Citrus Sinensis ID: 003942

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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-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780----
Protein Sequence
MAEEEVLAPASAAAADLKRKLDDLEPDEALEHAEGMRDDEAKNSDEVEKNVDGFAEAHGSEVKRPRLDDDKTEKPDGPVNVNGLKEEKPDEVVDAEQLTEDTTKEEELESAEVKTEQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYGGPPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAATQPSYDQSASQSTAYGVAQGTAAAGYGKTVSPQPGYPQYDSTQMYAAPR
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccHHHccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccHHHHHHcHHHccccccccccHHccccccccccHHHHHHHHccccHHHHHccccccHHccccccccccccccccccccccccccccccccccccccccEEEEEEEccccccEEEccccHHHHHHHHHHcccEEEEccccccccccccEEEEEccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccEEEEEEcccccEEEEEccHHHHHHHHHHHccEEEEEcccccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccEEEEcccccHHcccccccccccccccccccccccccEEEEccccccEEEEEccccEEcccEcccccEEcccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccEEEEEEcccccEEEEcccccEHHHHHHHcccEEEcccccccccccccccccHHHHHHHHHcHHHccccccccccccccccEEEEEEEccccEEEEEcccccEHHHHHHHcccEEEEEcccccccccccEEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccEEEEEEEHHHHHHHHcHHHHHHHHHHHHHccEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccc
Coil and Loop (DISEMBL)
maeeevlaPASAAAADLKRKlddlepdealehaegmrddeaknsdevEKNVDGFaeahgsevkrprldddktekpdgpvnvnglkeekpdevvdaeqltedttkeEELESaevkteqhssveeqasvdnqqisvkEETKEVLFSTEEAFIDVKEetkevtvkeeetvkeeesvepsnvvpqqvvdnsksddpsstddstmsrkievpnnkvgVLIGKAGDTIRYlqynsgakiqitrdadadphaatrpveiigtlsnIDKAEKLINAVIAeadaggspslVARGLATAQasgaaeqveikvpnekvgliigrggetikglqtrsgariqlipqhlpegdgskeRIVRVTGDMRQIEIAQEMIKEVLSQtvrpstlsggfnqqayrprvptgppqwgprgshpsqpmaydypqrgpypsqnphyphlpygnyppqqmaprsnyggppnmqgaaggydyyggqgghvsdrpvsvshstsipghpsvpaqapaggpppsqanynygqphtseyghqqpyahaapqqgyghgyddnhapvqhpygghsnsqpvysqgglqsgyhqhqygkppygmpaqgtqpqsygpprpgqpgdippyqsqvpsaqsygpnvphqqqypyatsgptqqtypsygsapapdsynqppasapgypqqagqavpnypqpggqqapsygqvaptagygqytntqqaypeqpatsnagygyqgtqdpsygssapgsayaaptgqpgyaqpaatqpsydqsasqsTAYGVAQGtaaagygktvspqpgypqydstqmyaapr
Flexible Loop (DISEMBL)
maeeevlapasaaaadlkRKLDDLEPDEALEHaegmrddeaknsdEVEKNVDgfaeahgsevkrprldddktekpdgpvnvnglkeekpdevvdaeqltedttkeeelesaevkteqhssveeqasvdnqqisvkEETKevlfsteeafidvkeetkevtvkeeetvkeeesvepsnvvpqqvvdnsksddpsstddstmsrkievpnnkvgvLIGKAGDTIRYLQYNSGAKiqitrdadadphaATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQAsgaaeqveikvpnekvgliiGRGGETIKGLQTRSGARIqlipqhlpegdgskerIVRVTGDMRQIEIAQEMIKEVLSQTVRPSTlsggfnqqayrprvPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYGGPPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAATQPSYDQSASQSTAYGVAQGTAAAgygktvspqpgypqydstqmyaapr
Low Complexity Region (SEG)
MaeeevlapasaaaadlkrklddlePDEALEHAEGMRDDEAKNSDEVEKNVDGFAEAHGSEVKRPRLDDDKTEKPDGPVNVNGLKEEKPDEVVDAeqltedttkeeelesaevkteQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDvkeetkevtvkeeetvkeeesvepsnvvpQQVVdnsksddpsstddsTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYGGPPNMqgaaggydyyggqggHVSDRPVSVSHSTSIPGHpsvpaqapaggpppsqaNYNYGQPHTSEYghqqpyahaapqqgyGHGYDDNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYgpprpgqpgdippYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQDpsygssapgsayaapTGQPGYAQPAATQPSYDQSASQSTAYGVAQGTAAAGYGKTVSPQPGYPQYDSTQMYAAPR
Disordered region (IsUnstruct)
****************************************************************************************************************************************************************************************************************NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA*****LVARGLA*********QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLI*************IVRVTGDMRQIEIAQEMIKEV******************************************************************************************DYY*************************************************************************************************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
******L**************************************************************************************************************************************************************************************************RKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD*****HAATRPVEIIGTLSNIDKAEKLINA*******************************IKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQH******SKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPRGSH**********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
**************ADLKRKLDDLEPDEALEHAEGMRDDEAKNSDEVEKNVDGFAEAHGSEVKRPRLDDDKTEKPDGPVNVNGLKEEK**************************************VDNQQISVKEETKEVLFSTEEAFIDVKEET**********************VPQQVV****************SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGL*********EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPT***********PSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYGGPPNMQGAAGGYDYYGGQGGHVSD**************************PPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSY************************QAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQ****************************************AYGVAQGTAAAGYGKTVSPQPGYPQYDSTQMYAAPR
Disordered Region (DISPRO)
**************************************DEAKNSDEVEKNVDGFAEAHGSEVKRPRLDDDKTEKPD***NVNG*KEEKPDEVVDAEQLTEDTTKEEELESAE***EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDN*********DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA******************AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYGGPPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAATQPSYDQSASQSTAYGVAQGTAAAGYGKTVSPQPGYPQYDSTQMYAAP*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAEEEVLAPASAAAADLKRKLDDLEPDEALEHAEGMRDDEAKNSDEVEKNVDGFAEAHGSEVKRPRLDDDKTEKPDGPVNVNGLKEEKPDEVVDAEQLTEDTTKEEELESAEVKTEQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYGGPPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAATQPSYDQSASQSTAYGVAQGTAAAGYGKTVSPQPGYPQYDSTQMYAAPR
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	784	2.2.26 [Sep-21-2011]
Q96I24	572	Far upstream element-bind	yes	no	0.201	0.276	0.341	2e-19
Q96AE4	644	Far upstream element-bind	no	no	0.200	0.243	0.358	5e-19
Q91WJ8	651	Far upstream element-bind	no	no	0.200	0.241	0.358	9e-19
Q32PX7	639	Far upstream element-bind	yes	no	0.200	0.245	0.358	1e-18
Q99PF5	721	Far upstream element-bind	no	no	0.225	0.245	0.32	2e-17
Q3U0V1	748	Far upstream element-bind	no	no	0.225	0.236	0.32	2e-17
Q92945	711	Far upstream element-bind	no	no	0.225	0.248	0.315	4e-17
Q8UVD9	769	Far upstream element-bind	no	no	0.200	0.204	0.327	1e-16
Q80WA4	474	RNA-binding protein Nova-	no	no	0.205	0.339	0.337	2e-13
Q2PFW9	483	RNA-binding protein Nova-	N/A	no	0.205	0.333	0.337	2e-13

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

 Score = 98.2 bits (243), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 59/173 (34%), Positives = 99/173 (57%), Gaps = 15/173 (8%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLS 257
           + ++ + +VP+  VG +IG+ G+ I  +Q  SG KIQI  ++   P    RP  + GT  
Sbjct: 76  TVITEEFKVPDKMVGFIIGRGGEQISRIQAESGCKIQIASESSGIPE---RPCVLTGTPE 132

Query: 258 NIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGET 317
           +I++A++L+  ++     G        G      S +  Q EI +P  KVGL+IGRGGET
Sbjct: 133 SIEQAKRLLGQIVDRCRNG-------PGFHNDIDSNSTIQ-EILIPASKVGLVIGRGGET 184

Query: 318 IKGLQTRSGARIQLIPQH-LPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369
           IK LQ R+G ++ +I    LP G    ++ +R+TGD  +++ A+EM+ E++ +
Sbjct: 185 IKQLQERTGVKMVMIQDGPLPTG---ADKPLRITGDAFKVQQAREMVLEIIRE 234

May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression.
Homo sapiens (taxid: 9606)

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

 Score = 97.1 bits (240), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 61/170 (35%), Positives = 100/170 (58%), Gaps = 13/170 (7%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLS 257
           S M+ + +VP+  VG +IG+ G+ I  +Q  SG KIQI  D+   P    R   + GT  
Sbjct: 99  SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPE---RSCMLTGTPE 155

Query: 258 NIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGET 317
           ++  A++L++ ++ +    G P   A G       G A Q EI +P  K GL+IG+GGET
Sbjct: 156 SVQSAKRLLDQIVEK----GRP---APGFHHGDGPGNAVQ-EIMIPASKAGLVIGKGGET 207

Query: 318 IKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVL 367
           IK LQ R+G ++ +I Q  P+  G+ ++ +R+TGD  +++ A+EM+ E++
Sbjct: 208 IKQLQERAGVKMVMI-QDGPQNTGA-DKPLRITGDPYKVQQAKEMVLELI 255

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

 Score = 96.3 bits (238), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 61/170 (35%), Positives = 100/170 (58%), Gaps = 13/170 (7%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLS 257
           S M+ + +VP+  VG +IG+ G+ I  +Q  SG KIQI  D+   P    R   + GT  
Sbjct: 95  SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPE---RSCMLTGTPE 151

Query: 258 NIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGET 317
           ++  A++L++ ++ +    G P   A G       G A Q EI +P  K GL+IG+GGET
Sbjct: 152 SVQSAKRLLDQIVEK----GRP---APGFHHGDGPGNAVQ-EIMIPASKAGLVIGKGGET 203

Query: 318 IKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVL 367
           IK LQ R+G ++ +I Q  P+  G+ ++ +R+TGD  +++ A+EM+ E++
Sbjct: 204 IKQLQERAGVKMVMI-QDGPQNTGA-DKPLRITGDPYKVQQAKEMVLELI 251

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

 Score = 95.9 bits (237), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/170 (35%), Positives = 100/170 (58%), Gaps = 13/170 (7%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLS 257
           S M+ + +VP+  VG +IG+ G+ I  +Q  SG KIQI  D+   P    R   + GT  
Sbjct: 94  SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPE---RSCMLTGTPE 150

Query: 258 NIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGET 317
           ++  A++L++ ++ +    G P   A G       G A Q EI +P  K GL+IG+GGET
Sbjct: 151 SVQSAKRLLDQIVEK----GRP---APGFHHGDGPGNAVQ-EIMIPASKAGLVIGKGGET 202

Query: 318 IKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVL 367
           IK LQ R+G ++ +I Q  P+  G+ ++ +R+TGD  +++ A+EM+ E++
Sbjct: 203 IKQLQERAGVKMVMI-QDGPQNTGA-DKPLRITGDPYKVQQAKEMVLELI 250

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

 Score = 91.7 bits (226), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 64/200 (32%), Positives = 111/200 (55%), Gaps = 23/200 (11%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLS 257
           ++M+ +  VP+  VG++IG+ G+ I  +Q +SG K+QI+ D+   P    R V + G   
Sbjct: 144 TSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPE---RSVSLTGAPE 200

Query: 258 NIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGET 317
           ++ KA+ +++ +++    GG P       A    +G  +  EI +P  K GL+IG+GGET
Sbjct: 201 SVQKAKMMLDDIVSRG-RGGPPGQFHDN-ANGGQNGTVQ--EIMIPAGKAGLVIGKGGET 256

Query: 318 IKGLQTRSGARIQLIPQHLPEGDGSK----ERIVRVTGDMRQIEIAQEMIKEVLSQTVRP 373
           IK LQ R+G ++ LI       DGS+    ++ +R+ GD  +++ A EM+ ++L +  + 
Sbjct: 257 IKQLQERAGVKMILIQ------DGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQ- 309

Query: 374 STLSGGF-NQQAYRPRVPTG 392
               GGF ++  Y  RV  G
Sbjct: 310 ----GGFGDRNEYGSRVGGG 325

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

 Score = 91.7 bits (226), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 64/200 (32%), Positives = 111/200 (55%), Gaps = 23/200 (11%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLS 257
           ++M+ +  VP+  VG++IG+ G+ I  +Q +SG K+QI+ D+   P    R V + G   
Sbjct: 144 TSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPE---RSVSLTGAPE 200

Query: 258 NIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGET 317
           ++ KA+ +++ +++    GG P       A    +G  +  EI +P  K GL+IG+GGET
Sbjct: 201 SVQKAKMMLDDIVSRG-RGGPPGQFHDN-ANGGQNGTVQ--EIMIPAGKAGLVIGKGGET 256

Query: 318 IKGLQTRSGARIQLIPQHLPEGDGSK----ERIVRVTGDMRQIEIAQEMIKEVLSQTVRP 373
           IK LQ R+G ++ LI       DGS+    ++ +R+ GD  +++ A EM+ ++L +  + 
Sbjct: 257 IKQLQERAGVKMILIQ------DGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQ- 309

Query: 374 STLSGGF-NQQAYRPRVPTG 392
               GGF ++  Y  RV  G
Sbjct: 310 ----GGFGDRNEYGSRVGGG 325

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

 Score = 90.9 bits (224), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 63/200 (31%), Positives = 111/200 (55%), Gaps = 23/200 (11%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLS 257
           ++M+ +  VP+  VG++IG+ G+ I  +Q +SG K+QI+ D+   P    R V + G   
Sbjct: 143 TSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPE---RSVSLTGAPE 199

Query: 258 NIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGET 317
           ++ KA+ +++ +++    GG P       A    +G  +  EI +P  K GL+IG+GGET
Sbjct: 200 SVQKAKMMLDDIVSRG-RGGPPGQFHDN-ANGGQNGTVQ--EIMIPAGKAGLVIGKGGET 255

Query: 318 IKGLQTRSGARIQLIPQHLPEGDGSK----ERIVRVTGDMRQIEIAQEMIKEVLSQTVRP 373
           IK LQ R+G ++ LI       DGS+    ++ +R+ GD  +++ A EM+ ++L +  + 
Sbjct: 256 IKQLQERAGVKMILIQ------DGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQ- 308

Query: 374 STLSGGF-NQQAYRPRVPTG 392
               GGF ++  Y  R+  G
Sbjct: 309 ----GGFGDRNEYGSRIGGG 324

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

 Score = 89.4 bits (220), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 58/177 (32%), Positives = 101/177 (57%), Gaps = 20/177 (11%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLS 257
           +T++ +  VP+  VG++IG+ G+ I  +Q +SG K+QI+ D+   P    R V + G+  
Sbjct: 207 TTVTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPE---RSVSLTGSPE 263

Query: 258 NIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQV-EIKVPNEKVGLIIGRGGE 316
            + KA+ +++ +++    GG P     G     A+G    V EI +P  K GL+IG+GGE
Sbjct: 264 AVQKAKLMLDDIVSRG-RGGPP-----GQFHDYANGQNGTVQEIMIPAGKAGLVIGKGGE 317

Query: 317 TIKGLQTRSGARIQLIPQHLPEGDGSK----ERIVRVTGDMRQIEIAQEMIKEVLSQ 369
           TIK LQ R+G ++  I       DGS+    ++ +R+ GD  +++ A EM+ ++L +
Sbjct: 318 TIKQLQERAGVKMIFIQ------DGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE 368

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|Q80WA4|NOVA1_RAT RNA-binding protein Nova-1 (Fragment) OS=Rattus norvegicus GN=Nova1 PE=2 SV=1

 Score = 78.6 bits (192), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 59/175 (33%), Positives = 88/175 (50%), Gaps = 14/175 (8%)

Query: 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT 255
           +D     K+ +P+   G +IGK G TI  LQ  +GA I++++  D  P    R   I GT
Sbjct: 45  EDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 104

Query: 256 LSNIDKAEKLINAVIAEADAGGSPSLVARG--LATAQASGAA-----EQVEIKVPNEKVG 308
           +  ++     I   I E      P  VA+   ++  Q          +QV+I VPN   G
Sbjct: 105 IEALNAVHGFIAEKIREM-----PQNVAKTEPVSILQPQTTVNPDRIKQVKIIVPNSTAG 159

Query: 309 LIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 363
           LIIG+GG T+K +  +SGA +QL     P+G   +ER+V V+G+  Q   A E+I
Sbjct: 160 LIIGKGGATVKAIMEQSGAWVQL--SQKPDGINLQERVVTVSGEPEQNRKAVELI 212

Functions to regulate alternative splicing in neurons by binding pre-mRNA in a sequence-specific manner to activate exon inclusion. It binds specifically to the sequence UCAUY (By similarity). Acts to regulate a novel glycine receptor alpha-2 chain splice variant (alpha-2N) in developing spinal cord.

Rattus norvegicus (taxid: 10116)

>sp|Q2PFW9|NOVA1_MACFA RNA-binding protein Nova-1 OS=Macaca fascicularis GN=NOVA1 PE=2 SV=1

 Score = 78.2 bits (191), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 59/175 (33%), Positives = 88/175 (50%), Gaps = 14/175 (8%)

Query: 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT 255
           +D     K+ +P+   G +IGK G TI  LQ  +GA I++++  D  P    R   I GT
Sbjct: 46  EDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 105

Query: 256 LSNIDKAEKLINAVIAEADAGGSPSLVARG--LATAQASGAA-----EQVEIKVPNEKVG 308
           +  ++     I   I E      P  VA+   ++  Q          +QV+I VPN   G
Sbjct: 106 VEALNAVHGFIAEKIREM-----PQNVAKTEPVSILQPQTTVNPDRIKQVKIIVPNSTAG 160

Query: 309 LIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 363
           LIIG+GG T+K +  +SGA +QL     P+G   +ER+V V+G+  Q   A E+I
Sbjct: 161 LIIGKGGATVKAIMEQSGAWVQL--SQKPDGINLQERVVTVSGEPEQNRKAVELI 213

May regulate RNA splicing or metabolism in a specific subset of developing neurons.

Macaca fascicularis (taxid: 9541)

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	784
359495228	772	PREDICTED: uncharacterized protein LOC10	0.955	0.970	0.592	0.0
255569106	798	nucleic acid binding protein, putative [	0.945	0.928	0.597	0.0
356495760	793	PREDICTED: uncharacterized protein LOC10	0.966	0.955	0.547	0.0
357481253	807	Far upstream element-binding protein [Me	0.950	0.923	0.540	0.0
356538917	794	PREDICTED: uncharacterized protein LOC10	0.945	0.933	0.537	0.0
224145055	581	predicted protein [Populus trichocarpa]	0.716	0.967	0.671	0.0
449447567	787	PREDICTED: uncharacterized protein LOC10	0.964	0.960	0.517	1e-175
145336377	763	far upstream element-binding protein [Ar	0.871	0.895	0.444	1e-131
22328551	725	KH domain-containing protein [Arabidopsi	0.887	0.96	0.445	1e-130
297813443	730	KH domain-containing protein [Arabidopsi	0.882	0.947	0.458	1e-128

>gi|359495228|ref|XP_002277528.2| PREDICTED: uncharacterized protein LOC100253453 [Vitis vinifera]

 Score =  750 bits (1936), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 478/807 (59%), Positives = 554/807 (68%), Gaps = 58/807 (7%)

Query: 1   MAEEEVL--APASAAAADLKRKLDDLEPDEALEHAEGMRDDEAKNSDEVEKNVDGFAEAH 58
           MAEEEV+  A AS A +D KRKL+DLEP EA E AE      A   D V  +        
Sbjct: 1   MAEEEVVVVAGASPAPSDHKRKLEDLEP-EAPEQAEPDGVQGADAGDYVANDE------- 52

Query: 59  GSEVKRPRLDDDKTEKPDGPVNVNGLKEEKPDEVVDAEQLTEDTTKEEELESAEVKTEQH 118
            SE KRPR++D      D     NG + EK DEV+           E  +E+A+ +   H
Sbjct: 53  -SEAKRPRVEDQD----DDLATENGYQREKEDEVIK-------ENVELTVENAQSQEAPH 100

Query: 119 SSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNV 178
            + E   +V+++Q S   E KE    T+E  I    E  ++   ++ T +E E  +P+  
Sbjct: 101 PTEEAPEAVNDEQPSTDNEQKE---DTQEPSI----ENPQLENPQQPTGEEFE--KPAEE 151

Query: 179 VPQQVVDNSKSDDPS---STDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQI 235
           +PQQ V +  S +     +++  TMSRK+EVPNNKVGVLIGKAGDTIR+LQYNSGAKIQI
Sbjct: 152 IPQQEVGDVPSAEVQQQPTSETQTMSRKMEVPNNKVGVLIGKAGDTIRFLQYNSGAKIQI 211

Query: 236 TRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAA 295
           TRDADADP++A+RPVE+IG+L NI+KAEKLI  VIAEADAGGSPSLVARG ATAQA GAA
Sbjct: 212 TRDADADPYSASRPVELIGSLENINKAEKLIKDVIAEADAGGSPSLVARGFATAQAVGAA 271

Query: 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ 355
           EQV+I+VPNEKVGLIIG+GGETIK LQTRSGARIQLIPQHLPEGD SKER VRVTGD +Q
Sbjct: 272 EQVQIQVPNEKVGLIIGKGGETIKSLQTRSGARIQLIPQHLPEGDQSKERTVRVTGDKKQ 331

Query: 356 IEIAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRG 415
           IE+A+EMIKEV++Q VR ST  G +NQQ YRPR PTGP QWGPRG HP QP  YDY QRG
Sbjct: 332 IEMAREMIKEVMNQPVRSSTYPGSYNQQGYRPRGPTGPSQWGPRGPHPGQPTGYDY-QRG 390

Query: 416 PYPSQNPHYPHLPYGNYPPQQMAPRSNYGG------PPNMQG--AAGGYDYYGGQGGHVS 467
            YPSQN  Y    YG YPPQQMAPRS++G       P NMQG   +GGYD+YGGQGGH  
Sbjct: 391 AYPSQNQQYAPPSYGGYPPQQMAPRSSFGSGWEQRPPANMQGPPQSGGYDFYGGQGGHGP 450

Query: 468 DRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAA-PQQGY 526
           D P +  HS S+  H   P+ +P  GPPPSQ NYNYGQP   +YG Q  Y+    PQQGY
Sbjct: 451 DAPAAAPHSASMSIHAPGPSPSPGMGPPPSQGNYNYGQPQGPDYGQQAQYSQTGPPQQGY 510

Query: 527 GHGYD----DNHAPVQHPYGGHSNSQPVYSQGGLQSGY-HQHQYGKP-PYGMPAQGTQPQ 580
           GHGYD    +  AP   PYGGH  SQPVY QGG QSGY  Q  YGKP  YGM +Q    Q
Sbjct: 511 GHGYDEPKYEGQAPTHPPYGGH-GSQPVYPQGGAQSGYPPQQPYGKPQSYGMASQAPAAQ 569

Query: 581 SYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSY 640
           SYGPPR  QPGD+ PYQ  + S QSYGPNVP  QQYPYA+SGP QQ+YP+YGS PA D Y
Sbjct: 570 SYGPPRASQPGDV-PYQGPMSSNQSYGPNVPP-QQYPYASSGPMQQSYPAYGSQPAADGY 627

Query: 641 NQP-PASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSN 699
           NQP PAS PGYPQQ GQ +  Y QPGGQQAP Y QV P  GYG Y  +Q  Y EQ   +N
Sbjct: 628 NQPQPASGPGYPQQGGQPMSGYSQPGGQQAPGYAQVGPQGGYGPYP-SQPGYAEQQTANN 686

Query: 700 AGYGYQGTQDPSYGSSAPGSAYAA-PTGQPGYAQPAATQPSYDQSA-SQSTAYGVAQGTA 757
           A YGYQG+ DP+Y +S P SAY A P+GQPGY QP  TQPSYDQS  +QS  YG    TA
Sbjct: 687 AAYGYQGSADPTY-NSGPASAYGAQPSGQPGYVQPTPTQPSYDQSIPAQSGGYGAVPATA 745

Query: 758 AAGYGKTVSPQPGYPQYDSTQMYAAPR 784
             GYGK++SPQPGYPQYD+TQMY A R
Sbjct: 746 PVGYGKSLSPQPGYPQYDATQMYGAHR 772

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255569106|ref|XP_002525522.1| nucleic acid binding protein, putative [Ricinus communis] gi|223535201|gb|EEF36880.1| nucleic acid binding protein, putative [Ricinus communis]

 Score =  740 bits (1911), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 476/796 (59%), Positives = 548/796 (68%), Gaps = 55/796 (6%)

Query: 18  KRKLDDLEPDEALEHAEGMRDDEAKNSDEVEKNVDGFAEAHGSEVKRPRLDDDKTEKPDG 77
           KRKL DLEP+EA   AE      A  SD+  K  D  AE    E KR R  D+   K DG
Sbjct: 29  KRKLQDLEPEEAQAPAE------ANPSDDANKKSDDVAEGDTQEAKRLRTVDEN--KSDG 80

Query: 78  PVNVNGLKEEKPD---EVVDA-EQLTEDTT------KEEELESAEVKTEQHSSVEEQASV 127
             + NG+ ++KP+   E  D  EQ  ED        K EE  +A+      +  +E ASV
Sbjct: 81  LASENGIGKDKPEGGQEKSDKDEQEEEDVNAQETVGKGEEPANADDNDTVDNDTKEAASV 140

Query: 128 DNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNS 187
                    ++K+     +    D+KE       K+++  ++++  +     P +     
Sbjct: 141 G--------DSKKDADDNDTVDNDIKEAASVGDSKKDDATEKQQEADEETARPPEEESEP 192

Query: 188 KSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAAT 247
           +SDD  +T     SRK+EVPN+KVGVLIGK GDTIRYLQYNSGAKIQITRD DADPH+ T
Sbjct: 193 ESDDAQTT-----SRKMEVPNDKVGVLIGKGGDTIRYLQYNSGAKIQITRDMDADPHSTT 247

Query: 248 RPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKV 307
           RPVE+IGTLS+I KAEKLINAVIAEADAGGSPSLVARGL +AQ +G  +Q+E++VPNEKV
Sbjct: 248 RPVELIGTLSSISKAEKLINAVIAEADAGGSPSLVARGLPSAQTAGVGDQIEMQVPNEKV 307

Query: 308 GLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVL 367
           GLIIGRGG+TIK LQ +SGARIQLIPQH PEGD SKER VRVTGD +QIEIA+EMIK+V+
Sbjct: 308 GLIIGRGGDTIKALQAKSGARIQLIPQHPPEGDASKERTVRVTGDRKQIEIAREMIKDVM 367

Query: 368 SQTVRPSTLSGGFN-QQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPH 426
           SQ VR S LSGG+N QQ+YRPR PTGP  WGPRG H SQP  YDY  RGPYPSQN  YP 
Sbjct: 368 SQNVRLSPLSGGYNQQQSYRPRGPTGPSHWGPRGPHSSQPSPYDYHHRGPYPSQNSQYPP 427

Query: 427 LPYGNYPPQQMAPRSNYGG-----PPNMQGAAG---GYDYYGGQGGHVSDRPVSVSHSTS 478
             YG YPPQ M PR N+G      PPNMQG      GYDYYGGQGGHV D P S   S  
Sbjct: 428 PSYGGYPPQHMGPRGNFGSGWEQRPPNMQGPVSHGGGYDYYGGQGGHVPDHPSSAPISNP 487

Query: 479 IPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYD----DNH 534
           I GH + P+  P  G PPSQANYNYGQ H  +YGHQ PY+ A  Q GYGHGYD    D+H
Sbjct: 488 ITGHATGPSPTPGMGHPPSQANYNYGQQHGPDYGHQAPYSQAVSQHGYGHGYDEPKYDSH 547

Query: 535 APVQHPYGGHSNSQPVYSQGGLQSGY-HQHQYGK-PPYGMPAQGTQPQSYGPPRPGQPGD 592
           A  QHPY GH N QPVY Q   Q GY  Q QYGK P YGM  QG  PQSYGPPRPGQPGD
Sbjct: 548 AQTQHPY-GHGNPQPVYPQASNQPGYGAQQQYGKQPSYGMLPQGP-PQSYGPPRPGQPGD 605

Query: 593 IPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQ-PPASAPGYP 651
           + PYQ+  PS+QSYG NVP QQQYPYA+SGP QQ YPSYG+  A D YNQ  PAS PGYP
Sbjct: 606 M-PYQAPNPSSQSYGSNVPPQQQYPYASSGPMQQAYPSYGAPSATDGYNQGLPASVPGYP 664

Query: 652 QQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQDPS 711
           QQAGQ+V +Y QPGGQQA +Y Q  P+ GYG Y ++QQAYPEQPA ++AGYGYQG+QDP+
Sbjct: 665 QQAGQSVASYGQPGGQQASAYVQ-GPSGGYGSYPSSQQAYPEQPAQNSAGYGYQGSQDPA 723

Query: 712 YGSSAPGSAYAAP-TGQPGYAQPAATQPSYDQSASQST--AYGVAQGTAAAGYGKTVSPQ 768
           Y ++ PGSAYAAP +GQ GYAQP  TQPSYDQS  QST  A      +A   YGKTVSPQ
Sbjct: 724 Y-ATGPGSAYAAPASGQQGYAQPTPTQPSYDQSVPQSTAYAAAAPPASAPVSYGKTVSPQ 782

Query: 769 PGYPQYDSTQMYAAPR 784
           PGYPQYDSTQMYAAPR
Sbjct: 783 PGYPQYDSTQMYAAPR 798

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356495760|ref|XP_003516741.1| PREDICTED: uncharacterized protein LOC100800173 [Glycine max]

 Score =  694 bits (1790), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 448/819 (54%), Positives = 539/819 (65%), Gaps = 61/819 (7%)

Query: 1   MAEEEVLAPA-SAAAADLKRKLDDLEPDEALEHAEGMRDDEAKNSDEVEKNVDGFAEAHG 59
           MAEEEV+APA S   +D KRKL+DL+P+    +A  +   +A+N+D         A +  
Sbjct: 1   MAEEEVVAPAASPVPSDNKRKLEDLQPENTESNANSISISDAENAD--------AAVSAE 52

Query: 60  SEVKRPRLDDDKTEKPDGPVN-VNGLKEEK-------PDEVVDAEQLTEDTTKEEELESA 111
           +E KR RLDD +    DG  N  NG ++E+        +E    E +T +  K   ++ +
Sbjct: 53  TENKRLRLDDHQ----DGLANNTNGHQDEQVAEPGKETEERSTLENVTPEHDKTISVDHS 108

Query: 112 EVKTEQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEET-VKEE 170
           E    + +S E     D ++  V++  +E   + EE   + ++++K+ T ++  +  K+ 
Sbjct: 109 EATANEQTSAENNEPADAKEPHVEDSGQE---NAEELSKETQQQSKDSTEQDASSGDKQP 165

Query: 171 ESVEPS--NV-VPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQY 227
            SV+ +  NV VP    D S      ++ D   +RKIEVPNNKVGVLIGKAGDTIRYLQY
Sbjct: 166 NSVDTALHNVEVPYNKQDTSSGQKQPTSGDEITTRKIEVPNNKVGVLIGKAGDTIRYLQY 225

Query: 228 NSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLA 287
           NSGAKIQITRDADADP  ATR VE+IG+L +IDKAEKL+NAVIAEADAGGSPSLVARGL+
Sbjct: 226 NSGAKIQITRDADADPLCATRSVELIGSLESIDKAEKLMNAVIAEADAGGSPSLVARGLS 285

Query: 288 TAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIV 347
            AQA+  +EQ++I+VPNEKVGLIIGRGGETIK LQT+SGARIQLIPQHLPEGD SKER V
Sbjct: 286 PAQATVGSEQIQIQVPNEKVGLIIGRGGETIKSLQTKSGARIQLIPQHLPEGDDSKERTV 345

Query: 348 RVTGDMRQIEIAQEMIKEVLSQTVRPSTLSGGFNQQAYR-PRVPTGPPQWGPRGSHPSQP 406
           +VTGD RQIEIAQE+IKEV++Q VRPS  SGGF QQAYR PR   GPPQWG RGSH  QP
Sbjct: 346 QVTGDKRQIEIAQELIKEVMNQPVRPS--SGGFGQQAYRPPRGSGGPPQWGQRGSHFGQP 403

Query: 407 MAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYG------------GPPNMQGAAG 454
            AYDY  RGPYPS N  Y   PYGNY PQ MAPRS++G            GPP   G   
Sbjct: 404 TAYDYQHRGPYPSHNQPYAPPPYGNY-PQHMAPRSSFGSGWEQRPHHSFQGPPPHNGGYE 462

Query: 455 GYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQ 514
            Y    GQGGH+S+ P S    +S P H + P+  P+  P P+Q NYNYGQP   +YGHQ
Sbjct: 463 YYG---GQGGHLSEAPPSTQLPSSAPPHGAGPSPVPSMVPTPAQVNYNYGQPQGQDYGHQ 519

Query: 515 QPYAHAA-PQQGYGHGYD----DNHAPVQHPYGGHSNSQPVYSQGGLQSGY-HQHQYGKP 568
             Y+ A  PQQGYG GYD    +N AP QH YGGH NSQ  Y Q   Q  Y    QYGKP
Sbjct: 520 TAYSQAGLPQQGYGQGYDESKYENRAPTQHSYGGHVNSQSTYPQAVAQPNYPAPQQYGKP 579

Query: 569 P-YGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQT 627
           P YGMP+QG  PQSYGPPR  QPGD+ PYQ   P AQSYG N+P QQ YPYA SGP+Q  
Sbjct: 580 PLYGMPSQGQPPQSYGPPRATQPGDM-PYQGSTP-AQSYGTNMPTQQPYPYAVSGPSQTA 637

Query: 628 YPSYGSAPAPDSYNQ-PPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTN 686
           YPSYGSAPA D Y+  PPAS P Y Q   Q  P Y QP  Q A SY QV PT GYG Y +
Sbjct: 638 YPSYGSAPAADGYSHPPPASGPPYTQPGAQ--PTYGQPAAQPAASYAQVGPT-GYGSYPS 694

Query: 687 TQQAYPEQPATSNAGYGYQGTQDPSYGS-SAPGSAYAAPTGQPGYAQPAATQPSYDQSAS 745
           +Q +YPEQPA +NA YGYQ  QDP Y + +AP  + A P+GQPGY QP  TQ  Y+QS +
Sbjct: 695 SQPSYPEQPAPNNAVYGYQAPQDPGYSTGAAPAYSTAQPSGQPGYVQPTPTQTGYEQSNT 754

Query: 746 QSTAYGVAQGTAAAGYGKTVSPQPGYPQYDSTQMYAAPR 784
           Q   Y     +A+A YGKT+SPQP   QYDSTQ+Y APR
Sbjct: 755 QPAGYAAVPASASAVYGKTLSPQPAAYQYDSTQVYGAPR 793

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357481253|ref|XP_003610912.1| Far upstream element-binding protein [Medicago truncatula] gi|355512247|gb|AES93870.1| Far upstream element-binding protein [Medicago truncatula]

 Score =  690 bits (1780), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 457/846 (54%), Positives = 537/846 (63%), Gaps = 101/846 (11%)

Query: 1   MAEEEVL--APASA-AAADLKRKLDDL--EPDEALEHAEGMRDDEAKNSDEVEKNVDGFA 55
           MAEEEV+  APA++  ++D KRK +DL  +P E+             N+D  E   D  A
Sbjct: 1   MAEEEVIVAAPATSPVSSDCKRKFEDLHSQPTES-------------NTDGAE--TDAAA 45

Query: 56  EAHGSEVKRPRLDDDKTEKPDGPVNVNGLKEEKPDEVVDAEQLTEDTTKEEELESAEVKT 115
            A     KRPRL+DD     +   N NG +E+K   V +AE    DT  EE   S EV+ 
Sbjct: 46  VAQDDVNKRPRLEDDNQ---NDLANTNGHQEKK---VAEAE---TDTDTEENAPSEEVQD 96

Query: 116 EQHSSVEEQAS-VDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESV- 173
               + EE A   D  +I V E+ KE+         D KE +K      +E+ +++ S  
Sbjct: 97  VSKDNSEETAEPTDTNEILV-EDVKEIPVEDSGKEND-KEPSKATEQPSKESTEQDASSG 154

Query: 174 ----EPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNS 229
               + S++ P    D S       +   T +RKIEVP+NKVGVLIGK+GDTIRYLQYNS
Sbjct: 155 DKQPDSSSIDPTLQHDTSSGQKQPISGSDTTTRKIEVPSNKVGVLIGKSGDTIRYLQYNS 214

Query: 230 GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATA 289
           GAKIQITRDADADPH++TRPVE+IGTL +IDKAEKL+NAVIAEADAGGSP+LVARGL+ A
Sbjct: 215 GAKIQITRDADADPHSSTRPVELIGTLESIDKAEKLMNAVIAEADAGGSPALVARGLSPA 274

Query: 290 QASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRV 349
           QA   ++Q++I+VPNEKVGLIIG+GGETIK LQT++GARIQLIPQHLPEGD SKER V+V
Sbjct: 275 QAIVGSDQIQIQVPNEKVGLIIGKGGETIKSLQTKTGARIQLIPQHLPEGDDSKERTVQV 334

Query: 350 TGDMRQIEIAQEMIKEVLSQT----------------VRP---------STLSGGFNQQA 384
           TGD RQIEIAQEMIKEVLSQ                 ++P          + SGGF QQA
Sbjct: 335 TGDKRQIEIAQEMIKEVLSQIWPLPFPWGQHCFLDVALKPPIAGCLMPIRSSSGGFGQQA 394

Query: 385 YR-PRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNY 443
           YR PR   GPPQWG RGSH  QP +YDY  RGPYPS N  Y   PYGNY PQ MAPRS+Y
Sbjct: 395 YRPPRGSGGPPQWGQRGSHYGQPPSYDYQHRGPYPSHNQSYAPPPYGNY-PQHMAPRSSY 453

Query: 444 G------------GPPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPA 491
           G            GPP+     GGYDYYGGQ GH S+ P S  H +S+P H + P+  P+
Sbjct: 454 GSGWEQRPHQSFQGPPSHN---GGYDYYGGQSGHSSEAPSSAQHPSSVPQHGTGPSPLPS 510

Query: 492 GGPPPSQANYNYGQPHTSEYGHQQPYAHAA-PQQGYGHGYD----DNHAPVQHPYGGHSN 546
            GP P+Q NYNYGQP   +YGHQ PY  A  PQQGYG GYD    +N  P Q+PYGGHSN
Sbjct: 511 MGPSPAQMNYNYGQPQGQDYGHQTPYQQAGHPQQGYGQGYDESKYENRGPAQYPYGGHSN 570

Query: 547 SQPVYSQGGLQSGYH-QHQYGKPP-YGM-PAQGTQPQSYGPPRPGQPGDIPPYQSQVPSA 603
            QP Y Q   Q+ Y    QYGKPP YG+ P+QG  PQSYG PR  QPG+I PYQ   P A
Sbjct: 571 PQPTYPQASAQANYAPPQQYGKPPLYGVPPSQGQHPQSYGHPRATQPGEI-PYQGSTP-A 628

Query: 604 QSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPG--YPQQAGQAVPNY 661
           QSYG     QQ YPYA+SGP+Q  YP+YGSAPA D Y+  P SAPG  Y Q  GQ  P+Y
Sbjct: 629 QSYGTV---QQPYPYASSGPSQAAYPTYGSAPAADGYSH-PQSAPGQVYAQPGGQ--PSY 682

Query: 662 PQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAY 721
            QPG Q   SY QV PT GYG Y ++QQ YPEQPA ++AGYGYQ  QDP+Y S A  +  
Sbjct: 683 GQPGAQAVASYAQVGPT-GYGSYPSSQQTYPEQPAPNSAGYGYQAPQDPAYSSGAAQTYS 741

Query: 722 AAPTGQPGYAQPAATQPSYDQSASQSTAY--GVAQGTAAAGYGKTVSPQP-GYPQYDSTQ 778
           AAPT QPGY QP  TQ  YDQS  Q   Y        A A YGKTVSPQP  Y QYDSTQ
Sbjct: 742 AAPTVQPGYVQPTPTQTGYDQSNPQPAGYAAVPPAAGAPAAYGKTVSPQPAAYAQYDSTQ 801

Query: 779 MYAAPR 784
           +Y APR
Sbjct: 802 VYGAPR 807

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538917|ref|XP_003537947.1| PREDICTED: uncharacterized protein LOC100786134 [Glycine max]

 Score =  652 bits (1681), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 433/806 (53%), Positives = 523/806 (64%), Gaps = 65/806 (8%)

Query: 16  DLKRKLDDLEPDEALEHAEGMRDDEAKNSDEVEKNVDGFAEAHGSEVKRPRLDDDKTEKP 75
           D KRKL+DL+P+ A  +A  + D  A N+D+   + +       +E KR RLDD +    
Sbjct: 17  DNKRKLEDLQPENAESNANSISD--AVNADDAAVSAE-------TENKRLRLDDHQ---- 63

