	2.3e-68
TAIR|locus:2012713	763	AT1G33680 "AT1G33680" [Arabido	0.533	0.467	0.355	2.3e-67
UNIPROTKB|F6Y140	602	KHSRP "Uncharacterized protein	0.352	0.392	0.338	1e-26
UNIPROTKB|F1SBT6	747	KHSRP "Uncharacterized protein	0.394	0.353	0.301	1.1e-26
UNIPROTKB|F1MHR6	708	LOC505564 "Uncharacterized pro	0.381	0.360	0.297	1.5e-26
ZFIN|ZDB-GENE-040426-2159	642	fubp1 "far upstream element (F	0.355	0.370	0.342	1.6e-26
RGD|1591892	639	Fubp1 "far upstream element (F	0.333	0.348	0.339	1.6e-26
UNIPROTKB|Q32PX7	639	Fubp1 "Far upstream element-bi	0.333	0.348	0.339	1.6e-26
UNIPROTKB|Q96AE4	644	FUBP1 "Far upstream element-bi	0.333	0.346	0.339	1.7e-26

TAIR|locus:2043530 AT2G25970 "AT2G25970" [Arabidopsis thaliana (taxid:3702)]

 Score = 1448 (514.8 bits), Expect = 2.7e-148, P = 2.7e-148
 Identities = 349/642 (54%), Positives = 406/642 (63%)

Query:     1 MADEPQYSSDGTPSKRKYEDQTTPPSAAARRPTGFSA-PDPAVA----------PTSYNS 49
             MADE QYSSD   +KRKYE+ T PP +  RRPTGFS+ P P+ +          P+SYNS
Sbjct:     1 MADESQYSSDTYSNKRKYEEPTAPPPST-RRPTGFSSGPIPSASVDPTAPTGLPPSSYNS 59

Query:    50 VPPPADEFQDFQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSAD-KGFSSPPSDL 108
             VPPP DE Q    AK++A++IAARL NS  A+AKRPRV+NG+  +D  D KGFSS PS+ 
Sbjct:    60 VPPPMDEIQ---IAKQKAQEIAARLLNS--ADAKRPRVDNGAS-YDYGDNKGFSSYPSEG 113

Query:   109 KSIPA--PSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR 166
             K +    PS+IPVSYG +Q  GT+KKI+IPN+RVGVIIGK GETIKYLQLQSGAKIQVTR
Sbjct:   114 KQMSGTVPSSIPVSYGSFQ--GTTKKIDIPNMRVGVIIGKGGETIKYLQLQSGAKIQVTR 171

Query:   167 DTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESG---GSGIVA-RRLTGQAGSDH 222
             D +AD N  TR+V+L GTP+QI+KAEQLI DVL EAE+G   GSG    RR+ GQAG+D 
Sbjct:   172 DMDADPNCATRTVDLTGTPDQISKAEQLITDVLQEAEAGNTAGSGGGGGRRMGGQAGADQ 231

Query:   223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIE 282
             F MKIPNNKVGL+IGKGGETIK+MQA+TGARIQVIPLHLPPGD + ERT+QIDG +EQIE
Sbjct:   232 FVMKIPNNKVGLIIGKGGETIKSMQAKTGARIQVIPLHLPPGDPTPERTLQIDGITEQIE 291

Query:   283 SAKQLVNEVIS-ENRIRNPAMAGGYSQQG-YQARPPTSWGTPGAPSMQQPGYG-YVQPGA 339
              AKQLVNE+IS ENR+RN AM GGY QQG YQARPP+SW  PG P  Q PGYG Y+QPGA
Sbjct:   292 HAKQLVNEIISGENRMRNSAMGGGYPQQGGYQARPPSSWAPPGGPPAQ-PGYGGYMQPGA 350

Query:   340 YPGQTPQYNMSQPPYGGYPSQPTPGGYPGNWDXXXXXXXXXXXXXXXXXXXXXXXXXXXX 399
             YPG  PQY  S  PYG YP Q + G Y                                 
Sbjct:   351 YPGP-PQYGQS--PYGSYPQQTSAGYYD---QSSVPPSQQSAQGEYDYYGQQQSQQPSSG 404

Query:   400 XXXXXXXXXXGYSYSQPPASGYNQQGQGYAQDSYGGYHAPQ-SGYGQAAPYDQQQGYNSA 458
                       GY+Y Q  ASGY Q GQGY QD YG Y+A Q SGYGQAA YDQQ      
Sbjct:   405 GSSAPPTDTTGYNYYQH-ASGYGQAGQGYQQDGYGAYNASQQSGYGQAAGYDQQ------ 457

Query:   459 AGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGT-GQQP----SPNTASY 513
              GYG+  N SQE          D++QA PP  SSA  GQ GYGT GQQP    S   A Y
Sbjct:   458 GGYGSTTNPSQEE---------DASQAAPP--SSAQSGQAGYGTTGQQPPAQGSTGQAGY 506

Query:   514 PPQGATQPSYGVPPTS--QSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYG-QTQQSPGS 570
                  +Q  Y   P +   SGYG+  PP S    YG  Q Q P A P +YG Q+  +  +
Sbjct:   507 GAPPTSQAGYSSQPAAAYNSGYGAP-PPASKPPTYGQSQ-QSPGA-PGSYGSQSGYAQPA 563

Query:   571 AGGYGQP-GYSHSQPPPS-----SYAQPDSGSQRAPPSNYGA 606
             A GYGQP  Y + Q P        Y QP +G   +   + GA
Sbjct:   564 ASGYGQPPAYGYGQAPQGYGSYGGYTQPAAGGGYSSDGSAGA 605

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005829 "cytosol" evidence=IDA

GO:0006606 "protein import into nucleus" evidence=RCA

TAIR|locus:2140513 AT4G10070 "AT4G10070" [Arabidopsis thaliana (taxid:3702)]

 Score = 543 (196.2 bits), Expect = 2.3e-68, Sum P(2) = 2.3e-68
 Identities = 124/258 (48%), Positives = 168/258 (65%)

Query:   123 GYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELM 182
             G QS  T+++I++P+ +VGV+IGK GETI+YLQ  SGAKIQ+ RD+EAD +S  R VE++
Sbjct:   172 GTQS--TTRRIDVPSSKVGVLIGKGGETIRYLQFNSGAKIQILRDSEADPSSALRPVEII 229

Query:   183 GTPEQIAKAEQLINDVLAEAESGGS-GIVARR--LTGQAG-SDHFAMKIPNNKVGLVIGK 238
             G+   I  AE+LI+ V+AEAE+GGS  +VAR    T   G  +   +K+PN+KVGL+IG+
Sbjct:   230 GSVACIESAEKLISAVIAEAEAGGSPALVARGHPSTHAIGIPEQIEIKVPNDKVGLIIGR 289

Query:   239 GGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENRIR 298
             GGETIKNMQ R+GAR Q+IP H   GD   ERTV+I G   QI+ A  ++ +V+++N  R
Sbjct:   290 GGETIKNMQTRSGARTQLIPQHAE-GDGLKERTVRISGDKMQIDIATDMIKDVMNQNA-R 347

Query:   299 NPAMAGGYSQQGYQAR-P--PTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYG 355
               + +GGY+Q  Y+ + P  P  WG+ G P    P Y Y   G Y  Q   YN   P +G
Sbjct:   348 PSSYSGGYNQPAYRPQGPGGPPQWGSRG-PHAPHP-YDYHPRGPYSSQGSYYN--SPGFG 403

Query:   356 GYPSQPTP--GGYPGNWD 371
             GYP Q  P  GGY  +WD
Sbjct:   404 GYPPQHMPPRGGYGTDWD 421

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

GO:0009688 "abscisic acid biosynthetic process" evidence=RCA

TAIR|locus:2012713 AT1G33680 "AT1G33680" [Arabidopsis thaliana (taxid:3702)]

 Score = 514 (186.0 bits), Expect = 2.3e-67, Sum P(2) = 2.3e-67
 Identities = 136/383 (35%), Positives = 202/383 (52%)

Query:     1 MADEPQYSSDGTPSKRKYEDQTTPPSAAARRPTGFSAPDPAVAPTSYNSVPPPADEFQDF 60
             + ++ Q + D   S  K ED   P       P   ++ D +V  +   ++    +E +D 
Sbjct:   102 LIEKVQETIDAEESDNKMEDNGKPEDNQLVTPEVVTSQDVSVEESKEVNISGSQNEGED- 160

Query:    61 QAAKRRAEQIAARLCNSVSAEA----KRPRVENGSGGFDSADKGFSSPPS---DLKSIPA 113
               +K   + +A +   + S E      +   E  +GG      G  S      + K +  
Sbjct:   161 -DSKETNDVVAQKEVENGSKEVTDCDSQKEDEANAGGESKEVNGSVSHDEIGDESKEVNG 219

Query:   114 PSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLN 173
              S         QS  T+++I++P+ +VG +IGK GE ++YLQ+ SGAKIQ+ RD EAD +
Sbjct:   220 GSTHK-EVDDTQS--TTRRIDVPSSKVGTLIGKGGEMVRYLQVNSGAKIQIRRDAEADPS 276

Query:   174 SPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVG 233
             S  R VE++GT   I KAE+LIN V+AE E+GG   +A R  G    +   +K+P++KVG
Sbjct:   277 SALRPVEIIGTVSCIEKAEKLINAVIAEVEAGGVPALAAR--GVP--EQMEIKVPSDKVG 332

Query:   234 LVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVIS 293
             ++IG+GGETIKNMQ ++ ARIQ+IP +   GD S ERTV+I G   QI+ A  L+ +V+ 
Sbjct:   333 VIIGRGGETIKNMQTKSRARIQLIPQN--EGDASKERTVRISGDKRQIDIATALIKDVMY 390

Query:   294 ENRIRNPAMAGGYSQQGYQAR-P--PTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMS 350
             ++   +P  +GG++QQ YQ R P  P  WG+ G        Y Y   G YP Q   +   
Sbjct:   391 QDGRPSP-YSGGFNQQAYQPRGPGGPPQWGSRGPHGPHSMPYNYHHGGPYPSQGSHFR-- 447

Query:   351 QPPYGGYPSQPTP--GGYPGNWD 371
              P  GGYP Q  P   GY   W+
Sbjct:   448 PPNSGGYPPQHMPPRSGYGSGWE 470

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005829 "cytosol" evidence=IDA

UNIPROTKB|F6Y140 KHSRP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 268 (99.4 bits), Expect = 1.0e-26, Sum P(2) = 1.0e-26
 Identities = 90/266 (33%), Positives = 124/266 (46%)

Query:   121 YGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVE 180
             YG    +G    + +P   VGV+IG+SGE IK +Q  +G +IQ  +D   D   P +   
Sbjct:   173 YGS--RIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD---DGTGPEKIAH 227

Query:   181 LMGTPEQIAKAEQLINDVLAEAESG------GSGIV--AR-RLTGQAG----SDHFAMKI 227
             +MG P++   A ++IND+L    SG      G G+    R R  GQ             I
Sbjct:   228 IMGPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQGNWGPPGGEMTFSI 287

Query:   228 PNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPP-GDTSTERTVQIDGTSEQIESAKQ 286
             P +K GLVIG+GGE +K +  +TGA ++ I   LPP GD + +  + I G+ +QI+ AKQ
Sbjct:   288 PTHKCGLVIGRGGENVKAINQQTGAFVE-ISRQLPPNGDPNFKLFI-IRGSPQQIDHAKQ 345

Query:   287 LVNEVISENRIRNPAMAGGYSQQGYQA--RP-PTSWGTPGAPSMQQPGYGYVQPGAYP-- 341
             L+ E I           GG    G      P P + G PGAP    P  G   P  YP  
Sbjct:   346 LIEEKIEGPLCPVGPGPGGPGPAGPMGPFNPGPFNQGPPGAP----PHAGGPPPHQYPPQ 401

Query:   342 GQTPQYNMSQPPYGGYPSQPTPGGYP 367
             G    Y   QPP    P++      P
Sbjct:   402 GWGNTYPQWQPPAPHDPNKAAAAADP 427

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1SBT6 KHSRP "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 274 (101.5 bits), Expect = 1.1e-26, Sum P(2) = 1.1e-26
 Identities = 84/279 (30%), Positives = 131/279 (46%)

Query:    24 PPSAAARRPTGFSAPDPAVAPTSYNSVPP----PADEFQDFQAAKRRAEQIAARLCNSVS 79
             PP    R   G     P        S PP    P      F  A +RA QIAA++    +
Sbjct:    34 PPGRXDRGGGGPGGGGPGGGSAGGPSQPPGGGGPGIRKDAFADAVQRARQIAAKIGGDAA 93

Query:    80 AEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGG-YQSMGTS--KKIEIP 136
                     + G GG     +    P S  K      +I    G  +    TS  ++  +P
Sbjct:    94 TTVNNSTPDFGFGGQKRQLEDGDQPESK-KLASQGDSISSQLGPIHPPPRTSMTEEYRVP 152

Query:   137 NIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLIN 196
             +  VG+IIG+ GE I  +Q  SG K+Q++ D+      P RSV L G PE + KA+ +++
Sbjct:   153 DGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGG---LPERSVSLTGAPESVQKAKMMLD 209

Query:   197 DVLAEAESGGSGIVARRLTG-QAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQ 255
             D+++    G  G       G Q G+    M IP  K GLVIGKGGETIK +Q R G  ++
Sbjct:   210 DIVSRGRGGPPGQFHDNANGGQNGTVQEIM-IPAGKAGLVIGKGGETIKQLQERAG--VK 266

Query:   256 VIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294
             +I +     +T+ ++ ++I G   +++ A ++V +++ E
Sbjct:   267 MILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE 305

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1MHR6 LOC505564 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 272 (100.8 bits), Expect = 1.5e-26, Sum P(2) = 1.5e-26
 Identities = 81/272 (29%), Positives = 132/272 (48%)

Query:    28 AARRPTGFSAPDPAVAPTSYNSVPPPADEFQDFQAAKRRAEQIAARLCNSVSAEAKRPRV 87
             A  R  G SA  P+  P        P      F  A +RA QIAA++    +        
Sbjct:     7 AGGRAGGXSAGGPSQPPGGGG----PGIRKDAFADAVQRARQIAAKIGGDAATTVNNSTP 62

Query:    88 ENGSGG----FDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVI 143
             + G GG     +  D+  S   +      +    P+      SM  +++  +P+  VG+I
Sbjct:    63 DFGFGGQKRQLEDGDQPESKKLASQGDSMSSQLGPIHPPPRTSM--TEEYRVPDGMVGLI 120

Query:   144 IGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE 203
             IG+ GE I  +Q  SG K+Q++ D+      P RSV L G PE + KA+ +++D+++   
Sbjct:   121 IGRGGEQINKIQQDSGCKVQISPDSGG---LPERSVSLTGAPESVQKAKMMLDDIVSRGR 177

Query:   204 SGGSGIVARRLTG-QAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLP 262
              G  G       G Q G+    M IP  K GLVIGKGGETIK +Q R G  +++I +   
Sbjct:   178 GGPPGQFHDNANGGQNGTVQEIM-IPAGKAGLVIGKGGETIKQLQERAG--VKMILIQDG 234

Query:   263 PGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294
               +T+ ++ ++I G   +++ A ++V +++ E
Sbjct:   235 SQNTNVDKPLRIIGDPYKVQQACEMVMDILRE 266

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

ZFIN|ZDB-GENE-040426-2159 fubp1 "far upstream element (FUSE) binding protein 1" [Danio rerio (taxid:7955)]

 Score = 293 (108.2 bits), Expect = 1.6e-26, Sum P(2) = 1.6e-26
 Identities = 90/263 (34%), Positives = 137/263 (52%)

Query:    42 VAPTSYNSVPPPADEFQDFQAAKRRAEQIAARLCNSVSAEAKRPR-VEN--GSGGFDSAD 98
             VAP S N+     D F+D   A +RA QIAA+    +  +   P  V N  G GG     
Sbjct:     7 VAPPSSNAGGGMNDAFKD---ALQRARQIAAK----IGGDGVPPSPVSNDFGYGGQKRPL 59

Query:    99 KGFSSPPSDLKSIPA--P-SAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQ 155
             +    P  + K +P   P SA+    GG      S++ ++P+  VG IIG+ GE I  LQ
Sbjct:    60 EDGDQP--ETKKVPPSDPFSAVMGGMGG-PPRSVSEEFKVPDGMVGFIIGRGGEQISRLQ 116

Query:   156 LQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLT 215
              +SG KIQ+  D+      P RSV L G+P+ I  A++L+++++   E G          
Sbjct:   117 QESGCKIQIAPDSGG---MPDRSVTLTGSPDAIMTAKRLLSEIV---EKGRPSPAFHHND 170

Query:   216 GQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQID 275
             G   S H  M IP +K GLVIGKGGETIK +Q R G  ++++ +   P +T  ++ ++I 
Sbjct:   171 GPGMSVH-EMMIPASKAGLVIGKGGETIKQLQERAG--VKMVMIQDGPQNTGADKPLRIS 227

Query:   276 GTSEQIESAKQLVNEVISENRIR 298
             G   +++ AK +V ++I +   R
Sbjct:   228 GDPFKVQQAKDMVMDLIRDQGFR 250

GO:0003723 "RNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

RGD|1591892 Fubp1 "far upstream element (FUSE) binding protein 1" [Rattus norvegicus (taxid:10116)]

 Score = 281 (104.0 bits), Expect = 1.6e-26, Sum P(2) = 1.6e-26
 Identities = 86/253 (33%), Positives = 121/253 (47%)

Query:   133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAE 192
             + IP   VG++IG++GE IK +Q  +G +IQ   D   D  +P R  ++ G P++   A 
Sbjct:   275 VPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD---DGTTPDRIAQITGPPDRCQHAA 331

Query:   193 QLINDVLAEAESG---GSGIVAR-RLTGQA--------GSDHFAMKIPNNKVGLVIGKGG 240
             ++I D+L   ++G   G G   R R  GQ         G   F   +P  K GL+IGKGG
Sbjct:   332 EIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGG 391

Query:   241 ETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE--NRIR 298
             ETIK++  ++GARI+ +  + PP      +   I GT +QI+ A+QL+ E I    N + 
Sbjct:   392 ETIKSISQQSGARIE-LQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKIGGPVNPLG 450

Query:   299 NPAMAGGYSQQGYQARP-PTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGY 357
              P   G +   G    P P   GTP  P    P   Y  PG  PG  P      PP   Y
Sbjct:   451 PPVPHGPHGVPGPHGPPGPPGPGTPMGPYNPAP---Y-NPGP-PGPAPH----GPP-APY 500

Query:   358 PSQPTPGGYPGNW 370
               Q     YP +W
Sbjct:   501 APQGWGNAYP-HW 512

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0010628 "positive regulation of gene expression" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|Q32PX7 Fubp1 "Far upstream element-binding protein 1" [Rattus norvegicus (taxid:10116)]

 Score = 281 (104.0 bits), Expect = 1.6e-26, Sum P(2) = 1.6e-26
 Identities = 86/253 (33%), Positives = 121/253 (47%)

Query:   133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAE 192
             + IP   VG++IG++GE IK +Q  +G +IQ   D   D  +P R  ++ G P++   A 
Sbjct:   275 VPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD---DGTTPDRIAQITGPPDRCQHAA 331

Query:   193 QLINDVLAEAESG---GSGIVAR-RLTGQA--------GSDHFAMKIPNNKVGLVIGKGG 240
             ++I D+L   ++G   G G   R R  GQ         G   F   +P  K GL+IGKGG
Sbjct:   332 EIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGG 391

Query:   241 ETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE--NRIR 298
             ETIK++  ++GARI+ +  + PP      +   I GT +QI+ A+QL+ E I    N + 
Sbjct:   392 ETIKSISQQSGARIE-LQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKIGGPVNPLG 450

Query:   299 NPAMAGGYSQQGYQARP-PTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGY 357
              P   G +   G    P P   GTP  P    P   Y  PG  PG  P      PP   Y
Sbjct:   451 PPVPHGPHGVPGPHGPPGPPGPGTPMGPYNPAP---Y-NPGP-PGPAPH----GPP-APY 500

Query:   358 PSQPTPGGYPGNW 370
               Q     YP +W
Sbjct:   501 APQGWGNAYP-HW 512

GO:0010628 "positive regulation of gene expression" evidence=IEA

UNIPROTKB|Q96AE4 FUBP1 "Far upstream element-binding protein 1" [Homo sapiens (taxid:9606)]

 Score = 281 (104.0 bits), Expect = 1.7e-26, Sum P(2) = 1.7e-26
 Identities = 86/253 (33%), Positives = 121/253 (47%)

Query:   133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAE 192
             + IP   VG++IG++GE IK +Q  +G +IQ   D   D  +P R  ++ G P++   A 
Sbjct:   280 VPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD---DGTTPERIAQITGPPDRCQHAA 336

Query:   193 QLINDVLAEAESG---GSGIVAR-RLTGQA--------GSDHFAMKIPNNKVGLVIGKGG 240
             ++I D+L   ++G   G G   R R  GQ         G   F   +P  K GL+IGKGG
Sbjct:   337 EIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGG 396

Query:   241 ETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE--NRIR 298
             ETIK++  ++GARI+ +  + PP      +   I GT +QI+ A+QL+ E I    N + 
Sbjct:   397 ETIKSISQQSGARIE-LQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKIGGPVNPLG 455

Query:   299 NPAMAGGYSQQGYQARP-PTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGY 357
              P   G +   G    P P   GTP  P    P   Y  PG  PG  P      PP   Y
Sbjct:   456 PPVPHGPHGVPGPHGPPGPPGPGTPMGPYNPAP---Y-NPGP-PGPAPH----GPP-APY 505

Query:   358 PSQPTPGGYPGNW 370
               Q     YP +W
Sbjct:   506 APQGWGNAYP-HW 517

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0010628 "positive regulation of gene expression" evidence=IDA

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

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0005730 "nucleolus" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00032165001 SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (590 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	669
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	4e-19
smart00322	68	smart00322, KH, K homology RNA-binding domain	1e-17
pfam00013	59	pfam00013, KH_1, KH domain	2e-17
smart00322	68	smart00322, KH, K homology RNA-binding domain	7e-16
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	7e-16
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	3e-15
pfam00013	59	pfam00013, KH_1, KH domain	1e-14
pfam13014	42	pfam13014, KH_3, KH domain	5e-11
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	3e-10
TIGR03665	172	TIGR03665, arCOG04150, arCOG04150 universal archae	8e-10
PRK13763	180	PRK13763, PRK13763, putative RNA-processing protei	1e-09
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	9e-09
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	1e-08
COG1094	194	COG1094, COG1094, Predicted RNA-binding protein (c	3e-08
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	1e-07
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	3e-07
pfam13014	42	pfam13014, KH_3, KH domain	4e-07
cd02409	68	cd02409, KH-II, KH-II (K homology RNA-binding doma	7e-07
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	9e-07
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	5e-06
PTZ00395	1560	PTZ00395, PTZ00395, Sec24-related protein; Provisi	9e-06
COG1855	604	COG1855, COG1855, ATPase (PilT family) [General fu	2e-05
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	2e-05
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	6e-05
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	6e-05
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	1e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-04
COG0195	190	COG0195, NusA, Transcription elongation factor [Tr	3e-04
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	3e-04
PRK08406	140	PRK08406, PRK08406, transcription elongation facto	4e-04
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	9e-04
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	0.001
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	0.001
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	0.001
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	0.001
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.001
pfam07650	77	pfam07650, KH_2, KH domain	0.002
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	0.003
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	0.003
PRK14086	617	PRK14086, dnaA, chromosomal replication initiation	0.003
PHA03375	844	PHA03375, PHA03375, hypothetical protein; Provisio	0.004

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

 Score = 81.5 bits (202), Expect = 4e-19
 Identities = 28/64 (43%), Positives = 41/64 (64%), Gaps = 4/64 (6%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + +P++ VG +IGKGG TIK ++  TGA+I++       G  S ER V I GT E +E A
Sbjct: 4   VLVPSSLVGRIIGKGGSTIKEIREETGAKIKIP----DSGSGSEERIVTITGTPEAVEKA 59

Query: 285 KQLV 288
           K+L+
Sbjct: 60  KELI 63

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

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

 Score = 77.0 bits (190), Expect = 1e-17
 Identities = 30/68 (44%), Positives = 43/68 (63%), Gaps = 6/68 (8%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IP +KVGL+IGKGG TIK ++  TG +I +      PG  S ER V+I G  E +E A
Sbjct: 7   VLIPADKVGLIIGKGGSTIKKIEEETGVKIDI------PGPGSEERVVEITGPPENVEKA 60

Query: 285 KQLVNEVI 292
            +L+ E++
Sbjct: 61  AELILEIL 68

Length = 68

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

 Score = 76.1 bits (188), Expect = 2e-17
 Identities = 26/64 (40%), Positives = 38/64 (59%), Gaps = 8/64 (12%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IP +KVG +IGKGG  IK ++  TG +I++            + TV I GT EQ+E A
Sbjct: 4   ILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD--------DRDDTVTISGTPEQVEKA 55

Query: 285 KQLV 288
           K+L+
Sbjct: 56  KELI 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 = 71.9 bits (177), Expect = 7e-16
 Identities = 27/71 (38%), Positives = 42/71 (59%), Gaps = 5/71 (7%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
            + ++ IP  +VG+IIGK G TIK ++ ++G KI +         S  R VE+ G PE +
Sbjct: 3   VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGP-----GSEERVVEITGPPENV 57

Query: 189 AKAEQLINDVL 199
            KA +LI ++L
Sbjct: 58  EKAAELILEIL 68

Length = 68

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

 Score = 72.1 bits (178), Expect = 7e-16
 Identities = 24/55 (43%), Positives = 34/55 (61%), Gaps = 3/55 (5%)

Query: 227 IPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQI 281
           +P+++ G +IGKGG TIK ++  TGA+I+V    LP    STER V I G    +
Sbjct: 6   VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPG---STERVVTISGKPSAV 57

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 = 70.3 bits (173), Expect = 3e-15
 Identities = 26/66 (39%), Positives = 42/66 (63%), Gaps = 3/66 (4%)

Query: 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIA 189
           ++++ +P+  VG IIGK G TIK ++ ++GAKI++         S  R V + GTPE + 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDS---GSGSEERIVTITGTPEAVE 57

Query: 190 KAEQLI 195
           KA++LI
Sbjct: 58  KAKELI 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 = 68.4 bits (168), Expect = 1e-14
 Identities = 26/66 (39%), Positives = 41/66 (62%), Gaps = 7/66 (10%)

Query: 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIA 189
           +++I IP  +VG IIGK G  IK ++ ++G KI++  D          +V + GTPEQ+ 
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDD-------RDDTVTISGTPEQVE 53

Query: 190 KAEQLI 195
           KA++LI
Sbjct: 54  KAKELI 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 = 57.6 bits (140), Expect = 5e-11
 Identities = 23/46 (50%), Positives = 28/46 (60%), Gaps = 4/46 (8%)

Query: 231 KVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDG 276
            VG +IGKGGETIK ++  TGA+IQ+      P   S ER V I G
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQI----PKPEPGSGERIVTITG 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|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 55.9 bits (136), Expect = 3e-10
 Identities = 24/61 (39%), Positives = 36/61 (59%), Gaps = 2/61 (3%)

Query: 135 IPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQL 194
           +P+ + G IIGK G TIK ++ ++GAKI+V++       S  R V + G P  + KA  L
Sbjct: 6   VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLP--GSTERVVTISGKPSAVQKALLL 63

Query: 195 I 195
           I
Sbjct: 64  I 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|211858 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain protein

 Score = 58.0 bits (141), Expect = 8e-10
 Identities = 46/179 (25%), Positives = 82/179 (45%), Gaps = 48/179 (26%)

Query: 133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVEL---MGTPEQIA 189
           ++IP  R+GV+IGK GET K ++ ++G K+        D++S T  V++      P  + 
Sbjct: 2   VKIPKDRIGVLIGKGGETKKEIEERTGVKL--------DIDSETGEVKIEEEDEDPLAVM 53

Query: 190 KAEQLINDVLAEAESGGSGI---VARRLTGQAGSDHFAMKI---------PNN---KVGL 234
           KA +++  +       G G     A +L      D + +++         PN      G 
Sbjct: 54  KAREVVKAI-------GRGFSPEKALKL----LDDDYMLEVIDLKEYGKSPNALRRIKGR 102

Query: 235 VIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVIS 293
           +IG+GG+T + ++  TG  I V             +TV I G  EQ++ A++ +  +I 
Sbjct: 103 IIGEGGKTRRIIEELTGVSISV-----------YGKTVGIIGDPEQVQIAREAIEMLIE 150

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

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

 Score = 58.0 bits (141), Expect = 1e-09
 Identities = 47/179 (26%), Positives = 80/179 (44%), Gaps = 49/179 (27%)

Query: 133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVEL----MGTPEQI 188
           ++IP  R+GV+IGK GET K ++ ++G K+        +++S T  V +       P  +
Sbjct: 7   VKIPKDRIGVLIGKKGETKKEIEERTGVKL--------EIDSETGEVIIEPTDGEDPLAV 58

Query: 189 AKAEQLINDVLAEAESGGSGI---VARRLTGQAGSDHFAMKI---------PNN---KVG 233
            KA  ++  +       G G     A RL      D + +++         PN      G
Sbjct: 59  LKARDIVKAI-------GRGFSPEKALRL----LDDDYVLEVIDLSDYGDSPNALRRIKG 107

Query: 234 LVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVI 292
            +IG+GG+T + ++  TG  I V             +TV I G  EQ+E A++ +  +I
Sbjct: 108 RIIGEGGKTRRIIEELTGVDISV-----------YGKTVAIIGDPEQVEIAREAIEMLI 155

Length = 180

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

 Score = 58.1 bits (142), Expect = 9e-09
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 11/71 (15%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS-EQIES 283
           +KIP +K+  VIG GG+TI+ +   TGA+I          D   + TV+I  T  E  E+
Sbjct: 558 IKIPPDKIRDVIGPGGKTIREITEETGAKI----------DIEDDGTVKIAATDGEAAEA 607

Query: 284 AKQLVNEVISE 294
           AK+ +  + +E
Sbjct: 608 AKERIEGITAE 618

Length = 693

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

 Score = 51.4 bits (124), Expect = 1e-08
 Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 11/66 (16%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS-EQIES 283
           MKIP +K+  VIG GG+TIK +   TG +I          D   + TV I  +  E  E 
Sbjct: 6   MKIPPDKIRDVIGPGGKTIKKIIEETGVKI----------DIEDDGTVYIAASDKEAAEK 55

Query: 284 AKQLVN 289
           AK+++ 
Sbjct: 56  AKKMIE 61

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

>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH domains) [General function prediction only]

 Score = 53.8 bits (130), Expect = 3e-08
 Identities = 44/186 (23%), Positives = 79/186 (42%), Gaps = 47/186 (25%)

Query: 126 SMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT- 184
           +  +S+ ++IP  R+GV+IGK GE  K ++ +    +++  D++      T SV +  T 
Sbjct: 5   AEKSSEAVKIPKDRIGVLIGKWGEVKKAIEEK--TGVKLRIDSK------TGSVTIRTTR 56

Query: 185 ----PEQIAKAEQLINDVLAEAESGGSGI-VARRLTGQAGSDHFA--------MKIPNNK 231
               P  + KA  ++     +A   G     A +L      D +         +   +  
Sbjct: 57  KTEDPLALLKARDVV-----KAIGRGFPPEKALKLL----EDDYYLEVIDLKDVVTLSGD 107

Query: 232 V-----GLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQ 286
                 G +IG+ G+T + ++  TG  I V             +TV I G  EQ+E A++
Sbjct: 108 HLRRIKGRIIGREGKTRRAIEELTGVYISV-----------YGKTVAIIGGFEQVEIARE 156

Query: 287 LVNEVI 292
            V  +I
Sbjct: 157 AVEMLI 162

Length = 194

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

 Score = 54.8 bits (133), Expect = 1e-07
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 11/71 (15%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS-EQIES 283
           +KI  +K+  VIG GG+ I+ +   TGA+I          D   + TV+I  +  E  E+
Sbjct: 555 IKINPDKIRDVIGPGGKVIREITEETGAKI----------DIEDDGTVKIAASDGEAAEA 604

Query: 284 AKQLVNEVISE 294
           A +++  + +E
Sbjct: 605 AIKMIEGITAE 615

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

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

 Score = 53.3 bits (129), Expect = 3e-07
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 11/71 (15%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS-EQIES 283
           +KI  +K+  VIG GG+TIK +   TG +I          D   + TV+I  +  E  + 
Sbjct: 556 IKIDPDKIRDVIGPGGKTIKAITEETGVKI----------DIEDDGTVKIAASDGESAKK 605

Query: 284 AKQLVNEVISE 294
           AK+ +  +  E
Sbjct: 606 AKERIEAITRE 616

Length = 692

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

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 20/44 (45%), Positives = 27/44 (61%), Gaps = 3/44 (6%)

Query: 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG 183
           VG IIGK GETIK ++ ++GAKIQ+ +       S  R V + G
Sbjct: 2   VGAIIGKGGETIKEIREETGAKIQIPKPEP---GSGERIVTITG 42

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

>gnl|CDD|239092 cd02409, KH-II, KH-II (K homology RNA-binding domain, type II)

 Score = 46.5 bits (111), Expect = 7e-07
 Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 7/71 (9%)

Query: 192 EQLINDVLAEAESGGSGIVARRLTGQAGSD-HFAMKIPNNKVGLVIGKGGETIKNMQART 250
            + +  +LA A  G SG+   R   +       A      + GLVIGK G+ I+ +Q   
Sbjct: 1   REFLKKLLAPA--GISGVEIERTPDRIEIIIVVA----RGQPGLVIGKKGQNIRALQKLL 54

Query: 251 GARIQVIPLHL 261
              ++   + +
Sbjct: 55  QKLLRKKRVKI 65

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. Length = 68

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

 Score = 46.0 bits (110), Expect = 9e-07
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 6/64 (9%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           ++IP      +IGK G  I+ +   TG +I+       P   S   T+ I G  E +E A
Sbjct: 4   VEIPKKLHRFIIGKKGSNIRKIMEETGVKIRF------PDPGSKSDTITITGPKENVEKA 57

Query: 285 KQLV 288
           K+ +
Sbjct: 58  KEEI 61

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

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 49.2 bits (118), Expect = 5e-06
 Identities = 28/193 (14%), Positives = 38/193 (19%), Gaps = 8/193 (4%)

Query: 468 SQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPP 527
           +     P+  + G   +A  P   +A             +          A  P    P 
Sbjct: 595 AGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPA---EASAAPAPGVAAPE 651

Query: 528 TSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPS 587
                         G           P A PPA          A   G    +   P P+
Sbjct: 652 HHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPA----PAPAAPAAPAGAAP-AQPAPAPA 706

Query: 588 SYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSYYGGGYSQPVYTA 647
           +          A      A        AA    P   +      P          P    
Sbjct: 707 ATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAP 766

Query: 648 DGNAAPAAQPVQQ 660
               A A  P   
Sbjct: 767 AAAPAAAPPPSPP 779

Length = 824

>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional

 Score = 48.9 bits (116), Expect = 9e-06
 Identities = 49/241 (20%), Positives = 73/241 (30%), Gaps = 28/241 (11%)

Query: 433 YGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQE-----GHTPSYGAQGDSTQAPP 487
           YGG+H        A       G  + A  G++N    +        P   A  +      
Sbjct: 339 YGGFHDGSPNAASAGA--PFNGLGNQADGGHINQVHPDARGAWAGGPHSNASYNCAAYSN 396

Query: 488 PVQSSAAMGQQGY---GTGQQPSPNTASYPPQGATQPSYGVPPTSQSGYGSQVPPQSGYA 544
             QS+AA    G+   G     + N        +  P Y  PP S + Y +  PP S   
Sbjct: 397 AAQSNAAQSNAGFSNAGYSNPGNSNPGYNNAPNSNTP-YNNPPNSNTPYSN--PPNSNPP 453

Query: 545 GYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQPDSGSQRAPPSNY 604
              +P +  P +N P       S           Y H      +   P +          
Sbjct: 454 YSNLPYSNTPYSNAPLSNAPPSSAKDHHSAYHAAYQHRAANQPAANLPTANQ-------- 505

Query: 605 GAATQPGYGSAAYGAPPGGSQAGYGQGPPSYYGGGYSQPVYTADGNAAPAAQPVQQGGVT 664
             A    +G+A        +   +G  P   YGG       TAD N     +   +GG  
Sbjct: 506 -PAANNFHGAAGNSVGNPFASRPFGSAP---YGG---NAATTADPNGIAKREDHPEGGTN 558

Query: 665 K 665
           +
Sbjct: 559 R 559

Length = 1560

>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction only]

 Score = 47.7 bits (114), Expect = 2e-05
 Identities = 45/145 (31%), Positives = 60/145 (41%), Gaps = 23/145 (15%)

Query: 135 IPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSV----------ELMGT 184
           IP I   VI  K GE  K  +L    K+  T  TE DL  P   V          E+   
Sbjct: 383 IPQIVDTVIFIKDGEVAKVYELSYTVKVP-TGMTEEDLARPVIEVRDFETGELEYEIYTF 441

Query: 185 PEQ-----IAKAEQLINDVLAEAESGGSGIVARRLTGQA-----GSDHFAMKIPNNKVGL 234
            EQ     + + E+     LAE E      + R L G       G     +K+P   +  
Sbjct: 442 GEQVVVVPVKEEEESPALKLAEEEI--EREIKRYLPGDVEVEVVGDGRAVVKVPEKYIPK 499

Query: 235 VIGKGGETIKNMQARTGARIQVIPL 259
           VIGKGG+ IK ++ + G +I V PL
Sbjct: 500 VIGKGGKRIKEIEKKLGIKIDVKPL 524

Length = 604

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 47.8 bits (114), Expect = 2e-05
 Identities = 45/273 (16%), Positives = 57/273 (20%), Gaps = 28/273 (10%)

Query: 298 RNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGY-GYVQPGAYP-----------GQTP 345
                                       S  Q GY     P   P              P
Sbjct: 73  AAVRYNQNAPGAPSVGPDSDLSQKTSTFSPCQSGYEASTDPEYIPDLQPDPSLWGTAPKP 132

Query: 346 QYNMSQPPYGGYPSQPTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAP 405
           +    Q P    P   TP     + ++   Q   +        Q P   QP         
Sbjct: 133 EPQPPQAPESQ-PQPQTPAQKMLSLEEVEAQLQQRQ-------QAPQLPQPPQQVLPQGM 184

Query: 406 ADSTGYSYSQPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVN 465
                    Q P     +Q  GY Q   G     Q      AP                 
Sbjct: 185 PPRQAAFPQQGPP----EQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQP 240

Query: 466 NTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGV 525
              Q+   P    Q      PPP Q      Q      Q P  N  +  P      +  +
Sbjct: 241 PPLQQPQFPGLSQQ----MPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPL 296

Query: 526 PPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANP 558
           PP  Q      V    G       + Q    + 
Sbjct: 297 PPPQQPQLLPLVQQPQGQQRGPQFREQLVQLSQ 329

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

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

 Score = 41.0 bits (97), Expect = 6e-05
 Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 5/66 (7%)

Query: 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIA 189
           ++++EIP      IIGK G  I+ +  ++G KI+          S + ++ + G  E + 
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP-----GSKSDTITITGPKENVE 55

Query: 190 KAEQLI 195
           KA++ I
Sbjct: 56  KAKEEI 61

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

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 45.9 bits (109), Expect = 6e-05
 Identities = 47/281 (16%), Positives = 61/281 (21%), Gaps = 31/281 (11%)

Query: 380 QGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQPPASGYNQQGQGYAQDSYGGYHAP 439
           + +     +         +   S      +GY  S  P    + Q       S  G    
Sbjct: 76  RYNQNAPGAPSVGPDSDLSQKTSTFSPCQSGYEASTDPEYIPDLQ----PDPSLWGTAPK 131

Query: 440 QSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQG 499
                  AP  Q Q               Q         +    Q     Q+        
Sbjct: 132 PEPQPPQAPESQPQP--------------QTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQ 177

Query: 500 YGTGQQPSPNTASYPPQGATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPP 559
               Q   P  A++P QG  +   G P   Q       P Q       +P   +  A PP
Sbjct: 178 QVLPQGMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQF------LPAPSQAPAQPP 231

Query: 560 AYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQPDSGSQRAPPSNYGAATQPGYGSAAYGA 619
              Q  Q P        PG S   PPP          Q   P                  
Sbjct: 232 LPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQ-QQPPQPQAQPPPQNQP------TP 284

Query: 620 PPGGSQAGYGQGPPSYYGGGYSQPVYTADGNAAPAAQPVQQ 660
            PG  Q      PP                   P  +    
Sbjct: 285 HPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQFREQLV 325

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

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

 Score = 44.9 bits (107), Expect = 1e-04
 Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 15/87 (17%)

Query: 132 KIEIPNI---RVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTP-EQ 187
           +IE   I   ++  +IG  G+TIK +  ++G KI +  D           V++  +  E 
Sbjct: 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDGT---------VKIAASDGES 602

Query: 188 IAKAEQLINDVLAEAESGG--SGIVAR 212
             KA++ I  +  E E G    G V R
Sbjct: 603 AKKAKERIEAITREVEVGEVYEGTVVR 629

Length = 692

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 23/121 (19%), Positives = 30/121 (24%), Gaps = 2/121 (1%)

Query: 514 PPQGATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQ--TQQSPGSA 571
              G         P++ +   +  P  +  A           A  PA         P  A
Sbjct: 386 GVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPA 445

Query: 572 GGYGQPGYSHSQPPPSSYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQG 631
           G     G     P  +  AQP      AP      A  P    A   AP   +      G
Sbjct: 446 GNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAG 505

Query: 632 P 632
            
Sbjct: 506 A 506

Length = 824

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 34/237 (14%), Positives = 46/237 (19%), Gaps = 26/237 (10%)

Query: 398 APGGSAAPADSTGYSYSQPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNS 457
             G +   A   G                            P +    AAP        +
Sbjct: 587 VVGPAPGAAGGEGPPAPASSGPPEEAA-------------RPAAPAAPAAPAAPAPAGAA 633

Query: 458 AAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQG 517
           AA                  A  +       V  ++  G          +P      P  
Sbjct: 634 AAP------AEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAP 687

Query: 518 ATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQP 577
           A   +      +Q        P +G       QA  P A PP   Q   +P  A     P
Sbjct: 688 AAPAAPAGAAPAQPAPAPAATPPAG-------QADDPAAQPPQAAQGASAPSPAADDPVP 740

Query: 578 GYSHSQPPPSSYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPS 634
                  PP     P        P+   A       S                    
Sbjct: 741 LPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDED 797

Length = 824

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

 Score = 42.2 bits (100), Expect = 3e-04
 Identities = 28/117 (23%), Positives = 45/117 (38%), Gaps = 27/117 (23%)

Query: 129 TSKKIEIPNI-RVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQ 187
            +    +  I  VG  IGK G  +K +  + G KI V              VE    P +
Sbjct: 75  AAVVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDV--------------VEWSEDPAE 120

Query: 188 IAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIK 244
             K      + LA AE     +  +   G        + +P +++ L IGKGG+ ++
Sbjct: 121 FIK------NALAPAEV--LSVNIKEDDGHV----AIVVVPPDQLSLAIGKGGQNVR 165

Length = 190

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 43.8 bits (103), Expect = 3e-04
 Identities = 64/312 (20%), Positives = 74/312 (23%), Gaps = 10/312 (3%)

Query: 301 AMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYPSQ 360
                  QQ  Q   P   G  G   MQQ G    Q    P    Q    Q         
Sbjct: 184 QQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQMDQQQG 243

Query: 361 PTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQPPASG 420
           P          Q                Q P  QQP       +          Q P  G
Sbjct: 244 PADAQAQMGQQQQGQGGMQPQQMQGGQMQVPMQQQPPQQQPQQSQLGMLPNQMQQMPGGG 303

Query: 421 YNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSYGAQG 480
               GQ            PQ G                      N   Q+        QG
Sbjct: 304 QGGPGQPMGPPPQRPGAVPQGGQAVQQGVMSAGQQQLKQ-MKLRNMRGQQQTQQQQQQQG 362

Query: 481 DSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPP--TSQSGYGSQVP 538
            +  A    Q +  +GQ G            +    GA     G P   +S S       
Sbjct: 363 GNHPAAHQQQMNQQVGQGGQMVALGYLNIQGNQGGLGANPMQQGQPGMMSSPSPVPQVQT 422

Query: 539 PQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQPDSGSQR 598
            QS      MPQ  +P   P   G   Q P S  G   P      P PS        SQR
Sbjct: 423 NQS------MPQPPQPS-VPSPGGPGSQPPQSVSGGMIPSPPALMPSPSPQMSQSPASQR 475

Query: 599 APPSNYGAATQP 610
               +  +   P
Sbjct: 476 TIQQDMVSPGGP 487

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|181413 PRK08406, PRK08406, transcription elongation factor NusA-like protein; Validated

 Score = 40.6 bits (96), Expect = 4e-04
 Identities = 11/31 (35%), Positives = 20/31 (64%)

Query: 227 IPNNKVGLVIGKGGETIKNMQARTGARIQVI 257
           +    +GL IGKGGE +K ++ + G  I+++
Sbjct: 38  VKEGDMGLAIGKGGENVKRLEEKLGKDIELV 68

Length = 140

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

 Score = 42.1 bits (100), Expect = 9e-04
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 8/74 (10%)

Query: 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKA 191
            I+I   ++  +IG  G+ I+ +  ++GAKI +  D    + +           E    A
Sbjct: 554 TIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAASDG--------EAAEAA 605

Query: 192 EQLINDVLAEAESG 205
            ++I  + AE E G
Sbjct: 606 IKMIEGITAEPEVG 619

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|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 42.0 bits (100), Expect = 0.001
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 10/74 (13%)

Query: 133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT-PEQIAKA 191
           I+IP  ++  +IG  G+TI+ +  ++GAKI    D E D      +V++  T  E    A
Sbjct: 558 IKIPPDKIRDVIGPGGKTIREITEETGAKI----DIEDD-----GTVKIAATDGEAAEAA 608

Query: 192 EQLINDVLAEAESG 205
           ++ I  + AE E G
Sbjct: 609 KERIEGITAEPEVG 622

Length = 693

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 41.9 bits (99), Expect = 0.001
 Identities = 30/162 (18%), Positives = 42/162 (25%), Gaps = 10/162 (6%)

Query: 501 GTGQQPSPNTASYPPQGATQPSYGVPPTSQSGYGSQVPPQ-----SGYAGYGMPQAQKPL 555
           G     +       P  +  P     P + +   +   P      +  A      A    
Sbjct: 589 GPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVA 648

Query: 556 ANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQPDSGSQRAPPSNYGAATQPGYGSA 615
           A             S GG G P  +    P +    P   +  AP     A   P     
Sbjct: 649 APEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPA---P 705

Query: 616 AYGAPPGGSQAGYGQGPPSYYGGGYSQPVYTADGNAAPAAQP 657
           A   P G +     Q P +    G S P   AD       +P
Sbjct: 706 AATPPAGQADDPAAQPPQA--AQGASAPSPAADDPVPLPPEP 745

Length = 824

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 41.9 bits (99), Expect = 0.001
 Identities = 33/197 (16%), Positives = 50/197 (25%), Gaps = 20/197 (10%)

Query: 355 GGYPSQPTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYS 414
           G  P      G P      P ++ ++ +     +   +     A    A  + +      
Sbjct: 589 GPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPA-PGV 647

Query: 415 QPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTP 474
             P           A D   G+ A   G   AAP         AA  G           P
Sbjct: 648 AAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAA---------P 698

Query: 475 SYGAQGDSTQAP----------PPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYG 524
           +  A   +   P          PP  +  A           P P     PP  A  P+  
Sbjct: 699 AQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQP 758

Query: 525 VPPTSQSGYGSQVPPQS 541
            PP + +   +      
Sbjct: 759 PPPPAPAPAAAPAAAPP 775

Length = 824

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 61/283 (21%), Positives = 74/283 (26%), Gaps = 29/283 (10%)

Query: 319 WGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYPSQPTPGGYPGNWDQTPTQQT 378
           +G   A       Y    PGA           +         P   GY  + D       
Sbjct: 64  FGGETAKLSAAVRYNQNAPGAPSVGPDSDLSQKTS----TFSPCQSGYEASTDPEYIPDL 119

Query: 379 SQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYS-QPPASGYNQQGQGYAQDSYGGYH 437
                    + +P  Q PQAP     P        S +   +   Q+ Q           
Sbjct: 120 QPDPSLWGTAPKPEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQV 179

Query: 438 APQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQ 497
            PQ    + A + QQ       GY            P          AP    +   +  
Sbjct: 180 LPQGMPPRQAAFPQQGPPEQPPGYP-----QPPQGHPEQVQPQQFLPAPSQAPAQPPLPP 234

Query: 498 QGYGTGQQPSPNTASYPPQGATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLAN 557
           Q     QQP P      P  + Q     P   Q     Q PPQ        PQAQ P  N
Sbjct: 235 Q---LPQQPPPLQQPQFPGLSQQMPPPPPQPPQ---QQQQPPQ--------PQAQPPPQN 280

Query: 558 PPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQPDSGSQRAP 600
            P        PG   G   P     QP      Q   G QR P
Sbjct: 281 QP-----TPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGP 318

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 20/125 (16%), Positives = 30/125 (24%), Gaps = 8/125 (6%)

Query: 282 ESAKQLVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYP 341
           E  +  + +   + + R   +  G    G   +PP  +   G P  Q  G     P    
Sbjct: 365 EQRRAHLQDQFMQLQPRMRQLPMGSPMGGAMGQPP--YYGQG-PQQQFNGQPLGWPRMSM 421

Query: 342 GQTPQYNMSQPPYGGYPSQPTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGG 401
             TP          G          P    Q   Q+             P+ Q       
Sbjct: 422 MPTPMGPGGPLRPNGLA-PMNAVRAPSRNAQNAAQKPPMQP----VMYPPNYQSLPLSQD 476

Query: 402 SAAPA 406
              P 
Sbjct: 477 LPQPQ 481

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|203707 pfam07650, KH_2, KH domain

 Score = 36.7 bits (86), Expect = 0.002
 Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 5/57 (8%)

Query: 120 SYGGYQSMGTSKKIEIPNIRV---GVIIGKSGETIKYLQLQSGAKIQVTRDTEADLN 173
                +   T  ++ +  IR    G++IGK G  IK L  +    I++    +  LN
Sbjct: 14  GISDIEIERTPNRVIV-VIRTSQPGIVIGKGGSNIKKLGKELRKLIEL-EGKKVYLN 68

Length = 77

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

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 10/65 (15%)

Query: 133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTP-EQIAKA 191
           ++IP  ++  +IG  G+TIK +  ++G KI +  D           V +  +  E   KA
Sbjct: 6   MKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGT---------VYIAASDKEAAEKA 56

Query: 192 EQLIN 196
           +++I 
Sbjct: 57  KKMIE 61

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

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 40.4 bits (95), Expect = 0.003
 Identities = 32/171 (18%), Positives = 44/171 (25%), Gaps = 6/171 (3%)

Query: 491 SSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPT--SQSGYGSQVPPQSGYAGYGM 548
           +  A G +G        P   +  P     P+    P     +   ++            
Sbjct: 591 APGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAP 650

Query: 549 PQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQPDSGSQRAPPSNYGAAT 608
               K +A P A       P  AGG        +  P +  A P   +   P     A  
Sbjct: 651 EHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAP-AAPAGAAPAQPAPAPAATP 709

Query: 609 QPGYGSAAYGAPPGGSQAGYGQGPPSYYGGGYSQPVYTADGNAAPAAQPVQ 659
             G        PP  +Q   G   PS             D    PA  P Q
Sbjct: 710 PAGQADDPAAQPPQAAQ---GASAPSPAADDPVPLPPEPDDPPDPAGAPAQ 757

Length = 824

>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein; Provisional

 Score = 40.6 bits (95), Expect = 0.003
 Identities = 24/145 (16%), Positives = 34/145 (23%), Gaps = 2/145 (1%)

Query: 514 PPQGATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGG 573
           P  G   P       +      +   +  Y GYG P+A       P   Q   +  +   
Sbjct: 90  PSAGEPAPPPPHARRTSEPELPRPGRR-PYEGYGGPRADDRPPGLPRQDQLPTARPAYPA 148

Query: 574 YGQPGYSHSQPPPSSYAQPDSGSQRAPPSN-YGAATQPGYGSAAYGAPPGGSQAGYGQGP 632
           Y Q     + P  +            PP   Y +             P    +  Y Q  
Sbjct: 149 YQQRPEPGAWPRAADDYGWQQQRLGFPPRAPYASPASYAPEQERDREPYDAGRPEYDQRR 208

Query: 633 PSYYGGGYSQPVYTADGNAAPAAQP 657
             Y            D    P   P
Sbjct: 209 RDYDHPRPDWDRPRRDRTDRPEPPP 233

Length = 617

>gnl|CDD|223064 PHA03375, PHA03375, hypothetical protein; Provisional

 Score = 40.2 bits (94), Expect = 0.004
 Identities = 24/89 (26%), Positives = 34/89 (38%), Gaps = 2/89 (2%)

Query: 7   YSSDGTPSKRKYEDQTTPPSAAARRPTGFSAPDPAVAPTSYNSVPPPADEFQDFQAAKRR 66
           YS D     R    + + P  +A  P   S   P+   +S +S PPPA          RR
Sbjct: 367 YSLDDNVGGRPRTARLSAPPPSAAPPVPRSGSSPSSLSSSSSSAPPPAT--DPSSDPTRR 424

Query: 67  AEQIAARLCNSVSAEAKRPRVENGSGGFD 95
             +I +RL      E  R R  + +  F 
Sbjct: 425 YVRIISRLSFVRYRERLRRRAADPAFDFT 453

Length = 844

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	669
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	99.97
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.93
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.91
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.89
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.89
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.86
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.86
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.85
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.74
PRK13763	180	putative RNA-processing protein; Provisional	99.72
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.33
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.32
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.16
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.15
COG1094	194	Predicted RNA-binding protein (contains KH domains	99.14
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.13
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.12
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	99.1
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.06
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.05
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.98
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.94
smart00322	69	KH K homology RNA-binding domain.	98.92
smart00322	69	KH K homology RNA-binding domain.	98.83
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.78
PF13014	43	KH_3: KH domain	98.78
KOG2113	394	consensus Predicted RNA binding protein, contains	98.76
PRK13763	180	putative RNA-processing protein; Provisional	98.73
PF13014	43	KH_3: KH domain	98.73
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.65
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.6
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.57
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.36
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.33
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.32
KOG0119	554	consensus Splicing factor 1/branch point binding p	98.32
PRK08406	140	transcription elongation factor NusA-like protein;	98.28
KOG0119	554	consensus Splicing factor 1/branch point binding p	98.17
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.14
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.93
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.87
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	97.7
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.6
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	97.55
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.54
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	97.5
COG0195	190	NusA Transcription elongation factor [Transcriptio	97.45
KOG1960	531	consensus Predicted RNA-binding protein, contains	97.41
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	97.4
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.38
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.17
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.16
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	97.14
PRK00106	535	hypothetical protein; Provisional	97.07
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	97.06
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.93
PRK12704	520	phosphodiesterase; Provisional	96.92
TIGR01953	341	NusA transcription termination factor NusA. This m	96.87
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.83
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.82
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.78
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.77
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.75
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.61
PRK09202	470	nusA transcription elongation factor NusA; Validat	96.46
COG1094	194	Predicted RNA-binding protein (contains KH domains	96.43
KOG2113	394	consensus Predicted RNA binding protein, contains	96.38
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.36
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.29
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.25
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.25
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.09
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	96.02
PRK12705	508	hypothetical protein; Provisional	95.96
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	95.92
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.92
PRK00106	535	hypothetical protein; Provisional	95.82
PRK02821	77	hypothetical protein; Provisional	95.72
PRK12704	520	phosphodiesterase; Provisional	95.67
PRK00468	75	hypothetical protein; Provisional	95.65
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.28
COG1782	637	Predicted metal-dependent RNase, consists of a met	95.13
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	94.93
PRK01064	78	hypothetical protein; Provisional	94.82
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	94.6
PRK00468	75	hypothetical protein; Provisional	94.51
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	94.37
PRK02821	77	hypothetical protein; Provisional	94.21
KOG1960	531	consensus Predicted RNA-binding protein, contains	94.17
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	93.73
COG1837	76	Predicted RNA-binding protein (contains KH domain)	93.38
PRK01064	78	hypothetical protein; Provisional	93.31
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	92.9
COG5166	657	Uncharacterized conserved protein [Function unknow	92.8
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	92.68
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	92.39
COG1855	604	ATPase (PilT family) [General function prediction	92.38
PRK12705	508	hypothetical protein; Provisional	92.2
PRK06418	166	transcription elongation factor NusA-like protein;	91.9
COG5166	657	Uncharacterized conserved protein [Function unknow	90.94
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	90.87
PRK08406	140	transcription elongation factor NusA-like protein;	90.79
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	90.78
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	90.33
PRK13764	602	ATPase; Provisional	90.31
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	90.09
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	89.76
TIGR03802	562	Asp_Ala_antiprt aspartate-alanine antiporter. All	89.63
PRK12328	374	nusA transcription elongation factor NusA; Provisi	88.78
PRK03818	552	putative transporter; Validated	88.62
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	88.57
KOG2874	356	consensus rRNA processing protein [Translation, ri	88.04
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	87.79
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	86.34
COG1782	637	Predicted metal-dependent RNase, consists of a met	86.2
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	85.48
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	84.25
TIGR01953	341	NusA transcription termination factor NusA. This m	83.97
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	83.86
PF07054	34	Pericardin_rpt: Pericardin like repeat; InterPro:	83.6
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	83.24
COG1855	604	ATPase (PilT family) [General function prediction	82.8
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	82.18
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	82.17
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	81.47
PRK09202	470	nusA transcription elongation factor NusA; Validat	81.11
KOG1423	379	consensus Ras-like GTPase ERA [Cell cycle control,	80.24
PRK15405	217	ethanolamine utilization protein EutL; Provisional	80.03

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

Probab=100.00  E-value=2.5e-36  Score=331.79  Aligned_cols=395  Identities=28%  Similarity=0.342  Sum_probs=260.7

Q ss_pred             CCCCCCCCCCCCcc---chHHHHHHHHHHHccccccCCC--CCCCCceecCCCCCCCCccccccCCcccccCCCCCCCCC
Q 005922           44 PTSYNSVPPPADEF---QDFQAAKRRAEQIAARLCNSVS--AEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIP  118 (669)
Q Consensus        44 p~s~~~v~pp~~~~---~~~e~IkkIaeEtaARI~I~~~--~~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~  118 (669)
                      ...+.+|+.+..++   ---+.|.+|-.+++|||.|...  ...+|.+++.|.  .+.+..+..+|.+++.+.....   
T Consensus        54 ~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~--pe~v~~aK~li~evv~r~~~~~---  128 (600)
T KOG1676|consen   54 QTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGS--PENVEVAKQLIGEVVSRGRPPG---  128 (600)
T ss_pred             cccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCC--cccHHHHHHhhhhhhhccCCCC---
Confidence            34677888887662   1124699999999999997632  358999999998  4557777777777766442111   


Q ss_pred             CCCCCCC-CCCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHH
Q 005922          119 VSYGGYQ-SMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLIND  197 (669)
Q Consensus       119 ~s~g~~~-~~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~e  197 (669)
                       .+...+ ..+++.+|+||..++|+||||+|+|||.|++++||+|.+..|+....+ .++.|.|+|+++.|++|+.||.|
T Consensus       129 -~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-~~KplritGdp~~ve~a~~lV~d  206 (600)
T KOG1676|consen  129 -GFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-ADKPLRITGDPDKVEQAKQLVAD  206 (600)
T ss_pred             -CccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-CCCceeecCCHHHHHHHHHHHHH
Confidence             111112 245899999999999999999999999999999999999988764444 78999999999999999999999


Q ss_pred             HHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC
Q 005922          198 VLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT  277 (669)
Q Consensus       198 lI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~  277 (669)
                      +|+|+.....+.............+++|.||.++||+||||+|++||+|+.+||+||+|++++.+   .+.||+++|.|+
T Consensus       207 il~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p---~speR~~~IiG~  283 (600)
T KOG1676|consen  207 ILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDP---SSPERPAQIIGT  283 (600)
T ss_pred             HHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCC---CCccceeeeecC
Confidence            99985543322211000111223488999999999999999999999999999999999988766   678999999999


Q ss_pred             HHHHHHHHHHHHHHHhhcccCCC-CCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCC
Q 005922          278 SEQIESAKQLVNEVISENRIRNP-AMAGGYSQQ---GYQARPPTSWGTPGAPSMQQPGYG-YVQPGAYPGQTPQYNMSQP  352 (669)
Q Consensus       278 peqVq~Ak~LI~dlL~e~~~r~~-~~~GG~~~~---gY~p~Pp~~~Gppg~~~~~q~gYg-y~~~g~Y~~~~~qy~~~q~  352 (669)
                      +++|+.|.+||.+||+++...++ ++.+|.+..   .|.-.|..-||..-+. ++...+. ....|+|-....+     .
T Consensus       284 ~d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGr-GGEtIK~in~qSGA~~el~r~-----~  357 (600)
T KOG1676|consen  284 VDQIEHAAELINEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGR-GGETIKQINQQSGARCELSRQ-----P  357 (600)
T ss_pred             HHHHHHHHHHHHHHHHHHhccCCCCcCCCCccceeeEEEeccccccccccCC-CccchhhhcccCCccccccCC-----C
Confidence            99999999999999999765543 344444433   4556788888765433 1122222 2333554432221     2


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCC-CCCCC-CCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCccCCCCCCC
Q 005922          353 PYGGYPSQPTPGGYPGNWDQTP-TQQTS-QGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQPPASGYNQQGQGYAQ  430 (669)
Q Consensus       353 pyggy~~~~~~~~y~~gwdq~~-~~~~~-~~~gy~yY~qq~~~~~~~~~~~~~~p~~~~~~~~~q~~~~~y~~~~~~~~~  430 (669)
                      |++++..- .-.-+   -|.++ .|-.+ --.-++++...... .   ..++..|. ...++|++...-.|++..+++.+
T Consensus       358 p~~~~~ek-tf~Ir---G~~~QIdhAk~LIr~kvg~~~~n~~~-~---~~~a~gp~-~q~~~~~p~~~g~~~~~~~~~~~  428 (600)
T KOG1676|consen  358 PNGNPKEK-TFVIR---GDKRQIDHAKQLIRDKVGDIAPNTPY-P---NPGAGGPQ-TQFGNYGPHAPGPFGQQQQGAPQ  428 (600)
T ss_pred             CCCCccce-EEEEe---cCcccchHHHHHHHHHhcccCCCCCC-C---CCCcCCCC-CCCCCCCCCCCCCCCCCCCCCCC
Confidence            33322221 11111   11222 11000 00112333333221 1   11122222 34455555422236777888999


Q ss_pred             CCCCCcCCCCCcCCCCCCccccCCCCCCCCCCCccCCCCC
Q 005922          431 DSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQE  470 (669)
Q Consensus       431 ~~y~~y~~~q~~y~q~~~~~~q~~~~~~~~~~~~~~~~~~  470 (669)
                      +.+++|.+.|..|++. .++.+-      -+.++.||+.+
T Consensus       429 p~~g~p~~s~~~~g~g-~~~p~~------q~~~~~~P~~~  461 (600)
T KOG1676|consen  429 PANGGPPASQQPYGQG-GQQPQV------QPQQTMAPSAA  461 (600)
T ss_pred             CCCCCCCcccCCCCcc-ccCCcc------cCCCCCCcccC
Confidence            9999998888888876 333221      15566677666

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

Probab=100.00  E-value=7.1e-34  Score=312.47  Aligned_cols=227  Identities=34%  Similarity=0.523  Sum_probs=185.2

Q ss_pred             HHHHHHHHHHccccccCCCC----CCCCceecCCCCCCCCccccccCCcccccCCCCCC-CCCCCCCCCCCCCceEEEEe
Q 005922           61 QAAKRRAEQIAARLCNSVSA----EAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPS-AIPVSYGGYQSMGTSKKIEI  135 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~~~----~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~-~~~~s~g~~~~~~vt~rIlV  135 (669)
                      |+||+++++++|++.+....    ...+.+.|+|+  .+.+..+..++.++|.+..... ......+.+.....+++|.|
T Consensus       159 ETikqlqe~sg~k~i~iqd~~~~~~~~KplritGd--p~~ve~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~V  236 (600)
T KOG1676|consen  159 ETIKQLQEQSGVKMILVQDGSIATGADKPLRITGD--PDKVEQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKV  236 (600)
T ss_pred             cHHHHHHhhcCCceEEEecCCcCCCCCCceeecCC--HHHHHHHHHHHHHHHHhcccCCCccccccCcCccccceeEEec
Confidence            89999999999998776433    25678888886  5668888888888876322111 11133444455567999999


Q ss_pred             ccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhccc
Q 005922          136 PNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLT  215 (669)
Q Consensus       136 P~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~  215 (669)
                      |...||.||||+|++||+|+.+||+||+|..|+  ++.+.||++.|.|++|.|++|.++|.+||++......+...... 
T Consensus       237 Pr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd--~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~~~~~~~G~-  313 (600)
T KOG1676|consen  237 PRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDD--DPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGAGGGMGGGA-  313 (600)
T ss_pred             cccceeeEEecCchHHHHHhhccCceeEeecCC--CCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccCCCCcCCCC-
Confidence            999999999999999999999999999999886  46899999999999999999999999999997765322111000 


Q ss_pred             CCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          216 GQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       216 ~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                       .....++.|.||.++||+||||+|+|||.|..+|||+|.+..+  ++..+..||+|+|.|++.+|+.|+.||+++|...
T Consensus       314 -P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~--~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~  390 (600)
T KOG1676|consen  314 -PGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ--PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDI  390 (600)
T ss_pred             -ccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC--CCCCCccceEEEEecCcccchHHHHHHHHHhccc
Confidence             1112278999999999999999999999999999999999876  5667889999999999999999999999999874

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

Probab=99.97  E-value=5.8e-30  Score=264.56  Aligned_cols=194  Identities=30%  Similarity=0.459  Sum_probs=163.0

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCC
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGS  207 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~  207 (669)
                      .+.+|||||+..+|.||||+|+||.+|+++|||+|+++|+.|++|+.+||||.|+|+.|+|...+++|.|+|+|......
T Consensus        38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~  117 (402)
T KOG2191|consen   38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVA  117 (402)
T ss_pred             ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhc
Confidence            38999999999999999999999999999999999999999999999999999999999999999999999999764322


Q ss_pred             Ccc-hhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHH
Q 005922          208 GIV-ARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQ  286 (669)
Q Consensus       208 ~~~-~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~  286 (669)
                      +.. ........+..+++|+||++.+|.||||+|.+||.|+|+++|.|+|.+.. +..-+..||+|+|.|+++++.+|..
T Consensus       118 k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk-pt~~sLqervvt~sge~e~~~~A~~  196 (402)
T KOG2191|consen  118 KPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK-PTGISLQERVVTVSGEPEQNMKAVS  196 (402)
T ss_pred             CCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC-CCCccceeEEEEecCCHHHHHHHHH
Confidence            211 00001123345689999999999999999999999999999999999643 3344677999999999999999999


Q ss_pred             HHHHHHhhcccCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCC
Q 005922          287 LVNEVISENRIRNPAMAGGYSQQGYQ--ARPPTSWGTPGAPSM  327 (669)
Q Consensus       287 LI~dlL~e~~~r~~~~~GG~~~~gY~--p~Pp~~~Gppg~~~~  327 (669)
                      ||+++|.|++     +++.|.+..|.  ..|..|++|.+.++.
T Consensus       197 ~IL~Ki~eDp-----qs~scln~sya~vsGpvaNsnPtGspya  234 (402)
T KOG2191|consen  197 LILQKIQEDP-----QSGSCLNISYANVSGPVANSNPTGSPYA  234 (402)
T ss_pred             HHHHHhhcCC-----cccceeccchhcccCcccccCCCCCCCC
Confidence            9999999986     44556667664  557788888776543

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

Probab=99.93  E-value=2.2e-26  Score=232.50  Aligned_cols=230  Identities=23%  Similarity=0.318  Sum_probs=184.7

Q ss_pred             CCCCCCCCCCccchHHHHHHHHHHHccccccCCCCCCCCceecCCCCCCCCccccccCCcccccCCCCCCCCCCCCCCCC
Q 005922           46 SYNSVPPPADEFQDFQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQ  125 (669)
Q Consensus        46 s~~~v~pp~~~~~~~e~IkkIaeEtaARI~I~~~~~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~g~~~  125 (669)
                      |.|+........   ++||+++.+.+|.|.|.+.+.+||+++|+.+  .+.+...+..|+..|++-.           ..
T Consensus        56 sk~agavigkgg---~nik~lr~d~na~v~vpds~~peri~tisad--~~ti~~ilk~iip~lee~f-----------~~  119 (390)
T KOG2192|consen   56 SKNAGAVIGKGG---KNIKALRTDYNASVSVPDSSGPERILTISAD--IETIGEILKKIIPTLEEGF-----------QL  119 (390)
T ss_pred             cccccceecccc---ccHHHHhhhccceeeccCCCCCceeEEEecc--HHHHHHHHHHHhhhhhhCC-----------CC
Confidence            566666666666   7999999999999999999999999999986  4445555555555555221           12


Q ss_pred             CCCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcC
Q 005922          126 SMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESG  205 (669)
Q Consensus       126 ~~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~  205 (669)
                      ...|++||||..+++|.||||+|++||+|+|++.|+++|...  .++++++|||.|.|...+|..|++.|+++|+|....
T Consensus       120 ~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~--c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pik  197 (390)
T KOG2192|consen  120 PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE--CCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIK  197 (390)
T ss_pred             CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc--cCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcC
Confidence            234899999999999999999999999999999999999754  589999999999999999999999999999985321


Q ss_pred             CC-----------------------------C----------------c---chh------------------cccC---
Q 005922          206 GS-----------------------------G----------------I---VAR------------------RLTG---  216 (669)
Q Consensus       206 ~~-----------------------------~----------------~---~~r------------------r~~~---  216 (669)
                      ++                             +                .   ..+                  .|..   
T Consensus       198 gsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~said  277 (390)
T KOG2192|consen  198 GSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAID  277 (390)
T ss_pred             CcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCC
Confidence            00                             0                0   000                  0000   


Q ss_pred             --------------------------------CCC-CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCC
Q 005922          217 --------------------------------QAG-SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPP  263 (669)
Q Consensus       217 --------------------------------~~~-~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~pp  263 (669)
                                                      ..+ .++..+.||.++-|.||||+|..||+|++++||.|+|..    +
T Consensus       278 tw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide----p  353 (390)
T KOG2192|consen  278 TWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE----P  353 (390)
T ss_pred             CcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC----c
Confidence                                            001 246789999999999999999999999999999999963    4


Q ss_pred             CCCCCccEEEEEcCHHHHHHHHHHHHHHHhhccc
Q 005922          264 GDTSTERTVQIDGTSEQIESAKQLVNEVISENRI  297 (669)
Q Consensus       264 ge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~~  297 (669)
                      .+.++||+|+|+|+.++|+.|+.|+...++.-++
T Consensus       354 leGsedrIitItGTqdQIqnAQYLlQn~Vkq~re  387 (390)
T KOG2192|consen  354 LEGSEDRIITITGTQDQIQNAQYLLQNSVKQYRE  387 (390)
T ss_pred             CCCCCceEEEEeccHHHHhhHHHHHHHHHHhhhc
Confidence            5578899999999999999999999998886443

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

Probab=99.91  E-value=4.9e-24  Score=236.93  Aligned_cols=229  Identities=25%  Similarity=0.314  Sum_probs=177.6

Q ss_pred             HHHHHHHHHHccccccCC--CCCCCCceecCC-------CCCCCCccccccCCcccccCCCCCCCCCCCCCCCCCCCceE
Q 005922           61 QAAKRRAEQIAARLCNSV--SAEAKRPRVENG-------SGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSK  131 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~--~~~~ERiisisg-------~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~g~~~~~~vt~  131 (669)
                      +.||+||+++.+||+|.+  .+|.|||++|.+       ....+++++++.+|..+++.............  ...++++
T Consensus        63 ~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~--~~~~v~~  140 (485)
T KOG2190|consen   63 DIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDA--SGPEVTC  140 (485)
T ss_pred             HHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcccccccccccCCccc--cCCceEE
Confidence            689999988888888885  459999999999       22267789999999988662111111111111  1124899


Q ss_pred             EEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh----cCC-
Q 005922          132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE----SGG-  206 (669)
Q Consensus       132 rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~----~~~-  206 (669)
                      |||||..++|+||||+|++||+|+++|||+|+|.+++  ++++++|.|+|.|+.+.|.+|+..|..+|.+..    ... 
T Consensus       141 RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~--lP~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~  218 (485)
T KOG2190|consen  141 RLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDM--LPNSTERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLV  218 (485)
T ss_pred             EEEechhheeeeeccCcHHHHHHHHhcCceEEecCCC--CCcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCC
Confidence            9999999999999999999999999999999999885  899999999999999999999999999998842    100 


Q ss_pred             -------------------CC-c-----------------------------------chh---------------cc--
Q 005922          207 -------------------SG-I-----------------------------------VAR---------------RL--  214 (669)
Q Consensus       207 -------------------~~-~-----------------------------------~~r---------------r~--  214 (669)
                                         .. .                                   ..+               +.  
T Consensus       219 st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~  298 (485)
T KOG2190|consen  219 STIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTDR  298 (485)
T ss_pred             CcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCcc
Confidence                               00 0                                   000               00  


Q ss_pred             ---------cC--------------------C----CCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCC
Q 005922          215 ---------TG--------------------Q----AGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHL  261 (669)
Q Consensus       215 ---------~~--------------------~----~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~  261 (669)
                               ..                    .    ...++.+|+||++++++||||+|++|.+||+.|||.|+|.....
T Consensus       299 ~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~  378 (485)
T KOG2190|consen  299 IVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEE  378 (485)
T ss_pred             eeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccc
Confidence                     00                    0    11156799999999999999999999999999999999985422


Q ss_pred             CCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          262 PPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       262 ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      .  ....|+.|+|++...+...++.+|...|...
T Consensus       379 ~--~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~  410 (485)
T KOG2190|consen  379 V--SGVREALVQITGMLREDLLAQYLIRARLSAP  410 (485)
T ss_pred             c--CCcceeEEEecchhHHHHhhhhhcccccccC
Confidence            1  1467999999999999999999997777653

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

Probab=99.89  E-value=4.8e-23  Score=229.06  Aligned_cols=161  Identities=29%  Similarity=0.437  Sum_probs=138.6

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC---------CHHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG---------TPEQIAKAEQLINDVL  199 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG---------t~E~V~kA~~lI~elI  199 (669)
                      .++|||++.+++|.||||+|++||+|+++|.++|+|...   +++|.+|+|+|+|         ..++|.+|+++|..++
T Consensus        43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~---~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~  119 (485)
T KOG2190|consen   43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNES---LPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKL  119 (485)
T ss_pred             ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecC---CCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcc
Confidence            458999999999999999999999999999999999754   6899999999999         9999999999999987


Q ss_pred             HhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHH
Q 005922          200 AEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSE  279 (669)
Q Consensus       200 ~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~pe  279 (669)
                      +++.........   ......++++|+||.++||.||||+|++||+|+++|||+|+|.++++|   .+++|.|+|.|.++
T Consensus       120 ~~d~~~~~d~~~---~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP---~ster~V~IsG~~~  193 (485)
T KOG2190|consen  120 EEDDEAAEDNGE---DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLP---NSTERAVTISGEPD  193 (485)
T ss_pred             cccccccccCCc---cccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCC---cccceeEEEcCchH
Confidence            754432211110   001114789999999999999999999999999999999999998887   67799999999999


Q ss_pred             HHHHHHHHHHHHHhhcccC
Q 005922          280 QIESAKQLVNEVISENRIR  298 (669)
Q Consensus       280 qVq~Ak~LI~dlL~e~~~r  298 (669)
                      .|.+|...|..+|.++..+
T Consensus       194 av~~al~~Is~~L~~~~~~  212 (485)
T KOG2190|consen  194 AVKKALVQISSRLLENPPR  212 (485)
T ss_pred             HHHHHHHHHHHHHHhcCCc
Confidence            9999999999999986433

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

Probab=99.89  E-value=4e-24  Score=226.62  Aligned_cols=223  Identities=24%  Similarity=0.315  Sum_probs=179.7

Q ss_pred             HHHHHHHHHHccccccCCCC---CCCCceecCCCCCCCCccccccCCcccccCCCCCCCCCCCCCCCCCCCceEEEEecc
Q 005922           61 QAAKRRAEQIAARLCNSVSA---EAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPN  137 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~~~---~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~g~~~~~~vt~rIlVP~  137 (669)
                      ++||.|...+.+||+|-...   ..||++++.+.  .+...+|..+|++++..-..      .+.  ...++.+||+..+
T Consensus       219 ~TIknItkqTqsriD~hrken~Gaaek~itvh~t--pEg~s~Ac~~ILeimqkEA~------~~k--~~~e~pLk~lAHN  288 (584)
T KOG2193|consen  219 ATIKNITKQTQSRIDVHRKENAGAAEKIITVHST--PEGTSKACKMILEIMQKEAV------DDK--VAEEIPLKILAHN  288 (584)
T ss_pred             ccccCcchhhhheeeeeecccCCcccCceEEecC--ccchHHHHHHHHHHHHHhhh------ccc--hhhhcchhhhhhc
Confidence            48999999999999987432   57999999998  55577888888888752110      000  1134889999999


Q ss_pred             ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCC----------
Q 005922          138 IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGS----------  207 (669)
Q Consensus       138 ~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~----------  207 (669)
                      .+||+||||.|.+||+|+.+||++|+|++-.|...-++||.|+|.|+.|+|.+|..+|..+|+|+-..+.          
T Consensus       289 ~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~  368 (584)
T KOG2193|consen  289 NLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLP  368 (584)
T ss_pred             chhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCC
Confidence            9999999999999999999999999999877766678899999999999999999999999998633210          


Q ss_pred             --------Ccchh--------------cc------cC-CCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922          208 --------GIVAR--------------RL------TG-QAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP  258 (669)
Q Consensus       208 --------~~~~r--------------r~------~~-~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~  258 (669)
                              +....              .+      .. ......++|.||...||.||||+|.+||.|.+.+||.|+|.+
T Consensus       369 P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIap  448 (584)
T KOG2193|consen  369 PGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAP  448 (584)
T ss_pred             cccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecC
Confidence                    00000              00      00 123456799999999999999999999999999999999986


Q ss_pred             CCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922          259 LHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR  296 (669)
Q Consensus       259 ~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~  296 (669)
                      -+.   .+..+|+|+|+|++++.-+|.-.|-.+|+|..
T Consensus       449 pE~---pdvseRMViItGppeaqfKAQgrifgKikEen  483 (584)
T KOG2193|consen  449 PEI---PDVSERMVIITGPPEAQFKAQGRIFGKIKEEN  483 (584)
T ss_pred             CCC---CCcceeEEEecCChHHHHhhhhhhhhhhhhhc
Confidence            543   46789999999999999999999999998853

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

Probab=99.86  E-value=5.4e-21  Score=193.58  Aligned_cols=152  Identities=26%  Similarity=0.417  Sum_probs=137.0

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG  208 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~  208 (669)
                      |+++|||-++.+|.||||+|++||.|+.+.+|.|.|.     +.+.++|||+|+-+.+.|...++.|.-.|++....   
T Consensus        48 ~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vp-----ds~~peri~tisad~~ti~~ilk~iip~lee~f~~---  119 (390)
T KOG2192|consen   48 VELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVP-----DSSGPERILTISADIETIGEILKKIIPTLEEGFQL---  119 (390)
T ss_pred             eeEEEEEecccccceeccccccHHHHhhhccceeecc-----CCCCCceeEEEeccHHHHHHHHHHHhhhhhhCCCC---
Confidence            8999999999999999999999999999999999997     45789999999999999988888888777764321   


Q ss_pred             cchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHH
Q 005922          209 IVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLV  288 (669)
Q Consensus       209 ~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI  288 (669)
                               ....+++|+|..++.|.|||++|++||+||++..||++|.-.+.+   .+++|+|.|.|.++.|..+.+.|
T Consensus       120 ---------~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p---~stdrv~l~~g~~k~v~~~i~~i  187 (390)
T KOG2192|consen  120 ---------PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCP---HSTDRVVLIGGKPKRVVECIKII  187 (390)
T ss_pred             ---------CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCC---CCcceEEEecCCcchHHHHHHHH
Confidence                     225789999999999999999999999999999999999877776   78899999999999999999999


Q ss_pred             HHHHhhcccCCC
Q 005922          289 NEVISENRIRNP  300 (669)
Q Consensus       289 ~dlL~e~~~r~~  300 (669)
                      +++|+|.+.+..
T Consensus       188 l~~i~e~pikgs  199 (390)
T KOG2192|consen  188 LDLISESPIKGS  199 (390)
T ss_pred             HHHhhcCCcCCc
Confidence            999999877654

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

Probab=99.86  E-value=1.1e-21  Score=203.49  Aligned_cols=277  Identities=24%  Similarity=0.244  Sum_probs=211.3

Q ss_pred             CCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCC--CCCCCCCCCCCCCCccchHHHHHHHHHHHccccccCCCC-----CC
Q 005922           10 DGTPSKRKYEDQTTPPSAAARRPTGFSAPDPA--VAPTSYNSVPPPADEFQDFQAAKRRAEQIAARLCNSVSA-----EA   82 (669)
Q Consensus        10 ~~~~~Kr~~~d~~~p~~~~~~r~~~~s~~p~~--~~p~s~~~v~pp~~~~~~~e~IkkIaeEtaARI~I~~~~-----~~   82 (669)
                      ..+++||..+...||+  .++|.+..+.....  +..+++.+-+...+..   ++|..+.+|++|||+++...     ..
T Consensus        11 ~~~s~kr~~~a~pe~~--~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG---~ti~~lqk~tgariklSks~dfyPGTT   85 (402)
T KOG2191|consen   11 APDSRKRPLEAPPEPG--STKRTNTGEDGQYFLKVLIPSYAAGSIIGKGG---QTIVQLQKETGARIKLSKSKDFYPGTT   85 (402)
T ss_pred             CCCCccccccCCCCcc--ccccccCCCCCceEEEEEeecccccceeccch---HHHHHHHhccCcEEEeccccccCCCcc
Confidence            4568899998887766  67899988888776  5677999989888888   89999999999999999654     58


Q ss_pred             CCceecCCCCCCCCccccccCCcccccCCCCCCCCCCCC-C-CCCCCCceEEEEeccccccceeccCCcchhHHHhhcCc
Q 005922           83 KRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSY-G-GYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGA  160 (669)
Q Consensus        83 ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~-g-~~~~~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGA  160 (669)
                      ||+|.|.|.  .+++...+..|.+++.+.+....-.+.. . -..+..-.+||+||+.-+|.||||+|.|||.|+|+++|
T Consensus        86 eRvcli~Gt--~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga  163 (402)
T KOG2191|consen   86 ERVCLIQGT--VEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGA  163 (402)
T ss_pred             ceEEEEecc--HHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCc
Confidence            999999998  6667777888888876444322211111 0 01223356899999999999999999999999999999


Q ss_pred             EEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcc----------hhccc----------CCCCC
Q 005922          161 KIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIV----------ARRLT----------GQAGS  220 (669)
Q Consensus       161 kI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~----------~rr~~----------~~~~~  220 (669)
                      .|+|+...++.-+..||+|+|+|++|++.+|+++|+++|.|+........          .+..+          .....
T Consensus       164 ~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpvaNsnPtGspya~~~~~~~as  243 (402)
T KOG2191|consen  164 WIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPVANSNPTGSPYAYQAHVLPAS  243 (402)
T ss_pred             ceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCcccccCCCCCCCCCCCcccccc
Confidence            99998555556788899999999999999999999999999864322110          01000          01112


Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      ....+-|+..++|..-|.++.++-.|...+|+.|.|... +........+ +.+.|....+..|..||..++...
T Consensus       244 tas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~-l~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~~~~a  316 (402)
T KOG2191|consen  244 TASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA-LNTMAGYGYN-TNILGLGLSILAAEGVLAAKVASA  316 (402)
T ss_pred             chhhccccccccccccccccccceeeecccccceeeccc-cccccccccc-ccccchhhhhhhhhhHHHHhhccc
Confidence            334567899999999999999999999999999988643 1112233344 788888999999999998887653

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

Probab=99.85  E-value=7.6e-22  Score=209.46  Aligned_cols=223  Identities=24%  Similarity=0.329  Sum_probs=171.3

Q ss_pred             HHHHHHHHHHccccccCCCC-----CCCCceecCCCCCCCCccccccCCccccc-----CC---------C---------
Q 005922           61 QAAKRRAEQIAARLCNSVSA-----EAKRPRVENGSGGFDSADKGFSSPPSDLK-----SI---------P---------  112 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~~~-----~~ERiisisg~~~~eav~kA~~~i~~~l~-----~i---------~---------  112 (669)
                      .++|+|.++++++|.|+.--     .+||-|++.|.  .+++.+|-..|..+|.     ++         +         
T Consensus       300 rnlKkIeq~TgTkITis~lqels~ynpERTItVkGs--iEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~  377 (584)
T KOG2193|consen  300 RNLKKIEQDTGTKITISKLQELSLYNPERTITVKGS--IEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALG  377 (584)
T ss_pred             ccHHHHHhhcCCceeeeehhhhcccCccceEEeccc--HHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccC
Confidence            47999999999999998432     68999999996  5666665444444432     10         0         


Q ss_pred             ---CC--C------CCCCCCCC-----CC-CCCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCC
Q 005922          113 ---AP--S------AIPVSYGG-----YQ-SMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSP  175 (669)
Q Consensus       113 ---~~--~------~~~~s~g~-----~~-~~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~  175 (669)
                         +.  .      ..++.+..     .+ .....++|+||...||.||||+|.+||+|.+.+||.|+|....  .++..
T Consensus       378 ~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE--~pdvs  455 (584)
T KOG2193|consen  378 LFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE--IPDVS  455 (584)
T ss_pred             CCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC--CCCcc
Confidence               00  0      00000000     01 1235689999999999999999999999999999999997543  56788


Q ss_pred             CccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEE
Q 005922          176 TRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQ  255 (669)
Q Consensus       176 eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIq  255 (669)
                      +|.|+|+|.+|...||-..|..+|+|+...+...        ....+.+|.||...+|+||||||.++++|++.|+|.|.
T Consensus       456 eRMViItGppeaqfKAQgrifgKikEenf~~Pke--------evklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~  527 (584)
T KOG2193|consen  456 ERMVIITGPPEAQFKAQGRIFGKIKEENFFLPKE--------EVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVV  527 (584)
T ss_pred             eeEEEecCChHHHHhhhhhhhhhhhhhccCCchh--------hheeeeeeeccchhhhhhhccccccHHHHhccccceEE
Confidence            9999999999999999999999999976433211        12345688999999999999999999999999999999


Q ss_pred             eccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhccc
Q 005922          256 VIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENRI  297 (669)
Q Consensus       256 I~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~~  297 (669)
                      |..+. .+ ++.+.-+|.|.|..-+.+.|...|.++|.+++.
T Consensus       528 vPrdq-tp-dEnd~vivriiGhfyatq~aQrki~~iv~qvkq  567 (584)
T KOG2193|consen  528 VPRDQ-TP-DENDQVIVRIIGHFYATQNAQRKIAHIVNQVKQ  567 (584)
T ss_pred             ccccC-CC-CccceeeeeeechhhcchHHHHHHHHHHHHHHH
Confidence            97665 33 344566799999999999999999999998653

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.74  E-value=6.6e-18  Score=165.60  Aligned_cols=138  Identities=28%  Similarity=0.454  Sum_probs=107.7

Q ss_pred             EEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccc---cCCHHHHHHHHHHHHHHHHhhhcCCCCc
Q 005922          133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVEL---MGTPEQIAKAEQLINDVLAEAESGGSGI  209 (669)
Q Consensus       133 IlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtI---tGt~E~V~kA~~lI~elI~e~~~~~~~~  209 (669)
                      |.||.+++|.|||++|++||.|+++|||+|+|+.+        +..|.|   +++++++.+|+.+|..++......    
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--------TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPE----   69 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--------CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHH----
Confidence            57899999999999999999999999999999743        234666   889999999999999987742211    


Q ss_pred             chhcccCCCCCcEEEEeeCC---------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHH
Q 005922          210 VARRLTGQAGSDHFAMKIPN---------NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQ  280 (669)
Q Consensus       210 ~~rr~~~~~~~~t~~I~VP~---------~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peq  280 (669)
                      ...++... ...-..+.|..         ..+|+|||++|++|+.|++.|||+|.|.           ++.|+|.|++++
T Consensus        70 ~A~~l~gd-~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~-----------~~~v~i~G~~~~  137 (172)
T TIGR03665        70 KALKLLDD-DYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY-----------GKTVGIIGDPEQ  137 (172)
T ss_pred             HHHHhcCC-cceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc-----------CCEEEEECCHHH
Confidence            00000000 00111223333         3689999999999999999999999995           368999999999


Q ss_pred             HHHHHHHHHHHHhh
Q 005922          281 IESAKQLVNEVISE  294 (669)
Q Consensus       281 Vq~Ak~LI~dlL~e  294 (669)
                      |+.|+++|++||+.
T Consensus       138 ~~~A~~~i~~li~~  151 (172)
T TIGR03665       138 VQIAREAIEMLIEG  151 (172)
T ss_pred             HHHHHHHHHHHHcC
Confidence            99999999999955

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=99.72  E-value=3.4e-17  Score=161.69  Aligned_cols=143  Identities=29%  Similarity=0.428  Sum_probs=109.5

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccc----cCCHHHHHHHHHHHHHHHHhhhc
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVEL----MGTPEQIAKAEQLINDVLAEAES  204 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtI----tGt~E~V~kA~~lI~elI~e~~~  204 (669)
                      +...|.||.+++|.|||++|++||.|+++|||+|+|+.+        +..|.|    +++++.+++|+++|.+++.....
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~--------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~   74 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE--------TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSP   74 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC--------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCH
Confidence            678999999999999999999999999999999999743        245556    58999999999999999884211


Q ss_pred             CCCCcchhcccCCC-CCcEEEEe--eC-----CCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEc
Q 005922          205 GGSGIVARRLTGQA-GSDHFAMK--IP-----NNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDG  276 (669)
Q Consensus       205 ~~~~~~~rr~~~~~-~~~t~~I~--VP-----~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG  276 (669)
                      .    ...++.+.. ..+.++|.  ..     ...+|+|||++|++||.|++.|||+|.|.           ++.|+|.|
T Consensus        75 e----~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~-----------~~~v~i~G  139 (180)
T PRK13763         75 E----KALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY-----------GKTVAIIG  139 (180)
T ss_pred             H----HHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc-----------CCEEEEEe
Confidence            0    000000000 00011110  11     13689999999999999999999999995           34699999


Q ss_pred             CHHHHHHHHHHHHHHHhh
Q 005922          277 TSEQIESAKQLVNEVISE  294 (669)
Q Consensus       277 ~peqVq~Ak~LI~dlL~e  294 (669)
                      ++++|+.|+++|++||+.
T Consensus       140 ~~~~~~~A~~~I~~li~g  157 (180)
T PRK13763        140 DPEQVEIAREAIEMLIEG  157 (180)
T ss_pred             CHHHHHHHHHHHHHHHcC
Confidence            999999999999999955

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.33  E-value=3.2e-12  Score=105.89  Aligned_cols=64  Identities=39%  Similarity=0.628  Sum_probs=57.7

Q ss_pred             EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHH
Q 005922          223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVN  289 (669)
Q Consensus       223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~  289 (669)
                      ++|+||.+++++||||+|++||+|+++|||+|.|.+...   ....+|+|+|+|+.++|++|+.||.
T Consensus         2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL---PGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC---CCCCceEEEEEeCHHHHHHHHHhhC
Confidence            689999999999999999999999999999999975432   2567899999999999999999983

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

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.32  E-value=1.9e-12  Score=107.32  Aligned_cols=65  Identities=37%  Similarity=0.563  Sum_probs=59.4

Q ss_pred             eEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHH
Q 005922          130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLIN  196 (669)
Q Consensus       130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~  196 (669)
                      +++|+||...+|+||||+|++||+|+++|||+|+|.++.  +.+..+|+|+|+|+.|+|.+|+.+|.
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~--~~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSV--LPGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCC--CCCCCceEEEEEeCHHHHHHHHHhhC
Confidence            379999999999999999999999999999999998654  34678999999999999999999883

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

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

Probab=99.16  E-value=9.8e-11  Score=96.27  Aligned_cols=59  Identities=39%  Similarity=0.586  Sum_probs=53.4

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHH
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVN  289 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~  289 (669)
                      +...|.||.+++++||||+|++||+|+++|||+|.|..          ++.|+|+|+ .+.|+.|+++|+
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            35678999999999999999999999999999999851          468999999 999999999984

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.15  E-value=5.9e-11  Score=96.91  Aligned_cols=61  Identities=30%  Similarity=0.474  Sum_probs=55.1

Q ss_pred             EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHH
Q 005922          223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVN  289 (669)
Q Consensus       223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~  289 (669)
                      .+|.||.+++++|||++|++|++|+++|||+|.|...      ++.++.|+|+|+.++|..|+.+|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~------~~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP------GSKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCC------CCCCCEEEEEcCHHHHHHHHHHhC
Confidence            5789999999999999999999999999999999642      256889999999999999999874

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.

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

Probab=99.14  E-value=8.9e-11  Score=116.26  Aligned_cols=145  Identities=28%  Similarity=0.401  Sum_probs=106.6

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-----CHHHHHHHHHHHHHHHHhhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-----TPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-----t~E~V~kA~~lI~elI~e~~  203 (669)
                      .++.+.||..+++.|||+.|++.|.|++.++++|.|+..        +..|+|..     ++..+.+|...|..+-.-..
T Consensus         8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~--------~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~   79 (194)
T COG1094           8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK--------TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFP   79 (194)
T ss_pred             ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC--------CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCC
Confidence            567899999999999999999999999999999999643        33444433     57788999988877644321


Q ss_pred             cCCCCcchhcccCC-CCCcEEE---Eee-CC----CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEE
Q 005922          204 SGGSGIVARRLTGQ-AGSDHFA---MKI-PN----NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQI  274 (669)
Q Consensus       204 ~~~~~~~~rr~~~~-~~~~t~~---I~V-P~----~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtI  274 (669)
                      ..    ..-++... .-.+.++   +.- +.    ...|+|||++|.+.+-|++.|+|.|.|.           +.+|.|
T Consensus        80 pe----~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~-----------g~tVai  144 (194)
T COG1094          80 PE----KALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY-----------GKTVAI  144 (194)
T ss_pred             HH----HHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe-----------CcEEEE
Confidence            10    00001000 0001111   111 11    2468999999999999999999999996           569999


Q ss_pred             EcCHHHHHHHHHHHHHHHhhcc
Q 005922          275 DGTSEQIESAKQLVNEVISENR  296 (669)
Q Consensus       275 tG~peqVq~Ak~LI~dlL~e~~  296 (669)
                      .|..++|+.|++.|+++|+...
T Consensus       145 iG~~~~v~iAr~AVemli~G~~  166 (194)
T COG1094         145 IGGFEQVEIAREAVEMLINGAP  166 (194)
T ss_pred             ecChhhhHHHHHHHHHHHcCCC
Confidence            9999999999999999998743

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.13  E-value=3.7e-11  Score=97.48  Aligned_cols=60  Identities=35%  Similarity=0.607  Sum_probs=54.3

Q ss_pred             EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHH
Q 005922          222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLV  288 (669)
Q Consensus       222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI  288 (669)
                      |++|.||.+++++|||++|++||+|+++|||+|.|..+      + ++..|+|+|+.++|++|++||
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            57899999999999999999999999999999999632      2 456999999999999999987

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.12  E-value=6.4e-11  Score=96.69  Aligned_cols=62  Identities=29%  Similarity=0.498  Sum_probs=56.3

Q ss_pred             eEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHH
Q 005922          130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLIN  196 (669)
Q Consensus       130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~  196 (669)
                      +++|.||..++++|||++|++||+|+++|||+|.|.+.     +..++.|+|+|+.++|.+|+.+|+
T Consensus         1 ~~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~-----~~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP-----GSKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             CeEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCC-----CCCCCEEEEEcCHHHHHHHHHHhC
Confidence            36899999999999999999999999999999999854     257899999999999999999873

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=2.1e-10  Score=93.35  Aligned_cols=63  Identities=43%  Similarity=0.647  Sum_probs=56.2

Q ss_pred             EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHH
Q 005922          223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVN  289 (669)
Q Consensus       223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~  289 (669)
                      ++|.||.+++++|||++|++|++|+++|+|+|.|....    ++..++.|+|.|+.++|+.|+.+|+
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~----~~~~~~~v~i~G~~~~v~~a~~~i~   64 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG----SGSEERIVTITGTPEAVEKAKELIL   64 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCC----CCCCceEEEEEcCHHHHHHHHHHhC
Confidence            57999999999999999999999999999999997432    1456899999999999999999874

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=99.10  E-value=3.7e-11  Score=97.51  Aligned_cols=60  Identities=42%  Similarity=0.732  Sum_probs=54.6

Q ss_pred             eEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHH
Q 005922          130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLI  195 (669)
Q Consensus       130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI  195 (669)
                      |++|+||...+++||||+|++||+|+++|+|+|.|+++     + .+..|+|+|+.++|++|+++|
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            57899999999999999999999999999999999754     2 345999999999999999987

; 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 ....

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

Probab=99.06  E-value=1.9e-10  Score=94.54  Aligned_cols=59  Identities=27%  Similarity=0.469  Sum_probs=53.8

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCC-HHHHHHHHHHHH
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT-PEQIAKAEQLIN  196 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt-~E~V~kA~~lI~  196 (669)
                      .+..|.||..++|+||||+|++||+|+++|||+|.|++         ++.|.|+|+ .++|++|+++|+
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            46889999999999999999999999999999999974         357999998 999999999884

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

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

Probab=99.05  E-value=2.7e-10  Score=92.67  Aligned_cols=63  Identities=41%  Similarity=0.655  Sum_probs=56.9

Q ss_pred             EEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHH
Q 005922          131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLIN  196 (669)
Q Consensus       131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~  196 (669)
                      .+|.||..++++|||++|++|++|+++|+|+|.|....+   ...+++|+|.|+.++|.+|+.+|.
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~~v~~a~~~i~   64 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVEKAKELIL   64 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHHHHHHHHHHhC
Confidence            689999999999999999999999999999999986432   467899999999999999998873

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.

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

Probab=98.98  E-value=2.6e-10  Score=126.14  Aligned_cols=211  Identities=19%  Similarity=0.217  Sum_probs=155.5

Q ss_pred             HHHHHHHHHHccccccCC-CCCCCCceecCCCCCCCCccccccCCcccccCCCCCCCCCCCCCCCCCCCceEEEEecccc
Q 005922           61 QAAKRRAEQIAARLCNSV-SAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPNIR  139 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~-~~~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~g~~~~~~vt~rIlVP~~~  139 (669)
                      .+||.|++.+.+||.+.. .+..||...+.+-  ...+.++...+..++....               .|.+.+-||...
T Consensus        88 snik~l~~~t~aKi~L~~ed~g~e~~~~~~~~--p~~v~~a~a~~~~~~~~~~---------------pvk~~lsvpqr~  150 (608)
T KOG2279|consen   88 SNIKQLRKQTGAKIDLDTEDVGDERVLLISGF--PVQVCKAKAAIHQILTENT---------------PVSEQLSVPQRS  150 (608)
T ss_pred             CCcchhhcccccceecCcccCCcccchhhccC--CCCCChHHHHHHHHHhcCC---------------cccccccchhhh
Confidence            379999999999999995 3477887777764  4456666666666655322               267888899999


Q ss_pred             ccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCC------------
Q 005922          140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGS------------  207 (669)
Q Consensus       140 vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~------------  207 (669)
                      +++|||++|++|+.|++-++|+|.+++.   -.+...+++.|.+...-++.|..+|.+.+.+++....            
T Consensus       151 ~~~i~grgget~~si~~ss~aki~~d~n---gr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvpr  227 (608)
T KOG2279|consen  151 VGRIIGRGGETIRSICKSSGAKITCDKN---GRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPR  227 (608)
T ss_pred             cccccccchhhhcchhcccccccccccc---cccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCC
Confidence            9999999999999999999999999865   2456678999999888888899999888776532100            


Q ss_pred             --Cc------------------chhc--cc---------------------------------CCCCCcEEEEeeCCCce
Q 005922          208 --GI------------------VARR--LT---------------------------------GQAGSDHFAMKIPNNKV  232 (669)
Q Consensus       208 --~~------------------~~rr--~~---------------------------------~~~~~~t~~I~VP~~~v  232 (669)
                        ..                  ..+.  +.                                 ........+|.||+.++
T Consensus       228 k~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~ls  307 (608)
T KOG2279|consen  228 KQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILS  307 (608)
T ss_pred             CCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccc
Confidence              00                  0000  00                                 00012345899999999


Q ss_pred             eeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHH
Q 005922          233 GLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVI  292 (669)
Q Consensus       233 G~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL  292 (669)
                      |.|||+.|++|+.+...+++++.|.-.... ..-....+++|.|....++.|.+||...+
T Consensus       308 g~lig~~gey~s~yssasn~~~hi~t~pyt-~~v~~~qic~~egkqh~~n~vl~ml~~~~  366 (608)
T KOG2279|consen  308 GDLIGHAGEYLSVYSSASNHPNHIWTQPYT-SRVLQLQICVNEGKQHYENSVLEMLTVHV  366 (608)
T ss_pred             cchhhhhhhhhhhhhhccCccceEEecccc-chhhhhhhheecchhHHHHHHHhhhhccC
Confidence            999999999999999999999998643211 00111256889999999999999988443

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

Probab=98.94  E-value=5.5e-10  Score=123.57  Aligned_cols=143  Identities=32%  Similarity=0.541  Sum_probs=122.5

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCC
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGS  207 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~  207 (669)
                      .+.+++.|+...|-+||||.|.+||.|++.+++||.+..+.    -..+++.++.|-+..+.+|+.+|++++.+..    
T Consensus        67 ~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed----~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~----  138 (608)
T KOG2279|consen   67 DIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED----VGDERVLLISGFPVQVCKAKAAIHQILTENT----  138 (608)
T ss_pred             heeeeEeecccceeeeeccccCCcchhhcccccceecCccc----CCcccchhhccCCCCCChHHHHHHHHHhcCC----
Confidence            37899999999999999999999999999999999997543    3457778888899999999999999888743    


Q ss_pred             CcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHH
Q 005922          208 GIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQL  287 (669)
Q Consensus       208 ~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~L  287 (669)
                                  .+.+.+.||...+++|||++|.+|++|+..++++|.+...    +.+-..+.+.|.+....++.|+.|
T Consensus       139 ------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n----gr~g~~~~~~i~~qqk~~~~a~~~  202 (608)
T KOG2279|consen  139 ------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN----GRLGLSRLIKISGQQKEVAAAKHL  202 (608)
T ss_pred             ------------cccccccchhhhcccccccchhhhcchhcccccccccccc----cccccccceecccccchHHHHHhh
Confidence                        3456778999999999999999999999999999998632    334557788888888889999999


Q ss_pred             HHHHHhh
Q 005922          288 VNEVISE  294 (669)
Q Consensus       288 I~dlL~e  294 (669)
                      +.+.|++
T Consensus       203 ~~~~~~e  209 (608)
T KOG2279|consen  203 ILEKVSE  209 (608)
T ss_pred             hhccccc
Confidence            9888866

>smart00322 KH K homology RNA-binding domain

Probab=98.92  E-value=6.8e-09  Score=83.67  Aligned_cols=67  Identities=42%  Similarity=0.698  Sum_probs=59.7

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHh
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVIS  293 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~  293 (669)
                      .+.+|.||.+++++|||++|++|++|++.|+|+|.+...      ......|+|.|+.+.|+.|+.+|.++|+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~------~~~~~~v~i~g~~~~v~~a~~~i~~~~~   69 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED------GSEERVVEITGPPENVEKAAELILEILE   69 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC------CCCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence            467899999999999999999999999999999999632      1257899999999999999999999873

>smart00322 KH K homology RNA-binding domain

Probab=98.83  E-value=9.1e-09  Score=82.92  Aligned_cols=66  Identities=42%  Similarity=0.711  Sum_probs=59.9

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL  199 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI  199 (669)
                      ++.+|.||...+++|||++|.+|++|+++|+++|.+....     ....+|+|.|+.+++..|+.+|.+++
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            6789999999999999999999999999999999997442     25688999999999999999999876

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.78  E-value=2.7e-09  Score=104.94  Aligned_cols=123  Identities=18%  Similarity=0.182  Sum_probs=83.3

Q ss_pred             HHHHHHHHHHccccccCCCCCCCCceec--CCCCCCCCccccccCCcccccCCC-CCCCCCCCCCCCCCCCceEEEEecc
Q 005922           61 QAAKRRAEQIAARLCNSVSAEAKRPRVE--NGSGGFDSADKGFSSPPSDLKSIP-APSAIPVSYGGYQSMGTSKKIEIPN  137 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~~~~~ERiisi--sg~~~~eav~kA~~~i~~~l~~i~-~~~~~~~s~g~~~~~~vt~rIlVP~  137 (669)
                      ++|++|.++++++|.+.+.   +..+.|  ... +.+++.+|...|........ ..+.......     -+..-+.|..
T Consensus        18 ~~Ik~I~~~tgv~I~Id~~---~g~V~I~~~t~-d~~~i~kA~~~I~~i~~gf~~e~A~~l~gd~-----y~~~Vi~I~~   88 (172)
T TIGR03665        18 ETKKEIEERTGVKLDIDSE---TGEVKIEEEDE-DPLAVMKAREVVKAIGRGFSPEKALKLLDDD-----YMLEVIDLKE   88 (172)
T ss_pred             hHHHHHHHHhCcEEEEEcC---CceEEEecCCC-CHHHHHHHHHHHHHHHcCCCHHHHHHhcCCc-----ceEEEEEhhh
Confidence            7999999999999999863   234555  221 34556666665544322100 0000000001     0112233333


Q ss_pred             ---------ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          138 ---------IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       138 ---------~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                               ..+|+|||++|+|+|.|++.|+|+|.|..          +.|.|.|+.++|+.|+++|++||+..
T Consensus        89 ~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665        89 YGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----------KTVGIIGDPEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             ccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC----------CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence                     36999999999999999999999999962          56999999999999999999999654

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.