Query: 76  DGPVNVNGLKEEK---PDEVVDAEQLTEDTTKEE-----ELESAEVKTEQHSSVEEQASV 127
           DG  N NG ++E+   P +  +     E+ T E      E  S E    + +S E     
Sbjct: 64  DGLANTNGHQDEQVAEPGKETEERSALENVTPEHDQTISEYPSLEATANEQTSAEISEPA 123

Query: 128 DNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEET-VKEEESVEPS--NV-VPQQV 183
           D+++  V++  +E   + EE   + ++++K+ T ++  +  K+  SV+ +  NV VP   
Sbjct: 124 DSKEPPVEDSGQE---NAEEPSKETQQQSKDSTEQDASSGDKQPNSVDTALHNVEVPYNK 180

Query: 184 VDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADP 243
            D S      ++ D   +RKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADP
Sbjct: 181 QDTSSGQKQPTSGDEITTRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADP 240

Query: 244 HAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVP 303
             ATR VE+IG+L +IDKAEKL+NAVIAEADAGGSPSLVARGL+ AQA+  +EQ++I+VP
Sbjct: 241 LCATRSVELIGSLESIDKAEKLMNAVIAEADAGGSPSLVARGLSPAQATVGSEQIQIQVP 300

Query: 304 NEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 363
           NEKVGLIIGR GETIK LQT+SGARIQLIPQHLPEGD SKER V+VTGD RQI+IAQE+I
Sbjct: 301 NEKVGLIIGRSGETIKSLQTKSGARIQLIPQHLPEGDDSKERTVQVTGDKRQIQIAQELI 360

Query: 364 KEVLSQTVRPSTLSGGFNQQAYR--PRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQN 421
           KEV++Q VRPS  SGGF QQA+        GPPQWG RGSH   P AYDY  RGP+P+ N
Sbjct: 361 KEVMNQPVRPS--SGGFGQQAHHPPRGGSGGPPQWGQRGSHFGHPTAYDYQHRGPFPAHN 418

Query: 422 PHYPHLPYGNYPPQQMAPRSNYG------------GPPNMQGAAGGYDYYGGQGGHVSDR 469
             Y   PYGNY PQ M PRS++G            GPP   G    Y    G GGH+SD 
Sbjct: 419 QPYAPAPYGNY-PQHMTPRSSFGSGWEQRPHHSFQGPPPHNGGYEYYG---GHGGHLSDA 474

Query: 470 PVSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAA-PQQGYGH 528
           P S    +S P + + P+  P+ GP P+Q NYNYGQP   +YGHQ  Y+ A  PQQGYG 
Sbjct: 475 PPSTQLPSSAPPYGAGPSPVPSMGPTPAQVNYNYGQPQGQDYGHQTTYSQAGLPQQGYGQ 534

Query: 529 GYD----DNHAPVQHPYGGHSNSQPVYSQGGLQSGY-HQHQYGKPP-YGMPAQGTQPQSY 582
           GYD    +N AP QH YGGH NSQ  Y Q G Q  Y    Q+GKPP YGMP+ G  PQSY
Sbjct: 535 GYDESKYENRAPTQHSYGGHVNSQSTYPQAGAQPNYPAPQQFGKPPLYGMPS-GQPPQSY 593

Query: 583 GPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQ 642
           GPPR  QPGD+ PYQ   P AQSYG N+P QQ YPYA SGP+Q  YPSYGSAPA D Y+ 
Sbjct: 594 GPPRATQPGDM-PYQGSTP-AQSYGTNMPTQQPYPYAVSGPSQTAYPSYGSAPATDGYSH 651

Query: 643 -PPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYG-QYTNTQQAYPEQPATSNA 700
            PPAS P Y Q A Q  P Y QP  Q A SY QV PT GYG  Y + Q +YPEQPA +NA
Sbjct: 652 PPPASFPPYTQPAAQ--PTYGQPAAQPAASYTQVGPT-GYGSSYPSLQPSYPEQPAPNNA 708

Query: 701 GYGYQGTQDPSYGS-SAPGSAYAAPTGQPGYAQPAATQPSYDQSASQSTAYGVAQGTAAA 759
            YGYQ  QDP Y + +AP  + A P+GQPGY QP  TQ  Y+QS +Q   Y     +A A
Sbjct: 709 VYGYQAPQDPGYSTGAAPAYSTAQPSGQPGYVQPTPTQTGYEQSNTQPAGYAAVPASAPA 768

Query: 760 GYGKTVSPQP-GYPQYDSTQMYAAPR 784
            YGKT+SPQP  YPQYDSTQ+Y APR
Sbjct: 769 AYGKTLSPQPAAYPQYDSTQVYGAPR 794

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224145055|ref|XP_002325510.1| predicted protein [Populus trichocarpa] gi|222862385|gb|EEE99891.1| predicted protein [Populus trichocarpa]

 Score =  646 bits (1667), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 397/591 (67%), Positives = 438/591 (74%), Gaps = 29/591 (4%)

Query: 210 KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAV 269
           +VGVLIGK GDTIRYLQYNSGAKIQITRD++AD  + TRPVE+IGTLS+I  AEKLINAV
Sbjct: 4   QVGVLIGKGGDTIRYLQYNSGAKIQITRDSEADSQSTTRPVELIGTLSSIRNAEKLINAV 63

Query: 270 IAEADAGGSPSLVARGLAT-AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGAR 328
           IAEADAGGSPSLVA GLA+ AQ +G  +Q+EI VPNEKVGLIIGRGGETIKGLQ +SGAR
Sbjct: 64  IAEADAGGSPSLVAMGLASGAQTAGVGDQLEIPVPNEKVGLIIGRGGETIKGLQAKSGAR 123

Query: 329 IQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPSTLSGGFN-QQAYRP 387
           IQLIPQHLPEGDGSKER VRVTGD RQ+E+A+EMI +V++QTVRPSTLS  FN QQ+YRP
Sbjct: 124 IQLIPQHLPEGDGSKERTVRVTGDKRQVEMAREMIMDVMNQTVRPSTLSSSFNQQQSYRP 183

Query: 388 RVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYGG-- 445
           R PTGP  WGPRG H +Q M YDY  RGPYPS    YP   YG+Y PQ MAPRSNY    
Sbjct: 184 RGPTGPAHWGPRGPHSNQKMPYDYQHRGPYPSHGSQYPPA-YGDY-PQHMAPRSNYSSGW 241

Query: 446 ---PPNMQGA---AGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQA 499
              P N+QG      GYDYY  QGGH SD PVS    T IPG  S  + AP  G PPSQ 
Sbjct: 242 EQRPANVQGPHTHTSGYDYY-SQGGHASDHPVSGPMPTPIPGPASRHSPAPVMGGPPSQV 300

Query: 500 NYNYGQPHTSEYGHQQPYAHAAP-QQGYGHGYDDNHAPVQHPYGGHSNSQPVYSQGGLQS 558
           NY+YGQ H  +YGHQ PY+ AAP  Q YGHGYD+     ++PY G+ +SQP YSQ G Q 
Sbjct: 301 NYSYGQSHGPDYGHQAPYSQAAPSHQSYGHGYDE----PKYPY-GYGSSQPAYSQAGNQP 355

Query: 559 GY-HQHQYGK-PPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNV--PHQQ 614
           GY  Q QYGK P +GMP+QG  PQSYGPPRPGQPGD+  YQ  + S+Q YGPN   P QQ
Sbjct: 356 GYGAQQQYGKQPSFGMPSQGPPPQSYGPPRPGQPGDM-SYQGPMQSSQLYGPNAPPPLQQ 414

Query: 615 QYPYATSGPTQQTYPSYGSAPAPDSYNQP-PASAPGYPQQAGQAVPNYPQPGGQQAPSYG 673
           QYPYA+SGP QQ YPSYGS    D YNQ   AS PGYPQQ GQ VP   QPGGQ A  Y 
Sbjct: 415 QYPYASSGPMQQPYPSYGSGSGSDGYNQAQTASGPGYPQQGGQPVPTPGQPGGQAAAGYA 474

Query: 674 QVAPTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQP 733
           Q  P  GYG Y + QQ YPEQ A +NAGYGYQG+QDP+YGS+    AY AP  Q GYAQP
Sbjct: 475 Q-GPAGGYGSYPSAQQGYPEQQAANNAGYGYQGSQDPAYGSAP---AYGAPASQQGYAQP 530

Query: 734 AATQPSYDQSASQSTAYGVAQGTAAAGYGKTVSPQPGYPQYDSTQMYAAPR 784
           A TQPSYDQS  QS  YG A  TA  GYGKTVSPQPGYPQYDSTQMYAAPR
Sbjct: 531 APTQPSYDQSVPQSAGYGAAPATAPVGYGKTVSPQPGYPQYDSTQMYAAPR 581

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447567|ref|XP_004141539.1| PREDICTED: uncharacterized protein LOC101203078 [Cucumis sativus] gi|449481514|ref|XP_004156205.1| PREDICTED: uncharacterized LOC101203078 [Cucumis sativus]

 Score =  621 bits (1601), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 422/815 (51%), Positives = 520/815 (63%), Gaps = 59/815 (7%)

Query: 1   MAEEEVLAPASAAA--ADLKRKLDDL--EPDEALE--HAEGMRDDEAKNSDEVEKNVDGF 54
           MAEE V+A  +A+    D KRKL DL  EP EA E  HAE +    A ++ +V  + +  
Sbjct: 1   MAEEVVVATGAASPEPLDHKRKLVDLDSEPTEATEENHAEPIEGSAAPDAADVPISDE-- 58

Query: 55  AEAHGSEVKRPRLDDDKTEKPDGPVNVNGLKEEKPDEVVDAEQLTEDTTKEEELESAEVK 114
                SE KRPRL+     KP+G  + NG +E+K +E+   E   + +++EE   S EV 
Sbjct: 59  -----SEYKRPRLEG----KPEGNASENGHEEKKEEELEPKEDYKQ-SSEEEPPASVEVL 108

Query: 115 TEQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVE 174
            E+  +  EQ + +  +    +++   +     A I  +++T+E++ KEE    E E+  
Sbjct: 109 PEKEGT--EQPTEEPHEAGDAQDSAAEISQDSAAEISQEDKTQELS-KEESQPSEVEAAP 165

Query: 175 PSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQ 234
           P   + ++ + N++ D PSS  ++T + K+EVPN+KVGVLIGKAGDTIRYLQYNSGAKIQ
Sbjct: 166 P---LQEEDISNAEQDQPSSESETT-TYKMEVPNSKVGVLIGKAGDTIRYLQYNSGAKIQ 221

Query: 235 ITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGA 294
           I RDA+ADP+  TRPVEIIGT  NI KAE+LINAVIAEADAGGSPSL+ARGL ++ +   
Sbjct: 222 IMRDAEADPNRLTRPVEIIGTSENIKKAEELINAVIAEADAGGSPSLIARGLTSSHSIAT 281

Query: 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMR 354
           AEQ++++VPNEKVGLIIGRGGETIK LQTRSGARIQLIPQ+LPEGD SKER +RVTGD +
Sbjct: 282 AEQIQLQVPNEKVGLIIGRGGETIKSLQTRSGARIQLIPQNLPEGDESKERTIRVTGDKK 341

Query: 355 QIEIAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQR 414
           QIEIA +MIKEV++QTVRPS  S GFNQQAYRPR P GP QWG RG HPS P  YDYP R
Sbjct: 342 QIEIATDMIKEVMNQTVRPSPHSTGFNQQAYRPRGPGGPTQWGHRGPHPSHPAGYDYPHR 401

Query: 415 GPYPSQNPHYPHLPYGNYPPQQMAPRSNYGG---------PPNMQGAAGGYDYYGGQGGH 465
           GPYPS N  Y H  YGNYP Q   PRS+YG                ++GGYDYY GQ  H
Sbjct: 402 GPYPSHNTQYQHPGYGNYPQQMGGPRSSYGSGWEQRPPPSMQGPPPSSGGYDYY-GQRSH 460

Query: 466 VSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQG 525
            SD P S     ++P H   P+ AP  GPP +Q++YNY Q     YGH  PY+ AAP Q 
Sbjct: 461 YSDAPPS-HFPGAMPSHAPGPSPAPTHGPPQTQSSYNYNQQQGQGYGHTAPYSQAAPHQS 519

Query: 526 YGHGYD---DNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPP--YGMPAQGTQPQ 580
           YGHGY+   D+HAP Q+PY GH N+Q  Y Q G Q  Y   QY   P  YG+  QG  PQ
Sbjct: 520 YGHGYEQKYDHHAPAQNPYSGHGNAQ-HYPQAGTQQVYPGQQYDNKPSSYGVSQQGPPPQ 578

Query: 581 SYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSY 640
           SYG PR GQP +  PYQ     A +YG N+  QQ YPY + G TQQ YP YG+AP+ D Y
Sbjct: 579 SYGAPRVGQPAE--PYQGGSAPA-TYGQNMQPQQTYPYQSGGSTQQ-YPPYGAAPSTDGY 634

Query: 641 NQ--PPASAPGYPQQAGQAVPNYPQPGGQQAPSYG-QVAPTAGYGQYTNTQQAYPEQ--P 695
           NQ    ++A GY QQ  QA   Y QP  QQ  +YG QVAP A YGQY  +QQ Y EQ   
Sbjct: 635 NQAPAASAAAGYSQQGAQA--GYGQPSVQQPSAYGQQVAPAAAYGQYPTSQQGYSEQAAA 692

Query: 696 ATSNAGYGYQGTQDP----SYGSSAPGSAYAAPTGQPGYAQPAATQPSYDQSASQSTAYG 751
            T+     YQ  QDP       ++A  +  A  +GQ GY Q  ATQP+YDQS  QS  YG
Sbjct: 693 NTAAGYAAYQAPQDPAAYSGGTAAAAAAYTAPASGQQGYTQQTATQPTYDQSIQQSGGYG 752

Query: 752 VAQGTAAAGYGKTVS--PQPGYPQYDSTQMYAAPR 784
               +A  GYGK+VS  PQPGYPQYDSTQ+Y A R
Sbjct: 753 TVPSSAPVGYGKSVSPQPQPGYPQYDSTQVYGASR 787

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145336377|ref|NP_174629.3| far upstream element-binding protein [Arabidopsis thaliana] gi|110739541|dbj|BAF01679.1| putative single-strand nucleic acid-binding protein [Arabidopsis thaliana] gi|110739658|dbj|BAF01737.1| putative single-strand nucleic acid-binding protein [Arabidopsis thaliana] gi|110739944|dbj|BAF01877.1| putative single-strand nucleic acid-binding protein [Arabidopsis thaliana] gi|332193492|gb|AEE31613.1| far upstream element-binding protein [Arabidopsis thaliana]

 Score =  474 bits (1221), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 372/836 (44%), Positives = 448/836 (53%), Gaps = 153/836 (18%)

Query: 1   MAEEEVLAPASAAAADLKRKLDDLEPDEALE--HAEGMRDDEAKNSDEVEKNVDGFAEAH 58
           MAEEEV+A      +D KRKL++LE  E LE  HA  + +D + + D   KN   + +  
Sbjct: 1   MAEEEVIA-IPVQPSDHKRKLENLE-SEILEQQHAGSIDNDVSVDDD---KNASDYCQP- 54

Query: 59  GSEVKRPRLDDDK----------------------TEKPDGPVNVNGLKE---EKPDEVV 93
               KRP+LDD+                       TEKP    + N       EK  E +
Sbjct: 55  ----KRPKLDDEAVDGLGIGGTVENSGDVESKEEGTEKPIAQSDENQDGNPLIEKVQETI 110

Query: 94  DAEQ---LTEDTTKEEE--LESAEVKTEQHSSVEEQASVD-----NQQISVKEETKEVLF 143
           DAE+     ED  K E+  L + EV T Q  SVEE   V+     N+     +ET +V+ 
Sbjct: 111 DAEESDNKMEDNGKPEDNQLVTPEVVTSQDVSVEESKEVNISGSQNEGEDDSKETNDVVA 170

Query: 144 STEEAFIDVKEETKEVT----VKEEETVKEEESVEPSNVVPQ-QVVDNSKSDDPSST--- 195
             E     V+  +KEVT     KE+E     ES E +  V   ++ D SK  +  ST   
Sbjct: 171 QKE-----VENGSKEVTDCDSQKEDEANAGGESKEVNGSVSHDEIGDESKEVNGGSTHKE 225

Query: 196 --DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEII 253
             D  + +R+I+VP++KVG LIGK G+ +RYLQ NSGAKIQI RDA+ADP +A RPVEII
Sbjct: 226 VDDTQSTTRRIDVPSSKVGTLIGKGGEMVRYLQVNSGAKIQIRRDAEADPSSALRPVEII 285

Query: 254 GTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGR 313
           GT+S I+KAEKLINAVIAE +AGG P+L ARG+         EQ+EIKVP++KVG+IIGR
Sbjct: 286 GTVSCIEKAEKLINAVIAEVEAGGVPALAARGVP--------EQMEIKVPSDKVGVIIGR 337

Query: 314 GGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRP 373
           GGETIK +QT+S ARIQLIPQ+  EGD SKER VR++GD RQI+IA  +IK+V+ Q  RP
Sbjct: 338 GGETIKNMQTKSRARIQLIPQN--EGDASKERTVRISGDKRQIDIATALIKDVMYQDGRP 395

Query: 374 STLSGGFNQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYP 433
           S  SGGFNQQAY+PR P GPPQWG RG H    M Y+Y   GPYPSQ  H+     G YP
Sbjct: 396 SPYSGGFNQQAYQPRGPGGPPQWGSRGPHGPHSMPYNYHHGGPYPSQGSHFRPPNSGGYP 455

Query: 434 PQQMAPRSNYGG-----PPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQ 488
           PQ M PRS YG      PP+    +G YDYYG QGG                       Q
Sbjct: 456 PQHMPPRSGYGSGWEQRPPH----SGPYDYYGRQGG-----------------------Q 488

Query: 489 APAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNH--APVQH------- 539
            P  GP PS               H   Y+ A  QQ YG  YD  H   P  H       
Sbjct: 489 NP--GPVPS---------------HGASYSQAGAQQTYGQMYDQPHYDNPPMHQSYGGYG 531

Query: 540 ------PYGGHSN-----SQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQ--SYGP-P 585
                 P  G  +     S+P   QG  + GY   +   PP  +P QG  P   SYG  P
Sbjct: 532 GSQQGYPSAGGQHQMQQPSRPYGMQGSAEQGYGPPRPAAPPGDVPYQGPTPAAPSYGSTP 591

Query: 586 RPGQPGDIP--PYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYN-- 641
                G  P  P     P+A SYG N+  QQQY YA+S PTQQTYPSY SA   D YN  
Sbjct: 592 AAASYGSTPAAPSYGSTPAAPSYGSNMAQQQQYGYASSAPTQQTYPSYSSAAPSDGYNGT 651

Query: 642 QPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSNAG 701
           QPPA AP Y Q   Q      Q  G     YGQV PT GY  Y +TQ AY   PA SN  
Sbjct: 652 QPPAVAPAYEQHGAQPASGVQQTSG----GYGQVPPTGGYSSYPSTQPAYGNTPAQSNGN 707

Query: 702 YGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAATQPSYDQSASQSTAYGVAQGTA 757
           YGY G+Q PSYG     SAYAAPTGQ  Y+Q A  Q  Y+QSA+QS  Y  A GTA
Sbjct: 708 YGYIGSQYPSYGGGN-ASAYAAPTGQTAYSQTAPPQAGYEQSATQSAGYAAAPGTA 762

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22328551|ref|NP_192745.2| KH domain-containing protein [Arabidopsis thaliana] gi|332657435|gb|AEE82835.1| KH domain-containing protein [Arabidopsis thaliana]

 Score =  473 bits (1216), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 362/813 (44%), Positives = 464/813 (57%), Gaps = 117/813 (14%)

Query: 1   MAEEEVLAPASAAAADLKRKLDDLEP-----DEALEHAEGMRDDEAKNSDEVEKNVD-GF 54
           M EE+ +   S    DLKRKLD++E      D++ + ++  +   AK  DE +  +D G 
Sbjct: 1   MTEEDFVV-ISTPPVDLKRKLDEVELNGNIVDDSNQTSDSSQAKRAKLEDEAQDGLDYGN 59

Query: 55  AEAHGS--EVKRPRLDDDKTEKPDGPVNVNGLKEEKPDEVVDAEQLTEDTTKEEELESAE 112
            + +GS  EVK    ++++ ++P         KEE  D V   E++ +D    +E E+  
Sbjct: 60  TQENGSSMEVK----EEEQLQEP---------KEENQDSVPLVEEV-QDPIHADESENKI 105

Query: 113 VKTEQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEES 172
              +Q +  ++    DNQQ  +++    V     +  ID  +++KEV     +   +EE+
Sbjct: 106 CSVDQPTD-DQVKPEDNQQGCIED----VNGGEHQKVID--DDSKEVNDGSSQENGKEEN 158

Query: 173 VEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAK 232
            E      Q+ VD ++S           +R+I+VP++KVGVLIGK G+TIRYLQ+NSGAK
Sbjct: 159 KEVDGEKSQKEVDGTQS----------TTRRIDVPSSKVGVLIGKGGETIRYLQFNSGAK 208

Query: 233 IQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQAS 292
           IQI RD++ADP +A RPVEIIG+++ I+ AEKLI+AVIAEA+AGGSP+LVARG  +  A 
Sbjct: 209 IQILRDSEADPSSALRPVEIIGSVACIESAEKLISAVIAEAEAGGSPALVARGHPSTHAI 268

Query: 293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD 352
           G  EQ+EIKVPN+KVGLIIGRGGETIK +QTRSGAR QLIPQH  EGDG KER VR++GD
Sbjct: 269 GIPEQIEIKVPNDKVGLIIGRGGETIKNMQTRSGARTQLIPQHA-EGDGLKERTVRISGD 327

Query: 353 MRQIEIAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYP 412
             QI+IA +MIK+V++Q  RPS+ SGG+NQ AYRP+ P GPPQWG RG H   P  YDY 
Sbjct: 328 KMQIDIATDMIKDVMNQNARPSSYSGGYNQPAYRPQGPGGPPQWGSRGPHAPHP--YDYH 385

Query: 413 QRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYGGPPNMQ-GAAGGYDYYGGQGGHVSDRPV 471
            RGPY SQ  +Y    +G YPPQ M PR  YG   + +   +G Y+YYG QG   +    
Sbjct: 386 PRGPYSSQGSYYNSPGFGGYPPQHMPPRGGYGTDWDQRPPYSGPYNYYGRQGAQSAGPVP 445

Query: 472 SVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYD 531
             S     P           GGPP SQ +Y YGQ H  EYGH  PY+    QQ YG  Y+
Sbjct: 446 PPSGPVPSPAF---------GGPPLSQVSYGYGQSHGPEYGHAAPYSQTGYQQTYGQTYE 496

Query: 532 ----DNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQY-GKPPYGMPAQGTQPQSYGPPR 586
               D++ P+Q PYGG   S P    GG QSGY+Q Q  G  PYGM  QG   Q YGPP+
Sbjct: 497 QPKYDSNPPMQPPYGG---SYP--PAGGGQSGYYQMQQPGVRPYGM-QQGPVQQGYGPPQ 550

Query: 587 P---GQPGDIPPYQSQVPSAQSYGPN--VPHQQQYPYATS-GPT-QQTYPSYGSAPAPDS 639
           P      GD+ PYQ   P+A SYG     P QQQY Y +S GP  QQTYPSY SAP  D+
Sbjct: 551 PAAAASSGDV-PYQGATPAAPSYGSTNMAPQQQQYGYTSSDGPVQQQTYPSYSSAPPSDA 609

Query: 640 YN---QPPASAPGYPQQAGQ-AVPNY---PQPGGQQAPSYGQVAPTAGYGQYTNTQQAYP 692
           YN   Q PA+ P Y QQ+ Q A   Y          A   GQVAPT GY         YP
Sbjct: 610 YNNGTQTPATGPAYQQQSVQPASSTYDQTGAQQAAAAGYGGQVAPTGGY--------TYP 661

Query: 693 EQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAATQPSYDQS-ASQSTAYG 751
                         T  P+YGS A             Y+Q A TQ  Y+Q  A+Q+  Y 
Sbjct: 662 --------------TSQPAYGSQA------------AYSQAAPTQTGYEQQPATQAAVYA 695

Query: 752 VAQGTAAAGYGKTVSPQPGYPQYDSTQMYAAPR 784
            A GTA     KT SPQ  Y QYD++Q+YA PR
Sbjct: 696 TAPGTAPV---KTQSPQSAYAQYDASQVYATPR 725

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297813443|ref|XP_002874605.1| KH domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297320442|gb|EFH50864.1| KH domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  466 bits (1198), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 377/822 (45%), Positives = 451/822 (54%), Gaps = 130/822 (15%)

Query: 1   MAEEEVLAPASAAAADLKRKLDDLEPDEALEHAEGMRDDEAKNSDEVEKNVDGFAEAHGS 60
           MAEEEV+   S    DLKRKLD+       +HA         N D V   VD    +  S
Sbjct: 1   MAEEEVVV-ISTPPVDLKRKLDE-------QHA-------GSNGDIV---VDSNPVSDSS 42

Query: 61  EVKRPRLDDDKTEKPDGPVNVNGLKEEKPDEVVDAEQLTEDTTKEEELESA----EVKTE 116
           + KR +LDD   E  DG  + N  +     EV + EQL E   K E  +S     EV+  
Sbjct: 43  QAKRAKLDD---EAQDGLDHGNTQENGSSMEVKEEEQLQE--PKYENQDSVPLVDEVQDP 97

Query: 117 QHSSVEEQASVD-------------NQQISVK----EETKEVLFSTEEAFIDVKEETKEV 159
            H++  E  + D             NQQ  ++    EE K V  +  E   +V EE K  
Sbjct: 98  IHANESENNTCDVAHAADDHVKPEDNQQGCIENNNVEECKNV--NGGEPQKEVDEEIK-- 153

Query: 160 TVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAG 219
            + +  + KE + V+  N        + + DD  ST     +R I+VPN+KVGVLIGK G
Sbjct: 154 VLNDGNSQKEIKEVDGEN-------SHKEVDDTQST-----TRTIDVPNSKVGVLIGKGG 201

Query: 220 DTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSP 279
           +TIRYLQ+NSGAKIQI RD++ADP++A RPVEIIGT++ I+ AE+LI+AVIAEA+AGGSP
Sbjct: 202 ETIRYLQFNSGAKIQILRDSEADPNSALRPVEIIGTVACIENAERLISAVIAEAEAGGSP 261

Query: 280 SLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEG 339
           +LVARG  +  A G  EQ+EIKVPN+KVGLIIGRGGETIK +QTRSGARIQLIPQH  EG
Sbjct: 262 ALVARGHPSTHAIGIPEQIEIKVPNDKVGLIIGRGGETIKDMQTRSGARIQLIPQHA-EG 320

Query: 340 DGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPR 399
           DG KER VR++GD  QI+IA +MIK+V++Q  RPS  SG +NQ AYRPR P GPPQWG R
Sbjct: 321 DGLKERTVRISGDKMQIDIATDMIKDVMNQNARPSPYSGCYNQPAYRPRGPGGPPQWGSR 380

Query: 400 GSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYG-GPPNMQGAAGGYDY 458
           G H   P  YDY  RGPY SQ  HY    YG YPPQ M PR  YG G       +G Y+Y
Sbjct: 381 GPHAPHP--YDYHPRGPYSSQGSHYNSPGYGGYPPQHMPPRGGYGPGWDQRPPYSGPYNY 438

Query: 459 YGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYA 518
           YG QG   S  PV         GH   PA    GGPPPSQ +Y Y Q H  EYG+  PY+
Sbjct: 439 YGRQGAQ-SSGPVPPPS-----GHVPSPA---LGGPPPSQVSYGYRQSHGPEYGNAAPYS 489

Query: 519 HAAPQQGYGHGYD----DNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQY-GKPPYGMP 573
               QQ YG  Y+    DN+ P+Q PYGG   S P    GG Q GY Q Q  G  PYGM 
Sbjct: 490 QTGYQQTYGQTYEQPKYDNNPPMQPPYGG---SYP--PAGGGQPGYSQMQQPGVRPYGM- 543

Query: 574 AQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPN--VPHQQQYPY-ATSGPT-QQTYP 629
            QG   Q YGPPRP       PYQ   P+A  YG     P QQQY Y +T GP  QQTYP
Sbjct: 544 QQGPVQQGYGPPRPAASSGDVPYQGATPAAAPYGSTNMAPQQQQYGYTSTGGPVQQQTYP 603

Query: 630 SYGSAPAPDSYN---QPPASAPGYPQQAGQAVPN----YPQPGGQQAPSYGQVAPTAGYG 682
           SY SAP  D YN   Q PA+ P Y QQ+ Q   +            A   GQVAPT GY 
Sbjct: 604 SYSSAPPSDGYNNGTQTPATGPAYQQQSVQPASSTHDQTGAQQAAAAGYGGQVAPTGGYS 663

Query: 683 QYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAATQPSYDQ 742
            Y  TQ                     P+YGS A  +   A   Q GY Q  ATQP+   
Sbjct: 664 SYPTTQ---------------------PAYGSQA--AYSQAAATQVGYEQQPATQPA--- 697

Query: 743 SASQSTAYGVAQGTAAAGYGKTVSPQPGYPQYDSTQMYAAPR 784
                  Y    G+A     KT SP   Y QY+++Q+YAAPR
Sbjct: 698 ------GYAATPGSAQV---KTQSPLSAYAQYEASQVYAAPR 730

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	784
TAIR|locus:2140513	725	AT4G10070 "AT4G10070" [Arabido	0.307	0.332	0.663	5.7e-123
TAIR|locus:2012713	763	AT1G33680 "AT1G33680" [Arabido	0.571	0.587	0.432	5e-89
TAIR|locus:2043530	632	AT2G25970 "AT2G25970" [Arabido	0.600	0.745	0.355	9.7e-64
RGD|621828	721	Khsrp "KH-type splicing regula	0.280	0.305	0.290	5.3e-25
UNIPROTKB|F6Y140	602	KHSRP "Uncharacterized protein	0.280	0.365	0.286	6.8e-25
UNIPROTKB|E2QVT3	743	KHSRP "Uncharacterized protein	0.280	0.296	0.286	1.6e-24
MGI|MGI:1336214	748	Khsrp "KH-type splicing regula	0.280	0.294	0.290	1.2e-22
UNIPROTKB|F1MHR6	708	LOC505564 "Uncharacterized pro	0.280	0.310	0.286	2.1e-22
UNIPROTKB|Q92945	711	KHSRP "Far upstream element-bi	0.280	0.309	0.286	2.1e-22
ZFIN|ZDB-GENE-040426-2159	642	fubp1 "far upstream element (F	0.281	0.344	0.332	1.1e-23

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

 Score = 839 (300.4 bits), Expect = 5.7e-123, Sum P(3) = 5.7e-123
 Identities = 162/244 (66%), Positives = 195/244 (79%)

Query:   201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNID 260
             +R+I+VP++KVGVLIGK G+TIRYLQ+NSGAKIQI RD++ADP +A RPVEIIG+++ I+
Sbjct:   177 TRRIDVPSSKVGVLIGKGGETIRYLQFNSGAKIQILRDSEADPSSALRPVEIIGSVACIE 236

Query:   261 KAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKG 320
              AEKLI+AVIAEA+AGGSP+LVARG  +  A G  EQ+EIKVPN+KVGLIIGRGGETIK 
Sbjct:   237 SAEKLISAVIAEAEAGGSPALVARGHPSTHAIGIPEQIEIKVPNDKVGLIIGRGGETIKN 296

Query:   321 LQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPSTLSGGF 380
             +QTRSGAR QLIPQH  EGDG KER VR++GD  QI+IA +MIK+V++Q  RPS+ SGG+
Sbjct:   297 MQTRSGARTQLIPQHA-EGDGLKERTVRISGDKMQIDIATDMIKDVMNQNARPSSYSGGY 355

Query:   381 NQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPR 440
             NQ AYRP+ P GPPQWG RG H   P  YDY  RGPY SQ  +Y    +G YPPQ M PR
Sbjct:   356 NQPAYRPQGPGGPPQWGSRGPHAPHP--YDYHPRGPYSSQGSYYNSPGFGGYPPQHMPPR 413

Query:   441 SNYG 444
               YG
Sbjct:   414 GGYG 417

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 = 858 (307.1 bits), Expect = 5.0e-89, Sum P(2) = 5.0e-89
 Identities = 209/483 (43%), Positives = 239/483 (49%)

Query:   283 ARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGS 342
             A G+    A G  EQ+EIKVP++KVG+IIGRGGETIK +QT+S ARIQLIPQ+  EGD S
Sbjct:   307 AGGVPALAARGVPEQMEIKVPSDKVGVIIGRGGETIKNMQTKSRARIQLIPQN--EGDAS 364

Query:   343 KERIVRVTGDMRQIEIAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPRGSH 402
             KER VR++GD RQI+IA  +IK+V+ Q  RPS  SGGFNQQAY+PR P GPPQWG RG H
Sbjct:   365 KERTVRISGDKRQIDIATALIKDVMYQDGRPSPYSGGFNQQAYQPRGPGGPPQWGSRGPH 424

Query:   403 PSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYGGPPNMXXXXXXXXXXXXX 462
                 M Y+Y   GPYPSQ  H+     G YPPQ M PRS YG                  
Sbjct:   425 GPHSMPYNYHHGGPYPSQGSHFRPPNSGGYPPQHMPPRSGYGSGWEQRPPHSGPYDYYGR 484

Query:   463 XXHVSDRPVSVSHSTSIPGHXXXXXXXXXXXXXXXXXNYNYGQPHTSEYXXXXXXXXXXX 522
                 +  PV  SH  S                        Y QPH   Y           
Sbjct:   485 QGGQNPGPVP-SHGASY-----------SQAGAQQTYGQMYDQPH---YDNPPMHQSYGG 529

Query:   523 XXXXGHGYDDNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQ-- 580
                   GY    A  QH       S+P   QG  + GY   +   PP  +P QG  P   
Sbjct:   530 YGGSQQGYPS--AGGQHQM--QQPSRPYGMQGSAEQGYGPPRPAAPPGDVPYQGPTPAAP 585

Query:   581 SYXXXXXXXXXXXX----XYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPA 636
             SY                 Y S  P+A SYG N+  QQQY YA+S PTQQTYPSY SA  
Sbjct:   586 SYGSTPAAASYGSTPAAPSYGS-TPAAPSYGSNMAQQQQYGYASSAPTQQTYPSYSSAAP 644

Query:   637 PDSYN--QPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQ 694
              D YN  QPPA AP Y Q   Q      Q  G     YGQV PT GY  Y +TQ AY   
Sbjct:   645 SDGYNGTQPPAVAPAYEQHGAQPASGVQQTSG----GYGQVPPTGGYSSYPSTQPAYGNT 700

Query:   695 PATSNAGYGYQGTQDXXXXXXXXXXXXXXXTGQPGYAQPAATQPSYDQSASQSTAYGVAQ 754
             PA SN  YGY G+Q                TGQ  Y+Q A  Q  Y+QSA+QS  Y  A 
Sbjct:   701 PAQSNGNYGYIGSQ-YPSYGGGNASAYAAPTGQTAYSQTAPPQAGYEQSATQSAGYAAAP 759

Query:   755 GTA 757
             GTA
Sbjct:   760 GTA 762

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

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

 Score = 650 (233.9 bits), Expect = 9.7e-64, P = 9.7e-64
 Identities = 179/503 (35%), Positives = 240/503 (47%)

Query:   201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNID 260
             ++KI++PN +VGV+IGK G+TI+YLQ  SGAKIQ+TRD DADP+ ATR V++ GT   I 
Sbjct:   135 TKKIDIPNMRVGVIIGKGGETIKYLQLQSGAKIQVTRDMDADPNCATRTVDLTGTPDQIS 194

Query:   261 KAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKG 320
             KAE+LI  V+ EA+AG +      G         A+Q  +K+PN KVGLIIG+GGETIK 
Sbjct:   195 KAEQLITDVLQEAEAGNTAGSGGGGGRRMGGQAGADQFVMKIPNNKVGLIIGKGGETIKS 254

Query:   321 LQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS--QTVRPSTLSG 378
             +Q ++GARIQ+IP HLP GD + ER +++ G   QIE A++++ E++S    +R S + G
Sbjct:   255 MQAKTGARIQVIPLHLPPGDPTPERTLQIDGITEQIEHAKQLVNEIISGENRMRNSAMGG 314

Query:   379 GFNQQA-YRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQM 437
             G+ QQ  Y+ R P+    W P G  P+QP    Y Q G YP   P Y   PYG+YP Q  
Sbjct:   315 GYPQQGGYQARPPSS---WAPPGGPPAQPGYGGYMQPGAYPGP-PQYGQSPYGSYPQQTS 370

Query:   438 APRSNYGG-PPNMXXXXXXXXXXXXXXXHVSDRPVSVSHSTSIPGHXXXXXXXXXXXXXX 496
             A   +    PP+                       S +  T   G+              
Sbjct:   371 AGYYDQSSVPPSQQSAQGEYDYYGQQQSQQPSSGGSSAPPTDTTGYNYYQHASGYGQAGQ 430

Query:   497 XXXNYNYGQPHTSEYXXXXXXXXXXXXXXXGHGYDDNHAPVQHPYGGHSNSQPVYSQGGL 556
                   YG  + S+                G+G   N  P Q      + + P  +Q G 
Sbjct:   431 GYQQDGYGAYNASQQSGYGQAAGYDQQG--GYGSTTN--PSQEEDASQA-APPSSAQSG- 484

Query:   557 QSGYHQHQYGKPPYGMPAQGTQPQSYXXXXXXXXXXXXXYQSQVPSAQSYGPNVPHQQQY 616
             Q+GY     G+ P   PAQG+  Q+              Y SQ  +A + G   P     
Sbjct:   485 QAGYGTT--GQQP---PAQGSTGQA---GYGAPPTSQAGYSSQPAAAYNSGYGAPPPASK 536

Query:   617 PYATSGPTQQT--YP-SYGSA-----PAPDSYNQPPASAPGYPQQAGQAVPNYPQPG-GQ 667
             P  T G +QQ+   P SYGS      PA   Y QPPA   G   Q   +   Y QP  G 
Sbjct:   537 P-PTYGQSQQSPGAPGSYGSQSGYAQPAASGYGQPPAYGYGQAPQGYGSYGGYTQPAAGG 595

Query:   668 QAPSYGQVAPTAGYGQYTNTQQA 690
                S G    TAG G  T   Q+
Sbjct:   596 GYSSDGSAGATAGGGGGTPASQS 618

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

RGD|621828 Khsrp "KH-type splicing regulatory protein" [Rattus norvegicus (taxid:10116)]

 Score = 256 (95.2 bits), Expect = 5.3e-25, Sum P(2) = 5.3e-25
 Identities = 70/241 (29%), Positives = 118/241 (48%)

Query:   204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAE 263
             + VP + VGV+IG++G+ I+ +Q ++G +IQ  +D    P    +   I+G     + A 
Sbjct:   328 VPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE---KIAHIMGPPDRCEHAA 384

Query:   264 KLINAVIAEADAG-----GSPSLVARGLATAQASG----AAEQVEIKVPNEKVGLIIGRG 314
             ++IN ++    +G     G+P +   G    +  G       ++   +P  K GL+IGRG
Sbjct:   385 RIINDLLQSLRSGPPGPPGAPGMPPGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLVIGRG 444

Query:   315 GETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPS 374
             GE +K +  ++GA +++  Q  P GD + +  V + G  +QI+ A+++I+E +   + P 
Sbjct:   445 GENVKAINQQTGAFVEISRQLPPNGDPNFKLFV-IRGSPQQIDHAKQLIEEKIEGPLCPV 503

Query:   375 TLSGGFNQQAYRPRVP--TGPPQWGPRGS--HPSQPMAYDYPQRG---PYPSQNPHYPHL 427
                 G    A  P  P   GP   GP G+  H   P  + YP +G    YP   P  PH 
Sbjct:   504 GPGPGGPGPA-GPMGPFHPGPFNQGPPGAPPHAGGPPPHQYPPQGWGNTYPEWQPPAPHD 562

Query:   428 P 428
             P
Sbjct:   563 P 563

GO:0003677 "DNA binding" evidence=IEA

GO:0003730 "mRNA 3'-UTR binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=IEA

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

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=ISO

GO:0030425 "dendrite" evidence=IDA

GO:0043025 "neuronal cell body" evidence=IDA

GO:0051028 "mRNA transport" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

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

 Score = 254 (94.5 bits), Expect = 6.8e-25, Sum P(2) = 6.8e-25
 Identities = 69/241 (28%), Positives = 117/241 (48%)

Query:   204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAE 263
             + VP + VGV+IG++G+ I+ +Q ++G +IQ  +D    P    +   I+G     + A 
Sbjct:   183 VPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE---KIAHIMGPPDRCEHAA 239

Query:   264 KLINAVIAEADAG-----GSPSLVARGLATAQASG----AAEQVEIKVPNEKVGLIIGRG 314
             ++IN ++    +G     G P +   G    +  G       ++   +P  K GL+IGRG
Sbjct:   240 RIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLVIGRG 299

Query:   315 GETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPS 374
             GE +K +  ++GA +++  Q  P GD + +  + + G  +QI+ A+++I+E +   + P 
Sbjct:   300 GENVKAINQQTGAFVEISRQLPPNGDPNFKLFI-IRGSPQQIDHAKQLIEEKIEGPLCPV 358