>PF13014 KH_3: KH domain

Probab=98.78  E-value=1.1e-08  Score=78.07  Aligned_cols=43  Identities=51%  Similarity=0.772  Sum_probs=37.4

Q ss_pred             ceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEc
Q 005922          231 KVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDG  276 (669)
Q Consensus       231 ~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG  276 (669)
                      +|++||||+|++||+|+++|+|+|+|..+.   ..++++++|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~---~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPEN---EPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCcc---CCCCCceEEEEEC
Confidence            589999999999999999999999997622   2367799999997

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

Probab=98.76  E-value=7.5e-09  Score=108.09  Aligned_cols=150  Identities=21%  Similarity=0.317  Sum_probs=112.8

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh---hc
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA---ES  204 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~---~~  204 (669)
                      .+++.+.||...|+.|+|++|.+||.|+.+|...|+....      ..|-++.++|..|.|+.|++.|...-+..   .-
T Consensus        25 nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr------~eePiF~vTg~~edv~~aRrei~saaeH~~l~~~   98 (394)
T KOG2113|consen   25 NVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR------GEEPIFPVTGRHEDVRRARREIPSAAEHFGLIRA   98 (394)
T ss_pred             ccceeeecCcccceeecccCccccchhhhhhcceeccCCC------CCCCcceeccCchhHHHHhhcCccccceeeeeee
Confidence            4899999999999999999999999999999999998532      34589999999999999999987632221   00


Q ss_pred             CCCCc-chhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHH-HH
Q 005922          205 GGSGI-VARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQ-IE  282 (669)
Q Consensus       205 ~~~~~-~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peq-Vq  282 (669)
                      ..... .... .......+..+.||...+++|+|..|++||.|++.+..-|.-.-       ...+.++.|+|-++. ++
T Consensus        99 s~s~Sgg~~~-~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v-------~~~~~Vf~Vtg~~~nC~k  170 (394)
T KOG2113|consen   99 SRSFSGGTNG-ASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV-------RCGEPVFCVTGAPKNCVK  170 (394)
T ss_pred             cccccCCCcc-ccccCCCceeeeccceeeeeccccccCccchheecccceEeeec-------cCCCceEEEecCCcchhh
Confidence            00000 0000 01234456778899999999999999999999999999887642       234778999998666 77


Q ss_pred             HHH-HHHHHH
Q 005922          283 SAK-QLVNEV  291 (669)
Q Consensus       283 ~Ak-~LI~dl  291 (669)
                      +|+ ..|+..
T Consensus       171 ra~s~eie~t  180 (394)
T KOG2113|consen  171 RARSCEIEQT  180 (394)
T ss_pred             hccccchhhh
Confidence            776 445443

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.73  E-value=4e-09  Score=104.52  Aligned_cols=123  Identities=17%  Similarity=0.198  Sum_probs=81.1

Q ss_pred             HHHHHHHHHHccccccCCCCCCCCceecC-C-CCCCCCccccccCCcccccCCC-CCCCCCCCCCCCCCCCceEEE-Eec
Q 005922           61 QAAKRRAEQIAARLCNSVSAEAKRPRVEN-G-SGGFDSADKGFSSPPSDLKSIP-APSAIPVSYGGYQSMGTSKKI-EIP  136 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~~~~~ERiisis-g-~~~~eav~kA~~~i~~~l~~i~-~~~~~~~s~g~~~~~~vt~rI-lVP  136 (669)
                      ++|+.|.++++++|++.+..   ..+.|. . ..+.+++.+|...|...+.... ..+.....      ..+..++ .|.
T Consensus        23 k~Ik~I~e~tg~~I~i~~~~---g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~g------d~y~~~Vi~i~   93 (180)
T PRK13763         23 ETKKEIEERTGVKLEIDSET---GEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLD------DDYVLEVIDLS   93 (180)
T ss_pred             hHHHHHHHHHCcEEEEECCC---CeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHHHHHhC------CCceEEEEEhh
Confidence            79999999999999999632   334443 1 1134556666655544332100 00000001      1122221 111


Q ss_pred             ---------cccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          137 ---------NIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       137 ---------~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                               ...+|+||||+|+|+|.|++.|||+|.|..          +.|.|.|+.++++.|.+.|++|++..
T Consensus        94 ~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763         94 DYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG----------KTVAIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             hccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----------CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence                     136999999999999999999999999963          33888999999999999999999654

>PF13014 KH_3: KH domain

Probab=98.73  E-value=8.3e-09  Score=78.80  Aligned_cols=43  Identities=44%  Similarity=0.643  Sum_probs=38.8

Q ss_pred             cccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC
Q 005922          139 RVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG  183 (669)
Q Consensus       139 ~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG  183 (669)
                      +||+||||+|++||+|+++|+|+|+|.++  ..++..+|+|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~--~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPE--NEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCc--cCCCCCceEEEEEC
Confidence            47999999999999999999999999873  36788899999987

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

Probab=98.65  E-value=9e-08  Score=89.17  Aligned_cols=67  Identities=25%  Similarity=0.390  Sum_probs=53.9

Q ss_pred             CCceeeeecCCchHHHHHHHHhCCeEEeccCCCCC-------------CCCCCccEEEEEcCH---HHHHHHHHHHHHHH
Q 005922          229 NNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPP-------------GDTSTERTVQIDGTS---EQIESAKQLVNEVI  292 (669)
Q Consensus       229 ~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~pp-------------ge~s~er~VtItG~p---eqVq~Ak~LI~dlL  292 (669)
                      .+++|+|||++|++||+|+++|||+|.|.++....             .+.+++-.|.|++..   +.+++|+++|+++|
T Consensus        14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll   93 (120)
T cd02395          14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL   93 (120)
T ss_pred             CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence            37899999999999999999999999998652111             112234679999975   89999999999999


Q ss_pred             hhc
Q 005922          293 SEN  295 (669)
Q Consensus       293 ~e~  295 (669)
                      ...
T Consensus        94 ~~~   96 (120)
T cd02395          94 KPA   96 (120)
T ss_pred             ccC
Confidence            864

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.

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

Probab=98.60  E-value=3.8e-08  Score=112.39  Aligned_cols=150  Identities=25%  Similarity=0.328  Sum_probs=102.4

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCC-CCC------ccccccCC-HHHH-------HHHH
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLN-SPT------RSVELMGT-PEQI-------AKAE  192 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~-~~e------RvVtItGt-~E~V-------~kA~  192 (669)
                      .+.++-.|..-.+|+|.-  |++.+-|.+..|-. .-..||++.-. +.+      .-+.|.|- .+-+       ..|.
T Consensus       452 GVPIk~pVAGIAMGLI~e--g~~~~vLsDI~G~E-DhlGDMDFKVAGT~~GiTAlQMDiKi~Git~eim~~AL~QAk~aR  528 (692)
T COG1185         452 GVPIKAPVAGIAMGLIKE--GDKYAVLSDILGDE-DHLGDMDFKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGAR  528 (692)
T ss_pred             CCcccccccchhccceec--CCceEeeccccccc-cccCCceeEEecCCCcceeeeeeeeecCCCHHHHHHHHHHHHHHH
Confidence            377888899899999955  55444444444433 11233332211 111      33567774 3322       3445


Q ss_pred             HHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEE
Q 005922          193 QLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTV  272 (669)
Q Consensus       193 ~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~V  272 (669)
                      ..|+++|.+........     ....-+..+.+.|+.+++..|||++|++||+|.++|||+|.|.          ++.+|
T Consensus       529 lhIL~~M~~ai~~pr~e-----ls~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie----------ddGtv  593 (692)
T COG1185         529 LHILIVMNEAISEPRKE-----LSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE----------DDGTV  593 (692)
T ss_pred             HHHHHHHHHHHhhhhhh-----hhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec----------CCCcE
Confidence            57777887765433211     1112245678999999999999999999999999999999994          36789


Q ss_pred             EEEcC-HHHHHHHHHHHHHHHhhc
Q 005922          273 QIDGT-SEQIESAKQLVNEVISEN  295 (669)
Q Consensus       273 tItG~-peqVq~Ak~LI~dlL~e~  295 (669)
                      .|.+. .+.+++|+++|++++++.
T Consensus       594 ~i~~s~~~~~~~ak~~I~~i~~e~  617 (692)
T COG1185         594 KIAASDGESAKKAKERIEAITREV  617 (692)
T ss_pred             EEEecchHHHHHHHHHHHHHHhhc
Confidence            99999 689999999999999874

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

Probab=98.57  E-value=1e-07  Score=88.85  Aligned_cols=73  Identities=36%  Similarity=0.496  Sum_probs=53.1

Q ss_pred             EEEEecc------ccccceeccCCcchhHHHhhcCcEEEEccCCcc---------------CCCCCCccccccCC--HHH
Q 005922          131 KKIEIPN------IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEA---------------DLNSPTRSVELMGT--PEQ  187 (669)
Q Consensus       131 ~rIlVP~------~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~---------------~p~~~eRvVtItGt--~E~  187 (669)
                      .||+||.      .++|+|||.+|.|||+|+++|||+|.|..+...               ..+.+..|++..-+  .+.
T Consensus         2 ~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~   81 (120)
T cd02395           2 EKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEA   81 (120)
T ss_pred             CEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHH
Confidence            4566665      458999999999999999999999999754100               01122333333445  699


Q ss_pred             HHHHHHHHHHHHHhhh
Q 005922          188 IAKAEQLINDVLAEAE  203 (669)
Q Consensus       188 V~kA~~lI~elI~e~~  203 (669)
                      +++|+.+|++||....
T Consensus        82 ~~~A~~~I~~ll~~~~   97 (120)
T cd02395          82 LAKAVEAIEELLKPAI   97 (120)
T ss_pred             HHHHHHHHHHHhccCC
Confidence            9999999999998644

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=98.36  E-value=1.7e-06  Score=100.93  Aligned_cols=89  Identities=31%  Similarity=0.445  Sum_probs=70.7

Q ss_pred             HHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCc
Q 005922          190 KAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTE  269 (669)
Q Consensus       190 kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~e  269 (669)
                      ++...|.++|++..... ...     ...-+....|.||.++++.|||.||++||.|+++|||+|.|.          ++
T Consensus       553 ~g~~~Il~~m~~al~~p-~~~-----s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~----------d~  616 (719)
T TIGR02696       553 DARLAILDVMAEAIDTP-DEM-----SPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE----------DD  616 (719)
T ss_pred             HHHHHHHHHHHHHHhCc-ccc-----ccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe----------cC
Confidence            34456777777765433 111     111245678999999999999999999999999999999995          26


Q ss_pred             cEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922          270 RTVQIDGT-SEQIESAKQLVNEVISE  294 (669)
Q Consensus       270 r~VtItG~-peqVq~Ak~LI~dlL~e  294 (669)
                      ..|.|.+. .+.+++|+++|+.++..
T Consensus       617 G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       617 GTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            78999998 89999999999999984

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.

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.33  E-value=9.7e-07  Score=104.38  Aligned_cols=140  Identities=23%  Similarity=0.356  Sum_probs=111.6

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG  208 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~  208 (669)
                      +...+.|-...+..||||+|.+|.+|++++.|+|.+.+.     +..+..|++++...++.+|++.|++++.+....   
T Consensus       347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-----~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~---  418 (753)
T KOG2208|consen  347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ-----GSNNKKVVITGVSANDEKAVEDVEKIIAEILNS---  418 (753)
T ss_pred             eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc-----cCCCCCeEEeccccchhHHHHHHHHHHHhhhcc---
Confidence            567788888999999999999999999999999999752     456788999999999999999999999885431   


Q ss_pred             cchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCC-eEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHH
Q 005922          209 IVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGA-RIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQL  287 (669)
Q Consensus       209 ~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGA-rIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~L  287 (669)
                                 ..+..+.||...+.+|||.+|..|..|++++++ .|++..      +......++|.|....|..++.+
T Consensus       419 -----------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~------~~~~~~~~~~~~~~~dv~~~~~~  481 (753)
T KOG2208|consen  419 -----------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQN------NNNSSDMVTIRGISKDVEKSVSL  481 (753)
T ss_pred             -----------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCC------CCcccccceEeccccccchhHHH
Confidence                       234678999999999999999999999999995 444421      23334557777776666666555


Q ss_pred             HHHHHh
Q 005922          288 VNEVIS  293 (669)
Q Consensus       288 I~dlL~  293 (669)
                      +..+..
T Consensus       482 ~~~~~~  487 (753)
T KOG2208|consen  482 LKALKA  487 (753)
T ss_pred             HHhhhh
Confidence            554443

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.32  E-value=7.5e-07  Score=105.30  Aligned_cols=189  Identities=17%  Similarity=0.225  Sum_probs=119.6

Q ss_pred             CCCCceecCCCCCCCCccccccCCcccccCCCCCCCCCCCCCCCCCCCceEEEEeccccccceeccCCcchhHHHhhcCc
Q 005922           81 EAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGA  160 (669)
Q Consensus        81 ~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~g~~~~~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGA  160 (669)
                      ..++.+.+.|.  .+++..|...+...+...             ....+..++.|....+.+|||++|.+|+.+++++.+
T Consensus       168 ~~~~~i~~~G~--~e~V~~a~~~~~~~~~~~-------------~~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~  232 (753)
T KOG2208|consen  168 KKDPQIKLQGV--VESVERAREPILNLIDRK-------------NERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKV  232 (753)
T ss_pred             ccCCeeeeecc--hhhhhhhhhhhhhhhhcc-------------cceeEEEEeeccccchhhhcccccccccccccccee
Confidence            44566666665  444444444444433322             112277899999999999999999999999999999


Q ss_pred             EEEEccCCccCCCCCCccccccC-------CHHHHHHHHHHHHH-HHHh-hhcCC--------CC---------------
Q 005922          161 KIQVTRDTEADLNSPTRSVELMG-------TPEQIAKAEQLIND-VLAE-AESGG--------SG---------------  208 (669)
Q Consensus       161 kI~Iskd~e~~p~~~eRvVtItG-------t~E~V~kA~~lI~e-lI~e-~~~~~--------~~---------------  208 (669)
                      .|+|..+.     .......|.+       ..-.+..++.+++. ++.. .....        .+               
T Consensus       233 ~i~ip~sn-----~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  307 (753)
T KOG2208|consen  233 HIHIPDSN-----KSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDS  307 (753)
T ss_pred             EEEccccc-----ccchhhhhccccccceehhhhhHHHHHHhcChhhhhhhhhccccccccccccchhhHHHhhcchhhh
Confidence            99996332     2222233333       23333333333322 1111 00000        00               


Q ss_pred             --------cchhcc-------------------cCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCC
Q 005922          209 --------IVARRL-------------------TGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHL  261 (669)
Q Consensus       209 --------~~~rr~-------------------~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~  261 (669)
                              .....+                   ..........+.|-...+..||||+|.+|.+|++++.|.|.+..   
T Consensus       308 i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~---  384 (753)
T KOG2208|consen  308 IFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK---  384 (753)
T ss_pred             hhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc---
Confidence                    000000                   00011245567788889999999999999999999999999852   


Q ss_pred             CCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          262 PPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       262 ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                         ..++++.|+|+|....+++|+++|++.+.+.
T Consensus       385 ---~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei  415 (753)
T KOG2208|consen  385 ---QGSNNKKVVITGVSANDEKAVEDVEKIIAEI  415 (753)
T ss_pred             ---ccCCCCCeEEeccccchhHHHHHHHHHHHhh
Confidence               2466889999999999999999988877663

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

Probab=98.32  E-value=5e-06  Score=91.83  Aligned_cols=65  Identities=29%  Similarity=0.396  Sum_probs=51.4

Q ss_pred             CceeeeecCCchHHHHHHHHhCCeEEeccCC-----------CCCCC-CCCccEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922          230 NKVGLVIGKGGETIKNMQARTGARIQVIPLH-----------LPPGD-TSTERTVQIDGT-SEQIESAKQLVNEVISE  294 (669)
Q Consensus       230 ~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~-----------~ppge-~s~er~VtItG~-peqVq~Ak~LI~dlL~e  294 (669)
                      ++||+|||..|.|.|+|+++|||||.|.++.           +.... ..++-.+.|+.+ .|.|++|.++|+.||.+
T Consensus       153 NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~  230 (554)
T KOG0119|consen  153 NFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS  230 (554)
T ss_pred             ceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence            7999999999999999999999999998630           11111 222334778877 88899999999999986

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.28  E-value=1.1e-06  Score=84.06  Aligned_cols=104  Identities=20%  Similarity=0.365  Sum_probs=76.1

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG  208 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~  208 (669)
                      -...|+|....+|..||++|++||.|++..|-+|.|-.-.                    +.+..+|.++|.-.......
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s--------------------~d~~~fI~n~l~Pa~V~~v~   91 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS--------------------DDPEEFIKNIFAPAAVRSVT   91 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcC--------------------CCHHHHHHHHcCCCEEEEEE
Confidence            3578888999999999999999999999999999885321                    12445565555442211100


Q ss_pred             cchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922          209 IVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI  257 (669)
Q Consensus       209 ~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~  257 (669)
                           .........+.+.|+.+..+++|||+|.+|+.++..++-++.|.
T Consensus        92 -----I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         92 -----IKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             -----EEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence                 00111134567889999999999999999999999999888774

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

Probab=98.17  E-value=2.3e-06  Score=94.38  Aligned_cols=76  Identities=32%  Similarity=0.371  Sum_probs=58.0

Q ss_pred             CceEEEEeccc------cccceeccCCcchhHHHhhcCcEEEEcc-----------C-CccCCCCC--CccccccCCHHH
Q 005922          128 GTSKKIEIPNI------RVGVIIGKSGETIKYLQLQSGAKIQVTR-----------D-TEADLNSP--TRSVELMGTPEQ  187 (669)
Q Consensus       128 ~vt~rIlVP~~------~vG~IIGKgGetIK~IqeeTGAkI~Isk-----------d-~e~~p~~~--eRvVtItGt~E~  187 (669)
                      .++.||.||.+      +||+|||..|.|+|+|++||||||.|..           + .....+..  +..+++.-+.|.
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            37788888864      4999999999999999999999999943           1 11122222  344455557899


Q ss_pred             HHHHHHHHHHHHHhhh
Q 005922          188 IAKAEQLINDVLAEAE  203 (669)
Q Consensus       188 V~kA~~lI~elI~e~~  203 (669)
                      |++|+++|+.||.+..
T Consensus       217 i~~Ai~vienli~~av  232 (554)
T KOG0119|consen  217 IKKAIAVIENLIQSAV  232 (554)
T ss_pred             HHHHHHHHHHHHHhhc
Confidence            9999999999999743

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.14  E-value=5.6e-06  Score=97.30  Aligned_cols=89  Identities=25%  Similarity=0.352  Sum_probs=67.2

Q ss_pred             HHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCcc
Q 005922          191 AEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTER  270 (669)
Q Consensus       191 A~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er  270 (669)
                      +...|.++|++.......     .....-+....+.||.++++.|||+||++||+|+++|||+|.|.          ++.
T Consensus       526 ~~~~I~~~m~~~l~~~~~-----~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~----------ddG  590 (684)
T TIGR03591       526 GRLHILGEMNKVISEPRA-----ELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE----------DDG  590 (684)
T ss_pred             HHHHHHHHHHHHHhhhhc-----cccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe----------cCe
Confidence            334566666665432211     11112245678999999999999999999999999999999995          256


Q ss_pred             EEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922          271 TVQIDGT-SEQIESAKQLVNEVISE  294 (669)
Q Consensus       271 ~VtItG~-peqVq~Ak~LI~dlL~e  294 (669)
                      .|.|.+. .+.+++|+++|+.++.+
T Consensus       591 ~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       591 TVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             EEEEEECcHHHHHHHHHHHHhhhcc
Confidence            8888876 88999999999998765

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).

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.93  E-value=1.6e-05  Score=94.92  Aligned_cols=88  Identities=22%  Similarity=0.339  Sum_probs=68.2

Q ss_pred             HHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCe-EEeccCCCCCCCCCCcc
Q 005922          192 EQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGAR-IQVIPLHLPPGDTSTER  270 (669)
Q Consensus       192 ~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGAr-IqI~~~~~ppge~s~er  270 (669)
                      ...|.++|++........     ....-.....|.|+.++++.|||.||.+||.|+++||++ |.|.          ++-
T Consensus       661 ~~~Il~~M~~~i~~pr~~-----~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~----------ddg  725 (891)
T PLN00207        661 RKHILAEMSKCSPPPSKR-----LSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ----------DDG  725 (891)
T ss_pred             HHHHHHHHHHHHhhhhhh-----hcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC----------CCe
Confidence            345666666655432211     111224567899999999999999999999999999999 8874          257


Q ss_pred             EEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922          271 TVQIDGT-SEQIESAKQLVNEVISE  294 (669)
Q Consensus       271 ~VtItG~-peqVq~Ak~LI~dlL~e  294 (669)
                      .|.|.+. .+.+++|+++|++++.+
T Consensus       726 ~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        726 TVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            8999987 89999999999999875

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.87  E-value=2.8e-05  Score=74.56  Aligned_cols=103  Identities=22%  Similarity=0.336  Sum_probs=72.7

Q ss_pred             eEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCc
Q 005922          130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGI  209 (669)
Q Consensus       130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~  209 (669)
                      ..-|+|....+|..||++|++||.|++..|-+|.|-.              .+.+++      .+|..+|.-......  
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe--------------ys~D~~------~fI~N~l~PA~V~~V--   91 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE--------------YSENLE------EFVANKLAPAEVKNV--   91 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE--------------cCCCHH------HHHHHcCCCceEEEE--
Confidence            5778899999999999999999999999999998842              222222      233333322111000  


Q ss_pred             chhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922          210 VARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI  257 (669)
Q Consensus       210 ~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~  257 (669)
                         ......+.....+.|+.+..++.|||+|.||+...+.++-++.|.
T Consensus        92 ---~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        92 ---TVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             ---EEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence               000011234567889999999999999999999999999888774

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.

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

Probab=97.70  E-value=0.00014  Score=75.60  Aligned_cols=75  Identities=15%  Similarity=0.271  Sum_probs=51.0

Q ss_pred             CcEEEEeeCC------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCC---------------CCC-ccEEEEEcC
Q 005922          220 SDHFAMKIPN------NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGD---------------TST-ERTVQIDGT  277 (669)
Q Consensus       220 ~~t~~I~VP~------~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge---------------~s~-er~VtItG~  277 (669)
                      ..+.+|.||.      ++||+|||..|.++|+|+++|+|+|.|-++......               +.. .-.|++..+
T Consensus        91 k~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p  170 (259)
T KOG1588|consen   91 KLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAP  170 (259)
T ss_pred             eEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCC
Confidence            3456777765      699999999999999999999999999865221110               011 112555566


Q ss_pred             HHH----HHHHHHHHHHHHhh
Q 005922          278 SEQ----IESAKQLVNEVISE  294 (669)
Q Consensus       278 peq----Vq~Ak~LI~dlL~e  294 (669)
                      +..    |..|.+.|+.+|.-
T Consensus       171 ~~ea~~rl~~AleeI~klL~P  191 (259)
T KOG1588|consen  171 PAEAYARLAYALEEIKKLLVP  191 (259)
T ss_pred             HHHHHHHHHHHHHHHHHhcCC
Confidence            544    44688888887743

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.60  E-value=6.8e-05  Score=88.33  Aligned_cols=65  Identities=25%  Similarity=0.345  Sum_probs=56.3

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE  201 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e  201 (669)
                      ....|.||.++++.|||++|++||+|+++|||+|.|..+        -.+.+...+.+.+++|+++|..++.+
T Consensus       551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd--------G~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD--------GTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC--------eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            678899999999999999999999999999999999743        24445555789999999999999775

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).

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=97.55  E-value=0.00011  Score=86.86  Aligned_cols=90  Identities=31%  Similarity=0.428  Sum_probs=67.7

Q ss_pred             HHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCc
Q 005922          190 KAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTE  269 (669)
Q Consensus       190 kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~e  269 (669)
                      ++...|.++|.+.........     .........+.|+.++++.|||.||.+||.|+++||++|.|.          ++
T Consensus       528 ~g~~~I~~~M~~aI~~~r~~~-----~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~----------d~  592 (693)
T PRK11824        528 EGRLHILGKMNEAISEPRAEL-----SPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE----------DD  592 (693)
T ss_pred             HHHHHHHHHHHHHhcCChhhh-----cccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC----------CC
Confidence            344566777777654322111     111234567788999999999999999999999999988873          25


Q ss_pred             cEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922          270 RTVQIDGT-SEQIESAKQLVNEVISE  294 (669)
Q Consensus       270 r~VtItG~-peqVq~Ak~LI~dlL~e  294 (669)
                      ..|.|.+. .+.+++|+++|+.++.+
T Consensus       593 G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        593 GTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             ceEEEEcccHHHHHHHHHHHHHhccc
Confidence            78999997 89999999999999865

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.54  E-value=0.0001  Score=86.33  Aligned_cols=64  Identities=25%  Similarity=0.409  Sum_probs=57.1

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHHh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAE  201 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e  201 (669)
                      ....|.|+.++++.|||.||.+||.|+++|||+|.|..+         -.|.|.+ +.+.+++|+.+|+.++..
T Consensus       578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~---------G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD---------GTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC---------cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            678999999999999999999999999999999999743         3466655 789999999999999985

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.

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=97.50  E-value=0.0013  Score=66.32  Aligned_cols=129  Identities=17%  Similarity=0.221  Sum_probs=95.1

Q ss_pred             EEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcc
Q 005922          131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIV  210 (669)
Q Consensus       131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~  210 (669)
                      +.|.+.....-+|+..+|..++.|-...||+|.+..+        +..|.|+|++..++.+...|.+++....       
T Consensus        28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~--------~~~i~I~g~k~~~~~i~~~i~~~l~~i~-------   92 (210)
T PF14611_consen   28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS--------ENRIRITGTKSTAEYIEASINEILSNIR-------   92 (210)
T ss_pred             eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC--------CcEEEEEccHHHHHHHHHHHHHHHhhcE-------
Confidence            4555567888899999999999998889999999754        4679999999999999999999988732       


Q ss_pred             hhcccCCCCCcEEEEeeCCCceeeee----cCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEc-----CHHHH
Q 005922          211 ARRLTGQAGSDHFAMKIPNNKVGLVI----GKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDG-----TSEQI  281 (669)
Q Consensus       211 ~rr~~~~~~~~t~~I~VP~~~vG~II----GKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG-----~peqV  281 (669)
                                 +.+|.++.-.--...    -.....|+.|++.|++.|...+         ++..+.|+.     ..+.+
T Consensus        93 -----------~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~---------~~~~~~i~~~~~~~~~~~~  152 (210)
T PF14611_consen   93 -----------TEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNP---------DGNKLKISWLASPENEKRA  152 (210)
T ss_pred             -----------EEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECC---------CCCeEEEEEEeeccccchH
Confidence                       233333321111111    1236679999999999999853         233455554     47889


Q ss_pred             HHHHHHHHHHHhh
Q 005922          282 ESAKQLVNEVISE  294 (669)
Q Consensus       282 q~Ak~LI~dlL~e  294 (669)
                      +.|++|+.-.+..
T Consensus       153 ~~a~RlL~~a~~~  165 (210)
T PF14611_consen  153 DRAKRLLLWALDY  165 (210)
T ss_pred             HHHHHHHHHhccC
Confidence            9999999998864

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=97.45  E-value=0.00028  Score=70.81  Aligned_cols=102  Identities=26%  Similarity=0.359  Sum_probs=71.6

Q ss_pred             eEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCc
Q 005922          130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGI  209 (669)
Q Consensus       130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~  209 (669)
                      ..-+++-.+.+|..||++|++||.|.++.|-+|.|-.-.                    +.-..+|.++|.-.....   
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s--------------------~d~~~fI~nal~Pa~v~~---  133 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS--------------------EDPAEFIKNALAPAEVLS---  133 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC--------------------CCHHHHHHHhcCcceEeE---
Confidence            345556667799999999999999999999888874321                    112334444444211100   


Q ss_pred             chhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922          210 VARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI  257 (669)
Q Consensus       210 ~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~  257 (669)
                      ....+.   ......+.|+.+..+++|||+|.+|+.+.+.||-+|.|.
T Consensus       134 V~~~~~---d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~  178 (190)
T COG0195         134 VNIKED---DGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE  178 (190)
T ss_pred             EEEEeC---CCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence            000000   112678889999999999999999999999999999996

>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]

Probab=97.41  E-value=0.00045  Score=75.01  Aligned_cols=158  Identities=14%  Similarity=0.027  Sum_probs=96.1

Q ss_pred             ccceeccCCcchhHHHhhcCcEEEEccCC---ccCC-CCCC--ccccccC-CHHHHHHHHHHHHHHHHhhhcCCCCc-c-
Q 005922          140 VGVIIGKSGETIKYLQLQSGAKIQVTRDT---EADL-NSPT--RSVELMG-TPEQIAKAEQLINDVLAEAESGGSGI-V-  210 (669)
Q Consensus       140 vG~IIGKgGetIK~IqeeTGAkI~Iskd~---e~~p-~~~e--RvVtItG-t~E~V~kA~~lI~elI~e~~~~~~~~-~-  210 (669)
                      +..++.| |.+..+|++++|+.|.+....   |..+ +..+  -+..|.+ +.|-+++|+..|.-+++.+....... + 
T Consensus       106 ~~~~~TR-g~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~~~~~~~~n~~~V~  184 (531)
T KOG1960|consen  106 TKATSTR-GTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPSTAEITSKAIERIKGVFMQDVEINNVRNVY  184 (531)
T ss_pred             ccceecc-chhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCccHHHHHHHHhhCccceeecccccccceEE
Confidence            5566666 999999999999999885321   1111 1222  3445666 78999999999997766543211100 0 


Q ss_pred             -hhcc---------cC----CCCC--cE---EEEeeCCCc-eeeeecCCchHHHHHHHHhCCeEEeccC---CCCC--CC
Q 005922          211 -ARRL---------TG----QAGS--DH---FAMKIPNNK-VGLVIGKGGETIKNMQARTGARIQVIPL---HLPP--GD  265 (669)
Q Consensus       211 -~rr~---------~~----~~~~--~t---~~I~VP~~~-vG~IIGKGGstIK~Iqe~TGArIqI~~~---~~pp--ge  265 (669)
                       ..++         ..    ..+.  ..   +-+.+|... -+.+=+++-.++.+|+.++++++.|.++   +..+  ++
T Consensus       185 i~~~~sP~~~i~~~V~~~~f~~G~~Y~~k~~v~~~~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~  264 (531)
T KOG1960|consen  185 ILVRASPLSEIENKVGVQLFSKGRYYPNKALATDKDPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGN  264 (531)
T ss_pred             EeecCCchhhhccccccccccccccchhheecccCCcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCccccc
Confidence             0000         00    0010  01   112234333 3445567778899999999999887554   2222  22


Q ss_pred             CCC-ccEEEEEcC-HHHHHHHHHHHHHHHhhcccC
Q 005922          266 TST-ERTVQIDGT-SEQIESAKQLVNEVISENRIR  298 (669)
Q Consensus       266 ~s~-er~VtItG~-peqVq~Ak~LI~dlL~e~~~r  298 (669)
                      ++. -+.|-|++. ++.+..|+++|.+|++.+...
T Consensus       265 EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~~  299 (531)
T KOG1960|consen  265 ESNEPMYIFSTHGNGNGENGAPRRKWNLEEKVYIN  299 (531)
T ss_pred             ccCCceeEEeecCCchhhccchhHHHhHHHHHHHH
Confidence            333 345777766 999999999999999886443

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

Probab=97.40  E-value=0.00018  Score=81.02  Aligned_cols=93  Identities=25%  Similarity=0.341  Sum_probs=71.6

Q ss_pred             HHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCc
Q 005922          190 KAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTE  269 (669)
Q Consensus       190 kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~e  269 (669)
                      .|+..|.++|.+.+.......     .....+...|.|+.+++..+||.+|.++|+|..+||+.-+|.           |
T Consensus       571 ~ar~~Il~~m~k~i~~Pr~~~-----~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-----------e  634 (760)
T KOG1067|consen  571 EARLQILDIMEKNINSPRGSD-----KEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-----------E  634 (760)
T ss_pred             HHHHHHHHHHHhhcCCcccCc-----cccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec-----------C
Confidence            345677777777654332211     122356678999999999999999999999999999777763           5


Q ss_pred             cEEEEEcC-HHHHHHHHHHHHHHHhhcccC
Q 005922          270 RTVQIDGT-SEQIESAKQLVNEVISENRIR  298 (669)
Q Consensus       270 r~VtItG~-peqVq~Ak~LI~dlL~e~~~r  298 (669)
                      .+|+|.-. ...+++|+++|..++..++..
T Consensus       635 ~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~  664 (760)
T KOG1067|consen  635 GTFSIFAPTQAAMEEAKEFIDGIIKDDQVQ  664 (760)
T ss_pred             ceEEEEecCHHHHHHHHHHHHHHhcCcccc
Confidence            68888887 888999999999999875443

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

Probab=97.38  E-value=0.00015  Score=79.42  Aligned_cols=69  Identities=32%  Similarity=0.439  Sum_probs=59.8

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR  296 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~  296 (669)
                      ..+.+.|-.++||.|||++|++||+|+..|.++|+|+.       ...+-.|+|.|..+.-.+|+..|..+++.+.
T Consensus        47 ~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~-------~~~e~kv~ifg~~~m~~kaka~id~~~~k~e  115 (629)
T KOG0336|consen   47 FPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIK-------CDLEVKVTIFGINHMRKKAKASIDRGQDKDE  115 (629)
T ss_pred             CchhhhhhhhhhheeeccCcchhhhhhcccceeEEEec-------cCceeEEEEechHHHHHHHHhhHhhhhhhhh
Confidence            34567889999999999999999999999999999984       2346789999999999999999988887643

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.17  E-value=0.0001  Score=88.07  Aligned_cols=66  Identities=18%  Similarity=0.366  Sum_probs=56.9

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcE-EEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHHhhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAK-IQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAk-I~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e~~  203 (669)
                      ....|.|+.++++.|||.||.|||.|.++||++ |.|..+         -.|.|.+ +.+.+++|+++|++++.+..
T Consensus       685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd---------g~V~I~a~d~~~i~~A~~~I~~l~~~~~  752 (891)
T PLN00207        685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD---------GTVKITAKDLSSLEKSKAIISSLTMVPT  752 (891)
T ss_pred             eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC---------eeEEEEeCCHHHHHHHHHHHHHHhcCcC
Confidence            688999999999999999999999999999999 999643         2355544 88999999999999988643

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

Probab=97.16  E-value=0.00028  Score=77.32  Aligned_cols=71  Identities=24%  Similarity=0.284  Sum_probs=62.5

Q ss_pred             CCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       127 ~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      .++.++|-|-+.+||.|||++|++||+|+..|+++|+|.+.      ..+-.|+|.|..+--.+|+..|...+++.+
T Consensus        45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~------~~e~kv~ifg~~~m~~kaka~id~~~~k~e  115 (629)
T KOG0336|consen   45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC------DLEVKVTIFGINHMRKKAKASIDRGQDKDE  115 (629)
T ss_pred             CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc------CceeEEEEechHHHHHHHHhhHhhhhhhhh
Confidence            45889999999999999999999999999999999999753      456789999999988899999988887654

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

Probab=97.14  E-value=0.00045  Score=71.85  Aligned_cols=37  Identities=32%  Similarity=0.579  Sum_probs=34.3

Q ss_pred             ceEEEEeccc------cccceeccCCcchhHHHhhcCcEEEEc
Q 005922          129 TSKKIEIPNI------RVGVIIGKSGETIKYLQLQSGAKIQVT  165 (669)
Q Consensus       129 vt~rIlVP~~------~vG~IIGKgGetIK~IqeeTGAkI~Is  165 (669)
                      ++.||+||.+      +||+|||.+|.|+|+|+++|+|+|.|.
T Consensus        92 ~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir  134 (259)
T KOG1588|consen   92 LTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR  134 (259)
T ss_pred             EEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence            7889999976      599999999999999999999999993

>PRK00106 hypothetical protein; Provisional

Probab=97.07  E-value=0.0026  Score=72.98  Aligned_cols=65  Identities=23%  Similarity=0.432  Sum_probs=55.3

Q ss_pred             EEEEeeCC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhhc
Q 005922          222 HFAMKIPN-NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISEN  295 (669)
Q Consensus       222 t~~I~VP~-~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e~  295 (669)
                      ...|.+|+ ++.|+||||.|.|||.|...|||.|.|.         ++...|+|++. +---+.|+.-++.||.+.
T Consensus       226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---------dtp~~v~lS~fdpvRReiAr~~le~Li~dg  292 (535)
T PRK00106        226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID---------DTPEVVVLSGFDPIRREIARMTLESLIKDG  292 (535)
T ss_pred             eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc---------CCCCeEEEeCCChHHHHHHHHHHHHHHHcC
Confidence            44677887 7899999999999999999999999994         45678999996 888888888888888664

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=97.06  E-value=0.0024  Score=73.11  Aligned_cols=65  Identities=23%  Similarity=0.430  Sum_probs=54.8

Q ss_pred             EEEEeeCC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhhc
Q 005922          222 HFAMKIPN-NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISEN  295 (669)
Q Consensus       222 t~~I~VP~-~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e~  295 (669)
                      ...|.+|+ ++.|+||||.|.|||.|...||+.|.|.         ++...|+|++. +---+.|+.-|+.||.+.
T Consensus       205 ~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid---------dtp~~v~ls~fdp~rreia~~~l~~li~dg  271 (514)
T TIGR03319       205 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---------DTPEAVILSGFDPVRREIARMALEKLIQDG  271 (514)
T ss_pred             eeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc---------CCCCeEEecCCchHHHHHHHHHHHHHHHcC
Confidence            34677887 7899999999999999999999999994         45678999996 777788888888888654

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

Probab=96.93  E-value=0.00088  Score=77.53  Aligned_cols=67  Identities=28%  Similarity=0.431  Sum_probs=57.2

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHHhhhc
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAEAES  204 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e~~~  204 (669)
                      -.+.|.|+.+.+..|||++|++||+|.++|||+|.|..+         -.|.|.+ +.+.+.+|++.|.+++++...
T Consensus       552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd---------Gtv~i~~s~~~~~~~ak~~I~~i~~e~ev  619 (692)
T COG1185         552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD---------GTVKIAASDGESAKKAKERIEAITREVEV  619 (692)
T ss_pred             ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC---------CcEEEEecchHHHHHHHHHHHHHHhhccc
Confidence            567888999999999999999999999999999999732         3466666 458999999999999987554

>PRK12704 phosphodiesterase; Provisional

Probab=96.92  E-value=0.0041  Score=71.44  Aligned_cols=64  Identities=22%  Similarity=0.422  Sum_probs=52.4

Q ss_pred             EEEEeeCC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922          222 HFAMKIPN-NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISE  294 (669)
Q Consensus       222 t~~I~VP~-~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e  294 (669)
                      ...|.+|+ ++.|+||||.|.|||.|...||+.|.|.         ++...|+|++. +-.-+.|+..++.+|..
T Consensus       211 ~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---------dtp~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        211 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---------DTPEAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             eeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---------CCCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence            34667887 7899999999999999999999999994         45678999996 66666777777777654

>TIGR01953 NusA transcription termination factor NusA

Probab=96.87  E-value=0.0017  Score=70.72  Aligned_cols=94  Identities=23%  Similarity=0.433  Sum_probs=65.2

Q ss_pred             cccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCC
Q 005922          139 RVGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQ  217 (669)
Q Consensus       139 ~vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~  217 (669)
                      -+|..||++|.+|+.|.++. |-+|.|-.-.+              +      -..+|...|.-......     .... 
T Consensus       244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~--------------d------~~~fi~nal~Pa~v~~v-----~i~~-  297 (341)
T TIGR01953       244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSD--------------D------PAEFIANALSPAKVISV-----EVLD-  297 (341)
T ss_pred             cceeeECCCCchHHHHHHHhCCCeEEEEEcCC--------------C------HHHHHHHhcCCceEEEE-----EEEc-
Confidence            39999999999999999998 88888853221              1      11123332221111000     0000 


Q ss_pred             CCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922          218 AGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP  258 (669)
Q Consensus       218 ~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~  258 (669)
                      .......+.|+.+..++.|||+|.|||...+.||++|.|..
T Consensus       298 ~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       298 EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            11246789999999999999999999999999999999973

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=96.83  E-value=0.0015  Score=71.72  Aligned_cols=95  Identities=20%  Similarity=0.256  Sum_probs=66.4

Q ss_pred             ccccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccC
Q 005922          138 IRVGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTG  216 (669)
Q Consensus       138 ~~vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~  216 (669)
                      +-+|..||++|.+|+.|.++. |-+|.|-.-.+              +      -..+|...|.-......      ...
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~--------------D------~~~fI~Nal~Pa~V~~V------~i~  304 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSN--------------V------PEIFIARALAPAIISSV------KIE  304 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCC--------------C------HHHHHHHhCCCceeeEE------EEc
Confidence            349999999999999999998 88888853221              1      11233333322111000      000


Q ss_pred             CCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 005922          217 QAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPL  259 (669)
Q Consensus       217 ~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~  259 (669)
                       .......+.|+.+..++.|||+|.|||...+.||.+|.|..-
T Consensus       305 -~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~  346 (374)
T PRK12328        305 -EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI  346 (374)
T ss_pred             -CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence             112467889999999999999999999999999999999854

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

Probab=96.82  E-value=0.0015  Score=69.87  Aligned_cols=68  Identities=22%  Similarity=0.395  Sum_probs=57.0

Q ss_pred             EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhhcc
Q 005922          223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISENR  296 (669)
Q Consensus       223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e~~  296 (669)
                      ..++|+..+++.|||+.|.|.|+|+++|+|+|.+..    +  +.....|+|+|- .++|.+|.+.|..+|.+++
T Consensus        59 ~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~----p--~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   59 SSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR----P--NTNKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             hhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC----C--CCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            467899999999999999999999999999999853    1  223445666655 9999999999999999876

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

Probab=96.78  E-value=0.001  Score=71.19  Aligned_cols=70  Identities=21%  Similarity=0.240  Sum_probs=59.9

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCC-CCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLN-SPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~-~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      +...|+|....++.|||++|.|.|+|++||+++|.+++.     + ..+.++.+....+.|.+|.+.|.-+|.+..
T Consensus        57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p-----~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP-----NTNKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC-----CCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            677889999999999999999999999999999999853     4 334455555689999999999999998865

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.77  E-value=0.0023  Score=66.31  Aligned_cols=62  Identities=31%  Similarity=0.365  Sum_probs=54.7

Q ss_pred             EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922          223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISE  294 (669)
Q Consensus       223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e  294 (669)
                      +.+.||.+++++|||++|.+|+.|.++|+|+|.|-          .+-.|.|++. .+.+++|+++|+++-++
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~  209 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG----------QNGRIWIKGPDEEDEEIAIEAIKKIERE  209 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc----------CCcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence            56889999999999999999999999999999983          1468999998 77899999999876655

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.75  E-value=0.0023  Score=70.19  Aligned_cols=94  Identities=19%  Similarity=0.345  Sum_probs=65.8

Q ss_pred             cccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCC
Q 005922          139 RVGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQ  217 (669)
Q Consensus       139 ~vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~  217 (669)
                      -+|..||++|.+|+.|.++. |-+|.|-.-.+              +      ...+|...|.-......      ....
T Consensus       246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~--------------d------~~~fi~nal~Pa~v~~v------~i~~  299 (362)
T PRK12327        246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSE--------------D------PAEFVANALSPAKVVSV------EVDD  299 (362)
T ss_pred             chheeECCCChhHHHHHHHhCCCeEEEEEcCC--------------C------HHHHHHHhCCCceEEEE------EEEc
Confidence            39999999999999999998 88888853221              1      12233333322111000      0000


Q ss_pred             CCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922          218 AGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP  258 (669)
Q Consensus       218 ~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~  258 (669)
                      .......+.|+.+..++.|||+|.|||...+.||++|.|..
T Consensus       300 ~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s  340 (362)
T PRK12327        300 EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS  340 (362)
T ss_pred             CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence            12346789999999999999999999999999999999974

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.61  E-value=0.0026  Score=70.93  Aligned_cols=92  Identities=28%  Similarity=0.437  Sum_probs=64.1

Q ss_pred             ccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCC
Q 005922          140 VGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQA  218 (669)
Q Consensus       140 vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~  218 (669)
                      ||..||++|.+|+.|.++. |=+|.|..-.+              +      -..+|...|.-......     .... .
T Consensus       279 vGacVG~kG~RI~~I~~eL~gEkIDVI~ys~--------------D------p~~fI~NaLsPA~V~~V-----~i~~-~  332 (449)
T PRK12329        279 VGACIGARGSRIQAVVNELRGEKIDVIRWSP--------------D------PATYIANALSPARVDEV-----RLVD-P  332 (449)
T ss_pred             hhccCCCCcchHHHHHHHhCCCeEEEEEcCC--------------C------HHHHHHHhcCCceeeEE-----EEEc-C
Confidence            9999999999999999998 88888853211              1      11233332222111000     0000 1


Q ss_pred             CCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922          219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI  257 (669)
Q Consensus       219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~  257 (669)
                      ......+.|+.+..++.|||+|.|||...+.||.+|.|.
T Consensus       333 ~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~  371 (449)
T PRK12329        333 EGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK  371 (449)
T ss_pred             CCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence            124578999999999999999999999999999999996

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=96.46  E-value=0.0045  Score=70.18  Aligned_cols=92  Identities=24%  Similarity=0.445  Sum_probs=64.8

Q ss_pred             ccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCC
Q 005922          140 VGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQA  218 (669)
Q Consensus       140 vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~  218 (669)
                      ||..||++|.+|+.|.++. |-+|.|..-.+              +      -..+|...|.-......      ... .
T Consensus       247 vga~vG~~G~ri~~i~~el~ge~Idiv~~s~--------------d------~~~fi~nal~pa~v~~v------~~~-~  299 (470)
T PRK09202        247 VGACVGMRGSRIQAISNELGGEKIDIILWSD--------------D------PAQFIINALSPAEVSSV------VVD-E  299 (470)
T ss_pred             hHccCCCCCchHHHHHHHhCCCeEEEEEcCC--------------C------HHHHHHHhCCCCEEEEE------EEe-C
Confidence            9999999999999999998 88888853211              1      11133332222111000      000 0


Q ss_pred             CCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922          219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP  258 (669)
Q Consensus       219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~  258 (669)
                      ....+.+.|+.+..++.|||+|.|||...+.||.+|.|..
T Consensus       300 ~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        300 DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            1246789999999999999999999999999999999975

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

Probab=96.43  E-value=0.0035  Score=62.93  Aligned_cols=55  Identities=27%  Similarity=0.419  Sum_probs=49.6

Q ss_pred             cccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          139 RVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       139 ~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      ..|+|||++|.|.+.|++-|+|.|.|-.          ..|.|.|..++|..|++.|+.||....
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG~~~~v~iAr~AVemli~G~~  166 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIGGFEQVEIAREAVEMLINGAP  166 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEecChhhhHHHHHHHHHHHcCCC
Confidence            4799999999999999999999999963          359999999999999999999988643

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

Probab=96.38  E-value=0.0027  Score=67.40  Aligned_cols=128  Identities=17%  Similarity=0.194  Sum_probs=87.3

Q ss_pred             HHHHHHHHHHccccccCCCCCCCCceecCCCCCCCCccccccCCccccc------CCCCCCCCCCCCCCCCCCCceEEEE
Q 005922           61 QAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLK------SIPAPSAIPVSYGGYQSMGTSKKIE  134 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~~~~~ERiisisg~~~~eav~kA~~~i~~~l~------~i~~~~~~~~s~g~~~~~~vt~rIl  134 (669)
                      ..||.|+.++..+|+-+- -..|.+..+++.  .+.+..|.+.|....+      .+.....  ..-+.......+..+-
T Consensus        46 ~kikalr~KTqtyi~tPs-r~eePiF~vTg~--~edv~~aRrei~saaeH~~l~~~s~s~Sg--g~~~~s~s~qt~sy~s  120 (394)
T KOG2113|consen   46 CKIKALRAKTQTYIKTPS-RGEEPIFPVTGR--HEDVRRARREIPSAAEHFGLIRASRSFSG--GTNGASASGQTTSYVS  120 (394)
T ss_pred             cccchhhhhhcceeccCC-CCCCCcceeccC--chhHHHHhhcCccccceeeeeeecccccC--CCccccccCCCceeee
Confidence            689999999999998763 234577777776  4556667666665332      1111111  1011111233678888


Q ss_pred             eccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHH-HHHHH-HHHHHHH
Q 005922          135 IPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQ-IAKAE-QLINDVL  199 (669)
Q Consensus       135 VP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~-V~kA~-~lI~elI  199 (669)
                      ||-..+|+|+|.+|.+||+|++.+..-|...      -.+.+.|+.++|-.++ ++++. +.|+..+
T Consensus       121 vP~rvvglvv~~~~~ti~~iqq~tnt~I~T~------v~~~~~Vf~Vtg~~~nC~kra~s~eie~ta  181 (394)
T KOG2113|consen  121 VPLRVVGLVVGPKGATIKRIQQFTNTYIATP------VRCGEPVFCVTGAPKNCVKRARSCEIEQTA  181 (394)
T ss_pred             ccceeeeeccccccCccchheecccceEeee------ccCCCceEEEecCCcchhhhccccchhhhh
Confidence            9999999999999999999999999887763      3556788999997776 66666 4555433

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

Probab=96.36  E-value=0.0049  Score=62.20  Aligned_cols=38  Identities=42%  Similarity=0.518  Sum_probs=33.8

Q ss_pred             CceEEEEecc------ccccceeccCCcchhHHHhhcCcEEEEc
Q 005922          128 GTSKKIEIPN------IRVGVIIGKSGETIKYLQLQSGAKIQVT  165 (669)
Q Consensus       128 ~vt~rIlVP~------~~vG~IIGKgGetIK~IqeeTGAkI~Is  165 (669)
                      .++.+|.||-      .+||+|||..|.|+|+|++.|+|+|-|.
T Consensus       147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIR  190 (269)
T COG5176         147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIR  190 (269)
T ss_pred             cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEe
Confidence            3778888885      4599999999999999999999999995

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.29  E-value=0.006  Score=63.20  Aligned_cols=66  Identities=27%  Similarity=0.324  Sum_probs=54.5

Q ss_pred             EEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhc
Q 005922          131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAES  204 (669)
Q Consensus       131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~  204 (669)
                      +.|.||..++++|||++|.+|+.|.++++++|.|-.+        -++.+..-+.+.+++|+.+|+++-++...
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N--------G~VwI~~~~~~~~~~a~~~I~~~e~~~~~  212 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN--------GRIWIKGPDEEDEEIAIEAIKKIEREAHT  212 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC--------cEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence            6688999999999999999999999999999999532        34444555778999999999988777543

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

Probab=96.25  E-value=0.0071  Score=49.83  Aligned_cols=36  Identities=28%  Similarity=0.668  Sum_probs=33.8

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEe
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQV  256 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI  256 (669)
                      ....+.|+.+.++.+|||+|.+|+.+++.++.+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            567899999999999999999999999999999886

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.25  E-value=0.0019  Score=76.48  Aligned_cols=64  Identities=30%  Similarity=0.485  Sum_probs=54.1

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHHh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAE  201 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e  201 (669)
                      ....+.|+.++++.|||.||.|||+|.++||++|.|..+         -.|.|++ +.+.+++|+++|+.++.+
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~---------G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD---------GTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC---------ceEEEEcccHHHHHHHHHHHHHhccc
Confidence            456777899999999999999999999999999988543         2355555 789999999999998865

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

Probab=96.09  E-value=0.0059  Score=50.31  Aligned_cols=36  Identities=25%  Similarity=0.586  Sum_probs=33.8

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEE
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQV  164 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~I  164 (669)
                      ...+|.|+.+.+|.+|||+|.+|+.+++.++-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            578999999999999999999999999999988876

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

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

Probab=96.02  E-value=0.0065  Score=61.06  Aligned_cols=151  Identities=17%  Similarity=0.235  Sum_probs=98.0

Q ss_pred             CceEEEEeccccccceeccCCcch-hHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCC
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETI-KYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGG  206 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetI-K~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~  206 (669)
                      .-+.+|.||..++--|--. ..+| .-|-+..+..|.++-.   .-....|.+.-+-+..++.++...|..++.-.....
T Consensus        73 ~e~Rkvpvpp~r~tplk~~-W~kIytPive~lklqiRmNlK---~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~D  148 (252)
T KOG3273|consen   73 IETRKVPVPPHRYTPLKDN-WMKIYTPIVEHLKLQIRMNLK---ARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDD  148 (252)
T ss_pred             cceeeccCCcccCChHHHh-hHhhhhHHHHhhhheeEeecc---cceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchh
Confidence            3577888888776554211 1122 3466777777766411   012234666667778899999999988876543221


Q ss_pred             CCcchhcccCCCCCcEEEE--------eeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCH
Q 005922          207 SGIVARRLTGQAGSDHFAM--------KIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS  278 (669)
Q Consensus       207 ~~~~~rr~~~~~~~~t~~I--------~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~p  278 (669)
                      .-..- |+.. .-.++++|        .-=...+|+|+||+|.+--.|.+.|..||.+.           +..|+|-|.-
T Consensus       149 AiALl-rldd-lflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla-----------d~kIHiLG~~  215 (252)
T KOG3273|consen  149 AIALL-RLDD-LFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA-----------DSKIHILGAF  215 (252)
T ss_pred             HHHHH-hhhh-hhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec-----------CceEEEeecc
Confidence            10000 0000 00111221        11224579999999999999999999999986           5689999999


Q ss_pred             HHHHHHHHHHHHHHhhc
Q 005922          279 EQIESAKQLVNEVISEN  295 (669)
Q Consensus       279 eqVq~Ak~LI~dlL~e~  295 (669)
                      ++|..|+..|+.||..+
T Consensus       216 ~niriAR~avcsLIlGs  232 (252)
T KOG3273|consen  216 QNIRIARDAVCSLILGS  232 (252)
T ss_pred             hhhHHHHHhhHhhhccC
Confidence            99999999999999764

>PRK12705 hypothetical protein; Provisional

Probab=95.96  E-value=0.017  Score=66.07  Aligned_cols=64  Identities=22%  Similarity=0.372  Sum_probs=47.9

Q ss_pred             EEEEeeCC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922          222 HFAMKIPN-NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISE  294 (669)
Q Consensus       222 t~~I~VP~-~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e  294 (669)
                      ...+.+|+ ++.|+||||.|.|||.+...||+.|.|.         ++.+.|+|.+. +.--+.|+..++.+|..
T Consensus       199 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---------dtp~~V~ls~fdp~rreia~~~l~~Li~d  264 (508)
T PRK12705        199 VSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID---------DTPEAVVISSFNPIRREIARLTLEKLLAD  264 (508)
T ss_pred             eeeeecCChHhhccccCccchhHHHHHHhhCCceEec---------CCccchhhcccCccchHHHHHHHHHHHhc
Confidence            34566776 6899999999999999999999999994         33455667766 55556666666655544

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=95.92  E-value=0.013  Score=67.30  Aligned_cols=64  Identities=27%  Similarity=0.459  Sum_probs=44.6

Q ss_pred             ceEEEEecc-ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPN-IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLA  200 (669)
Q Consensus       129 vt~rIlVP~-~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~  200 (669)
                      ++-.|.+|+ ++-|+||||.|.|||.|+..|||+|.|+...+        +|+|++ ++-.-+.|+..|+.||.
T Consensus       204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp~--------~v~ls~fdp~rreia~~~l~~li~  269 (514)
T TIGR03319       204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPE--------AVILSGFDPVRREIARMALEKLIQ  269 (514)
T ss_pred             eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCCC--------eEEecCCchHHHHHHHHHHHHHHH
Confidence            445566776 67899999999999999999999999975432        355666 44333444444444443

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

Probab=95.92  E-value=0.0099  Score=60.07  Aligned_cols=66  Identities=26%  Similarity=0.308  Sum_probs=44.7

Q ss_pred             CceeeeecCCchHHHHHHHHhCCeEEeccCCC-CCCCCCC---------cc---EEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          230 NKVGLVIGKGGETIKNMQARTGARIQVIPLHL-PPGDTST---------ER---TVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       230 ~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~-ppge~s~---------er---~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      ++||+|||..|.|+|+|++.|+|+|-|-+... ..+..+.         +.   .+.+.-..+.|.+++.++..+|.+.
T Consensus       163 NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a  241 (269)
T COG5176         163 NFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREA  241 (269)
T ss_pred             ceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHH
Confidence            79999999999999999999999999976411 0111111         11   1223333666777777777777764

>PRK00106 hypothetical protein; Provisional

Probab=95.82  E-value=0.015  Score=66.85  Aligned_cols=64  Identities=25%  Similarity=0.434  Sum_probs=45.0

Q ss_pred             ceEEEEecc-ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPN-IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLA  200 (669)
Q Consensus       129 vt~rIlVP~-~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~  200 (669)
                      ++-.|.+|+ ++-|+||||.|.|||.|+..|||+|.|+...+        .|+|++ ++-.-+.|+..|+.||.
T Consensus       225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~--------~v~lS~fdpvRReiAr~~le~Li~  290 (535)
T PRK00106        225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPE--------VVVLSGFDPIRREIARMTLESLIK  290 (535)
T ss_pred             eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCCC--------eEEEeCCChHHHHHHHHHHHHHHH
Confidence            445566776 67899999999999999999999999975432        355666 44444444444444443

>PRK02821 hypothetical protein; Provisional

Probab=95.72  E-value=0.018  Score=50.07  Aligned_cols=32  Identities=22%  Similarity=0.536  Sum_probs=28.4

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhC
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTG  251 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TG  251 (669)
                      ...++|.|..+.+|+||||+|.+|+.||..-.
T Consensus        30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             cEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            36789999999999999999999999997654

>PRK12704 phosphodiesterase; Provisional

Probab=95.67  E-value=0.017  Score=66.36  Aligned_cols=65  Identities=25%  Similarity=0.437  Sum_probs=46.3

Q ss_pred             ceEEEEecc-ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHHh
Q 005922          129 TSKKIEIPN-IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAE  201 (669)
Q Consensus       129 vt~rIlVP~-~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e  201 (669)
                      ++-.|.+|+ ++-|+||||.|.|||.|+.-||++|.|+...        .+|+|++ ++-.-+.|+..|+.++.+
T Consensus       210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp--------~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP--------EAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC--------CeEEEecCChhhHHHHHHHHHHHHhc
Confidence            344555666 6789999999999999999999999997443        3466776 444434555555555543

>PRK00468 hypothetical protein; Provisional

Probab=95.65  E-value=0.017  Score=49.92  Aligned_cols=32  Identities=28%  Similarity=0.431  Sum_probs=28.2

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhC
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTG  251 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TG  251 (669)
                      ...++|.|..+.+|+||||+|.+|+.||..-.
T Consensus        29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~   60 (75)
T PRK00468         29 SVILELKVAPEDMGKVIGKQGRIAKAIRTVVK   60 (75)
T ss_pred             eEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence            46789999999999999999999999997643

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

Probab=95.28  E-value=0.034  Score=48.16  Aligned_cols=32  Identities=25%  Similarity=0.477  Sum_probs=28.2

Q ss_pred             CCcEEEEeeCCCceeeeecCCchHHHHHHHHh
Q 005922          219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQART  250 (669)
Q Consensus       219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~T  250 (669)
                      ...+++|.|..+.+|+||||+|.+|+.||..-
T Consensus        28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             CeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            35678999999999999999999999999753

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

Probab=95.13  E-value=0.025  Score=63.83  Aligned_cols=96  Identities=27%  Similarity=0.390  Sum_probs=71.0

Q ss_pred             ccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCC
Q 005922          140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAG  219 (669)
Q Consensus       140 vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~  219 (669)
                      .-.+|-+.|+.||+|-++..-+|.|..|...          +    ..-++|++.|.+++-++..-..    -.+    .
T Consensus        40 ~P~~~~~~~dlik~lAk~lrKRI~iR~dPsv----------l----~~~e~A~~~I~eivP~ea~i~~----i~F----d   97 (637)
T COG1782          40 NPELFAKDGDLIKDLAKDLRKRIIIRPDPSV----------L----KPPEEARKIILEIVPEEAGITD----IYF----D   97 (637)
T ss_pred             CHHHhccchhHHHHHHHHHhhceEeccCchh----------c----CCHHHHHHHHHHhCccccCcee----EEe----c
Confidence            3556778899999999999999999755321          1    1236788899999866432110    001    1


Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI  257 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~  257 (669)
                      .++-+++|-.++-|+||||+|+++++|..+||-.-.|.
T Consensus        98 ~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~iv  135 (637)
T COG1782          98 DDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIV  135 (637)
T ss_pred             CCCceEEEEecCCceEEecCchHHHHHHHHhCCcceee
Confidence            34557888999999999999999999999999887775

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

Probab=94.93  E-value=0.07  Score=51.53  Aligned_cols=94  Identities=26%  Similarity=0.391  Sum_probs=66.9

Q ss_pred             ceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCCc
Q 005922          142 VIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSD  221 (669)
Q Consensus       142 ~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~  221 (669)
                      .++=..++.||+|-++..-+|.|..|...              ...=++|.++|.+++-++.. -.+.   .+    ..+
T Consensus        19 ~~~~~~~dli~~lAk~lrKRIvvR~dps~--------------l~~~e~A~~~I~~ivP~ea~-i~di---~F----d~~   76 (145)
T cd02410          19 ELFAEDGDLVKDLAKDLRKRIVIRPDPSV--------------LKPPEEAIKIILEIVPEEAG-ITDI---YF----DDD   76 (145)
T ss_pred             HHHhcccHHHHHHHHHHhceEEEcCChhh--------------cCCHHHHHHHHHHhCCCccC-ceee---Ee----cCC
Confidence            44556689999999999999999644210              01125688899998865421 0000   01    123


Q ss_pred             EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922          222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI  257 (669)
Q Consensus       222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~  257 (669)
                      +-++.|-.++-|+||||+|.++++|..+||-+-.|.
T Consensus        77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vv  112 (145)
T cd02410          77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVV  112 (145)
T ss_pred             CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEE
Confidence            457888889999999999999999999999988885

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.

>PRK01064 hypothetical protein; Provisional

Probab=94.82  E-value=0.041  Score=47.91  Aligned_cols=32  Identities=25%  Similarity=0.492  Sum_probs=28.1

Q ss_pred             CCcEEEEeeCCCceeeeecCCchHHHHHHHHh
Q 005922          219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQART  250 (669)
Q Consensus       219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~T  250 (669)
                      ..+.+++.|..+.+|+||||+|.+|+.||...
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            34678999999999999999999999999754

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

Probab=94.60  E-value=0.02  Score=65.04  Aligned_cols=66  Identities=17%  Similarity=0.358  Sum_probs=55.4

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccc-cCCHHHHHHHHHHHHHHHHhhh
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVEL-MGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtI-tGt~E~V~kA~~lI~elI~e~~  203 (669)
                      .+.+.|.|+.+.+..|||.+|.+.|+|+.|||+...|+.          ..+.| .-+...+++|+++|..++..+.
T Consensus       596 P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe----------~t~~i~A~~~~am~~Ak~~I~~i~~~~~  662 (760)
T KOG1067|consen  596 PVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDE----------GTFSIFAPTQAAMEEAKEFIDGIIKDDQ  662 (760)
T ss_pred             ceeeEEeecchhhheeecCccceeeeEeeeccceeeecC----------ceEEEEecCHHHHHHHHHHHHHHhcCcc
Confidence            378999999999999999999999999999997777752          22444 3478999999999999998754

>PRK00468 hypothetical protein; Provisional

Probab=94.51  E-value=0.031  Score=48.32  Aligned_cols=29  Identities=21%  Similarity=0.375  Sum_probs=26.9

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQ  157 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~Iqee  157 (669)
                      +.++|.|....+|+||||+|.+|+.||.-
T Consensus        30 ~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         30 VILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             EEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            78899999999999999999999999864

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

Probab=94.37  E-value=0.016  Score=69.96  Aligned_cols=72  Identities=22%  Similarity=0.251  Sum_probs=63.1

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      ...++.||...+.+|||++|.||+.|++-|||.|.|.+-.  ..|-.||.+.+.|.++.++.|...|.-+|.+.
T Consensus      1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq--~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--PDNQAERSKAPKGRPPSQRVATSPIGLPIIDP 1411 (2131)
T ss_pred             cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--CccchhhhcccCCCChhhhhhhccccceeecC
Confidence            5568889999999999999999999999999999998632  23577999999999999999999998877663

>PRK02821 hypothetical protein; Provisional

Probab=94.21  E-value=0.04  Score=47.88  Aligned_cols=31  Identities=19%  Similarity=0.358  Sum_probs=27.7

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSG  159 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTG  159 (669)
                      +.++|.|....+|+||||+|.+|+.||.-..
T Consensus        31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         31 RTLEVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             EEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            7899999999999999999999999986533

>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]

Probab=94.17  E-value=0.022  Score=62.31  Aligned_cols=148  Identities=15%  Similarity=0.086  Sum_probs=100.6

Q ss_pred             EEEeccc-----cccceeccCCcchhHHHhhcCcEEEEccC--------CccCCCCCCccccccCCHHHHHHHHHHHHHH
Q 005922          132 KIEIPNI-----RVGVIIGKSGETIKYLQLQSGAKIQVTRD--------TEADLNSPTRSVELMGTPEQIAKAEQLINDV  198 (669)
Q Consensus       132 rIlVP~~-----~vG~IIGKgGetIK~IqeeTGAkI~Iskd--------~e~~p~~~eRvVtItGt~E~V~kA~~lI~el  198 (669)
                      |++|+.+     +-+..-+++-.++..|+.++++++-++..        .....+.+.+|.++.+.++.+.+|.++|.+|
T Consensus       213 k~~v~~~~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl  292 (531)
T KOG1960|consen  213 KALATDKDPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNL  292 (531)
T ss_pred             heecccCCcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhH
Confidence            4555544     23445567777888899999998777321        1123456668999999999999999999999


Q ss_pred             HHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCC-----CCCCC--ccE
Q 005922          199 LAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPP-----GDTST--ERT  271 (669)
Q Consensus       199 I~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~pp-----ge~s~--er~  271 (669)
                      ++..-...+.++                    ..-.|+|.-|.++|+|+.++-.+++|++.....     .....  -.+
T Consensus       293 ~~~v~~~~sr~~--------------------~~~~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~p~~~~~~~~p~~~  352 (531)
T KOG1960|consen  293 EEKVYINLSRGF--------------------HRQAIVGPQGAYVKHIQQETRTRVQIKGQGSAFIEPSTNRESDEPIHL  352 (531)
T ss_pred             HHHHHHHhhhhh--------------------hhcccccCCcccccccCCCCCcceeccCccceeecCCCCCCCCCCccc
Confidence            887433221111                    011366778889999999999999998652211     11111  234


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHhhcccCC
Q 005922          272 VQIDGTSEQIESAKQLVNEVISENRIRN  299 (669)
Q Consensus       272 VtItG~peqVq~Ak~LI~dlL~e~~~r~  299 (669)
                      ..|.-++..|+.|+-||.++|..+....
T Consensus       353 ~~~~~~~~~~~~~~~~~~~~i~~v~~qy  380 (531)
T KOG1960|consen  353 CIMSHDPNAIQRAKVLCEDLIASVHQQY  380 (531)
T ss_pred             ccccCChhhhhhhhhcccccCCcccccC
Confidence            5677779999999999999998765443

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

Probab=93.73  E-value=0.018  Score=69.59  Aligned_cols=70  Identities=23%  Similarity=0.262  Sum_probs=59.8

Q ss_pred             EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922          222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e  294 (669)
                      ..++.||...+.+|||++|.+|+.||..||+.|.|.+-+   .++-.||.+.+.|.++.+..|..+|.-+|.+
T Consensus      1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq---~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ---PDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC---CccchhhhcccCCCChhhhhhhccccceeec
Confidence            346778988999999999999999999999999996422   2356699999999999999999999877755

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

Probab=93.38  E-value=0.069  Score=46.31  Aligned_cols=29  Identities=24%  Similarity=0.473  Sum_probs=27.0

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQ  157 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~Iqee  157 (669)
                      +.++|.|....+|.||||+|.+|+.||.-
T Consensus        30 ~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          30 VTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             EEEEEEECcccccceecCCChhHHHHHHH
Confidence            78999999999999999999999999864

>PRK01064 hypothetical protein; Provisional

Probab=93.31  E-value=0.073  Score=46.35  Aligned_cols=30  Identities=30%  Similarity=0.462  Sum_probs=27.4

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhh
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQ  157 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~Iqee  157 (669)
                      .+.++|.|....+|+||||+|.||+.|+.-
T Consensus        29 ~~~~~l~v~~~D~g~vIGk~G~~i~air~l   58 (78)
T PRK01064         29 TIIYELTVAKPDIGKIIGKEGRTIKAIRTL   58 (78)
T ss_pred             EEEEEEEECcccceEEECCCCccHHHHHHH
Confidence            378999999999999999999999999874

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

Probab=92.90  E-value=0.057  Score=54.48  Aligned_cols=57  Identities=18%  Similarity=0.313  Sum_probs=50.2

Q ss_pred             ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhc
Q 005922          138 IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAES  204 (669)
Q Consensus       138 ~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~  204 (669)
                      ..+|+|+||+|.|--.|++-|..+|.+..          ..|.|-|..++|.-|...|+.||.-...
T Consensus       178 RAIGRiaGk~GkTkfaIEn~trtrIVlad----------~kIHiLG~~~niriAR~avcsLIlGspp  234 (252)
T KOG3273|consen  178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD----------SKIHILGAFQNIRIARDAVCSLILGSPP  234 (252)
T ss_pred             HHHHHhhcCCCcceeeeeccceeEEEecC----------ceEEEeecchhhHHHHHhhHhhhccCCc
Confidence            45999999999999999999999999963          3488889999999999999999987544

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=92.80  E-value=0.09  Score=59.43  Aligned_cols=128  Identities=16%  Similarity=0.115  Sum_probs=81.6

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCcc-ccccC---CHHHHHHHHHHHHHHHHhhhc
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRS-VELMG---TPEQIAKAEQLINDVLAEAES  204 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRv-VtItG---t~E~V~kA~~lI~elI~e~~~  204 (669)
                      ..+.|.|+...+..|||.||..|.+++.+.++.|++...-+.. -+--+- |+|..   +.++|.-++.-+.+++++-..
T Consensus       449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~-qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~  527 (657)
T COG5166         449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFG-QSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQQCR  527 (657)
T ss_pred             hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcc-hhhhhcceEEECCccCccchhcccccHHHHHhhhcc
Confidence            5688999999999999999999999999999999996544321 111121 44433   456777777777888876431


Q ss_pred             C-CCCcch-------------------hcccCC----CCCcEEEEeeCCCceeeeec---CCchHHHHHHHHhCCeEEec
Q 005922          205 G-GSGIVA-------------------RRLTGQ----AGSDHFAMKIPNNKVGLVIG---KGGETIKNMQARTGARIQVI  257 (669)
Q Consensus       205 ~-~~~~~~-------------------rr~~~~----~~~~t~~I~VP~~~vG~IIG---KGGstIK~Iqe~TGArIqI~  257 (669)
                      - ..+..+                   |-.-+.    .-..++.+-++.+.++..||   -.|++|-.+...-.-.|...
T Consensus       528 f~~Kgdirf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~~  607 (657)
T COG5166         528 FNLKGDIRFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEFS  607 (657)
T ss_pred             cccccceEEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcccccccchhhhhhhhhccceee
Confidence            1 111000                   000000    01223445567788888999   67888887776656666554

>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein

Probab=92.68  E-value=0.15  Score=60.15  Aligned_cols=96  Identities=26%  Similarity=0.352  Sum_probs=69.1

Q ss_pred             cceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCC
Q 005922          141 GVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGS  220 (669)
Q Consensus       141 G~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~  220 (669)
                      -.++-+.++.||+|-++..-+|.|..|...          +    ..-++|+++|.+++-++..- .+.   .+    ..
T Consensus        35 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~----------~----~~~~~~~~~i~~~~~~~~~~-~~~---~f----~~   92 (630)
T TIGR03675        35 PELFAKDDDLVKELAKKLRKRIVIRPDPSV----------L----LPPEEAIEKIKEIVPEEAGI-TDI---YF----DD   92 (630)
T ss_pred             HHHhccchHHHHHHHHHhhceEEEecChhh----------c----CCHHHHHHHHHHhCCCcCCc-eeE---Ee----cC
Confidence            345567789999999999999999644310          0    11255888898888664210 000   01    13


Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP  258 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~  258 (669)
                      ++-++.|-.++-|+||||+|.++++|.++||-+..|..
T Consensus        93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~  130 (630)
T TIGR03675        93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR  130 (630)
T ss_pred             CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence            45578889999999999999999999999999988863

This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=92.39  E-value=1  Score=45.46  Aligned_cols=66  Identities=27%  Similarity=0.475  Sum_probs=57.4

Q ss_pred             EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922          222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR  296 (669)
Q Consensus       222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~  296 (669)
                      .+.+.+.....-+|+..+|..+++|....||+|.|.         ..+..|.|+|+...|+.+...|.+++...+
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~---------~~~~~i~I~g~k~~~~~i~~~i~~~l~~i~   92 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVS---------RSENRIRITGTKSTAEYIEASINEILSNIR   92 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEe---------cCCcEEEEEccHHHHHHHHHHHHHHHhhcE
Confidence            456666788899999999999999988889999995         346799999999999999999999997743

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

Probab=92.38  E-value=0.23  Score=55.96  Aligned_cols=67  Identities=30%  Similarity=0.535  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 005922          187 QIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPL  259 (669)
Q Consensus       187 ~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~  259 (669)
                      ....|.++|++.|+....+....   .+   .+.....+.||+.+++.||||+|.+|++|.++.|-+|.|...
T Consensus       458 ~~~~a~~~i~~~i~r~~p~~~eV---e~---~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~  524 (604)
T COG1855         458 ALKLAEEEIEREIKRYLPGDVEV---EV---VGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL  524 (604)
T ss_pred             hhHHHHHHHHHHHHHhCCCCceE---EE---ecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence            45667777777777755431110   01   123456789999999999999999999999999999999854

>PRK12705 hypothetical protein; Provisional

Probab=92.20  E-value=0.15  Score=58.60  Aligned_cols=38  Identities=24%  Similarity=0.462  Sum_probs=31.5

Q ss_pred             eEEEEecc-ccccceeccCCcchhHHHhhcCcEEEEccC
Q 005922          130 SKKIEIPN-IRVGVIIGKSGETIKYLQLQSGAKIQVTRD  167 (669)
Q Consensus       130 t~rIlVP~-~~vG~IIGKgGetIK~IqeeTGAkI~Iskd  167 (669)
                      +-.|.+|+ ++-|+||||.|.|||.|+..||+.|.|+..
T Consensus       199 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt  237 (508)
T PRK12705        199 VSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT  237 (508)
T ss_pred             eeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence            33444554 678999999999999999999999999754

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=91.90  E-value=0.56  Score=46.46  Aligned_cols=103  Identities=17%  Similarity=0.223  Sum_probs=63.8

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG  208 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~  208 (669)
                      -.+-|+|-... |..|||+|++||+|++..|-+|.|-...              .+      ...+|.+++.-....+. 
T Consensus        61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s--------------~d------~~~fl~Nl~~PA~V~gV-  118 (166)
T PRK06418         61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEKT--------------ND------IKKLAVQLLSPARVLGV-  118 (166)
T ss_pred             CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEcC--------------CC------HHHHHHhcCCCcEEEEE-
Confidence            35667777777 9999999999999999999999995332              11      33455555443221110 


Q ss_pred             cchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEe
Q 005922          209 IVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQV  256 (669)
Q Consensus       209 ~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI  256 (669)
                        +-++.. .+...+.+.|.......|-.|--..-+-+++.||..|.|
T Consensus       119 --~i~~~~-dG~~~~kV~Vd~~Dk~~l~~k~e~~~~v~~kltgk~v~~  163 (166)
T PRK06418        119 --NTVWLP-DGTVQYVIRVSRRDRRRLPAKPELLESILSKITGTEVKI  163 (166)
T ss_pred             --EEEEeC-CCcEEEEEEECHHHhhcccccHHHHHHHHHHHHCCcEEE
Confidence              001111 123444577777666665555554444567778888776

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=90.94  E-value=0.17  Score=57.27  Aligned_cols=128  Identities=14%  Similarity=0.157  Sum_probs=85.1

Q ss_pred             ccceeccCCcchhHHHhhcCcEEEEc--cCCccCCCCCCccc-cccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccC
Q 005922          140 VGVIIGKSGETIKYLQLQSGAKIQVT--RDTEADLNSPTRSV-ELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTG  216 (669)
Q Consensus       140 vG~IIGKgGetIK~IqeeTGAkI~Is--kd~e~~p~~~eRvV-tItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~  216 (669)
                      --+|-||+--++.+|++...|-+.+.  ++.    +  .+++ .+.|..-...+++.+|..-+                 
T Consensus       391 EdFl~gkkngK~TrIm~~v~c~~~~~i~~~~----g--s~~~~~~~g~~~~F~k~~~~~~~EF-----------------  447 (657)
T COG5166         391 EDFLRGKKNGKATRIMKGVSCSELSSIVSST----G--SIVETNGIGEKMSFSKKLSIPPTEF-----------------  447 (657)
T ss_pred             HHHhccccCcchhhhhhhcccceeeEEEecC----C--cEEEEeccCcchhhHHHhcCCcccC-----------------
Confidence            34788888888999999988885543  221    1  2333 34566666665555443211                 


Q ss_pred             CCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCH---HHHHHHHHHHHHHHh
Q 005922          217 QAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS---EQIESAKQLVNEVIS  293 (669)
Q Consensus       217 ~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~p---eqVq~Ak~LI~dlL~  293 (669)
                         ..++.+.|++..+..|||-||..|.+++.+.++.|+++.... .+.+-....|.|.-+.   +.|-.+|.=++++|.
T Consensus       448 ---pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~-~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~  523 (657)
T COG5166         448 ---PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYK-FGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVK  523 (657)
T ss_pred             ---chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhh-cchhhhhcceEEECCccCccchhcccccHHHHHh
Confidence               235678999999999999999999999999999999875411 1112223337777663   345566766777776


Q ss_pred             h
Q 005922          294 E  294 (669)
Q Consensus       294 e  294 (669)
                      +
T Consensus       524 ~  524 (657)
T COG5166         524 Q  524 (657)
T ss_pred             h
Confidence            5

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

Probab=90.87  E-value=0.52  Score=49.07  Aligned_cols=47  Identities=36%  Similarity=0.541  Sum_probs=38.8

Q ss_pred             EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHH
Q 005922          223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSE  279 (669)
Q Consensus       223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~pe  279 (669)
                      .-+.|+..+|.+||||+|+.|+.|.++|+|+|.|--          .-.|.|.+..+
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~----------NG~IWV~~~~~  194 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ----------NGRIWVDGENE  194 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec----------CCEEEecCCCc
Confidence            457899999999999999999999999999999841          34666666644

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=90.79  E-value=0.28  Score=47.17  Aligned_cols=38  Identities=32%  Similarity=0.716  Sum_probs=34.8

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP  258 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~  258 (669)
                      ..+.+.|+...+|..||++|++||.|++..|-+|.|..
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve   69 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE   69 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence            46778899999999999999999999999999999875

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

Probab=90.78  E-value=0.32  Score=39.22  Aligned_cols=34  Identities=26%  Similarity=0.347  Sum_probs=27.4

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEE
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKI  162 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI  162 (669)
                      ....+.+.....|.+|||+|++|+.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            4556666666789999999999999999988443

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=90.33  E-value=0.14  Score=43.40  Aligned_cols=35  Identities=29%  Similarity=0.460  Sum_probs=29.7

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeE
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARI  254 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArI  254 (669)
                      ...+.+.|..+..|+||||+|.+|+.||.....-+
T Consensus        28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~   62 (73)
T PF13083_consen   28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA   62 (73)
T ss_dssp             TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence            45788899999999999999999999997765433

>PRK13764 ATPase; Provisional

Probab=90.31  E-value=0.49  Score=55.53  Aligned_cols=67  Identities=27%  Similarity=0.433  Sum_probs=49.4

Q ss_pred             HHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 005922          187 QIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPL  259 (669)
Q Consensus       187 ~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~  259 (669)
                      ....|.++|++.|+....+.....   +   .......+.||...++.||||+|.+|++|.++.|.+|.|...
T Consensus       453 ~~~~~~~~~~~~~~~~~~~~~~~~---~---~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~  519 (602)
T PRK13764        453 VWRLAEKEIEREIKRYLPGPVEVE---V---VSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL  519 (602)
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEE---E---ecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence            445567777777776552221110   0   123467889999999999999999999999999999999865

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=90.09  E-value=0.14  Score=43.31  Aligned_cols=32  Identities=31%  Similarity=0.440  Sum_probs=28.0

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCc
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGA  160 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGA  160 (669)
                      ..+.+.|..+..|+||||.|.|++.||.-...
T Consensus        29 ~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   29 DTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             eEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            67888899999999999999999999876543

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

Probab=89.76  E-value=0.29  Score=41.56  Aligned_cols=38  Identities=34%  Similarity=0.510  Sum_probs=31.0

Q ss_pred             ceEEEEecccc-----ccceeccCCcchhHHHhhc-CcEEEEcc
Q 005922          129 TSKKIEIPNIR-----VGVIIGKSGETIKYLQLQS-GAKIQVTR  166 (669)
Q Consensus       129 vt~rIlVP~~~-----vG~IIGKgGetIK~IqeeT-GAkI~Isk  166 (669)
                      ...+|.|-...     +|.+||++|.+||.|.++. |-+|.|-.
T Consensus         3 ~r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    3 NRTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             TEEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             ceEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            35677777777     9999999999999999999 99999853

>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter

Probab=89.63  E-value=1.7  Score=50.85  Aligned_cols=144  Identities=18%  Similarity=0.268  Sum_probs=80.8

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEE---ccCCccC-CCC-----CCccccccCCHHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQV---TRDTEAD-LNS-----PTRSVELMGTPEQIAKAEQLINDVL  199 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~I---skd~e~~-p~~-----~eRvVtItGt~E~V~kA~~lI~elI  199 (669)
                      +...+.|++.  ..+|||   ||++|+.....+|.|   .++.+.. +..     ...++.|.|+.|++++..+.+-..+
T Consensus       218 ~~r~~~V~~~--s~liGk---Tl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~L~~l~~~~G~~~  292 (562)
T TIGR03802       218 VGRAYRVNRA--SSLIGK---TVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDAVVQFGAEIGEEV  292 (562)
T ss_pred             eeEEEEECCC--cccCCC---cHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHHHHHHHHhcCCcc
Confidence            4566777665  346666   899998776544444   2222111 111     1256788999999987776654332


Q ss_pred             HhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHH------HHhCCeEEeccCC---CCCCC---CC
Q 005922          200 AEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQ------ARTGARIQVIPLH---LPPGD---TS  267 (669)
Q Consensus       200 ~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iq------e~TGArIqI~~~~---~ppge---~s  267 (669)
                      .+...     ..      ......++.+++   ..+|||   +|++|+      ++.|+.|.-..+.   .....   -.
T Consensus       293 ~~~~~-----~~------~~~~~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~  355 (562)
T TIGR03802       293 QEVEG-----LD------VPMETKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQ  355 (562)
T ss_pred             CCccc-----cC------CceEEEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEec
Confidence            21100     00      011233444553   456766   788886      2667777655441   11100   11


Q ss_pred             CccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922          268 TERTVQIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       268 ~er~VtItG~peqVq~Ak~LI~dlL~e  294 (669)
                      .-.+|+|.|+++.++++++.+-+...+
T Consensus       356 ~GD~LlV~G~~~~l~~~~~~lG~~~~~  382 (562)
T TIGR03802       356 RGDVVTLVGTPQDVDRAAKQLGYAIAP  382 (562)
T ss_pred             CCCEEEEEeCHHHHHHHHHHcCCchhh
Confidence            235699999999999988876554443

All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=88.78  E-value=0.35  Score=53.51  Aligned_cols=37  Identities=19%  Similarity=0.336  Sum_probs=34.8

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEc
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVT  165 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Is  165 (669)
                      -...+.|+....++.|||+|.|||-..+-||.+|.|.
T Consensus       308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~  344 (374)
T PRK12328        308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN  344 (374)
T ss_pred             cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence            4678899999999999999999999999999999995

>PRK03818 putative transporter; Validated

Probab=88.62  E-value=1.9  Score=50.19  Aligned_cols=139  Identities=19%  Similarity=0.298  Sum_probs=77.8

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEc---cCCcc-CC-----CCCCccccccCCHHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVT---RDTEA-DL-----NSPTRSVELMGTPEQIAKAEQLINDVL  199 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Is---kd~e~-~p-----~~~eRvVtItGt~E~V~kA~~lI~elI  199 (669)
                      ...++.|+++.   +||   +||+++++....++.|.   ++... .+     -....++.|.|+.|.++++.+.+-..+
T Consensus       205 ~~r~~~V~~s~---liG---kTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~  278 (552)
T PRK03818        205 QTINIRVENPN---LHG---KAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEV  278 (552)
T ss_pred             eeEEEEEeCCC---CCC---CcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCcc
Confidence            44667777443   454   59999998877666652   22111 11     112356788999998887776654322


Q ss_pred             HhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHH--HHHhCCeEEeccC---CCCCCCC---CCccE
Q 005922          200 AEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNM--QARTGARIQVIPL---HLPPGDT---STERT  271 (669)
Q Consensus       200 ~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~I--qe~TGArIqI~~~---~~ppge~---s~er~  271 (669)
                      .++.          .......+..++.++++   .++||   +|++|  +++.|+.|.-..+   ......+   ..-.+
T Consensus       279 ~~~~----------~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~  342 (552)
T PRK03818        279 DTSL----------STRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDI  342 (552)
T ss_pred             Cccc----------cccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCE
Confidence            1100          00001122334445543   67776   67777  5667777654433   1111110   12356


Q ss_pred             EEEEcCHHHHHHHHHHHH
Q 005922          272 VQIDGTSEQIESAKQLVN  289 (669)
Q Consensus       272 VtItG~peqVq~Ak~LI~  289 (669)
                      |.|.|+++.+++..+.+.
T Consensus       343 LlVvG~~~~i~~l~~~Lg  360 (552)
T PRK03818        343 LNLVGRPEAIDAVANVLG  360 (552)
T ss_pred             EEEEECHHHHHHHHHHhC
Confidence            999999999999877644

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

Probab=88.57  E-value=0.64  Score=37.44  Aligned_cols=34  Identities=26%  Similarity=0.433  Sum_probs=27.4

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeE
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARI  254 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArI  254 (669)
                      .+..+.+.....++||||+|++|+.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            4455666666789999999999999999988554

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=88.04  E-value=0.8  Score=48.58  Aligned_cols=52  Identities=23%  Similarity=0.357  Sum_probs=45.9

Q ss_pred             eeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922          232 VGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       232 vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e  294 (669)
                      .-+|||.+|+++|.|+-.|.|-|-|.           ..+|.+.|.-..++.++.+|+|.|.+
T Consensus       160 RqRLiGpng~TLKAlelLT~CYilVq-----------G~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  160 RQRLIGPNGSTLKALELLTNCYILVQ-----------GNTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHHhcCCCchhHHHHHHHhhcEEEee-----------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence            35699999999999999999999996           35899999999999999998887765

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

Probab=87.79  E-value=0.86  Score=47.51  Aligned_cols=35  Identities=31%  Similarity=0.573  Sum_probs=32.4

Q ss_pred             EEEEeccccccceeccCCcchhHHHhhcCcEEEEc
Q 005922          131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVT  165 (669)
Q Consensus       131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Is  165 (669)
                      .-|.|+..+|-++|||+|+.|++|.++|+|+|-|-
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG  182 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVG  182 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEe
Confidence            56778999999999999999999999999999994

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=86.34  E-value=4.4  Score=48.45  Aligned_cols=22  Identities=9%  Similarity=0.279  Sum_probs=11.7

Q ss_pred             EEEcCHHHHHHHHHHHHHHHhh
Q 005922          273 QIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       273 tItG~peqVq~Ak~LI~dlL~e  294 (669)
                      .|++.-+....+-+|+...+++
T Consensus       376 dir~emDd~~~~f~lL~n~vkd  397 (1102)
T KOG1924|consen  376 DIRAEMDDANEVFELLANTVKD  397 (1102)
T ss_pred             hhhhhhccHHHHHHHHHHhhhh
Confidence            3455545555555555555544

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

Probab=86.20  E-value=0.78  Score=52.32  Aligned_cols=39  Identities=23%  Similarity=0.479  Sum_probs=33.4

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRD  167 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd  167 (669)
                      .+-+++|-.++=|+||||+|+++++|..+||-.-.|.+.
T Consensus        99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~  137 (637)
T COG1782          99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT  137 (637)
T ss_pred             CCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence            456777888899999999999999999999988777653

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=85.48  E-value=0.77  Score=39.40  Aligned_cols=33  Identities=27%  Similarity=0.521  Sum_probs=26.5

Q ss_pred             eEEEEeccccccceeccCCcchhHHHhhcCcEE
Q 005922          130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKI  162 (669)
Q Consensus       130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI  162 (669)
                      .++|.|.....|+||||.|+|++.|+--+..-+
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~   57 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL   57 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence            466777788899999999999999887655433

The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

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

Probab=84.25  E-value=0.56  Score=39.86  Aligned_cols=36  Identities=31%  Similarity=0.555  Sum_probs=28.4

Q ss_pred             EEEeeCCCc-----eeeeecCCchHHHHHHHHh-CCeEEecc
Q 005922          223 FAMKIPNNK-----VGLVIGKGGETIKNMQART-GARIQVIP  258 (669)
Q Consensus       223 ~~I~VP~~~-----vG~IIGKGGstIK~Iqe~T-GArIqI~~  258 (669)
                      ..+.|-...     +|.+||++|.+||.|.++. |-+|.|..
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            345555555     8999999999999999999 99999874

>TIGR01953 NusA transcription termination factor NusA

Probab=83.97  E-value=0.85  Score=50.05  Aligned_cols=38  Identities=24%  Similarity=0.486  Sum_probs=35.5

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEcc
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR  166 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Isk  166 (669)
                      -...+.|+....++.|||+|.|||-..+-||.+|.|..
T Consensus       301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            46889999999999999999999999999999999964

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.

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=83.86  E-value=1.3  Score=42.89  Aligned_cols=37  Identities=30%  Similarity=0.624  Sum_probs=33.7

Q ss_pred             EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922          222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP  258 (669)
Q Consensus       222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~  258 (669)
                      .+-+.|....+|..||++|++||.|++..|-+|.|..
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe   70 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE   70 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence            5677899999999999999999999999999998874

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.

>PF07054 Pericardin_rpt: Pericardin like repeat; InterPro: IPR009765 This entry represents a repeated sequence of around 34 residues in length, which is found in multiple copies in Drosophila pericardin and other extracellular matrix proteins [, ]

Probab=83.60  E-value=1  Score=33.03  Aligned_cols=22  Identities=50%  Similarity=1.055  Sum_probs=12.0

Q ss_pred             CCCCC-CCCCCCCCCCCCCCCCC
Q 005922          609 QPGYG-SAAYGAPPGGSQAGYGQ  630 (669)
Q Consensus       609 ~~~~~-~~~~~~~~~~~~~~~~~  630 (669)
                      ||||| .|..|.-++++|++||-
T Consensus         1 QpgyG~QpGvggQ~g~gQpGYg~   23 (34)
T PF07054_consen    1 QPGYGSQPGVGGQTGAGQPGYGT   23 (34)
T ss_pred             CCccccCCccccccCCCCCcccc
Confidence            45555 44554444556666664

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=83.24  E-value=1.1  Score=38.37  Aligned_cols=35  Identities=29%  Similarity=0.557  Sum_probs=28.7

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEE
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQ  255 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIq  255 (669)
                      ..+.+.|..+..|+||||.|++|+.||-.+..-+.
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            35677788889999999999999999987765444

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.

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

Probab=82.80  E-value=0.84  Score=51.70  Aligned_cols=37  Identities=30%  Similarity=0.516  Sum_probs=34.1

Q ss_pred             eEEEEeccccccceeccCCcchhHHHhhcCcEEEEcc
Q 005922          130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR  166 (669)
Q Consensus       130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Isk  166 (669)
                      ...+.||...++.||||+|.+|++|+++.|.+|.|..
T Consensus       487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~  523 (604)
T COG1855         487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP  523 (604)
T ss_pred             eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence            4678899999999999999999999999999999963

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=82.18  E-value=0.56  Score=39.99  Aligned_cols=34  Identities=26%  Similarity=0.412  Sum_probs=28.5

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEE
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKI  162 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI  162 (669)
                      ....|.|...+.+.||||+|++|++|.++..-++
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            3577888999999999999999999988765544

; 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 ....

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=82.17  E-value=0.63  Score=39.69  Aligned_cols=35  Identities=29%  Similarity=0.553  Sum_probs=29.7

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEE
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQ  255 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIq  255 (669)
                      ....+.|...+.+.|||++|++|++|.+...-++.
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            45778899999999999999999999887765553

; 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 ....

>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein

Probab=81.47  E-value=1.6  Score=51.64  Aligned_cols=39  Identities=26%  Similarity=0.480  Sum_probs=33.9

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRD  167 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd  167 (669)
                      .+-+++|-.++-|+||||+|.|+++|.++||-+..|.+.
T Consensus        93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~  131 (630)
T TIGR03675        93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT  131 (630)
T ss_pred             CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence            456777778889999999999999999999999888654

This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=81.11  E-value=1.1  Score=51.21  Aligned_cols=39  Identities=23%  Similarity=0.507  Sum_probs=35.9

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRD  167 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd  167 (669)
                      -...+.|+....++.|||+|.|||...+-||.+|.|...
T Consensus       302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            478899999999999999999999999999999999653

>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]

Probab=80.24  E-value=5.7  Score=43.32  Aligned_cols=31  Identities=32%  Similarity=0.546  Sum_probs=24.8

Q ss_pred             CcEEEEeeCCC-ceeeeecCCchHHHHHHHHh
Q 005922          220 SDHFAMKIPNN-KVGLVIGKGGETIKNMQART  250 (669)
Q Consensus       220 ~~t~~I~VP~~-~vG~IIGKGGstIK~Iqe~T  250 (669)
                      .++.++++|.+ ...+||||||..|++|-++.
T Consensus       327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a  358 (379)
T KOG1423|consen  327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRA  358 (379)
T ss_pred             EEEEEEEcCCCcceeEEEcCCCccHHHHHHHH
Confidence            35668889975 57789999999999986654

>PRK15405 ethanolamine utilization protein EutL; Provisional

Probab=80.03  E-value=33  Score=35.54  Aligned_cols=136  Identities=14%  Similarity=0.155  Sum_probs=77.4

Q ss_pred             hhHHHhhcCcEEEEccCCc------cCCCCCCccccccC-CHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCCcE-
Q 005922          151 IKYLQLQSGAKIQVTRDTE------ADLNSPTRSVELMG-TPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDH-  222 (669)
Q Consensus       151 IK~IqeeTGAkI~Iskd~e------~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t-  222 (669)
                      +.++.|.++++|-+.++..      .-+.+.+.+++|.| +...|+.|++...+.|++....-.       .+..+..+ 
T Consensus        51 aDeA~KAAnVevv~a~~~~gGaghg~~~~~G~viiIi~G~dvsdVrsAveaa~~~i~~~~~f~~-------~n~~g~~~~  123 (217)
T PRK15405         51 LDEATKQAMVEVVYARSFYAGAAHASTPLAGEVIGILAGPNPAEVRAGLDAMVAFIENGAAFQS-------ANDDDSTAF  123 (217)
T ss_pred             HHHHHhhcceEEEEEEeeccccccCCCCCCccEEEEEeCCCHHHHHHHHHHHHHHHHhhhceEe-------eCCCCCEEE
Confidence            3556677888888876641      11234456789999 999999999999988887532100       00001111 


Q ss_pred             -------------EEEeeCC-CceeeeecCCchHHHHHHHHhC-CeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHH
Q 005922          223 -------------FAMKIPN-NKVGLVIGKGGETIKNMQARTG-ARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQL  287 (669)
Q Consensus       223 -------------~~I~VP~-~~vG~IIGKGGstIK~Iqe~TG-ArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~L  287 (669)
                                   ..+-+|. +-.+.|||.=+.-+--+=.... +.|+|..-..|+.+.+ -.-++|+|+...|..|.+.
T Consensus       124 ~a~~~aRag~~l~k~~g~~~G~a~~~li~~P~~~~~~~D~AlKaA~V~~~~~~~P~~~t~-f~~~~ltG~~~A~r~A~~a  202 (217)
T PRK15405        124 FAHVVSRTGSYLSKTAGIAEGEPLAYLIAPPLEAMYGIDAALKAADVQLVTFVGPPSETN-FGGALLTGSQSACKAACNA  202 (217)
T ss_pred             EEEEcccHHHHHHHHcCCCCCceeEEEecCcHHHHHHHHHHHhhcCceEEEEeCCCCCce-ecCeeEEeCHHHHHHHHHH
Confidence                         1223444 3467788766554433322221 3444432222333322 2239999998888887777


Q ss_pred             HHHHHhh
Q 005922          288 VNEVISE  294 (669)
Q Consensus       288 I~dlL~e  294 (669)
                      -.+.++.
T Consensus       203 ~~e~v~~  209 (217)
T PRK15405        203 FTDAVLE  209 (217)
T ss_pred             HHHHHHH
Confidence            6666655

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	669
1j4w_A	174	Complex Of The Kh3 And Kh4 Domains Of Fbp With A Si		2e-15
1j4w_A	174	Complex Of The Kh3 And Kh4 Domains Of Fbp With A Si		1e-04
2jvz_A	164	Solution Nmr Structure Of The Second And Third Kh D		2e-14
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		1e-11
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		1e-08
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		1e-08
1x4n_A	92	Solution Structure Of Kh Domain In Fuse Binding Pro		5e-08
2opu_A	89	Solution Nmr Structure Of The First Domain Of Ksrp		2e-07
2opu_A	89	Solution Nmr Structure Of The First Domain Of Ksrp		1e-06
2hh2_A	107	Solution Structure Of The Fourth Kh Domain Of Ksrp		3e-07
1x4m_A	94	Solution Structure Of Kh Domain In Far Upstream Ele		1e-06
4b8t_A	106	Rna Binding Protein Solution Structure Of The Third		2e-06
2hh3_A	106	Solution Structure Of The Third Kh Domain Of Ksrp L		2e-06
2opv_A	85	Solution Nmr Structure Of The Second Domain Of Ksrp		2e-05
2opv_A	85	Solution Nmr Structure Of The Second Domain Of Ksrp		7e-05
3vke_A	76	Contribution Of The First K-Homology Domain Of Poly		7e-05
1ztg_A	74	Human Alpha Polyc Binding Protein Kh1 Length = 74		3e-04
1we8_A	104	Solution Structure Of Kh Domain In Protein Bab28342		3e-04
1we8_A	104	Solution Structure Of Kh Domain In Protein Bab28342		5e-04
2cte_A	94	Solution Structure Of The 1st Kh Type I Domain From		5e-04

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

Iteration: 1
 Score = 80.9 bits (198), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 58/170 (34%), Positives = 90/170 (52%), Gaps = 16/170 (9%)
Query: 135 IPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQL 194
           IP   VG++IG++GE IK +Q  +G +IQ   D   D  +P R  ++ G P++   A ++
Sbjct: 9   IPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD---DGTTPERIAQITGPPDRAQHAAEI 65
Query: 195 INDVLAEAESGGSGIVARRLTGQA------------GSDHFAMKIPNNKVGLVIGKGGET 242
           I D+L   ++G  G       G+             G   F   +P  K GL+IGKGGET
Sbjct: 66  ITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGET 125
Query: 243 IKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVI 292
           IK++  ++GARI+ +  + PP      +   I GT +QI+ A+QL+ E I
Sbjct: 126 IKSISQQSGARIE-LQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 6/75 (8%)
Query: 219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTST-ERTVQIDGT 277
           GS    + IP   VG+VIG+ GE IK +Q   G RIQ       P D +T ER  QI G 
Sbjct: 1   GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQ-----FKPDDGTTPERIAQITGP 55
Query: 278 SEQIESAKQLVNEVI 292
            ++ + A +++ +++
Sbjct: 56  PDRAQHAAEIITDLL 70

>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains Of Ksrp Length = 164

Iteration: 1
 Score = 78.2 bits (191), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 56/172 (32%), Positives = 94/172 (54%), Gaps = 13/172 (7%)
Query: 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRD--TEADLNSPTRSVELMGTP 185
           GT ++I IP  + G++IGK GETIK LQ ++G K+ + +D     +++ P R   ++G P
Sbjct: 1   GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLR---IIGDP 57
Query: 186 EQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKN 245
            ++ +A +++ D+L E + GG G   R   G        + +P + VG+VIG+ GE IK 
Sbjct: 58  YKVQQACEMVMDILRERDQGGFG--DRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKK 115
Query: 246 MQARTGARIQVIPLHLPPGD-TSTERTVQIDGTSEQIESAKQLVNEVISENR 296
           +Q   G RIQ         D T  E+   I G  ++ E A +++N+++   R
Sbjct: 116 IQNDAGVRIQ-----FKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLR 162

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

Iteration: 1
 Score = 68.6 bits (166), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 52/153 (33%), Positives = 78/153 (50%), Gaps = 20/153 (13%)
Query: 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL 199
           VG IIGK GE++K ++ +SGA+I ++       N P R + L G    I KA  +I D L
Sbjct: 16  VGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKL 70
Query: 200 AEAESGGSGIVARRLTGQAGSDH----FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQ 255
            E        ++  +T    +        + +P ++ G +IGKGG  IK ++  TGA++Q
Sbjct: 71  EED-------ISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQ 123
Query: 256 VIPLHLPPGDTSTERTVQIDGTSEQ-IESAKQL 287
           V    LP    STER + I G  +  IE  KQ+
Sbjct: 124 VAGDMLP---NSTERAITIAGIPQSIIECVKQI 153

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 50/170 (29%), Positives = 86/170 (50%), Gaps = 8/170 (4%)
Query: 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKA 191
           K+ IP+   G IIGK G+TI  LQ ++GA I++++  +    +  R   + GT E +   
Sbjct: 9   KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAV 68
Query: 192 EQLINDVLAE-----AESGGSGIVARRLTGQ-AGSDHFAMKIPNNKVGLVIGKGGETIKN 245
              I + + E     A++    I+  + T     ++   + +PN+  GL+IGKGG T+K 
Sbjct: 69  HGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKA 128
Query: 246 MQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN 295
           +  ++GA +Q+     P G     R V + G  EQ   A +L+ + I E+
Sbjct: 129 IMEQSGAWVQL--SQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 50/170 (29%), Positives = 86/170 (50%), Gaps = 8/170 (4%)
Query: 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKA 191
           K+ IP+   G IIGK G+TI  LQ ++GA I++++  +    +  R   + GT E +   
Sbjct: 9   KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAV 68
Query: 192 EQLINDVLAE-----AESGGSGIVARRLTGQ-AGSDHFAMKIPNNKVGLVIGKGGETIKN 245
              I + + E     A++    I+  + T     ++   + +PN+  GL+IGKGG T+K 
Sbjct: 69  HGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKA 128
Query: 246 MQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN 295
           +  ++GA +Q+     P G     R V + G  EQ   A +L+ + I E+
Sbjct: 129 IXEQSGAWVQL--SQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176

>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1 Length = 92

Iteration: 1
 Score = 56.2 bits (134), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 46/73 (63%), Gaps = 8/73 (10%)
Query: 226 KIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLH--LPPGDTSTERTVQIDGTSEQIES 283
           K+P+  VG +IG+GGE I  +Q  +G +IQ+ P    LP      ER+  + GT E ++S
Sbjct: 20  KVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP------ERSCMLTGTPESVQS 73
Query: 284 AKQLVNEVISENR 296
           AK+L+++++ + R
Sbjct: 74  AKRLLDQIVEKGR 86