Query:   375 TLSGGFNQQAYRPRVP--TGPPQWGPRGS--HPSQPMAYDYPQRG---PYPSQNPHYPHL 427
                 G    A  P  P   GP   GP G+  H   P  + YP +G    YP   P  PH 
Sbjct:   359 GPGPGGPGPA-GPMGPFNPGPFNQGPPGAPPHAGGPPPHQYPPQGWGNTYPQWQPPAPHD 417

Query:   428 P 428
             P
Sbjct:   418 P 418

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|E2QVT3 KHSRP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 254 (94.5 bits), Expect = 1.6e-24, Sum P(2) = 1.6e-24
 Identities = 69/241 (28%), Positives = 117/241 (48%)

Query:   204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAE 263
             + VP + VGV+IG++G+ I+ +Q ++G +IQ  +D    P    +   I+G     + A 
Sbjct:   324 VPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE---KIAHIMGPPDRCEHAA 380

Query:   264 KLINAVIAEADAG-----GSPSLVARGLATAQASG----AAEQVEIKVPNEKVGLIIGRG 314
             ++IN ++    +G     G P +   G    +  G       ++   +P  K GL+IGRG
Sbjct:   381 RIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLVIGRG 440

Query:   315 GETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPS 374
             GE +K +  ++GA +++  Q  P GD + +  + + G  +QI+ A+++I+E +   + P 
Sbjct:   441 GENVKAINQQTGAFVEISRQLPPNGDPNFKLFI-IRGSPQQIDHAKQLIEEKIEGPLCPV 499

Query:   375 TLSGGFNQQAYRPRVP--TGPPQWGPRGS--HPSQPMAYDYPQRG---PYPSQNPHYPHL 427
                 G    A  P  P   GP   GP G+  H   P  + YP +G    YP   P  PH 
Sbjct:   500 GPGPGGPGPA-GPMGPFNPGPFNQGPPGAPPHAGGPPPHQYPPQGWGNTYPQWQPPAPHD 558

Query:   428 P 428
             P
Sbjct:   559 P 559

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

MGI|MGI:1336214 Khsrp "KH-type splicing regulatory protein" [Mus musculus (taxid:10090)]

 Score = 256 (95.2 bits), Expect = 1.2e-22, Sum P(2) = 1.2e-22
 Identities = 70/241 (29%), Positives = 118/241 (48%)

Query:   204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAE 263
             + VP + VGV+IG++G+ I+ +Q ++G +IQ  +D    P    +   I+G     + A 
Sbjct:   328 VPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE---KIAHIMGPPDRCEHAA 384

Query:   264 KLINAVIAEADAG-----GSPSLVARGLATAQASG----AAEQVEIKVPNEKVGLIIGRG 314
             ++IN ++    +G     G+P +   G    +  G       ++   +P  K GL+IGRG
Sbjct:   385 RIINDLLQSLRSGPPGPPGAPGMPPGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLVIGRG 444

Query:   315 GETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPS 374
             GE +K +  ++GA +++  Q  P GD + +  V + G  +QI+ A+++I+E +   + P 
Sbjct:   445 GENVKAINQQTGAFVEISRQLPPNGDPNFKLFV-IRGSPQQIDHAKQLIEEKIEGPLCPV 503

Query:   375 TLSGGFNQQAYRPRVP--TGPPQWGPRGS--HPSQPMAYDYPQRG---PYPSQNPHYPHL 427
                 G    A  P  P   GP   GP G+  H   P  + YP +G    YP   P  PH 
Sbjct:   504 GPGPGGPGPA-GPMGPFNPGPFNQGPPGAPPHAGGPPPHQYPPQGWGNTYPQWQPPAPHD 562

Query:   428 P 428
             P
Sbjct:   563 P 563

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003730 "mRNA 3'-UTR binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

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

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0030425 "dendrite" evidence=ISO

GO:0043025 "neuronal cell body" evidence=ISO

GO:0051028 "mRNA transport" evidence=IEA

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

 Score = 254 (94.5 bits), Expect = 2.1e-22, Sum P(2) = 2.1e-22
 Identities = 69/241 (28%), Positives = 117/241 (48%)

Query:   204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAE 263
             + VP + VGV+IG++G+ I+ +Q ++G +IQ  +D    P    +   I+G     + A 
Sbjct:   288 VPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE---KIAHIMGPPDRCEHAA 344

Query:   264 KLINAVIAEADAG-----GSPSLVARGLATAQASG----AAEQVEIKVPNEKVGLIIGRG 314
             ++IN ++    +G     G P +   G    +  G       ++   +P  K GL+IGRG
Sbjct:   345 RIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLVIGRG 404

Query:   315 GETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPS 374
             GE +K +  ++GA +++  Q  P GD + +  + + G  +QI+ A+++I+E +   + P 
Sbjct:   405 GENVKAINQQTGAFVEISRQLPPNGDPNFKLFI-IRGSPQQIDHAKQLIEEKIEGPLCPV 463

Query:   375 TLSGGFNQQAYRPRVP--TGPPQWGPRGS--HPSQPMAYDYPQRG---PYPSQNPHYPHL 427
                 G    A  P  P   GP   GP G+  H   P  + YP +G    YP   P  PH 
Sbjct:   464 GPGPGGPGPA-GPMGPFNPGPFNQGPPGAPPHAGGPPPHQYPPQGWGNTYPQWQPPAPHD 522

Query:   428 P 428
             P
Sbjct:   523 P 523

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q92945 KHSRP "Far upstream element-binding protein 2" [Homo sapiens (taxid:9606)]

 Score = 254 (94.5 bits), Expect = 2.1e-22, Sum P(2) = 2.1e-22
 Identities = 69/241 (28%), Positives = 117/241 (48%)

Query:   204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAE 263
             + VP + VGV+IG++G+ I+ +Q ++G +IQ  +D    P    +   I+G     + A 
Sbjct:   327 VPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE---KIAHIMGPPDRCEHAA 383

Query:   264 KLINAVIAEADAG-----GSPSLVARGLATAQASG----AAEQVEIKVPNEKVGLIIGRG 314
             ++IN ++    +G     G P +   G    +  G       ++   +P  K GL+IGRG
Sbjct:   384 RIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLVIGRG 443

Query:   315 GETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPS 374
             GE +K +  ++GA +++  Q  P GD + +  + + G  +QI+ A+++I+E +   + P 
Sbjct:   444 GENVKAINQQTGAFVEISRQLPPNGDPNFKLFI-IRGSPQQIDHAKQLIEEKIEGPLCPV 502

Query:   375 TLSGGFNQQAYRPRVP--TGPPQWGPRGS--HPSQPMAYDYPQRG---PYPSQNPHYPHL 427
                 G    A  P  P   GP   GP G+  H   P  + YP +G    YP   P  PH 
Sbjct:   503 GPGPGGPGPA-GPMGPFNPGPFNQGPPGAPPHAGGPPPHQYPPQGWGNTYPQWQPPAPHD 561

Query:   428 P 428
             P
Sbjct:   562 P 562

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0008380 "RNA splicing" evidence=TAS

GO:0000375 "RNA splicing, via transesterification reactions" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

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

 Score = 275 (101.9 bits), Expect = 1.1e-23, Sum P(2) = 1.1e-23
 Identities = 83/250 (33%), Positives = 118/250 (47%)

Query:   201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNID 260
             S  + VP   VG++IG++G+ I+ +Q ++G +IQ   D  + P    R  +I+G      
Sbjct:   269 SLDVPVPRFAVGIVIGRSGEMIKKIQNDTGVRIQFKPDDGSTPE---RIAQIMGPPDRAQ 325

Query:   261 KAEKLINAVIAEADAGGSPSLVA--------RGLATAQAS------GAAEQVEIKVPNEK 306
              A  +I  ++    AGG P            RG    Q +      G  ++    VP  K
Sbjct:   326 HAADIITDLLRSVQAGGPPGHGGGGGGGGGGRGRGRGQGNWNMGPPGGLQEFTFTVPTMK 385

Query:   307 VGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEV 366
              GLIIG+GGETIK +  +SGARI+L     P  D +  +I  V G  +QI+ A+++++E 
Sbjct:   386 TGLIIGKGGETIKNISQQSGARIELQRNPPPNSDPNI-KIFTVRGSPQQIDYARQLVEEK 444

Query:   367 LSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPRGSH-PSQPMAYDYPQRGPYPSQNPHYP 425
             +   V P    GG     + P  P G P  GP G   P  PM    P  GPY  Q P  P
Sbjct:   445 IGGPVSPM---GG----PHGPPGPHGGPSHGPPGPQGPPAPMGPYNP--GPY-GQGPPGP 494

Query:   426 HLPYGNYPPQ 435
             H P   Y PQ
Sbjct:   495 HGPPAPYQPQ 504

GO:0003723 "RNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	784
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	7e-18
smart00322	68	smart00322, KH, K homology RNA-binding domain	1e-17
pfam00013	59	pfam00013, KH_1, KH domain	3e-16
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	1e-13
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-13
smart00322	68	smart00322, KH, K homology RNA-binding domain	4e-13
pfam00013	59	pfam00013, KH_1, KH domain	8e-13
TIGR03665	172	TIGR03665, arCOG04150, arCOG04150 universal archae	4e-12
pfam13014	42	pfam13014, KH_3, KH domain	8e-11
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	5e-10
PRK13763	180	PRK13763, PRK13763, putative RNA-processing protei	5e-10
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	6e-08
pfam13014	42	pfam13014, KH_3, KH domain	3e-07
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	3e-07
COG1094	194	COG1094, COG1094, Predicted RNA-binding protein (c	4e-07
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	6e-07
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	9e-07
TIGR03927	150	TIGR03927, T7SS_EssA_Firm, type VII secretion prot	1e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-05
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	1e-05
pfam07415	489	pfam07415, Herpes_LMP2, Gammaherpesvirus latent me	3e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	4e-05
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	4e-05
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	8e-05
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	1e-04
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-04
pfam13083	71	pfam13083, KH_4, KH domain	2e-04
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	2e-04
pfam07650	77	pfam07650, KH_2, KH domain	2e-04
TIGR03665	172	TIGR03665, arCOG04150, arCOG04150 universal archae	3e-04
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	4e-04
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	4e-04
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	5e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	7e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	8e-04
PRK14086	617	PRK14086, dnaA, chromosomal replication initiation	8e-04
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	9e-04
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	9e-04
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.001
COG0195	190	COG0195, NusA, Transcription elongation factor [Tr	0.001
PTZ00395	1560	PTZ00395, PTZ00395, Sec24-related protein; Provisi	0.001
TIGR00592	1172	TIGR00592, pol2, DNA polymerase (pol2)	0.001
PRK13763	180	PRK13763, PRK13763, putative RNA-processing protei	0.002
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	0.002
cd02409	68	cd02409, KH-II, KH-II (K homology RNA-binding doma	0.002
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.004
PRK05896	605	PRK05896, PRK05896, DNA polymerase III subunits ga	0.004

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

 Score = 78.0 bits (193), Expect = 7e-18
 Identities = 30/67 (44%), Positives = 43/67 (64%), Gaps = 4/67 (5%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
             + VP+  VG IIG+GG TIK ++  +GA+I+ IP     G GS+ERIV +TG    +E
Sbjct: 2   ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIK-IP---DSGSGSEERIVTITGTPEAVE 57

Query: 358 IAQEMIK 364
            A+E+I 
Sbjct: 58  KAKELIL 64

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

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

 Score = 77.3 bits (191), Expect = 1e-17
 Identities = 30/72 (41%), Positives = 46/72 (63%), Gaps = 6/72 (8%)

Query: 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ 355
             +E+ +P +KVGLIIG+GG TIK ++  +G +I +       G GS+ER+V +TG    
Sbjct: 3   VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI------PGPGSEERVVEITGPPEN 56

Query: 356 IEIAQEMIKEVL 367
           +E A E+I E+L
Sbjct: 57  VEKAAELILEIL 68

Length = 68

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

 Score = 73.0 bits (180), Expect = 3e-16
 Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 8/66 (12%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
             I +P +KVG IIG+GG  IK ++  +G +I++           ++  V ++G   Q+E
Sbjct: 2   ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD--------DRDDTVTISGTPEQVE 53

Query: 358 IAQEMI 363
            A+E+I
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|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 65.6 bits (161), Expect = 1e-13
 Identities = 24/62 (38%), Positives = 39/62 (62%), Gaps = 3/62 (4%)

Query: 302 VPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQE 361
           VP+ + G IIG+GG TIK ++  +GA+I++    LP   GS ER+V ++G    ++ A  
Sbjct: 6   VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLP---GSTERVVTISGKPSAVQKALL 62

Query: 362 MI 363
           +I
Sbjct: 63  LI 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|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 65.3 bits (160), Expect = 2e-13
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 3/64 (4%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
           ++ VP++ VG +IGK G TI+ ++  +GAKI+I            R V I GT   ++KA
Sbjct: 3   RVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSE---ERIVTITGTPEAVEKA 59

Query: 263 EKLI 266
           ++LI
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 = 64.6 bits (158), Expect = 4e-13
 Identities = 24/68 (35%), Positives = 40/68 (58%), Gaps = 5/68 (7%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
           ++ +P +KVG++IGK G TI+ ++  +G KI I      +     R VEI G   N++KA
Sbjct: 6   EVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEE-----RVVEITGPPENVEKA 60

Query: 263 EKLINAVI 270
            +LI  ++
Sbjct: 61  AELILEIL 68

Length = 68

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

 Score = 63.3 bits (155), Expect = 8e-13
 Identities = 24/64 (37%), Positives = 37/64 (57%), Gaps = 7/64 (10%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
           +I +P +KVG +IGK G  I+ ++  +G KI+I  D D         V I GT   ++KA
Sbjct: 3   RILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDRD-------DTVTISGTPEQVEKA 55

Query: 263 EKLI 266
           ++LI
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|211858 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain protein

 Score = 64.9 bits (159), Expect = 4e-12
 Identities = 46/176 (26%), Positives = 81/176 (46%), Gaps = 48/176 (27%)

Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQI--------TRDADADPHAATRPVEIIGT 255
           +++P +++GVLIGK G+T + ++  +G K+ I          + D DP A  +  E++  
Sbjct: 2   VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKA 61

Query: 256 LS---NIDKAEKLIN-----AVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKV 307
           +    + +KA KL++      VI   + G SP+ + R               IK      
Sbjct: 62  IGRGFSPEKALKLLDDDYMLEVIDLKEYGKSPNALRR---------------IK------ 100

Query: 308 GLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 363
           G IIG GG+T + ++  +G  I +             + V + GD  Q++IA+E I
Sbjct: 101 GRIIGEGGKTRRIIEELTGVSISV-----------YGKTVGIIGDPEQVQIAREAI 145

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|221895 pfam13014, KH_3, KH domain

 Score = 57.2 bits (139), Expect = 8e-11
 Identities = 26/46 (56%), Positives = 33/46 (71%), Gaps = 4/46 (8%)

Query: 306 KVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG 351
            VG IIG+GGETIK ++  +GA+IQ IP+  P   GS ERIV +TG
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQ-IPKPEP---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|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 55.6 bits (135), Expect = 5e-10
 Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 2/61 (3%)

Query: 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKL 265
           VP+++ G +IGK G TI+ ++  +GAKI++++          R V I G  S + KA  L
Sbjct: 6   VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTE--RVVTISGKPSAVQKALLL 63

Query: 266 I 266
           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|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional

 Score = 59.1 bits (144), Expect = 5e-10
 Identities = 46/177 (25%), Positives = 81/177 (45%), Gaps = 49/177 (27%)

Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQ---------ITRDADADPHAATRPVEIIG 254
           +++P +++GVLIGK G+T + ++  +G K++         I      DP A  +  +I+ 
Sbjct: 7   VKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTDGEDPLAVLKARDIVK 66

Query: 255 TLS---NIDKAEKLIN-----AVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEK 306
            +    + +KA +L++      VI  +D G SP+ + R               IK     
Sbjct: 67  AIGRGFSPEKALRLLDDDYVLEVIDLSDYGDSPNALRR---------------IK----- 106

Query: 307 VGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 363
            G IIG GG+T + ++  +G  I +             + V + GD  Q+EIA+E I
Sbjct: 107 -GRIIGEGGKTRRIIEELTGVDISV-----------YGKTVAIIGDPEQVEIAREAI 151

Length = 180

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

 Score = 56.3 bits (136), Expect = 6e-08
 Identities = 46/216 (21%), Positives = 54/216 (25%), Gaps = 25/216 (11%)

Query: 486 PAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGHS 545
           P QAP   P P             E   QQ        Q           P Q  +    
Sbjct: 136 PPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAF---- 191

Query: 546 NSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQS 605
              P         GY Q   G P    P Q     S  P +P  P  +P     +   Q 
Sbjct: 192 ---PQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQF 248

Query: 606 YGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQP- 664
            G +   QQ  P           P       P    QPP      PQ      P  PQ  
Sbjct: 249 PGLS---QQMPP-------PPPQPPQQQQQPPQPQAQPP------PQNQPTPHPGLPQGQ 292

Query: 665 -GGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSN 699
                 P   Q+ P     Q       + EQ    +
Sbjct: 293 NAPLPPPQQPQLLPLVQQPQGQQRGPQFREQLVQLS 328

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

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

 Score = 47.2 bits (113), Expect = 3e-07
 Identities = 19/45 (42%), Positives = 27/45 (60%), Gaps = 3/45 (6%)

Query: 210 KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG 254
            VG +IGK G+TI+ ++  +GAKIQI      +P +  R 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|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

 Score = 47.9 bits (115), Expect = 3e-07
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 11/66 (16%)

Query: 300 IKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEI 358
           +K+P +K+  +IG GG+TIK +   +G +I +      E DG+    V +   D    E 
Sbjct: 6   MKIPPDKIRDVIGPGGKTIKKIIEETGVKIDI------EDDGT----VYIAASDKEAAEK 55

Query: 359 AQEMIK 364
           A++MI+
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 = 50.8 bits (122), Expect = 4e-07
 Identities = 42/183 (22%), Positives = 74/183 (40%), Gaps = 51/183 (27%)

Query: 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQI----------TRDADADPHAATRPV 250
           S  +++P +++GVLIGK G+  + ++  +G K++I          T     DP A  +  
Sbjct: 9   SEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKAR 68

Query: 251 EIIGTLS---NIDKAEKLIN-----AVIAEAD-AGGSPSLVARGLATAQASGAAEQVEIK 301
           +++  +      +KA KL+       VI   D    S   + R                 
Sbjct: 69  DVVKAIGRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRR----------------- 111

Query: 302 VPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQE 361
                 G IIGR G+T + ++  +G  I +         G     V + G   Q+EIA+E
Sbjct: 112 ----IKGRIIGREGKTRRAIEELTGVYISV--------YGKT---VAIIGGFEQVEIARE 156

Query: 362 MIK 364
            ++
Sbjct: 157 AVE 159

Length = 194

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

 Score = 46.7 bits (112), Expect = 6e-07
 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 6/67 (8%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
            E+++P +    IIG+ G  I+ +   +G +I+  P       GSK   + +TG    +E
Sbjct: 2   EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIR-FPD-----PGSKSDTITITGPKENVE 55

Query: 358 IAQEMIK 364
            A+E I 
Sbjct: 56  KAKEEIL 62

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

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

 Score = 52.0 bits (126), Expect = 9e-07
 Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 11/67 (16%)

Query: 300 IKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEI 358
           IK+P +K+  +IG GG+TI+ +   +GA+I +      E DG     V++   D    E 
Sbjct: 558 IKIPPDKIRDVIGPGGKTIREITEETGAKIDI------EDDG----TVKIAATDGEAAEA 607

Query: 359 AQEMIKE 365
           A+E I+ 
Sbjct: 608 AKERIEG 614

Length = 693

>gnl|CDD|200340 TIGR03927, T7SS_EssA_Firm, type VII secretion protein EssA

 Score = 48.5 bits (116), Expect = 1e-06
 Identities = 31/122 (25%), Positives = 56/122 (45%), Gaps = 21/122 (17%)

Query: 70  DKTEKPDGPVNVNGLKEEKPDEVVDAEQLTEDTTKEEELESAEVKTE----QHSSVEEQA 125
           D   + DG + V   + EK D  ++ + L E+T  ++EL + E + +    +H    EQ 
Sbjct: 15  DSAAENDGKLQVKPNRYEKKDIEINTDYLQEETELDKELFTPEEQKKITFQKHKEKPEQE 74

Query: 126 SVDNQ-------QISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNV 178
            + NQ       + +  + TK+ LFS+E           E T    E+  EEE+ + S++
Sbjct: 75  ELKNQLFSENATENNTVKATKKQLFSSE----------YEQTSSSSESTSEEETKKTSSI 124

Query: 179 VP 180
           + 
Sbjct: 125 LL 126

Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions [Protein fate, Protein and peptide secretion and trafficking]. Length = 150

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

 Score = 51.5 bits (124), Expect = 1e-06
 Identities = 25/184 (13%), Positives = 34/184 (18%), Gaps = 5/184 (2%)

Query: 567 KPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQ 626
             P          +   P  P  P   P       +              P         
Sbjct: 601 PAPASSGPPEEAARPAAPAAPAAPAA-PAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAV 659

Query: 627 TYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAG----YG 682
              S G    P        +AP                  Q AP+     P         
Sbjct: 660 PDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAA 719

Query: 683 QYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAATQPSYDQ 742
           Q     Q        ++         D     +   +    P      A PAA  P    
Sbjct: 720 QPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPP 779

Query: 743 SASQ 746
           S  +
Sbjct: 780 SEEE 783

Length = 824

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 49.0 bits (116), Expect = 1e-05
 Identities = 51/229 (22%), Positives = 88/229 (38%), Gaps = 21/229 (9%)

Query: 4    EEVLAPASAAAADLKRKLDDLEPDEALEHAEGMRDDEAKNSDEVEKNVDG--FAEAHGSE 61
            EE      A  A+ K+K D+L+  E L+ AE  +  E     E +KN+      EA  +E
Sbjct: 1531 EEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAE 1590

Query: 62   VKRPRLDDDKTEKPDGPVNVNGLKEE----KPDEVVDAEQLTEDTTKEEELESAEV-KTE 116
              R        E+          K E    K +E+  AE+  +   + ++ E+ E  K E
Sbjct: 1591 EARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAE 1650

Query: 117  QHSSVEEQASVDNQQISVKEE-----------TKEVLFSTEEAFIDVKEETK---EVTVK 162
            +    EE+  +   + + K E            +E      EA     EE K   E+  K
Sbjct: 1651 ELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKK 1710

Query: 163  EEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKV 211
            E E  K+ E ++ +    +   + +K +       +  ++K E    K+
Sbjct: 1711 EAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKI 1759

Length = 2084

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

 Score = 48.6 bits (117), Expect = 1e-05
 Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 11/67 (16%)

Query: 300 IKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEI 358
           IK+  +K+  +IG GG+ I+ +   +GA+I +      E DG     V++   D    E 
Sbjct: 555 IKINPDKIRDVIGPGGKVIREITEETGAKIDI------EDDG----TVKIAASDGEAAEA 604

Query: 359 AQEMIKE 365
           A +MI+ 
Sbjct: 605 AIKMIEG 611

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|219404 pfam07415, Herpes_LMP2, Gammaherpesvirus latent membrane protein (LMP2) protein

 Score = 47.2 bits (112), Expect = 3e-05
 Identities = 28/112 (25%), Positives = 35/112 (31%), Gaps = 11/112 (9%)

Query: 445 GPPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYG 504
           G P    + GG D  G +G      P S   S   PG P           PP      YG
Sbjct: 12  GGP---RSHGGPD--GDEGDSNPYYPSSFGSSWDRPGPPVPEDYDAPSHRPPP-----YG 61

Query: 505 QPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGHSN-SQPVYSQGG 555
             +   +G  QP     P    G G +        PY      S+ VY +  
Sbjct: 62  GSNGDRHGGYQPLGQQDPSLYAGLGQNGGGGLPPPPYSPRDQGSEHVYEEPR 113

This family consists of several Gammaherpesvirus latent membrane protein (LMP2) proteins. Epstein-Barr virus is a human Gammaherpesvirus that infects and establishes latency in B lymphocytes in vivo. The latent membrane protein 2 (LMP2) gene is expressed in latently infected B cells and encodes two protein isoforms, LMP2A and LMP2B, that are identical except for an additional N-terminal 119 aa cytoplasmic domain which is present in the LMP2A isoform. LMP2A is thought to play a key role in either the establishment or the maintenance of latency and/or the reactivation of productive infection from the latent state. The significance of LMP2B and its role in pathogenesis remain unclear. Length = 489

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

 Score = 46.9 bits (112), Expect = 4e-05
 Identities = 32/206 (15%), Positives = 50/206 (24%), Gaps = 7/206 (3%)

Query: 576 GTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAP 635
           G  P + G   P  P    P +     A    P  P       A + P + +        
Sbjct: 589 GPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVA 648

Query: 636 APDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQP 695
           AP+ + +  A         G              P+    AP A  G         P   
Sbjct: 649 APEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAAT 708

Query: 696 ATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAATQPSYDQSASQSTAYGVAQG 755
             +          DP+          +AP+       P   +P      +          
Sbjct: 709 PPA------GQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAG-APAQPPPP 761

Query: 756 TAAAGYGKTVSPQPGYPQYDSTQMYA 781
            A A      +  P  P  +  +M  
Sbjct: 762 PAPAPAAAPAAAPPPSPPSEEEEMAE 787

Length = 824

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 46.9 bits (111), Expect = 4e-05
 Identities = 76/400 (19%), Positives = 102/400 (25%), Gaps = 44/400 (11%)

Query: 383  QAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSN 442
            Q+ RPR P          + PS      +    P PS +P          P      R  
Sbjct: 2594 QSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPR 2653

Query: 443  YGGPPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGP------PP 496
                P                   + R    + ++S P  P   A  P  G       PP
Sbjct: 2654 DDPAPGRVSRP-----------RRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPP 2702

Query: 497  SQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGHSNSQPVYSQGGL 556
                     PH        P   AA +Q          A    P      + P    G  
Sbjct: 2703 PPPPTPEPAPHALVSATPLPPGPAAARQASP-------ALPAAPAPPAVPAGPATPGGPA 2755

Query: 557  QSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQY 616
            +        G P    PA         P          P  + +  ++   P+       
Sbjct: 2756 RPARPPTTAGPPAPAPPA--------APAAGPPRRLTRPAVASLSESRESLPSPWDPADP 2807

Query: 617  PYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVA 676
            P A   P     P+  ++PA      P ++ P  P       P     GG  AP  G V 
Sbjct: 2808 PAAVLAPAAALPPA--ASPAGPL-PPPTSAQPTAPPPPPGPPPPSLPLGGSVAPG-GDVR 2863

Query: 677  --PTAGYGQYTNTQQAYPE-----QPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPG 729
              P +          A P      +PA S +   +    D       P +    P  QP 
Sbjct: 2864 RRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAP-PPPQPQPQ 2922

Query: 730  YAQPAATQPSYDQSASQSTAYGVAQGTAAAGYGKTVSPQP 769
               P   QP                  A AG      PQP
Sbjct: 2923 PPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQP 2962

Length = 3151

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 46.1 bits (109), Expect = 8e-05
 Identities = 41/187 (21%), Positives = 75/187 (40%), Gaps = 19/187 (10%)

Query: 22   DDLEPDEALEHAEGMRDDEAKNSDEVEKNVDGFAEAHGSEVKRPRLDDDKTEKPDGPVNV 81
            DDLE   A E     + D    S+  E   D       S V      D + E  D    V
Sbjct: 3835 DDLEEL-ANEEDTANQSDL-DESEARELESDMNGVTKDSVVSENENSDSEEENQDLDEEV 3892

Query: 82   NGLKEEKPDEVVDAEQLTEDTTKEEELESAEVKTEQHSSVEEQASVDNQQISVKEETKEV 141
            N + E+  + +   E+L ++  +E+ LE     TEQ S+ E+ A+ +   +  KE+  + 
Sbjct: 3893 NDIPEDLSNSL--NEKLWDEPNEEDLLE-----TEQKSN-EQSAANNESDLVSKEDDNKA 3944

Query: 142  LF-STEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQ-QVVD-----NSKSDDPSS 194
            L     +   D +E + +V + +E  ++ +     S   P+ + +D          +   
Sbjct: 3945 LEDKDRQEKEDEEEMSDDVGIDDE--IQPDIQENNSQPPPENEDLDLPEDLKLDEKEGDV 4002

Query: 195  TDDSTMS 201
            + DS + 
Sbjct: 4003 SKDSDLE 4009

Length = 4600

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

 Score = 45.1 bits (107), Expect = 1e-04
 Identities = 42/226 (18%), Positives = 52/226 (23%), Gaps = 46/226 (20%)

Query: 394 PQWGPRGSHPSQPM--AYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYGGPPNMQG 451
           P+  P+   P+Q M    +   +     Q P     P     PQ M PR     P     
Sbjct: 140 PESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQ-LPQPPQQVLPQGMPPR-QAAFPQQGPP 197

Query: 452 AAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEY 511
                    G        P  V     +P     PAQ P     P Q      QP     
Sbjct: 198 EQPP-----GYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPP-PLQQPQFPGL 251

Query: 512 GHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYG 571
             Q P     P Q                                     Q Q  +P   
Sbjct: 252 SQQMPPPPPQPPQ------------------------------------QQQQPPQPQAQ 275

Query: 572 MPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYP 617
            P Q       G P+       PP Q Q+              Q+ 
Sbjct: 276 PPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQFR 321

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

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 44.9 bits (106), Expect = 2e-04
 Identities = 66/361 (18%), Positives = 88/361 (24%), Gaps = 44/361 (12%)

Query: 386  RPRVPTGPPQ-WGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYG 444
            R    + PPQ    R + P+           P P   P        +  P    P +   
Sbjct: 2672 RAAQASSPPQRPRRRAARPTVGSLTSL-ADPPPPPPTPEPAPHALVSATPLPPGPAAARQ 2730

Query: 445  GPPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYG 504
              P +  A        G          +   +T+ P  P+ PA APA GPP         
Sbjct: 2731 ASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPA-APAAGPPRRLTRPAVA 2789

Query: 505  QPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQ 564
                S      P+  A P            A V  P      +                 
Sbjct: 2790 SLSESRESLPSPWDPADPP-----------AAVLAPAAALPPAAS--------------- 2823

Query: 565  YGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYP--YATSG 622
                P G     T  Q   PP P       P    +P   S  P    +++ P     + 
Sbjct: 2824 ----PAGPLPPPTSAQPTAPPPPP-----GPPPPSLPLGGSVAPGGDVRRRPPSRSPAAK 2874

Query: 623  PTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYG 682
            P     P       P       + A    Q      P  P P   Q        P     
Sbjct: 2875 PAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPP 2934

Query: 683  QYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYA----APTGQPGYAQPAATQP 738
                 Q         + AG        P  G+  PG         P   P    PA++ P
Sbjct: 2935 PPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTP 2994

Query: 739  S 739
             
Sbjct: 2995 P 2995

Length = 3151

>gnl|CDD|221909 pfam13083, KH_4, KH domain

 Score = 40.1 bits (95), Expect = 2e-04
 Identities = 11/27 (40%), Positives = 17/27 (62%)

Query: 297 QVEIKVPNEKVGLIIGRGGETIKGLQT 323
            +E+ V  E +G +IG+ G T+  LQT
Sbjct: 29  VIELNVAGEDLGKLIGKRGRTLDALQT 55

Length = 71

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

 Score = 44.9 bits (107), Expect = 2e-04
 Identities = 32/143 (22%), Positives = 58/143 (40%), Gaps = 38/143 (26%)

Query: 229 SGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLAT 288
            G   +I + A      A   + I+           ++N  I+E     SP         
Sbjct: 510 KGITKEIMKKALEQAKGAR--LHILI----------VMNEAISEPRKELSPY-------- 549

Query: 289 AQASGAAEQVE-IKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIV 347
                 A ++E IK+  +K+  +IG GG+TIK +   +G +I +      E DG+    V
Sbjct: 550 ------APRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDI------EDDGT----V 593

Query: 348 RVTG-DMRQIEIAQEMIKEVLSQ 369
           ++   D    + A+E I+ +  +
Sbjct: 594 KIAASDGESAKKAKERIEAITRE 616

Length = 692

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

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 5/58 (8%)

Query: 279 PSLVARGLATAQASG-----AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQL 331
              +A  L  A  S         +V + +   + G++IG+GG  IK L       I+L
Sbjct: 3   REFLAVELKKAGISDIEIERTPNRVIVVIRTSQPGIVIGKGGSNIKKLGKELRKLIEL 60

Length = 77

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

 Score = 41.8 bits (99), Expect = 3e-04
 Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 12/69 (17%)

Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVT---GDMRQ 355
            +K+P +++G++IG+GGET K ++ R+G ++ +        D S+   V++     D   
Sbjct: 1   YVKIPKDRIGVLIGKGGETKKEIEERTGVKLDI--------D-SETGEVKIEEEDEDPLA 51

Query: 356 IEIAQEMIK 364
           +  A+E++K
Sbjct: 52  VMKAREVVK 60

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

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 10/65 (15%)

Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT-LSNIDKA 262
           +++P +K+  +IG  G TI+ +   +G KI I  D           V I  +     +KA
Sbjct: 6   MKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGT---------VYIAASDKEAAEKA 56

Query: 263 EKLIN 267
           +K+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|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 43.8 bits (103), Expect = 4e-04
 Identities = 45/197 (22%), Positives = 86/197 (43%), Gaps = 21/197 (10%)

Query: 13   AAADLKRKLDDLEPD-EALEHA-EGMRDDEAKNSDEVEKNVDGFAEAHGSEVKRPRLDDD 70
            +AA+ +  L   E D +ALE      ++DE + SD+V  + D           +P  +++
Sbjct: 3927 SAANNESDLVSKEDDNKALEDKDRQEKEDEEEMSDDVGID-DEIQPDIQENNSQPPPENE 3985

Query: 71   KTEKPDGPVNVNGLKEEKPDEVVDAEQLTEDTTKEEELES---------AEVKTEQHSSV 121
              + P+  + ++  KE    +  D E +  +   E + E+          E   E+++++
Sbjct: 3986 DLDLPED-LKLDE-KEGDVSKDSDLEDMDMEAADENKEEADAEKDEPMQDEDPLEENNTL 4043

Query: 122  EEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQ 181
            +E    D+     +++ K      E+ F +  +E +E T   E+ VK +E +E   V   
Sbjct: 4044 DEDIQQDDFSDLAEDDEKM----NEDGFEENVQENEEST---EDGVKSDEELEQGEVPED 4096

Query: 182  QVVDNSKSDDPSSTDDS 198
            Q +DN    D  ST  S
Sbjct: 4097 QAIDNHPKMDAKSTFAS 4113

Length = 4600

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

 Score = 43.1 bits (103), Expect = 5e-04
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 10/74 (13%)

Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT-LSNIDKA 262
           I++P +K+  +IG  G TIR +   +GAKI I  D        T  V+I  T     + A
Sbjct: 558 IKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD-------GT--VKIAATDGEAAEAA 608

Query: 263 EKLINAVIAEADAG 276
           ++ I  + AE + G
Sbjct: 609 KERIEGITAEPEVG 622

Length = 693

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

 Score = 42.7 bits (101), Expect = 7e-04
 Identities = 28/193 (14%), Positives = 44/193 (22%), Gaps = 9/193 (4%)

Query: 483 PSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYG 542
           P+  A    G P P+ +         +        A  AP        + + AP      
Sbjct: 590 PAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAA 649

Query: 543 GHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPS 602
              + + V        G             PA      +   P     G  P   +  P+
Sbjct: 650 PEHHPKHVAVPDASDGGDGWPAKAGGA--APAAPPPAPAPAAPAAPA-GAAPAQPAPAPA 706

Query: 603 AQSYGPNVPHQQQYPYATSGPTQQTYPSYGSA----PAPDSYNQPPASAPGYPQQAGQAV 658
           A    P                  + PS  +       P+  + P  +          A 
Sbjct: 707 ATP--PAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAP 764

Query: 659 PNYPQPGGQQAPS 671
                P     PS
Sbjct: 765 APAAAPAAAPPPS 777

Length = 824

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.8 bits (100), Expect = 8e-04
 Identities = 50/187 (26%), Positives = 75/187 (40%), Gaps = 23/187 (12%)

Query: 2    AEEEVLAPASAAAADLKRKLDDLEPDEALEHAEGMRDDEAKNSDEVEK--NVDGFAEAHG 59
            A E       A  A+  +K D+ +  E     E  + DEAK ++E +K   +    E   
Sbjct: 1505 AAEAKKKADEAKKAEEAKKADEAKKAE-----EAKKADEAKKAEEKKKADELKKAEELKK 1559

Query: 60   SEVKRPRLDDDKTEKPDGPVNVNGLK-----EEKPDEVVDAEQLTEDTTKEEEL---ESA 111
            +E K+ + ++ K  + D  + +   +     EE   E V      E   K EE    E A
Sbjct: 1560 AEEKK-KAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEA 1618

Query: 112  EVKTEQHSSVEEQASVDNQQISVKEETK----EVLFSTEEAFIDVKEETK---EVTVKEE 164
            ++K E+    EE+     Q    + E K    E+  + EE  I   EE K   E   K E
Sbjct: 1619 KIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAE 1678

Query: 165  ETVKEEE 171
            E  K EE
Sbjct: 1679 EAKKAEE 1685

Length = 2084

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

 Score = 42.5 bits (100), Expect = 8e-04
 Identities = 35/195 (17%), Positives = 51/195 (26%), Gaps = 16/195 (8%)

Query: 568 PPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQT 627
           PP     + ++P+   P R    G   P     P        +P        T+ P    
Sbjct: 97  PPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLP--------TARPA--- 145

Query: 628 YPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNT 687
           YP+Y   P P ++  P A+     QQ     P         + +  Q      Y      
Sbjct: 146 YPAYQQRPEPGAW--PRAADDYGWQQQRLGFPPRAPYASPASYAPEQERDREPYDAGRPE 203

Query: 688 QQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAATQPSYDQSASQS 747
                         +              PG+ +    G     +  A       SA   
Sbjct: 204 YDQRRRDYDHPRPDWDRPRRDRTDRPEPPPGAGHVHRGGPGPPERDDAPVVPIRPSAPGP 263

Query: 748 TAYGVAQGTAAAGYG 762
            A   AQ   A G G
Sbjct: 264 LA---AQPAPAPGPG 275

Length = 617

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

 Score = 42.7 bits (101), Expect = 9e-04
 Identities = 30/197 (15%), Positives = 36/197 (18%), Gaps = 7/197 (3%)

Query: 481 GHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQ---GYGHGYDDNHAPV 537
             P          P  S       +P              A                   
Sbjct: 590 PAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAA 649

Query: 538 QHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGP----PRPGQPGDI 593
              +  H         G              P   PA        G     P P      
Sbjct: 650 PEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATP 709

Query: 594 PPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQ 653
           P  Q+  P+AQ            P A         P     PA      PP  AP     
Sbjct: 710 PAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAA 769

Query: 654 AGQAVPNYPQPGGQQAP 670
              A P  P    ++  
Sbjct: 770 PAAAPPPSPPSEEEEMA 786

Length = 824

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 42.8 bits (100), Expect = 9e-04
 Identities = 57/332 (17%), Positives = 89/332 (26%), Gaps = 31/332 (9%)

Query: 446 PPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYGQ 505
           PP     A        Q   +S       H   +P          A    P     +   
Sbjct: 204 PPQGSPIAAQPAPQPQQPSPLSLISAPSLHPQRLPSPHPPLQPQTASQQSPQPPAPSSRH 263

Query: 506 PHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQY 565
           P +S +G   P  HA  Q            PV   +   +  QP              Q 
Sbjct: 264 PQSSHHGPGPPMPHALQQG-----------PVFLQHPSSNPPQPFGLA----------QS 302

Query: 566 GKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQ 625
             PP  +P+Q        P +       PP +  +P A S  P++      P        
Sbjct: 303 QVPPLPLPSQAQPHSHTPPSQSALQPQQPPREQPLPPAPS-MPHIKPPPTTPIPQLPNQS 361

Query: 626 QTYPSYGSAPAP----DSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGY 681
             +P +   P+P     S   PP +            P+   P  Q  P    +      
Sbjct: 362 HKHPPHLQGPSPFPQMPSNLPPPPALKPLSSLPTHHPPSAHPPPLQLMPQSQPLQSVPAQ 421

Query: 682 GQYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAATQPSYD 741
                  Q+ P + +T      + G     +             G P    P +   S  
Sbjct: 422 PPVLTQSQSLPPKASTHPHSGLHSGPPQSPFAQHP-----FTSGGLPAIGPPPSLPTSTP 476

Query: 742 QSASQSTAYGVAQGTAAAGYGKTVSPQPGYPQ 773
            +  ++++     G+A    G    P P  P 
Sbjct: 477 AAPPRASSGSQPPGSALPSSGGCAGPGPPLPP 508

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

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

 Score = 41.7 bits (99), Expect = 0.001
 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 10/75 (13%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT-LSNIDK 261
            I++  +K+  +IG  G  IR +   +GAKI I  D           V+I  +     + 
Sbjct: 554 TIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDDGT---------VKIAASDGEAAEA 604

Query: 262 AEKLINAVIAEADAG 276
           A K+I  + AE + G
Sbjct: 605 AIKMIEGITAEPEVG 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|223273 COG0195, NusA, Transcription elongation factor [Transcription]

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 35/187 (18%), Positives = 69/187 (36%), Gaps = 52/187 (27%)

Query: 134 VKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPS 193
           V++E K  +  +      + E+  E+ V E      +  +E         +    + DP 
Sbjct: 30  VQKEAKGQIELSRTIPELL-EKLFEIEVPE----IGDGVIE---------IK-CVARDPR 74

Query: 194 STDDSTMSRKIEVPN-NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEI 252
           +      +    V   + VG  IGK G  ++ +    G KI +   ++            
Sbjct: 75  A------AVVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE------------ 116

Query: 253 IGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIG 312
                  D AE + NA+        +P+ V   +   +  G      + VP +++ L IG
Sbjct: 117 -------DPAEFIKNAL--------APAEVL-SVNIKEDDG--HVAIVVVPPDQLSLAIG 158

Query: 313 RGGETIK 319
           +GG+ ++
Sbjct: 159 KGGQNVR 165

Length = 190

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

 Score = 42.4 bits (99), Expect = 0.001
 Identities = 84/403 (20%), Positives = 121/403 (30%), Gaps = 51/403 (12%)

Query: 381 NQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPR 440
           NQQ+    +P G P    RG HP+     +  +     +Q+ H      G+ PP      
Sbjct: 121 NQQS---NIPIGDPVNHLRG-HPNFGEPRERAEDAAPHAQHNHSGK-TNGDNPPTGGQYH 175

Query: 441 SNYGGPPNMQ--------GAAGGYDYYGGQGGH-----VSDRPVSVS-HSTSIPG--HPS 484
            + G   N Q         A   ++     G H       D P  +   S    G    +
Sbjct: 176 QSGGTSRNHQMMDSNKNCPADALFNETNPSGEHKRNSIDGDIPSDIYIDSQPNEGDVQKT 235

Query: 485 VPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDN---HAP----- 536
            P Q   G    S           S    QQ  A +A + GY H    N   H P     
Sbjct: 236 NPWQGKQGNSATSPPANENNAVTLSCSNDQQRGASSAAESGYAHHRGSNIASHTPNDNIM 295

Query: 537 --VQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIP 594
               +P    +++Q    QG L  G       K  +    + T  Q YG    G P    
Sbjct: 296 HAANNPLNNTNDAQRNAIQGDLVRGAPND---KNSFDRGNEKTY-QIYGGFHDGSPNAAS 351

Query: 595 P-YQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQ 653
                     Q+ G ++                +  SY  A    +Y+    S       
Sbjct: 352 AGAPFNGLGNQADGGHINQVHPDARGAWAGGPHSNASYNCA----AYSNAAQSNAAQ-SN 406

Query: 654 AGQAVPNYPQPGGQQAPSYGQVAPTAGYGQ--YTNTQQAYP--EQPATSNAGYGYQGTQD 709
           AG +   Y  PG               Y     +NT  + P    P  SN  Y      +
Sbjct: 407 AGFSNAGYSNPGNSNPGYNNAPNSNTPYNNPPNSNTPYSNPPNSNPPYSNLPYSNTPYSN 466

Query: 710 PSYGSSAPGSAYAAPTG-QPGYA-----QPAATQPSYDQSASQ 746
               ++ P SA    +     Y      QPAA  P+ +Q A+ 
Sbjct: 467 APLSNAPPSSAKDHHSAYHAAYQHRAANQPAANLPTANQPAAN 509

Length = 1560

>gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2)

 Score = 42.0 bits (98), Expect = 0.001
 Identities = 39/180 (21%), Positives = 64/180 (35%), Gaps = 25/180 (13%)

Query: 45  DEVEKNVDGFAEAHGSEVKRPRLDDDKTEKPDGPVNVNGLKEEKPDEVVDAEQLTEDTTK 104
           D + ++VD   E   S+  + +  DD   K DG   V   +E  PDE  D   L +D   
Sbjct: 6   DYIYEDVD---EEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDED-DILDLDKDDGS 61

Query: 105 EEELESAEVKTEQHSSVEEQASVDNQQISVKEETKEV-----------------LFSTEE 147
             E +      E H  V +  ++   +I+   + K+                  L  TE 
Sbjct: 62  AAEAKK--KDKENHKKVTKPNNIKAVRIACAPKKKKDRKKSLGKDGLLGDILQELNKTET 119

Query: 148 AFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVP 207
           A   +      V   +  +  +  ++   +     VVD  K   P ST    +  KI +P
Sbjct: 120 AQRKITPRLVSVPKLKFSSPADVPAINDFSNHHPAVVDIVKKAIPVSTRY--LLEKILIP 177

All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1172

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

 Score = 39.9 bits (94), Expect = 0.002
 Identities = 11/33 (33%), Positives = 26/33 (78%)

Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQL 331
            +K+P +++G++IG+ GET K ++ R+G ++++
Sbjct: 6   YVKIPKDRIGVLIGKKGETKKEIEERTGVKLEI 38

Length = 180

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

 Score = 41.1 bits (97), Expect = 0.002
 Identities = 36/192 (18%), Positives = 52/192 (27%), Gaps = 4/192 (2%)

Query: 363 IKEVLSQTVRPS----TLSGGFNQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYP 418
           + E L    +         G    +       +GPP+   R + P+ P A   P      
Sbjct: 574 LAEELGGDWQVEAVVGPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAA 633

Query: 419 SQNPHYPHLPYGNYPPQQMAPRSNYGGPPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTS 478
           +        P       +  P+       +  G        G         P   + +  
Sbjct: 634 AAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAP 693

Query: 479 IPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQ 538
               P+ PA APA  PP  QA+    QP  +  G   P   A          DD   P  
Sbjct: 694 AGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAG 753

Query: 539 HPYGGHSNSQPV 550
            P        P 
Sbjct: 754 APAQPPPPPAPA 765

Length = 824

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

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 10/27 (37%), Positives = 17/27 (62%)

Query: 296 EQVEIKVPNEKVGLIIGRGGETIKGLQ 322
            ++ I V   + GL+IG+ G+ I+ LQ
Sbjct: 25  IEIIIVVARGQPGLVIGKKGQNIRALQ 51

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|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 40.4 bits (94), Expect = 0.004
 Identities = 31/181 (17%), Positives = 65/181 (35%), Gaps = 13/181 (7%)

Query: 22   DDLEPDEALEHAEGMRDDEAKNSDEVEKNVDGFAE---AHGSEVKRPRLDDDKTEKPDGP 78
            D LE +  L+      D      D+ + N DGF E    +    +     D++ E+ + P
Sbjct: 4035 DPLEENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENVQENEESTEDGVKSDEELEQGEVP 4094

Query: 79   VNVNGLK-EEKPD-EVVDAEQLTEDTTKEEELESAEVKTEQHSSVEEQASVDNQQISVKE 136
                 +    K D +   A    ++   ++ +     +  +   V    + D +   V+E
Sbjct: 4095 -EDQAIDNHPKMDAKSTFASAEADEENTDKGIVGENEELGEEDGVRGNGTADGEFEQVQE 4153

Query: 137  ETKEVLFSTEEAFI-------DVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKS 189
            +T     +  EA          ++E  +   + E E + E +S    +     V ++ + 
Sbjct: 4154 DTSTPKEAMSEADRQYQSLGDHLREWQQANRIHEWEDLTESQSQAFDDSEFMHVKEDEEE 4213

Query: 190  D 190
            D
Sbjct: 4214 D 4214

Length = 4600

>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau; Validated

 Score = 40.2 bits (94), Expect = 0.004
 Identities = 21/117 (17%), Positives = 47/117 (40%), Gaps = 8/117 (6%)

Query: 69  DDKTEKPDGPVNVNGL--KEEKPDEVVDAEQL--TEDTTKEEELESAEVKTEQH--SSVE 122
           + KT      +    +   EE     V  + L  T+    ++++     + +      +E
Sbjct: 380 EKKTINNSQIITTKKINIVEESNKNSVHFDTLYKTKIFYHKKKINQNNKEQDIKKEELLE 439

Query: 123 EQASVDNQQISVKEETKEVLFSTEEAFID-VKEETKEVTVKEEETVKEEESVEPSNV 178
           ++    +++I   +E  + L   ++ F +   E +K +  K  +  K EES E S +
Sbjct: 440 KEFVKKSEKIPKNDELLDNLELAKQKFFNKDIELSKNMLQKFNK-FKNEESAENSFI 495

Length = 605

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	784
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.97
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.95
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.95
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.94
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.93
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.93
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.86
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.84
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.74
PRK13763	180	putative RNA-processing protein; Provisional	99.72
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.55
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.55
PRK13763	180	putative RNA-processing protein; Provisional	99.53
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.34
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.27
COG1094	194	Predicted RNA-binding protein (contains KH domains	99.26
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.15
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.15
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.14
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.14
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.06
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.05
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.04
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.01
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.01
smart00322	69	KH K homology RNA-binding domain.	98.9
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.82
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.79
PF13014	43	KH_3: KH domain	98.78
smart00322	69	KH K homology RNA-binding domain.	98.77
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.76
KOG2113	394	consensus Predicted RNA binding protein, contains	98.7
PF13014	43	KH_3: KH domain	98.65
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.63
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.57
KOG0119	554	consensus Splicing factor 1/branch point binding p	98.48
PRK08406	140	transcription elongation factor NusA-like protein;	98.26
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.2
KOG0119	554	consensus Splicing factor 1/branch point binding p	98.2
KOG2113	394	consensus Predicted RNA binding protein, contains	98.18
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.92
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.92
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.84
PRK08406	140	transcription elongation factor NusA-like protein;	97.81
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.77
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	97.76
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.74
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	97.64
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	97.63
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.63
COG0195	190	NusA Transcription elongation factor [Transcriptio	97.61
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.6
COG5176	269	MSL5 Splicing factor (branch point binding protein	97.5
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.47
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.47
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	97.44
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	97.35
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.26
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	97.23
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.23
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.2
PRK00106	535	hypothetical protein; Provisional	97.01
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	97.0
TIGR01953	341	NusA transcription termination factor NusA. This m	97.0
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.92
PRK12704	520	phosphodiesterase; Provisional	96.91
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.89
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.87
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.86
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.82
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.7
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.7
PRK00106	535	hypothetical protein; Provisional	96.67
PRK09202	470	nusA transcription elongation factor NusA; Validat	96.66
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.65
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.59
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.51
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.5
PRK12704	520	phosphodiesterase; Provisional	96.5
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.38
KOG1960	531	consensus Predicted RNA-binding protein, contains	96.35
PRK12705	508	hypothetical protein; Provisional	96.19
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.18
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	96.17
TIGR01953	341	NusA transcription termination factor NusA. This m	95.97
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.84
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.71
KOG1960	531	consensus Predicted RNA-binding protein, contains	95.71
PRK12705	508	hypothetical protein; Provisional	95.69
PRK00468	75	hypothetical protein; Provisional	95.64
COG1782	637	Predicted metal-dependent RNase, consists of a met	95.61
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.56
PRK02821	77	hypothetical protein; Provisional	95.45
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	95.32
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	95.2
COG5166	657	Uncharacterized conserved protein [Function unknow	95.16
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.15
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	95.14
PRK01064	78	hypothetical protein; Provisional	94.83
PRK00468	75	hypothetical protein; Provisional	94.56
PRK02821	77	hypothetical protein; Provisional	94.42
COG1782	637	Predicted metal-dependent RNase, consists of a met	94.34
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	94.02
COG1837	76	Predicted RNA-binding protein (contains KH domain)	93.91
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	93.73
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	93.7
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	93.45
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	93.41
PRK01064	78	hypothetical protein; Provisional	93.39
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	92.53
PRK06418	166	transcription elongation factor NusA-like protein;	92.2
KOG2874	356	consensus rRNA processing protein [Translation, ri	92.06
KOG2874	356	consensus rRNA processing protein [Translation, ri	91.83
COG5166	657	Uncharacterized conserved protein [Function unknow	91.81
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	91.58
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	91.52
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	90.51
COG1855	604	ATPase (PilT family) [General function prediction	90.21
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	89.5
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	89.45
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	89.43
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	88.89
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	87.86
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	87.34
COG1855	604	ATPase (PilT family) [General function prediction	87.28
TIGR03802	562	Asp_Ala_antiprt aspartate-alanine antiporter. All	86.93
PRK03818	552	putative transporter; Validated	86.29
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	85.65
PRK13764	602	ATPase; Provisional	85.21
PRK13764	602	ATPase; Provisional	85.14
PF10446	458	DUF2457: Protein of unknown function (DUF2457); In	84.74
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	84.46
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	83.73
KOG0299	479	consensus U3 snoRNP-associated protein (contains W	83.26
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	81.03
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	80.89
PRK03818	552	putative transporter; Validated	80.41
PRK06418	166	transcription elongation factor NusA-like protein;	80.01

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

Probab=100.00  E-value=4.7e-47  Score=421.12  Aligned_cols=249  Identities=33%  Similarity=0.521  Sum_probs=209.5

Q ss_pred             ccceeeeccccccccccCCCchhhhhhhcccCceeeeccccc-c-cccceeeecCchhchhhhhhhhhHhhhcCCCCCCC
Q 003942          116 EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETK-E-VTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPS  193 (784)
Q Consensus       116 ~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~-~-~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~  193 (784)
                      +++.+|.||.+++|+||||+||+||.|++.+++++.+..+.. . ...|.|.|+|+.+.|++|+.|++++|+++..+...
T Consensus       138 ~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g  217 (600)
T KOG1676|consen  138 ETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVPG  217 (600)
T ss_pred             ceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCCc
Confidence            467899999999999999999999999987777765554443 3 37899999999999999999999999854332221


Q ss_pred             ------CCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHH
Q 003942          194 ------STDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN  267 (784)
Q Consensus       194 ------~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~  267 (784)
                            .......+++|.||+++||.||||+|+|||+|+.+||+||+|..|+  ++.+.+|.+.|+|+++.|.+|.+||.
T Consensus       218 ~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd--~p~speR~~~IiG~~d~ie~Aa~lI~  295 (600)
T KOG1676|consen  218 SGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDD--DPSSPERPAQIIGTVDQIEHAAELIN  295 (600)
T ss_pred             cccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCC--CCCCccceeeeecCHHHHHHHHHHHH
Confidence                  2223456999999999999999999999999999999999999875  45788999999999999999999999


Q ss_pred             HHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEE
Q 003942          268 AVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIV  347 (784)
Q Consensus       268 elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V  347 (784)
                      +||++...+... -+.+|..     .....+.|.||.++||+||||+|+|||.|.++|||+|.+.++  ++..+..+|+|
T Consensus       296 eii~~~~~~~~~-~~~~G~P-----~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~--~p~~~~~ektf  367 (600)
T KOG1676|consen  296 EIIAEAEAGAGG-GMGGGAP-----GLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ--PPNGNPKEKTF  367 (600)
T ss_pred             HHHHHHhccCCC-CcCCCCc-----cceeeEEEeccccccccccCCCccchhhhcccCCccccccCC--CCCCCccceEE
Confidence            999998653110 0111211     123389999999999999999999999999999999999987  46778899999


Q ss_pred             EEEcCHHHHHHHHHHHHHHHhcccCCC
Q 003942          348 RVTGDMRQIEIAQEMIKEVLSQTVRPS  374 (784)
Q Consensus       348 ~I~Gt~~qV~~Ak~lI~~~L~~~~r~~  374 (784)
                      +|+|++.+|++|+.||+++|....++.
T Consensus       368 ~IrG~~~QIdhAk~LIr~kvg~~~~n~  394 (600)
T KOG1676|consen  368 VIRGDKRQIDHAKQLIRDKVGDIAPNT  394 (600)
T ss_pred             EEecCcccchHHHHHHHHHhcccCCCC
Confidence            999999999999999999998766654

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

Probab=100.00  E-value=5.6e-37  Score=340.99  Aligned_cols=248  Identities=27%  Similarity=0.446  Sum_probs=212.3

Q ss_pred             ceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCC--C
Q 003942          118 HSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSS--T  195 (784)
Q Consensus       118 ~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~--~  195 (784)
                      +.+..||..+|+.||||+|+-|..|..+++|++.|..+......|.|.++|..++|+.|+.||.+++++......+.  .
T Consensus        55 ~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~~~~~~q  134 (600)
T KOG1676|consen   55 TERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGRPPGGFPDNQ  134 (600)
T ss_pred             ccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHHHhhhhhhhccCCCCCccccC
Confidence            34678999999999999999999999999999999999988899999999999999999999999998664322221  1


Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhc
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA  275 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~  275 (784)
                      ....++.+|+||.+++|+||||+|+|||.|++.+||+|.+..++....+ .++.|.|+|+.+.|+.|+.||.++|+|++.
T Consensus       135 ~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-~~KplritGdp~~ve~a~~lV~dil~e~~~  213 (600)
T KOG1676|consen  135 GSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-ADKPLRITGDPDKVEQAKQLVADILREEDD  213 (600)
T ss_pred             CccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-CCCceeecCCHHHHHHHHHHHHHHHHhccc
Confidence            2456899999999999999999999999999999999999998765433 789999999999999999999999998643


Q ss_pred             CCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHH
Q 003942          276 GGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ  355 (784)
Q Consensus       276 ~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~q  355 (784)
                      .........+.    ......+++|.||+++||.||||+|+|||+|+.+||+||+|++++.+   .+.||.+.|+|+.++
T Consensus       214 ~~~g~~~~~g~----~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p---~speR~~~IiG~~d~  286 (600)
T KOG1676|consen  214 EVPGSGGHAGV----RGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDP---SSPERPAQIIGTVDQ  286 (600)
T ss_pred             CCCccccccCc----CccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCC---CCccceeeeecCHHH
Confidence            32222111111    11234589999999999999999999999999999999999988754   688999999999999


Q ss_pred             HHHHHHHHHHHHhcccCC
Q 003942          356 IEIAQEMIKEVLSQTVRP  373 (784)
Q Consensus       356 V~~Ak~lI~~~L~~~~r~  373 (784)
                      |++|.+||.+||++..+.
T Consensus       287 ie~Aa~lI~eii~~~~~~  304 (600)
T KOG1676|consen  287 IEHAAELINEIIAEAEAG  304 (600)
T ss_pred             HHHHHHHHHHHHHHHhcc
Confidence            999999999999876554

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

Probab=99.97  E-value=3.7e-30  Score=260.83  Aligned_cols=240  Identities=23%  Similarity=0.336  Sum_probs=191.7

Q ss_pred             ccceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCC
Q 003942          116 EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSST  195 (784)
Q Consensus       116 ~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~  195 (784)
                      .++.+|++.++.++.||||+|+|||.|+.+.++.+.|.+...  .+|+|.|+.+.+.|-...+.|.-.|+ +.+.     
T Consensus        47 r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~--peri~tisad~~ti~~ilk~iip~le-e~f~-----  118 (390)
T KOG2192|consen   47 RVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSG--PERILTISADIETIGEILKKIIPTLE-EGFQ-----  118 (390)
T ss_pred             ceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCC--CceeEEEeccHHHHHHHHHHHhhhhh-hCCC-----
Confidence            577899999999999999999999999999999999887654  46888887776665544333333332 1121     


Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhc
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA  275 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~  275 (784)
                      ....+.+||||.++++|.||||+|+.||+||+++.|+++|..  ++++++++|+|.|.|..++|..|++.|+++|+|...
T Consensus       119 ~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift--~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pi  196 (390)
T KOG2192|consen  119 LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT--ECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPI  196 (390)
T ss_pred             CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh--ccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCc
Confidence            233589999999999999999999999999999999999985  589999999999999999999999999999998641


Q ss_pred             CCC------------------C-------c--------------------cc---ccc-----------cchh-------
Q 003942          276 GGS------------------P-------S--------------------LV---ARG-----------LATA-------  289 (784)
Q Consensus       276 ~g~------------------p-------~--------------------~~---~~g-----------~~~~-------  289 (784)
                      .++                  +       .                    ++   .+|           |...       
T Consensus       197 kgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~sai  276 (390)
T KOG2192|consen  197 KGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAI  276 (390)
T ss_pred             CCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcC
Confidence            100                  0       0                    00   000           0000       


Q ss_pred             --------------------------------hccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCC
Q 003942          290 --------------------------------QASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLP  337 (784)
Q Consensus       290 --------------------------------~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p  337 (784)
                                                      .......+.++.||.++-|.||||+|+.||+|++++||.|.|..    
T Consensus       277 dtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide----  352 (390)
T KOG2192|consen  277 DTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE----  352 (390)
T ss_pred             CCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC----
Confidence                                            01123567899999999999999999999999999999999964    


Q ss_pred             CCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          338 EGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       338 ~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      +-+.+.+|+|+|+|+.++|+.|+.|+...+++
T Consensus       353 pleGsedrIitItGTqdQIqnAQYLlQn~Vkq  384 (390)
T KOG2192|consen  353 PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ  384 (390)
T ss_pred             cCCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence            34678899999999999999999999998863

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

Probab=99.95  E-value=1.1e-28  Score=262.88  Aligned_cols=246  Identities=25%  Similarity=0.302  Sum_probs=207.3

Q ss_pred             ceeeeccccccccccCCCchhhhhhhcccCceeeeccccc-ccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCC
Q 003942          118 HSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETK-EVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTD  196 (784)
Q Consensus       118 ~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~-~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~  196 (784)
                      ..+++||...++.||||+|.+||+|.+.+.++|++.+... ...+|.+.|.++.|...+|.++|.+++..+..+....  
T Consensus       200 PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~k~~--  277 (584)
T KOG2193|consen  200 PLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDDKVA--  277 (584)
T ss_pred             ceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHHhhhccchh--
Confidence            4589999999999999999999999999999998887654 6778999999999999999999999997665544433  


Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcC
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAG  276 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~  276 (784)
                       .++.++|+..+++||+||||.|.+||+|+.+||++|+|++--+..--+.+|.|+|.|+.|+|.+|..+|+.+|+++-+.
T Consensus       278 -~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEn  356 (584)
T KOG2193|consen  278 -EEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYEN  356 (584)
T ss_pred             -hhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhh
Confidence             5688999999999999999999999999999999999998666555567999999999999999999999999987532


Q ss_pred             CC----------Cccc--ccccch-----------------------hhccCCccEEEEEecCCceeeeecCCchHHHHH
Q 003942          277 GS----------PSLV--ARGLAT-----------------------AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGL  321 (784)
Q Consensus       277 g~----------p~~~--~~g~~~-----------------------~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~I  321 (784)
                      ..          +.++  .-+.++                       .......+.++|.||...||.||||+|.+||.|
T Consensus       357 Dl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql  436 (584)
T KOG2193|consen  357 DLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQL  436 (584)
T ss_pred             hHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHH
Confidence            11          1111  001000                       011235678999999999999999999999999


Q ss_pred             HHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          322 QTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       322 q~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      .+.+||.|+|...   +.++..+|.|+|+|.+++.-+|.-.|..+|.+
T Consensus       437 ~RfagASiKIapp---E~pdvseRMViItGppeaqfKAQgrifgKikE  481 (584)
T KOG2193|consen  437 SRFAGASIKIAPP---EIPDVSERMVIITGPPEAQFKAQGRIFGKIKE  481 (584)
T ss_pred             HHhccceeeecCC---CCCCcceeEEEecCChHHHHhhhhhhhhhhhh
Confidence            9999999999764   45678999999999999999999999988876

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

Probab=99.95  E-value=4.1e-27  Score=266.23  Aligned_cols=252  Identities=24%  Similarity=0.349  Sum_probs=206.3

Q ss_pred             eeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecC---------chhchhhhhhhhhHhhhcCCC
Q 003942          119 SSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVK---------EEESVEPSNVVPQQVVDNSKS  189 (784)
Q Consensus       119 ~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G---------~~e~Ve~A~~lI~~ii~~~~~  189 (784)
                      ++++|+.+++|.||||+|++|++||.++.++|+|.+....+.+|++.|.|         ..+++.+|..+|...++++..
T Consensus        45 ~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~  124 (485)
T KOG2190|consen   45 YRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDE  124 (485)
T ss_pred             EEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccccccc
Confidence            89999999999999999999999999999999999999999999999999         999999999999887763332


Q ss_pred             CCCCC---CCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHH
Q 003942          190 DDPSS---TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLI  266 (784)
Q Consensus       190 ~~~~~---~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I  266 (784)
                      .....   .....+++||+||.+.+|.||||+|++||+||++|||+|+|..+  .+|.+++|.|+|.|..+.|.+|+..|
T Consensus       125 ~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~lP~ster~V~IsG~~~av~~al~~I  202 (485)
T KOG2190|consen  125 AAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD--MLPNSTERAVTISGEPDAVKKALVQI  202 (485)
T ss_pred             ccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC--CCCcccceeEEEcCchHHHHHHHHHH
Confidence            22111   12225899999999999999999999999999999999999986  68999999999999999999999999


Q ss_pred             HHHHHhhh----c-CCC-----C----------ccc---------------------------------ccc--------
Q 003942          267 NAVIAEAD----A-GGS-----P----------SLV---------------------------------ARG--------  285 (784)
Q Consensus       267 ~elI~e~~----~-~g~-----p----------~~~---------------------------------~~g--------  285 (784)
                      ..+|.+..    . ..+     +          .+.                                 ..+        
T Consensus       203 s~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~  282 (485)
T KOG2190|consen  203 SSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALR  282 (485)
T ss_pred             HHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhh
Confidence            99998842    0 000     0          000                                 000        


Q ss_pred             ------------cc------hh----h--------c-----------c----CCccEEEEEecCCceeeeecCCchHHHH
Q 003942          286 ------------LA------TA----Q--------A-----------S----GAAEQVEIKVPNEKVGLIIGRGGETIKG  320 (784)
Q Consensus       286 ------------~~------~~----~--------~-----------~----~~~~~~~i~VP~~~vG~VIGkgG~~IK~  320 (784)
                                  +.      ..    .        +           .    ....+.+|+||++++|+||||+|++|.+
T Consensus       283 ~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~ise  362 (485)
T KOG2190|consen  283 NETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISE  362 (485)
T ss_pred             hhcCCceEeccccCcceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHH
Confidence                        00      00    0        0           0    2236789999999999999999999999


Q ss_pred             HHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccCCC
Q 003942          321 LQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPS  374 (784)
Q Consensus       321 Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~r~~  374 (784)
                      ||+.|||.|.|....  ......++.|+|+|...+...+..+|...|+...+..
T Consensus       363 ir~~tgA~I~I~~~~--~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~  414 (485)
T KOG2190|consen  363 IRQRTGASISILNKE--EVSGVREALVQITGMLREDLLAQYLIRARLSAPKSSM  414 (485)
T ss_pred             HHHhcCCceEEcccc--ccCCcceeEEEecchhHHHHhhhhhcccccccCccCC
Confidence            999999999998643  1126789999999999999999999988887666554

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

Probab=99.94  E-value=3.1e-26  Score=238.69  Aligned_cols=170  Identities=34%  Similarity=0.532  Sum_probs=145.9

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcC
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAG  276 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~  276 (784)
                      +..+.+|||||+..+|.||||+|++|.+|+++|||+|++++..|..|+.++|+|.|.|+.++|...+++|.++|+|....
T Consensus        36 ~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~  115 (402)
T KOG2191|consen   36 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQA  115 (402)
T ss_pred             CCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHh
Confidence            44589999999999999999999999999999999999999999999999999999999999999999999999997531


Q ss_pred             CC-CcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHH
Q 003942          277 GS-PSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ  355 (784)
Q Consensus       277 g~-p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~q  355 (784)
                      .. +..+    +..+..++..+++|.||+..+|.||||+|++||.|++++||.|+|.+.. +..-...+|+|+|+|++++
T Consensus       116 ~~k~v~~----~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk-pt~~sLqervvt~sge~e~  190 (402)
T KOG2191|consen  116 VAKPVDI----LQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK-PTGISLQERVVTVSGEPEQ  190 (402)
T ss_pred             hcCCccc----cCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC-CCCccceeEEEEecCCHHH
Confidence            11 1111    0111134556799999999999999999999999999999999999643 3556788999999999999


Q ss_pred             HHHHHHHHHHHHhccc
Q 003942          356 IEIAQEMIKEVLSQTV  371 (784)
Q Consensus       356 V~~Ak~lI~~~L~~~~  371 (784)
                      +.+|..||.++|.++-
T Consensus       191 ~~~A~~~IL~Ki~eDp  206 (402)
T KOG2191|consen  191 NMKAVSLILQKIQEDP  206 (402)
T ss_pred             HHHHHHHHHHHhhcCC
Confidence            9999999999887653

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

Probab=99.93  E-value=2.4e-25  Score=232.09  Aligned_cols=251  Identities=23%  Similarity=0.184  Sum_probs=200.4

Q ss_pred             cceeeeccccccccccCCCchhhhhhhcccCceeeeccccc---ccccceeeecCchhchhhhhhhhhHhhhcCCCCCCC
Q 003942          117 QHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETK---EVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPS  193 (784)
Q Consensus       117 ~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~---~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~  193 (784)
                      .++||+||+..+|.||||+|++|..|+.+++++|+++++.+   ..++|+|.|.|+.++|....++|.++|++.......
T Consensus        39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~k  118 (402)
T KOG2191|consen   39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVAK  118 (402)
T ss_pred             eEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhcC
Confidence            78999999999999999999999999999999999998876   688999999999999999999999999844432211


Q ss_pred             -------CCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHH
Q 003942          194 -------STDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLI  266 (784)
Q Consensus       194 -------~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I  266 (784)
                             ...++...++|+||++.+|.||||+|.|||.|+++++|-|+|.......-+..+|+|+|+|++|++.+|+++|
T Consensus       119 ~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~I  198 (402)
T KOG2191|consen  119 PVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLI  198 (402)
T ss_pred             CccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHH
Confidence                   1123345689999999999999999999999999999999999544455577899999999999999999999


Q ss_pred             HHHHHhhhcCCCCccccc-------------c---cchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEE
Q 003942          267 NAVIAEADAGGSPSLVAR-------------G---LATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQ  330 (784)
Q Consensus       267 ~elI~e~~~~g~p~~~~~-------------g---~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIq  330 (784)
                      +++|.|+...++..-...             |   ..............+.|+..++|.+-|++|.++-.|-..+|+.|.
T Consensus       199 L~Ki~eDpqs~scln~sya~vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~  278 (402)
T KOG2191|consen  199 LQKIQEDPQSGSCLNISYANVSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIA  278 (402)
T ss_pred             HHHhhcCCcccceeccchhcccCcccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeeccccccee
Confidence            999999864322111000             0   001122334455667899999999999999999999999999988


Q ss_pred             eccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          331 LIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       331 I~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      |.... ..-.....+ +.+.|...++..|..||..++..
T Consensus       279 itq~l-~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~~~~  315 (402)
T KOG2191|consen  279 ITQAL-NTMAGYGYN-TNILGLGLSILAAEGVLAAKVAS  315 (402)
T ss_pred             ecccc-ccccccccc-ccccchhhhhhhhhhHHHHhhcc
Confidence            87532 112233444 77888889999999999887754

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

Probab=99.93  E-value=7.8e-26  Score=241.26  Aligned_cols=242  Identities=21%  Similarity=0.246  Sum_probs=201.0

Q ss_pred             ccceeeeccccccccccCCCchhhhhhhcccCceeeeccccc---ccccceeeecCchhchhhhhhhhhHhhhcC---CC
Q 003942          116 EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETK---EVTVKEEETVKEEESVEPSNVVPQQVVDNS---KS  189 (784)
Q Consensus       116 ~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~---~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~---~~  189 (784)
                      +...||+.-+..+|+||||.|.+||+|..+++++|.|+.-.+   ...+|.+.++|+.|+|..|..+|.++|+++   ++
T Consensus       279 e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl  358 (584)
T KOG2193|consen  279 EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDL  358 (584)
T ss_pred             hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhH
Confidence            445588999999999999999999999999999999987654   566899999999999999999998887611   00


Q ss_pred             ------C--------------CCCC----------------------CCCCCeEEEEEecCCccceeeccCcchHhhHHh
Q 003942          190 ------D--------------DPSS----------------------TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQY  227 (784)
Q Consensus       190 ------~--------------~~~~----------------------~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~  227 (784)
                            +              ...+                      -..+...++|.||...||.||||+|.+||.|.+
T Consensus       359 ~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~R  438 (584)
T KOG2193|consen  359 AAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSR  438 (584)
T ss_pred             HHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHH
Confidence                  0              0000                      002345679999999999999999999999999


Q ss_pred             hcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCce
Q 003942          228 NSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKV  307 (784)
Q Consensus       228 ~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~v  307 (784)
                      .+||.|+|...  ..+...+|.|+|+|..+...||.-.|.-+|+|+..+..            ..+...+.+|.||...+
T Consensus       439 fagASiKIapp--E~pdvseRMViItGppeaqfKAQgrifgKikEenf~~P------------keevklethirVPs~~a  504 (584)
T KOG2193|consen  439 FAGASIKIAPP--EIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFLP------------KEEVKLETHIRVPSSAA  504 (584)
T ss_pred             hccceeeecCC--CCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccCCc------------hhhheeeeeeeccchhh
Confidence            99999999864  35668899999999999999999999999999753211            11345567899999999


Q ss_pred             eeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccCC
Q 003942          308 GLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRP  373 (784)
Q Consensus       308 G~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~r~  373 (784)
                      |+||||||.|+++|++.|+|.|.|.++..  .+..+..+|.|+|..-+++.|.+.|.++|.+.++.
T Consensus       505 GRvIGKGGktVnELQnlt~AeV~vPrdqt--pdEnd~vivriiGhfyatq~aQrki~~iv~qvkq~  568 (584)
T KOG2193|consen  505 GRVIGKGGKTVNELQNLTSAEVVVPRDQT--PDENDQVIVRIIGHFYATQNAQRKIAHIVNQVKQS  568 (584)
T ss_pred             hhhhccccccHHHHhccccceEEccccCC--CCccceeeeeeechhhcchHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999988763  33455667899999999999999999999987664

>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=1.1e-20  Score=192.23  Aligned_cols=147  Identities=22%  Similarity=0.401  Sum_probs=130.7

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCC
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGS  278 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~  278 (784)
                      .+.++|||-+..+|.||||+|++||+|+.+++|+|+|.+.     +..+|+|+|+.+.+.|...++.|.-.|++...   
T Consensus        47 r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds-----~~peri~tisad~~ti~~ilk~iip~lee~f~---  118 (390)
T KOG2192|consen   47 RVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS-----SGPERILTISADIETIGEILKKIIPTLEEGFQ---  118 (390)
T ss_pred             ceeEEEEEecccccceeccccccHHHHhhhccceeeccCC-----CCCceeEEEeccHHHHHHHHHHHhhhhhhCCC---
Confidence            4799999999999999999999999999999999999864     46799999999999988888777777766411   


Q ss_pred             CcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHH
Q 003942          279 PSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEI  358 (784)
Q Consensus       279 p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~  358 (784)
                                   .....+++|+|..+++|.||||+|++||+||++..||++|..++.|   .+++|+|.|.|.++.|-.
T Consensus       119 -------------~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p---~stdrv~l~~g~~k~v~~  182 (390)
T KOG2192|consen  119 -------------LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCP---HSTDRVVLIGGKPKRVVE  182 (390)
T ss_pred             -------------CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCC---CCcceEEEecCCcchHHH
Confidence                         1245788999999999999999999999999999999999987655   789999999999999999


Q ss_pred             HHHHHHHHHhc
Q 003942          359 AQEMIKEVLSQ  369 (784)
Q Consensus       359 Ak~lI~~~L~~  369 (784)
                      ++++|+++|++
T Consensus       183 ~i~~il~~i~e  193 (390)
T KOG2192|consen  183 CIKIILDLISE  193 (390)
T ss_pred             HHHHHHHHhhc
Confidence            99999999987

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

Probab=99.84  E-value=1.4e-20  Score=213.24  Aligned_cols=159  Identities=29%  Similarity=0.484  Sum_probs=134.9

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec---------chhhHHHHHHHHHHH
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG---------TLSNIDKAEKLINAV  269 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G---------~~e~V~kA~~~I~el  269 (784)
                      ..++||+++-..||.||||+|++||+||++|.++|+|..   .++++.+|+|+|+|         ..++|.+|.++|...
T Consensus        42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~---~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~  118 (485)
T KOG2190|consen   42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNE---SLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFK  118 (485)
T ss_pred             cceEEEEeccccceeEEccCcHHHHHHhhcccccceeec---CCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhc
Confidence            345899999999999999999999999999999999985   36788999999999         999999999999988


Q ss_pred             HHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEE
Q 003942          270 IAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRV  349 (784)
Q Consensus       270 I~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I  349 (784)
                      +.+++...    .+.+.   ......++++|+||.++||.||||+|++||+|+++|||+|+|..+.+|   .+++|.|+|
T Consensus       119 ~~~d~~~~----~d~~~---~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP---~ster~V~I  188 (485)
T KOG2190|consen  119 LEEDDEAA----EDNGE---DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLP---NSTERAVTI  188 (485)
T ss_pred             cccccccc----ccCCc---cccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCC---cccceeEEE
Confidence            77442210    00010   001114789999999999999999999999999999999999998777   678999999


Q ss_pred             EcCHHHHHHHHHHHHHHHhcc
Q 003942          350 TGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       350 ~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      .|..+.|.+|...|..+|.+.
T Consensus       189 sG~~~av~~al~~Is~~L~~~  209 (485)
T KOG2190|consen  189 SGEPDAVKKALVQISSRLLEN  209 (485)
T ss_pred             cCchHHHHHHHHHHHHHHHhc
Confidence            999999999999999988764

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.74  E-value=1.1e-17  Score=167.12  Aligned_cols=139  Identities=27%  Similarity=0.444  Sum_probs=109.0

Q ss_pred             EEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEE---ecchhhHHHHHHHHHHHHHhhhcCCCCc
Q 003942          204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEI---IGTLSNIDKAEKLINAVIAEADAGGSPS  280 (784)
Q Consensus       204 I~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I---~G~~e~V~kA~~~I~elI~e~~~~g~p~  280 (784)
                      |.||.+++|.|||++|++||.|+++|+|+|.|..+        +..|.|   +++.+.+.+|+++|..+.....    +.
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--------TGEVKIEEEDEDPLAVMKAREVVKAIGRGFS----PE   69 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--------CceEEEecCCCCHHHHHHHHHHHHHHHcCCC----HH
Confidence            67899999999999999999999999999999854        356788   6799999999999999876421    10


Q ss_pred             ccccccchhhccCCccEEEEEecC---------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEc
Q 003942          281 LVARGLATAQASGAAEQVEIKVPN---------EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG  351 (784)
Q Consensus       281 ~~~~g~~~~~~~~~~~~~~i~VP~---------~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~G  351 (784)
                      .. ..+    .........+.|..         +.+|+|||++|++|+.|++.|||+|.|.           +++|+|.|
T Consensus        70 ~A-~~l----~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~-----------~~~v~i~G  133 (172)
T TIGR03665        70 KA-LKL----LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY-----------GKTVGIIG  133 (172)
T ss_pred             HH-HHh----cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc-----------CCEEEEEC
Confidence            00 000    00111222233433         3799999999999999999999999994           36899999


Q ss_pred             CHHHHHHHHHHHHHHHhcc
Q 003942          352 DMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       352 t~~qV~~Ak~lI~~~L~~~  370 (784)
                      +.++|+.|+++|+++|+..
T Consensus       134 ~~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665       134 DPEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             CHHHHHHHHHHHHHHHcCC
Confidence            9999999999999999643

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=5.5e-17  Score=163.23  Aligned_cols=143  Identities=27%  Similarity=0.426  Sum_probs=110.8

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEe----cchhhHHHHHHHHHHHHHhhhc
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEII----GTLSNIDKAEKLINAVIAEADA  275 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~----G~~e~V~kA~~~I~elI~e~~~  275 (784)
                      +...|.||.+++|.|||++|++||.|+++|||+|+|..+        +..|.|.    ++.+.+.+|+++|++++...+.
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            578999999999999999999999999999999999854        3577885    6999999999999998873210


Q ss_pred             CCCCcccccccchhhccCCccEEEEEec----C-----CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceE
Q 003942          276 GGSPSLVARGLATAQASGAAEQVEIKVP----N-----EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERI  346 (784)
Q Consensus       276 ~g~p~~~~~g~~~~~~~~~~~~~~i~VP----~-----~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~  346 (784)
                      ...-.++.         .......+.|.    +     ..+|+|||++|++||.|++.|||+|.|.           ++.
T Consensus        75 e~A~~l~g---------d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~-----------~~~  134 (180)
T PRK13763         75 EKALRLLD---------DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY-----------GKT  134 (180)
T ss_pred             HHHHHHhC---------CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc-----------CCE
Confidence            00000000         01111111111    1     3789999999999999999999999995           345


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          347 VRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       347 V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      |+|.|+.++|+.|+++|+.+++..
T Consensus       135 v~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        135 VAIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             EEEEeCHHHHHHHHHHHHHHHcCC
Confidence            999999999999999999999643

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.55  E-value=5.6e-15  Score=147.71  Aligned_cols=141  Identities=23%  Similarity=0.285  Sum_probs=110.5

Q ss_pred             eeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCC-CCCCC
Q 003942          121 VEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSS-TDDST  199 (784)
Q Consensus       121 i~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~-~~~~~  199 (784)
                      +.||.++++.|||++|++|+.|++.++++|+|.+++.....+  ..+++.+++.+|+.+|..+...+....... ..+..
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~--~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~gd~y   79 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIE--EEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDY   79 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEe--cCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcCCcc
Confidence            568999999999999999999999999999999764322111  248999999999999999887544321110 11222


Q ss_pred             eEEEEEecC---------CccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHH
Q 003942          200 MSRKIEVPN---------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVI  270 (784)
Q Consensus       200 ~t~rI~VP~---------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI  270 (784)
                      +..-|.|..         ..+|+|||++|+|||.|++.|+|+|.|..          +.|+|+|+.++|+.|+++|++||
T Consensus        80 ~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~~~i~~li  149 (172)
T TIGR03665        80 MLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----------KTVGIIGDPEQVQIAREAIEMLI  149 (172)
T ss_pred             eEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC----------CEEEEECCHHHHHHHHHHHHHHH
Confidence            233344444         36999999999999999999999999973          57999999999999999999999


Q ss_pred             Hhh
Q 003942          271 AEA  273 (784)
Q Consensus       271 ~e~  273 (784)
                      ...
T Consensus       150 ~~~  152 (172)
T TIGR03665       150 EGA  152 (172)
T ss_pred             cCC
Confidence            543

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.