>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp Length = 89

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 3/72 (4%)
Query: 134 EIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQ 193
            +P+  VG+IIG+ GE I  +Q  SG K+Q++ D+      P RSV L G PE + KA+ 
Sbjct: 21  RVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGG---LPERSVSLTGAPESVQKAKM 77
Query: 194 LINDVLAEAESG 205
           +++D+++    G
Sbjct: 78  MLDDIVSRGRGG 89

>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp Length = 89

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 45/73 (61%), Gaps = 8/73 (10%)
Query: 226 KIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLH--LPPGDTSTERTVQIDGTSEQIES 283
           ++P+  VGL+IG+GGE I  +Q  +G ++Q+ P    LP      ER+V + G  E ++ 
Sbjct: 21  RVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP------ERSVSLTGAPESVQK 74
Query: 284 AKQLVNEVISENR 296
           AK ++++++S  R
Sbjct: 75  AKMMLDDIVSRGR 87

>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp Length = 107

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/67 (43%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 227 IPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQ 286
           IP +K GLVIG+GGE +K +  +TGA ++ I   LPP      +   I G+ +QI+ AKQ
Sbjct: 13  IPTHKCGLVIGRGGENVKAINQQTGAFVE-ISRQLPPNGDPNFKLFIIRGSPQQIDHAKQ 71
Query: 287 LVNEVIS 293
           L+ E I 
Sbjct: 72  LIEEKIE 78

>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element Binding Protein 1 Length = 94

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 47/70 (67%), Gaps = 2/70 (2%)
Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IP +K GLVIGKGGETIK +Q R G  ++++ +   P +T  ++ ++I G   +++ A
Sbjct: 19  IMIPASKAGLVIGKGGETIKQLQERAG--VKMVMIQDGPQNTGADKPLRITGDPYKVQQA 76
Query: 285 KQLVNEVISE 294
           K++V E+I +
Sbjct: 77  KEMVLELIRD 86

>pdb|4B8T|A Chain A, Rna Binding Protein Solution Structure Of The Third Kh Domain Of Ksrp In Complex With The G-rich Target Sequence Length = 106

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 3/70 (4%)
Query: 135 IPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQL 194
           +P   VGV+IG+SGE IK +Q  +G +IQ  +D   D   P +   +MG P++   A ++
Sbjct: 17  VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD---DGTGPEKIAHIMGPPDRCEHAARI 73
Query: 195 INDVLAEAES 204
           IND+L    S
Sbjct: 74  INDLLQSLRS 83

>pdb|2HH3|A Chain A, Solution Structure Of The Third Kh Domain Of Ksrp Length = 106

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 3/70 (4%)
Query: 135 IPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQL 194
           +P   VGV+IG+SGE IK +Q  +G +IQ  +D   D   P +   +MG P++   A ++
Sbjct: 17  VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD---DGTGPEKIAHIMGPPDRCEHAARI 73
Query: 195 INDVLAEAES 204
           IND+L    S
Sbjct: 74  INDLLQSLRS 83

>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp Length = 85

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 48/74 (64%), Gaps = 1/74 (1%)
Query: 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQ 187
           GT ++I IP  + G++IGK GETIK LQ ++G K+ + +D   + N   + + ++G P +
Sbjct: 13  GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNV-DKPLRIIGDPYK 71
Query: 188 IAKAEQLINDVLAE 201
           + +A +++ D+L E
Sbjct: 72  VQQACEMVMDILRE 85

>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp Length = 85

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 29/79 (36%), Positives = 49/79 (62%), Gaps = 3/79 (3%)
Query: 216 GQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQID 275
           GQ G+    M IP  K GLVIGKGGETIK +Q R G  +++I +     +T+ ++ ++I 
Sbjct: 10  GQNGTVQEIM-IPAGKAGLVIGKGGETIKQLQERAG--VKMILIQDGSQNTNVDKPLRII 66
Query: 276 GTSEQIESAKQLVNEVISE 294
           G   +++ A ++V +++ E
Sbjct: 67  GDPYKVQQACEMVMDILRE 85

>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 = 45.8 bits (107), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL 199
           VG IIGK GE++K ++ +SGA+I ++       NSP R + L G    I KA  +I D L
Sbjct: 14  VGSIIGKKGESVKRIREESGARINISEG-----NSPERIITLTGPTNAIFKAFAMIIDKL 68
Query: 200 AE 201
            E
Sbjct: 69  EE 70

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL 199
           VG IIGK GE++K ++ +SGA+I ++       N P R + L G    I KA  +I D L
Sbjct: 14  VGSIIGKKGESVKRIREESGARINISEG-----NCPERIITLTGPTNAIFKAFAMIIDKL 68
Query: 200 AE 201
            E
Sbjct: 69  EE 70

>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342 Length = 104

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 26/73 (35%), Positives = 47/73 (64%), Gaps = 1/73 (1%)
Query: 131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAK 190
           +++ +P   VG IIG+ GETI+ +   SGAKI   +++E  L   +R +++ GT +++A 
Sbjct: 17  EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTL-LLSRLIKISGTQKEVAA 75
Query: 191 AEQLINDVLAEAE 203
           A+ LI + ++E E
Sbjct: 76  AKHLILEKVSEDE 88

>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342 Length = 104

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 2/71 (2%)
Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + +P   VG +IG+GGETI+++   +GA+I         G     R ++I GT +++ +A
Sbjct: 19  LSVPQRSVGRIIGRGGETIRSICKASGAKITCD--KESEGTLLLSRLIKISGTQKEVAAA 76
Query: 285 KQLVNEVISEN 295
           K L+ E +SE+
Sbjct: 77  KHLILEKVSED 87

>pdb|2CTE|A Chain A, Solution Structure Of The 1st Kh Type I Domain From Human Vigilin Length = 94

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 34/96 (35%), Positives = 51/96 (53%), Gaps = 9/96 (9%)
Query: 204 SGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPP 263
           SG SG +  RL  QA +    + IP      VIGK GE +++++ +T  +IQ IP    P
Sbjct: 3   SGSSGDIVARLQTQASA---TVAIPKEHHRFVIGKNGEKLQDLELKTATKIQ-IP---RP 55
Query: 264 GDTSTERTVQIDGTSEQIESAKQLVNEVISENRIRN 299
            D S +  ++I GT E IE A+  V  + +E   R+
Sbjct: 56  DDPSNQ--IKITGTKEGIEKARHEVLLISAEQDKRS 89

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	669
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-49
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	5e-20
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-19
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-48
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	6e-20
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-17
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-47
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	1e-17
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	4e-46
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-19
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-16
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-45
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-22
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-17
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	3e-28
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	3e-09
1tua_A	191	Hypothetical protein APE0754; structural genomics,	9e-25
1tua_A	191	Hypothetical protein APE0754; structural genomics,	1e-07
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	2e-23
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	2e-20
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-23
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-21
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-21
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	4e-20
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-21
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	7e-21
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	6e-21
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-19
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-20
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	5e-19
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-20
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-19
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-20
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	8e-20
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	6e-20
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	3e-12
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	4e-09
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	7e-20
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-19
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	1e-19
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	2e-18
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-19
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	3e-15
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	2e-19
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	2e-17
1we8_A	104	Tudor and KH domain containing protein; structural	1e-18
1we8_A	104	Tudor and KH domain containing protein; structural	1e-15
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	1e-17
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	7e-16
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	2e-15
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	1e-12
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	5e-14
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	1e-11
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	2e-13
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	6e-12
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	3e-13
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	1e-11
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	1e-12
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	6e-11
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-12
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-11
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	5e-11
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-10
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-10
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-09
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-09
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-09
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-09
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-08
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-06
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	4e-12
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	6e-10
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-09
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-06
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	1e-05
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	6e-04
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-09
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	3e-08
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	4e-09
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	8e-05
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	4e-09
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	1e-07
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	6e-07
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	2e-06
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	9e-09
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	3e-04
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	2e-08
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	7e-08
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	3e-06
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	5e-04
2cxc_A	144	NUSA; transcription termination, RNA binding prote	1e-04
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	1e-04
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	3e-04
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	1e-04
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	3e-04

>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 =  168 bits (428), Expect = 2e-49
 Identities = 52/169 (30%), Positives = 91/169 (53%), Gaps = 7/169 (4%)

Query: 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQ 187
           GT ++I IP  + G++IGK GETIK LQ ++G K+ + +D   +  +  + + ++G P +
Sbjct: 1   GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN-TNVDKPLRIIGDPYK 59

Query: 188 IAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQ 247
           + +A +++ D+L E + GG G       G        + +P + VG+VIG+ GE IK +Q
Sbjct: 60  VQQACEMVMDILRERDQGGFGDRNE--YGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQ 117

Query: 248 ARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR 296
              G RIQ          T  E+   I G  ++ E A +++N+++   R
Sbjct: 118 NDAGVRIQF----KQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLR 162

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

 Score = 86.8 bits (215), Expect = 5e-20
 Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 2/86 (2%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IP  K GLVIGKGGETIK +Q R G ++ +I         + ++ ++I G   +++ A
Sbjct: 6   IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNT--NVDKPLRIIGDPYKVQQA 63

Query: 285 KQLVNEVISENRIRNPAMAGGYSQQG 310
            ++V +++ E           Y  + 
Sbjct: 64  CEMVMDILRERDQGGFGDRNEYGSRI 89

>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 = 84.8 bits (210), Expect = 2e-19
 Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 3/81 (3%)

Query: 125 QSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT 184
             +G    + +P   VGV+IG+SGE IK +Q  +G +IQ  +D   D   P +   +MG 
Sbjct: 87  SRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD---DGTGPEKIAHIMGP 143

Query: 185 PEQIAKAEQLINDVLAEAESG 205
           P++   A ++IND+L    SG
Sbjct: 144 PDRCEHAARIINDLLQSLRSG 164

>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 =  166 bits (423), Expect = 2e-48
 Identities = 47/173 (27%), Positives = 80/173 (46%), Gaps = 8/173 (4%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
              K+ IP+   G IIGK G+TI  LQ ++GA I++++  +    +  R   + GT E +
Sbjct: 6   YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEAL 65

Query: 189 AKAEQLINDVLAEAESGGSGIVARRLTGQAGSD------HFAMKIPNNKVGLVIGKGGET 242
                 I + + E     +      +     +          + +PN+  GL+IGKGG T
Sbjct: 66  NAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGAT 125

Query: 243 IKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN 295
           +K +  ++GA +Q+     P G     R V + G  EQ   A +L+ + I E+
Sbjct: 126 VKAIMEQSGAWVQLSQ--KPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176

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

 Score = 86.8 bits (215), Expect = 6e-20
 Identities = 28/104 (26%), Positives = 38/104 (36%), Gaps = 1/104 (0%)

Query: 218 AGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT 277
                  + IP+   G +IGKGG+TI  +Q  TGA I++         T TER   I GT
Sbjct: 3   GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGT-TERVCLIQGT 61

Query: 278 SEQIESAKQLVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGT 321
            E + +    + E I E              Q      P     
Sbjct: 62  IEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQ 105

>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 = 79.1 bits (195), Expect = 3e-17
 Identities = 31/99 (31%), Positives = 46/99 (46%), Gaps = 1/99 (1%)

Query: 105 PSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQV 164
           P ++      S +              KI +PN   G+IIGK G T+K +  QSGA +Q+
Sbjct: 80  PQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQL 139

Query: 165 TRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE 203
           ++  +   N   R V + G PEQ  KA +LI   + E  
Sbjct: 140 SQKPDGI-NLQNRVVTVSGEPEQNRKAVELIIQKIQEDP 177

>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 =  162 bits (411), Expect = 5e-47
 Identities = 51/170 (30%), Positives = 82/170 (48%), Gaps = 11/170 (6%)

Query: 125 QSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT 184
           +++  + ++ +    VG IIGK GE++K ++ +SGA+I ++       N P R + L G 
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGP 55

Query: 185 PEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIK 244
              I KA  +I D L E  S                    + +P ++ G +IGKGG  IK
Sbjct: 56  TNAIFKAFAMIIDKLEEDISSSMT---NSTAASRPPVTLRLVVPASQCGSLIGKGGCKIK 112

Query: 245 NMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294
            ++  TGA++QV    LP    STER + I G  + I    + +  V+ E
Sbjct: 113 EIRESTGAQVQVAGDMLP---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 = 79.8 bits (197), Expect = 1e-17
 Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 2/89 (2%)

Query: 113 APSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADL 172
             S+   +         + ++ +P  + G +IGK G  IK ++  +GA++QV  D     
Sbjct: 73  DISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLP-- 130

Query: 173 NSPTRSVELMGTPEQIAKAEQLINDVLAE 201
           NS  R++ + G P+ I +  + I  V+ E
Sbjct: 131 NSTERAITIAGIPQSIIECVKQICVVMLE 159

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

 Score =  159 bits (405), Expect = 4e-46
 Identities = 45/171 (26%), Positives = 77/171 (45%), Gaps = 12/171 (7%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
              ++ IP   VG IIGK G+ IK L   + A I++      D  S  R V + G PE  
Sbjct: 3   EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPD--SKVRMVIITGPPEAQ 60

Query: 189 AKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQA 248
            KA+  I   L E    G          +       +++P +  G VIGKGG+T+  +Q 
Sbjct: 61  FKAQGRIYGKLKEENFFGPK--------EEVKLETHIRVPASAAGRVIGKGGKTVNELQN 112

Query: 249 RTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENRIRN 299
            T A + V     P    + +  V+I G     + A++ + +++++ + ++
Sbjct: 113 LTAAEVVVPRDQTPD--ENDQVIVKIIGHFYASQMAQRKIRDILAQVKQQH 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 = 84.8 bits (210), Expect = 2e-19
 Identities = 23/83 (27%), Positives = 32/83 (38%), Gaps = 3/83 (3%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IP   VG +IGK G+ IK +     A I++ P   P    S  R V I G  E    A
Sbjct: 7   VFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETP---DSKVRMVIITGPPEAQFKA 63

Query: 285 KQLVNEVISENRIRNPAMAGGYS 307
           +  +   + E     P       
Sbjct: 64  QGRIYGKLKEENFFGPKEEVKLE 86

>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 = 76.7 bits (189), Expect = 1e-16
 Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 1/84 (1%)

Query: 121 YGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVE 180
           +G  + +     I +P    G +IGK G+T+  LQ  + A++ V RD   D N     V+
Sbjct: 77  FGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQ-VIVK 135

Query: 181 LMGTPEQIAKAEQLINDVLAEAES 204
           ++G       A++ I D+LA+ + 
Sbjct: 136 IIGHFYASQMAQRKIRDILAQVKQ 159

>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 =  157 bits (399), Expect = 4e-45
 Identities = 56/176 (31%), Positives = 89/176 (50%), Gaps = 16/176 (9%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
               + IP   VG++IG++GE IK +Q  +G +IQ   D   D  +P R  ++ G P++ 
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD---DGTTPERIAQITGPPDRA 59

Query: 189 AKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFA------------MKIPNNKVGLVI 236
             A ++I D+L   ++G  G       G+                     +P  K GL+I
Sbjct: 60  QHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLII 119

Query: 237 GKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVI 292
           GKGGETIK++  ++GARI++   + PP      +   I GT +QI+ A+QL+ E I
Sbjct: 120 GKGGETIKSISQQSGARIELQR-NPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

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

 Score = 93.4 bits (232), Expect = 3e-22
 Identities = 32/108 (29%), Positives = 51/108 (47%), Gaps = 4/108 (3%)

Query: 219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS 278
           GS    + IP   VG+VIG+ GE IK +Q   G RIQ      P   T+ ER  QI G  
Sbjct: 1   GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQF----KPDDGTTPERIAQITGPP 56

Query: 279 EQIESAKQLVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGTPGAPS 326
           ++ + A +++ +++   +  NP   G   +   + +   + G PG   
Sbjct: 57  DRAQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQ 104

>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 = 78.4 bits (193), Expect = 4e-17
 Identities = 27/88 (30%), Positives = 42/88 (47%)

Query: 112 PAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEAD 171
                      G           +P  + G+IIGK GETIK +  QSGA+I++ R+   +
Sbjct: 87  GRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPN 146

Query: 172 LNSPTRSVELMGTPEQIAKAEQLINDVL 199
            +   +   + GTP+QI  A QLI + +
Sbjct: 147 ADPNMKLFTIRGTPQQIDYARQLIEEKI 174

>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 =  112 bits (280), Expect = 3e-28
 Identities = 37/196 (18%), Positives = 71/196 (36%), Gaps = 21/196 (10%)

Query: 103 SPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKI 162
               +  +                    + ++IP  R+ V+IGK G+T K ++ ++  KI
Sbjct: 9   MKKFENVNKDGEIVEDEDEWEEFFK-QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKI 67

Query: 163 QVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDH 222
            +  +T         S +    P  + KA  ++  +        +  +          + 
Sbjct: 68  TIDSETGEV---WITSTKETEDPLAVWKARDIVLAIGRGFSPERAFRLLNEGEYLEIINL 124

Query: 223 FAMKIPNNK------VGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDG 276
             + I N K       G +IG+ G T + ++  +GA + V             +TV I G
Sbjct: 125 TDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSV-----------YGKTVAIIG 173

Query: 277 TSEQIESAKQLVNEVI 292
              QIE AK  + ++ 
Sbjct: 174 NPIQIEIAKTAIEKLA 189

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219

 Score = 57.0 bits (137), Expect = 3e-09
 Identities = 19/84 (22%), Positives = 31/84 (36%), Gaps = 10/84 (11%)

Query: 122 GGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVEL 181
                +    +        G IIG+ G T + ++  SGA + V   T          V +
Sbjct: 122 INLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYGKT----------VAI 171

Query: 182 MGTPEQIAKAEQLINDVLAEAESG 205
           +G P QI  A+  I  +   +  G
Sbjct: 172 IGNPIQIEIAKTAIEKLARGSPHG 195

>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 =  101 bits (252), Expect = 9e-25
 Identities = 33/185 (17%), Positives = 65/185 (35%), Gaps = 41/185 (22%)

Query: 127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT-- 184
           M     +++   R+G +IG  GE    +  ++G  I V        ++    V +     
Sbjct: 2   MKPRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITV--------DTENSMVIVEPEAE 53

Query: 185 ---PEQIAKAEQLINDV-----------LAEAESGGSGIVARRLTGQAGSDHFAMKIPNN 230
              P  + KA +++  +           L E +     +  +++ G + +          
Sbjct: 54  GIPPVNLMKAAEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHL------KR 107

Query: 231 KVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNE 290
             G +IG+GG   + ++  T   I V            E  V I G  E+  +AKQ +  
Sbjct: 108 IKGRIIGEGGRARRTIEEMTDTYINV-----------GEYEVAIIGDYERAMAAKQAIEM 156

Query: 291 VISEN 295
           +    
Sbjct: 157 LAEGR 161

>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 = 51.5 bits (123), Expect = 1e-07
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 11/80 (13%)

Query: 126 SMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTP 185
            +    +  +  I+ G IIG+ G   + ++  +   I V              V ++G  
Sbjct: 96  QVVGDSQNHLKRIK-GRIIGEGGRARRTIEEMTDTYINVGEYE----------VAIIGDY 144

Query: 186 EQIAKAEQLINDVLAEAESG 205
           E+   A+Q I  +       
Sbjct: 145 ERAMAAKQAIEMLAEGRMHS 164

>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 = 93.6 bits (233), Expect = 2e-23
 Identities = 23/82 (28%), Positives = 41/82 (50%)

Query: 127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPE 186
           M    +I +P   VG I+GK G+T+   Q  +GA+IQ+++  E    +  R V + G+P 
Sbjct: 1   MKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPA 60

Query: 187 QIAKAEQLINDVLAEAESGGSG 208
               A+ LI+  +   +   + 
Sbjct: 61  ATQAAQYLISQRVTYEQGVRAS 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 = 85.5 bits (212), Expect = 2e-20
 Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + +P N VG ++GKGG+T+   Q  TGARIQ I         +  R V I G+    ++A
Sbjct: 7   IAVPENLVGAILGKGGKTLVEYQELTGARIQ-ISKKGEFLPGTRNRRVTITGSPAATQAA 65

Query: 285 KQLVNEVISENRIRNPA 301
           + L+++ ++  +    +
Sbjct: 66  QYLISQRVTYEQGVRAS 82

>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 = 93.1 bits (232), Expect = 2e-23
 Identities = 22/75 (29%), Positives = 39/75 (52%)

Query: 127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPE 186
           M    ++ +P   VG I+GK G+T+   Q  +GA+IQ+++  E    +  R V + G+P 
Sbjct: 1   MKELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPA 60

Query: 187 QIAKAEQLINDVLAE 201
               A+ LI+  +  
Sbjct: 61  ATQAAQYLISQRVTY 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 = 87.7 bits (218), Expect = 2e-21
 Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           M +P N VG ++GKGG+T+   Q  TGARIQ+          +  R V I G+    ++A
Sbjct: 7   MAVPENLVGAILGKGGKTLVEYQELTGARIQISK-KGEFLPGTRNRRVTITGSPAATQAA 65

Query: 285 KQLVNEVISE 294
           + L+++ ++ 
Sbjct: 66  QYLISQRVTY 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 = 87.3 bits (217), Expect = 2e-21
 Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 217 QAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDG 276
           +  +    + +   +VG +IGK GE++K M+  +GARI +   + P      ER + + G
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP------ERIITLAG 54

Query: 277 TSEQIESAKQLVNEVISEN 295
            +  I  A  ++ + + E+
Sbjct: 55  PTNAIFKAFAMIIDKLEED 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 = 83.9 bits (208), Expect = 4e-20
 Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 5/77 (6%)

Query: 125 QSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT 184
           +++  + ++ +    VG IIGK GE++K ++ +SGA+I +     ++ N P R + L G 
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI-----SEGNCPERIITLAGP 55

Query: 185 PEQIAKAEQLINDVLAE 201
              I KA  +I D L E
Sbjct: 56  TNAIFKAFAMIIDKLEE 72

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

 Score = 87.8 bits (218), Expect = 2e-21
 Identities = 25/70 (35%), Positives = 44/70 (62%), Gaps = 2/70 (2%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IP  K GLVIGKGGETIK +Q R G ++ +I       +T+ ++ ++I G   +++ A
Sbjct: 18  IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG--SQNTNVDKPLRIIGDPYKVQQA 75

Query: 285 KQLVNEVISE 294
            ++V +++ E
Sbjct: 76  CEMVMDILRE 85

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

 Score = 86.3 bits (214), Expect = 7e-21
 Identities = 26/74 (35%), Positives = 48/74 (64%), Gaps = 1/74 (1%)

Query: 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQ 187
           GT ++I IP  + G++IGK GETIK LQ ++G K+ + +D   + N   + + ++G P +
Sbjct: 13  GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVD-KPLRIIGDPYK 71

Query: 188 IAKAEQLINDVLAE 201
           + +A +++ D+L E
Sbjct: 72  VQQACEMVMDILRE 85

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

 Score = 86.6 bits (215), Expect = 6e-21
 Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 3/79 (3%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
           T+ ++ IPN  +G IIG+ G  I  ++  SGA+I++    E    S  R V + G+   I
Sbjct: 6   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE---GSSGRQVTITGSAASI 62

Query: 189 AKAEQLINDVLAEAESGGS 207
           + A+ LIN  L+  +  G 
Sbjct: 63  SLAQYLINARLSSEKGMGC 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 = 82.3 bits (204), Expect = 2e-19
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 4/72 (5%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IPNN +G +IG+ G  I  ++  +GA+I++      P + S+ R V I G++  I  A
Sbjct: 10  LTIPNNLIGCIIGRQGANINEIRQMSGAQIKIA----NPVEGSSGRQVTITGSAASISLA 65

Query: 285 KQLVNEVISENR 296
           + L+N  +S  +
Sbjct: 66  QYLINARLSSEK 77

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

 Score = 85.8 bits (213), Expect = 1e-20
 Identities = 26/87 (29%), Positives = 44/87 (50%), Gaps = 3/87 (3%)

Query: 118 PVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTR 177
            +SYG       + ++ IP    G IIGK G+ IK ++ +SGA I++    E    S  R
Sbjct: 3   HMSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE---GSEDR 59

Query: 178 SVELMGTPEQIAKAEQLINDVLAEAES 204
            + + GT +QI  A+ L+ + + +   
Sbjct: 60  IITITGTQDQIQNAQYLLQNSVKQYSG 86

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

 Score = 81.2 bits (201), Expect = 5e-19
 Identities = 23/74 (31%), Positives = 43/74 (58%), Gaps = 4/74 (5%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IP +  G +IGKGG+ IK ++  +GA I++      P + S +R + I GT +QI++A
Sbjct: 18  VTIPKDLAGSIIGKGGQRIKQIRHESGASIKID----EPLEGSEDRIITITGTQDQIQNA 73

Query: 285 KQLVNEVISENRIR 298
           + L+   + +   +
Sbjct: 74  QYLLQNSVKQYSGK 87

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

 Score = 86.4 bits (214), Expect = 1e-20
 Identities = 30/100 (30%), Positives = 47/100 (47%), Gaps = 3/100 (3%)

Query: 120 SYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSV 179
           +      +G    + +P   VGV+IG+SGE IK +Q  +G +IQ  +D       P +  
Sbjct: 2   AMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG---TGPEKIA 58

Query: 180 ELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAG 219
            +MG P++   A ++IND+L    SG  G          G
Sbjct: 59  HIMGPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPGG 98

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

 Score = 82.1 bits (203), Expect = 4e-19
 Identities = 28/105 (26%), Positives = 43/105 (40%), Gaps = 4/105 (3%)

Query: 216 GQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQID 275
           G        + +P + VG+VIG+ GE IK +Q   G RIQ          T  E+   I 
Sbjct: 6   GSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFK----QDDGTGPEKIAHIM 61

Query: 276 GTSEQIESAKQLVNEVISENRIRNPAMAGGYSQQGYQARPPTSWG 320
           G  ++ E A +++N+++   R   P   GG              G
Sbjct: 62  GPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQG 106

>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 = 84.6 bits (210), Expect = 2e-20
 Identities = 23/74 (31%), Positives = 43/74 (58%), Gaps = 4/74 (5%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IP +  G +IGKGG+ IK ++  +GA I++      P + S +R + I GT +QI++A
Sbjct: 11  VTIPKDLAGSIIGKGGQRIKQIRHESGASIKID----EPLEGSEDRIITITGTQDQIQNA 66

Query: 285 KQLVNEVISENRIR 298
           + L+   + +   +
Sbjct: 67  QYLLQNSVKQYSGK 80

>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 = 83.1 bits (206), Expect = 8e-20
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
            + ++ IP    G IIGK G+ IK ++ +SGA I++    E    S  R + + GT +QI
Sbjct: 7   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE---GSEDRIITITGTQDQI 63

Query: 189 AKAEQLINDVLAEAES 204
             A+ L+ + + +   
Sbjct: 64  QNAQYLLQNSVKQYSG 79

>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 = 85.8 bits (212), Expect = 6e-20
 Identities = 29/167 (17%), Positives = 56/167 (33%), Gaps = 31/167 (18%)

Query: 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIA 189
            ++  +    +G+ IG  G  I+  +   G        T  DL+  T +  + G  +   
Sbjct: 5   HEQFIVREDLMGLAIGTHGANIQQARKVPGV-------TAIDLDEDTCTFHIYGEDQDAV 57

Query: 190 KAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQAR 249
           K  +   +                           +++P N VG VIGK G+ I+ +  +
Sbjct: 58  KKARSFLEF----------------------AEDVIQVPRNLVGKVIGKNGKLIQEIVDK 95

Query: 250 TGARIQVIPLHLPPGDTS--TERTVQIDGTSEQIESAKQLVNEVISE 294
           +G     I                    GT + I +A  L++  ++ 
Sbjct: 96  SGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNY 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 = 63.5 bits (154), Expect = 3e-12
 Identities = 21/94 (22%), Positives = 40/94 (42%), Gaps = 3/94 (3%)

Query: 111 IPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGA-KIQVTRDTE 169
           I       V             I++P   VG +IGK+G+ I+ +  +SG  ++++  + E
Sbjct: 49  IYGEDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENE 108

Query: 170 ADLNS--PTRSVELMGTPEQIAKAEQLINDVLAE 201
            ++           +GT + IA A  L++  L  
Sbjct: 109 KNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNY 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 = 54.6 bits (131), Expect = 4e-09
 Identities = 13/74 (17%), Positives = 24/74 (32%), Gaps = 9/74 (12%)

Query: 218 AGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDG- 276
           A   H    +  + +GL IG  G  I+  +   G     +             T  I G 
Sbjct: 1   ASRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLD--------EDTCTFHIYGE 52

Query: 277 TSEQIESAKQLVNE 290
             + ++ A+  +  
Sbjct: 53  DQDAVKKARSFLEF 66

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

 Score = 83.1 bits (206), Expect = 7e-20
 Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 3/77 (3%)

Query: 125 QSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT 184
           ++  TS ++ IPN  +G IIG+ G  I  ++  SGA+I++    E    S  R V + G+
Sbjct: 1   KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVE---GSTDRQVTITGS 57

Query: 185 PEQIAKAEQLINDVLAE 201
              I+ A+ LIN  L+ 
Sbjct: 58  AASISLAQYLINVRLSS 74

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

 Score = 82.7 bits (205), Expect = 1e-19
 Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 4/70 (5%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IPN+ +G +IG+ G  I  ++  +GA+I++      P + ST+R V I G++  I  A
Sbjct: 9   LTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIA----NPVEGSTDRQVTITGSAASISLA 64

Query: 285 KQLVNEVISE 294
           + L+N  +S 
Sbjct: 65  QYLINVRLSS 74

>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 = 83.2 bits (206), Expect = 1e-19
 Identities = 29/86 (33%), Positives = 49/86 (56%), Gaps = 2/86 (2%)

Query: 216 GQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQID 275
              G+    + IP +K GLVIGKGGETIK +Q R G ++ +I     P +T  ++ ++I 
Sbjct: 10  DGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMI--QDGPQNTGADKPLRIT 67

Query: 276 GTSEQIESAKQLVNEVISENRIRNPA 301
           G   +++ AK++V E+I +      +
Sbjct: 68  GDPYKVQQAKEMVLELIRDQGSGPSS 93

>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 = 79.8 bits (197), Expect = 2e-18
 Identities = 24/87 (27%), Positives = 48/87 (55%), Gaps = 1/87 (1%)

Query: 122 GGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVEL 181
            G       ++I IP  + G++IGK GETIK LQ ++G K+ + +D         + + +
Sbjct: 8   HGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQD-GPQNTGADKPLRI 66

Query: 182 MGTPEQIAKAEQLINDVLAEAESGGSG 208
            G P ++ +A++++ +++ +  SG S 
Sbjct: 67  TGDPYKVQQAKEMVLELIRDQGSGPSS 93

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

 Score = 83.4 bits (206), Expect = 1e-19
 Identities = 33/97 (34%), Positives = 45/97 (46%), Gaps = 1/97 (1%)

Query: 217 QAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDG 276
            A        IP +K GLVIG+GGE +K +  +TGA ++ I   LPP      +   I G
Sbjct: 3   MAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVE-ISRQLPPNGDPNFKLFIIRG 61

Query: 277 TSEQIESAKQLVNEVISENRIRNPAMAGGYSQQGYQA 313
           + +QI+ AKQL+ E I           GG    G   
Sbjct: 62  SPQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAGPMG 98

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

 Score = 71.1 bits (174), Expect = 3e-15
 Identities = 21/80 (26%), Positives = 41/80 (51%)

Query: 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQ 187
           G      IP  + G++IG+ GE +K +  Q+GA ++++R    + +   +   + G+P+Q
Sbjct: 6   GGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQ 65

Query: 188 IAKAEQLINDVLAEAESGGS 207
           I  A+QLI + +        
Sbjct: 66  IDHAKQLIEEKIEGPLCPVG 85

>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 = 82.1 bits (203), Expect = 2e-19
 Identities = 30/84 (35%), Positives = 49/84 (58%), Gaps = 3/84 (3%)

Query: 125 QSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT 184
           Q    +++ ++P+  VG IIG+ GE I  +Q +SG KIQ+  D+      P RS  L GT
Sbjct: 11  QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG---GLPERSCMLTGT 67

Query: 185 PEQIAKAEQLINDVLAEAESGGSG 208
           PE +  A++L++ ++ +  SG S 
Sbjct: 68  PESVQSAKRLLDQIVEKGRSGPSS 91

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

 Score = 76.7 bits (189), Expect = 2e-17
 Identities = 25/72 (34%), Positives = 44/72 (61%), Gaps = 4/72 (5%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
            K+P+  VG +IG+GGE I  +Q  +G +IQ+     P      ER+  + GT E ++SA
Sbjct: 19  YKVPDGMVGFIIGRGGEQISRIQQESGCKIQIA----PDSGGLPERSCMLTGTPESVQSA 74

Query: 285 KQLVNEVISENR 296
           K+L+++++ + R
Sbjct: 75  KRLLDQIVEKGR 86

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

 Score = 80.6 bits (199), Expect = 1e-18
 Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 2/86 (2%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + +P   VG +IG+GGETI+++   +GA+I         G     R ++I GT +++ +A
Sbjct: 19  LSVPQRSVGRIIGRGGETIRSICKASGAKITCDK--ESEGTLLLSRLIKISGTQKEVAAA 76

Query: 285 KQLVNEVISENRIRNPAMAGGYSQQG 310
           K L+ E +SE+      +A   S   
Sbjct: 77  KHLILEKVSEDEELRKRIAHSASGPS 102

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

 Score = 72.2 bits (177), Expect = 1e-15
 Identities = 27/91 (29%), Positives = 49/91 (53%), Gaps = 1/91 (1%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
             +++ +P   VG IIG+ GETI+ +   SGAKI   +++E      +R +++ GT +++
Sbjct: 15  VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT-LLLSRLIKISGTQKEV 73

Query: 189 AKAEQLINDVLAEAESGGSGIVARRLTGQAG 219
           A A+ LI + ++E E     I        +G
Sbjct: 74  AAAKHLILEKVSEDEELRKRIAHSASGPSSG 104

>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 = 77.8 bits (192), Expect = 1e-17
 Identities = 31/101 (30%), Positives = 49/101 (48%), Gaps = 9/101 (8%)

Query: 204 SGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPP 263
           SG SG +  RL  QA +    + IP      VIGK GE +++++ +T  +IQ+      P
Sbjct: 3   SGSSGDIVARLQTQASAT---VAIPKEHHRFVIGKNGEKLQDLELKTATKIQI------P 53

Query: 264 GDTSTERTVQIDGTSEQIESAKQLVNEVISENRIRNPAMAG 304
                   ++I GT E IE A+  V  + +E   R+   +G
Sbjct: 54  RPDDPSNQIKITGTKEGIEKARHEVLLISAEQDKRSGPSSG 94

>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 = 72.5 bits (178), Expect = 7e-16
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 5/76 (6%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
            S  + IP      +IGK+GE ++ L+L++  KIQ+ R      + P+  +++ GT E I
Sbjct: 17  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-----DDPSNQIKITGTKEGI 71

Query: 189 AKAEQLINDVLAEAES 204
            KA   +  + AE + 
Sbjct: 72  EKARHEVLLISAEQDK 87

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

 Score = 70.5 bits (173), Expect = 2e-15
 Identities = 14/69 (20%), Positives = 33/69 (47%), Gaps = 6/69 (8%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + I +     +IGK G  I  ++ +    +++      P D+     ++I+G  + ++ A
Sbjct: 9   INIDHKFHRHLIGKSGANINRIKDQYKVSVRI------PPDSEKSNLIRIEGDPQGVQQA 62

Query: 285 KQLVNEVIS 293
           K+ + E+ S
Sbjct: 63  KRELLELAS 71

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

 Score = 62.4 bits (152), Expect = 1e-12
 Identities = 13/72 (18%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
              +I I +     +IGKSG  I  ++ Q    +++  D     +  +  + + G P+ +
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-----SEKSNLIRIEGDPQGV 59

Query: 189 AKAEQLINDVLA 200
            +A++ + ++ +
Sbjct: 60  QQAKRELLELAS 71

>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 = 67.5 bits (165), Expect = 5e-14
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 6/70 (8%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           +++P +    VIG+ G  I+ M       I V      P        + I G +  ++ A
Sbjct: 21  VEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV------PAPELQSDIIAITGLAANLDRA 74

Query: 285 KQLVNEVISE 294
           K  + E + E
Sbjct: 75  KAGLLERVKE 84

>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 = 61.0 bits (148), Expect = 1e-11
 Identities = 11/75 (14%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIA 189
           + ++E+P      +IG+ G  I+ +  +    I V           +  + + G    + 
Sbjct: 18  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-----ELQSDIIAITGLAANLD 72

Query: 190 KAEQLINDVLAEAES 204
           +A+  + + + E ++
Sbjct: 73  RAKAGLLERVKELQA 87

>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 = 65.2 bits (159), Expect = 2e-13
 Identities = 15/90 (16%), Positives = 31/90 (34%), Gaps = 3/90 (3%)

Query: 205 GGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPG 264
           G SG    +      S   ++ +       +IG+ G  I  ++      IQ         
Sbjct: 1   GSSGSSGEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPD---KDD 57

Query: 265 DTSTERTVQIDGTSEQIESAKQLVNEVISE 294
               +  + I G  +  E+A+  +  ++ E
Sbjct: 58  GNQPQDQITITGYEKNTEAARDAILRIVGE 87

>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 = 61.4 bits (149), Expect = 6e-12
 Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 2/77 (2%)

Query: 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQ 187
                + +       IIG+ G  I  ++L+    IQ     + D N P   + + G  + 
Sbjct: 16  SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPD--KDDGNQPQDQITITGYEKN 73

Query: 188 IAKAEQLINDVLAEAES 204
              A   I  ++ E E 
Sbjct: 74  TEAARDAILRIVGELEQ 90

>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 = 64.6 bits (157), Expect = 3e-13
 Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           +++P   VGLV+G  G TIK +Q RT   I              E    + G  E ++ A
Sbjct: 14  VRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTP-------GRDKEPVFAVTGMPENVDRA 66

Query: 285 KQLVNEVISENR 296
           ++ +   I+   
Sbjct: 67  REEIEAHITLRS 78

>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 = 60.3 bits (146), Expect = 1e-11
 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 8/81 (9%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQV-TRDTEADLNSPTRSVELMGTPEQ 187
           T+ ++ +P   VG+++G  G TIK +Q ++   I    RD E           + G PE 
Sbjct: 10  TTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKE-------PVFAVTGMPEN 62

Query: 188 IAKAEQLINDVLAEAESGGSG 208
           + +A + I   +       SG
Sbjct: 63  VDRAREEIEAHITLRSGPSSG 83

>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 = 63.3 bits (154), Expect = 1e-12
 Identities = 13/80 (16%), Positives = 27/80 (33%), Gaps = 5/80 (6%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + + +     +IG  G+ I+ +       I+      P         V + G  E +E A
Sbjct: 21  VPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-----PQSGAPDPNCVTVTGLPENVEEA 75

Query: 285 KQLVNEVISENRIRNPAMAG 304
              +  +  E    +   +G
Sbjct: 76  IDHILNLEEEYLADSGPSSG 95

>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 = 58.6 bits (142), Expect = 6e-11
 Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 4/76 (5%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
            S+ + + +     IIG  G+ I+ +  +    I+  +    D       V + G PE +
Sbjct: 17  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPD----PNCVTVTGLPENV 72

Query: 189 AKAEQLINDVLAEAES 204
            +A   I ++  E  +
Sbjct: 73  EEAIDHILNLEEEYLA 88

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 69.5 bits (169), Expect = 2e-12
 Identities = 28/166 (16%), Positives = 43/166 (25%), Gaps = 6/166 (3%)

Query: 497 QQGYGTGQQPSPNTASYPPQGATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLA 556
           ++ Y   Q               QP+  +PP   +  G             +P   +   
Sbjct: 6   KRVYPQAQLQYG----QNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQF 61

Query: 557 NPPAYGQTQQSPGSAGGYGQPGYSHSQP--PPSSYAQPDSGSQRAPPSNYGAATQPGYGS 614
             PA  Q  Q    A       + H+ P   P++Y QP    Q   P             
Sbjct: 62  LTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAY 121

Query: 615 AAYGAPPGGSQAGYGQGPPSYYGGGYSQPVYTADGNAAPAAQPVQQ 660
               A  G +     Q  P         P+        P   P ++
Sbjct: 122 GQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPER 167

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 66.8 bits (162), Expect = 2e-11
 Identities = 20/147 (13%), Positives = 29/147 (19%)

Query: 474 PSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPTSQSGY 533
             YG      Q P            G   GQ   P   + P  G  Q             
Sbjct: 14  LQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQI 73

Query: 534 GSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQPD 593
                  +    + +P         P       +P           ++ QP  +      
Sbjct: 74  DQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMR 133

Query: 594 SGSQRAPPSNYGAATQPGYGSAAYGAP 620
             +Q  P         P         P
Sbjct: 134 PMNQLYPIDLLTELPPPITDLTLPPPP 160

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 64.8 bits (157), Expect = 5e-11
 Identities = 34/199 (17%), Positives = 40/199 (20%), Gaps = 21/199 (10%)

Query: 349 MSQPPYGGYPSQPTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADS 408
           MS      YP      G      Q P Q                    Q          S
Sbjct: 1   MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQD-----PAAAGMSYGQMGMPPQGAVPS 55

Query: 409 TGYSYSQPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTS 468
            G      PA     Q    A  S    H           Y Q Q               
Sbjct: 56  MGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQ--------------- 100

Query: 469 QEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSP-NTASYPPQGATQPSYGVPP 527
                 +   Q     A P     +A   Q      Q  P +  +  P   T  +   PP
Sbjct: 101 VPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPP 160

Query: 528 TSQSGYGSQVPPQSGYAGY 546
                    VP +   A  
Sbjct: 161 LVIPPERMLVPSELSNASP 179

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 63.7 bits (154), Expect = 1e-10
 Identities = 27/178 (15%), Positives = 35/178 (19%), Gaps = 23/178 (12%)

Query: 435 GYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAA 494
            Y   Q  YGQ A   QQ                                      S   
Sbjct: 8   VYPQAQLQYGQNATPLQQPAQFMP-----------------------PQDPAAAGMSYGQ 44

Query: 495 MGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKP 554
           MG    G            P Q           TS +       P      Y  PQ    
Sbjct: 45  MGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQ 104

Query: 555 LANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQPDSGSQRAPPSNYGAATQPGY 612
           +  P    Q   +  + G        + +P    Y          P ++      P  
Sbjct: 105 MGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLV 162

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 62.5 bits (151), Expect = 3e-10
 Identities = 32/153 (20%), Positives = 40/153 (26%), Gaps = 6/153 (3%)

Query: 519 TQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPG 578
           +     V P +Q  YG    P    A +  PQ   P A   +YGQ    P   G     G
Sbjct: 2   SHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQD--PAAAGMSYGQMGMPP--QGAVPSMG 57

Query: 579 YSHSQPPPSSYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSYYGG 638
                 P                ++      P     AY  P    Q G           
Sbjct: 58  QQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMA 117

Query: 639 G--YSQPVYTADGNAAPAAQPVQQGGVTKSPQS 669
              Y QP      N  P  Q      +T+ P  
Sbjct: 118 APAYGQPSAAMGQNMRPMNQLYPIDLLTELPPP 150

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 60.6 bits (146), Expect = 1e-09
 Identities = 21/173 (12%), Positives = 33/173 (19%), Gaps = 8/173 (4%)

Query: 304 GGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYPSQPTP 363
             + ++ Y  +    +G    P  Q   +   Q  A  G +    M  PP G  PS    
Sbjct: 2   SHHKKRVY-PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYG-QMGMPPQGAVPSMGQQ 59

Query: 364 GGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQPPASGYNQ 423
                     P Q+          +          P                       Q
Sbjct: 60  QFLT------PAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQ 113

Query: 424 QGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSY 476
           Q               Q+       Y             ++         P  
Sbjct: 114 QPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPE 166

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 59.8 bits (144), Expect = 2e-09
 Identities = 30/185 (16%), Positives = 40/185 (21%), Gaps = 12/185 (6%)

Query: 414 SQPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHT 473
           S      Y Q    Y Q++       Q    Q                        +G  
Sbjct: 2   SHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGM--------PPQGAV 53

Query: 474 PSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPTSQSGY 533
           PS G Q      P   Q    + Q           N     P    QP   V   +    
Sbjct: 54  PSMGQQQ--FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQ 111

Query: 534 GSQ--VPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQPPPSSYAQ 591
             Q    P  G     M Q  +P+          + P        P      PP      
Sbjct: 112 QQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVP 171

Query: 592 PDSGS 596
            +  +
Sbjct: 172 SELSN 176

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 59.8 bits (144), Expect = 2e-09
 Identities = 19/155 (12%), Positives = 26/155 (16%), Gaps = 4/155 (2%)

Query: 301 AMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYPSQ 360
                  Q G  A P         P               P Q    +M Q  +     +
Sbjct: 8   VYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQE 67

Query: 361 PTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQPPASG 420
                      Q  T                +  QPQ P     P        + P    
Sbjct: 68  QLHQQID----QATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQ 123

Query: 421 YNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGY 455
            +       +     Y             D     
Sbjct: 124 PSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPP 158

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 59.5 bits (143), Expect = 2e-09
 Identities = 25/202 (12%), Positives = 44/202 (21%), Gaps = 9/202 (4%)

Query: 333 GYVQPGAYPGQTPQYN-----MSQPPYGGYPSQPTPGGYPGNWDQTPTQQTSQGSGYDYY 387
            + +   YP    QY      + QP     P  P   G        P Q      G    
Sbjct: 2   SHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQ-QQ 60

Query: 388 SQQPSSQQPQAPGGSAAPADSTGYSYSQP---PASGYNQQGQGYAQDSYGGYHAPQSGYG 444
              P+ +Q       A  + +  + ++ P   P +    Q              P +   
Sbjct: 61  FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPA 120

Query: 445 QAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQ 504
              P                 +   E   P             P +      +    +  
Sbjct: 121 YGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPD 180

Query: 505 QPSPNTASYPPQGATQPSYGVP 526
                  + P   +      +P
Sbjct: 181 YIRSTLNAVPKNSSLLKKSKLP 202

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 57.5 bits (138), Expect = 1e-08
 Identities = 24/170 (14%), Positives = 31/170 (18%), Gaps = 3/170 (1%)

Query: 300 PAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGY--VQPGAYPGQTPQYNMSQPPYGGY 357
           P     Y Q     + P  +  P  P+     YG   + P        Q     P     
Sbjct: 10  PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQL 69

Query: 358 PSQPTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQPP 417
             Q        N            + Y    Q P              A       S   
Sbjct: 70  HQQIDQATTSMNDMHLHNVPLVDPNAY-MQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAM 128

Query: 418 ASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNT 467
                   Q Y  D       P +      P                N +
Sbjct: 129 GQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNAS 178

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 49.8 bits (118), Expect = 3e-06
 Identities = 18/132 (13%), Positives = 26/132 (19%), Gaps = 2/132 (1%)

Query: 299 NPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYP 358
            PA                  G P   ++   G       A      Q + +        
Sbjct: 25  QPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMH 84

Query: 359 SQPTPGGYPGNWDQ--TPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQP 416
               P   P  + Q   P Q  +           P+  QP A  G      +  Y     
Sbjct: 85  LHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLL 144

Query: 417 PASGYNQQGQGY 428
                       
Sbjct: 145 TELPPPITDLTL 156

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 69.0 bits (168), Expect = 4e-12
 Identities = 56/299 (18%), Positives = 79/299 (26%), Gaps = 40/299 (13%)

Query: 299  NPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYP 358
             P                    +P   S           G        Y  +  P+G Y 
Sbjct: 1471 TPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMA---GGFTAYGGADYGEATSPFGAYG 1527

Query: 359  SQPTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQPPA 418
              PT  G+           +S G     +S    +  P +P  S      +  S S  P 
Sbjct: 1528 EAPTSPGFGV---------SSPG-----FSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPT 1573

Query: 419  S-GYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSYG 477
            S  Y+     Y+  S   Y      Y   +P        ++  Y   +        PSY 
Sbjct: 1574 SPSYSPTSPSYSPTS-PSYSPTSPSYSPTSP----SYSPTSPSYSPTS--------PSYS 1620

Query: 478  AQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPTSQSGYGSQV 537
                S     P  S  +           P+  + S      +  S    PTS   Y    
Sbjct: 1621 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTS-PSYSPTS 1679

Query: 538  PPQSGYAGYGMPQAQKPLANPPAYGQT--QQSPGSAGGYGQPGYSHSQPPPSSYAQPDS 594
            P  S  +    P +       P+Y  T    SPGS      P YS  Q         +S
Sbjct: 1680 PSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGS------PAYSPKQDEQKHNENENS 1732

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 61.6 bits (149), Expect = 6e-10
 Identities = 50/229 (21%), Positives = 69/229 (30%), Gaps = 22/229 (9%)

Query: 457  SAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASY--- 513
            S       N+    G T   GA      +P      A        +    SP + +Y   
Sbjct: 1493 SPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPT 1552

Query: 514  -PPQGATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQT-QQSPGSA 571
             P    T PSY   PTS   Y    P  S  +    P +       P+Y  T      ++
Sbjct: 1553 SPAYSPTSPSYS--PTSP-SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1609

Query: 572  GGYG---------QPGYSHSQPPPSSYAQPDSGS--QRAPPSNYGAATQPGYGSAAYGAP 620
              Y           P YS + P  S  +   S +    +P S   + T P Y   +    
Sbjct: 1610 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYS 1669

Query: 621  PGGSQAGYGQGPPSYYGGGYS-QPVYTADGNAAPAAQPVQQGGVTKSPQ 668
            P  +   Y    PSY     S  P        +P+  P   G    SP 
Sbjct: 1670 P--TSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPA 1716

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 60.1 bits (145), Expect = 2e-09
 Identities = 55/301 (18%), Positives = 85/301 (28%), Gaps = 39/301 (12%)

Query: 389  QQPSSQQPQAPGGSAAPADSTGYSYSQPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAP 448
             +   +Q             T YS      +                  +  +  G    
Sbjct: 1451 VKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTA 1510

Query: 449  YDQQQGYNSAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSP 508
            Y       + + +G         +  +  + G    +P    +S         T    SP
Sbjct: 1511 YGGADYGEATSPFG--------AYGEAPTSPGFGVSSPGFSPTSPTYS----PTSPAYSP 1558

Query: 509  NTASYPPQGATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQ-- 566
             + SY P   T PSY   PTS   Y    P  S  +    P +       P+Y  T    
Sbjct: 1559 TSPSYSP---TSPSYS--PTS-PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1612

Query: 567  SPGSAG-GYGQPGYSHSQPPPSSYAQPDSGS---------QRAPPSNYGAATQPGYGSAA 616
            SP S       P YS + P  S  +   S +           +P S   + T P Y   +
Sbjct: 1613 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTS 1672

Query: 617  YGAPP-----GGSQAGYGQGPPSYYGG--GYSQ--PVYTADGNAAPAAQPVQQGGVTKSP 667
                P       +   Y    P+Y      YS   P Y+    A    Q  Q+    ++ 
Sbjct: 1673 PSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENS 1732

Query: 668  Q 668
            +
Sbjct: 1733 R 1733

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 48.9 bits (116), Expect = 5e-06
 Identities = 45/197 (22%), Positives = 64/197 (32%), Gaps = 20/197 (10%)

Query: 486  PPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPTSQSGYGSQVPPQSGYAG 545
            P    +    GQ G  T    S  +         +      P   SG    +    G+  
Sbjct: 1455 PEQKITEIEDGQDGGVT--PYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAG--GFTA 1510

Query: 546  YGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQP---PPSSYAQPDSGSQRAPPS 602
            YG     +  +   AYG+   SPG       PG+S + P   P S    P S S  +P S
Sbjct: 1511 YGGADYGEATSPFGAYGEAPTSPGFGVSS--PGFSPTSPTYSPTSPAYSPTSPSY-SPTS 1567

Query: 603  NYGAATQPGYGSAAYGAPPG-----GSQAGYGQGPPSYYGG--GYS--QPVYTADGNA-A 652
               + T P Y   +    P       +   Y    PSY      YS   P Y+    + +
Sbjct: 1568 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1627

Query: 653  PAAQPVQQGGVTKSPQS 669
            P +        + SP S
Sbjct: 1628 PTSPSYSPTSPSYSPTS 1644

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 47.8 bits (113), Expect = 1e-05
 Identities = 42/219 (19%), Positives = 64/219 (29%), Gaps = 31/219 (14%)

Query: 452  QQGYNSAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTA 511
            + G +      +  +               S         + A G   YG G      T+
Sbjct: 1463 EDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYG-GADYGEATS 1521

Query: 512  SYPPQGATQPSYGVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSA 571
             +   G    S G   +S  G+    P  S  +    P +       P+Y     SP S 
Sbjct: 1522 PFGAYGEAPTSPGFGVSS-PGFSPTSPTYSPTSPAYSPTSPSYSPTSPSY-----SPTS- 1574