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

Probab=99.55  E-value=9e-15  Score=162.34  Aligned_cols=235  Identities=22%  Similarity=0.247  Sum_probs=179.3

Q ss_pred             ccceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCC
Q 003942          116 EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSST  195 (784)
Q Consensus       116 ~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~  195 (784)
                      ....+++++...+-++|||.|.+|+.|+..+.++|.+.+++..+ .+...+.+-...+.+|+.+|..++.++        
T Consensus        67 ~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~-e~~~~~~~~p~~v~~a~a~~~~~~~~~--------  137 (608)
T KOG2279|consen   67 DIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGD-ERVLLISGFPVQVCKAKAAIHQILTEN--------  137 (608)
T ss_pred             heeeeEeecccceeeeeccccCCcchhhcccccceecCcccCCc-ccchhhccCCCCCChHHHHHHHHHhcC--------
Confidence            34568999999999999999999999999999999888777654 444555568889999999988888533        


Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhc
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA  275 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~  275 (784)
                        ..+.+.+-||...+++||||+|++|+.|++.++++|.+.....   ....+...|.+...-++.|..+|.+.+.+...
T Consensus       138 --~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr---~g~~~~~~i~~qqk~~~~a~~~~~~~~~edee  212 (608)
T KOG2279|consen  138 --TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR---LGLSRLIKISGQQKEVAAAKHLILEKVSEDEE  212 (608)
T ss_pred             --Ccccccccchhhhcccccccchhhhcchhcccccccccccccc---cccccceecccccchHHHHHhhhhccccchhH
Confidence              3477889999999999999999999999999999999987632   34578888888888888999999888776541


Q ss_pred             C-------------------------------CCCccc-------ccc--------------c-----c-h-----hhcc
Q 003942          276 G-------------------------------GSPSLV-------ARG--------------L-----A-T-----AQAS  292 (784)
Q Consensus       276 ~-------------------------------g~p~~~-------~~g--------------~-----~-~-----~~~~  292 (784)
                      .                               +.+.+-       ..+              +     + .     ....
T Consensus       213 lv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~  292 (608)
T KOG2279|consen  213 LVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKS  292 (608)
T ss_pred             HhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccc
Confidence            0                               000000       000              0     0 0     0011


Q ss_pred             CCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCC-CceEEEEEcCHHHHHHHHHHHHHH
Q 003942          293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGS-KERIVRVTGDMRQIEIAQEMIKEV  366 (784)
Q Consensus       293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~-~er~V~I~Gt~~qV~~Ak~lI~~~  366 (784)
                      ......+|.||+.++|+|||+.|++|+.+...|++++.|.-..  ..... .-.+|+|.|+...++++..||..+
T Consensus       293 ~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~p--yt~~v~~~qic~~egkqh~~n~vl~ml~~~  365 (608)
T KOG2279|consen  293 EALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQP--YTSRVLQLQICVNEGKQHYENSVLEMLTVH  365 (608)
T ss_pred             cccccceeecCcccccchhhhhhhhhhhhhhccCccceEEecc--ccchhhhhhhheecchhHHHHHHHhhhhcc
Confidence            2234578899999999999999999999999999999886543  11111 124688999999999999999844

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.53  E-value=9.5e-15  Score=147.07  Aligned_cols=144  Identities=20%  Similarity=0.267  Sum_probs=110.8

Q ss_pred             ceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCC-CC
Q 003942          118 HSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSS-TD  196 (784)
Q Consensus       118 ~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~-~~  196 (784)
                      ...+.||.++++.|||++|++|+.|++.++++|+|.+++.....+.+. +++.+++++|+.+|..++..+....... ..
T Consensus         4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~-~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~g   82 (180)
T PRK13763          4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTD-GEDPLAVLKARDIVKAIGRGFSPEKALRLLD   82 (180)
T ss_pred             eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCC-CCCHHHHHHHHHHHHHHhcCCCHHHHHHHhC
Confidence            457899999999999999999999999999999999865333222223 6899999999999999987543221100 01


Q ss_pred             CCCeEEEEEecC---------CccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHH
Q 003942          197 DSTMSRKIEVPN---------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN  267 (784)
Q Consensus       197 ~~~~t~rI~VP~---------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~  267 (784)
                      +.....-+.|..         ..+|+|||++|+|+|.|++.|+|+|.|..          +.|+|+|+.++++.|+++|+
T Consensus        83 d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~~~I~  152 (180)
T PRK13763         83 DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG----------KTVAIIGDPEQVEIAREAIE  152 (180)
T ss_pred             CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----------CEEEEEeCHHHHHHHHHHHH
Confidence            111112222221         36999999999999999999999999973          34899999999999999999


Q ss_pred             HHHHh
Q 003942          268 AVIAE  272 (784)
Q Consensus       268 elI~e  272 (784)
                      +||..
T Consensus       153 ~li~g  157 (180)
T PRK13763        153 MLIEG  157 (180)
T ss_pred             HHHcC
Confidence            99954

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.34  E-value=2.7e-12  Score=108.04  Aligned_cols=65  Identities=35%  Similarity=0.630  Sum_probs=58.5

Q ss_pred             EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 003942          297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIK  364 (784)
Q Consensus       297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~  364 (784)
                      +++|+||.+++|+||||+|++||+|+++|||+|.|.+...   ....+|+|+|.|+.++|.+|+.||.
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL---PGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC---CCCCceEEEEEeCHHHHHHHHHhhC
Confidence            3689999999999999999999999999999999986432   3578999999999999999999983

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=99.27  E-value=6.5e-12  Score=105.68  Aligned_cols=65  Identities=35%  Similarity=0.567  Sum_probs=59.1

Q ss_pred             EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHH
Q 003942          201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN  267 (784)
Q Consensus       201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~  267 (784)
                      +++|+||.+++|+||||+|++||+|+++|||+|.|..+.+  ....+|+|+|+|+.++|.+|+.+|.
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--CCCCceEEEEEeCHHHHHHHHHhhC
Confidence            4799999999999999999999999999999999987542  4577899999999999999999983

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

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

Probab=99.26  E-value=6.2e-11  Score=118.45  Aligned_cols=140  Identities=28%  Similarity=0.463  Sum_probs=109.2

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecc-----hhhHHHHHHHHHHHHHhh
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT-----LSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~-----~e~V~kA~~~I~elI~e~  273 (784)
                      ...+.+.||...++.|||++|++.|.|.+.++++|.|+.+        +..|+|..+     +-.+.+|+++|..+=   
T Consensus         7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~--------~~~V~i~~~~~t~Dp~~~~ka~d~VkAIg---   75 (194)
T COG1094           7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK--------TGSVTIRTTRKTEDPLALLKARDVVKAIG---   75 (194)
T ss_pred             cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC--------CCeEEEEecCCCCChHHHHHHHHHHHHHh---
Confidence            3567899999999999999999999999999999999854        467777654     457888888887753   


Q ss_pred             hcCCCCcccccccchhhcc----CCccEEEEEe------cC----CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCC
Q 003942          274 DAGGSPSLVARGLATAQAS----GAAEQVEIKV------PN----EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEG  339 (784)
Q Consensus       274 ~~~g~p~~~~~g~~~~~~~----~~~~~~~i~V------P~----~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~  339 (784)
                                +||.+..+.    .......|.|      ..    ...|+|||++|.|-+.|.+.|+|.|.|-       
T Consensus        76 ----------rGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~-------  138 (194)
T COG1094          76 ----------RGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY-------  138 (194)
T ss_pred             ----------cCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe-------
Confidence                      344433221    1222222222      11    3569999999999999999999999994       


Q ss_pred             CCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          340 DGSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       340 ~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                          ..+|.|.|..++|+.|++.|+.+|+..
T Consensus       139 ----g~tVaiiG~~~~v~iAr~AVemli~G~  165 (194)
T COG1094         139 ----GKTVAIIGGFEQVEIAREAVEMLINGA  165 (194)
T ss_pred             ----CcEEEEecChhhhHHHHHHHHHHHcCC
Confidence                568999999999999999999999754

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

Probab=99.15  E-value=9.8e-11  Score=97.43  Aligned_cols=58  Identities=29%  Similarity=0.514  Sum_probs=53.1

Q ss_pred             EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHH
Q 003942          297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIK  364 (784)
Q Consensus       297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~  364 (784)
                      ...|.||.+++|+||||+|++||+|+++|||+|.|..          ++.|+|+|+ .+.|+.|+++|+
T Consensus         3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~----------~g~v~I~G~~~~~v~~A~~~I~   61 (61)
T cd02393           3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED----------DGTVYIAASDKEAAEKAKKMIE   61 (61)
T ss_pred             EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC----------CCEEEEEeCCHHHHHHHHHHhC
Confidence            5679999999999999999999999999999999953          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.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.15  E-value=3.9e-11  Score=99.07  Aligned_cols=60  Identities=37%  Similarity=0.629  Sum_probs=54.5

Q ss_pred             EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 003942          297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI  363 (784)
Q Consensus       297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI  363 (784)
                      +.+|.||.+++++|||++|++||+|+++|||+|.|.++      + ....|+|+|+.++|+.|++||
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            57899999999999999999999999999999999642      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=99.14  E-value=6e-11  Score=98.59  Aligned_cols=61  Identities=28%  Similarity=0.499  Sum_probs=55.5

Q ss_pred             EEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 003942          298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIK  364 (784)
Q Consensus       298 ~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~  364 (784)
                      .+|.||.+++++|||++|++|++|+++|||+|.|.+..      ..++.|+|+|+.++|+.|+.+|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~------~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG------SKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC------CCCCEEEEEcCHHHHHHHHHHhC
Confidence            57999999999999999999999999999999996532      56899999999999999999873

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=99.14  E-value=1.4e-10  Score=96.41  Aligned_cols=63  Identities=43%  Similarity=0.695  Sum_probs=56.8

Q ss_pred             EEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 003942          298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIK  364 (784)
Q Consensus       298 ~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~  364 (784)
                      .+|.||.+++++|||++|++|++|+++|||+|.|....    +...++.|+|.|+.++|+.|+.+|+
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            57999999999999999999999999999999997632    2467899999999999999999873

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=99.06  E-value=1.6e-10  Score=129.00  Aligned_cols=144  Identities=30%  Similarity=0.527  Sum_probs=123.3

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCC
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGG  277 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g  277 (784)
                      ..+.++++|+...|-+||||.|.+||.|++.+++||.+..+.    ...+++..+.|....|.+|..+|+.++.+.    
T Consensus        66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed----~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~----  137 (608)
T KOG2279|consen   66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED----VGDERVLLISGFPVQVCKAKAAIHQILTEN----  137 (608)
T ss_pred             hheeeeEeecccceeeeeccccCCcchhhcccccceecCccc----CCcccchhhccCCCCCChHHHHHHHHHhcC----
Confidence            457889999999999999999999999999999999998653    233566666779999999999999988775    


Q ss_pred             CCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHH
Q 003942          278 SPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE  357 (784)
Q Consensus       278 ~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~  357 (784)
                                      ..++..+.||.+.+++||||+|++|+.|+..|+++|.+...    +-....+.+.|.+...-++
T Consensus       138 ----------------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n----gr~g~~~~~~i~~qqk~~~  197 (608)
T KOG2279|consen  138 ----------------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN----GRLGLSRLIKISGQQKEVA  197 (608)
T ss_pred             ----------------Ccccccccchhhhcccccccchhhhcchhcccccccccccc----cccccccceecccccchHH
Confidence                            33567788999999999999999999999999999998753    3445678888889888999


Q ss_pred             HHHHHHHHHHhc
Q 003942          358 IAQEMIKEVLSQ  369 (784)
Q Consensus       358 ~Ak~lI~~~L~~  369 (784)
                      .|+.||.+.|++
T Consensus       198 ~a~~~~~~~~~e  209 (608)
T KOG2279|consen  198 AAKHLILEKVSE  209 (608)
T ss_pred             HHHhhhhccccc
Confidence            999999988765

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.05  E-value=1.9e-10  Score=95.58  Aligned_cols=62  Identities=27%  Similarity=0.506  Sum_probs=56.4

Q ss_pred             EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHH
Q 003942          201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN  267 (784)
Q Consensus       201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~  267 (784)
                      +++|.||..++++|||++|++|++|+++|||+|.|....     ..++.|+|+|+.++|.+|+.+|+
T Consensus         1 ~~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-----~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-----SKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             CeEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-----CCCCEEEEEcCHHHHHHHHHHhC
Confidence            368999999999999999999999999999999999652     55789999999999999999874

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.04  E-value=1.1e-10  Score=96.25  Aligned_cols=60  Identities=40%  Similarity=0.668  Sum_probs=54.8

Q ss_pred             EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHH
Q 003942          201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLI  266 (784)
Q Consensus       201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I  266 (784)
                      |.+|+||..++|+|||++|++||+|+++|+|+|+|.++     . .+..|+|+|+.++|++|+++|
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            67999999999999999999999999999999999854     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 ....

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

Probab=99.01  E-value=5.6e-10  Score=92.73  Aligned_cols=64  Identities=38%  Similarity=0.601  Sum_probs=57.3

Q ss_pred             EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHH
Q 003942          201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN  267 (784)
Q Consensus       201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~  267 (784)
                      +.+|.||.+++++|||++|++|++|+++|+|+|.|....+   ...++.|+|.|+.++|.+|+.+|.
T Consensus         1 ~~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~~v~~a~~~i~   64 (64)
T cd00105           1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVEKAKELIL   64 (64)
T ss_pred             CEEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHHHHHHHHHHhC
Confidence            3689999999999999999999999999999999997532   456889999999999999999873

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

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

Probab=99.01  E-value=5.2e-10  Score=93.09  Aligned_cols=59  Identities=29%  Similarity=0.470  Sum_probs=53.8

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecc-hhhHHHHHHHHH
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT-LSNIDKAEKLIN  267 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~-~e~V~kA~~~I~  267 (784)
                      .+..|.||.+++|+||||+|++||+|+++|||+|.|.+         ++.|+|+|+ .++|++|+++|+
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            46789999999999999999999999999999999985         357999997 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.

>smart00322 KH K homology RNA-binding domain

Probab=98.90  E-value=7.6e-09  Score=85.68  Aligned_cols=67  Identities=42%  Similarity=0.746  Sum_probs=60.0

Q ss_pred             cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942          296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS  368 (784)
Q Consensus       296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~  368 (784)
                      .+.+|.|+.+++++|||++|++|++|++.|+|+|.+....      ...++|+|.|+.++|+.|+.+|.++|+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~------~~~~~v~i~g~~~~v~~a~~~i~~~~~   69 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG------SEERVVEITGPPENVEKAAELILEILE   69 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC------CCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence            5688999999999999999999999999999999996432      257899999999999999999998873

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

Probab=98.82  E-value=8.2e-09  Score=103.41  Aligned_cols=146  Identities=17%  Similarity=0.224  Sum_probs=116.5

Q ss_pred             ceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCC-
Q 003942          118 HSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTD-  196 (784)
Q Consensus       118 ~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~-  196 (784)
                      ...+.||...++.|||+.|++.+.|...+++++.|...+.....+...-+.+.-++.+|+.+|..+-..++........ 
T Consensus         9 ~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL~   88 (194)
T COG1094           9 SEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALKLLE   88 (194)
T ss_pred             eeeeecCchhheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHHHhc
Confidence            4468999999999999999999999988888888887776665555555678889999999999988766654443211 


Q ss_pred             CCCeEEEEEecC----------CccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHH
Q 003942          197 DSTMSRKIEVPN----------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLI  266 (784)
Q Consensus       197 ~~~~t~rI~VP~----------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I  266 (784)
                      +..+...|.|-.          ...|+|||++|.|.+.|++-|+|.|.|-.          ..|.|.|..++|..|++.|
T Consensus        89 d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG~~~~v~iAr~AV  158 (194)
T COG1094          89 DDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIGGFEQVEIAREAV  158 (194)
T ss_pred             CCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEecChhhhHHHHHHH
Confidence            233333343321          24799999999999999999999999984          4899999999999999999


Q ss_pred             HHHHHhh
Q 003942          267 NAVIAEA  273 (784)
Q Consensus       267 ~elI~e~  273 (784)
                      +.+|.-.
T Consensus       159 emli~G~  165 (194)
T COG1094         159 EMLINGA  165 (194)
T ss_pred             HHHHcCC
Confidence            9998754

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.79  E-value=2.2e-08  Score=120.51  Aligned_cols=213  Identities=18%  Similarity=0.193  Sum_probs=149.7

Q ss_pred             cceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCC
Q 003942          117 QHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTD  196 (784)
Q Consensus       117 ~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~  196 (784)
                      ......+.....-.+++..|+.|..|..... ++.+...+.......+++.+....+..+.+....++.+.        .
T Consensus       273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~  343 (753)
T KOG2208|consen  273 FDYDEIIYRRLPRFIRGIPGEEINQLRDYMP-EVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNS--------E  343 (753)
T ss_pred             hhhhhhhhccccccccccccchhhHHHhhcc-hhhhhhccccccceeEeecccccchhhhhhHHHHHHHHh--------h
Confidence            3445666677777899999999999973221 222222222233344566666666555554333333211        1


Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcC
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAG  276 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~  276 (784)
                      ...+...+.|-...+..||||+|.+|.+|++++.|+|.+...     .+.+..|.|++...++.+|.+.|+.++.+... 
T Consensus       344 ~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-----~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n-  417 (753)
T KOG2208|consen  344 ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ-----GSNNKKVVITGVSANDEKAVEDVEKIIAEILN-  417 (753)
T ss_pred             ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc-----cCCCCCeEEeccccchhHHHHHHHHHHHhhhc-
Confidence            223677888888999999999999999999999999999874     34578999999999999999999999998632 


Q ss_pred             CCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCC-eEEeccCCCCCCCCCCceEEEEEcCHHH
Q 003942          277 GSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGA-RIQLIPQHLPEGDGSKERIVRVTGDMRQ  355 (784)
Q Consensus       277 g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGa-rIqI~~~~~p~~~~~~er~V~I~Gt~~q  355 (784)
                                       ...+..+.||...+.+|||.+|..|..|..++++ .|++.+..      +....++|.|....
T Consensus       418 -----------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~------~~~~~~~~~~~~~d  474 (753)
T KOG2208|consen  418 -----------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN------NSSDMVTIRGISKD  474 (753)
T ss_pred             -----------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC------cccccceEeccccc
Confidence                             1346679999999999999999999999999995 45554322      33445666666555


Q ss_pred             HHHHHHHHHHHH
Q 003942          356 IEIAQEMIKEVL  367 (784)
Q Consensus       356 V~~Ak~lI~~~L  367 (784)
                      |..++.++..+.
T Consensus       475 v~~~~~~~~~~~  486 (753)
T KOG2208|consen  475 VEKSVSLLKALK  486 (753)
T ss_pred             cchhHHHHHhhh
Confidence            555555544433

>PF13014 KH_3: KH domain

Probab=98.78  E-value=1e-08  Score=79.21  Aligned_cols=43  Identities=51%  Similarity=0.883  Sum_probs=38.1

Q ss_pred             ceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEc
Q 003942          306 KVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG  351 (784)
Q Consensus       306 ~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~G  351 (784)
                      +||+||||+|++||+|+++|||+|+|.++   ......+|+|+|+|
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            58999999999999999999999999873   33467899999997

>smart00322 KH K homology RNA-binding domain

Probab=98.77  E-value=2.6e-08  Score=82.43  Aligned_cols=67  Identities=37%  Similarity=0.677  Sum_probs=60.2

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHH
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVI  270 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI  270 (784)
                      .++.+|.|+.+++++|||++|++|+.|++.|+++|.+....     .....|+|.|..+++..|+.+|.+++
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-----~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-----SEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-----CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            36789999999999999999999999999999999998542     14678999999999999999999876

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.76  E-value=8.9e-09  Score=123.78  Aligned_cols=218  Identities=16%  Similarity=0.243  Sum_probs=160.6

Q ss_pred             ccccceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCC
Q 003942          114 KTEQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPS  193 (784)
Q Consensus       114 ~~~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~  193 (784)
                      +.+..+++.|....+.-++||+|.+|.+|++++++.|.+.....  ..+.+.+++...++++|.+.|.+++.+....   
T Consensus       344 ~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~--~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~---  418 (753)
T KOG2208|consen  344 ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGS--NNKKVVITGVSANDEKAVEDVEKIIAEILNS---  418 (753)
T ss_pred             ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccC--CCCCeEEeccccchhHHHHHHHHHHHhhhcc---
Confidence            34566788888889999999999999999999999999988443  3467888999999999999998888533221   


Q ss_pred             CCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcC-CEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942          194 STDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSG-AKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE  272 (784)
Q Consensus       194 ~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TG-akI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e  272 (784)
                           .+...+.||...+.+|||.+|..|..|.++++ +.|.+...     .+....+++.+....|.+++.++..+...
T Consensus       419 -----~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-----~~~~~~~~~~~~~~dv~~~~~~~~~~~~~  488 (753)
T KOG2208|consen  419 -----IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-----NNSSDMVTIRGISKDVEKSVSLLKALKAD  488 (753)
T ss_pred             -----cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-----CcccccceEeccccccchhHHHHHhhhhh
Confidence                 45778999999999999999999999999999 66666543     33445678888777777777776665554


Q ss_pred             hhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC
Q 003942          273 ADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD  352 (784)
Q Consensus       273 ~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt  352 (784)
                      ....              ......+.+.+.+..+++.++|+.|.    |++..+.+..|..     .+...+..++|.|.
T Consensus       489 a~~~--------------~~~~~~~~d~~~~~~~~~~~~g~~~~----i~d~~~~~~i~~~-----~~~~~~~~i~i~gk  545 (753)
T KOG2208|consen  489 AKNL--------------KFRDVVTKDKLLPVKYIGKEIGKNGT----IRDSLGDKSIFPP-----NEDEDHEKITIEGK  545 (753)
T ss_pred             hhcc--------------hhhhhhhccccchHHhhcccccCcee----eeccCCceeeccc-----ccccccceeeeccc
Confidence            3210              00122344556666777777776665    4555555544432     22345678999999


Q ss_pred             HHHHHHHHHHHHHHHhc
Q 003942          353 MRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       353 ~~qV~~Ak~lI~~~L~~  369 (784)
                      .+.|..|.++|..+++.
T Consensus       546 ~~~v~~a~~~L~~~~~~  562 (753)
T KOG2208|consen  546 LELVLEAPAELKALIEA  562 (753)
T ss_pred             ccchhhhHHHHHhcchh
Confidence            99999999999877764

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

Probab=98.70  E-value=1.3e-08  Score=106.88  Aligned_cols=153  Identities=22%  Similarity=0.333  Sum_probs=113.6

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhc-C
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA-G  276 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~-~  276 (784)
                      ..+++.+.||..+|+.|+|++|.+||.|+.+|.+.|......      .+-+|.++|..+.|+.|++.|...-+..-. .
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~------eePiF~vTg~~edv~~aRrei~saaeH~~l~~   97 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG------EEPIFPVTGRHEDVRRARREIPSAAEHFGLIR   97 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC------CCCcceeccCchhHHHHhhcCccccceeeeee
Confidence            568899999999999999999999999999999999988653      256899999999999999999763222100 0


Q ss_pred             CCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHH-H
Q 003942          277 GSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMR-Q  355 (784)
Q Consensus       277 g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~-q  355 (784)
                      .++... .+.. ........+....||-+.||+|+|..|++||.|++.+...|...-.       ..+.++.|+|-.. +
T Consensus        98 ~s~s~S-gg~~-~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~-------~~~~Vf~Vtg~~~nC  168 (394)
T KOG2113|consen   98 ASRSFS-GGTN-GASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR-------CGEPVFCVTGAPKNC  168 (394)
T ss_pred             eccccc-CCCc-cccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc-------CCCceEEEecCCcch
Confidence            000000 0000 0112345677889999999999999999999999999998876432       3578899999755 4


Q ss_pred             HHHHH-HHHHH
Q 003942          356 IEIAQ-EMIKE  365 (784)
Q Consensus       356 V~~Ak-~lI~~  365 (784)
                      |++|+ ..|+.
T Consensus       169 ~kra~s~eie~  179 (394)
T KOG2113|consen  169 VKRARSCEIEQ  179 (394)
T ss_pred             hhhccccchhh
Confidence            77777 44554

>PF13014 KH_3: KH domain

Probab=98.65  E-value=3.1e-08  Score=76.46  Aligned_cols=43  Identities=44%  Similarity=0.696  Sum_probs=38.5

Q ss_pred             ccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec
Q 003942          210 KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG  254 (784)
Q Consensus       210 ~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G  254 (784)
                      +||+||||+|++||+|+++|+|+|+|.+  +..+...+|.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~--~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPP--ENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECC--ccCCCCCceEEEEEC
Confidence            4899999999999999999999999998  345577899999987

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

Probab=98.63  E-value=1.2e-07  Score=89.61  Aligned_cols=67  Identities=28%  Similarity=0.416  Sum_probs=53.7

Q ss_pred             CceeeeecCCchHHHHHHHHhCCeEEeccCCCCC-------------CCCCCceEEEEEcCH---HHHHHHHHHHHHHHh
Q 003942          305 EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPE-------------GDGSKERIVRVTGDM---RQIEIAQEMIKEVLS  368 (784)
Q Consensus       305 ~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~-------------~~~~~er~V~I~Gt~---~qV~~Ak~lI~~~L~  368 (784)
                      |++|+|||.+|.+||+|+++|||+|.|..+..-.             .+....-.|.|++..   +++++|+++|+.+|.
T Consensus        15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~   94 (120)
T cd02395          15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK   94 (120)
T ss_pred             CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence            8999999999999999999999999998653111             112334678899964   899999999999997


Q ss_pred             ccc
Q 003942          369 QTV  371 (784)
Q Consensus       369 ~~~  371 (784)
                      ...
T Consensus        95 ~~~   97 (120)
T cd02395          95 PAI   97 (120)
T ss_pred             cCC
Confidence            543

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

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

Probab=98.57  E-value=1.2e-07  Score=89.43  Aligned_cols=71  Identities=30%  Similarity=0.434  Sum_probs=56.1

Q ss_pred             EEEecC------CccceeeccCcchHhhHHhhcCCEEEEccCCCCCC--------------CCCCCcEEEec-c--hhhH
Q 003942          203 KIEVPN------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADP--------------HAATRPVEIIG-T--LSNI  259 (784)
Q Consensus       203 rI~VP~------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p--------------~s~eR~V~I~G-~--~e~V  259 (784)
                      +|.||.      +++|+|||.+|+|||+|+++|||+|.|..+.....              ......|.|++ +  .+.+
T Consensus         3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~   82 (120)
T cd02395           3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEAL   82 (120)
T ss_pred             EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHH
Confidence            555554      68999999999999999999999999997631110              11235788888 5  6999


Q ss_pred             HHHHHHHHHHHHhh
Q 003942          260 DKAEKLINAVIAEA  273 (784)
Q Consensus       260 ~kA~~~I~elI~e~  273 (784)
                      ++|+.+|+.+|...
T Consensus        83 ~~A~~~I~~ll~~~   96 (120)
T cd02395          83 AKAVEAIEELLKPA   96 (120)
T ss_pred             HHHHHHHHHHhccC
Confidence            99999999999865

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.

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

Probab=98.48  E-value=4.1e-07  Score=101.12  Aligned_cols=75  Identities=31%  Similarity=0.419  Sum_probs=60.6

Q ss_pred             CeEEEEEecC------CccceeeccCcchHhhHHhhcCCEEEEccCCC-------------CCCCCCCCcEEEec-chhh
Q 003942          199 TMSRKIEVPN------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDAD-------------ADPHAATRPVEIIG-TLSN  258 (784)
Q Consensus       199 ~~t~rI~VP~------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~-------------~~p~s~eR~V~I~G-~~e~  258 (784)
                      .++.||.||.      ++||+|||.+|.|+|+|+++|||||.|..+..             ......+..|.|++ +.|.
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            5777888875      68999999999999999999999999987321             11112345678888 8899


Q ss_pred             HHHHHHHHHHHHHhh
Q 003942          259 IDKAEKLINAVIAEA  273 (784)
Q Consensus       259 V~kA~~~I~elI~e~  273 (784)
                      |++|+++|+.||.+.
T Consensus       217 i~~Ai~vienli~~a  231 (554)
T KOG0119|consen  217 IKKAIAVIENLIQSA  231 (554)
T ss_pred             HHHHHHHHHHHHHhh
Confidence            999999999999974

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.26  E-value=1.8e-06  Score=83.74  Aligned_cols=104  Identities=21%  Similarity=0.363  Sum_probs=76.2

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCC
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSP  279 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p  279 (784)
                      -.+.|+|....+|..||++|++||.|++..|-+|.|...++                    .+.++|..+|.-..     
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~--------------------d~~~fI~n~l~Pa~-----   86 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD--------------------DPEEFIKNIFAPAA-----   86 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC--------------------CHHHHHHHHcCCCE-----
Confidence            46788999999999999999999999999999998885432                    23444555443221     


Q ss_pred             cccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEec
Q 003942          280 SLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLI  332 (784)
Q Consensus       280 ~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~  332 (784)
                        +..-..  ........+.+.|+.+..|++|||+|.||+.++..++-++.|.
T Consensus        87 --V~~v~I--~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         87 --VRSVTI--KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             --EEEEEE--EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence              000000  0012234567789999999999999999999999999998774

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.20  E-value=5.6e-06  Score=98.31  Aligned_cols=89  Identities=27%  Similarity=0.380  Sum_probs=69.6

Q ss_pred             HHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCC
Q 003942          261 KAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGD  340 (784)
Q Consensus       261 kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~  340 (784)
                      +|+..|.++|++....- ..+         .........|.|+.+++|.|||.||.+||.|+++|||+|.|.+       
T Consensus       553 ~g~~~Il~~m~~al~~p-~~~---------s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-------  615 (719)
T TIGR02696       553 DARLAILDVMAEAIDTP-DEM---------SPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-------  615 (719)
T ss_pred             HHHHHHHHHHHHHHhCc-ccc---------ccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-------
Confidence            44455677777764321 111         1123467889999999999999999999999999999999953       


Q ss_pred             CCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003942          341 GSKERIVRVTGD-MRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       341 ~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~  369 (784)
                         +.+|.|.+. .+.+++|+++|+.++..
T Consensus       616 ---~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       616 ---DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             ---CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence               578999997 89999999999999983

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.

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

Probab=98.20  E-value=6.2e-06  Score=91.98  Aligned_cols=75  Identities=24%  Similarity=0.329  Sum_probs=55.7

Q ss_pred             ccEEEEEecC------CceeeeecCCchHHHHHHHHhCCeEEeccCCC-----------CCCC-CCCceEEEEEcC-HHH
Q 003942          295 AEQVEIKVPN------EKVGLIIGRGGETIKGLQTRSGARIQLIPQHL-----------PEGD-GSKERIVRVTGD-MRQ  355 (784)
Q Consensus       295 ~~~~~i~VP~------~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~-----------p~~~-~~~er~V~I~Gt-~~q  355 (784)
                      ..+.+|.||-      ||||+|||-+|.|.|+|+++|||||.|.....           .... ..++--|.|+.+ .+.
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            3445555554      79999999999999999999999999985221           0011 112223677776 789


Q ss_pred             HHHHHHHHHHHHhc
Q 003942          356 IEIAQEMIKEVLSQ  369 (784)
Q Consensus       356 V~~Ak~lI~~~L~~  369 (784)
                      |++|+++|+.||.+
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999986

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

Probab=98.18  E-value=3e-06  Score=89.60  Aligned_cols=146  Identities=15%  Similarity=0.171  Sum_probs=111.7

Q ss_pred             ccceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCC-------
Q 003942          116 EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSK-------  188 (784)
Q Consensus       116 ~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~-------  188 (784)
                      ++...+.+|..+++.|.|++|..||.|+.++.+.|+-..+.+.   -++.++|..++|+.||+.|....+...       
T Consensus        25 nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~ee---PiF~vTg~~edv~~aRrei~saaeH~~l~~~s~s  101 (394)
T KOG2113|consen   25 NVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEE---PIFPVTGRHEDVRRARREIPSAAEHFGLIRASRS  101 (394)
T ss_pred             ccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCC---CcceeccCchhHHHHhhcCccccceeeeeeeccc
Confidence            4555677889999999999999999999888888876655544   578899999999999999987333111       


Q ss_pred             C--CCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhh-HHHHH-H
Q 003942          189 S--DDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN-IDKAE-K  264 (784)
Q Consensus       189 ~--~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~-V~kA~-~  264 (784)
                      +  .....-.....+..+.||...||+|+|.+|.+||+|++.+..-|....      .+.+.++.++|-.++ +++|+ .
T Consensus       102 ~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v------~~~~~Vf~Vtg~~~nC~kra~s~  175 (394)
T KOG2113|consen  102 FSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV------RCGEPVFCVTGAPKNCVKRARSC  175 (394)
T ss_pred             ccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeec------cCCCceEEEecCCcchhhhcccc
Confidence            1  111112345678889999999999999999999999999998887664      344679999997777 66676 5


Q ss_pred             HHHHHH
Q 003942          265 LINAVI  270 (784)
Q Consensus       265 ~I~elI  270 (784)
                      .|+..+
T Consensus       176 eie~ta  181 (394)
T KOG2113|consen  176 EIEQTA  181 (394)
T ss_pred             chhhhh
Confidence            555443

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.92  E-value=3.3e-05  Score=74.98  Aligned_cols=103  Identities=18%  Similarity=0.319  Sum_probs=74.4

Q ss_pred             EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCc
Q 003942          201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPS  280 (784)
Q Consensus       201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~  280 (784)
                      ..-|+|....+|..||++|++||.|++..|-+|.|..-++      +                  +.++|++..   +|.
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~------D------------------~~~fI~N~l---~PA   86 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSE------N------------------LEEFVANKL---APA   86 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCC------C------------------HHHHHHHcC---CCc
Confidence            7788999999999999999999999999999998875432      1                  333333321   121


Q ss_pred             ccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEec
Q 003942          281 LVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLI  332 (784)
Q Consensus       281 ~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~  332 (784)
                      .+..-..  ....+.....+.|+.+..+++|||+|.||+...+.++-++.|.
T Consensus        87 ~V~~V~i--~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        87 EVKNVTV--SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             eEEEEEE--EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            1110000  0012345677889999999999999999999999999998774

This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.92  E-value=2.7e-05  Score=93.71  Aligned_cols=65  Identities=25%  Similarity=0.455  Sum_probs=57.4

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~  369 (784)
                      .....|.|+.++++.|||+||++||.|+++|||+|.|.+          +..|.|.+. .+.+++|+++|+.++..
T Consensus       550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d----------dG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED----------DGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec----------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            456789999999999999999999999999999999953          467888776 78999999999998764

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).

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.84  E-value=3.1e-05  Score=92.18  Aligned_cols=67  Identities=28%  Similarity=0.409  Sum_probs=60.7

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHh
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAE  272 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e  272 (784)
                      .......|.|+.+++|.|||.+|++||.|.++|||+|.|.++         ..|.|.+ +.+.+++|+++|+.++..
T Consensus       575 ~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~---------G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       575 YAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD---------GTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             CCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC---------cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            446788999999999999999999999999999999999853         5888888 889999999999999884

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

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.81  E-value=1.7e-05  Score=77.00  Aligned_cols=102  Identities=14%  Similarity=0.103  Sum_probs=71.7

Q ss_pred             ceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCC-CCCC
Q 003942          118 HSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDP-SSTD  196 (784)
Q Consensus       118 ~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~-~~~~  196 (784)
                      ...+++....+|..||++|++|+.|++..+.+|.+-.-+                 +.++.+|..++.......- ....
T Consensus        33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s-----------------~d~~~fI~n~l~Pa~V~~v~I~~~   95 (140)
T PRK08406         33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS-----------------DDPEEFIKNIFAPAAVRSVTIKKK   95 (140)
T ss_pred             EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcC-----------------CCHHHHHHHHcCCCEEEEEEEEec
Confidence            446777888999999999999999986666565554422                 1234455555543322111 1112


Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEc
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT  236 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~  236 (784)
                      .......|.|+...+|++|||+|.||+.++.-++-++.|.
T Consensus        96 ~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         96 NGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             CCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            2345677889999999999999999999999999888764

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.77  E-value=1.1e-05  Score=97.65  Aligned_cols=68  Identities=22%  Similarity=0.434  Sum_probs=60.3

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCE-EEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhh
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAK-IQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGak-I~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~  273 (784)
                      .......|.|+.++++.|||.+|.|||.|.++||++ |.|.++         -.|.|.+ +.+.+++|+++|+.++.+.
T Consensus       682 ~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd---------g~V~I~a~d~~~i~~A~~~I~~l~~~~  751 (891)
T PLN00207        682 YAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD---------GTVKITAKDLSSLEKSKAIISSLTMVP  751 (891)
T ss_pred             cCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC---------eeEEEEeCCHHHHHHHHHHHHHHhcCc
Confidence            446788999999999999999999999999999999 888753         4788888 8899999999999998753

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

Probab=97.76  E-value=0.0001  Score=77.28  Aligned_cols=75  Identities=23%  Similarity=0.324  Sum_probs=51.3

Q ss_pred             CccEEEEEecC------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCC-------------CCCCc---eEEEEEc
Q 003942          294 AAEQVEIKVPN------EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEG-------------DGSKE---RIVRVTG  351 (784)
Q Consensus       294 ~~~~~~i~VP~------~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~-------------~~~~e---r~V~I~G  351 (784)
                      ...+.+|.||-      |+||+|||.+|.++|+|+++|||||.|....+-..             +...+   -.|++..
T Consensus        90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~  169 (259)
T KOG1588|consen   90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEA  169 (259)
T ss_pred             eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeC
Confidence            34566677765      79999999999999999999999999985432111             01111   2355666


Q ss_pred             CHHHH----HHHHHHHHHHHh
Q 003942          352 DMRQI----EIAQEMIKEVLS  368 (784)
Q Consensus       352 t~~qV----~~Ak~lI~~~L~  368 (784)
                      +.+.+    ..|++.|+.+|-
T Consensus       170 p~~ea~~rl~~AleeI~klL~  190 (259)
T KOG1588|consen  170 PPAEAYARLAYALEEIKKLLV  190 (259)
T ss_pred             CHHHHHHHHHHHHHHHHHhcC
Confidence            65433    457888888774

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.74  E-value=5.1e-05  Score=91.35  Aligned_cols=67  Identities=30%  Similarity=0.418  Sum_probs=59.0

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHh
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAE  272 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e  272 (784)
                      .......|.|+.++++.|||++|++||.|+++|||+|.|..+         ..|.|.+ +.+.+++|+++|..++.+
T Consensus       548 ~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd---------G~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       548 YAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD---------GTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             cCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC---------eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            346788999999999999999999999999999999999853         4677776 889999999999998765

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).