Query: 572  GGYGQPGYSHSQPPPSSYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQG 631
                 P YS + P  S            P S   + T P Y   +    P  +   Y   
Sbjct: 1575 -----PSYSPTSPSYS------------PTSPSYSPTSPSYSPTSPSYSP--TSPSYSPT 1615

Query: 632  PPSYYGGGYSQPVYT-ADGNAAPAAQPVQQGGVTKSPQS 669
             PSY     + P Y+    + +P +        + SP S
Sbjct: 1616 SPSYS---PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1651

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 42.4 bits (99), Expect = 6e-04
 Identities = 28/132 (21%), Positives = 44/132 (33%), Gaps = 8/132 (6%)

Query: 298  RNPAMAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGY-VQPGAYPGQTPQYNMSQPPYGG 356
                 +  YS       P +   +P +PS       Y     +Y   +P Y+ + P Y  
Sbjct: 1604 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSP 1663

Query: 357  YP---SQPTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSY 413
                 S  +P   P +   +PT  +   +  +Y    PS   P +PG S     S  YS 
Sbjct: 1664 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPS-YSPTSPGYS---PGSPAYSP 1719

Query: 414  SQPPASGYNQQG 425
             Q        + 
Sbjct: 1720 KQDEQKHNENEN 1731

>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 = 54.0 bits (130), Expect = 2e-09
 Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 7/81 (8%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQAR-TGARIQVIPLHLPPGDTSTERTVQIDGTSEQIES 283
           + IP      +IG  G  I+++     G  I        P + S   TV I G S  +E 
Sbjct: 21  VSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHF------PVEGSGSDTVVIRGPSSDVEK 74

Query: 284 AKQLVNEVISENRIRNPAMAG 304
           AK+ +  +  E + ++   +G
Sbjct: 75  AKKQLLHLAEEKQTKSGPSSG 95

>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 = 50.6 bits (121), Expect = 3e-08
 Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGA-KIQVTRDTEADLNSPTRSVELMGTPEQ 187
              ++ IP      +IG  G  I+ +  + G   I    +      S + +V + G    
Sbjct: 17  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-----GSGSDTVVIRGPSSD 71

Query: 188 IAKAEQLINDVLAEAES 204
           + KA++ +  +  E ++
Sbjct: 72  VEKAKKQLLHLAEEKQT 88

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

 Score = 58.7 bits (143), Expect = 4e-09
 Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 11/71 (15%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS-EQIES 283
           + IP +K+  VIG GG+ I+ + A TGA++          D + +  V++  +   +I++
Sbjct: 574 INIPTDKIREVIGSGGKVIREIVATTGAKV----------DINDDGVVKVSASDGAKIKA 623

Query: 284 AKQLVNEVISE 294
           A   +  +  E
Sbjct: 624 AIDWIKSITDE 634

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

 Score = 44.8 bits (107), Expect = 8e-05
 Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 12/84 (14%)

Query: 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT-PEQIAK 190
            I IP  ++  +IG  G+ I+ +   +GAK+    D   D       V++  +   +I  
Sbjct: 573 TINIPTDKIREVIGSGGKVIREIVATTGAKV----DINDD-----GVVKVSASDGAKIKA 623

Query: 191 AEQLINDVLAEAESGG--SGIVAR 212
           A   I  +  EAE G    G V +
Sbjct: 624 AIDWIKSITDEAEVGKIYDGKVVK 647

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 59.3 bits (143), Expect = 4e-09
 Identities = 66/327 (20%), Positives = 94/327 (28%), Gaps = 54/327 (16%)

Query: 322  PGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYPSQPTPGGYPGNWDQTPTQQTSQG 381
             G       G G        G    Y  S     G+   P    +      +P  Q    
Sbjct: 1461 LGTAVPTLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDAAAF------SPLVQGGSE 1514

Query: 382  SGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQPPASGYNQQGQGYAQDSYGGYHAPQS 441
                +             G  +    S    +S   + GY      Y+  S G   +P  
Sbjct: 1515 GREGFGDYGLLGAASPYKGVQSPGYTS---PFSSAMSPGYGLTSPSYSPSSPGYSTSP-- 1569

Query: 442  GYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYG 501
                         Y  ++   +  + S    +PSY     S  +P    +S +       
Sbjct: 1570 ------------AYMPSSPSYSPTSPSYSPTSPSY-----SPTSPSYSPTSPSYSATSPS 1612

Query: 502  ---TGQQPSPNTASYPPQGATQPSY-----GVPPTSQSGYGSQVPPQSGYAGYGMPQAQK 553
               T    SP + SY P   T PSY        PTS   Y    P  S       P +  
Sbjct: 1613 YSPTSPSYSPTSPSYSP---TSPSYSPTSPSYSPTS-PSYSPTSPSYS-------PTSPS 1661

Query: 554  PLANPPAYGQT--QQSPGSAGGYG-QPGYSHSQPP--PSSYAQPDSGSQRAPPSNYGAAT 608
                 P+Y  T    SP S       P YS + P   P+S +   +    +P S   + T
Sbjct: 1662 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1721

Query: 609  QPGYGSAAYGAPPGGSQAGYGQGPPSY 635
             P Y   +    P  +   Y    PSY
Sbjct: 1722 SPSYSPTSPSYSP--TSPSYSPTSPSY 1746

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 54.3 bits (130), Expect = 1e-07
 Identities = 63/270 (23%), Positives = 89/270 (32%), Gaps = 36/270 (13%)

Query: 302  MAGGYSQQGYQARPPTSWGTPGAPSMQQPGYGYVQPGAYPGQTPQYNMSQPPYGGYPS-Q 360
               G+   G      + +    +P    P    + PG Y   +P Y+ S P Y   P+  
Sbjct: 1515 GREGFGDYGLLG-AASPYKGVQSPGYTSPFSSAMSPG-YGLTSPSYSPSSPGYSTSPAYM 1572

Query: 361  PTPGGYPGNWDQTPTQQT-SQGSGYDYYSQQPSSQQPQAPGGSAA-PADSTGYSYSQPPA 418
            P+   Y      +PT  + S  S    YS    S  P +P  SA  P+ S       P +
Sbjct: 1573 PSSPSY------SPTSPSYSPTSP--SYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTS 1624

Query: 419  SGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQEGHTPSYGA 478
              Y+     Y+  S   Y      Y   +P       + +    + + TS      S   
Sbjct: 1625 PSYSPTSPSYSPTSP-SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1683

Query: 479  QGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYGVPPTSQSGYGSQVP 538
               S    P   +S +       T    SP + SY P   T PSY   PTS   Y    P
Sbjct: 1684 SPTSPSYSP---TSPSYS----PTSPSYSPTSPSYSP---TSPSYS--PTS-PSYSPTSP 1730

Query: 539  PQSGYAGYGMPQAQKPLANPPAYGQTQQSP 568
              S       P +       P+Y  T  SP
Sbjct: 1731 SYS-------PTSPSYSPTSPSYSPT--SP 1751

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 52.0 bits (124), Expect = 6e-07
 Identities = 68/326 (20%), Positives = 95/326 (29%), Gaps = 53/326 (16%)

Query: 345  PQYNMSQPPYGGYPSQPTPGGYPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAA 404
              Y++         S       P     TP +++         S   ++  P   GGS  
Sbjct: 1457 MNYSLGTAVPTLAGSGMGTSQLPEG-AGTPYERSPMVDSGFVGSPDAAAFSPLVQGGSEG 1515

Query: 405  PADSTGYSYSQPPASGYNQQGQGYAQDSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNV 464
                  Y      AS Y           +    +P  G    +      GY+++  Y   
Sbjct: 1516 REGFGDYGLL-GAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPS 1574

Query: 465  NNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSYG 524
                    +PSY     S     P  S          T    SP + SY     T PSY 
Sbjct: 1575 --------SPSYSPTSPSYSPTSPSYS---------PTSPSYSPTSPSYSA---TSPSYS 1614

Query: 525  VPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQTQQSPGSAGGYGQPGYSHSQP 584
              PTS S Y    P  S       P +       P+Y     SP S      P YS    
Sbjct: 1615 --PTSPS-YSPTSPSYS-------PTSPSYSPTSPSY-----SPTS------PSYS---- 1649

Query: 585  PPSSYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSYYGG--GYSQ 642
             P+S +   +    +P S   + T P Y   +       +   Y    PSY      YS 
Sbjct: 1650 -PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS--PSYSPTSPSYSPTSPSYSPTSPSYS- 1705

Query: 643  PVYTADGNAAPAAQPVQQGGVTKSPQ 668
            P   +    +P+  P        SP 
Sbjct: 1706 PTSPSYSPTSPSYSPTSPSYSPTSPS 1731

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 50.5 bits (120), Expect = 2e-06
 Identities = 42/188 (22%), Positives = 61/188 (32%), Gaps = 13/188 (6%)

Query: 464  VNNTSQEGHTPSYGAQGDSTQAPPPVQSSAAMGQQGYGTGQQPSPNTASYPPQGATQPSY 523
            + N S     P+    G  T   P    +         +G   SP+ A++ P        
Sbjct: 1456 LMNYSLGTAVPTLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDAAAFSPLVQGGSEG 1515

Query: 524  GVPPTSQSGYGSQVPPQSGYAGYGMPQAQKPLANPPAYGQT--QQSPGSAGGYGQPGYSH 581
                      G+  P +   +          ++  P YG T    SP S G    P Y  
Sbjct: 1516 REGFGDYGLLGAASPYKGVQSPGYTSPFSSAMS--PGYGLTSPSYSPSSPGYSTSPAYMP 1573

Query: 582  SQP---PPSSYAQPDSGSQRAPPSNYGAATQPGYGSAAYGAPPGGSQAGYGQGPPSYYGG 638
            S P   P S    P S S  +P S   + T P Y + +    P  +   Y    PSY   
Sbjct: 1574 SSPSYSPTSPSYSPTSPSY-SPTSPSYSPTSPSYSATSPSYSP--TSPSYSPTSPSY--- 1627

Query: 639  GYSQPVYT 646
              + P Y+
Sbjct: 1628 SPTSPSYS 1635

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

 Score = 57.5 bits (140), Expect = 9e-09
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 11/71 (15%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS-EQIES 283
           +KI  +K+  VIGKGG  I+ +   TG  I          +   + TV+I  T  E+ + 
Sbjct: 564 IKINPDKIKDVIGKGGSVIRALTEETGTTI----------EIEDDGTVKIAATDGEKAKH 613

Query: 284 AKQLVNEVISE 294
           A + + E+ +E
Sbjct: 614 AIRRIEEITAE 624

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

 Score = 42.9 bits (102), Expect = 3e-04
 Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 12/83 (14%)

Query: 133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT-PEQIAKA 191
           I+I   ++  +IGK G  I+ L  ++G  I    + E D      +V++  T  E+   A
Sbjct: 564 IKINPDKIKDVIGKGGSVIRALTEETGTTI----EIEDD-----GTVKIAATDGEKAKHA 614

Query: 192 EQLINDVLAEAESGG--SGIVAR 212
            + I ++ AE E G   +G V R
Sbjct: 615 IRRIEEITAEIEVGRVYTGKVTR 637

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

 Score = 56.8 bits (138), Expect = 2e-08
 Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 11/69 (15%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS-EQIES 283
           +++P +K    +G GG  +K +QA TG  I              E T  +   +   +  
Sbjct: 571 VQVPLSKRAKFVGPGGYNLKKLQAETGVTI----------SQVDEETFSVFAPTPSAMHE 620

Query: 284 AKQLVNEVI 292
           A+  + E+ 
Sbjct: 621 ARDFITEIC 629

>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 = 54.9 bits (133), Expect = 7e-08
 Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 11/71 (15%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS-EQIES 283
           +KIP +K+G VIG   + I  +Q  TGA I              + T+ I        E+
Sbjct: 602 VKIPVDKIGEVIGPKRQMINQIQEDTGAEI----------TIEDDGTIYIGAADGPAAEA 651

Query: 284 AKQLVNEVISE 294
           A+  +N + + 
Sbjct: 652 ARATINGIANP 662

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score = 48.8 bits (115), Expect = 3e-06
 Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 5/74 (6%)

Query: 225 MKIPNNKVGLVIGKGG--ETIKNMQARTGARIQVIPLHLPPGDTSTE--RTVQIDGTSEQ 280
           M+  +    L+    G  E + ++ A T   IQ +P     G T     + V I G    
Sbjct: 34  MEFESQYYSLMTSDNGDHENVASIMAETNTLIQ-LPDRSVGGTTPDPFAQQVTITGYFGD 92

Query: 281 IESAKQLVNEVISE 294
           ++ A+ L+      
Sbjct: 93  VDRARMLMRRNCHF 106

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score = 41.8 bits (97), Expect = 5e-04
 Identities = 12/163 (7%), Positives = 51/163 (31%), Gaps = 16/163 (9%)

Query: 133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQ-IAKA 191
           + +  +++ +   ++        +Q+     V    +  + +    +      +  + +A
Sbjct: 110 MALSKMKMPLHELQAHVRQN--PIQNVEMSFVDAPEKNGIVTTYLRITAREKNQHELIEA 167

Query: 192 EQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGK--GGETIKNMQAR 249
            + +N++L                           +    V  V+G     + +  ++  
Sbjct: 168 AKRLNEILFRESPAPENNFT-----------LHFTLSTYYVDQVLGSSSTAQLMPVIERE 216

Query: 250 TGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVI 292
           T   I     +           +++ G  + +  A++ + +++
Sbjct: 217 TTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLL 259

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A Length = 144

 Score = 41.9 bits (99), Expect = 1e-04
 Identities = 24/125 (19%), Positives = 44/125 (35%), Gaps = 25/125 (20%)

Query: 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKA 191
              +     G  IG+ G  IK L+   G  I+V   +  DL                   
Sbjct: 39  IFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSS-DL------------------- 78

Query: 192 EQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTG 251
           E+++ ++    +     I +  +  + G     +K+  +  G  IGKGG+ +K  +    
Sbjct: 79  ERIVKNLFPGVK-----IESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLS 133

Query: 252 ARIQV 256
               V
Sbjct: 134 KLFGV 138

>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 Length = 102

 Score = 40.7 bits (95), Expect = 1e-04
 Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 9/82 (10%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
           T   +  P+     IIGK G+ +  +  Q   K+ +      +       + L G  E +
Sbjct: 27  TVSSVAAPSWLHRFIIGKKGQNLAKITQQMP-KVHI------EFTEGEDKITLEGPTEDV 79

Query: 189 AKAEQLINDVLAE--AESGGSG 208
           + A++ I  ++ +    SG S 
Sbjct: 80  SVAQEQIEGMVKDLINRSGPSS 101

>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 Length = 102

 Score = 39.5 bits (92), Expect = 3e-04
 Identities = 12/71 (16%), Positives = 29/71 (40%), Gaps = 10/71 (14%)

Query: 225 MKIPNNKVGLVIGKGGETIKN-MQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIES 283
           +  P+     +IGK G+ +    Q      I+          T  E  + ++G +E +  
Sbjct: 31  VAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEF---------TEGEDKITLEGPTEDVSV 81

Query: 284 AKQLVNEVISE 294
           A++ +  ++ +
Sbjct: 82  AQEQIEGMVKD 92

>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 Length = 131

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 23/102 (22%), Positives = 39/102 (38%), Gaps = 24/102 (23%)

Query: 123 GYQSMGTSKKIEIP-------NIRVGVIIGKSGETIKYLQLQSGAKIQV----------- 164
           G  +   S K+ IP       N  VG++IG  G T+K ++ +  AKI +           
Sbjct: 1   GAMATRVSDKVMIPQDEYPEINF-VGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKV 59

Query: 165 ---TRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAEA 202
                      + P     +   T E + KA + I ++L + 
Sbjct: 60  GRKDGQMLPGEDEPLH-ALVTANTMENVKKAVEQIRNILKQG 100

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 42.8 bits (100), Expect = 3e-04
 Identities = 26/146 (17%), Positives = 35/146 (23%), Gaps = 12/146 (8%)

Query: 307 SQQGYQARPPTSWGTPGAPSMQQP-GYGYVQPGAYPGQTPQYNMSQPPYGGYPSQPTPGG 365
           +Q       PT  G+  APS+    G G   PG          +S P  G  P       
Sbjct: 18  TQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPIS--TLSSPINGMGPPFSVISS 75

Query: 366 YPGNWDQTPTQQTSQGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQPPASGYNQQG 425
             G    +     + G                +      P    G        SG     
Sbjct: 76  PMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMASF 135

Query: 426 QGYA----QDSYGGYHAPQSGYGQAA 447
             +      D   G H     YG  +
Sbjct: 136 TKHICAICGDRSSGKH-----YGVYS 156

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	669
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.95
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
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.94
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.94
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.82
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.74
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.72
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.68
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.67
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.66
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.64
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.64
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.62
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.54
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.53
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.52
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.5
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.5
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.5
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.49
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.48
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.48
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	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	99.47
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.47
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.47
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.46
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.46
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.46
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.46
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.45
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.44
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.43
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.43
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.43
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.42
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.41
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.41
1we8_A	104	Tudor and KH domain containing protein; structural	99.41
1we8_A	104	Tudor and KH domain containing protein; structural	99.4
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.34
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.33
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.33
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.31
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.31
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.3
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.27
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.27
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.26
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.23
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.22
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.22
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.14
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.13
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.06
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.89
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.85
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.85
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.8
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.79
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.79
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.75
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	98.64
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.48
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.43
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.32
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.14
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.98
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.85
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.8
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.74
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.43
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.33
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	97.14
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	96.83
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.74
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.61
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.89
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	95.69
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	94.52
2cxc_A	144	NUSA; transcription termination, RNA binding prote	87.13
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	83.96
4hhu_A	170	OR280; engineered protein, PSI-biology, structural	81.69

>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=99.95  E-value=1.5e-28  Score=238.28  Aligned_cols=168  Identities=27%  Similarity=0.418  Sum_probs=137.2

Q ss_pred             CCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCC
Q 005922          127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGG  206 (669)
Q Consensus       127 ~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~  206 (669)
                      ..++++|+||.+++|+||||+|++||+|+++|||+|+|.++.+..+++.+|+|+|+|+.++|.+|+.+|.+++.+.....
T Consensus         4 ~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~~~~   83 (178)
T 2anr_A            4 SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQNV   83 (178)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCCCC-
T ss_pred             CCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhccCCcc
Confidence            34899999999999999999999999999999999999876556678899999999999999999999999998754321


Q ss_pred             CCcc------hhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHH
Q 005922          207 SGIV------ARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQ  280 (669)
Q Consensus       207 ~~~~------~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peq  280 (669)
                      ....      ...........+++|+||.+++|+||||+|++||+|+++|||+|+|..+.  ...++++++|+|+|+.++
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~--~~~~~~~~~v~I~G~~~~  161 (178)
T 2anr_A           84 AKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKP--DGINLQNRVVTVSGEPEQ  161 (178)
T ss_dssp             ----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC------CCEEEEEEESSHHH
T ss_pred             ccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCC--CCCCCCceEEEEEcCHHH
Confidence            1000      00000112246789999999999999999999999999999999997542  122457899999999999


Q ss_pred             HHHHHHHHHHHHhhcc
Q 005922          281 IESAKQLVNEVISENR  296 (669)
Q Consensus       281 Vq~Ak~LI~dlL~e~~  296 (669)
                      |++|+.||+++|+++.
T Consensus       162 v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          162 NRKAVELIIQKIQEDP  177 (178)
T ss_dssp             HHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHhCC
Confidence            9999999999998853

>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=1e-27  Score=229.20  Aligned_cols=158  Identities=28%  Similarity=0.388  Sum_probs=134.8

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG  208 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~  208 (669)
                      .+++|+||.+.+|+||||+|++||+|+++|||+|+|.++.  .+++.+|+|+|+|+.+++.+|+.+|.++|.+...... 
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~--~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~~~~-   79 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPE--TPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFGP-   79 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCS--STTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTSSCS-
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCC--CCCCCceEEEEEcCHHHHHHHHHHHHHHHhccccccc-
Confidence            5799999999999999999999999999999999998753  5678999999999999999999999999988632111 


Q ss_pred             cchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHH
Q 005922          209 IVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLV  288 (669)
Q Consensus       209 ~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI  288 (669)
                             ......+.+|.||.+++|+||||+|++||+|+++|||+|.|..+..+  ...+++.|+|+|++++|++|+.||
T Consensus        80 -------~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~--~~~~~~~v~I~G~~~~v~~A~~~I  150 (163)
T 3krm_A           80 -------KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTP--DENDQVIVKIIGHFYASQMAQRKI  150 (163)
T ss_dssp             -------SCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCC--CTTSEEEEEEEECHHHHHHHHHHH
T ss_pred             -------ccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCC--CCCCceEEEEEeCHHHHHHHHHHH
Confidence                   01124567999999999999999999999999999999999765433  133455899999999999999999


Q ss_pred             HHHHhhcccC
Q 005922          289 NEVISENRIR  298 (669)
Q Consensus       289 ~dlL~e~~~r  298 (669)
                      +++|++.+..
T Consensus       151 ~~~i~~~~~~  160 (163)
T 3krm_A          151 RDILAQVKQQ  160 (163)
T ss_dssp             HHHHHHHTC-
T ss_pred             HHHHHHHHHh
Confidence            9999986543

>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=1.4e-27  Score=227.67  Aligned_cols=160  Identities=31%  Similarity=0.540  Sum_probs=133.4

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG  208 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~  208 (669)
                      ++++|+||.+++|+||||+|++||+|+++|||+|+|.++.. .++..+|+|+|+|+.++|++|+.+|+++|.+.......
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~-~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~~~~~   80 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQGGFG   80 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTT-SSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSSSCCCS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCC-CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhccCCCCC
Confidence            68999999999999999999999999999999999976542 45678899999999999999999999999886532111


Q ss_pred             cchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHH
Q 005922          209 IVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLV  288 (669)
Q Consensus       209 ~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI  288 (669)
                      ..  .........+++|.||.+++|+||||+|++||+|+++|||+|+|....    +.+.++.|+|+|+.++|++|++||
T Consensus        81 ~~--~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~----~~~~~~~v~I~G~~~~v~~A~~~I  154 (164)
T 2jvz_A           81 DR--NEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD----GTGPEKIAHIMGPPDRCEHAARII  154 (164)
T ss_dssp             SC--SSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC----TTSSEEEEEEESCHHHHHHHHHHH
T ss_pred             Cc--cccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC----CCCCcEEEEEEcCHHHHHHHHHHH
Confidence            00  000011124578999999999999999999999999999999997432    245689999999999999999999


Q ss_pred             HHHHhhc
Q 005922          289 NEVISEN  295 (669)
Q Consensus       289 ~dlL~e~  295 (669)
                      +++|++.
T Consensus       155 ~~~i~~~  161 (164)
T 2jvz_A          155 NDLLQSL  161 (164)
T ss_dssp             HHHHHHH
T ss_pred             HHHHhhh
Confidence            9999874

>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=99.94  E-value=1.7e-27  Score=230.33  Aligned_cols=160  Identities=36%  Similarity=0.634  Sum_probs=130.1

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG  208 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~  208 (669)
                      .+++|+||.+++|+||||+|++||+|+++|||+|+|.++   ..++++|+|+|+|+.++|++|+.+|.++|.+.......
T Consensus         3 ~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~---~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~~   79 (174)
T 1j4w_A            3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD---DGTTPERIAQITGPPDRAQHAAEIITDLLRSVQAGNPG   79 (174)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECC---TTSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC-----
T ss_pred             eEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecC---CCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcccCCCC
Confidence            689999999999999999999999999999999999754   34678899999999999999999999999886432110


Q ss_pred             c----------chhcc--cCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEc
Q 005922          209 I----------VARRL--TGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDG  276 (669)
Q Consensus       209 ~----------~~rr~--~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG  276 (669)
                      .          ....+  ......++++|.||.+++|+||||+|++||+|+++|||+|+|..+. ++..++.+++|+|+|
T Consensus        80 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~-~~~~~~~~~~v~I~G  158 (174)
T 1j4w_A           80 GPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP-PPNADPNMKLFTIRG  158 (174)
T ss_dssp             ------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCC-TTTSCTTEEEEEEEC
T ss_pred             CCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCC-CCCCCCCceEEEEEC
Confidence            0          00000  0011245789999999999999999999999999999999997643 233456789999999


Q ss_pred             CHHHHHHHHHHHHHHH
Q 005922          277 TSEQIESAKQLVNEVI  292 (669)
Q Consensus       277 ~peqVq~Ak~LI~dlL  292 (669)
                      +.++|++|++||+++|
T Consensus       159 ~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          159 TPQQIDYARQLIEEKI  174 (174)
T ss_dssp             CHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHhC
Confidence            9999999999999975

>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=1.3e-27  Score=227.82  Aligned_cols=156  Identities=33%  Similarity=0.480  Sum_probs=133.7

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCC
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGS  207 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~  207 (669)
                      .++++|+||.+.+|+||||+|++||+|+++|||+|+|+++     ++++|+|+|+|+.++|.+|+.+|.++|.++.....
T Consensus         4 ~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~-----~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~~~~   78 (160)
T 2jzx_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKLEEDISSSM   78 (160)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC-----TTTEEEEEEEEEHHHHHHHHHHHHHHHHHHHTSCC
T ss_pred             cEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC-----CCCceEEEEEeCHHHHHHHHHHHHHHHHhhccccC
Confidence            4889999999999999999999999999999999999753     46789999999999999999999999988654221


Q ss_pred             CcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHH
Q 005922          208 GIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQL  287 (669)
Q Consensus       208 ~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~L  287 (669)
                      ...   ........+++|.||.+++|+||||+|++||+|+++|||+|+|..+.++   +++++.|+|+|++++|++|+++
T Consensus        79 ~~~---~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~---~~~~~~v~I~G~~~~v~~A~~~  152 (160)
T 2jzx_A           79 TNS---TAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLP---NSTERAITIAGIPQSIIECVKQ  152 (160)
T ss_dssp             CSS---SCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCST---TCCEEEEEEEECHHHHHHHHHH
T ss_pred             CCC---ccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCC---CCCceEEEEEcCHHHHHHHHHH
Confidence            100   0011224688999999999999999999999999999999999764433   4678999999999999999999


Q ss_pred             HHHHHhh
Q 005922          288 VNEVISE  294 (669)
Q Consensus       288 I~dlL~e  294 (669)
                      |+++|.|
T Consensus       153 I~~~i~e  159 (160)
T 2jzx_A          153 ICVVMLE  159 (160)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHhc
Confidence            9999987

>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=9.5e-21  Score=179.07  Aligned_cols=136  Identities=19%  Similarity=0.272  Sum_probs=108.7

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG  208 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~  208 (669)
                      ++++|+||.+.||++|||+|++||.|++++|++|....      ..+++.+....+++.|.+|+.+|.            
T Consensus         4 ~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~------~~~~~~i~~~~~p~~v~~~~~~l~------------   65 (144)
T 2qnd_A            4 FHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLD------EDTCTFHIYGEDQDAVKKARSFLE------------   65 (144)
T ss_dssp             CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEE------TTTTEEEEEESSHHHHHHHHHHHC------------
T ss_pred             eEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccC------CCchheeeccCCHHHHHHHHHhhh------------
Confidence            78999999999999999999999999999994443321      234566666678999988865331            


Q ss_pred             cchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCC-eEEeccCCCCCCCCCCc--cEEEEEcCHHHHHHHH
Q 005922          209 IVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGA-RIQVIPLHLPPGDTSTE--RTVQIDGTSEQIESAK  285 (669)
Q Consensus       209 ~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGA-rIqI~~~~~ppge~s~e--r~VtItG~peqVq~Ak  285 (669)
                                 ..+.+|.||.++++++|||+|++||.|++.||| +|+|..+..... ..++  +.|+|+|+.++|++|+
T Consensus        66 -----------~~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~-~~~~~~~~vtI~G~~~~v~~Ak  133 (144)
T 2qnd_A           66 -----------FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV-PQEEGMVPFVFVGTKDSIANAT  133 (144)
T ss_dssp             -----------EEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC-CCCTTEEEEEEEEEHHHHHHHH
T ss_pred             -----------cceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc-cccCCeeEEEEEeCHHHHHHHH
Confidence                       013789999999999999999999999999997 999986432211 1223  3589999999999999


Q ss_pred             HHHHHHHhh
Q 005922          286 QLVNEVISE  294 (669)
Q Consensus       286 ~LI~dlL~e  294 (669)
                      .||+++|.+
T Consensus       134 ~li~~~l~~  142 (144)
T 2qnd_A          134 VLLDYHLNY  142 (144)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHh
Confidence            999999976

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.74  E-value=1.9e-18  Score=173.93  Aligned_cols=143  Identities=27%  Similarity=0.384  Sum_probs=109.0

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-----CHHHHHHHHHHHHHHHHhhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-----TPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-----t~E~V~kA~~lI~elI~e~~  203 (669)
                      .+++|.||..++|.|||++|++||.|+++|||+|+|+.+        ++.|+|.+     +.+.+++|+++|.++++...
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~--------~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg~~  105 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE--------TGEVWITSTKETEDPLAVWKARDIVLAIGRGFS  105 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT--------TCEEEEEECTTCCSHHHHHHHHHHHHHHHTTCC
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC--------CCEEEEecCCCCCCHHHHHHHHHHHHHHhccCC
Confidence            578999999999999999999999999999999999733        34455554     47999999999999984321


Q ss_pred             cCCCCcchhcccCCCCCcEEEEee-----CC------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEE
Q 005922          204 SGGSGIVARRLTGQAGSDHFAMKI-----PN------NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTV  272 (669)
Q Consensus       204 ~~~~~~~~rr~~~~~~~~t~~I~V-----P~------~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~V  272 (669)
                      ..    ....+... ......+.|     +.      ..+|+||||+|++||.|++.|||+|.|.           +++|
T Consensus       106 ~e----~g~~ll~d-d~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~-----------~~~v  169 (219)
T 2e3u_A          106 PE----RAFRLLNE-GEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY-----------GKTV  169 (219)
T ss_dssp             HH----HHGGGGST-TCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE-----------TTEE
T ss_pred             cc----ccceeccC-CccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC-----------CeEE
Confidence            10    00000000 001111222     22      2689999999999999999999999995           4689


Q ss_pred             EEEcCHHHHHHHHHHHHHHHhhc
Q 005922          273 QIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       273 tItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      +|.|+.++|+.|+.+|+++|.+.
T Consensus       170 ~i~G~~~~i~~A~~~i~~li~g~  192 (219)
T 2e3u_A          170 AIIGNPIQIEIAKTAIEKLARGS  192 (219)
T ss_dssp             EEEECHHHHHHHHHHHHHHHTTC
T ss_pred             EEEeCHHHHHHHHHHHHHHHcCC
Confidence            99999999999999999999663

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

Probab=99.72  E-value=1.1e-17  Score=179.57  Aligned_cols=165  Identities=10%  Similarity=0.169  Sum_probs=120.6

Q ss_pred             CceEEEEeccccccceeccCC--cchhHHHhhcCcEEEEccCC--ccCCCCCCccccccCCHHHHHHHHHHHHHH-----
Q 005922          128 GTSKKIEIPNIRVGVIIGKSG--ETIKYLQLQSGAKIQVTRDT--EADLNSPTRSVELMGTPEQIAKAEQLINDV-----  198 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgG--etIK~IqeeTGAkI~Iskd~--e~~p~~~eRvVtItGt~E~V~kA~~lI~el-----  198 (669)
                      .++++|.||...+.+||||+|  ++|++|+++|+|+|+|..+.  ...+......|+|+|.+++|++|+++|.++     
T Consensus        29 ~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l~Pl~i  108 (376)
T 3n89_A           29 RVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNCHFTV  108 (376)
T ss_dssp             EEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHSCEEEE
T ss_pred             EEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhcCCceE
Confidence            499999999999999999999  99999999999999997543  111224457899999999999999999874     


Q ss_pred             -----------------HHhhhcCCC---------------Ccc--h--h---------------cccC----CCCCcEE
Q 005922          199 -----------------LAEAESGGS---------------GIV--A--R---------------RLTG----QAGSDHF  223 (669)
Q Consensus       199 -----------------I~e~~~~~~---------------~~~--~--r---------------r~~~----~~~~~t~  223 (669)
                                       |.......+               ...  +  .               .+..    ....+++
T Consensus       109 ~~elp~~~i~~~~l~~~I~qq~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~~nv~~akeA~~~Ll~~l~~~e~~~~~~~s~  188 (376)
T 3n89_A          109 FMALSKMKMPLHELQAHVRQNPIQNVEMSFVDAPEKNGIVTTYLRITAREKNQHELIEAAKRLNEILFRESPAPENNFTL  188 (376)
T ss_dssp             EEECTTCSSCHHHHHHHHHHCCCTTCEEEEEEEC-----CEEEEEEEEEGGGHHHHHHHHHHHHHHHCC--CCCSSCEEE
T ss_pred             EEEccccccCcchhhhhhccceeCceEEEeCCcccccCCCCCEEEEEcChhhHHHHHHHHHHHHHHHHhhhcccccceEE
Confidence                             111000000               000  0  0               0001    1134678


Q ss_pred             EEeeCCCceeeeecCCc--hHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHH
Q 005922          224 AMKIPNNKVGLVIGKGG--ETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVI  292 (669)
Q Consensus       224 ~I~VP~~~vG~IIGKGG--stIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL  292 (669)
                      .|.|+..++..||||+|  ..|++|+++|||+|.|...............|+|+|..++|+.|+++|+++|
T Consensus       189 ~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lL  259 (376)
T 3n89_A          189 HFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLL  259 (376)
T ss_dssp             EEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTS
T ss_pred             EEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhC
Confidence            89999999999999999  6679999999999999532211100123467999999999999999999988

>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=99.68  E-value=6.8e-18  Score=163.39  Aligned_cols=139  Identities=28%  Similarity=0.356  Sum_probs=106.2

Q ss_pred             HHHHHHHHHHccccccCCCC-----CCCCceecCCCCCCCCccccccCCcccccCCCCCCCCC--CC-----CCCCCCCC
Q 005922           61 QAAKRRAEQIAARLCNSVSA-----EAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIP--VS-----YGGYQSMG  128 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~~~-----~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~--~s-----~g~~~~~~  128 (669)
                      ++|++|+++++|+|+|.+..     +.+|+++|.|.  .+++.+|+.+|.+.+..........  ..     .....+..
T Consensus        26 ~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~--~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (178)
T 2anr_A           26 QTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT--IEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRA  103 (178)
T ss_dssp             HHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEEC--HHHHHHHHHHHHHHHTCCCCC-----------------CGGG
T ss_pred             HHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeC--HHHHHHHHHHHHHHHhccCCccccCCcccccCCccCCCCCCc
Confidence            68999999999999998532     67899999997  4567778777777665332211000  00     00011234


Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      ++++|+||.+++|+||||+|++||+|+++|||+|+|.++.+ +++..+|+|+|+|+.++|++|+.+|.++|+++
T Consensus       104 ~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~-~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~  176 (178)
T 2anr_A          104 NQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD-GINLQNRVVTVSGEPEQNRKAVELIIQKIQED  176 (178)
T ss_dssp             GEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC-----CCEEEEEEESSHHHHHHHHHHHHHHHHSC
T ss_pred             eEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCC-CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhC
Confidence            78999999999999999999999999999999999986542 45677899999999999999999999999875

>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=99.67  E-value=3.4e-18  Score=162.68  Aligned_cols=134  Identities=25%  Similarity=0.326  Sum_probs=109.4

Q ss_pred             HHHHHHHHHHccccccCCCCCCCCceecCCCCCCCCccccccCCcccccC-CCCCCCCCCCCCCCCCCCceEEEEecccc
Q 005922           61 QAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLKS-IPAPSAIPVSYGGYQSMGTSKKIEIPNIR  139 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~~~~~ERiisisg~~~~eav~kA~~~i~~~l~~-i~~~~~~~~s~g~~~~~~vt~rIlVP~~~  139 (669)
                      ++|++|+++++|+|+|.+..+.+|.++|.|.  .+++.+|+..|.+.+.+ +.....  .+. ......++++|+||..+
T Consensus        25 ~~Ik~i~~~tg~~I~i~~~~~~~r~v~I~G~--~~~v~~A~~~I~~~i~e~~~~~~~--~~~-~~~~~~~~~~i~vp~~~   99 (160)
T 2jzx_A           25 ESVKKMREESGARINISEGNCPERIITLAGP--TNAIFKAFAMIIDKLEEDISSSMT--NST-AASRPPVTLRLVVPASQ   99 (160)
T ss_dssp             HHHHHHHHHHCSEEEEECCTTTEEEEEEEEE--HHHHHHHHHHHHHHHHHHHTSCCC--SSS-CCCCCSEEEEEEEEHHH
T ss_pred             HHHHHHHHHHCCEEEEcCCCCCceEEEEEeC--HHHHHHHHHHHHHHHHhhccccCC--CCc-cCCCCCEEEEEEEChhh
Confidence            6899999999999999987788999999997  55677888877766542 211111  000 01123489999999999


Q ss_pred             ccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922          140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE  201 (669)
Q Consensus       140 vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e  201 (669)
                      +|+||||+|++||+|+++|||+|+|.++.  .+++.+++|+|+|+.++|++|+++|+++|.|
T Consensus       100 ~g~iIGkgG~~Ik~i~~~tga~I~i~~~~--~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          100 CGSLIGKGGCKIKEIRESTGAQVQVAGDM--LPNSTERAITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             HHHHHCGGGHHHHHHHHHHSSEECCCCCC--STTCCEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             eeeEECCCCHHHHHHHHHhCCeEEECCCC--CCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999998653  5678899999999999999999999999987

>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=99.66  E-value=5.5e-17  Score=160.03  Aligned_cols=142  Identities=23%  Similarity=0.296  Sum_probs=111.2

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCcccccc-----CCHHHHHHHHHHHHHHHHhhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELM-----GTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtIt-----Gt~E~V~kA~~lI~elI~e~~  203 (669)
                      ..++++||..++|.|||++|+++|.|+++++++|+|+..        ++.|+|.     ++++.+.+|.++|.+++....
T Consensus         4 ~~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~~--------~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf~   75 (191)
T 1tua_A            4 PRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE--------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFP   75 (191)
T ss_dssp             CCEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT--------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCC
T ss_pred             cceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEcC--------CCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCC
Confidence            457999999999999999999999999999999999632        4555555     999999999999999887543


Q ss_pred             cCCCCcchhcccCCCCCcEEEEeeC----------CCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEE
Q 005922          204 SGGSGIVARRLTGQAGSDHFAMKIP----------NNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQ  273 (669)
Q Consensus       204 ~~~~~~~~rr~~~~~~~~t~~I~VP----------~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~Vt  273 (669)
                      ...    ..++.. .......|.|.          ...+|+||||+|.+||.|++.|||+|.|.           +++|+
T Consensus        76 ~e~----A~~Ll~-Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~-----------~~~v~  139 (191)
T 1tua_A           76 PEK----AFRLLE-EDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG-----------EYEVA  139 (191)
T ss_dssp             HHH----HGGGGS-TTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC-----------SSEEE
T ss_pred             HHH----hhhccc-CcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc-----------CCEEE
Confidence            210    001111 00011122232          23589999999999999999999999995           35999


Q ss_pred             EEcCHHHHHHHHHHHHHHHhh
Q 005922          274 IDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       274 ItG~peqVq~Ak~LI~dlL~e  294 (669)
                      |.|+.+.|+.|+..|+++|..
T Consensus       140 i~G~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          140 IIGDYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             EEEEHHHHHHHHHHHHHHHTT
T ss_pred             EEeChHHHHHHHHHHHHHHcC
Confidence            999999999999999999975

>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=99.64  E-value=4.8e-17  Score=154.80  Aligned_cols=136  Identities=24%  Similarity=0.389  Sum_probs=106.8

Q ss_pred             HHHHHHHHHHccccccCCC----CCCCCceecCCCCCCCCccccccCCcccccCCCCC-CCCCCCCCCCCCCCceEEEEe
Q 005922           61 QAAKRRAEQIAARLCNSVS----AEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAP-SAIPVSYGGYQSMGTSKKIEI  135 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~~----~~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~-~~~~~s~g~~~~~~vt~rIlV  135 (669)
                      ++||+|+++++|+|.|...    .+.+|+++|.|.  .+++.+|+..|.+.+.+.... ......++.  ...++++|+|
T Consensus        22 ~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~--~~~v~~A~~~I~~ii~e~~~~~~~~~~~~~~--~~~~~~~i~v   97 (164)
T 2jvz_A           22 ETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGD--PYKVQQACEMVMDILRERDQGGFGDRNEYGS--RIGGGIDVPV   97 (164)
T ss_dssp             HHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEEC--HHHHHHHHHHHHHHTTCSSSCCCSSCSSCTT--SCSSSBCCEE
T ss_pred             HHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcC--HHHHHHHHHHHHHHHHhccCCCCCCccccCC--CCCceEEEEE
Confidence            6899999999999999743    256899999996  556778888777776643211 111111221  1135789999


Q ss_pred             ccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          136 PNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       136 P~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      |..++|+||||+|++||+|+++|||+|+|.++.   .+..+|+|+|+|+.++|++|+.+|.++|++..
T Consensus        98 p~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~---~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~  162 (164)
T 2jvz_A           98 PRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD---GTGPEKIAHIMGPPDRCEHAARIINDLLQSLR  162 (164)
T ss_dssp             ETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC---TTSSEEEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             ChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC---CCCCcEEEEEEcCHHHHHHHHHHHHHHHhhhh
Confidence            999999999999999999999999999998653   35568999999999999999999999998754

>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=99.64  E-value=4.5e-17  Score=155.35  Aligned_cols=132  Identities=23%  Similarity=0.246  Sum_probs=106.4

Q ss_pred             HHHHHHHHHHccccccCCC---CCCCCceecCCCCCCCCccccccCCcccccCCCCCCCCCCCCCCCCCCCceEEEEecc
Q 005922           61 QAAKRRAEQIAARLCNSVS---AEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPN  137 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~~---~~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~g~~~~~~vt~rIlVP~  137 (669)
                      ++|++|+++++|+|+|.+.   .+.+|+++|.|.  .+++.+|+..|.+.+......       ....+..++.+|+||.
T Consensus        23 ~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~--~e~v~~A~~~I~~~~~e~~~~-------~~~~~~~~~~~i~vp~   93 (163)
T 3krm_A           23 QHIKQLSRFASASIKIAPPETPDSKVRMVIITGP--PEAQFKAQGRIYGKLKEENFF-------GPKEEVKLETHIRVPA   93 (163)
T ss_dssp             HHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEEC--HHHHHHHHHHHHHHHHHTTSS-------CSSCCCCEEEEEEEET
T ss_pred             HHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcC--HHHHHHHHHHHHHHHhccccc-------ccccCCceEEEEEcCh
Confidence            6899999999999999974   358899999996  566777877777766522100       0112234788999999


Q ss_pred             ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCC-ccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          138 IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPT-RSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       138 ~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~e-RvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      ..+|+||||+|++||+|+++|||+|+|.++.  .++..+ ++|+|+|+.++|++|+.+|+++|++..
T Consensus        94 ~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~--~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~  158 (163)
T 3krm_A           94 SAAGRVIGKGGKTVNELQNLTAAEVVVPRDQ--TPDENDQVIVKIIGHFYASQMAQRKIRDILAQVK  158 (163)
T ss_dssp             TTHHHHHCGGGHHHHHHHHHHCCEEECCTTC--CCCTTSEEEEEEEECHHHHHHHHHHHHHHHHHHT
T ss_pred             hheeeEEcCCChHHHHHHHHhCCeEEECCCC--CCCCCCceEEEEEeCHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999998654  344444 489999999999999999999999854

>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=99.62  E-value=3.5e-17  Score=158.00  Aligned_cols=137  Identities=27%  Similarity=0.365  Sum_probs=102.8

Q ss_pred             HHHHHHHHHHccccccCC--CCCCCCceecCCCCCCCCccccccCCcccccCCCCC-CCCC-----------CCCC-CCC
Q 005922           61 QAAKRRAEQIAARLCNSV--SAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAP-SAIP-----------VSYG-GYQ  125 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~--~~~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~-~~~~-----------~s~g-~~~  125 (669)
                      ++||+|+++++|+|+|..  ..+.+|+++|.|.  .+++.+|+.+|.+.+...... ....           ..+. ...
T Consensus        23 ~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~--~~~v~~A~~~I~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~  100 (174)
T 1j4w_A           23 EMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP--PDRAQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPP  100 (174)
T ss_dssp             HHHHHHHHHHCCEEEEECCTTSCSEEEEEEEEC--HHHHHHHHHHHHHHHHHHC--------------------------
T ss_pred             hHHHHHHHHhCCEEEEecCCCCCCccEEEEEeC--HHHHHHHHHHHHHHHHhcccCCCCCCCCCCCCCCCCCCccccCCC
Confidence            689999999999999974  3467899999997  556778877776665422100 0000           0000 001


Q ss_pred             CCCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHH
Q 005922          126 SMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL  199 (669)
Q Consensus       126 ~~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI  199 (669)
                      +..++++|+||..++|+||||+|++||+|+++|||+|+|.++.....+..+|+|+|+|+.++|++|+.+|+++|
T Consensus       101 ~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          101 GGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             ---CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             CCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            12368999999999999999999999999999999999987643334577899999999999999999999875

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

Probab=99.54  E-value=4.3e-15  Score=133.69  Aligned_cols=74  Identities=35%  Similarity=0.586  Sum_probs=65.8

Q ss_pred             EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922          222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR  296 (669)
Q Consensus       222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~  296 (669)
                      +++|+||.++|++||||+|++||+|+++|||+|+|..+..+ ..+..+++|+|+|+.++|++|++||+++|++..
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 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPP-NGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCT-TCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCC-CCCCCceEEEEECCHHHHHHHHHHHHHHHhccc
Confidence            68999999999999999999999999999999999765332 234568999999999999999999999998864

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

Probab=99.53  E-value=8.3e-15  Score=131.82  Aligned_cols=74  Identities=31%  Similarity=0.547  Sum_probs=64.5

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcccC
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENRIR  298 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~~r  298 (669)
                      .+++|+||.+++++||||+|++||+|+++|+|+|+|..+.    .+..||+|+|+|++++|++|++||+++|++....
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~----~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~~g   84 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD----GTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSG   84 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC----SSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC--
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC----CCCceeEEEEEeCHHHHHHHHHHHHHHHhccccC
Confidence            4689999999999999999999999999999999997432    2456899999999999999999999999986543

>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=99.52  E-value=5.2e-15  Score=124.51  Aligned_cols=73  Identities=29%  Similarity=0.448  Sum_probs=67.5

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE  201 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e  201 (669)
                      ++++|+||.+++|+||||+|++||+|+++|||+|+|.++.+..++..+|+|+|+|+.++|++|+.+|.++|.+
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            6899999999999999999999999999999999999875556778899999999999999999999999876

>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=99.50  E-value=1.3e-14  Score=125.61  Aligned_cols=75  Identities=29%  Similarity=0.450  Sum_probs=69.8

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      ++++|+||.+.+|+||||+|++||+|+++|||+|+|.++.+..++..+|+|+|+|+.++|++|+.+|+++|.+..
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   77 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQ   77 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccc
Confidence            689999999999999999999999999999999999976555678889999999999999999999999998854

>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=99.50  E-value=8.1e-15  Score=123.06  Aligned_cols=70  Identities=36%  Similarity=0.549  Sum_probs=65.0

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      .++++|+||.+.+|+||||+|++||+|+++|||+|+|+++     ++++|+|+|+|+.++|.+|+.+|.++|+|+
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~-----~~~er~v~I~G~~~~v~~A~~~I~~~l~ed   73 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKLEED   73 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-----CCSEEEEEEEECHHHHHHHHHHHHHHHHC-
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-----CCCcEEEEEEeCHHHHHHHHHHHHHHHhcC
Confidence            3899999999999999999999999999999999999854     467999999999999999999999999874

>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=99.50  E-value=2e-14  Score=123.07  Aligned_cols=73  Identities=30%  Similarity=0.460  Sum_probs=67.2

Q ss_pred             CCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       127 ~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      ..++++|+||.+++|+||||+|++||+|+++|||+|+|+++   .++..+|+|+|+|+.++|++|+.+|+++|++.
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~---~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT---TSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC---CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            34899999999999999999999999999999999999754   35678899999999999999999999999874

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

Probab=99.49  E-value=1.6e-14  Score=129.95  Aligned_cols=75  Identities=27%  Similarity=0.505  Sum_probs=67.2

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      .+++|+||.++||+||||+|++||+|+++|||+|+|.++.+...+..+|+|+|+|+.|+|++|+++|+++|++..
T Consensus         7 ~~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~   81 (107)
T 2hh2_A            7 GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CCEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCC
T ss_pred             CeEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhccc
Confidence            378999999999999999999999999999999999876533345678999999999999999999999998754

>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=99.48  E-value=3.9e-14  Score=123.99  Aligned_cols=74  Identities=34%  Similarity=0.650  Sum_probs=66.3

Q ss_pred             CCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922          219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR  296 (669)
Q Consensus       219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~  296 (669)
                      ..++++|+||.+++|+||||+|++||+|+++|||+|+|..+.    +...+|+|+|+|++++|++|++||+++|++.+
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 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS----GGLPERSCMLTGTPESVQSAKRLLDQIVEKGR   86 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC----TTCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC----CCCCccEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            356789999999999999999999999999999999997532    24568999999999999999999999999864

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

Probab=99.48  E-value=2.5e-14  Score=120.05  Aligned_cols=70  Identities=27%  Similarity=0.487  Sum_probs=63.7

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      ..+++|+||.+++|.||||+|++||+|+++|||+|+|..+      +..+|+|+|+|++++|++|++||+++|+|+
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~------~~~er~v~I~G~~~~v~~A~~~I~~~l~ed   73 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG------NCPERIITLAGPTNAIFKAFAMIIDKLEED   73 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS------CCSEEEEEEEECHHHHHHHHHHHHHHHHC-
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC------CCCcEEEEEEeCHHHHHHHHHHHHHHHhcC
Confidence            4678999999999999999999999999999999999743      346899999999999999999999999874

>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=99.48  E-value=2.7e-14  Score=125.00  Aligned_cols=75  Identities=36%  Similarity=0.611  Sum_probs=68.1

Q ss_pred             CCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhc
Q 005922          127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAES  204 (669)
Q Consensus       127 ~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~  204 (669)
                      ..++++|+||.+++|+||||+|++||+|+++|||+|+|.++.   .+..+|+|+|+|+.++|++|+.+|+++|++...
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~---~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~~   87 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCMLTGTPESVQSAKRLLDQIVEKGRS   87 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC---TTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHHhccc
Confidence            348999999999999999999999999999999999998653   356789999999999999999999999998643

>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=120.02  Aligned_cols=72  Identities=31%  Similarity=0.522  Sum_probs=64.6

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      ..+++|.||.+++|+||||+|++||+|+++|||+|+|...    ..++++|.|+|+|++++|++|++||+++|++.
T Consensus         6 ~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~----~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            6 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT----TSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC----CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            4678999999999999999999999999999999999642    12456899999999999999999999999873

>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=99.47  E-value=1.8e-14  Score=123.37  Aligned_cols=72  Identities=33%  Similarity=0.523  Sum_probs=65.5

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      .++++|+||.+++|+||||+|++||+|+++|||+|+|.++   .++..+|+|+|+|+.++|++|+.+|.++|.++
T Consensus         5 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~---~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            5 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP---VEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC---CTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             cEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC---CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            4889999999999999999999999999999999999864   35678999999999999999999999999875

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

Probab=99.47  E-value=1.8e-14  Score=121.51  Aligned_cols=72  Identities=35%  Similarity=0.511  Sum_probs=66.7

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      .++++|+||.+++|+||||+|++||+|+++|||+|+|.+.   .++..+|+|+|+|+.++|++|+.+|.++|+++
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~---~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP---VEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC---CTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC---CCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            3889999999999999999999999999999999999863   46778999999999999999999999999864

>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=99.47  E-value=4.1e-14  Score=121.10  Aligned_cols=72  Identities=31%  Similarity=0.542  Sum_probs=63.9

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      .++++|+||.+++|+||||+|++||+|+++|||+|+|...    .+.+.++.|+|+|++++|++|++||+++|+++
T Consensus         5 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~----~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            5 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP----VEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC----CTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             cEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC----CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            4678999999999999999999999999999999999742    23567999999999999999999999999875

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

Probab=99.46  E-value=6.4e-14  Score=117.85  Aligned_cols=73  Identities=32%  Similarity=0.483  Sum_probs=63.5

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e  294 (669)
                      ++++|.||.+++|+||||+|++||+|+++|||+|+|..+.. ....+.++.|+|+|++++|++|+.||+++|++
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 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGE-FLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTC-CSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCC-CCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            57899999999999999999999999999999999975421 11245689999999999999999999999865

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

Probab=99.46  E-value=4.1e-14  Score=127.32  Aligned_cols=74  Identities=36%  Similarity=0.658  Sum_probs=66.1