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

Probab=97.64  E-value=0.00019  Score=75.33  Aligned_cols=44  Identities=30%  Similarity=0.539  Sum_probs=38.8

Q ss_pred             CCCCeEEEEEecC------CccceeeccCcchHhhHHhhcCCEEEEccCC
Q 003942          196 DDSTMSRKIEVPN------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDA  239 (784)
Q Consensus       196 ~~~~~t~rI~VP~------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~  239 (784)
                      ....++.+|+||-      ++||+|||.+|.++|+|+++|+|+|.|....
T Consensus        88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrg  137 (259)
T KOG1588|consen   88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRG  137 (259)
T ss_pred             CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCC
Confidence            4456788999987      5899999999999999999999999998754

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=97.63  E-value=0.00095  Score=68.99  Aligned_cols=129  Identities=17%  Similarity=0.238  Sum_probs=95.7

Q ss_pred             EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCc
Q 003942          201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPS  280 (784)
Q Consensus       201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~  280 (784)
                      .+.|.+.....-+|+..+|..++.|-...||+|.|..+        +..|.|+|++..|+.++..|.+++...       
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~--------~~~i~I~g~k~~~~~i~~~i~~~l~~i-------   91 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS--------ENRIRITGTKSTAEYIEASINEILSNI-------   91 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC--------CcEEEEEccHHHHHHHHHHHHHHHhhc-------
Confidence            34455557788899999999999998889999999864        468999999999999999999988764       


Q ss_pred             ccccccchhhccCCccEEEEEecCCceeeee----cCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEc-----
Q 003942          281 LVARGLATAQASGAAEQVEIKVPNEKVGLII----GRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-----  351 (784)
Q Consensus       281 ~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VI----GkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~G-----  351 (784)
                                     .+.+|.++.-..-...    -.....|+.|++.|++.|+...+         ...+.|..     
T Consensus        92 ---------------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~---------~~~~~i~~~~~~~  147 (210)
T PF14611_consen   92 ---------------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD---------GNKLKISWLASPE  147 (210)
T ss_pred             ---------------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC---------CCeEEEEEEeecc
Confidence                           2344444432111111    11367899999999999998643         23344443     


Q ss_pred             CHHHHHHHHHHHHHHHh
Q 003942          352 DMRQIEIAQEMIKEVLS  368 (784)
Q Consensus       352 t~~qV~~Ak~lI~~~L~  368 (784)
                      ..+.++.|++||.-.+.
T Consensus       148 ~~~~~~~a~RlL~~a~~  164 (210)
T PF14611_consen  148 NEKRADRAKRLLLWALD  164 (210)
T ss_pred             ccchHHHHHHHHHHhcc
Confidence            47899999999998886

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.63  E-value=9.5e-05  Score=89.86  Aligned_cols=67  Identities=25%  Similarity=0.430  Sum_probs=58.8

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCe-EEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhccc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGAR-IQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQTV  371 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGar-IqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~~~  371 (784)
                      .....|.|+.++++.|||.||.+||.|.++||++ |.|.+          +..|.|.+. .+.+++|+++|++++.+..
T Consensus       684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d----------dg~V~I~a~d~~~i~~A~~~I~~l~~~~~  752 (891)
T PLN00207        684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD----------DGTVKITAKDLSSLEKSKAIISSLTMVPT  752 (891)
T ss_pred             CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC----------CeeEEEEeCCHHHHHHHHHHHHHHhcCcC
Confidence            4678899999999999999999999999999999 88743          567888886 8999999999999986543

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=97.61  E-value=0.00017  Score=73.33  Aligned_cols=103  Identities=22%  Similarity=0.354  Sum_probs=72.1

Q ss_pred             EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCc
Q 003942          201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPS  280 (784)
Q Consensus       201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~  280 (784)
                      .+-+++-.+.||..||++|.+||.|.++.|-+|.|...++                    .-.++|..+|.       |.
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~--------------------d~~~fI~nal~-------Pa  129 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE--------------------DPAEFIKNALA-------PA  129 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCC--------------------CHHHHHHHhcC-------cc
Confidence            4555556678999999999999999999998888875431                    11223333332       11


Q ss_pred             ccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942          281 LVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP  333 (784)
Q Consensus       281 ~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~  333 (784)
                      .+..-.   ..........+.|+.+..+++|||+|.+|+-+.+.||-+|.|..
T Consensus       130 ~v~~V~---~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         130 EVLSVN---IKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             eEeEEE---EEeCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            000000   00011227788899999999999999999999999999999964

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

Probab=97.60  E-value=0.00012  Score=85.49  Aligned_cols=94  Identities=23%  Similarity=0.302  Sum_probs=71.5

Q ss_pred             HHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCC
Q 003942          261 KAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGD  340 (784)
Q Consensus       261 kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~  340 (784)
                      .|+..|+.+|.+....-...         ...-......+.|+.++++.|||++|++||.|.++|||+|.|.        
T Consensus       526 ~aRlhIL~~M~~ai~~pr~e---------ls~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie--------  588 (692)
T COG1185         526 GARLHILIVMNEAISEPRKE---------LSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE--------  588 (692)
T ss_pred             HHHHHHHHHHHHHHhhhhhh---------hhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec--------
Confidence            44556777776653211001         1112345678999999999999999999999999999999995        


Q ss_pred             CCCceEEEEEcC-HHHHHHHHHHHHHHHhcccCC
Q 003942          341 GSKERIVRVTGD-MRQIEIAQEMIKEVLSQTVRP  373 (784)
Q Consensus       341 ~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~~~r~  373 (784)
                        ++.+|.|.++ .+.+++|+++|.+++++....
T Consensus       589 --ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg  620 (692)
T COG1185         589 --DDGTVKIAASDGESAKKAKERIEAITREVEVG  620 (692)
T ss_pred             --CCCcEEEEecchHHHHHHHHHHHHHHhhcccc
Confidence              3567999998 589999999999999876443

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

Probab=97.50  E-value=0.00016  Score=72.87  Aligned_cols=70  Identities=33%  Similarity=0.457  Sum_probs=50.3

Q ss_pred             CCCeEEEEEecC------CccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHH
Q 003942          197 DSTMSRKIEVPN------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAV  269 (784)
Q Consensus       197 ~~~~t~rI~VP~------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~el  269 (784)
                      ...++.+|.||-      ++||+|||..|.|+|+|++.|+|+|-|.....      ...+.|+. +.+.+..|.+.|+.+
T Consensus       145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gs------vKegk~ssd~p~~~~N~e~~lhcL  218 (269)
T COG5176         145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGS------VKEGKISSDTPESLKNAEAVLHCL  218 (269)
T ss_pred             cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccc------cccCcccccCchhhhhhHHhHHHH
Confidence            345777888874      68999999999999999999999999987532      23444544 355555555555555


Q ss_pred             HHh
Q 003942          270 IAE  272 (784)
Q Consensus       270 I~e  272 (784)
                      |..
T Consensus       219 I~a  221 (269)
T COG5176         219 IEA  221 (269)
T ss_pred             hhc
Confidence            544

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

Probab=97.47  E-value=0.00014  Score=80.03  Aligned_cols=75  Identities=21%  Similarity=0.310  Sum_probs=64.1

Q ss_pred             CCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          195 TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       195 ~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      .....+.+.|.|-++.||.|||++|++||+|+..|+++|+|.+-      ..+-.|+|.|..+--.+|...|...++..+
T Consensus        42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~------~~e~kv~ifg~~~m~~kaka~id~~~~k~e  115 (629)
T KOG0336|consen   42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC------DLEVKVTIFGINHMRKKAKASIDRGQDKDE  115 (629)
T ss_pred             cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc------CceeEEEEechHHHHHHHHhhHhhhhhhhh
Confidence            34567888999999999999999999999999999999999863      236688999998888888888888887665


Q ss_pred             c
Q 003942          275 A  275 (784)
Q Consensus       275 ~  275 (784)
                      .
T Consensus       116 ~  116 (629)
T KOG0336|consen  116 R  116 (629)
T ss_pred             h
Confidence            4

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

Probab=97.47  E-value=9.5e-05  Score=81.36  Aligned_cols=72  Identities=29%  Similarity=0.360  Sum_probs=60.7

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccC
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVR  372 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~r  372 (784)
                      ..-.+.|.|-+++||.|||++|++||.||..|.++|+|++..       .+..|+|.|....-.+|+..|...++...+
T Consensus        45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~-------~e~kv~ifg~~~m~~kaka~id~~~~k~e~  116 (629)
T KOG0336|consen   45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD-------LEVKVTIFGINHMRKKAKASIDRGQDKDER  116 (629)
T ss_pred             CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC-------ceeEEEEechHHHHHHHHhhHhhhhhhhhh
Confidence            344567889999999999999999999999999999998643       478899999988888899888877765443

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

Probab=97.44  E-value=0.00012  Score=73.45  Aligned_cols=149  Identities=19%  Similarity=0.283  Sum_probs=102.7

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEe-----cchhhHHHHHHHHHHHHHh
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEII-----GTLSNIDKAEKLINAVIAE  272 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~-----G~~e~V~kA~~~I~elI~e  272 (784)
                      ...+.+|.||.+++--+--.+-....-|-+..+..|.+.-+        .|.|.|.     -+..++.++..+|..++.-
T Consensus        72 k~e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK--------~r~VelRt~~~t~D~s~Lqk~adfv~Af~lG  143 (252)
T KOG3273|consen   72 KIETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLK--------ARSVELRTCKDTEDPSALQKGADFVRAFILG  143 (252)
T ss_pred             ccceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecc--------cceeEeecCCCCCChHHHHHHHHHHHHHHhC
Confidence            34578899999998887666666677788888888877532        3555554     3556899999999888765


Q ss_pred             hhcCCCCccc------ccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceE
Q 003942          273 ADAGGSPSLV------ARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERI  346 (784)
Q Consensus       273 ~~~~g~p~~~------~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~  346 (784)
                      .+....-.|.      -..|.    .....+++=.--...+|+|+||+|.|--.|.+.|.+||.+.           +..
T Consensus       144 F~i~DAiALlrlddlflesFE----i~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla-----------d~k  208 (252)
T KOG3273|consen  144 FDIDDAIALLRLDDLFLESFE----IKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA-----------DSK  208 (252)
T ss_pred             CcchhHHHHHhhhhhhheeee----ecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec-----------Cce
Confidence            4321111110      00000    00111111111235789999999999999999999999984           557


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHhc
Q 003942          347 VRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       347 V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      |+|.|....+..|+..|+.+|-.
T Consensus       209 IHiLG~~~niriAR~avcsLIlG  231 (252)
T KOG3273|consen  209 IHILGAFQNIRIARDAVCSLILG  231 (252)
T ss_pred             EEEeecchhhHHHHHhhHhhhcc
Confidence            99999999999999999998853

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

Probab=97.35  E-value=0.00025  Score=71.13  Aligned_cols=106  Identities=16%  Similarity=0.285  Sum_probs=80.7

Q ss_pred             ccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCC--CCCCCeEEEEEecC----------CccceeeccCcchHhhH
Q 003942          158 EVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSS--TDDSTMSRKIEVPN----------NKVGVLIGKAGDTIRYL  225 (784)
Q Consensus       158 ~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~--~~~~~~t~rI~VP~----------~~vG~IIGkgG~tIK~I  225 (784)
                      ....|.+.-+-+..++.++...|..++-.++++....  ..+..+..+|.|-.          ..+|+|+||+|.|--.|
T Consensus       115 ~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DAiALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaI  194 (252)
T KOG3273|consen  115 SVELRTCKDTEDPSALQKGADFVRAFILGFDIDDAIALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAI  194 (252)
T ss_pred             eeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhHHHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeee
Confidence            4445667777788888898888888887666544331  11233444454433          45899999999999999


Q ss_pred             HhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          226 QYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       226 q~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      ++.|.++|.|..          ..|+|.|..++|..|+..|+.+|--.
T Consensus       195 En~trtrIVlad----------~kIHiLG~~~niriAR~avcsLIlGs  232 (252)
T KOG3273|consen  195 ENVTRTRIVLAD----------SKIHILGAFQNIRIARDAVCSLILGS  232 (252)
T ss_pred             eccceeEEEecC----------ceEEEeecchhhHHHHHhhHhhhccC
Confidence            999999999973          47999999999999999999998743

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

Probab=97.26  E-value=0.00037  Score=81.64  Aligned_cols=68  Identities=28%  Similarity=0.426  Sum_probs=59.6

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhhh
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~~  274 (784)
                      ....+.+.|+..+...|||++|++||.|.++|||+|.|..+         ..|.|.+ +.+.+.+|+++|..++++..
T Consensus       550 aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd---------Gtv~i~~s~~~~~~~ak~~I~~i~~e~e  618 (692)
T COG1185         550 APRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD---------GTVKIAASDGESAKKAKERIEAITREVE  618 (692)
T ss_pred             CCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC---------CcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence            34577889999999999999999999999999999999843         4788888 56899999999999998763

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=97.23  E-value=0.00036  Score=84.26  Aligned_cols=64  Identities=28%  Similarity=0.514  Sum_probs=55.9

Q ss_pred             cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003942          296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~  369 (784)
                      ....+.|+.++++.|||.||.+||.|.++||++|.|..          +..|.|.+. .+.+++|+++|+.++.+
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d----------~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED----------DGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC----------CceEEEEcccHHHHHHHHHHHHHhccc
Confidence            45677889999999999999999999999999988742          567888886 88999999999998865

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.23  E-value=0.00023  Score=69.20  Aligned_cols=102  Identities=15%  Similarity=0.087  Sum_probs=68.8

Q ss_pred             ceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCC-CCCC
Q 003942          118 HSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDP-SSTD  196 (784)
Q Consensus       118 ~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~-~~~~  196 (784)
                      -.-+++-...+|..||++|.+|+.|++..+.+|.|-+-+..                 -+.+|...+.-.....- ....
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D-----------------~~~fI~N~l~PA~V~~V~i~~~   96 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN-----------------LEEFVANKLAPAEVKNVTVSEF   96 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC-----------------HHHHHHHcCCCceEEEEEEEcC
Confidence            34567777899999999999999998766666665542221                 11223332221111110 0111


Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEc
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT  236 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~  236 (784)
                      +......+.|+.+..+++|||+|.|||..++-++-++.|.
T Consensus        97 ~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        97 NGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             CCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            2345678999999999999999999999999998888765

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.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.20  E-value=0.00098  Score=74.07  Aligned_cols=95  Identities=18%  Similarity=0.273  Sum_probs=68.1

Q ss_pred             CccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccc
Q 003942          209 NKVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLA  287 (784)
Q Consensus       209 ~~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~  287 (784)
                      +-||..||++|.+|+.|.++. |-+|.|..-++.                        +.++|++..   +|.-+.+-. 
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D------------------------~~~fI~Nal---~Pa~V~~V~-  302 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV------------------------PEIFIARAL---APAIISSVK-  302 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC------------------------HHHHHHHhC---CCceeeEEE-
Confidence            359999999999999999998 888888764321                        222333321   111111000 


Q ss_pred             hhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 003942          288 TAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQ  334 (784)
Q Consensus       288 ~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~  334 (784)
                         .........+.|+.+..++.|||+|.|||-..+.||.+|.|..-
T Consensus       303 ---i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~  346 (374)
T PRK12328        303 ---IEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI  346 (374)
T ss_pred             ---EcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence               01233577899999999999999999999999999999999853

>PRK00106 hypothetical protein; Provisional

Probab=97.01  E-value=0.0027  Score=74.04  Aligned_cols=66  Identities=23%  Similarity=0.411  Sum_probs=55.5

Q ss_pred             ccEEEEEecC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003942          295 AEQVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       295 ~~~~~i~VP~-~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~  369 (784)
                      .....+.+|+ ++.|+||||.|.|||.|...|||.|.|++         +...|+|++. +-.-+.|+.-|+.+|.+
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd---------tp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD---------TPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC---------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            3456778899 78999999999999999999999999953         4567889995 77778888888888764

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=97.00  E-value=0.0025  Score=74.47  Aligned_cols=66  Identities=27%  Similarity=0.427  Sum_probs=55.0

Q ss_pred             ccEEEEEecC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003942          295 AEQVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       295 ~~~~~i~VP~-~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~  369 (784)
                      .....+.+|+ ++.|+||||.|.|||.+...|||.|.|++         +...|+|++. +-.-+.|+.-|+.+|.+
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd---------tp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD---------TPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC---------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            3455678888 78999999999999999999999999953         4567889985 66778888888888764

>TIGR01953 NusA transcription termination factor NusA

Probab=97.00  E-value=0.0019  Score=71.66  Aligned_cols=94  Identities=28%  Similarity=0.422  Sum_probs=67.1

Q ss_pred             ccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccch
Q 003942          210 KVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLAT  288 (784)
Q Consensus       210 ~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~  288 (784)
                      -||..||++|.+|+.|.++. |-+|.|..-++.                        +.++|.+..   +|..+.+-.- 
T Consensus       244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d------------------------~~~fi~nal---~Pa~v~~v~i-  295 (341)
T TIGR01953       244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSDD------------------------PAEFIANAL---SPAKVISVEV-  295 (341)
T ss_pred             cceeeECCCCchHHHHHHHhCCCeEEEEEcCCC------------------------HHHHHHHhc---CCceEEEEEE-
Confidence            59999999999999999998 888888764321                        222333321   1111111000 


Q ss_pred             hhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942          289 AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP  333 (784)
Q Consensus       289 ~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~  333 (784)
                        .........+.|+.+..++.|||+|.|||-..+.||++|.|..
T Consensus       296 --~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       296 --LDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             --EcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence              0112357889999999999999999999999999999999974

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

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

Probab=96.92  E-value=0.00088  Score=72.28  Aligned_cols=71  Identities=27%  Similarity=0.373  Sum_probs=60.6

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhhh
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~~  274 (784)
                      .....|+|...+.+.|||++|.|.|+|+++|+++|.+++.     +.....|+|+| ..+.|.+|++.|..+|.+..
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p-----~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP-----NTNKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC-----CCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            3566789999999999999999999999999999999965     33345666666 89999999999999998864

>PRK12704 phosphodiesterase; Provisional

Probab=96.91  E-value=0.0035  Score=73.44  Aligned_cols=65  Identities=28%  Similarity=0.420  Sum_probs=53.0

Q ss_pred             cEEEEEecC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003942          296 EQVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       296 ~~~~i~VP~-~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~  369 (784)
                      ....+.+|+ ++.|+||||.|.|||.+...|||.|.|++         +..+|.|+|. +-.-+.|+..|+.+|.+
T Consensus       210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd---------tp~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD---------TPEAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC---------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence            445677888 78999999999999999999999999953         4667889995 55656788887777654

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.89  E-value=0.0018  Score=73.06  Aligned_cols=94  Identities=26%  Similarity=0.369  Sum_probs=66.7

Q ss_pred             ccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccch
Q 003942          210 KVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLAT  288 (784)
Q Consensus       210 ~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~  288 (784)
                      -||..||++|.+|+.|.++. |-+|.|..-++      +                  +..+|++..   +|..+..-.. 
T Consensus       278 PvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~------D------------------p~~fI~NaL---sPA~V~~V~i-  329 (449)
T PRK12329        278 PVGACIGARGSRIQAVVNELRGEKIDVIRWSP------D------------------PATYIANAL---SPARVDEVRL-  329 (449)
T ss_pred             hhhccCCCCcchHHHHHHHhCCCeEEEEEcCC------C------------------HHHHHHHhc---CCceeeEEEE-
Confidence            59999999999999999998 88888875432      1                  222233221   1211111000 


Q ss_pred             hhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942          289 AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP  333 (784)
Q Consensus       289 ~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~  333 (784)
                        .........+.|+.+..++.|||+|.|||-....||.+|.|..
T Consensus       330 --~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        330 --VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             --EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence              0112356789999999999999999999999999999999964

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.87  E-value=0.00073  Score=81.68  Aligned_cols=67  Identities=31%  Similarity=0.473  Sum_probs=57.4

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhh
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~  273 (784)
                      ......+.|+.++++.|||.+|.|||.|.++||++|.+..+         -.|.|.+ +.+.+++|+++|..++.+.
T Consensus       552 ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~---------G~v~i~~~~~~~~~~a~~~I~~~~~~~  619 (693)
T PRK11824        552 APRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD---------GTVKIAATDGEAAEAAKERIEGITAEP  619 (693)
T ss_pred             CchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC---------ceEEEEcccHHHHHHHHHHHHHhcccC
Confidence            34566777899999999999999999999999999998643         4778887 8899999999999988653

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.86  E-value=0.0026  Score=71.07  Aligned_cols=94  Identities=21%  Similarity=0.330  Sum_probs=67.5

Q ss_pred             ccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccch
Q 003942          210 KVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLAT  288 (784)
Q Consensus       210 ~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~  288 (784)
                      -||..||++|.+|+.|.++. |-+|.|..-++.                        +.++|++..   +|..+.+-.- 
T Consensus       246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d------------------------~~~fi~nal---~Pa~v~~v~i-  297 (362)
T PRK12327        246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSED------------------------PAEFVANAL---SPAKVVSVEV-  297 (362)
T ss_pred             chheeECCCChhHHHHHHHhCCCeEEEEEcCCC------------------------HHHHHHHhC---CCceEEEEEE-
Confidence            59999999999999999988 888888764321                        222333321   1211111000 


Q ss_pred             hhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942          289 AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP  333 (784)
Q Consensus       289 ~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~  333 (784)
                        .........+.|+.+..++.|||+|.||+-....||++|.|..
T Consensus       298 --~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s  340 (362)
T PRK12327        298 --DDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS  340 (362)
T ss_pred             --EcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence              0123357889999999999999999999999999999999975

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

Probab=96.82  E-value=0.0042  Score=62.86  Aligned_cols=69  Identities=25%  Similarity=0.273  Sum_probs=47.4

Q ss_pred             CceeeeecCCchHHHHHHHHhCCeEEeccCCC----------CCCCCCCceE---EEEEcCHHHHHHHHHHHHHHHhccc
Q 003942          305 EKVGLIIGRGGETIKGLQTRSGARIQLIPQHL----------PEGDGSKERI---VRVTGDMRQIEIAQEMIKEVLSQTV  371 (784)
Q Consensus       305 ~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~----------p~~~~~~er~---V~I~Gt~~qV~~Ak~lI~~~L~~~~  371 (784)
                      |+||+|||..|.|+|.|++.|+|+|-|.....          ++.-...+.+   +++.-+.+.+++++.+|..+|.+.+
T Consensus       163 NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a~  242 (269)
T COG5176         163 NFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREAR  242 (269)
T ss_pred             ceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHHh
Confidence            89999999999999999999999999974321          1110111111   2333446778888888888877665


Q ss_pred             CC
Q 003942          372 RP  373 (784)
Q Consensus       372 r~  373 (784)
                      +.
T Consensus       243 ~~  244 (269)
T COG5176         243 RN  244 (269)
T ss_pred             cC
Confidence            54

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.70  E-value=0.0035  Score=73.32  Aligned_cols=90  Identities=20%  Similarity=0.321  Sum_probs=61.2

Q ss_pred             hchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCC-ccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCc
Q 003942          171 ESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNN-KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRP  249 (784)
Q Consensus       171 e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~-~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~  249 (784)
                      ++-.+|+.+|..-+......    .....++..|.+|++ .-|+||||.|.|||.|..-|||+|.|++.        ...
T Consensus       179 ~a~~~a~~i~~~aiqr~a~~----~~~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt--------p~~  246 (514)
T TIGR03319       179 EADKKAKEILATAIQRYAGD----HVAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT--------PEA  246 (514)
T ss_pred             HHHHHHHHHHHHHHHhccch----hhhhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC--------CCe
Confidence            34455666666655433221    123356677888884 78999999999999999999999999853        246


Q ss_pred             EEEec-chhhHHHHHHHHHHHHHh
Q 003942          250 VEIIG-TLSNIDKAEKLINAVIAE  272 (784)
Q Consensus       250 V~I~G-~~e~V~kA~~~I~elI~e  272 (784)
                      |+|++ ++-.-+.|+..|..||.+
T Consensus       247 v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       247 VILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             EEecCCchHHHHHHHHHHHHHHHc
Confidence            77887 555445555555555543

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.70  E-value=0.0014  Score=66.72  Aligned_cols=101  Identities=18%  Similarity=0.178  Sum_probs=67.7

Q ss_pred             eeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCC-CCCCCC
Q 003942          120 SVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDP-SSTDDS  198 (784)
Q Consensus       120 ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~-~~~~~~  198 (784)
                      ...+-...+|..||++|.+|+.|.++.+.+|+|-.-...                 -..+|...|.-.....- ....+.
T Consensus        79 ~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d-----------------~~~fI~nal~Pa~v~~V~~~~~d~  141 (190)
T COG0195          79 SNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED-----------------PAEFIKNALAPAEVLSVNIKEDDG  141 (190)
T ss_pred             EeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC-----------------HHHHHHHhcCcceEeEEEEEeCCC
Confidence            445555677899999999999999777655555443321                 12223333321111000 011112


Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD  238 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~  238 (784)
                      . ...+.|+.+..+++|||+|.+++.+.+-||.+|.|...
T Consensus       142 ~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~  180 (190)
T COG0195         142 H-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI  180 (190)
T ss_pred             c-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence            2 78899999999999999999999999999999999753

>PRK00106 hypothetical protein; Provisional

Probab=96.67  E-value=0.0039  Score=72.81  Aligned_cols=90  Identities=18%  Similarity=0.269  Sum_probs=62.4

Q ss_pred             hchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCC-ccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCc
Q 003942          171 ESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNN-KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRP  249 (784)
Q Consensus       171 e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~-~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~  249 (784)
                      ++-.+|+.+|..-+.....+.    ....++..|.+|++ .-|+||||.|.|||.|..-|||+|.|++.        ...
T Consensus       200 ~a~~~a~~ii~~aiqr~a~~~----~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt--------p~~  267 (535)
T PRK00106        200 RSDKMAKDLLAQAMQRLAGEY----VTEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT--------PEV  267 (535)
T ss_pred             HHHHHHHHHHHHHHHHhcchh----hhhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC--------CCe
Confidence            344556666666554332211    23356777888984 78999999999999999999999999853        346


Q ss_pred             EEEec-chhhHHHHHHHHHHHHHh
Q 003942          250 VEIIG-TLSNIDKAEKLINAVIAE  272 (784)
Q Consensus       250 V~I~G-~~e~V~kA~~~I~elI~e  272 (784)
                      |+|++ ++-.-+.|+..|+.||.+
T Consensus       268 v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        268 VVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             EEEeCCChHHHHHHHHHHHHHHHc
Confidence            77888 555555566666655554

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=96.66  E-value=0.0029  Score=72.98  Aligned_cols=103  Identities=26%  Similarity=0.425  Sum_probs=71.6

Q ss_pred             eEEEEEecCC-----ccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          200 MSRKIEVPNN-----KVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       200 ~t~rI~VP~~-----~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      ...+|-|-++     -||..||++|++|+.|.++. |-+|.|..-++      +                  +..+|.+.
T Consensus       231 ~RaKvAV~s~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~------d------------------~~~fi~na  286 (470)
T PRK09202        231 SRAKIAVKSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSD------D------------------PAQFIINA  286 (470)
T ss_pred             ceeEEEEEcCCCCCChhHccCCCCCchHHHHHHHhCCCeEEEEEcCC------C------------------HHHHHHHh
Confidence            3445555443     49999999999999999998 78888875432      1                  22233332


Q ss_pred             hcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942          274 DAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP  333 (784)
Q Consensus       274 ~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~  333 (784)
                      .   +|..+.+-.    .......+.+.|+.+..++.|||+|.|||-..+.||.+|.|..
T Consensus       287 l---~pa~v~~v~----~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        287 L---SPAEVSSVV----VDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             C---CCCEEEEEE----EeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            1   111111100    0112357889999999999999999999999999999999975

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.65  E-value=0.0031  Score=66.61  Aligned_cols=65  Identities=25%  Similarity=0.328  Sum_probs=56.4

Q ss_pred             EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhccc
Q 003942          297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQTV  371 (784)
Q Consensus       297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~~~  371 (784)
                      -+.|.||.+++++|||++|.+|+.|.++++|+|.|-.          +..|.|.+. .+.+.+|+.+|+.+-++..
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~  211 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ----------NGRIWIKGPDEEDEEIAIEAIKKIEREAH  211 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC----------CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence            4678999999999999999999999999999999843          467888888 6799999999998776543

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

Probab=96.59  E-value=0.0024  Score=69.03  Aligned_cols=71  Identities=21%  Similarity=0.316  Sum_probs=57.5

Q ss_pred             cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcccC
Q 003942          296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEIAQEMIKEVLSQTVR  372 (784)
Q Consensus       296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~G-t~~qV~~Ak~lI~~~L~~~~r  372 (784)
                      ....+.|...+++.|||++|.|-|+|+++|+|+|.+.+..      .....|+|+| ..++|..|.+.|..+|.+.++
T Consensus        57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~  128 (345)
T KOG2814|consen   57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN------TNKEEIKIIGISRNCVIQALERIAKLIDSDRK  128 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC------CCcceEEEeehhHHHHHHHHHHHHHHHHhhhh
Confidence            4556889999999999999999999999999999996532      2333455554 589999999999999987653

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.51  E-value=0.0038  Score=65.94  Aligned_cols=65  Identities=26%  Similarity=0.335  Sum_probs=56.5

Q ss_pred             EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhhh
Q 003942          201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~~  274 (784)
                      -+.|.|+.+++++|||++|.+|+.|.++|+++|.|-.         +-.|.|.+ +.+.+.+|+.+|+.+-++..
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~---------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~  211 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ---------NGRIWIKGPDEEDEEIAIEAIKKIEREAH  211 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC---------CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence            3578899999999999999999999999999999974         35789998 67799999999998777654

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

Probab=96.50  E-value=0.003  Score=52.61  Aligned_cols=37  Identities=32%  Similarity=0.614  Sum_probs=34.4

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEE
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQI  235 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V  235 (784)
                      ....+|.|+.+.+|.+|||+|.+|+.+++.++.+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3688999999999999999999999999999988876

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

>PRK12704 phosphodiesterase; Provisional

Probab=96.50  E-value=0.0053  Score=71.91  Aligned_cols=90  Identities=20%  Similarity=0.335  Sum_probs=62.1

Q ss_pred             hchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCC-ccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCc
Q 003942          171 ESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNN-KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRP  249 (784)
Q Consensus       171 e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~-~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~  249 (784)
                      ++-.+|+.+|..-+.......    ....++..|.+|++ .-|+||||.|.|||.|+.-|||+|.|++.        ..+
T Consensus       185 ~a~~~a~~i~~~a~qr~a~~~----~~e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt--------p~~  252 (520)
T PRK12704        185 EADKKAKEILAQAIQRCAADH----VAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT--------PEA  252 (520)
T ss_pred             HHHHHHHHHHHHHHHhhcchh----hhhhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC--------CCe
Confidence            344556666666554332211    23345667888884 88999999999999999999999999853        347


Q ss_pred             EEEec-chhhHHHHHHHHHHHHHh
Q 003942          250 VEIIG-TLSNIDKAEKLINAVIAE  272 (784)
Q Consensus       250 V~I~G-~~e~V~kA~~~I~elI~e  272 (784)
                      |.|++ ++-.-+.|+..|+.+|.+
T Consensus       253 v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        253 VILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             EEEecCChhhHHHHHHHHHHHHhc
Confidence            77888 454445666666666654

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

Probab=96.38  E-value=0.0052  Score=51.21  Aligned_cols=37  Identities=27%  Similarity=0.680  Sum_probs=34.6

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEe
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQL  331 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI  331 (784)
                      .....+.|+.+.+|.+|||+|.+|+.|++.++.+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3688999999999999999999999999999999887

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.

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

Probab=96.35  E-value=0.016  Score=63.88  Aligned_cols=163  Identities=15%  Similarity=0.010  Sum_probs=99.9

Q ss_pred             CcchHhhHHhhcCCEEEEccCCCC------CCCCCCCcEEEec-chhhHHHHHHHHHHHHHhhhcCCCCccc---cc---
Q 003942          218 AGDTIRYLQYNSGAKIQITRDADA------DPHAATRPVEIIG-TLSNIDKAEKLINAVIAEADAGGSPSLV---AR---  284 (784)
Q Consensus       218 gG~tIK~Iq~~TGakI~V~~~~~~------~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~~~~g~p~~~---~~---  284 (784)
                      +|.+..+|.+.+|+.|.+...-..      .+++.-.+.+|.+ +.|-+++|+..|.-++..+....+...+   .+   
T Consensus       112 Rg~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~~~~~~~~n~~~V~i~~~~sP  191 (531)
T KOG1960|consen  112 RGTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPSTAEITSKAIERIKGVFMQDVEINNVRNVYILVRASP  191 (531)
T ss_pred             cchhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCccHHHHHHHHhhCccceeecccccccceEEEeecCCc
Confidence            588899999999999988764221      1222334678888 8899999999998666544221111000   00   


Q ss_pred             ------c-----cchhhccCCccEEEEEecC-CceeeeecCCchHHHHHHHHhCCeEEeccCC----CC--CCCCCCceE
Q 003942          285 ------G-----LATAQASGAAEQVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQLIPQH----LP--EGDGSKERI  346 (784)
Q Consensus       285 ------g-----~~~~~~~~~~~~~~i~VP~-~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~----~p--~~~~~~er~  346 (784)
                            -     |.....-.....+.+.+|. ++.+++=+++-.++.+|+.+|++++.|..+.    .|  ..+..+-+.
T Consensus       192 ~~~i~~~V~~~~f~~G~~Y~~k~~v~~~~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMY  271 (531)
T KOG1960|consen  192 LSEIENKVGVQLFSKGRYYPNKALATDKDPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMY  271 (531)
T ss_pred             hhhhccccccccccccccchhheecccCCcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcccccccCCcee
Confidence                  0     0000000011122223444 4567777888889999999999998774322    11  123444567


Q ss_pred             EEEEcC-HHHHHHHHHHHHHHHhcccCCCCCCCCCCC
Q 003942          347 VRVTGD-MRQIEIAQEMIKEVLSQTVRPSTLSGGFNQ  382 (784)
Q Consensus       347 V~I~Gt-~~qV~~Ak~lI~~~L~~~~r~~~~~gg~~~  382 (784)
                      |.|++. .+.+.+|+++|.++++.+...  ++.+|++
T Consensus       272 I~i~h~~~~g~~~A~r~~~nl~~~v~~~--~sr~~~~  306 (531)
T KOG1960|consen  272 IFSTHGNGNGENGAPRRKWNLEEKVYIN--LSRGFHR  306 (531)
T ss_pred             EEeecCCchhhccchhHHHhHHHHHHHH--hhhhhhh
Confidence            777765 899999999999999765443  2344443

>PRK12705 hypothetical protein; Provisional

Probab=96.19  E-value=0.0088  Score=69.49  Aligned_cols=64  Identities=22%  Similarity=0.353  Sum_probs=47.7

Q ss_pred             cEEEEEecC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHh
Q 003942          296 EQVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLS  368 (784)
Q Consensus       296 ~~~~i~VP~-~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~  368 (784)
                      ....+.+|+ ++.|+||||.|.|||.+...||+.|.|++         +.+.|+|++. +..-+.|+..+..+|.
T Consensus       198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd---------tp~~V~ls~fdp~rreia~~~l~~Li~  263 (508)
T PRK12705        198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD---------TPEAVVISSFNPIRREIARLTLEKLLA  263 (508)
T ss_pred             eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC---------CccchhhcccCccchHHHHHHHHHHHh
Confidence            445677888 78999999999999999999999999954         3445666665 4455556665555554

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.18  E-value=0.0048  Score=68.68  Aligned_cols=95  Identities=14%  Similarity=0.129  Sum_probs=62.6

Q ss_pred             cccccccCCCchhhhhhhccc-CceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEE
Q 003942          126 SVDNQQISVKEETKEVLFSTE-EAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKI  204 (784)
Q Consensus       126 ~~vg~iIGk~Ge~Ik~iq~~s-~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI  204 (784)
                      +-+|..||++|.+|+.|..+- +.+|+|-.-....                 ..+|...|.-.....-.. ........+
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~-----------------~~fI~Nal~Pa~V~~V~i-~~~~~~~~V  312 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVP-----------------EIFIARALAPAIISSVKI-EEEEKKAIV  312 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhCCCceeeEEEE-cCCCcEEEE
Confidence            345699999999999997443 5555554433321                 112222221111100000 122357899


Q ss_pred             EecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942          205 EVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD  238 (784)
Q Consensus       205 ~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~  238 (784)
                      .|+....++.|||+|.|||...+-||.+|.|..-
T Consensus       313 ~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~  346 (374)
T PRK12328        313 TLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI  346 (374)
T ss_pred             EEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence            9999999999999999999999999999999864

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

Probab=96.17  E-value=0.0089  Score=68.41  Aligned_cols=66  Identities=24%  Similarity=0.310  Sum_probs=56.4

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhccc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQTV  371 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~~~  371 (784)
                      .....|.|+.+++..+||.+|.++|+|..+||+.-.++           +.+|+|.-. ...+++|+++|..++....
T Consensus       596 P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-----------e~t~~i~A~~~~am~~Ak~~I~~i~~~~~  662 (760)
T KOG1067|consen  596 PVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-----------EGTFSIFAPTQAAMEEAKEFIDGIIKDDQ  662 (760)
T ss_pred             ceeeEEeecchhhheeecCccceeeeEeeeccceeeec-----------CceEEEEecCHHHHHHHHHHHHHHhcCcc
Confidence            45678899999999999999999999999999777663           556887776 7899999999999886543

>TIGR01953 NusA transcription termination factor NusA

Probab=95.97  E-value=0.0065  Score=67.46  Aligned_cols=95  Identities=17%  Similarity=0.238  Sum_probs=61.9

Q ss_pred             ccccccCCCchhhhhhhccc-CceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEE
Q 003942          127 VDNQQISVKEETKEVLFSTE-EAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIE  205 (784)
Q Consensus       127 ~vg~iIGk~Ge~Ik~iq~~s-~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~  205 (784)
                      -+|..||++|.+|+.|..+- +.+|+|-.-....                 ..+|...|.-.....-...........+.
T Consensus       244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~-----------------~~fi~nal~Pa~v~~v~i~~~~~~~~~v~  306 (341)
T TIGR01953       244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSDDP-----------------AEFIANALSPAKVISVEVLDEDKHSAEVV  306 (341)
T ss_pred             cceeeECCCCchHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhcCCceEEEEEEEcCCCcEEEEE
Confidence            46699999999999997443 5555554433221                 11122212111100000001123578999


Q ss_pred             ecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942          206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD  238 (784)
Q Consensus       206 VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~  238 (784)
                      |+.+..++.|||+|.|||...+-||.+|.|...
T Consensus       307 V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~  339 (341)
T TIGR01953       307 VPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE  339 (341)
T ss_pred             EChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence            999999999999999999999999999999753

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.

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.84  E-value=0.0061  Score=69.00  Aligned_cols=94  Identities=18%  Similarity=0.232  Sum_probs=61.4

Q ss_pred             ccccccCCCchhhhhhhccc-CceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEE
Q 003942          127 VDNQQISVKEETKEVLFSTE-EAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIE  205 (784)
Q Consensus       127 ~vg~iIGk~Ge~Ik~iq~~s-~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~  205 (784)
                      -+|..||++|.+|+.|..+. +.+|+|-.-....                 ..+|...|.-.....-...........|.
T Consensus       278 PvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp-----------------~~fI~NaLsPA~V~~V~i~~~~~k~a~V~  340 (449)
T PRK12329        278 PVGACIGARGSRIQAVVNELRGEKIDVIRWSPDP-----------------ATYIANALSPARVDEVRLVDPEGRHAHVL  340 (449)
T ss_pred             hhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhcCCceeeEEEEEcCCCcEEEEE
Confidence            45699999999999997443 5555554433221                 11222222111110000001223467899


Q ss_pred             ecCCccceeeccCcchHhhHHhhcCCEEEEcc
Q 003942          206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITR  237 (784)
Q Consensus       206 VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~  237 (784)
                      |+.+..++.|||+|.|||...+-||.+|.|..
T Consensus       341 V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        341 VPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             EChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            99999999999999999999999999999974

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.71  E-value=0.0086  Score=66.95  Aligned_cols=95  Identities=18%  Similarity=0.259  Sum_probs=62.6

Q ss_pred             ccccccCCCchhhhhhhccc-CceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEE
Q 003942          127 VDNQQISVKEETKEVLFSTE-EAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIE  205 (784)
Q Consensus       127 ~vg~iIGk~Ge~Ik~iq~~s-~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~  205 (784)
                      -+|..||++|.+|+.|..+. +.+|+|-.-....                 ..+|...|.-.....-...........+.
T Consensus       246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~-----------------~~fi~nal~Pa~v~~v~i~~~~~~~~~v~  308 (362)
T PRK12327        246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDP-----------------AEFVANALSPAKVVSVEVDDEEEKAARVV  308 (362)
T ss_pred             chheeECCCChhHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhCCCceEEEEEEEcCCCcEEEEE
Confidence            46799999999999997444 5555554433221                 11222222111110000001223578999


Q ss_pred             ecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942          206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD  238 (784)
Q Consensus       206 VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~  238 (784)
                      |+.+..++.|||+|.|||...+-||.+|.|...
T Consensus       309 V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        309 VPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             EChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            999999999999999999999999999999854

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

Probab=95.71  E-value=0.011  Score=64.92  Aligned_cols=215  Identities=12%  Similarity=0.051  Sum_probs=127.1

Q ss_pred             ccCCCchhhhhhhcccCceeeeccccc-------cccc--ceeeec-CchhchhhhhhhhhHhhhcCCCC----------
Q 003942          131 QISVKEETKEVLFSTEEAFIDVKEETK-------EVTV--KEEETV-KEEESVEPSNVVPQQVVDNSKSD----------  190 (784)
Q Consensus       131 iIGk~Ge~Ik~iq~~s~a~I~I~~~~~-------~~s~--r~~~i~-G~~e~Ve~A~~lI~~ii~~~~~~----------  190 (784)
                      -.-..|.+...|...+++.+.+.....       .+.+  ..++|. -+.|-+.+|...|.-++..+...          
T Consensus       108 ~~~TRg~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~~~~~~~~n~~~V~i~~  187 (531)
T KOG1960|consen  108 ATSTRGTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPSTAEITSKAIERIKGVFMQDVEINNVRNVYILV  187 (531)
T ss_pred             ceeccchhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCccHHHHHHHHhhCccceeecccccccceEEEee
Confidence            334567888888888888877665532       2233  334444 35677778888887544311100          


Q ss_pred             --------------CCCCCCCCCeEEEEEecCC-----ccceeeccCcchHhhHHhhcCCEEEEccCCC--CCCCC----
Q 003942          191 --------------DPSSTDDSTMSRKIEVPNN-----KVGVLIGKAGDTIRYLQYNSGAKIQITRDAD--ADPHA----  245 (784)
Q Consensus       191 --------------~~~~~~~~~~t~rI~VP~~-----~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~--~~p~s----  245 (784)
                                    ..+. ......-+++|+.+     +-+++=+++-.+|..|+.++++++.++.+..  ..+++    
T Consensus       188 ~~sP~~~i~~~V~~~~f~-~G~~Y~~k~~v~~~~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~Es  266 (531)
T KOG1960|consen  188 RASPLSEIENKVGVQLFS-KGRYYPNKALATDKDPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNES  266 (531)
T ss_pred             cCCchhhhcccccccccc-ccccchhheecccCCcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCccccccc
Confidence                          0000 00111112333322     3344556677788999999999987754321  11111    


Q ss_pred             --CCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHH
Q 003942          246 --ATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQT  323 (784)
Q Consensus       246 --~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~  323 (784)
                        ...++.+-++.+.+.+|+++|.+|++.....-     .|+|..                   =.|+|.-|..+|+|+.
T Consensus       267 nEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~~~-----sr~~~~-------------------~~~~~p~~~y~~~~~~  322 (531)
T KOG1960|consen  267 NEPMYIFSTHGNGNGENGAPRRKWNLEEKVYINL-----SRGFHR-------------------QAIVGPQGAYVKHIQQ  322 (531)
T ss_pred             CCceeEEeecCCchhhccchhHHHhHHHHHHHHh-----hhhhhh-------------------cccccCCcccccccCC
Confidence              22244444599999999999998877643211     111111                   1356777889999999


Q ss_pred             HhCCeEEeccCCCCCCC-------CCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          324 RSGARIQLIPQHLPEGD-------GSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       324 ~SGarIqI~~~~~p~~~-------~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      .+-.++.|+....-..+       +.--.++.|.-.+.+|+.|+-||.++|..+
T Consensus       323 ~~~~~~~~~g~~s~~i~p~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~~v  376 (531)
T KOG1960|consen  323 ETRTRVQIKGQGSAFIEPSTNRESDEPIHLCIMSHDPNAIQRAKVLCEDLIASV  376 (531)
T ss_pred             CCCcceeccCccceeecCCCCCCCCCCcccccccCChhhhhhhhhcccccCCcc
Confidence            99999998754311111       122345778888999999999998888654

>PRK12705 hypothetical protein; Provisional

Probab=95.69  E-value=0.014  Score=67.75  Aligned_cols=89  Identities=18%  Similarity=0.276  Sum_probs=56.7

Q ss_pred             hchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCC-ccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCc
Q 003942          171 ESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNN-KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRP  249 (784)
Q Consensus       171 e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~-~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~  249 (784)
                      ++-.+|+.+|..-+.....+.    ....++..|.+|++ .-|+||||.|.|||.|+..||+.|.|++..        +.
T Consensus       173 ~a~~~A~~ii~~aiqr~a~~~----~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp--------~~  240 (508)
T PRK12705        173 EAERKAQNILAQAMQRIASET----ASDLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP--------EA  240 (508)
T ss_pred             HHHHHHHHHHHHHHHHhccch----hhhheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc--------cc
Confidence            344456666666664333221    22345667778875 789999999999999999999999998542        34


Q ss_pred             EEEec-chhhHHHHHHHHHHHHH
Q 003942          250 VEIIG-TLSNIDKAEKLINAVIA  271 (784)
Q Consensus       250 V~I~G-~~e~V~kA~~~I~elI~  271 (784)
                      |.|++ ++..-+.|+..+..+|.
T Consensus       241 V~ls~fdp~rreia~~~l~~Li~  263 (508)
T PRK12705        241 VVISSFNPIRREIARLTLEKLLA  263 (508)
T ss_pred             hhhcccCccchHHHHHHHHHHHh
Confidence            55555 33333344444444433

>PRK00468 hypothetical protein; Provisional

Probab=95.64  E-value=0.0077  Score=52.38  Aligned_cols=33  Identities=18%  Similarity=0.395  Sum_probs=29.3

Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhh
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN  228 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~  228 (784)
                      .+..+.++|.|..+.+|+||||+|.+|+.||.-
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            345588999999999999999999999999874

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

Probab=95.61  E-value=0.023  Score=64.72  Aligned_cols=96  Identities=25%  Similarity=0.442  Sum_probs=71.6

Q ss_pred             ceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhc
Q 003942          212 GVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQA  291 (784)
Q Consensus       212 G~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~  291 (784)
                      -.+|-+.|+.||+|-++...+|.|..+...              ...-++|++.|+++|-++-.  ...+.   |     
T Consensus        41 P~~~~~~~dlik~lAk~lrKRI~iR~dPsv--------------l~~~e~A~~~I~eivP~ea~--i~~i~---F-----   96 (637)
T COG1782          41 PELFAKDGDLIKDLAKDLRKRIIIRPDPSV--------------LKPPEEARKIILEIVPEEAG--ITDIY---F-----   96 (637)
T ss_pred             HHHhccchhHHHHHHHHHhhceEeccCchh--------------cCCHHHHHHHHHHhCccccC--ceeEE---e-----
Confidence            446778899999999999999999865211              13356899999999966421  11111   1     


Q ss_pred             cCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942          292 SGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP  333 (784)
Q Consensus       292 ~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~  333 (784)
                        ...+-++.|-.++=|+||||+|+++++|..+||-+-+|.+
T Consensus        97 --d~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR  136 (637)
T COG1782          97 --DDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR  136 (637)
T ss_pred             --cCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence              2245678888999999999999999999999998877765

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

Probab=95.56  E-value=0.011  Score=51.52  Aligned_cols=33  Identities=27%  Similarity=0.487  Sum_probs=29.6

Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhh
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN  228 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~  228 (784)
                      .+..+.++|.|....+|+||||+|.+|+.||.-
T Consensus        26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             cCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            356678999999999999999999999999974

>PRK02821 hypothetical protein; Provisional

Probab=95.45  E-value=0.0089  Score=52.23  Aligned_cols=35  Identities=20%  Similarity=0.342  Sum_probs=30.1

Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhhcC
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSG  230 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TG  230 (784)
                      ....+.++|.|..+.+|+||||+|.+|+.||.-..
T Consensus        27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            34457899999999999999999999999997544

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

Probab=95.32  E-value=0.028  Score=64.45  Aligned_cols=69  Identities=22%  Similarity=0.385  Sum_probs=59.5

Q ss_pred             CCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhh
Q 003942          195 TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       195 ~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~  273 (784)
                      .....+.+.+.|+.+++..+||.+|.++|+|..+||+.-.|+          +..|+|.. +...+++|+++|..++...
T Consensus       592 ~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD----------e~t~~i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  592 KEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD----------EGTFSIFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             cccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec----------CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence            345678899999999999999999999999999999666665          35788887 8889999999999999875

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

Probab=95.20  E-value=0.052  Score=52.82  Aligned_cols=94  Identities=26%  Similarity=0.479  Sum_probs=67.8

Q ss_pred             eeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhccC
Q 003942          214 LIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASG  293 (784)
Q Consensus       214 IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~  293 (784)
                      ++=.+++.||+|-++..-+|.|..|.+           +   ...=+.|.++|.++|-++-  +...+.   |       
T Consensus        20 ~~~~~~dli~~lAk~lrKRIvvR~dps-----------~---l~~~e~A~~~I~~ivP~ea--~i~di~---F-------   73 (145)
T cd02410          20 LFAEDGDLVKDLAKDLRKRIVIRPDPS-----------V---LKPPEEAIKIILEIVPEEA--GITDIY---F-------   73 (145)
T ss_pred             HHhcccHHHHHHHHHHhceEEEcCChh-----------h---cCCHHHHHHHHHHhCCCcc--CceeeE---e-------
Confidence            344568899999999988898875421           0   0123569999999886541  111111   1       


Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP  333 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~  333 (784)
                      ...+-++.|-.++-|+||||+|.++++|..+||-+-.|.+
T Consensus        74 d~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR  113 (145)
T cd02410          74 DDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR  113 (145)
T ss_pred             cCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence            2245578888899999999999999999999999988864

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

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=95.16  E-value=0.032  Score=63.35  Aligned_cols=192  Identities=12%  Similarity=0.033  Sum_probs=122.3

Q ss_pred             ccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEe
Q 003942          127 VDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEV  206 (784)
Q Consensus       127 ~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~V  206 (784)
                      ..+-|-||+--.+.+|....++.+.+.-....++.-.-.+.|..-++.++.+++...+              ...+.|.|
T Consensus       390 ~EdFl~gkkngK~TrIm~~v~c~~~~~i~~~~gs~~~~~~~g~~~~F~k~~~~~~~EF--------------pae~~f~i  455 (657)
T COG5166         390 NEDFLRGKKNGKATRIMKGVSCSELSSIVSSTGSIVETNGIGEKMSFSKKLSIPPTEF--------------PAEIAFII  455 (657)
T ss_pred             hHHHhccccCcchhhhhhhcccceeeEEEecCCcEEEEeccCcchhhHHHhcCCcccC--------------chheEEEe
Confidence            4446666666567888777888866665555555333444566666666655554433              23678999


Q ss_pred             cCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCC-cEEEecc---hhhHHHHHHHHHHHHHhhhcCCCCcc-
Q 003942          207 PNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATR-PVEIIGT---LSNIDKAEKLINAVIAEADAGGSPSL-  281 (784)
Q Consensus       207 P~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR-~V~I~G~---~e~V~kA~~~I~elI~e~~~~g~p~~-  281 (784)
                      +...+-.|||-+|..|.++..+.++.|.+...-+ .+.+.-+ -|.|...   .++|.-++.-++++|.+.....+..+ 
T Consensus       456 ~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~-~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdi  534 (657)
T COG5166         456 MESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYK-FGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDI  534 (657)
T ss_pred             ecccceeeeccCchhhHHhhhhhhhhhhhhhhhh-cchhhhhcceEEECCccCccchhcccccHHHHHhhhcccccccce
Confidence            9999999999999999999999999998875321 2222222 3677764   44666677778888887653211111 


Q ss_pred             -cccc---------cch--hhc-------cCCccEEEEEecCCceeeeec---CCchHHHHHHHHhCCeEEecc
Q 003942          282 -VARG---------LAT--AQA-------SGAAEQVEIKVPNEKVGLIIG---RGGETIKGLQTRSGARIQLIP  333 (784)
Q Consensus       282 -~~~g---------~~~--~~~-------~~~~~~~~i~VP~~~vG~VIG---kgG~~IK~Iq~~SGarIqI~~  333 (784)
                       ...+         ...  .+.       .+-.....+.++.+.++..||   -+|++|..+.....-.|....
T Consensus       535 rf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~~~  608 (657)
T COG5166         535 RFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEFST  608 (657)
T ss_pred             EEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcccccccchhhhhhhhhccceeec
Confidence             0000         000  000       111233455677788899999   788998888887777777653

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.15  E-value=0.015  Score=67.14  Aligned_cols=94  Identities=16%  Similarity=0.232  Sum_probs=61.7

Q ss_pred             ccccccCCCchhhhhhhccc-CceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEE
Q 003942          127 VDNQQISVKEETKEVLFSTE-EAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIE  205 (784)
Q Consensus       127 ~vg~iIGk~Ge~Ik~iq~~s-~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~  205 (784)
                      -+|..||++|.+|+.|..+- +.+|.|-.-+...                 ..+|...|.-.....-.. +.......|.
T Consensus       246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~-----------------~~fi~nal~pa~v~~v~~-~~~~~~~~v~  307 (470)
T PRK09202        246 PVGACVGMRGSRIQAISNELGGEKIDIILWSDDP-----------------AQFIINALSPAEVSSVVV-DEDEHSADVV  307 (470)
T ss_pred             hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhCCCCEEEEEEE-eCCCCEEEEE
Confidence            45699999999999997443 5556554433321                 111222121111000000 1112488999


Q ss_pred             ecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942          206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD  238 (784)
Q Consensus       206 VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~  238 (784)
                      |+....++.|||+|.|||..++-||.+|.|...
T Consensus       308 V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        308 VPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             ECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            999999999999999999999999999999864

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

Probab=95.14  E-value=0.035  Score=53.95  Aligned_cols=95  Identities=16%  Similarity=0.197  Sum_probs=64.6

Q ss_pred             cccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcC-CCCCCCCCCCCCeEEEEEecC
Q 003942          130 QQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNS-KSDDPSSTDDSTMSRKIEVPN  208 (784)
Q Consensus       130 ~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~-~~~~~~~~~~~~~t~rI~VP~  208 (784)
                      ..+-.+++.|++|-.+-.-+|.|..+...           ...-+.|+++|.+++-.+ .++.-..   ...+-+|.|-.
T Consensus        19 ~~~~~~~dli~~lAk~lrKRIvvR~dps~-----------l~~~e~A~~~I~~ivP~ea~i~di~F---d~~tGEV~Iea   84 (145)
T cd02410          19 ELFAEDGDLVKDLAKDLRKRIVIRPDPSV-----------LKPPEEAIKIILEIVPEEAGITDIYF---DDDTGEVIIEA   84 (145)
T ss_pred             HHHhcccHHHHHHHHHHhceEEEcCChhh-----------cCCHHHHHHHHHHhCCCccCceeeEe---cCCCcEEEEEE
Confidence            55566788888886555545554433321           112367899999988432 2211111   12356788888


Q ss_pred             CccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942          209 NKVGVLIGKAGDTIRYLQYNSGAKIQITRD  238 (784)
Q Consensus       209 ~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~  238 (784)
                      .+-|+||||+|.++++|..+||-+-.|.+.
T Consensus        85 eKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          85 EKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             cCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence            899999999999999999999998888753

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=94.83  E-value=0.021  Score=50.03  Aligned_cols=33  Identities=27%  Similarity=0.472  Sum_probs=29.5

Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhh
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN  228 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~  228 (784)
                      ....+.++|.|..+.+|+||||+|.||+.||.-
T Consensus        26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l   58 (78)
T PRK01064         26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTL   58 (78)
T ss_pred             CCCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence            356688999999999999999999999999874

>PRK00468 hypothetical protein; Provisional

Probab=94.56  E-value=0.034  Score=48.43  Aligned_cols=32  Identities=31%  Similarity=0.522  Sum_probs=28.1

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHh
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS  325 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~S  325 (784)
                      ....++|.|..+-+|+||||+|.+|+.||..-
T Consensus        28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            44678889999999999999999999999754

>PRK02821 hypothetical protein; Provisional

Probab=94.42  E-value=0.036  Score=48.48  Aligned_cols=33  Identities=33%  Similarity=0.629  Sum_probs=28.8

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhC
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSG  326 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SG  326 (784)
                      ....++|.|..+-+|+||||+|.+|+.||..-.
T Consensus        29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             CcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            446789999999999999999999999997643

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

Probab=94.34  E-value=0.055  Score=61.77  Aligned_cols=97  Identities=16%  Similarity=0.203  Sum_probs=71.1

Q ss_pred             cccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCC-CCCCCCCCCCCeEEEEEe
Q 003942          128 DNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSK-SDDPSSTDDSTMSRKIEV  206 (784)
Q Consensus       128 vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~-~~~~~~~~~~~~t~rI~V  206 (784)
                      ...+|-++|+.|++|-.+-..+|.|..+-..           ...-+.|+++|.+++-.+. +..-.   -...+.+|+|
T Consensus        40 ~P~~~~~~~dlik~lAk~lrKRI~iR~dPsv-----------l~~~e~A~~~I~eivP~ea~i~~i~---Fd~~tGEViI  105 (637)
T COG1782          40 NPELFAKDGDLIKDLAKDLRKRIIIRPDPSV-----------LKPPEEARKIILEIVPEEAGITDIY---FDDDTGEVII  105 (637)
T ss_pred             CHHHhccchhHHHHHHHHHhhceEeccCchh-----------cCCHHHHHHHHHHhCccccCceeEE---ecCCCceEEE
Confidence            3477888899999998777777777655432           2356788999999884322 21111   1224567888


Q ss_pred             cCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942          207 PNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD  238 (784)
Q Consensus       207 P~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~  238 (784)
                      -..+-|+||||+|+++++|..+||-.-.|.+.
T Consensus       106 ea~KPGlvigk~g~~~reI~~~tgW~p~ivR~  137 (637)
T COG1782         106 EAKKPGLVIGKGGSTLREITAETGWAPKIVRT  137 (637)
T ss_pred             EecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence            88999999999999999999999987777753

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

Probab=94.02  E-value=0.016  Score=70.65  Aligned_cols=72  Identities=24%  Similarity=0.237  Sum_probs=61.7

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ..+-++.||.+.+.+|||++|.+|+.|+.-||+.|.|.+-+   .+...||.+.+.|.++.+..|..+|.-+|.+
T Consensus      1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq---~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ---PDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC---CccchhhhcccCCCChhhhhhhccccceeec
Confidence            44567789999999999999999999999999999997633   2346799999999999999999999876654

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

Probab=93.91  E-value=0.058  Score=46.97  Aligned_cols=33  Identities=30%  Similarity=0.567  Sum_probs=28.7

Q ss_pred             CCccEEEEEecCCceeeeecCCchHHHHHHHHh
Q 003942          293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS  325 (784)
Q Consensus       293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~S  325 (784)
                      +....++|.|...-+|+||||+|.+|+.||..-
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            345678899999999999999999999999753

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

Probab=93.73  E-value=0.019  Score=69.98  Aligned_cols=74  Identities=20%  Similarity=0.225  Sum_probs=63.9

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      ....++.||-....+|||++|.||+.||.-|||.|.|.+-  ...+-.+|.+.+.|..+.+..|..+|..+|.+-+
T Consensus      1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm--q~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpd 1412 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM--QPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPD 1412 (2131)
T ss_pred             ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhc--CCccchhhhcccCCCChhhhhhhccccceeecCC
Confidence            4566889999999999999999999999999999999862  1224568999999999999999999998887754

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=93.70  E-value=0.48  Score=48.96  Aligned_cols=66  Identities=24%  Similarity=0.447  Sum_probs=57.3

Q ss_pred             cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      ..+.+.+.....-+|...+|..++.|....||+|.+..         .+..|.|+|+...|+.+...|.++|...
T Consensus        26 g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~---------~~~~i~I~g~k~~~~~i~~~i~~~l~~i   91 (210)
T PF14611_consen   26 GDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR---------SENRIRITGTKSTAEYIEASINEILSNI   91 (210)
T ss_pred             ceeEEEecchheeeeecCCchHHHHHHHhcCceEEEec---------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence            45566667888999999999999999888899999975         3678999999999999999999998753

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=93.45  E-value=0.021  Score=49.07  Aligned_cols=34  Identities=29%  Similarity=0.470  Sum_probs=29.1

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcC
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSG  230 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TG  230 (784)
                      .....+.|.|..+..|+||||+|.||+.||.-..
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~   59 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN   59 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence            4456888999999999999999999999987544

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

Probab=93.41  E-value=0.14  Score=53.65  Aligned_cols=59  Identities=22%  Similarity=0.389  Sum_probs=47.2

Q ss_pred             EEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhh-HHHHHHHHHHH
Q 003942          202 RKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN-IDKAEKLINAV  269 (784)
Q Consensus       202 ~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~-V~kA~~~I~el  269 (784)
                      .-|.|+..+|-++|||+|++|+.|+++|+|+|.|-.+         -.|.|.+..+. ...|.+.|..+
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N---------G~IWV~~~~~~~e~~~~~aI~~i  207 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN---------GRIWVDGENESLEELAIEAIRKI  207 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC---------CEEEecCCCcchHHHHHHHHHHH
Confidence            4688999999999999999999999999999999753         47888886663 44455555443

>PRK01064 hypothetical protein; Provisional

Probab=93.39  E-value=0.09  Score=46.14  Aligned_cols=33  Identities=33%  Similarity=0.484  Sum_probs=28.5

Q ss_pred             CCccEEEEEecCCceeeeecCCchHHHHHHHHh
Q 003942          293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS  325 (784)
Q Consensus       293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~S  325 (784)
                      .....++|.|..+-+|+||||+|++|+.||...
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            345678889999999999999999999999753

>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein

Probab=92.53  E-value=0.2  Score=60.31  Aligned_cols=96  Identities=24%  Similarity=0.412  Sum_probs=70.3

Q ss_pred             eeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhcc
Q 003942          213 VLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQAS  292 (784)
Q Consensus       213 ~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~  292 (784)
                      .++=..++.||+|-++..-+|.|..+..           +   ...=++|+++|.++|-++-  +...+.   |      
T Consensus        36 ~~~~~~~~~~~~~~~~~~~r~~~~~~~~-----------~---~~~~~~~~~~i~~~~~~~~--~~~~~~---f------   90 (630)
T TIGR03675        36 ELFAKDDDLVKELAKKLRKRIVIRPDPS-----------V---LLPPEEAIEKIKEIVPEEA--GITDIY---F------   90 (630)
T ss_pred             HHhccchHHHHHHHHHhhceEEEecChh-----------h---cCCHHHHHHHHHHhCCCcC--CceeEE---e------
Confidence            4556778999999999999999975421           1   1223568999999887641  111111   1      


Q ss_pred             CCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 003942          293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQ  334 (784)
Q Consensus       293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~  334 (784)
                       ...+-++.|-.++-|+||||+|.++++|..+||-+.+|.+.
T Consensus        91 -~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~  131 (630)
T TIGR03675        91 -DDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT  131 (630)
T ss_pred             -cCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence             23456788889999999999999999999999999888653

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.

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=92.20  E-value=0.54  Score=47.08  Aligned_cols=103  Identities=17%  Similarity=0.226  Sum_probs=61.7

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCC
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSP  279 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p  279 (784)
                      -.+-|+|-... |..|||+|.+||+|++..|-+|.|...++      +              ..++|.+++.       |
T Consensus        61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s~------d--------------~~~fl~Nl~~-------P  112 (166)
T PRK06418         61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEKTN------D--------------IKKLAVQLLS-------P  112 (166)
T ss_pred             CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEcCC------C--------------HHHHHHhcCC-------C
Confidence            45677787777 99999999999999999999999986532      1              2233333332       1


Q ss_pred             cccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEe
Q 003942          280 SLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQL  331 (784)
Q Consensus       280 ~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI  331 (784)
                      ..+.. ........+...+.+.|..+....|-.|--..-+-+++.||..+.|
T Consensus       113 A~V~g-V~i~~~~dG~~~~kV~Vd~~Dk~~l~~k~e~~~~v~~kltgk~v~~  163 (166)
T PRK06418        113 ARVLG-VNTVWLPDGTVQYVIRVSRRDRRRLPAKPELLESILSKITGTEVKI  163 (166)
T ss_pred             cEEEE-EEEEEeCCCcEEEEEEECHHHhhcccccHHHHHHHHHHHHCCcEEE
Confidence            11100 0000001223344477777666665555544444557778877766

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

Probab=92.06  E-value=0.22  Score=52.89  Aligned_cols=51  Identities=18%  Similarity=0.384  Sum_probs=46.8

Q ss_pred             eeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          308 GLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       308 G~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      -+|||.+|.|+|.|+-.|.|-|-|.           ..+|.+.|....++.++.+|.++|.+
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVq-----------G~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQ-----------GNTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEee-----------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence            5799999999999999999999984           45799999999999999999999976

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

Probab=91.83  E-value=0.2  Score=53.20  Aligned_cols=93  Identities=15%  Similarity=0.235  Sum_probs=63.1

Q ss_pred             eecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCC
Q 003942          165 ETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPH  244 (784)
Q Consensus       165 ~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~  244 (784)
                      .+.+...-++.|.+++.+.+.++-+........   ..+|   -.+--+|||.+|.|+|.|+--|.|-|-|..       
T Consensus       120 KLlaRsVp~eqAvkiLqDev~CdiIkIgn~V~n---kerF---vKRRqRLiGpng~TLKAlelLT~CYilVqG-------  186 (356)
T KOG2874|consen  120 KLLARSVPFEQAVKILQDEVACDIIKIGNLVRN---KERF---VKRRQRLIGPNGSTLKALELLTNCYILVQG-------  186 (356)
T ss_pred             HHHHcCCCHHHHHHHHhhccceeeeehhhhhcc---HHHH---HHHHHHhcCCCchhHHHHHHHhhcEEEeeC-------
Confidence            344555666777777766664443322221000   0000   012357999999999999999999999985       


Q ss_pred             CCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          245 AATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       245 s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                         ..|.+.|....|..++++|.+.|...
T Consensus       187 ---~TVsaiGpfkGlkevr~IV~DcM~Ni  212 (356)
T KOG2874|consen  187 ---NTVSAIGPFKGLKEVRKIVEDCMKNI  212 (356)
T ss_pred             ---cEEEeecCcchHHHHHHHHHHHHhcc
Confidence               37899999999999999888887764

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=91.81  E-value=0.37  Score=55.15  Aligned_cols=127  Identities=13%  Similarity=0.066  Sum_probs=81.4

Q ss_pred             ccceeeccCcchHhhHHhhcCCEEEE--ccCCCCCCCCCCCcE-EEecchhhHHHHHHHHHHHHHhhhcCCCCccccccc
Q 003942          210 KVGVLIGKAGDTIRYLQYNSGAKIQI--TRDADADPHAATRPV-EIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGL  286 (784)
Q Consensus       210 ~vG~IIGkgG~tIK~Iq~~TGakI~V--~~~~~~~p~s~eR~V-~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~  286 (784)
                      .--.|-||+--.+.+|++...|.+.+  ....    +  .++. .+.|..-...++++++..-+                
T Consensus       390 ~EdFl~gkkngK~TrIm~~v~c~~~~~i~~~~----g--s~~~~~~~g~~~~F~k~~~~~~~EF----------------  447 (657)
T COG5166         390 NEDFLRGKKNGKATRIMKGVSCSELSSIVSST----G--SIVETNGIGEKMSFSKKLSIPPTEF----------------  447 (657)
T ss_pred             hHHHhccccCcchhhhhhhcccceeeEEEecC----C--cEEEEeccCcchhhHHHhcCCcccC----------------
Confidence            34477888877799999999988544  3321    1  2333 33455555555555543321                


Q ss_pred             chhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceE-EEEEcCH---HHHHHHHHH
Q 003942          287 ATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERI-VRVTGDM---RQIEIAQEM  362 (784)
Q Consensus       287 ~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~-V~I~Gt~---~qV~~Ak~l  362 (784)
                              ..++.|.|+...+..|||-||..|.+++.+.++.|++...-  ....+..+- |.|.-+.   +.+..+|.=
T Consensus       448 --------pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~--~~~qs~~~dNV~I~~PrKn~~ni~~~KNd  517 (657)
T COG5166         448 --------PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFY--KFGQSQWHDNVLIEAPRKNQDNISGKKND  517 (657)
T ss_pred             --------chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhh--hcchhhhhcceEEECCccCccchhccccc
Confidence                    23567999999999999999999999999999999987532  111222222 5565542   345555555


Q ss_pred             HHHHHh
Q 003942          363 IKEVLS  368 (784)
Q Consensus       363 I~~~L~  368 (784)
                      +++++.
T Consensus       518 ~~~~V~  523 (657)
T COG5166         518 KLDKVK  523 (657)
T ss_pred             HHHHHh
Confidence            555554

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=91.58  E-value=0.15  Score=44.40  Aligned_cols=32  Identities=31%  Similarity=0.612  Sum_probs=26.1

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCC
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGA  231 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGa  231 (784)
                      ..+.|.|.....|+||||+|+||+.|+.-+..
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~   55 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANL   55 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHHHH
Confidence            35667777889999999999999999875543

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.

>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein

Probab=91.52  E-value=0.21  Score=60.16  Aligned_cols=96  Identities=16%  Similarity=0.199  Sum_probs=67.7

Q ss_pred             ccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcC-CCCCCCCCCCCCeEEEEEec
Q 003942          129 NQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNS-KSDDPSSTDDSTMSRKIEVP  207 (784)
Q Consensus       129 g~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~-~~~~~~~~~~~~~t~rI~VP  207 (784)
                      .+++-++++.|++|-.+-.-+|.|+.+...           ...-+.|+++|.+++-.+ .++.-.   -...+-+|+|-
T Consensus        35 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~-----------~~~~~~~~~~i~~~~~~~~~~~~~~---f~~~~~~v~i~  100 (630)
T TIGR03675        35 PELFAKDDDLVKELAKKLRKRIVIRPDPSV-----------LLPPEEAIEKIKEIVPEEAGITDIY---FDDVTGEVIIE  100 (630)
T ss_pred             HHHhccchHHHHHHHHHhhceEEEecChhh-----------cCCHHHHHHHHHHhCCCcCCceeEE---ecCCCceEEEE
Confidence            366777889999997666555555544321           123367889999988533 221111   12345688888


Q ss_pred             CCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942          208 NNKVGVLIGKAGDTIRYLQYNSGAKIQITRD  238 (784)
Q Consensus       208 ~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~  238 (784)
                      ..+-|+||||+|.++++|.++||-+..|.+.
T Consensus       101 ~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~  131 (630)
T TIGR03675       101 AEKPGLVIGKGGSTLREITAETGWTPKVVRT  131 (630)
T ss_pred             EcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence            8999999999999999999999998888764

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.

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

Probab=90.51  E-value=0.53  Score=49.52  Aligned_cols=48  Identities=25%  Similarity=0.430  Sum_probs=40.2

Q ss_pred             EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHH
Q 003942          297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMR  354 (784)
Q Consensus       297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~  354 (784)
                      -.-+.|+..+|-+||||+|.+|+.|.++|+|+|.|-.          ...|-|.+..+
T Consensus       147 G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~----------NG~IWV~~~~~  194 (239)
T COG1097         147 GQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ----------NGRIWVDGENE  194 (239)
T ss_pred             CEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec----------CCEEEecCCCc
Confidence            3567899999999999999999999999999999853          44677777644

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

Probab=90.21  E-value=0.49  Score=53.95  Aligned_cols=66  Identities=26%  Similarity=0.403  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 003942          259 IDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQ  334 (784)
Q Consensus       259 V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~  334 (784)
                      ...|.+.|++.|+....+  +..        -...+.....+.||...++.||||+|.+|++|.++.|.+|.|...
T Consensus       459 ~~~a~~~i~~~i~r~~p~--~~e--------Ve~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~  524 (604)
T COG1855         459 LKLAEEEIEREIKRYLPG--DVE--------VEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL  524 (604)
T ss_pred             hHHHHHHHHHHHHHhCCC--Cce--------EEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence            555777777777765321  110        011234567899999999999999999999999999999999853

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

Probab=89.50  E-value=0.47  Score=39.03  Aligned_cols=34  Identities=32%  Similarity=0.406  Sum_probs=27.8

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEE
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKI  233 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI  233 (784)
                      ....+.+.....|.+|||+|.+|+.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            5556666666799999999999999999887554

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=89.45  E-value=0.19  Score=43.17  Aligned_cols=37  Identities=24%  Similarity=0.458  Sum_probs=31.1

Q ss_pred             CCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeE
Q 003942          293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARI  329 (784)
Q Consensus       293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarI  329 (784)
                      .....+.+.|..+..|+||||+|+||+.||.....-+
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~   62 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA   62 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence            3567888999999999999999999999997765443

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

Probab=89.43  E-value=0.26  Score=42.27  Aligned_cols=39  Identities=31%  Similarity=0.509  Sum_probs=30.9

Q ss_pred             EEEEEecCCc-----cceeeccCcchHhhHHhhc-CCEEEEccCC
Q 003942          201 SRKIEVPNNK-----VGVLIGKAGDTIRYLQYNS-GAKIQITRDA  239 (784)
Q Consensus       201 t~rI~VP~~~-----vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~  239 (784)
                      ..+|.|-...     +|.+||++|.+||.|.++. |-+|.|...+
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~s   48 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEYS   48 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE--
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEcC
Confidence            4567777777     9999999999999999999 9999998653

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

Probab=88.89  E-value=0.58  Score=38.50  Aligned_cols=34  Identities=29%  Similarity=0.473  Sum_probs=27.0

Q ss_pred             cEEEEEecCCceeeeecCCchHHHHHHHHhCCeE
Q 003942          296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARI  329 (784)
Q Consensus       296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarI  329 (784)
                      ..+.+.+.....|.+|||+|++|+.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            4445555555689999999999999999988554

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

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

Probab=87.86  E-value=0.34  Score=41.54  Aligned_cols=37  Identities=27%  Similarity=0.566  Sum_probs=29.3

Q ss_pred             EEEEEecCCc-----eeeeecCCchHHHHHHHHh-CCeEEecc
Q 003942          297 QVEIKVPNEK-----VGLIIGRGGETIKGLQTRS-GARIQLIP  333 (784)
Q Consensus       297 ~~~i~VP~~~-----vG~VIGkgG~~IK~Iq~~S-GarIqI~~  333 (784)
                      ++.+.|-.+.     +|..||++|.+||.|.++. |-+|.|..
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            4556666655     9999999999999999999 99999864

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

Probab=87.34  E-value=0.99  Score=39.92  Aligned_cols=37  Identities=19%  Similarity=0.375  Sum_probs=31.0

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEe
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQL  331 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI  331 (784)
                      ...+++.|-...-|.|||++|++|++|++...-+..+
T Consensus        29 ~~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~   65 (81)
T cd02413          29 PTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF   65 (81)
T ss_pred             CCeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence            4568899999999999999999999999876555544

S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

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

Probab=87.28  E-value=0.39  Score=54.73  Aligned_cols=39  Identities=26%  Similarity=0.420  Sum_probs=35.8

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD  238 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~  238 (784)
                      ....|.||...++.||||+|.+|++|+++.|.+|.|...
T Consensus       486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~  524 (604)
T COG1855         486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL  524 (604)
T ss_pred             CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence            456788999999999999999999999999999999864

>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter

Probab=86.93  E-value=6.9  Score=46.77  Aligned_cols=143  Identities=20%  Similarity=0.290  Sum_probs=76.6

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEc---cCCCC-CC-----CCCCCcEEEecchhhHHHHHHHHHHH
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT---RDADA-DP-----HAATRPVEIIGTLSNIDKAEKLINAV  269 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~---~~~~~-~p-----~s~eR~V~I~G~~e~V~kA~~~I~el  269 (784)
                      .+...+.|+..  ..+|   |.+|++|......+|.|.   ++.+. .+     -....++.|.|+.++|+++++.+...
T Consensus       217 ~~~r~~~V~~~--s~li---GkTl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~L~~l~~~~G~~  291 (562)
T TIGR03802       217 LVGRAYRVNRA--SSLI---GKTVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDAVVQFGAEIGEE  291 (562)
T ss_pred             eeeEEEEECCC--cccC---CCcHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHHHHHHHHhcCCc
Confidence            34556667654  2244   457888876654333332   21110 01     11235779999999998877665443


Q ss_pred             HHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHH-H-----HhCCeEEeccCC---CCC--
Q 003942          270 IAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQ-T-----RSGARIQLIPQH---LPE--  338 (784)
Q Consensus       270 I~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq-~-----~SGarIqI~~~~---~p~--  338 (784)
                      +.+..          ..    . ......++.+++   ..+|||   +|++|+ +     +.|+.|.-..+.   ++.  
T Consensus       292 ~~~~~----------~~----~-~~~~~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~  350 (562)
T TIGR03802       292 VQEVE----------GL----D-VPMETKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILP  350 (562)
T ss_pred             cCCcc----------cc----C-CceEEEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCC
Confidence            32210          00    0 011233445554   345654   888887 2     568775444321   110  


Q ss_pred             -CCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 003942          339 -GDGSKERIVRVTGDMRQIEIAQEMIKEVL  367 (784)
Q Consensus       339 -~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L  367 (784)
                       ..-..-.++.|.|+.+.++++++.+-+..
T Consensus       351 d~~L~~GD~LlV~G~~~~l~~~~~~lG~~~  380 (562)
T TIGR03802       351 ETVLQRGDVVTLVGTPQDVDRAAKQLGYAI  380 (562)
T ss_pred             CCEecCCCEEEEEeCHHHHHHHHHHcCCch
Confidence             01122356899999999999877755433

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).

>PRK03818 putative transporter; Validated

Probab=86.29  E-value=6.2  Score=47.04  Aligned_cols=140  Identities=18%  Similarity=0.288  Sum_probs=77.3

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEcc---CCCC------CCCCCCCcEEEecchhhHHHHHHHHHHHH
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITR---DADA------DPHAATRPVEIIGTLSNIDKAEKLINAVI  270 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~---~~~~------~p~s~eR~V~I~G~~e~V~kA~~~I~elI  270 (784)
                      ..+++.|+++.   +|   |++|++++.....++.|.+   +.+.      ..-....++.|.|+.++++++++.+...+
T Consensus       205 ~~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~  278 (552)
T PRK03818        205 QTINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEV  278 (552)
T ss_pred             eeEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCcc
Confidence            34677777443   34   5689999887766554432   2110      11122357889999999887776655332


Q ss_pred             HhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHH--HHHhCCeEEeccC-C--CCCCC---CC
Q 003942          271 AEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGL--QTRSGARIQLIPQ-H--LPEGD---GS  342 (784)
Q Consensus       271 ~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~I--q~~SGarIqI~~~-~--~p~~~---~~  342 (784)
                      .+.            .  ..........++.++++   .++||   +|++|  +++.|+.|.-.++ .  ++...   -.
T Consensus       279 ~~~------------~--~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq  338 (552)
T PRK03818        279 DTS------------L--STRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQ  338 (552)
T ss_pred             Ccc------------c--cccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEe
Confidence            110            0  00011223344445543   56655   78888  4667776443322 1  11111   12


Q ss_pred             CceEEEEEcCHHHHHHHHHHHHH
Q 003942          343 KERIVRVTGDMRQIEIAQEMIKE  365 (784)
Q Consensus       343 ~er~V~I~Gt~~qV~~Ak~lI~~  365 (784)
                      .-.++.|.|+.+++++..+.+.+
T Consensus       339 ~GD~LlVvG~~~~i~~l~~~Lg~  361 (552)
T PRK03818        339 FGDILNLVGRPEAIDAVANVLGN  361 (552)
T ss_pred             cCCEEEEEECHHHHHHHHHHhCC
Confidence            23468999999999998776543

>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]

Probab=85.65  E-value=3.4  Score=43.44  Aligned_cols=37  Identities=24%  Similarity=0.539  Sum_probs=29.1

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHH----HhCC-eEEe
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQT----RSGA-RIQL  331 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~----~SGa-rIqI  331 (784)
                      ...+++.|....=|.||||+|++|+.|++    .+|. .|+|
T Consensus        50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I   91 (233)
T COG0092          50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQI   91 (233)
T ss_pred             CCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceE
Confidence            45678888899999999999999998864    4565 3444

>PRK13764 ATPase; Provisional

Probab=85.21  E-value=0.72  Score=55.12  Aligned_cols=66  Identities=15%  Similarity=0.180  Sum_probs=47.1

Q ss_pred             hhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCC
Q 003942          174 EPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDA  239 (784)
Q Consensus       174 e~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~  239 (784)
                      ..|.+.|.+.|...-...-...........|.|+...++.+|||+|.+|++|+++.|.+|.|....
T Consensus       455 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~  520 (602)
T PRK13764        455 RLAEKEIEREIKRYLPGPVEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD  520 (602)
T ss_pred             HHHHHHHHHHHHHhcCCceEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence            445566666664333111111112445778999999999999999999999999999999998654

>PRK13764 ATPase; Provisional

Probab=85.14  E-value=1.1  Score=53.77  Aligned_cols=66  Identities=26%  Similarity=0.373  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 003942          259 IDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQ  334 (784)
Q Consensus       259 V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~  334 (784)
                      ...|.+.|++.|+....+...          -......+..+.|+...++.||||+|.+|++|.++.|.+|.|...
T Consensus       454 ~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~  519 (602)
T PRK13764        454 WRLAEKEIEREIKRYLPGPVE----------VEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL  519 (602)
T ss_pred             HHHHHHHHHHHHHHhcCCceE----------EEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence            345677777777765311000          011245678899999999999999999999999999999999753

>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins

Probab=84.74  E-value=0.64  Score=52.64  Aligned_cols=21  Identities=10%  Similarity=0.113  Sum_probs=11.2

Q ss_pred             eecccccccccceeeecCchh
Q 003942          151 DVKEETKEVTVKEEETVKEEE  171 (784)
Q Consensus       151 ~I~~~~~~~s~r~~~i~G~~e  171 (784)
                      +|...+.........|.|+.+
T Consensus       181 ~~Rp~tP~LPDSTDFVCGTLD  201 (458)
T PF10446_consen  181 KIRPGTPELPDSTDFVCGTLD  201 (458)
T ss_pred             CCCCCCCCCCCcccccCCCcC
Confidence            444444455555566666643

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=84.46  E-value=0.97  Score=39.31  Aligned_cols=36  Identities=28%  Similarity=0.635  Sum_probs=29.4

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEE
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQ  330 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIq  330 (784)
                      ...+.+.|-.+..|+||||+|++|+.||--+...+.
T Consensus        23 ~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          23 GDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             CCEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            346778888899999999999999999977665444

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.