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESG  205 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~  205 (669)
                      .+++|+||.+++++||||+|+|||+|+++|+|+|+|+++.   .+.++|+|+|+|+.|+|++|+++|+++|++....
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~---~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~~g   84 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD---GTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSG   84 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC---SSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC--
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC---CCCceeEEEEEeCHHHHHHHHHHHHHHHhccccC
Confidence            5799999999999999999999999999999999998653   3567899999999999999999999999987543

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

Probab=99.46  E-value=4.5e-14  Score=119.08  Aligned_cols=72  Identities=31%  Similarity=0.551  Sum_probs=64.9

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      .++++|.||.+++|+||||+|++||+|+++|||+|+|...    ...+.++.|+|+|++++|++|+.||+++|++.
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~----~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP----VEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC----CTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC----CCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            4578999999999999999999999999999999999742    23567999999999999999999999999864

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

Probab=99.46  E-value=2.5e-14  Score=124.48  Aligned_cols=73  Identities=30%  Similarity=0.460  Sum_probs=67.3

Q ss_pred             CCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       127 ~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      ..++++|+||.+++|+||||+|++||+|+++|||+|+|++.   .+++.+|+|+|+|+.++|++|+++|+++|++.
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 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC---CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC---CCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            45899999999999999999999999999999999999754   45678999999999999999999999999874

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

Probab=99.45  E-value=1.6e-13  Score=118.21  Aligned_cols=73  Identities=34%  Similarity=0.586  Sum_probs=64.5

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e  294 (669)
                      ...++|.||.+++|+||||+|++||+|+++|||+|.|..+...  ....+|.|+|+|++++|++|++||+++|+|
T Consensus        13 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~--~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ--NTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCS--STTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCC--CCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            4578999999999999999999999999999999999764321  245689999999999999999999999864

>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=99.44  E-value=8e-14  Score=122.48  Aligned_cols=75  Identities=37%  Similarity=0.646  Sum_probs=66.3

Q ss_pred             CCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      +.++++|+||.+++++||||+|++||+|+++|||+|+|..+...  ...++|.|+|+|++++|++|++||+++|++.
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 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQ--NTGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCC--SSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCC--CCCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            45788999999999999999999999999999999999754321  2346899999999999999999999999874

>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=99.43  E-value=4.5e-14  Score=124.11  Aligned_cols=76  Identities=26%  Similarity=0.531  Sum_probs=67.9

Q ss_pred             CCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       127 ~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      ..++++|+||.+++|+||||+|++||+|+++|||+|+|.++.. .....+|+|+|+|+.++|++|+++|+++|++..
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~-~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   88 (94)
T 1x4m_A           13 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGP-QNTGADKPLRITGDPYKVQQAKEMVLELIRDQG   88 (94)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCC-CSSCSCEEEEEEECTTTHHHHHHHHHHHHCCCS
T ss_pred             CcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCC-CCCCCceEEEEEeCHHHHHHHHHHHHHHHhccC
Confidence            4489999999999999999999999999999999999987642 124578999999999999999999999998754

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

Probab=99.43  E-value=1.1e-13  Score=119.33  Aligned_cols=72  Identities=33%  Similarity=0.595  Sum_probs=65.6

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE  201 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e  201 (669)
                      .+++|+||.+++|+||||+|++||+|+++|||+|+|.++.. .....+|+|+|+|+++.|++|+.+|+++++|
T Consensus        14 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~-~~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           14 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             EEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSC-SSTTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             EEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCC-CCCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            78999999999999999999999999999999999987542 3467789999999999999999999999864

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=4.9e-14  Score=121.51  Aligned_cols=70  Identities=29%  Similarity=0.472  Sum_probs=62.3

Q ss_pred             CCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922          218 AGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       218 ~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e  294 (669)
                      .+..+++|.||.+++|+||||+|++||+|+++|||+|+|..+       .++++|+|+|++++|++|++||+++|..
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            345788999999999999999999999999999999999631       2368999999999999999999998765

>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=7.5e-14  Score=121.39  Aligned_cols=72  Identities=31%  Similarity=0.522  Sum_probs=64.6

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      .++++|.||.+++++||||+|++||+|+++|||+|+|...    ..++++|.|+|+|++++|++|++||+++|++.
T Consensus        13 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~----~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           13 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             EEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC----CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC----CCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            4578999999999999999999999999999999999642    12456899999999999999999999999873

>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=99.41  E-value=1.4e-13  Score=118.96  Aligned_cols=75  Identities=29%  Similarity=0.473  Sum_probs=65.3

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR  296 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~  296 (669)
                      ++++|.||.+++|+||||+|++||+|+++|||+|+|..+.. ....+.++.|+|+|++++|++|+.||+++|.+..
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~-~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   77 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGE-FLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQ   77 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTC-BSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCC-CCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccc
Confidence            57899999999999999999999999999999999975321 1124568999999999999999999999998743

>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=99.41  E-value=7.2e-14  Score=120.48  Aligned_cols=69  Identities=23%  Similarity=0.393  Sum_probs=62.9

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      .++++|+||.+++|+||||+|++||+|+++|||+|+|.+..      .+++|+|+|+.++|++|+.+|++++...
T Consensus         9 ~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~------~~~~v~ItG~~e~v~~A~~~I~~~i~~r   77 (83)
T 2dgr_A            9 QTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD------KEPVFAVTGMPENVDRAREEIEAHITLR   77 (83)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS------SCCEEEEEECTTTHHHHHHHHHHHHHSC
T ss_pred             ceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC------CCCeEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            48999999999999999999999999999999999997532      2689999999999999999999987753

>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=99.41  E-value=2.8e-13  Score=121.18  Aligned_cols=75  Identities=32%  Similarity=0.530  Sum_probs=65.1

Q ss_pred             CCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      ...+++|+||.+++|+||||+|++||+|+++|||+|+|.....  ...+.++.|+|+|+.++|++|++||+++|+++
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 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE--GTLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSC--CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCC--CCCCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            3567899999999999999999999999999999999975321  11245899999999999999999999999774

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

Probab=99.40  E-value=1.8e-13  Score=122.38  Aligned_cols=74  Identities=34%  Similarity=0.546  Sum_probs=66.1

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      ++++|+||.+++|+||||+|++||+|+++|||+|+|.++.+. ....+|+|+|+|+.++|++|+.+|+++|.++.
T Consensus        15 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~-~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T 1we8_A           15 VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG-TLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             EEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC-SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCC-CCCCcceEEEEcCHHHHHHHHHHHHHHHhhCh
Confidence            789999999999999999999999999999999999865421 13468999999999999999999999998754

>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=99.34  E-value=9.3e-13  Score=115.76  Aligned_cols=72  Identities=32%  Similarity=0.540  Sum_probs=64.9

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhc
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAES  204 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~  204 (669)
                      .++++|.||.+++|+||||+|++||+|+++|||+|+|++.     +..++.|+|+|+.++|++|+.+|++++.+...
T Consensus        16 ~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~-----~~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~~   87 (94)
T 2cte_A           16 QASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-----DDPSNQIKITGTKEGIEKARHEVLLISAEQDK   87 (94)
T ss_dssp             CEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-----TSSCCEEEEEECHHHHHHHHHHHHHHHHHHHT
T ss_pred             ceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCC-----CCCCCeEEEEECHHHHHHHHHHHHHHhhcccc
Confidence            3899999999999999999999999999999999999743     23458999999999999999999999988654

>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=99.33  E-value=1.4e-12  Score=115.47  Aligned_cols=74  Identities=22%  Similarity=0.328  Sum_probs=66.9

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhc
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAES  204 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~  204 (669)
                      ++++|.||..++++||||+|++||+|+++|||+|+|.++.  .++..+|.|+|+|+.++|++|+.+|++++.+...
T Consensus        17 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g--~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~e~   90 (97)
T 2ctl_A           17 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKD--DGNQPQDQITITGYEKNTEAARDAILRIVGELEQ   90 (97)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTT--TCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHHH
T ss_pred             eeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCC--CCCCCccEEEEEeCHHHHHHHHHHHHHHHHHHHh
Confidence            7999999999999999999999999999999999998654  2345789999999999999999999999987543

>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=99.33  E-value=2.4e-12  Score=113.86  Aligned_cols=73  Identities=16%  Similarity=0.268  Sum_probs=63.8

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      ..++.|.||.++++.||||+|++||+|+++|||+|+|..+..   .+..++.|+|+|+.++|++|+.+|++++.+.
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~---~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~   88 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD---GNQPQDQITITGYEKNTEAARDAILRIVGEL   88 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT---CSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            357899999999999999999999999999999999964321   1235789999999999999999999999773

>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=99.31  E-value=2.2e-12  Score=113.37  Aligned_cols=72  Identities=28%  Similarity=0.457  Sum_probs=63.7

Q ss_pred             CCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922          219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR  296 (669)
Q Consensus       219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~  296 (669)
                      ..++++|.||.++++.|||++|++||+|+++|||+|.|...      ++.++.|+|+|+.++|++|++||++++++..
T Consensus        15 ~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~------~~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~   86 (94)
T 2cte_A           15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP------DDPSNQIKITGTKEGIEKARHEVLLISAEQD   86 (94)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT------TSSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCC------CCCCCeEEEEECHHHHHHHHHHHHHHhhccc
Confidence            35678999999999999999999999999999999999532      2336799999999999999999999998854

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

Probab=99.31  E-value=1.5e-12  Score=108.78  Aligned_cols=67  Identities=19%  Similarity=0.366  Sum_probs=60.0

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHH
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVI  292 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL  292 (669)
                      ..+.+|.||.++++.|||++|++||+|+++|||+|.|..+      ...++.|+|+|+.+.|++|+++|++++
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~------g~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD------SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC------CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCC------CCcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999999999999632      235689999999999999999999875

>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=99.30  E-value=4.7e-12  Score=111.69  Aligned_cols=72  Identities=17%  Similarity=0.227  Sum_probs=63.8

Q ss_pred             CCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      ..++++|.||.++++.|||++|++||+|+++|||+|+|..+    + +..++.|+|+|.+++|++|+++|++++++.
T Consensus        15 ~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~----g-~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   86 (95)
T 2ctm_A           15 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQS----G-APDPNCVTVTGLPENVEEAIDHILNLEEEY   86 (95)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCT----T-CSCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCC----C-CCCCcEEEEEcCHHHHHHHHHHHHHHHHHH
Confidence            35788999999999999999999999999999999999532    1 234789999999999999999999999874

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

Probab=99.27  E-value=4.2e-12  Score=111.97  Aligned_cols=73  Identities=19%  Similarity=0.251  Sum_probs=65.6

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhc
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAES  204 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~  204 (669)
                      .++++|.||..++++||||+|++||+|+++|||+|+|.++.    ...+|.|+|+|+.++|++|+++|++++++...
T Consensus        16 ~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           16 MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG----APDPNCVTVTGLPENVEEAIDHILNLEEEYLA   88 (95)
T ss_dssp             CCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT----CSCTTEEEEESCHHHHHHHHHHHHHHHHHHHT
T ss_pred             cEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC----CCCCcEEEEEcCHHHHHHHHHHHHHHHHHHHH
Confidence            38899999999999999999999999999999999997542    23578999999999999999999999988653

>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=99.27  E-value=2.7e-13  Score=121.19  Aligned_cols=89  Identities=16%  Similarity=0.317  Sum_probs=76.7

Q ss_pred             cccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHH-hCCeEEecc
Q 005922          180 ELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQAR-TGARIQVIP  258 (669)
Q Consensus       180 tItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~-TGArIqI~~  258 (669)
                      .|+|++++|.+|+.+|.+++.+                  .++.+|.||..+++.|||++|++||+|+++ ++++|.|..
T Consensus         4 ~i~G~~~~V~~A~~~i~~~~~~------------------~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~   65 (102)
T 2ctf_A            4 GSSGEPEKLGQALTEVYAKANS------------------FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE   65 (102)
T ss_dssp             CCCCCCCCCCCSCCCCCCCCCC------------------CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS
T ss_pred             ccCcCHHHHHHHHHHHHHHhcC------------------eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC
Confidence            5788888888888888765532                  257899999999999999999999999997 589999842


Q ss_pred             CCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          259 LHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       259 ~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                               .++.|+|+|+++.|++|+.+|+++|++.
T Consensus        66 ---------~~~~ItI~G~~~~V~~a~~~I~~~v~el   93 (102)
T 2ctf_A           66 ---------GEDKITLEGPTEDVSVAQEQIEGMVKDL   93 (102)
T ss_dssp             ---------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             ---------CCCEEEEECCHHHHHHHHHHHHHHHHHH
Confidence                     3679999999999999999999999874

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

Probab=99.26  E-value=1.8e-12  Score=108.25  Aligned_cols=66  Identities=20%  Similarity=0.341  Sum_probs=60.7

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL  199 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI  199 (669)
                      +++.|.||.+++|+||||+|++||+|+++|||+|+|.++.     ..+|.|+|+|+.++|++|+.+|++++
T Consensus         5 ~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-----~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            5 DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-----EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             EEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-----SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             EEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-----CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            7899999999999999999999999999999999998643     36789999999999999999999874

>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=99.23  E-value=6.3e-12  Score=112.60  Aligned_cols=70  Identities=16%  Similarity=0.256  Sum_probs=63.5

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      +++.|.||.+++|+|||++|++||+|+++|||+|+|.++.     ...+.|+|+|+.++|++|+.+|++++++..
T Consensus        17 ~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g-----~~~~~V~I~G~~e~v~~A~~~I~~i~~e~e   86 (104)
T 2ctk_A           17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-----LQSDIIAITGLAANLDRAKAGLLERVKELQ   86 (104)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-----TTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-----CCcceEEEEcCHHHHHHHHHHHHHHHhhHH
Confidence            7899999999999999999999999999999999998543     235689999999999999999999998754

>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=99.22  E-value=9.2e-12  Score=111.54  Aligned_cols=69  Identities=22%  Similarity=0.304  Sum_probs=61.7

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e  294 (669)
                      ..+..|.||.++++.|||++|++||+|+++|||+|.|..+      ....+.|+|+|+.++|++|+++|++++++
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~------g~~~~~V~I~G~~e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP------ELQSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT------TTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCC------CCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            4678999999999999999999999999999999999632      22356999999999999999999999876

>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=99.22  E-value=1.9e-11  Score=109.17  Aligned_cols=90  Identities=19%  Similarity=0.301  Sum_probs=74.2

Q ss_pred             ecCCCCCCCCccccccCCcccccCCCCCCCCCCCCCCCCCCCceEEEEeccccccceeccCCcchhHHHhh-cCcEEEEc
Q 005922           87 VENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQ-SGAKIQVT  165 (669)
Q Consensus        87 sisg~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~g~~~~~~vt~rIlVP~~~vG~IIGKgGetIK~Iqee-TGAkI~Is  165 (669)
                      .+.|+  .+++.+|+..+.+.+...                 ++.+|.||..++++||||+|++||+|+++ ++++|+|.
T Consensus         4 ~i~G~--~~~V~~A~~~i~~~~~~~-----------------~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp   64 (102)
T 2ctf_A            4 GSSGE--PEKLGQALTEVYAKANSF-----------------TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFT   64 (102)
T ss_dssp             CCCCC--CCCCCCSCCCCCCCCCCC-----------------EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEEC
T ss_pred             ccCcC--HHHHHHHHHHHHHHhcCe-----------------EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeC
Confidence            34565  455667776666554311                 78999999999999999999999999997 58999997


Q ss_pred             cCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          166 RDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       166 kd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      +        .+++|+|+|.++.|++|+.+|++++++..
T Consensus        65 ~--------~~~~ItI~G~~~~V~~a~~~I~~~v~el~   94 (102)
T 2ctf_A           65 E--------GEDKITLEGPTEDVSVAQEQIEGMVKDLI   94 (102)
T ss_dssp             S--------SSCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             C--------CCCEEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            4        35789999999999999999999998754

>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=99.14  E-value=5.7e-12  Score=118.95  Aligned_cols=72  Identities=26%  Similarity=0.457  Sum_probs=61.1

Q ss_pred             eEEEEeccccccceeccCCcchhHHHhhcCc-EEEEccCCccCCCCCCc--cccccCCHHHHHHHHHHHHHHHHh
Q 005922          130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGA-KIQVTRDTEADLNSPTR--SVELMGTPEQIAKAEQLINDVLAE  201 (669)
Q Consensus       130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGA-kI~Iskd~e~~p~~~eR--vVtItGt~E~V~kA~~lI~elI~e  201 (669)
                      ..+|.||.+.+|++|||+|+|||.|++.||| +|+|..+.+......++  .|+|+|+.++|++|+.+|+++|.+
T Consensus        68 e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A           68 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             EEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            3889999999999999999999999999997 99998754322222333  489999999999999999999975

>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=99.13  E-value=9.5e-11  Score=103.42  Aligned_cols=72  Identities=25%  Similarity=0.348  Sum_probs=63.8

Q ss_pred             CCcEEEEeeCCCceeeeecCCchHHHHHHHHh-CCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922          219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQART-GARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR  296 (669)
Q Consensus       219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~T-GArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~  296 (669)
                      ..++..|.||.++++.|||++|++||+|+++| ||+|.|..+      .+..+.|+|+|+.+.|++|+++|++++++..
T Consensus        15 ~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~------g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~e   87 (95)
T 2ctj_A           15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   87 (95)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT------TTTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             hcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC------CCCcceEEEEcCHHHHHHHHHHHHHHHhhhh
Confidence            45688999999999999999999999999999 999999532      3446799999998899999999999998743

>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=99.06  E-value=9.5e-11  Score=103.42  Aligned_cols=72  Identities=19%  Similarity=0.324  Sum_probs=64.9

Q ss_pred             CCceEEEEeccccccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       127 ~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      ..+++.|.||.++++.|||++|++||+|+++| ||+|+|.++     +...+.|+|+|..+.|++|+++|++++.+..
T Consensus        15 ~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~-----g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~e   87 (95)
T 2ctj_A           15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-----GSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   87 (95)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-----TTTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             hcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC-----CCCcceEEEEcCHHHHHHHHHHHHHHHhhhh
Confidence            34789999999999999999999999999999 999999754     3456789999999999999999999998754

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.89  E-value=2.5e-09  Score=98.04  Aligned_cols=75  Identities=17%  Similarity=0.156  Sum_probs=58.8

Q ss_pred             cEEEEeeCC-------CceeeeecCCchHHHHHHHHhCCeEEeccCCCC------CCCCCCccEEEEEcC-HHHHHHHHH
Q 005922          221 DHFAMKIPN-------NKVGLVIGKGGETIKNMQARTGARIQVIPLHLP------PGDTSTERTVQIDGT-SEQIESAKQ  286 (669)
Q Consensus       221 ~t~~I~VP~-------~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~p------pge~s~er~VtItG~-peqVq~Ak~  286 (669)
                      .+.+|.||.       ++++.|||++|++||+|+++|||+|.|.++...      ..+..++-.|.|++. .+.|++|++
T Consensus        12 ~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~~   91 (119)
T 2yqr_A           12 VQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKK   91 (119)
T ss_dssp             EEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHHH
T ss_pred             EEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHHH
Confidence            455666664       488999999999999999999999999754211      111234568999987 999999999


Q ss_pred             HHHHHHhhc
Q 005922          287 LVNEVISEN  295 (669)
Q Consensus       287 LI~dlL~e~  295 (669)
                      ||++||.+.
T Consensus        92 ~Ie~Ll~~v  100 (119)
T 2yqr_A           92 LCENLLQTV  100 (119)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHhhch
Confidence            999999874

>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=98.85  E-value=4.4e-09  Score=97.96  Aligned_cols=75  Identities=20%  Similarity=0.303  Sum_probs=61.8

Q ss_pred             CcEEEEeeCCC------ceeeeecCCchHHHHHHHHhCCeEEeccCCCC------------CCCCCCccEEEEEcC-HHH
Q 005922          220 SDHFAMKIPNN------KVGLVIGKGGETIKNMQARTGARIQVIPLHLP------------PGDTSTERTVQIDGT-SEQ  280 (669)
Q Consensus       220 ~~t~~I~VP~~------~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~p------------pge~s~er~VtItG~-peq  280 (669)
                      ..+.+|.||.+      ++|+|||++|++||+|+++|||+|.|.++..-            ..+..++-.|.|+++ .+.
T Consensus         6 k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~   85 (131)
T 1k1g_A            6 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   85 (131)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             eEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHH
Confidence            45778999987      89999999999999999999999999764210            011234678999997 899


Q ss_pred             HHHHHHHHHHHHhh
Q 005922          281 IESAKQLVNEVISE  294 (669)
Q Consensus       281 Vq~Ak~LI~dlL~e  294 (669)
                      |++|+++|+++|.+
T Consensus        86 ~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           86 VKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999976

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=98.85  E-value=3.8e-10  Score=113.54  Aligned_cols=124  Identities=17%  Similarity=0.151  Sum_probs=85.2

Q ss_pred             HHHHHHHHHHccccccCCCCCCCCceecCCCC---CCCCccccccCCcccccCCC-CCCCCCCCCCCCCCCCceEEEEec
Q 005922           61 QAAKRRAEQIAARLCNSVSAEAKRPRVENGSG---GFDSADKGFSSPPSDLKSIP-APSAIPVSYGGYQSMGTSKKIEIP  136 (669)
Q Consensus        61 e~IkkIaeEtaARI~I~~~~~~ERiisisg~~---~~eav~kA~~~i~~~l~~i~-~~~~~~~s~g~~~~~~vt~rIlVP  136 (669)
                      ++|+.|.++++++|+|...   ++.+.|.+..   +.+++.+|...|...+.... ..+..+..     +..+...|.|.
T Consensus        54 k~Ik~I~e~tgvkI~I~~~---~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg~~~e~g~~ll~-----dd~~~e~i~i~  125 (219)
T 2e3u_A           54 QTKKEIEKRTKTKITIDSE---TGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPERAFRLLN-----EGEYLEIINLT  125 (219)
T ss_dssp             HHHHHHHHHHTEEEEECTT---TCEEEEEECTTCCSHHHHHHHHHHHHHHHTTCCHHHHGGGGS-----TTCEEEEEEGG
T ss_pred             HHHHHHHHHHCcEEEEEcC---CCEEEEecCCCCCCHHHHHHHHHHHHHHhccCCccccceecc-----CCccceeEEcc
Confidence            7999999999999999832   4556666542   23446666666554431000 00000000     11122333333


Q ss_pred             c-----------ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          137 N-----------IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       137 ~-----------~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      .           ..+|+||||+|+|||.|++.|||+|.|.          ++.|+|.|+.++|+.|+.+|+++|...
T Consensus       126 ~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~----------~~~v~i~G~~~~i~~A~~~i~~li~g~  192 (219)
T 2e3u_A          126 DIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY----------GKTVAIIGNPIQIEIAKTAIEKLARGS  192 (219)
T ss_dssp             GCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE----------TTEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             cccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC----------CeEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence            2           2699999999999999999999999996          256999999999999999999999663

>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=98.80  E-value=1e-09  Score=96.03  Aligned_cols=66  Identities=21%  Similarity=0.346  Sum_probs=58.4

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCe-EEeccCCCCCCCCCCccEEEEEc-CHHHHHHHHHHHHHHHhh
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGAR-IQVIPLHLPPGDTSTERTVQIDG-TSEQIESAKQLVNEVISE  294 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGAr-IqI~~~~~ppge~s~er~VtItG-~peqVq~Ak~LI~dlL~e  294 (669)
                      .....|.||.++++.|||++|++||+|+++|||+ |.|.         +++.+|+|.| +.+++++|++||+.+.+.
T Consensus        14 ~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~---------eddG~V~I~g~~~ea~~~A~~~I~~ie~~   81 (91)
T 2cpq_A           14 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD---------EDTGTFRIYGESADAVKKARGFLEFVEDF   81 (91)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE---------TTTTEEEEEESSHHHHHHHHHHHSCCCCC
T ss_pred             ceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEE---------cCCCEEEEEECCHHHHHHHHHHHHhhheE
Confidence            4567899999999999999999999999999998 9995         2358999999 599999999999876554

>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=98.79  E-value=1.3e-09  Score=95.47  Aligned_cols=62  Identities=21%  Similarity=0.393  Sum_probs=56.0

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcE-EEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAK-IQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDV  198 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAk-I~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~el  198 (669)
                      +.+.|.||.+++|.|||++|.+||+|+++|||+ |.|..+        +..|+|+| +.|.+++|+++|+.+
T Consensus        15 ~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~ed--------dG~V~I~g~~~ea~~~A~~~I~~i   78 (91)
T 2cpq_A           15 FHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED--------TGTFRIYGESADAVKKARGFLEFV   78 (91)
T ss_dssp             EEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT--------TTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             eEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEcC--------CCEEEEEECCHHHHHHHHHHHHhh
Confidence            899999999999999999999999999999998 999632        36799999 899999999988754

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.79  E-value=5.1e-09  Score=96.00  Aligned_cols=74  Identities=18%  Similarity=0.211  Sum_probs=59.1

Q ss_pred             ceEEEEeccc-------cccceeccCCcchhHHHhhcCcEEEEccCCc--------cCCCCCCccccccCCHHHHHHHHH
Q 005922          129 TSKKIEIPNI-------RVGVIIGKSGETIKYLQLQSGAKIQVTRDTE--------ADLNSPTRSVELMGTPEQIAKAEQ  193 (669)
Q Consensus       129 vt~rIlVP~~-------~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e--------~~p~~~eRvVtItGt~E~V~kA~~  193 (669)
                      ++.||.||.+       ++|+|||++|.|||+|+++|||+|.|.....        ...+.+.+|++...+.+.|++|++
T Consensus        12 ~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~~   91 (119)
T 2yqr_A           12 VQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKK   91 (119)
T ss_dssp             EEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHHH
T ss_pred             EEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHHH
Confidence            7889998876       5999999999999999999999999962210        011233466666678999999999


Q ss_pred             HHHHHHHhh
Q 005922          194 LINDVLAEA  202 (669)
Q Consensus       194 lI~elI~e~  202 (669)
                      +|++||.+.
T Consensus        92 ~Ie~Ll~~v  100 (119)
T 2yqr_A           92 LCENLLQTV  100 (119)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHhhch
Confidence            999999874

>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=7.1e-09  Score=96.56  Aligned_cols=74  Identities=28%  Similarity=0.445  Sum_probs=58.5

Q ss_pred             ceEEEEeccc------cccceeccCCcchhHHHhhcCcEEEEccCCc--------------cCCCCCCccccccCCHHHH
Q 005922          129 TSKKIEIPNI------RVGVIIGKSGETIKYLQLQSGAKIQVTRDTE--------------ADLNSPTRSVELMGTPEQI  188 (669)
Q Consensus       129 vt~rIlVP~~------~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e--------------~~p~~~eRvVtItGt~E~V  188 (669)
                      ++.+|.||.+      ++|+|||.+|.|||+|+++|||+|.|.....              ...+.+..|++..-+.+.|
T Consensus         7 ~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~~   86 (131)
T 1k1g_A            7 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENV   86 (131)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHH
T ss_pred             EEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHHH
Confidence            7899999988      8999999999999999999999999964210              0011233444444579999


Q ss_pred             HHHHHHHHHHHHhh
Q 005922          189 AKAEQLINDVLAEA  202 (669)
Q Consensus       189 ~kA~~lI~elI~e~  202 (669)
                      ++|+++|++||.+.
T Consensus        87 ~~A~~~I~~ll~~~  100 (131)
T 1k1g_A           87 KKAVEQIRNILKQG  100 (131)
T ss_dssp             HHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHhcc
Confidence            99999999999874

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

Probab=98.64  E-value=1.2e-08  Score=109.73  Aligned_cols=73  Identities=18%  Similarity=0.241  Sum_probs=61.2

Q ss_pred             CCcEEEEeeCCCceeeeecCCc--hHHHHHHHHhCCeEEeccCCC-CCCCCCCccEEEEEcCHHHHHHHHHHHHHH
Q 005922          219 GSDHFAMKIPNNKVGLVIGKGG--ETIKNMQARTGARIQVIPLHL-PPGDTSTERTVQIDGTSEQIESAKQLVNEV  291 (669)
Q Consensus       219 ~~~t~~I~VP~~~vG~IIGKGG--stIK~Iqe~TGArIqI~~~~~-ppge~s~er~VtItG~peqVq~Ak~LI~dl  291 (669)
                      ..++++|.||..++..||||+|  ++|++|+++|+|+|+|..+.. .....+....|+|+|.++.|++|+.+|.++
T Consensus        28 ~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l  103 (376)
T 3n89_A           28 TRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRN  103 (376)
T ss_dssp             TEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHS
T ss_pred             CEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhc
Confidence            4678999999999999999999  999999999999999954320 001124457899999999999999999985

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.48  E-value=1e-07  Score=89.63  Aligned_cols=74  Identities=24%  Similarity=0.329  Sum_probs=56.5

Q ss_pred             EEEEeeCC------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCC---------C-----CCCCccEEEEEcC-HH-
Q 005922          222 HFAMKIPN------NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPP---------G-----DTSTERTVQIDGT-SE-  279 (669)
Q Consensus       222 t~~I~VP~------~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~pp---------g-----e~s~er~VtItG~-pe-  279 (669)
                      +.+|.||.      +++|+|||++|++||+|+++|||+|.|.++....         +     +..++-.|.|++. .+ 
T Consensus         3 ~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~   82 (140)
T 2bl5_A            3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQN   82 (140)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCH
T ss_pred             eeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCchh
Confidence            45666764      5699999999999999999999999998753210         0     1233457889986 43 


Q ss_pred             ----HHHHHHHHHHHHHhhc
Q 005922          280 ----QIESAKQLVNEVISEN  295 (669)
Q Consensus       280 ----qVq~Ak~LI~dlL~e~  295 (669)
                          .|++|+++|+++|..+
T Consensus        83 ~~~~~l~~A~~~I~~lL~p~  102 (140)
T 2bl5_A           83 RAELKLKRAVEEVKKLLVPA  102 (140)
T ss_dssp             HHHHHHHHHHHHHHHHSSCC
T ss_pred             hHHHHHHHHHHHHHHHCCCC
Confidence                7999999999999753

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

Probab=98.43  E-value=1.7e-07  Score=107.28  Aligned_cols=64  Identities=23%  Similarity=0.420  Sum_probs=55.8

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHh
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVIS  293 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~  293 (669)
                      ...+.|.||.++++.|||+||++||.|+++|||+|.|.          ++..|.|.+. .+.+++|+++|+++++
T Consensus       566 p~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~----------d~G~V~I~~~~~~~~~~A~~~I~~i~~  630 (630)
T 3u1k_A          566 PVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV----------DEETFSVFAPTPSAMHEARDFITEICK  630 (630)
T ss_dssp             CEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC----------SSSEEEEEESSHHHHHHHHHHTTC---
T ss_pred             CeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc----------CCcEEEEEeCCHHHHHHHHHHHHHHhC
Confidence            45678999999999999999999999999999999994          2579999998 7899999999998763

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.32  E-value=2.3e-07  Score=87.24  Aligned_cols=72  Identities=25%  Similarity=0.392  Sum_probs=53.8

Q ss_pred             ceEEEEecccc------ccceeccCCcchhHHHhhcCcEEEEccCCcc----------------CCCCCCccccccC-CH
Q 005922          129 TSKKIEIPNIR------VGVIIGKSGETIKYLQLQSGAKIQVTRDTEA----------------DLNSPTRSVELMG-TP  185 (669)
Q Consensus       129 vt~rIlVP~~~------vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~----------------~p~~~eRvVtItG-t~  185 (669)
                      ++.||.||.+.      +|+|||.+|.|||+|+++|||+|.|......                ..+.+..|+ |++ +.
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~-Isa~~~   80 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVL-ITVEDA   80 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEE-EEECSC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEE-EEecCc
Confidence            67899999766      9999999999999999999999999642200                012223433 444 33


Q ss_pred             H-----HHHHHHHHHHHHHHh
Q 005922          186 E-----QIAKAEQLINDVLAE  201 (669)
Q Consensus       186 E-----~V~kA~~lI~elI~e  201 (669)
                      +     .|++|+++|+++|..
T Consensus        81 ~~~~~~~l~~A~~~I~~lL~p  101 (140)
T 2bl5_A           81 QNRAELKLKRAVEEVKKLLVP  101 (140)
T ss_dssp             CHHHHHHHHHHHHHHHHHSSC
T ss_pred             hhhHHHHHHHHHHHHHHHCCC
Confidence            3     799999999999864

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=98.14  E-value=1.7e-06  Score=85.35  Aligned_cols=64  Identities=23%  Similarity=0.351  Sum_probs=58.4

Q ss_pred             EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEE-----cCHHHHHHHHHHHHHHHhh
Q 005922          222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQID-----GTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtIt-----G~peqVq~Ak~LI~dlL~e  294 (669)
                      ++++.||.+.+|.|||++|+++|.|+++++|+|+|.         ..++.|+|.     |++..+.+|++||..++..
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id---------~~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rg   73 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVD---------TENSMVIVEPEAEGIPPVNLMKAAEVVKAISLG   73 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEE---------TTTTEEEEEESSTTSCHHHHHHHHHHHHHHHHT
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEE---------cCCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcC
Confidence            478999999999999999999999999999999995         347888988     9999999999999888764

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

Probab=97.98  E-value=3.2e-06  Score=97.91  Aligned_cols=65  Identities=26%  Similarity=0.539  Sum_probs=13.1

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISE  294 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e  294 (669)
                      +....|.||.++++.|||+||++||.|+++||++|.|.          ++..|.|.+. .+.+++|+++|+.++.+
T Consensus       569 p~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~----------ddG~v~I~~~~~~~~~~A~~~i~~i~~~  634 (726)
T 4aid_A          569 PKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN----------DDGVVKVSASDGAKIKAAIDWIKSITDE  634 (726)
T ss_dssp             CC-----------------------------------------------------CCSCHHHHHHHHHC-------
T ss_pred             CeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE----------CCceEEEEeCCHHHHHHHHHHHHHHhhh
Confidence            44578899999999999999999999999999999984          2568888888 89999999999999876

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.85  E-value=2.1e-05  Score=73.23  Aligned_cols=69  Identities=14%  Similarity=0.216  Sum_probs=60.5

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e  294 (669)
                      .-+.+.|...+++.|||++|+.|++|+..|.+.|+|+.-     +.+.+-.|+|.|++..=.+|+.||+.+++-
T Consensus        56 dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~-----~s~g~tEVtIfG~~~~Q~rak~MI~sLA~~  124 (140)
T 3v69_A           56 DPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVW-----GPERRAEIWIFGPPPFRRDVDRMLTDLAHY  124 (140)
T ss_dssp             SCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECC-----CTTSCEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEecc-----CCCCcEEEEEECCHHHHHHHHHHHHHHHHH
Confidence            356788999999999999999999999999999999742     334577899999999999999999988764

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.80  E-value=6.4e-06  Score=77.81  Aligned_cols=104  Identities=21%  Similarity=0.346  Sum_probs=75.5

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG  208 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~  208 (669)
                      -...|+|....+|..||++|++||.|++++|-+|.|-...+              +      -..+|...|.-...... 
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~--------------d------~~~fI~naLsPA~V~~V-   94 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSS--------------D------LERIVKNLFPGVKIESI-   94 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCS--------------S------HHHHHHHHSTTSCEEEE-
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCC--------------C------HHHHHHHhcCCceEEEE-
Confidence            46889999999999999999999999999999998854321              1      22233333332111000 


Q ss_pred             cchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922          209 IVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI  257 (669)
Q Consensus       209 ~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~  257 (669)
                        .-.+.  .+.....+.|+.+..++.|||+|.||+-..+.||.+|.|.
T Consensus        95 --~i~~~--~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           95 --NVRER--NGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             --EEEEE--TTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             --EEeec--CCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence              00000  1235678899999999999999999999999999998875

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

Probab=97.74  E-value=8.6e-06  Score=93.23  Aligned_cols=63  Identities=19%  Similarity=0.441  Sum_probs=53.2

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLA  200 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~  200 (669)
                      ..+.|.||.++++.|||+||++||+|+++|||+|.|.++         -.|.|.+ +.+.+++|+++|+++++
T Consensus       567 ~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d~---------G~V~I~~~~~~~~~~A~~~I~~i~~  630 (630)
T 3u1k_A          567 VVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDE---------ETFSVFAPTPSAMHEARDFITEICK  630 (630)
T ss_dssp             EEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS---------SEEEEEESSHHHHHHHHHHTTC---
T ss_pred             eEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcCC---------cEEEEEeCCHHHHHHHHHHHHHHhC
Confidence            678999999999999999999999999999999999733         3466666 57899999999988763

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.43  E-value=0.00017  Score=67.24  Aligned_cols=70  Identities=17%  Similarity=0.249  Sum_probs=61.5

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      ..+.|.|....++.|||++|+.|+.|+..|.+.|+|++-.   + +.+-.|+|.|+...-.+|+.+|.+++.-.
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---P-ERRAEIWIFGPPPFRRDVDRMLTDLAHYC  125 (140)
T ss_dssp             SCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC---T-TSCEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC---C-CCcEEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            5688899999999999999999999999999999998642   2 35678999999999999999999987654

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

Probab=97.33  E-value=5.1e-05  Score=88.02  Aligned_cols=68  Identities=25%  Similarity=0.373  Sum_probs=12.5

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhc
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAES  204 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~  204 (669)
                      ....|.||.++++.|||+||.+||.|+++||++|.|..+        .++.+...+.+.+++|+++|+.++.+...
T Consensus       570 ~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~dd--------G~v~I~~~~~~~~~~A~~~i~~i~~~~~v  637 (726)
T 4aid_A          570 KIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDD--------GVVKVSASDGAKIKAAIDWIKSITDEAEV  637 (726)
T ss_dssp             C---------------------------------------------------CCSCHHHHHHHHHC----------
T ss_pred             eEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEECC--------ceEEEEeCCHHHHHHHHHHHHHHhhhhcC
Confidence            567889999999999999999999999999999999633        23444455799999999999999876543

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

Probab=97.14  E-value=0.00014  Score=84.42  Aligned_cols=65  Identities=32%  Similarity=0.521  Sum_probs=0.0

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISE  294 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e  294 (669)
                      +..+.|.|+.++++.|||++|.+||.|.++||+.|.|.          ++..|+|... .+.+++|+++|+.++.+
T Consensus       559 p~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~----------~dg~v~I~~~~~~~~~~a~~~i~~i~~~  624 (723)
T 3cdi_A          559 PRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIE----------DDGTVKIAATDGEKAKHAIRRIEEITAE  624 (723)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             ceEEEEEECHHHhcccccccceeeeeeehhhCceEEec----------CCccEEEecCCHHHHHHHHHHHHHHhhh
Confidence            34567889999999999999999999999999999884          2568888887 77889999999888755

>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=96.83  E-value=0.00012  Score=85.42  Aligned_cols=62  Identities=31%  Similarity=0.491  Sum_probs=23.1

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHH
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVI  292 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL  292 (669)
                      ....|.||.++++.|||++|++||.|+++||+.|.|.          .+..|+|+.. .+.+++|+++|+.++
T Consensus       598 ~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~----------~dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          598 RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE----------DDGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             BCCCC------------------CTTCCCCCSCC------------------CCCBSSHHHHCC---------
T ss_pred             eeEEEEEChHHeehcccccceeeehhhHhhCCEEEec----------CCceEEEecCCHHHHHHHHHHHHHhc
Confidence            3456789999999999999999999999999999984          1578999888 788888988888876

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=96.74  E-value=0.00064  Score=69.46  Aligned_cols=95  Identities=21%  Similarity=0.339  Sum_probs=66.7

Q ss_pred             cccceeccCCcchhHH-HhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCC
Q 005922          139 RVGVIIGKSGETIKYL-QLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQ  217 (669)
Q Consensus       139 ~vG~IIGKgGetIK~I-qeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~  217 (669)
                      -+|..||++|.+|+.| ++..|-+|.|-...+              +      ...+|...|.-.......     .. .
T Consensus       127 pvGacIG~~G~rI~~i~~eL~gekIDIi~~s~--------------d------p~~fi~nalsPA~V~~V~-----i~-~  180 (251)
T 2asb_A          127 AKGACIGPMGQRVRNVMSELSGEKIDIIDYDD--------------D------PARFVANALSPAKVVSVS-----VI-D  180 (251)
T ss_dssp             HHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS--------------S------HHHHHHHHTTTSCCSEEE-----EE-E
T ss_pred             HHHHHhCCCchHHHHHHHHhCCCeEEEEEecC--------------C------HHHHHHhccCCcceEEEE-----EE-c
Confidence            3999999999999999 677889999954321              1      222333333321111000     00 0


Q ss_pred             CCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 005922          218 AGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPL  259 (669)
Q Consensus       218 ~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~  259 (669)
                      .......+.|+.+..++.|||+|.||+...+.||.+|.|...
T Consensus       181 ~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  222 (251)
T 2asb_A          181 QTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  222 (251)
T ss_dssp             TTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             CCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEH
Confidence            112468899999999999999999999999999999999743

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=96.61  E-value=0.0009  Score=71.81  Aligned_cols=102  Identities=21%  Similarity=0.349  Sum_probs=71.7

Q ss_pred             EEEEecc-----ccccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhc
Q 005922          131 KKIEIPN-----IRVGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAES  204 (669)
Q Consensus       131 ~rIlVP~-----~~vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~  204 (669)
                      .||-|-.     +-+|..||++|.+|+.|.++. |-+|.|....+              +      ...+|...|.-...
T Consensus       237 aKIAV~s~d~~iDpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~--------------d------p~~fi~nalsPA~V  296 (366)
T 1k0r_A          237 SKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYDD--------------D------PARFVANALSPAKV  296 (366)
T ss_dssp             EEEEEEESSTTCCHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS--------------S------HHHHHHHHTTTSCC
T ss_pred             EEEEEEeCCCCCCCcccccCCcchHHHHHHHHhCCCeEEEEEcCC--------------C------HHHHHHHhcCCcce
Confidence            3555543     459999999999999999998 89999964321              1      22234333332211


Q ss_pred             CCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922          205 GGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP  258 (669)
Q Consensus       205 ~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~  258 (669)
                      ....     .. ........+.|+.+..++.|||+|.||+...+.||.+|.|..
T Consensus       297 ~~V~-----~~-~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~  344 (366)
T 1k0r_A          297 VSVS-----VI-DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG  344 (366)
T ss_dssp             SEEE-----EE-ETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEE
T ss_pred             eEEE-----EE-cCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeE
Confidence            1100     00 112456889999999999999999999999999999999974

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

Probab=95.89  E-value=0.0013  Score=76.36  Aligned_cols=67  Identities=25%  Similarity=0.339  Sum_probs=0.0

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      ..+.|.|+.++++.|||++|.+||+|.+++|+.|.|..+        -++++...+.+.+++|+++|++++.+..
T Consensus       560 ~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~d--------g~v~I~~~~~~~~~~a~~~i~~i~~~~~  626 (723)
T 3cdi_A          560 RIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDD--------GTVKIAATDGEKAKHAIRRIEEITAEIE  626 (723)
T ss_dssp             ---------------------------------------------------------------------------
T ss_pred             eEEEEEECHHHhcccccccceeeeeeehhhCceEEecCC--------ccEEEecCCHHHHHHHHHHHHHHhhhhh
Confidence            567888999999999999999999999999999988632        2344444567888899988888876543

>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=95.69  E-value=0.0069  Score=64.61  Aligned_cols=94  Identities=27%  Similarity=0.401  Sum_probs=65.7

Q ss_pred             cccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCC
Q 005922          139 RVGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQ  217 (669)
Q Consensus       139 ~vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~  217 (669)
                      -+|..||.+|.+|+.|.++. |-+|.|..-.+              +      -..+|...|.-......      ....
T Consensus       246 pvGacvg~~G~ri~~i~~el~ge~Idii~~s~--------------d------~~~fi~nal~Pa~v~~v------~~~d  299 (344)
T 1hh2_P          246 PIGACIGEGGSRIAAILKELKGEKLDVLKWSD--------------D------PKQLIANALAPATVIEV------EILD  299 (344)
T ss_dssp             HHHHHHCTTSTTHHHHHHHTTTCEEEEEECCS--------------S------HHHHHHHHTCSSCCSEE------EEEE
T ss_pred             ccceeeccCCcEeHHHHHHhCCCeeeEEecCC--------------C------HHHHHHHhcCccEEEEE------EEEc
Confidence            48999999999999999998 78888853221              1      11233333321111000      0000


Q ss_pred             CCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922          218 AGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP  258 (669)
Q Consensus       218 ~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~  258 (669)
                      .......+.||.+..++-|||+|.||+...+.||.+|.|..
T Consensus       300 ~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          300 KENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             TTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            12346889999999999999999999999999999999963

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

Probab=94.52  E-value=0.0022  Score=74.85  Aligned_cols=62  Identities=21%  Similarity=0.341  Sum_probs=21.7

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCcccccc-CCHHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELM-GTPEQIAKAEQLINDVL  199 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtIt-Gt~E~V~kA~~lI~elI  199 (669)
                      ....|.||.++++.|||++|.+||.|++++|+.|.|..         +..|.|+ .+.+.+++|+++|..++
T Consensus       598 ~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~---------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          598 RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED---------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             BCCCC------------------CTTCCCCCSCC-----------------CCCBSSHHHHCC---------
T ss_pred             eeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC---------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            45678899999999999999999999999999999963         2334444 46788888888888776

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=87.13  E-value=0.3  Score=45.96  Aligned_cols=39  Identities=26%  Similarity=0.552  Sum_probs=35.9

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPL  259 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~  259 (669)
                      ..+.+.|....+|..||++|++|+.|++++|-+|.|...
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~   74 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEY   74 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEEC
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEc
Confidence            467899999999999999999999999999999998754

>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=83.96  E-value=0.33  Score=52.17  Aligned_cols=40  Identities=20%  Similarity=0.516  Sum_probs=36.8

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDT  168 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~  168 (669)
                      ....+.|+....++.|||+|.|||-..+-||.+|.|..+.
T Consensus       307 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  346 (366)
T 1k0r_A          307 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  346 (366)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESS
T ss_pred             cEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHH
Confidence            5789999999999999999999999999999999997543

>4hhu_A OR280; engineered protein, PSI-biology, structural genomi unknown function; HET: AE4 PG4; 2.00A {Synthetic construct}

Probab=81.69  E-value=14  Score=33.53  Aligned_cols=28  Identities=21%  Similarity=0.222  Sum_probs=22.2

Q ss_pred             CccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          176 TRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       176 eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      +-+|.|+|.+|.|.|-+.+-.|.|+.+.
T Consensus        42 ~l~i~itgvpeqvrkelakeaerl~~ef   69 (170)
T 4hhu_A           42 RLVIVITGVPEQVRKELAKEAERLKAEF   69 (170)
T ss_dssp             EEEEEEESCCHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCCcHHHHHHHHHHHHHHHHhc
Confidence            4578999999999998887777766543

---

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	669
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	3e-22
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	4e-18
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	9e-22
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	4e-20
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	4e-21
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	7e-20
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-20
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	5e-19
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	2e-20
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	1e-17
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-19
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	9e-18
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-18
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	3e-18
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	3e-18
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	3e-16
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	3e-18
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	8e-18
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	8e-18
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-15
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	9e-18
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	2e-15
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-17
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	9e-17
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-17
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	6e-17
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	9e-16
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	4e-15
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-15
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	6e-15
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	2e-14
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	1e-12
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	3e-14
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	2e-13
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	5e-14
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	6e-14
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	2e-12
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	5e-12
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	2e-10
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	2e-09
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	1e-09
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	2e-07
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	1e-09
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	7e-06
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	7e-09
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	2e-07
d2bl5a1	134	d.51.1.1 (A:1-134) Quaking protein A (Xqua) {Afric	0.001
d2bl5a1	134	d.51.1.1 (A:1-134) Quaking protein A (Xqua) {Afric	0.002
d1k1ga_	122	d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo s	0.003

>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 = 88.4 bits (219), Expect = 3e-22
 Identities = 30/70 (42%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIE 282
           F   +P  K GL+IGKGGETIK++  ++GARI+ +  + PP      +   I GT +QI+
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIE-LQRNPPPNADPNMKLFTIRGTPQQID 61

Query: 283 SAKQLVNEVI 292
            A+QL+ 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 = 76.9 bits (189), Expect = 4e-18
 Identities = 26/68 (38%), Positives = 41/68 (60%)

Query: 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKA 191
              +P  + G+IIGK GETIK +  QSGA+I++ R+   + +   +   + GTP+QI  A
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYA 63

Query: 192 EQLINDVL 199
            QLI + +
Sbjct: 64  RQLIEEKI 71

>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 = 87.6 bits (217), Expect = 9e-22
 Identities = 25/72 (34%), Positives = 44/72 (61%), Gaps = 4/72 (5%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
            K+P+  VG +IG+GGE I  +Q  +G +IQ+     P      ER+  + GT E ++SA
Sbjct: 12  YKVPDGMVGFIIGRGGEQISRIQQESGCKIQIA----PDSGGLPERSCMLTGTPESVQSA 67

Query: 285 KQLVNEVISENR 296
           K+L+++++ + R
Sbjct: 68  KRLLDQIVEKGR 79

>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 = 82.6 bits (204), Expect = 4e-20
 Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 3/78 (3%)

Query: 125 QSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT 184
           Q    +++ ++P+  VG IIG+ GE I  +Q +SG KIQ+  D+      P RS  L GT
Sbjct: 4   QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG---GLPERSCMLTGT 60

Query: 185 PEQIAKAEQLINDVLAEA 202
           PE +  A++L++ ++ + 
Sbjct: 61  PESVQSAKRLLDQIVEKG 78

>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 = 85.3 bits (211), Expect = 4e-21
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           M +P N VG ++GKGG+T+   Q  TGARIQ+          +  R V I G+    ++A
Sbjct: 7   MAVPENLVGAILGKGGKTLVEYQELTGARIQISKKG-EFLPGTRNRRVTITGSPAATQAA 65

Query: 285 KQLVNEVIS 293
           + L+++ ++
Sbjct: 66  QYLISQRVT 74

>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 = 81.8 bits (202), Expect = 7e-20
 Identities = 21/69 (30%), Positives = 38/69 (55%)

Query: 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKA 191
           ++ +P   VG I+GK G+T+   Q  +GA+IQ+++  E    +  R V + G+P     A
Sbjct: 6   EMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAA 65

Query: 192 EQLINDVLA 200
           + LI+  + 
Sbjct: 66  QYLISQRVT 74

>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 = 83.7 bits (207), Expect = 2e-20
 Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + +   +VG +IGK GE++K M+  +GARI +            ER + + G +  I  A
Sbjct: 8   LLMHGKEVGSIIGKKGESVKKMREESGARINISE------GNCPERIITLAGPTNAIFKA 61

Query: 285 KQLVNEVISE 294
             ++ + + E
Sbjct: 62  FAMIIDKLEE 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 = 79.4 bits (196), Expect = 5e-19
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
            + ++ +    VG IIGK GE++K ++ +SGA+I ++       N P R + L G    I
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAI 58

Query: 189 AKAEQLINDVLAE 201
            KA  +I D L E
Sbjct: 59  FKAFAMIIDKLEE 71

>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 = 83.8 bits (207), Expect = 2e-20
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS 278
           GS    + IP   VG+VIG+ GE IK +Q   G RIQ      P   T+ ER  QI G  
Sbjct: 1   GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQ----FKPDDGTTPERIAQITGPP 56

Query: 279 EQIESAKQLVNEVISE 294
           ++ + A +++ +++  
Sbjct: 57  DRAQHAAEIITDLLRS 72

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.7 bits (186), Expect = 1e-17
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKA 191
            + IP   VG++IG++GE IK +Q  +G +IQ   D      +P R  ++ G P++   A
Sbjct: 6   DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG---TTPERIAQITGPPDRAQHA 62

Query: 192 EQLINDVLAEAE 203
            ++I D+L   +
Sbjct: 63  AEIITDLLRSVQ 74

>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 = 80.5 bits (199), Expect = 3e-19
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IP      VIGK GE +++++ +T  +IQ+      P        ++I GT E IE A
Sbjct: 14  VAIPKEHHRFVIGKNGEKLQDLELKTATKIQI------PRPDDPSNQIKITGTKEGIEKA 67

Query: 285 KQLVNEVISENRIR 298
           +  V  + +E   R
Sbjct: 68  RHEVLLISAEQDKR 81

>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 = 76.3 bits (188), Expect = 9e-18
 Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 5/75 (6%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
            S  + IP      +IGK+GE ++ L+L++  KIQ+ R      + P+  +++ GT E I
Sbjct: 10  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-----DDPSNQIKITGTKEGI 64

Query: 189 AKAEQLINDVLAEAE 203
            KA   +  + AE +
Sbjct: 65  EKARHEVLLISAEQD 79

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 78.0 bits (192), Expect = 2e-18
 Identities = 11/70 (15%), Positives = 25/70 (35%), Gaps = 3/70 (4%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + +       +IG+ G  I  ++      IQ             +  + I G  +  E+A
Sbjct: 14  VTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPD---KDDGNQPQDQITITGYEKNTEAA 70

Query: 285 KQLVNEVISE 294
           +  +  ++ E
Sbjct: 71  RDAILRIVGE 80

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.6 bits (191), Expect = 3e-18
 Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 2/80 (2%)

Query: 125 QSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT 184
                   + +       IIG+ G  I  ++L+    IQ     +   N P   + + G 
Sbjct: 6   ALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG--NQPQDQITITGY 63

Query: 185 PEQIAKAEQLINDVLAEAES 204
            +    A   I  ++ E E 
Sbjct: 64  EKNTEAARDAILRIVGELEQ 83

>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 = 77.2 bits (190), Expect = 3e-18
 Identities = 23/69 (33%), Positives = 40/69 (57%), Gaps = 4/69 (5%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IPNN +G +IG+ G  I  ++  +GA+I++      P + S+ R V I G++  I  A
Sbjct: 6   LTIPNNLIGCIIGRQGANINEIRQMSGAQIKIA----NPVEGSSGRQVTITGSAASISLA 61

Query: 285 KQLVNEVIS 293
           + L+N  +S
Sbjct: 62  QYLINARLS 70

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.8 bits (176), Expect = 3e-16
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
           T+ ++ IPN  +G IIG+ G  I  ++  SGA+I++    E    S  R V + G+   I
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE---GSSGRQVTITGSAASI 58

Query: 189 AKAEQLINDVLA 200
           + A+ LIN  L+
Sbjct: 59  SLAQYLINARLS 70

>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 = 77.9 bits (192), Expect = 3e-18
 Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 10/75 (13%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + I   +V  VIGK G  IK +++    +I V               + ++G   ++  A
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVV----------GQNGLIWVNGDRRKVSIA 54

Query: 285 KQLVNEVISENRIRN 299
           ++ +  +  E     
Sbjct: 55  EEAIYLIEQEAHTEG 69

>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 = 76.3 bits (188), Expect = 8e-18
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 9/74 (12%)

Query: 133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAE 192
           + I   RV  +IGK G  IK L+ +   +I V ++           + + G   +++ AE
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQN---------GLIWVNGDRRKVSIAE 55

Query: 193 QLINDVLAEAESGG 206
           + I  +  EA + G
Sbjct: 56  EAIYLIEQEAHTEG 69

>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 = 76.1 bits (187), Expect = 8e-18
 Identities = 28/70 (40%), Positives = 46/70 (65%), Gaps = 2/70 (2%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IP +K GLVIGKGGETIK +Q R G ++ +I     P +T  ++ ++I G   +++ A
Sbjct: 12  IMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQ--DGPQNTGADKPLRITGDPYKVQQA 69

Query: 285 KQLVNEVISE 294
           K++V E+I +
Sbjct: 70  KEMVLELIRD 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 = 70.4 bits (172), Expect = 1e-15
 Identities = 20/73 (27%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
             ++I IP  + G++IGK GETIK LQ ++G K+ + +D   +     + + + G P ++
Sbjct: 8   AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN-TGADKPLRITGDPYKV 66

Query: 189 AKAEQLINDVLAE 201
            +A++++ +++ +
Sbjct: 67  QQAKEMVLELIRD 79

>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 = 75.9 bits (187), Expect = 9e-18
 Identities = 14/69 (20%), Positives = 33/69 (47%), Gaps = 6/69 (8%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + I +     +IGK G  I  ++ +    +++      P D+     ++I+G  + ++ A
Sbjct: 9   INIDHKFHRHLIGKSGANINRIKDQYKVSVRI------PPDSEKSNLIRIEGDPQGVQQA 62

Query: 285 KQLVNEVIS 293
           K+ + E+ S
Sbjct: 63  KRELLELAS 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 = 69.4 bits (170), Expect = 2e-15
 Identities = 14/72 (19%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
              +I I +     +IGKSG  I  ++ Q    +++  D+E         + + G P+ +
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKS-----NLIRIEGDPQGV 59

Query: 189 AKAEQLINDVLA 200
            +A++ + ++ +
Sbjct: 60  QQAKRELLELAS 71

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.6 bits (186), Expect = 2e-17
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 6/70 (8%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           +++P +    VIG+ G  I+ M       I V      P        + I G +  ++ A
Sbjct: 14  VEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV------PAPELQSDIIAITGLAANLDRA 67

Query: 285 KQLVNEVISE 294
           K  + E + E
Sbjct: 68  KAGLLERVKE 77

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.7 bits (181), Expect = 9e-17
 Identities = 11/75 (14%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIA 189
           + ++E+P      +IG+ G  I+ +  +    I V           +  + + G    + 
Sbjct: 11  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-----ELQSDIIAITGLAANLD 65

Query: 190 KAEQLINDVLAEAES 204
           +A+  + + + E ++
Sbjct: 66  RAKAGLLERVKELQA 80

>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 = 74.9 bits (184), Expect = 2e-17
 Identities = 23/70 (32%), Positives = 42/70 (60%), Gaps = 4/70 (5%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + IP +  G +IGKGG+ IK ++  +GA I++      P + S +R + I GT +QI++A
Sbjct: 8   VTIPKDLAGSIIGKGGQRIKQIRHESGASIKID----EPLEGSEDRIITITGTQDQIQNA 63

Query: 285 KQLVNEVISE 294
           + L+   + +
Sbjct: 64  QYLLQNSVKQ 73

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.8 bits (181), Expect = 6e-17
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
            + ++ IP    G IIGK G+ IK ++ +SGA I++    E    S  R + + GT +QI
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE---GSEDRIITITGTQDQI 60

Query: 189 AKAEQLINDVLAE 201
             A+ L+ + + +
Sbjct: 61  QNAQYLLQNSVKQ 73

>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 = 71.2 bits (174), Expect = 9e-16
 Identities = 26/83 (31%), Positives = 45/83 (54%), Gaps = 2/83 (2%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + +P   VG +IG+GGETI+++   +GA+I         G     R ++I GT +++ +A
Sbjct: 19  LSVPQRSVGRIIGRGGETIRSICKASGAKITCDK--ESEGTLLLSRLIKISGTQKEVAAA 76

Query: 285 KQLVNEVISENRIRNPAMAGGYS 307
           K L+ E +SE+      +A   S
Sbjct: 77  KHLILEKVSEDEELRKRIAHSAS 99

>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 = 69.2 bits (169), Expect = 4e-15
 Identities = 25/74 (33%), Positives = 46/74 (62%), Gaps = 1/74 (1%)

Query: 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIA 189
            +++ +P   VG IIG+ GETI+ +   SGAKI   +++E      +R +++ GT +++A
Sbjct: 16  FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT-LLLSRLIKISGTQKEVA 74

Query: 190 KAEQLINDVLAEAE 203
            A+ LI + ++E E
Sbjct: 75  AAKHLILEKVSEDE 88

>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 = 70.2 bits (172), Expect = 1e-15
 Identities = 12/70 (17%), Positives = 24/70 (34%), Gaps = 5/70 (7%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           + + +     +IG  G+ I+ +       I+      P         V + G  E +E A
Sbjct: 14  VPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-----PQSGAPDPNCVTVTGLPENVEEA 68

Query: 285 KQLVNEVISE 294
              +  +  E
Sbjct: 69  IDHILNLEEE 78

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.9 bits (166), Expect = 6e-15
 Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 4/73 (5%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
            S+ + + +     IIG  G+ I+ +  +    I+  +    D       V + G PE +
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPD----PNCVTVTGLPENV 65

Query: 189 AKAEQLINDVLAE 201
            +A   I ++  E
Sbjct: 66  EEAIDHILNLEEE 78

>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 = 66.3 bits (162), Expect = 2e-14
 Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 11/75 (14%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS-EQIES 283
           + I   KV  VIGK     + + +++G  I V          +    +     S    E 
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFV----------ANNGRIWATCPSRFSEEI 54

Query: 284 AKQLVNEVISENRIR 298
             + + ++ +E+ I+
Sbjct: 55  LIEAIRKIENESHIK 69

>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 = 61.3 bits (149), Expect = 1e-12
 Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 8/71 (11%)

Query: 133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAE 192
           I+I  ++V  +IGK+    + L  +SG  I V  +       P        +        
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCP--------SRFSEEILI 56

Query: 193 QLINDVLAEAE 203
           + I  +  E+ 
Sbjct: 57  EAIRKIENESH 67

>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 = 66.3 bits (162), Expect = 3e-14
 Identities = 12/76 (15%), Positives = 27/76 (35%), Gaps = 11/76 (14%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS-EQIES 283
           ++I   KV  VIG+    +K ++ +T  +I V               + ++  + +    
Sbjct: 5   VEISPAKVPRVIGRKMSMLKTLEEKTECKIFV-------ARNG---RIHLECPNEDLEAI 54

Query: 284 AKQLVNEVISENRIRN 299
           A   +  +  E     
Sbjct: 55  AVMAIKIIDEEAYTSG 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 = 64.0 bits (156), Expect = 2e-13
 Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 10/78 (12%)

Query: 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT-PEQI 188
            K +EI   +V  +IG+    +K L+ ++  KI V R+           + L     +  
Sbjct: 2   GKIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNGR---------IHLECPNEDLE 52

Query: 189 AKAEQLINDVLAEAESGG 206
           A A   I  +  EA + G
Sbjct: 53  AIAVMAIKIIDEEAYTSG 70

>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 = 65.3 bits (159), Expect = 5e-14
 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 7/75 (9%)

Query: 225 MKIPNNKVGLVIGKGGETIKN-MQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIES 283
           + IP      +IG  G  I++ M+   G  I          + S   TV I G S  +E 
Sbjct: 14  VSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV------EGSGSDTVVIRGPSSDVEK 67

Query: 284 AKQLVNEVISENRIR 298
           AK+ +  +  E + +
Sbjct: 68  AKKQLLHLAEEKQTK 82

>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 = 65.3 bits (159), Expect = 6e-14
 Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQ 187
              ++ IP      +IG  G  I+ +  +  G  I    +      S + +V + G    
Sbjct: 10  AEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-----GSGSDTVVIRGPSSD 64

Query: 188 IAKAEQLINDVLAEAES 204
           + KA++ +  +  E ++
Sbjct: 65  VEKAKKQLLHLAEEKQT 81

>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 = 61.0 bits (148), Expect = 2e-12
 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 8/69 (11%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTST--ERTVQIDGTSEQIE 282
           +K+   ++G VIG  GE    +  RTG  I V        + S               + 
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVITV------DTENSMVIVEPEAEGIPPVNLM 60

Query: 283 SAKQLVNEV 291
            A ++V  +
Sbjct: 61  KAAEVVKAI 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 = 59.8 bits (145), Expect = 5e-12
 Identities = 12/66 (18%), Positives = 26/66 (39%), Gaps = 3/66 (4%)

Query: 133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAE 192
           +++   R+G +IG  GE    +  ++G  I V  +                 P  + KA 
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENS---MVIVEPEAEGIPPVNLMKAA 63

Query: 193 QLINDV 198
           +++  +
Sbjct: 64  EVVKAI 69

>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 = 55.9 bits (135), Expect = 2e-10
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 11/80 (13%)

Query: 126 SMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTP 185
            +    +  +  I+ G IIG+ G   + ++  +   I V              V ++G  
Sbjct: 11  QVVGDSQNHLKRIK-GRIIGEGGRARRTIEEMTDTYINVGEYE----------VAIIGDY 59

Query: 186 EQIAKAEQLINDVLAEAESG 205
           E+   A+Q I  +       
Sbjct: 60  ERAMAAKQAIEMLAEGRMHS 79

>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 = 52.8 bits (127), Expect = 2e-09
 Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 11/63 (17%)

Query: 232 VGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEV 291
            G +IG+GG   + ++  T   I V            E  V I G  E+  +AKQ +  +
Sbjct: 24  KGRIIGEGGRARRTIEEMTDTYINV-----------GEYEVAIIGDYERAMAAKQAIEML 72

Query: 292 ISE 294
              
Sbjct: 73  AEG 75

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.0 bits (127), Expect = 1e-09
 Identities = 13/71 (18%), Positives = 25/71 (35%), Gaps = 9/71 (12%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS-EQIES 283
             +  + +GL IG  G  I+  +   G     +             T +I G S + ++ 
Sbjct: 12  FVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED--------TGTFRIYGESADAVKK 63

Query: 284 AKQLVNEVISE 294
           A+  +  V   
Sbjct: 64  ARGFLEFVEDF 74

>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 = 46.8 bits (111), Expect = 2e-07
 Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 8/75 (10%)

Query: 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQI 188
            ++  +    +G+ IG  G  I+  +   G            L+  T +  + G + + +
Sbjct: 9   HEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIE-------LDEDTGTFRIYGESADAV 61

Query: 189 AKAEQLINDVLAEAE 203
            KA   +  V    +
Sbjct: 62  KKARGFLEFVEDFIQ 76

>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 = 52.0 bits (125), Expect = 1e-09
 Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 12/60 (20%)

Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
           +KIP +K+G VIG   + I  +Q  TGA I +            + T+ I        +A
Sbjct: 7   VKIPVDKIGEVIGPKRQMINQIQEDTGAEITI----------EDDGTIYIGAADG--PAA 54

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 41.6 bits (98), Expect = 7e-06
 Identities = 11/44 (25%), Positives = 23/44 (52%)

Query: 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSP 175
            ++IP  ++G +IG   + I  +Q  +GA+I +  D    + + 
Sbjct: 6   TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDDGTIYIGAA 49

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.0 bits (122), Expect = 7e-09
 Identities = 18/113 (15%), Positives = 43/113 (38%), Gaps = 28/113 (24%)

Query: 183 GTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGET 242
           G PE++ +A   + +V A+A S                    +  P+     +IGK G+ 
Sbjct: 1   GEPEKLGQA---LTEVYAKANS----FTVSS-----------VAAPSWLHRFIIGKKGQN 42

Query: 243 IKNMQAR-TGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294
           +  +  +     I+             E  + ++G +E +  A++ +  ++ +
Sbjct: 43  LAKITQQMPKVHIE-FTEG--------EDKITLEGPTEDVSVAQEQIEGMVKD 86

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.2 bits (112), Expect = 2e-07
 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 9/77 (11%)

Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQ-SGAKIQVTRDTEADLNSPTRSVELMGTPEQ 187
           T   +  P+     IIGK G+ +  +  Q     I+ T             + L G  E 
Sbjct: 21  TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE--------GEDKITLEGPTED 72

Query: 188 IAKAEQLINDVLAEAES 204
           ++ A++ I  ++ +  +
Sbjct: 73  VSVAQEQIEGMVKDLIN 89

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 134

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-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]

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 230 NKVGLVIGKGGETIKNMQARTGARIQV 256
           N VG ++G  G T K ++A TG +I V
Sbjct: 17  NFVGRILGPRGLTAKQLEAETGCKIMV 43

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 134

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-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]

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 8/42 (19%)

Query: 130 SKKIEIP-------NIRVGVIIGKSGETIKYLQLQSGAKIQV 164
            +K+ +P       N   G I+G  G T K L+ ++G KI V
Sbjct: 3   QEKLYVPVKEYPDFNFV-GRILGPRGLTAKQLEAETGCKIMV 43

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 122

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-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]

 Score = 36.0 bits (83), Expect = 0.003
 Identities = 21/96 (21%), Positives = 38/96 (39%), Gaps = 24/96 (25%)

Query: 129 TSKKIEIP-------NIRVGVIIGKSGETIKYLQLQSGAKIQV-----TRD--------- 167
            S K+ IP       N   G++IG  G T+K ++ +  AKI +      ++         
Sbjct: 3   VSDKVMIPQDEYPEINFV-GLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQ 61

Query: 168 TEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAEA 202
                + P     +   T E + KA + I ++L + 
Sbjct: 62  MLPGEDEP-LHALVTANTMENVKKAVEQIRNILKQG 96

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	669
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.54
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.54
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.54
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.54
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.53
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.53
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.52
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.52
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.51
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.51
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.5
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.5
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.49
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.48
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.48
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.48
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.47
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.45
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.38
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.37
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.35
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.33
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.32
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.29
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.29
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.28
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.26
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.26
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.26
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.22
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.2
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.2
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.1
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.1
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.89
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.84
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.84
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.8
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.79
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.64
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.62
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.5
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.49
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.41
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.4
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.4
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.2
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.97
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.27
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.06
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.04
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	92.73
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	88.64
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	87.65
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	82.83
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	80.06

>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=99.54  E-value=2.7e-15  Score=123.24  Aligned_cols=70  Identities=41%  Similarity=0.695  Sum_probs=62.7

Q ss_pred             EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHH
Q 005922          222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVI  292 (669)
Q Consensus       222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL  292 (669)
                      +++|.||++++|+||||+|++||+|+++|||+|+|..+..+ ...+.+|+|+|+|++++|++|++||.++|
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 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPP-NADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTT-TSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCC-CCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            57899999999999999999999999999999999765432 33567899999999999999999999975

>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=99.54  E-value=2.6e-15  Score=124.23  Aligned_cols=72  Identities=31%  Similarity=0.477  Sum_probs=66.6

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      .++++|+||..++|+||||+|++||+|+++|||+|+|.++   ..++.+|+|+|+|+.++|++|+.+|.++|+|.
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 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT---TSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccC---CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            3789999999999999999999999999999999999754   35678899999999999999999999999874

>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=99.54  E-value=1.3e-15  Score=125.31  Aligned_cols=69  Identities=36%  Similarity=0.558  Sum_probs=64.4

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE  201 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e  201 (669)
                      .++++|+||...+|+||||+|++||+|+++|||+|+|.++     +.++|+|+|+|++++|.+|+.+|.++|+|
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~-----~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-----CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC-----CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            4899999999999999999999999999999999999743     56789999999999999999999999975

>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=99.54  E-value=1.6e-15  Score=124.59  Aligned_cols=70  Identities=37%  Similarity=0.605  Sum_probs=64.4

Q ss_pred             eEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHH
Q 005922          130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL  199 (669)
Q Consensus       130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI  199 (669)
                      +++|+||+..+|+||||+|++||+|+++|||+|+|+++.+....+.+|+|+|+|++++|++|+++|.++|
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            4689999999999999999999999999999999987765566778899999999999999999999875

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=2.6e-15  Score=124.12  Aligned_cols=72  Identities=35%  Similarity=0.603  Sum_probs=64.6

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      ...++|.||.+++|+||||+|++||+|+++|||+|+|....    ++..+|.|+|+|++++|++|++||+++|++.
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~----~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD----GTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT----TSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCC----CCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            35689999999999999999999999999999999997532    3456899999999999999999999999864

>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=7e-15  Score=121.63  Aligned_cols=71  Identities=31%  Similarity=0.536  Sum_probs=64.4

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e  294 (669)
                      .++++|.||.+++|+||||+|++||+|+++|||+|+|...    .+++++|+|+|+|++++|++|+.||.++|++
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~----~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT----TSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccC----CCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            3578999999999999999999999999999999999642    2356789999999999999999999999986

>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=99.52  E-value=2.7e-15  Score=124.20  Aligned_cols=71  Identities=30%  Similarity=0.470  Sum_probs=66.5

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL  199 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI  199 (669)
                      .+++|+||+..+|+||||+|++||+|+++|||+|+|.++.+..++..+|+|+|+|+.++|++|+.+|.++|
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            46899999999999999999999999999999999988776677888999999999999999999999886

>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=2.4e-15  Score=124.41  Aligned_cols=71  Identities=34%  Similarity=0.647  Sum_probs=65.9

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      ..++|+||.+.+|+||||+|+|||+|+++|||+|+|.++   ..+..+|+|+|+|+.++|++|+.+|.++|++.
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 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD---DGTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECC---TTSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccC---CCCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            689999999999999999999999999999999999865   34677899999999999999999999999874

>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=99.51  E-value=7.4e-15  Score=121.53  Aligned_cols=71  Identities=32%  Similarity=0.502  Sum_probs=63.0

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHH
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVI  292 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL  292 (669)
                      +.++|.||++++|+||||+|++||+|+++|||+|+|..+.. ...++++|+|+|+|+.++|++|++||.++|
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 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGE-FLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTC-CSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCC-CCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            46799999999999999999999999999999999976432 223567899999999999999999999987

>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=99.51  E-value=6.2e-15  Score=120.90  Aligned_cols=69  Identities=32%  Similarity=0.559  Sum_probs=62.2

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHh
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVIS  293 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~  293 (669)
                      .+.+|.||++++|+||||+|++||+|+++|||+|+|.+.    .++..+|+|+|+|++++|++|+.||+++|.
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~----~~~~~~r~v~I~G~~~~v~~A~~~I~~~is   70 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP----VEGSSGRQVTITGSAASISLAQYLINARLS   70 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC----CTTCSEEEEEEEECHHHHHHHHHHHHHHTC
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCC----CCCCCcEEEEEEeCHHHHHHHHHHHHHHcC
Confidence            478999999999999999999999999999999999643    235678999999999999999999999873

>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=3.9e-15  Score=125.31  Aligned_cols=74  Identities=27%  Similarity=0.550  Sum_probs=67.3

Q ss_pred             CCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922          127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE  201 (669)
Q Consensus       127 ~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e  201 (669)
                      ..++++|+||...+|+||||+|++||+|+++|||+|+|.++.. .....+|+|+|+|++++|++|+.+|+++|+|
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 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGP-QNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCC-CSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             ccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCC-CCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            3489999999999999999999999999999999999987543 3456789999999999999999999999976

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=6.3e-15  Score=121.09  Aligned_cols=69  Identities=28%  Similarity=0.483  Sum_probs=63.2

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e  294 (669)
                      .++++|+||.+++|+||||+|++||+|+++|||+|+|...      ...||+|+|+|++++|.+|+.||.++|+|
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~------~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG------NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC------CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            4688999999999999999999999999999999999642      34589999999999999999999999975

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=5.8e-15  Score=121.09  Aligned_cols=68  Identities=35%  Similarity=0.553  Sum_probs=63.2

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL  199 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI  199 (669)
                      ++.+|+||...+|+||||+|.+||+|+++|||+|.|.+.   ..++.+|+|+|+|++++|++|+.+|.++|
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~---~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP---VEGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC---CTTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCC---CCCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            689999999999999999999999999999999999765   45678899999999999999999999876

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.48  E-value=1e-14  Score=122.74  Aligned_cols=74  Identities=39%  Similarity=0.693  Sum_probs=65.9

Q ss_pred             CCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922          219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e  294 (669)
                      ..++++|+||.+++++||||+|++||+|+++|||+|+|..+.  +...+.+|+|+|+|++++|++|++||+++|+|
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 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG--PQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSC--CCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             ccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCC--CCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            457889999999999999999999999999999999997542  22345789999999999999999999999976

>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=1.1e-14  Score=121.84  Aligned_cols=73  Identities=36%  Similarity=0.611  Sum_probs=67.4

Q ss_pred             CCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       127 ~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      ..++.+|+||..++|+|||++|.+||+|+++|||+|+|.+.   ..++.+|+|+|+|+.++|++|+.+|.++|.|+
T Consensus         6 ~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~---~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           6 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD---SGGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSC---CTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCC---CCCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            34899999999999999999999999999999999999865   34677899999999999999999999999974

>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=1.8e-14  Score=120.45  Aligned_cols=73  Identities=34%  Similarity=0.660  Sum_probs=66.1

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR  296 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~  296 (669)
                      .++.+|.||.+++|+|||++|.+||+|+++|||+|+|.+.    .+++.++.|+|+|++++|++|+.||.++|++++
T Consensus         7 ~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~----~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~r   79 (79)
T d1x4na1           7 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD----SGGLPERSCMLTGTPESVQSAKRLLDQIVEKGR   79 (79)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSC----CTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             cEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCC----CCCCCceEEEEEeCHHHHHHHHHHHHHHHHccC
Confidence            5678999999999999999999999999999999999642    235678999999999999999999999999864

>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=99.47  E-value=1.3e-14  Score=127.54  Aligned_cols=75  Identities=33%  Similarity=0.530  Sum_probs=67.5

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      .++++|+||..++|+||||+|.+||+|+++|||+|+|.++.+ .....+|+|+|+|++++|++|+.+|.++|+++.
T Consensus        14 ~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~-~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T d1we8a_          14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE-GTLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             EEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSC-CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCC-CCCCCccEEEEEeCHHHHHHHHHHHHHHHhCcH
Confidence            388999999999999999999999999999999999976543 334568999999999999999999999998754

>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=99.45  E-value=4.2e-14  Score=124.28  Aligned_cols=76  Identities=32%  Similarity=0.521  Sum_probs=66.1

Q ss_pred             CCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          218 AGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       218 ~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      ...++++|+||.+++++||||+|++||+|+++|||+|+|..+..  .....+|+|+|+|++++|++|+.||+++|+++
T Consensus        12 ~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~--~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE--GTLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSC--CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCC--CCCCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            34577899999999999999999999999999999999964322  22456899999999999999999999999764

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=2e-13  Score=115.30  Aligned_cols=73  Identities=22%  Similarity=0.331  Sum_probs=66.8

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      ++++|+||..++++||||+|++||+|+++|||+|+|++..  ..+..+++|+|+|+.++|++|+.+|.++|++..
T Consensus        10 ~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~--~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~e   82 (84)
T d2ctla1          10 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKD--DGNQPQDQITITGYEKNTEAARDAILRIVGELE   82 (84)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTT--TCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCC--CCCCCcceEEEECCHHHHHHHHHHHHHHHHhHh
Confidence            7899999999999999999999999999999999997543  356778999999999999999999999998853

>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=99.37  E-value=4.2e-13  Score=113.33  Aligned_cols=73  Identities=16%  Similarity=0.268  Sum_probs=64.7

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      ..+++|.||..++++|||++|++||+|+++|||+|+|.+...   .+..+++|+|+|+.++|++|+.+|+++|++.
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~---~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD---GNQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT---CSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC---CCCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            356889999999999999999999999999999999965432   2566889999999999999999999999873

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=6.1e-13  Score=111.75  Aligned_cols=70  Identities=16%  Similarity=0.214  Sum_probs=62.3

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e  294 (669)
                      .++.+|.||..++++|||++|++||+|+++|||+|+|...     ++..++.|+|+|+++.|++|+++|++++++
T Consensus         9 ~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-----~~~~~~~v~I~G~~~~V~~A~~~I~~i~~e   78 (81)
T d2ctma1           9 MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQS-----GAPDPNCVTVTGLPENVEEAIDHILNLEEE   78 (81)
T ss_dssp             CCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCT-----TCSCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCc-----cCCCCCEEEEeCCHHHHHHHHHHHHHHHHH
Confidence            4578999999999999999999999999999999999532     123457899999999999999999999987

>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=99.34  E-value=4e-13  Score=112.87  Aligned_cols=70  Identities=29%  Similarity=0.484  Sum_probs=63.5

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      ..+.+|.||.+++++|||++|++|++|+++|||+|+|..      .++.++.|+|+|+.++|++|+.+|+++|++.
T Consensus         9 ~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~------~~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           9 QASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR------PDDPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCC------TTSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECC------CCCCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999999953      2456789999999999999999999999874

>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=99.34  E-value=4.9e-13  Score=112.40  Aligned_cols=71  Identities=25%  Similarity=0.374  Sum_probs=63.1

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHH-hCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQAR-TGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR  296 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~-TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~  296 (669)
                      .++++|.||.+++++||||+|++|++|+++ ++|+|+|..      .++.++.|+|+|++++|++|+.+|++++++.+
T Consensus         9 ~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~------~~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~~   80 (82)
T d2ctja1           9 IAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV------EGSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   80 (82)
T ss_dssp             SCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCC------TTTTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             cEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeC------CCCCCceEEEeCCHHHHHHHHHHHHHHHhhhh
Confidence            567899999999999999999999999987 589999842      24567899999999999999999999999854

>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=99.33  E-value=5.4e-13  Score=112.07  Aligned_cols=71  Identities=20%  Similarity=0.266  Sum_probs=64.0

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      .++.+|.||...+++||||+|++||+|+++|||+|+|.+..    ...+++|+|+|+.++|++|+++|+++++|.
T Consensus         9 ~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~----~~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           9 MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG----APDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             CCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT----CSCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCcc----CCCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            37899999999999999999999999999999999997543    233578999999999999999999999885

>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=99.32  E-value=3.6e-13  Score=113.18  Aligned_cols=71  Identities=32%  Similarity=0.547  Sum_probs=65.2

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      .++.+|.||...+|+||||+|++|++|+++|||+|+|.+.     +..+++|+|+|+.++|++|+++|++++++..
T Consensus         9 ~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-----~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~~   79 (81)
T d2ctea1           9 QASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-----DDPSNQIKITGTKEGIEKARHEVLLISAEQD   79 (81)
T ss_dssp             CEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-----TSSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC-----CCCCCEEEEEeCHHHHHHHHHHHHHHHHHHh
Confidence            3789999999999999999999999999999999999743     4567899999999999999999999999854

>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=99.29  E-value=1.1e-12  Score=107.44  Aligned_cols=67  Identities=21%  Similarity=0.409  Sum_probs=60.3

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHH
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVI  292 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL  292 (669)
                      .+..+|.||.+++++|||++|++||+|+++|||+|+|..      ++++++.|+|+|++++|++|+++|++++
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~------~~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPP------DSEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCC------CCSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCC------CCCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            356799999999999999999999999999999999953      2456789999999999999999999874

>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=99.29  E-value=6.8e-14  Score=120.19  Aligned_cols=67  Identities=15%  Similarity=0.346  Sum_probs=60.7

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHh-CCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQART-GARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~T-GArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      .++.+|.||..++++|||++|++|++|++++ +|+|.|.         +.++.|+|+|+++.|++|+++|+++|++-
T Consensus        20 ~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~---------~~~~~v~i~G~~~~ve~Ak~~I~~iv~el   87 (90)
T d2ctfa1          20 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFT---------EGEDKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEEC---------SSSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeC---------CCCceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            5688999999999999999999999999994 8999994         23578999999999999999999999873

>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=99.28  E-value=1e-12  Score=110.40  Aligned_cols=71  Identities=20%  Similarity=0.340  Sum_probs=64.0

Q ss_pred             CceEEEEeccccccceeccCCcchhHHHhh-cCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQ-SGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       128 ~vt~rIlVP~~~vG~IIGKgGetIK~Iqee-TGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      .++++|.||...+|+||||+|++||+|+++ ++|+|+|.+.     +..+++|+|+|+.++|++|+++|+++++|..
T Consensus         9 ~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~-----~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~~   80 (82)
T d2ctja1           9 IAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-----GSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   80 (82)
T ss_dssp             SCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-----TTTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             cEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC-----CCCCceEEEeCCHHHHHHHHHHHHHHHhhhh
Confidence            378999999999999999999999999988 5999999743     4567999999999999999999999999854

>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=99.26  E-value=9.4e-13  Score=107.96  Aligned_cols=66  Identities=20%  Similarity=0.338  Sum_probs=60.8

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL  199 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI  199 (669)
                      ++.+|.||...+++|||++|++||+|+++|||+|+|.++     +..+++|+|+|+.++|++|+++|++|+
T Consensus         5 ~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~-----~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           5 DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-----SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             EEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC-----CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             EEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC-----CCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            678999999999999999999999999999999999743     456789999999999999999999874

>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=99.26  E-value=2e-12  Score=110.76  Aligned_cols=69  Identities=22%  Similarity=0.312  Sum_probs=62.8

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e  294 (669)
                      .++.+|.||.++++.|||++|++||+|+++|||+|.|..      .++.++.|+|+|+.++|++|+++|+++|.+
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~------~~~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA------PELQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCC------TTTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECC------CCCCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            568899999999999999999999999999999999953      245578999999999999999999999976

>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=99.26  E-value=4.1e-12  Score=108.91  Aligned_cols=67  Identities=22%  Similarity=0.365  Sum_probs=61.4

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      ++..|.||...+++|||++|++||+|++++ +++|.+.++        +.+|+|+|++++|++|+++|++++++..
T Consensus        21 ~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~--------~~~v~i~G~~~~ve~Ak~~I~~iv~el~   88 (90)
T d2ctfa1          21 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG--------EDKITLEGPTEDVSVAQEQIEGMVKDLI   88 (90)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS--------SCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC--------CceEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            899999999999999999999999999995 899999743        4679999999999999999999998843

>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=99.22  E-value=2.6e-12  Score=109.99  Aligned_cols=70  Identities=16%  Similarity=0.261  Sum_probs=64.4

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      ++.+|.||...+++|||++|.+||+|+++|||+|.|.+.     +..+++|+|+|+.++|++|+.+|++++++..
T Consensus        10 vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-----~~~~~~v~I~G~~~~V~~A~~~I~~~v~e~~   79 (91)
T d2ctka1          10 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-----ELQSDIIAITGLAANLDRAKAGLLERVKELQ   79 (91)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT-----TTTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC-----CCCcceEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999999999999999999999999743     4557899999999999999999999998753

>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=99.20  E-value=8.5e-13  Score=110.50  Aligned_cols=67  Identities=19%  Similarity=0.314  Sum_probs=58.3

Q ss_pred             CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEc-CHHHHHHHHHHHHHHHhh
Q 005922          220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDG-TSEQIESAKQLVNEVISE  294 (669)
Q Consensus       220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG-~peqVq~Ak~LI~dlL~e  294 (669)
                      ..+.+|.||.+++|+|||++|++||+|+++|||+|.|.        +.++++|+|.| ++++|++|++||+.+.++
T Consensus         7 ~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~--------~~~~g~v~I~g~~~eav~~A~~~Ie~~~~~   74 (78)
T d2cpqa1           7 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIEL--------DEDTGTFRIYGESADAVKKARGFLEFVEDF   74 (78)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEE--------ETTTTEEEEEESSHHHHHHHHHHHSCCCCC
T ss_pred             CceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEe--------cCCCceEEEEECCHHHHHHHHHHHHHhhee
Confidence            35678999999999999999999999999999999985        23467999999 599999999999765543

>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=99.20  E-value=8.5e-12  Score=105.76  Aligned_cols=64  Identities=22%  Similarity=0.299  Sum_probs=58.1

Q ss_pred             EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922          223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR  296 (669)
Q Consensus       223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~  296 (669)
                      ..|.||.+++++||||+|++||+|+++|||+|.|.          .++.|+|+|++++|+.|+++|++++++..
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~----------~~g~v~I~G~~e~v~~A~~~I~~i~~ea~   66 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVG----------QNGLIWVNGDRRKVSIAEEAIYLIEQEAH   66 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEEC----------TTSEEEEESCHHHHHHHHHHHHHHHHCSC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEEC----------CCCEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            35789999999999999999999999999999994          24689999999999999999999998743

>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=99.10  E-value=4.2e-12  Score=106.19  Aligned_cols=64  Identities=17%  Similarity=0.279  Sum_probs=57.0

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHH
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVL  199 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI  199 (669)
                      ++.+|.||.+++|+|||++|++||+|+++|||+|.+..+       .++.|+|+| +.++|++|+++|+.+.
T Consensus         8 ~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~-------~~g~v~I~g~~~eav~~A~~~Ie~~~   72 (78)
T d2cpqa1           8 FHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-------DTGTFRIYGESADAVKKARGFLEFVE   72 (78)
T ss_dssp             EEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-------TTTEEEEEESSHHHHHHHHHHHSCCC
T ss_pred             ceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC-------CCceEEEEECCHHHHHHHHHHHHHhh
Confidence            889999999999999999999999999999999998643       246788888 7999999999996554

>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=2.2e-11  Score=103.14  Aligned_cols=64  Identities=28%  Similarity=0.356  Sum_probs=58.4

Q ss_pred             EEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922          131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~  203 (669)
                      .-|.||.+++|+||||+|++||+|+++|||+|+|.+         +..|+|+|+.++|.+|+.+|++++++..
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~---------~g~v~I~G~~e~v~~A~~~I~~i~~ea~   66 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ---------NGLIWVNGDRRKVSIAEEAIYLIEQEAH   66 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT---------TSEEEEESCHHHHHHHHHHHHHHHHCSC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC---------CCEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            568899999999999999999999999999999964         3579999999999999999999988743

>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=98.89  E-value=2.8e-11  Score=98.84  Aligned_cols=63  Identities=19%  Similarity=0.223  Sum_probs=49.5

Q ss_pred             EEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhhcc
Q 005922          224 AMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISENR  296 (669)
Q Consensus       224 ~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e~~  296 (669)
                      .|.||.+++++||||+|++||.|+++|||+|.|.          ++..|+|+|. .+.|++|+++|++++++..
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 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVA----------NNGRIWATCPSRFSEEILIEAIRKIENESH   67 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEEC----------TTSEEEC-----CTTCCTHHHHTTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEc----------CCCEEEEEeCCHHHHHHHHHHHHHHHHhhc
Confidence            4789999999999999999999999999999994          1457999997 7889999999998887743

>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=98.84  E-value=1e-09  Score=92.71  Aligned_cols=63  Identities=24%  Similarity=0.346  Sum_probs=52.2

Q ss_pred             EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEE-----cCHHHHHHHHHHHHHHHhh
Q 005922          223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQID-----GTSEQIESAKQLVNEVISE  294 (669)
Q Consensus       223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtIt-----G~peqVq~Ak~LI~dlL~e  294 (669)
                      +.|.||.+++|+||||+|++||+|+++|||+|+|..         ++..|.|.     +.+.++++|+++|.++.+.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~---------d~g~v~i~~~~~~~~~~a~~~a~~iI~aI~rG   72 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT---------ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLG   72 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET---------TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHT
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEc---------CCCeEEEecCCccccHHHHHHHHHHHHHHhCC
Confidence            568999999999999999999999999999999952         23455554     4588899999999887653

>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=98.84  E-value=6.3e-10  Score=94.09  Aligned_cols=68  Identities=18%  Similarity=0.254  Sum_probs=55.1

Q ss_pred             EEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922          131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE  201 (669)
Q Consensus       131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e  201 (669)
                      +.|.||.+++|+||||+|++||+|+++|||+|+|+.+..   ....+...+.+...++.+|+++|.++.+.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g---~v~i~~~~~~~~~~a~~~a~~iI~aI~rG   72 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENS---MVIVEPEAEGIPPVNLMKAAEVVKAISLG   72 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTT---EEEEEESSTTSCHHHHHHHHHHHHHHHHT
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCC---eEEEecCCccccHHHHHHHHHHHHHHhCC
Confidence            468999999999999999999999999999999975421   11223445677889999999999888654

>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=98.80  E-value=7.8e-11  Score=96.15  Aligned_cols=63  Identities=21%  Similarity=0.189  Sum_probs=48.8

Q ss_pred             EEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCC-HHHHHHHHHHHHHHHHhh
Q 005922          131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT-PEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt-~E~V~kA~~lI~elI~e~  202 (669)
                      ..|.||.+++|+||||+|++||+|+++|||+|+|.++         ..|+|+|. .+++++|+++|+++++|.
T Consensus         3 ~vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~---------g~v~I~g~~~~~v~~A~~~I~~i~~ea   66 (69)
T d2je6i3           3 IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN---------GRIWATCPSRFSEEILIEAIRKIENES   66 (69)
T ss_dssp             CEEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT---------SEEEC-----CTTCCTHHHHTTTTTTT
T ss_pred             EEEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC---------CEEEEEeCCHHHHHHHHHHHHHHHHhh
Confidence            3578999999999999999999999999999999643         35888884 789999999998887764

>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=98.79  E-value=3.8e-09  Score=89.70  Aligned_cols=62  Identities=19%  Similarity=0.265  Sum_probs=56.3

Q ss_pred             EEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhhc
Q 005922          224 AMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISEN  295 (669)
Q Consensus       224 ~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e~  295 (669)
                      .|.||.++++.|||++|++||.|+++|||+|.|.          ++..|+|.|. .+.+..|+.+|+.+.++.
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~----------d~G~V~I~g~~~~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVA----------RNGRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEE----------TTTEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEEC----------CCcEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            5789999999999999999999999999999995          1458999997 899999999999998874

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.64  E-value=1.3e-08  Score=86.30  Aligned_cols=64  Identities=28%  Similarity=0.280  Sum_probs=56.1

Q ss_pred             EEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHHhhh
Q 005922          131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAEAE  203 (669)
Q Consensus       131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e~~  203 (669)
                      .-|.||.+++++|||++|++||+|+++|||+|.|..+         -.|.|.| +.+.+++|+.+|..+.++..
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~---------G~V~I~g~~~~~~~~A~~~I~~I~~ea~   67 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN---------GRIHLECPNEDLEAIAVMAIKIIDEEAY   67 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETT---------TEEEEECSCHHHHHHHHHHHHHHHHCSC
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCC---------cEEEEEeCCHHHHHHHHHHHHHHHHhch
Confidence            4578999999999999999999999999999999643         2588888 58999999999999888753

>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=98.62  E-value=9.3e-09  Score=89.99  Aligned_cols=54  Identities=30%  Similarity=0.378  Sum_probs=48.9

Q ss_pred             ceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922          231 KVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN  295 (669)
Q Consensus       231 ~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~  295 (669)
                      ..|+|||++|++||.|++.|||+|.|.           +..|+|.|..++|+.|+++|+++|.+.
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~-----------d~~v~iig~~e~i~~A~~~Ie~li~~~   76 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVG-----------EYEVAIIGDYERAMAAKQAIEMLAEGR   76 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEEC-----------SSEEEEEEEHHHHHHHHHHHHHHHTTC
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEe-----------CCeEEEEECchhHHHHHHHHHHHHcCC
Confidence            378999999999999999999999994           347888999999999999999999763

>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=98.50  E-value=1.1e-07  Score=85.38  Aligned_cols=74  Identities=20%  Similarity=0.318  Sum_probs=58.6

Q ss_pred             cEEEEeeCCC------ceeeeecCCchHHHHHHHHhCCeEEeccCCCC----------C--CCCCCccEEEEEcC-HHHH
Q 005922          221 DHFAMKIPNN------KVGLVIGKGGETIKNMQARTGARIQVIPLHLP----------P--GDTSTERTVQIDGT-SEQI  281 (669)
Q Consensus       221 ~t~~I~VP~~------~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~p----------p--ge~s~er~VtItG~-peqV  281 (669)
                      .+.+|.||-+      ++|+|||.+|+++|+|+++|||+|.|.++..-          .  .+..++-.|.|+++ .+.|
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            4567888765      59999999999999999999999999875220          0  01223456889998 8899


Q ss_pred             HHHHHHHHHHHhh
Q 005922          282 ESAKQLVNEVISE  294 (669)
Q Consensus       282 q~Ak~LI~dlL~e  294 (669)
                      +.|+.+|+++|..
T Consensus        83 ~~A~~~i~~ll~~   95 (122)
T d1k1ga_          83 KKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999964

>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=98.49  E-value=4.4e-09  Score=81.69  Aligned_cols=46  Identities=35%  Similarity=0.550  Sum_probs=14.7

Q ss_pred             EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC
Q 005922          222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT  277 (669)
Q Consensus       222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~  277 (669)
                      .+.|.||.++++.|||++|++||.|+++|||+|.|.          +|..|+|+|.
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~----------ddg~v~I~a~   49 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE----------DDGTIYIGAA   49 (54)
T ss_dssp             CC---------------------CHHHHSCCCC------------------CCCCB
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEe----------CCeEEEEEec
Confidence            457899999999999999999999999999999984          2578888775

>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=98.41  E-value=1.2e-07  Score=85.10  Aligned_cols=74  Identities=28%  Similarity=0.444  Sum_probs=58.8

Q ss_pred             ceEEEEecccc------ccceeccCCcchhHHHhhcCcEEEEcc-----CC--c-----cC--CCCCCccccccCCHHHH
Q 005922          129 TSKKIEIPNIR------VGVIIGKSGETIKYLQLQSGAKIQVTR-----DT--E-----AD--LNSPTRSVELMGTPEQI  188 (669)
Q Consensus       129 vt~rIlVP~~~------vG~IIGKgGetIK~IqeeTGAkI~Isk-----d~--e-----~~--p~~~eRvVtItGt~E~V  188 (669)
                      ++.+|+||-+.      ||+|||.+|.|+|+|+++|||+|.|..     +.  +     ..  .+.+..+++..-+.+.|
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            78999999875      999999999999999999999999942     10  0     01  12334666666688999


Q ss_pred             HHHHHHHHHHHHhh
Q 005922          189 AKAEQLINDVLAEA  202 (669)
Q Consensus       189 ~kA~~lI~elI~e~  202 (669)
                      ++|+.+|+++|.+.
T Consensus        83 ~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          83 KKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999764

>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=98.40  E-value=1.7e-08  Score=78.35  Aligned_cols=47  Identities=21%  Similarity=0.399  Sum_probs=15.1

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT  184 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt  184 (669)
                      ..++|.||.+++|.|||++|++||.|+++|||+|.|..         +..|+|++.
T Consensus         3 ~~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d---------dg~v~I~a~   49 (54)
T d1e3ha4           3 RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED---------DGTIYIGAA   49 (54)
T ss_dssp             BCC---------------------CHHHHSCCCC-----------------CCCCB
T ss_pred             eEEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC---------CeEEEEEec
Confidence            45678999999999999999999999999999999963         356777774

>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=98.40  E-value=3.8e-08  Score=86.06  Aligned_cols=54  Identities=24%  Similarity=0.310  Sum_probs=47.7

Q ss_pred             cccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922          139 RVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA  202 (669)
Q Consensus       139 ~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~  202 (669)
                      ..|+||||+|.|||.|++.|||+|.|..+          .|.|.|+.++++.|+++|++||.+.
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d~----------~v~iig~~e~i~~A~~~Ie~li~~~   76 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGEY----------EVAIIGDYERAMAAKQAIEMLAEGR   76 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECSS----------EEEEEEEHHHHHHHHHHHHHHHTTC
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeCC----------eEEEEECchhHHHHHHHHHHHHcCC
Confidence            38999999999999999999999999632          3666789999999999999999763

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=98.20  E-value=5.5e-07  Score=81.86  Aligned_cols=73  Identities=23%  Similarity=0.281  Sum_probs=56.2

Q ss_pred             EEEEeeCC------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCC--------------CCCCCccEEEEEcC-H--
Q 005922          222 HFAMKIPN------NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPP--------------GDTSTERTVQIDGT-S--  278 (669)
Q Consensus       222 t~~I~VP~------~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~pp--------------ge~s~er~VtItG~-p--  278 (669)
                      +.+|.||.      +++|+|||.+|.++|+|+++|||+|.|.++....              .+..++-.|.|++. +  
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            45677764      6899999999999999999999999998763210              01234667889887 2  


Q ss_pred             ---HHHHHHHHHHHHHHhh
Q 005922          279 ---EQIESAKQLVNEVISE  294 (669)
Q Consensus       279 ---eqVq~Ak~LI~dlL~e  294 (669)
                         ..|.+|+.+|+.+|..
T Consensus        83 ~a~~kl~~A~~~I~~lL~p  101 (134)
T d2bl5a1          83 RAELKLKRAVEEVKKLLVP  101 (134)
T ss_dssp             HHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHHHHHHHcCC
Confidence               3588999999999954

>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=97.97  E-value=1.4e-06  Score=79.03  Aligned_cols=73  Identities=25%  Similarity=0.343  Sum_probs=51.8

Q ss_pred             ceEEEEeccc------cccceeccCCcchhHHHhhcCcEEEEccCCc----------------cCCCCCCccccccCCH-
Q 005922          129 TSKKIEIPNI------RVGVIIGKSGETIKYLQLQSGAKIQVTRDTE----------------ADLNSPTRSVELMGTP-  185 (669)
Q Consensus       129 vt~rIlVP~~------~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e----------------~~p~~~eRvVtItGt~-  185 (669)
                      +..||+||.+      ++|+|||.+|.|+|+|+++|||+|.|.....                ...+.+..|++..-+. 
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            5789999864      5899999999999999999999999943110                0112333443333232 


Q ss_pred             ----HHHHHHHHHHHHHHHh
Q 005922          186 ----EQIAKAEQLINDVLAE  201 (669)
Q Consensus       186 ----E~V~kA~~lI~elI~e  201 (669)
                          ..|.+|+.+|+++|..
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                3588899999988854

>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=94.27  E-value=0.011  Score=46.78  Aligned_cols=38  Identities=26%  Similarity=0.393  Sum_probs=35.5

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP  258 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~  258 (669)
                      ..+.+.|+.+...+.|||+|.|||-..+.||.+|.|..
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            46789999999999999999999999999999999974

>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=94.06  E-value=0.014  Score=46.31  Aligned_cols=37  Identities=27%  Similarity=0.479  Sum_probs=34.9

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI  257 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~  257 (669)
                      ..+.+.|+.+..++.|||+|.|||-..+.||.+|.|.
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~   63 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIK   63 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeE
Confidence            4678999999999999999999999999999999996

>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=94.04  E-value=0.015  Score=46.10  Aligned_cols=40  Identities=20%  Similarity=0.516  Sum_probs=36.5

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCC
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDT  168 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~  168 (669)
                      -...++|+.+...+.|||+|.|||-..+-||.+|.|..+.
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~es   65 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA   65 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeCC
Confidence            4688999999999999999999999999999999997653

>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=92.73  E-value=0.027  Score=44.63  Aligned_cols=38  Identities=21%  Similarity=0.461  Sum_probs=35.2

Q ss_pred             ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEcc
Q 005922          129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR  166 (669)
Q Consensus       129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Isk  166 (669)
                      -...+.|+.+...+.|||+|.|||-..+-||.+|.|..
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            36889999999999999999999999999999999964

>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=88.64  E-value=0.16  Score=41.61  Aligned_cols=59  Identities=8%  Similarity=0.043  Sum_probs=46.1

Q ss_pred             EEEeeCCCceeeeecCCch-HHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHH
Q 005922          223 FAMKIPNNKVGLVIGKGGE-TIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEV  291 (669)
Q Consensus       223 ~~I~VP~~~vG~IIGKGGs-tIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dl  291 (669)
                      +-+.|+.+++..|||+.++ .|+.|.+++.|+|.|-          ....|-|.+. .+.+..+.+.|.+.
T Consensus         3 ~v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG----------~NGrIWi~~~~~~~~i~i~~aI~~~   63 (85)
T d2ja9a2           3 MIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIG----------LNGKIWVKCEELSNTLACYRTIMEC   63 (85)
T ss_dssp             EEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEE----------TTTEEEEECSSHHHHHHHHHHHHHH
T ss_pred             EEEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEe----------cCcEEEEECCCHHHHHHHHHHHHHH
Confidence            3467899999999999998 8999999999999984          2458999996 66655555545443

>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=87.65  E-value=0.27  Score=40.26  Aligned_cols=62  Identities=6%  Similarity=0.008  Sum_probs=45.2

Q ss_pred             EEEEeccccccceeccCCc-chhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHHh
Q 005922          131 KKIEIPNIRVGVIIGKSGE-TIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAE  201 (669)
Q Consensus       131 ~rIlVP~~~vG~IIGKgGe-tIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e  201 (669)
                      .-+.|+-.++.+|||+++. -|+.|.+++.++|.|=..        -| |-|.+ +.+.+..+.+.|.++-++
T Consensus         3 ~v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~N--------Gr-IWi~~~~~~~~i~i~~aI~~~e~~   66 (85)
T d2ja9a2           3 MIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLN--------GK-IWVKCEELSNTLACYRTIMECCQK   66 (85)
T ss_dssp             EEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETT--------TE-EEEECSSHHHHHHHHHHHHHHHHH
T ss_pred             EEEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecC--------cE-EEEECCCHHHHHHHHHHHHHHHHh
Confidence            3467899999999999998 789999999999999432        24 55555 666666665555554443

>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=82.83  E-value=0.22  Score=41.41  Aligned_cols=31  Identities=19%  Similarity=0.312  Sum_probs=26.9

Q ss_pred             cEEEEeeCCCceeeeecCCchHHHHHHHHhC
Q 005922          221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTG  251 (669)
Q Consensus       221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TG  251 (669)
                      ..++|.|....-|.|||++|++|++|+++..
T Consensus        35 ~~i~I~I~tarPGivIGrkG~~I~~L~~~l~   65 (92)
T d1wh9a_          35 TRTEIIILATRTQNVLGEKGRRIRELTAVVQ   65 (92)
T ss_dssp             SCEEEEEEESCHHHHHCGGGHHHHHHHHHHH
T ss_pred             CeEEEEEEeCCCceeeccCchhHHHHHHHHH
Confidence            4578889999999999999999999987653

>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=80.06  E-value=0.22  Score=41.36  Aligned_cols=29  Identities=24%  Similarity=0.342  Sum_probs=25.5

Q ss_pred             eEEEEeccccccceeccCCcchhHHHhhc
Q 005922          130 SKKIEIPNIRVGVIIGKSGETIKYLQLQS  158 (669)
Q Consensus       130 t~rIlVP~~~vG~IIGKgGetIK~IqeeT  158 (669)
                      .++|.|...+-|.||||+|++|++|+++.
T Consensus        36 ~i~I~I~tarPGivIGrkG~~I~~L~~~l   64 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGEKGRRIRELTAVV   64 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHHH
T ss_pred             eEEEEEEeCCCceeeccCchhHHHHHHHH
Confidence            47788999999999999999999988654