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=83.73  E-value=0.56  Score=40.67  Aligned_cols=35  Identities=23%  Similarity=0.518  Sum_probs=30.2

Q ss_pred             cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEE
Q 003942          296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQ  330 (784)
Q Consensus       296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIq  330 (784)
                      ..+.+.|-....|.|||++|++|++|.+.+.-++.
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            56788899999999999999999999887766654

; 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 ....

>KOG0299 consensus U3 snoRNP-associated protein (contains WD40 repeats) [RNA processing and modification]

Probab=83.26  E-value=3  Score=47.48  Aligned_cols=40  Identities=30%  Similarity=0.289  Sum_probs=21.6

Q ss_pred             hcCCccccccCchhhccccccccccCCCccCCccccCCCC
Q 003942           33 AEGMRDDEAKNSDEVEKNVDGFAEAHGSEVKRPRLDDDKT   72 (784)
Q Consensus        33 ~~~~~~~e~~~~~e~~~~~~~~~~~d~~e~Krpr~ddd~~   72 (784)
                      +++|.-||++|+.+.++-..++.+..+..+||.||-++.+
T Consensus        44 ~eei~Sd~Een~~~g~~e~e~e~~~Eta~ekr~RlA~e~L   83 (479)
T KOG0299|consen   44 AEEIESDEEENSLAGEEEEEDEFEEETAGEKRLRLAEEYL   83 (479)
T ss_pred             hhhhccccccccccchhhhcccchhcchhHHHHHHHHHHH
Confidence            4455544555555553333333344445558888777765

>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]

Probab=81.03  E-value=1.2  Score=46.73  Aligned_cols=51  Identities=16%  Similarity=0.294  Sum_probs=34.9

Q ss_pred             hhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhh
Q 003942          177 NVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN  228 (784)
Q Consensus       177 ~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~  228 (784)
                      ++.|.+.+.+..+..-.... ....++|.|-..+-|.||||+|++|++|++.
T Consensus        29 re~l~k~l~~Ag~s~veIeR-~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~   79 (233)
T COG0092          29 REFLEKELSNAGISGVEIER-TPKGTRVTIHAARPGLVIGKKGSNIEKLRKE   79 (233)
T ss_pred             HHHHHHHHHhCCcceEEEEe-cCCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence            34555555555443322211 2457789999999999999999999988764

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=80.89  E-value=0.81  Score=39.65  Aligned_cols=35  Identities=20%  Similarity=0.376  Sum_probs=29.6

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEE
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQ  234 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~  234 (784)
                      ....|.|-....|.|||++|++|++|+....-.+.
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            46788889999999999999999999887665554

; 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 ....

>PRK03818 putative transporter; Validated

Probab=80.41  E-value=5.9  Score=47.21  Aligned_cols=96  Identities=20%  Similarity=0.275  Sum_probs=56.8

Q ss_pred             ceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhH--HhhcCCEEEEccCC
Q 003942          162 KEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYL--QYNSGAKIQITRDA  239 (784)
Q Consensus       162 r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~I--q~~TGakI~V~~~~  239 (784)
                      ..+.+.|+.++++++...+...+..    .....+.....++|+++++   .++||   +|++|  +++.|+.|.-.++.
T Consensus       256 DiLlV~G~~e~l~~l~~~~Gl~~~~----~~~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~  325 (552)
T PRK03818        256 DLLHLVGQPEDLHKAQLVIGEEVDT----SLSTRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRA  325 (552)
T ss_pred             CEEEEEECHHHHHHHHHhcCCccCc----cccccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeEC
Confidence            5677888999888877665544321    0111122345666777764   55655   78777  46677766443332


Q ss_pred             CCCC-CC------CCCcEEEecchhhHHHHHHHHH
Q 003942          240 DADP-HA------ATRPVEIIGTLSNIDKAEKLIN  267 (784)
Q Consensus       240 ~~~p-~s------~eR~V~I~G~~e~V~kA~~~I~  267 (784)
                      +..- ..      .-.++.+.|+++++++..+.+.
T Consensus       326 g~~l~~~~d~~Lq~GD~LlVvG~~~~i~~l~~~Lg  360 (552)
T PRK03818        326 GVELVASPDLSLQFGDILNLVGRPEAIDAVANVLG  360 (552)
T ss_pred             CeecCCCCCCEEecCCEEEEEECHHHHHHHHHHhC
Confidence            2111 11      1236789999999999877644

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=80.01  E-value=2.2  Score=42.81  Aligned_cols=39  Identities=23%  Similarity=0.488  Sum_probs=34.2

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP  333 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~  333 (784)
                      ....+-|.|-... |..|||+|.+||.+++..|-+|.|..
T Consensus        59 ~ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE   97 (166)
T PRK06418         59 VDDLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE   97 (166)
T ss_pred             eCCEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence            3467788887777 99999999999999999999999974

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	784
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		9e-14
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		1e-13
2jvz_A	164	Solution Nmr Structure Of The Second And Third Kh D		5e-12
1j4w_A	174	Complex Of The Kh3 And Kh4 Domains Of Fbp With A Si		1e-09
1j4w_A	174	Complex Of The Kh3 And Kh4 Domains Of Fbp With A Si		8e-05
1x4m_A	94	Solution Structure Of Kh Domain In Far Upstream Ele		1e-07
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		6e-07
2opv_A	85	Solution Nmr Structure Of The Second Domain Of Ksrp		2e-06
1x4n_A	92	Solution Structure Of Kh Domain In Fuse Binding Pro		6e-06
1x4n_A	92	Solution Structure Of Kh Domain In Fuse Binding Pro		9e-05
2opu_A	89	Solution Nmr Structure Of The First Domain Of Ksrp		1e-05
2opu_A	89	Solution Nmr Structure Of The First Domain Of Ksrp		1e-05
2hh2_A	107	Solution Structure Of The Fourth Kh Domain Of Ksrp		4e-05
1we8_A	104	Solution Structure Of Kh Domain In Protein Bab28342		7e-05
3krm_A	163	Imp1 Kh34 Length = 163		2e-04
1ec6_A	87	Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Bind		7e-04
3vke_A	76	Contribution Of The First K-Homology Domain Of Poly		7e-04
1dt4_A	73	Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Bind		8e-04
2e3u_A	219	Crystal Structure Analysis Of Dim2p From Pyrococcus		8e-04

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

Iteration: 1
 Score = 75.9 bits (185), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 57/164 (34%), Positives = 83/164 (50%), Gaps = 6/164 (3%)
Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
           K+ +P+   G +IGK G TI  LQ  +GA I++++  D  P    R   I GT+  ++  
Sbjct: 9   KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAV 68
Query: 263 EKLINAVIAEA---DAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIK 319
              I   I E     A   P  + +   T      A QV+I VPN   GLIIG+GG T+K
Sbjct: 69  HGFIAEKIREMPQNVAKTEPVSILQPQTTVNPD-RANQVKIIVPNSTAGLIIGKGGATVK 127
Query: 320 GLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 363
            +  +SGA +QL     P+G   + R+V V+G+  Q   A E+I
Sbjct: 128 AIMEQSGAWVQL--SQKPDGINLQNRVVTVSGEPEQNRKAVELI 169

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

Iteration: 1
 Score = 75.5 bits (184), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 57/164 (34%), Positives = 83/164 (50%), Gaps = 6/164 (3%)
Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
           K+ +P+   G +IGK G TI  LQ  +GA I++++  D  P    R   I GT+  ++  
Sbjct: 9   KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAV 68
Query: 263 EKLINAVIAEA---DAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIK 319
              I   I E     A   P  + +   T      A QV+I VPN   GLIIG+GG T+K
Sbjct: 69  HGFIAEKIREXPQNVAKTEPVSILQPQTTVNPD-RANQVKIIVPNSTAGLIIGKGGATVK 127
Query: 320 GLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 363
            +  +SGA +QL     P+G   + R+V V+G+  Q   A E+I
Sbjct: 128 AIXEQSGAWVQL--SQKPDGINLQNRVVTVSGEPEQNRKAVELI 169

>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains Of Ksrp Length = 164

Iteration: 1
 Score = 69.7 bits (169), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 53/171 (30%), Positives = 91/171 (53%), Gaps = 14/171 (8%)
Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
           +I +P  K G++IGK G+TI+ LQ  +G K+ + +D   + +   +P+ IIG    + +A
Sbjct: 5   EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNV-DKPLRIIGDPYKVQQA 63
Query: 263 EKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQ 322
            +++  ++ E D GG       G      S     +++ VP   VG++IGR GE IK +Q
Sbjct: 64  CEMVMDILRERDQGGF------GDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQ 117
Query: 323 TRSGARIQLIPQHLPEGDGSK-ERIVRVTGDMRQIEIAQEMIKEVLSQTVR 372
             +G RIQ       + DG+  E+I  + G   + E A  +I ++L Q++R
Sbjct: 118 NDAGVRIQ-----FKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL-QSLR 162

>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 = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 50/168 (29%), Positives = 81/168 (48%), Gaps = 12/168 (7%)
Query: 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKL 265
           +P   VG++IG+ G+ I+ +Q ++G +IQ   D    P    R  +I G       A ++
Sbjct: 9   IPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPE---RIAQITGPPDRAQHAAEI 65
Query: 266 INAVIAEADAGGSPSLVARGLATAQAS--------GAAEQVEIKVPNEKVGLIIGRGGET 317
           I  ++    AG        G    +          G  ++    VP  K GLIIG+GGET
Sbjct: 66  ITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGET 125
Query: 318 IKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKE 365
           IK +  +SGARI+L     P  D    ++  + G  +QI+ A+++I+E
Sbjct: 126 IKSISQQSGARIELQRNPPPNAD-PNMKLFTIRGTPQQIDYARQLIEE 172

>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 = 45.8 bits (107), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 6/74 (8%)
Query: 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSK-ERIVRVTGDM 353
           +  +++ +P   VG++IGR GE IK +Q  +G RIQ  P      DG+  ERI ++TG  
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD-----DGTTPERIAQITGPP 56
Query: 354 RQIEIAQEMIKEVL 367
            + + A E+I ++L
Sbjct: 57  DRAQHAAEIITDLL 70

>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element Binding Protein 1 Length = 94

Iteration: 1
 Score = 55.5 bits (132), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/69 (43%), Positives = 50/69 (72%), Gaps = 2/69 (2%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEI 358
           EI +P  K GL+IG+GGETIK LQ R+G ++ +I Q  P+  G+ ++ +R+TGD  +++ 
Sbjct: 18  EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMI-QDGPQNTGA-DKPLRITGDPYKVQQ 75
Query: 359 AQEMIKEVL 367
           A+EM+ E++
Sbjct: 76  AKEMVLELI 84

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 40/161 (24%), Positives = 78/161 (48%), Gaps = 31/161 (19%)
Query: 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN 258
           T++ ++ +   +VG +IGK G++++ ++  SGA+I I+     + +   R + + G  + 
Sbjct: 4   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINIS-----EGNCPERIITLAGPTNA 58
Query: 259 I--------DKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLI 310
           I        DK E+ I++ +  + A   P +  R               + VP  + G +
Sbjct: 59  IFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLR---------------LVVPASQCGSL 103
Query: 311 IGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG 351
           IG+GG  IK ++  +GA++Q+    LP    S ER + + G
Sbjct: 104 IGKGGCKIKEIRESTGAQVQVAGDMLPN---STERAITIAG 141

>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp Length = 85

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 48/75 (64%), Gaps = 10/75 (13%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSK----ERIVRVTGDMR 354
           EI +P  K GL+IG+GGETIK LQ R+G ++ LI       DGS+    ++ +R+ GD  
Sbjct: 17  EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQ------DGSQNTNVDKPLRIIGDPY 70
Query: 355 QIEIAQEMIKEVLSQ 369
           +++ A EM+ ++L +
Sbjct: 71  KVQQACEMVMDILRE 85

>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1 Length = 92

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 3/78 (3%)
Query: 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN 258
            M+ + +VP+  VG +IG+ G+ I  +Q  SG KIQI  D+   P    R   + GT  +
Sbjct: 14  VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPE---RSCMLTGTPES 70
Query: 259 IDKAEKLINAVIAEADAG 276
           +  A++L++ ++ +  +G
Sbjct: 71  VQSAKRLLDQIVEKGRSG 88

>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1 Length = 92

Iteration: 1
 Score = 45.8 bits (107), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 4/69 (5%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEI 358
           E KVP+  VG IIGRGGE I  +Q  SG +IQ+     P+  G  ER   +TG    ++ 
Sbjct: 18  EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQI----APDSGGLPERSCMLTGTPESVQS 73
Query: 359 AQEMIKEVL 367
           A+ ++ +++
Sbjct: 74  AKRLLDQIV 82

>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp Length = 89

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 46/78 (58%), Gaps = 3/78 (3%)
Query: 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN 258
           +M+ +  VP+  VG++IG+ G+ I  +Q +SG K+QI+ D+   P    R V + G   +
Sbjct: 15  SMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPE---RSVSLTGAPES 71
Query: 259 IDKAEKLINAVIAEADAG 276
           + KA+ +++ +++    G
Sbjct: 72  VQKAKMMLDDIVSRGRGG 89

>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp Length = 89

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 44/71 (61%), Gaps = 4/71 (5%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEI 358
           E +VP+  VGLIIGRGGE I  +Q  SG ++Q+     P+  G  ER V +TG    ++ 
Sbjct: 19  EYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQI----SPDSGGLPERSVSLTGAPESVQK 74
Query: 359 AQEMIKEVLSQ 369
           A+ M+ +++S+
Sbjct: 75  AKMMLDDIVSR 85

>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp Length = 107

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 44/69 (63%), Gaps = 1/69 (1%)
Query: 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQI 356
           ++   +P  K GL+IGRGGE +K +  ++GA +++  Q  P GD + +  + + G  +QI
Sbjct: 8   EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFI-IRGSPQQI 66
Query: 357 EIAQEMIKE 365
           + A+++I+E
Sbjct: 67  DHAKQLIEE 75

>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342 Length = 104

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 25/71 (35%), Positives = 43/71 (60%), Gaps = 2/71 (2%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEI 358
           ++ VP   VG IIGRGGETI+ +   SGA+I    +   EG     R+++++G  +++  
Sbjct: 18  QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKE--SEGTLLLSRLIKISGTQKEVAA 75
Query: 359 AQEMIKEVLSQ 369
           A+ +I E +S+
Sbjct: 76  AKHLILEKVSE 86

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 73/165 (44%), Gaps = 16/165 (9%)
Query: 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKL 265
           +P   VG +IGK G  I+ L   + A I+I       P +  R V I G      KA+  
Sbjct: 9   IPAQAVGAIIGKKGQHIKQLSRFASASIKIA--PPETPDSKVRMVIITGPPEAQFKAQGR 66
Query: 266 INAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325
           I   + E +  G    V              +  I+VP    G +IG+GG+T+  LQ  +
Sbjct: 67  IYGKLKEENFFGPKEEVKL------------ETHIRVPASAAGRVIGKGGKTVNELQNLT 114
Query: 326 GARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT 370
            A + +     P  D + + IV++ G     ++AQ  I+++L+Q 
Sbjct: 115 AAEVVVPRDQTP--DENDQVIVKIIGHFYASQMAQRKIRDILAQV 157

>pdb|1EC6|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding Domain Bound To 20-Mer Rna Hairpin Length = 87

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 48/83 (57%), Gaps = 7/83 (8%)
Query: 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP--QHLPEGDGSKERIVRVTGDM 353
           E VEI VP   VG I+G+GG+T+   Q  +GARIQ+    + LP   G++ R V +TG  
Sbjct: 3   ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP---GTRNRRVTITGSP 59
Query: 354 RQIEIAQEMIKEVLS--QTVRPS 374
              + AQ +I + ++  Q VR S
Sbjct: 60  AATQAAQYLISQRVTYEQGVRAS 82

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 27/70 (38%), Positives = 42/70 (60%), Gaps = 6/70 (8%)
Query: 305 EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIK 364
           ++VG IIG+ GE++K ++  SGARI     ++ EG+ S ERI+ +TG    I  A  MI 
Sbjct: 12  KEVGSIIGKKGESVKRIREESGARI-----NISEGN-SPERIITLTGPTNAIFKAFAMII 65
Query: 365 EVLSQTVRPS 374
           + L + +  S
Sbjct: 66  DKLEEDINSS 75

>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding Domain Length = 73

Iteration: 1
 Score = 42.7 bits (99), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 25/68 (36%), Positives = 36/68 (52%)
Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
           +I VP N VG ++GK G T+   Q  +G +IQI++  +  P    R V I GT +    A
Sbjct: 6   EIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAA 65
Query: 263 EKLINAVI 270
           + LI   I
Sbjct: 66  QYLITQRI 73

>pdb|2E3U|A Chain A, Crystal Structure Analysis Of Dim2p From Pyrococcus Horikoshii Ot3 Length = 219

Iteration: 1
 Score = 42.7 bits (99), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 45/169 (26%), Positives = 78/169 (46%), Gaps = 24/169 (14%)
Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAE 263
           +++P +++ VLIGK G T + ++  +  K +IT D++      T   E    L+ + KA 
Sbjct: 38  VKIPKDRIAVLIGKKGQTKKEIEKRT--KTKITIDSETGEVWITSTKETEDPLA-VWKAR 94
Query: 264 KLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGL------IIGRGGET 317
            ++ A+      G SP    R L   +        +I + NEK  L      IIGR G T
Sbjct: 95  DIVLAI----GRGFSPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRT 150
Query: 318 IKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEV 366
            + ++  SGA + +             + V + G+  QIEIA+  I+++
Sbjct: 151 RQIIEEMSGASVSVY-----------GKTVAIIGNPIQIEIAKTAIEKL 188

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	784
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-46
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	6e-18
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	6e-18
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	7e-46
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	9e-18
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-16
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-44
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-19
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-18
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	5e-44
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-19
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	7e-17
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	6e-42
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	4e-16
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	4e-27
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	5e-23
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	5e-20
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	6e-23
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	3e-22
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	5e-22
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	6e-22
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	3e-21
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-15
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-20
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-18
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	1e-20
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	3e-19
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-20
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-19
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	3e-20
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-17
1tua_A	191	Hypothetical protein APE0754; structural genomics,	1e-19
1tua_A	191	Hypothetical protein APE0754; structural genomics,	8e-09
1we8_A	104	Tudor and KH domain containing protein; structural	1e-19
1we8_A	104	Tudor and KH domain containing protein; structural	2e-15
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-19
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	3e-19
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-19
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	7e-18
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	2e-19
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	4e-18
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	2e-19
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-18
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-17
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	6e-10
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	1e-09
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-17
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	1e-15
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	9e-16
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	5e-10
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	1e-14
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	7e-11
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	1e-13
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	5e-11
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	2e-13
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	1e-09
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-13
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-12
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-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	4e-10
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	5e-10
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	5e-09
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	5e-08
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-07
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-05
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-12
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-10
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-12
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	9e-12
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-06
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	6e-12
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	3e-09
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	9e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-10
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	5e-09
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	1e-06
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	2e-06
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	2e-06
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	5e-05
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	6e-06
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	5e-05
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	6e-06
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	2e-04
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	1e-05
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	3e-05
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	7e-05
2cxc_A	144	NUSA; transcription termination, RNA binding prote	8e-05
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	2e-04
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	9e-04
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	3e-04
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	4e-04
2z73_A	448	Rhodopsin; visual pigment, GQ-type, G-protein coup	9e-04

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

 Score =  160 bits (407), Expect = 5e-46
 Identities = 43/174 (24%), Positives = 86/174 (49%), Gaps = 15/174 (8%)

Query: 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTL 256
           + T++ ++ +   +VG +IGK G++++ ++  SGA+I I     ++ +   R + + G  
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI-----SEGNCPERIITLAGPT 56

Query: 257 SNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGE 316
           + I KA  +I   + E  +    +       +  AS     + + VP  + G +IG+GG 
Sbjct: 57  NAIFKAFAMIIDKLEEDISSSMTN-------STAASRPPVTLRLVVPASQCGSLIGKGGC 109

Query: 317 TIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT 370
            IK ++  +GA++Q+    LP    S ER + + G  + I    + I  V+ +T
Sbjct: 110 KIKEIRESTGAQVQVAGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLET 160

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

 Score = 80.6 bits (199), Expect = 6e-18
 Identities = 23/88 (26%), Positives = 47/88 (53%), Gaps = 2/88 (2%)

Query: 185 DNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPH 244
            +S   + ++     ++ ++ VP ++ G LIGK G  I+ ++ ++GA++Q+    D  P+
Sbjct: 74  ISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG--DMLPN 131

Query: 245 AATRPVEIIGTLSNIDKAEKLINAVIAE 272
           +  R + I G   +I +  K I  V+ E
Sbjct: 132 STERAITIAGIPQSIIECVKQICVVMLE 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 = 80.6 bits (199), Expect = 6e-18
 Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 6/87 (6%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
           + + +  ++VG IIG+ GE++K ++  SGARI +            ERI+ + G    I 
Sbjct: 7   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISE------GNCPERIITLAGPTNAIF 60

Query: 358 IAQEMIKEVLSQTVRPSTLSGGFNQQA 384
            A  MI + L + +  S  +     + 
Sbjct: 61  KAFAMIIDKLEEDISSSMTNSTAASRP 87

>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 =  160 bits (407), Expect = 7e-46
 Identities = 56/174 (32%), Positives = 86/174 (49%), Gaps = 4/174 (2%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLS 257
           S    K+ +P+   G +IGK G TI  LQ  +GA I++++  D  P    R   I GT+ 
Sbjct: 4   SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIE 63

Query: 258 NIDKAEKLINAVIAEADAGGSPSLVARGLATAQASG--AAEQVEIKVPNEKVGLIIGRGG 315
            ++     I   I E     + +     L          A QV+I VPN   GLIIG+GG
Sbjct: 64  ALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGG 123

Query: 316 ETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369
            T+K +  +SGA +QL  +  P+G   + R+V V+G+  Q   A E+I + + +
Sbjct: 124 ATVKAIMEQSGAWVQLSQK--PDGINLQNRVVTVSGEPEQNRKAVELIIQKIQE 175

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

 Score = 80.7 bits (199), Expect = 9e-18
 Identities = 22/97 (22%), Positives = 42/97 (43%), Gaps = 1/97 (1%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
           +++ +P+   G IIG+GG+TI  LQ  +GA I+L         G+ ER+  + G +  + 
Sbjct: 8   LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFY-PGTTERVCLIQGTIEALN 66

Query: 358 IAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPTGPP 394
                I E + +  +    +   +    +  V     
Sbjct: 67  AVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRA 103

>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 = 77.2 bits (190), Expect = 1e-16
 Identities = 28/99 (28%), Positives = 44/99 (44%), Gaps = 1/99 (1%)

Query: 174 EPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKI 233
           E    V +    +      +   D     KI VPN+  G++IGK G T++ +   SGA +
Sbjct: 78  EMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWV 137

Query: 234 QITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE 272
           Q+++  D   +   R V + G      KA +LI   I E
Sbjct: 138 QLSQKPD-GINLQNRVVTVSGEPEQNRKAVELIIQKIQE 175

>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 =  156 bits (395), Expect = 3e-44
 Identities = 48/169 (28%), Positives = 82/169 (48%), Gaps = 11/169 (6%)

Query: 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNID 260
            ++I +P  K G++IGK G+TI+ LQ  +G K+ + +D         +P+ IIG    + 
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRIIGDPYKVQ 61

Query: 261 KAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKG 320
           +A +++  ++ E D GG              S     +++ VP   VG++IGR GE IK 
Sbjct: 62  QACEMVMDILRERDQGGFGD------RNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKK 115

Query: 321 LQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369
           +Q  +G RIQ       +     E+I  + G   + E A  +I ++L  
Sbjct: 116 IQNDAGVRIQF----KQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQS 160

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

 Score = 84.8 bits (210), Expect = 3e-19
 Identities = 27/86 (31%), Positives = 47/86 (54%), Gaps = 2/86 (2%)

Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEI 358
           EI +P  K GL+IG+GGETIK LQ R+G ++ LI       + + ++ +R+ GD  +++ 
Sbjct: 5   EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQD--GSQNTNVDKPLRIIGDPYKVQQ 62

Query: 359 AQEMIKEVLSQTVRPSTLSGGFNQQA 384
           A EM+ ++L +  +            
Sbjct: 63  ACEMVMDILRERDQGGFGDRNEYGSR 88

>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 = 81.8 bits (202), Expect = 3e-18
 Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 3/92 (3%)

Query: 185 DNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPH 244
                D             + VP + VGV+IG++G+ I+ +Q ++G +IQ  +D    P 
Sbjct: 76  QGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP- 134

Query: 245 AATRPVEIIGTLSNIDKAEKLINAVIAEADAG 276
              +   I+G     + A ++IN ++    +G
Sbjct: 135 --EKIAHIMGPPDRCEHAARIINDLLQSLRSG 164

>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 =  155 bits (394), Expect = 5e-44
 Identities = 48/177 (27%), Positives = 85/177 (48%), Gaps = 12/177 (6%)

Query: 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN 258
           +    + +P   VG++IG+ G+ I+ +Q ++G +IQ   D   D     R  +I G    
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD---DGTTPERIAQITGPPDR 58

Query: 259 IDKAEKLINAVIAEADAGGSPSLVARGLATAQASG--------AAEQVEIKVPNEKVGLI 310
              A ++I  ++    AG        G    +  G          ++    VP  K GLI
Sbjct: 59  AQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLI 118

Query: 311 IGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVL 367
           IG+GGETIK +  +SGARI+ + ++ P       ++  + G  +QI+ A+++I+E +
Sbjct: 119 IGKGGETIKSISQQSGARIE-LQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

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

 Score = 85.3 bits (211), Expect = 2e-19
 Identities = 26/106 (24%), Positives = 45/106 (42%), Gaps = 4/106 (3%)

Query: 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ 355
             +++ +P   VG++IGR GE IK +Q  +G RIQ      P+   + ERI ++TG   +
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQF----KPDDGTTPERIAQITGPPDR 58

Query: 356 IEIAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPRGS 401
            + A E+I ++L      +    G   +                  
Sbjct: 59  AQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQ 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 = 78.0 bits (192), Expect = 7e-17
 Identities = 26/108 (24%), Positives = 46/108 (42%), Gaps = 1/108 (0%)

Query: 164 EETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTM-SRKIEVPNNKVGVLIGKAGDTI 222
            + ++  ++  P    P          + +      +      VP  K G++IGK G+TI
Sbjct: 67  TDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETI 126

Query: 223 RYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVI 270
           + +   SGA+I++ R+   +     +   I GT   ID A +LI   I
Sbjct: 127 KSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

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

 Score =  149 bits (378), Expect = 6e-42
 Identities = 44/174 (25%), Positives = 76/174 (43%), Gaps = 18/174 (10%)

Query: 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT 255
           +   +  ++ +P   VG +IGK G  I+ L   + A I+I       P +  R V I G 
Sbjct: 1   EQEMV--QVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPET--PDSKVRMVIITGP 56

Query: 256 LSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGG 315
                KA+  I   + E +  G                   +  I+VP    G +IG+GG
Sbjct: 57  PEAQFKAQGRIYGKLKEENFFGPKE------------EVKLETHIRVPASAAGRVIGKGG 104

Query: 316 ETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369
           +T+  LQ  + A + +     P  D + + IV++ G     ++AQ  I+++L+Q
Sbjct: 105 KTVNELQNLTAAEVVVPRDQTP--DENDQVIVKIIGHFYASQMAQRKIRDILAQ 156

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

 Score = 75.6 bits (186), Expect = 4e-16
 Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 1/85 (1%)

Query: 190 DDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRP 249
           +     ++  +   I VP +  G +IGK G T+  LQ  + A++ + RD           
Sbjct: 75  NFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRD-QTPDENDQVI 133

Query: 250 VEIIGTLSNIDKAEKLINAVIAEAD 274
           V+IIG       A++ I  ++A+  
Sbjct: 134 VKIIGHFYASQMAQRKIRDILAQVK 158

>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 =  109 bits (272), Expect = 4e-27
 Identities = 45/205 (21%), Positives = 80/205 (39%), Gaps = 25/205 (12%)

Query: 170 EESVEPSNVVPQQVVDNSKSDDPSSTDD-STMSRKIEVPNNKVGVLIGKAGDTIRYLQYN 228
           EE  +          D    +D    ++       +++P +++ VLIGK G T + ++  
Sbjct: 3   EEFEKLMKKFENVNKDGEIVEDEDEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKR 62

Query: 229 SGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLAT 288
           +  KI I  +            +       + KA  ++ A+      G SP    R L  
Sbjct: 63  TKTKITIDSETGEVWI---TSTKETEDPLAVWKARDIVLAIG----RGFSPERAFRLLNE 115

Query: 289 AQASGAAEQVEIKVPNEK------VGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGS 342
            +        +I + NEK       G IIGR G T + ++  SGA + +           
Sbjct: 116 GEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSV----------- 164

Query: 343 KERIVRVTGDMRQIEIAQEMIKEVL 367
             + V + G+  QIEIA+  I+++ 
Sbjct: 165 YGKTVAIIGNPIQIEIAKTAIEKLA 189

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

 Score = 92.8 bits (231), Expect = 5e-23
 Identities = 28/81 (34%), Positives = 47/81 (58%), Gaps = 2/81 (2%)

Query: 289 AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVR 348
           A         EI +P  K GL+IG+GGETIK LQ R+G ++ LI       + + ++ +R
Sbjct: 7   ANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG--SQNTNVDKPLR 64

Query: 349 VTGDMRQIEIAQEMIKEVLSQ 369
           + GD  +++ A EM+ ++L +
Sbjct: 65  IIGDPYKVQQACEMVMDILRE 85

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

 Score = 84.3 bits (209), Expect = 5e-20
 Identities = 22/83 (26%), Positives = 46/83 (55%), Gaps = 1/83 (1%)

Query: 190 DDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRP 249
            D ++   +   ++I +P  K G++IGK G+TI+ LQ  +G K+ + +D   +     +P
Sbjct: 4   HDNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNT-NVDKP 62

Query: 250 VEIIGTLSNIDKAEKLINAVIAE 272
           + IIG    + +A +++  ++ E
Sbjct: 63  LRIIGDPYKVQQACEMVMDILRE 85

>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 = 91.9 bits (229), Expect = 6e-23
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ 355
           E VE+ VP   VG I+G+GG+T+   Q  +GARIQ I +      G++ R V +TG    
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQ-ISKKGEFLPGTRNRRVTITGSPAA 61

Query: 356 IEIAQEMIKEVLSQ 369
            + AQ +I + ++ 
Sbjct: 62  TQAAQYLISQRVTY 75

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

 Score = 90.0 bits (224), Expect = 3e-22
 Identities = 23/70 (32%), Positives = 38/70 (54%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
           ++ VP N VG ++GK G T+   Q  +GA+IQI++  +  P    R V I G+ +    A
Sbjct: 6   EMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAA 65

Query: 263 EKLINAVIAE 272
           + LI+  +  
Sbjct: 66  QYLISQRVTY 75

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

 Score = 90.1 bits (224), Expect = 5e-22
 Identities = 24/73 (32%), Positives = 38/73 (52%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
           +I VP N VG ++GK G T+   Q  +GA+IQI++  +  P    R V I G+ +    A
Sbjct: 6   EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAA 65

Query: 263 EKLINAVIAEADA 275
           + LI+  +     
Sbjct: 66  QYLISQRVTYEQG 78

>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 = 89.7 bits (223), Expect = 6e-22
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ 355
           E VEI VP   VG I+G+GG+T+   Q  +GARIQ I +      G++ R V +TG    
Sbjct: 3   ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQ-ISKKGEFLPGTRNRRVTITGSPAA 61

Query: 356 IEIAQEMIKEVLSQ 369
            + AQ +I + ++ 
Sbjct: 62  TQAAQYLISQRVTY 75

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

 Score = 88.4 bits (219), Expect = 3e-21
 Identities = 31/116 (26%), Positives = 53/116 (45%), Gaps = 13/116 (11%)

Query: 291 ASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVT 350
           A     ++   +P  K GL+IGRGGE +K +  ++GA ++ I + LP       ++  + 
Sbjct: 2   AMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVE-ISRQLPPNGDPNFKLFIIR 60

Query: 351 GDMRQIEIAQEMIKEVLSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPRGSHPSQP 406
           G  +QI+ A+++I+E +   + P                P GP   GP G     P
Sbjct: 61  GSPQQIDHAKQLIEEKIEGPLCP------------VGPGPGGPGPAGPMGPFNPGP 104

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

 Score = 72.2 bits (177), Expect = 1e-15
 Identities = 21/91 (23%), Positives = 39/91 (42%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
              +P +K G++IG+ G+ ++ +   +GA ++I+R    +     +   I G+   ID A
Sbjct: 10  TFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHA 69

Query: 263 EKLINAVIAEADAGGSPSLVARGLATAQASG 293
           ++LI   I        P     G A      
Sbjct: 70  KQLIEEKIEGPLCPVGPGPGGPGPAGPMGPF 100

>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 = 85.8 bits (213), Expect = 1e-20
 Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 4/79 (5%)

Query: 291 ASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVT 350
           A G     ++ +P +  G IIG+GG+ IK ++  SGA I++        +GS++RI+ +T
Sbjct: 2   AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL----EGSEDRIITIT 57

Query: 351 GDMRQIEIAQEMIKEVLSQ 369
           G   QI+ AQ +++  + Q
Sbjct: 58  GTQDQIQNAQYLLQNSVKQ 76

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

 Score = 79.6 bits (197), Expect = 2e-18
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN 258
            ++ ++ +P +  G +IGK G  I+ +++ SGA I+I    +    +  R + I GT   
Sbjct: 6   IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQ 62

Query: 259 IDKAEKLINAVIAEADA 275
           I  A+ L+   + +   
Sbjct: 63  IQNAQYLLQNSVKQYSG 79

>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 = 85.9 bits (213), Expect = 1e-20
 Identities = 31/97 (31%), Positives = 53/97 (54%), Gaps = 4/97 (4%)

Query: 283 ARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGS 342
           + G +           EI +P  K GL+IG+GGETIK LQ R+G ++ +I       +  
Sbjct: 2   SSGSSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQD--GPQNTG 59

Query: 343 KERIVRVTGDMRQIEIAQEMIKEVLSQTVRPSTLSGG 379
            ++ +R+TGD  +++ A+EM+ E++    + S  S G
Sbjct: 60  ADKPLRITGDPYKVQQAKEMVLELIRD--QGSGPSSG 94

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

 Score = 82.1 bits (203), Expect = 3e-19
 Identities = 23/88 (26%), Positives = 46/88 (52%), Gaps = 1/88 (1%)

Query: 192 PSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVE 251
                     ++I +P +K G++IGK G+TI+ LQ  +G K+ + +D       A +P+ 
Sbjct: 7   GHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQD-GPQNTGADKPLR 65

Query: 252 IIGTLSNIDKAEKLINAVIAEADAGGSP 279
           I G    + +A++++  +I +  +G S 
Sbjct: 66  ITGDPYKVQQAKEMVLELIRDQGSGPSS 93

>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 = 85.4 bits (212), Expect = 2e-20
 Identities = 26/81 (32%), Positives = 46/81 (56%), Gaps = 3/81 (3%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLS 257
           S  + ++ +PNN +G +IG+ G  I  ++  SGA+I+I   A+    ++ R V I G+ +
Sbjct: 4   SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKI---ANPVEGSSGRQVTITGSAA 60

Query: 258 NIDKAEKLINAVIAEADAGGS 278
           +I  A+ LINA ++     G 
Sbjct: 61  SISLAQYLINARLSSEKGMGC 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 = 82.7 bits (205), Expect = 2e-19
 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD 352
           G+    E+ +PN  +G IIGR G  I  ++  SGA+I++        +GS  R V +TG 
Sbjct: 3   GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIA----NPVEGSSGRQVTITGS 58

Query: 353 MRQIEIAQEMIKEVLSQ 369
              I +AQ +I   LS 
Sbjct: 59  AASISLAQYLINARLSS 75

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

 Score = 85.6 bits (212), Expect = 3e-20
 Identities = 30/107 (28%), Positives = 44/107 (41%), Gaps = 5/107 (4%)

Query: 287 ATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERI 346
           A A  S     +++ VP   VG++IGR GE IK +Q  +G RIQ       +     E+I
Sbjct: 2   AMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFK----QDDGTGPEKI 57

Query: 347 VRVTGDMRQIEIAQEMIKEVLSQT-VRPSTLSGGFNQQAYRPRVPTG 392
             + G   + E A  +I ++L      P    GG            G
Sbjct: 58  AHIMGPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRG 104

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

 Score = 78.3 bits (193), Expect = 1e-17
 Identities = 22/99 (22%), Positives = 45/99 (45%), Gaps = 3/99 (3%)

Query: 191 DPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPV 250
             ++         + VP + VGV+IG++G+ I+ +Q ++G +IQ  +D    P    +  
Sbjct: 2   AMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP---EKIA 58

Query: 251 EIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATA 289
            I+G     + A ++IN ++    +G        G+   
Sbjct: 59  HIMGPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPG 97

>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 = 86.6 bits (214), Expect = 1e-19
 Identities = 30/185 (16%), Positives = 63/185 (34%), Gaps = 33/185 (17%)

Query: 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNI 259
               ++V   ++G +IG  G+    +   +G  I +  +           V +      I
Sbjct: 4   PRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE--------NSMVIVEPEAEGI 55

Query: 260 D-----KAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEK-----VGL 309
                 KA +++ A+      G  P    R L   Q     +  ++   ++       G 
Sbjct: 56  PPVNLMKAAEVVKAIS----LGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGR 111

Query: 310 IIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369
           IIG GG   + ++  +   I +            E  V + GD  +   A++ I+ +   
Sbjct: 112 IIGEGGRARRTIEEMTDTYINV-----------GEYEVAIIGDYERAMAAKQAIEMLAEG 160

Query: 370 TVRPS 374
            +  +
Sbjct: 161 RMHST 165

>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 = 55.0 bits (132), Expect = 8e-09
 Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKE-RIVRVTG 351
               ++ +KV  E++G +IG  GE    +  R+G  I +  +     +            
Sbjct: 1   AMKPRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE-----NSMVIVEPEAEGI 55

Query: 352 DMRQIEIAQEMIKEV 366
               +  A E++K +
Sbjct: 56  PPVNLMKAAEVVKAI 70

>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 = 83.7 bits (207), Expect = 1e-19
 Identities = 26/87 (29%), Positives = 46/87 (52%), Gaps = 2/87 (2%)

Query: 283 ARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGS 342
           + G +           ++ VP   VG IIGRGGETI+ +   SGA+I    +   EG   
Sbjct: 2   SSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKE--SEGTLL 59

Query: 343 KERIVRVTGDMRQIEIAQEMIKEVLSQ 369
             R+++++G  +++  A+ +I E +S+
Sbjct: 60  LSRLIKISGTQKEVAAAKHLILEKVSE 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 = 72.2 bits (177), Expect = 2e-15
 Identities = 24/80 (30%), Positives = 46/80 (57%), Gaps = 1/80 (1%)

Query: 195 TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG 254
           T+++ +  ++ VP   VG +IG+ G+TIR +   SGAKI   ++++      +R ++I G
Sbjct: 10  TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTL-LLSRLIKISG 68

Query: 255 TLSNIDKAEKLINAVIAEAD 274
           T   +  A+ LI   ++E +
Sbjct: 69  TQKEVAAAKHLILEKVSEDE 88

>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 = 83.2 bits (206), Expect = 1e-19
 Identities = 27/92 (29%), Positives = 47/92 (51%), Gaps = 3/92 (3%)

Query: 187 SKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAA 246
           S          S M+ + +VP+  VG +IG+ G+ I  +Q  SG KIQI  D+   P   
Sbjct: 2   SSGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP--- 58

Query: 247 TRPVEIIGTLSNIDKAEKLINAVIAEADAGGS 278
            R   + GT  ++  A++L++ ++ +  +G S
Sbjct: 59  ERSCMLTGTPESVQSAKRLLDQIVEKGRSGPS 90

>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 = 3e-19
 Identities = 28/87 (32%), Positives = 45/87 (51%), Gaps = 4/87 (4%)

Query: 283 ARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGS 342
           + G +  Q   +    E KVP+  VG IIGRGGE I  +Q  SG +IQ+ P       G 
Sbjct: 2   SSGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS----GGL 57

Query: 343 KERIVRVTGDMRQIEIAQEMIKEVLSQ 369
            ER   +TG    ++ A+ ++ +++ +
Sbjct: 58  PERSCMLTGTPESVQSAKRLLDQIVEK 84

>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 = 82.3 bits (204), Expect = 1e-19
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
           + + +  ++VG IIG+ GE++K ++  SGARI +   + P      ERI+ + G    I 
Sbjct: 7   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP------ERIITLAGPTNAIF 60

Query: 358 IAQEMIKEVLSQ 369
            A  MI + L +
Sbjct: 61  KAFAMIIDKLEE 72

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

 Score = 77.7 bits (192), Expect = 7e-18
 Identities = 19/77 (24%), Positives = 42/77 (54%), Gaps = 5/77 (6%)

Query: 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT 255
            + T++ ++ +   +VG +IGK G++++ ++  SGA+I I     ++ +   R + + G 
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI-----SEGNCPERIITLAGP 55

Query: 256 LSNIDKAEKLINAVIAE 272
            + I KA  +I   + E
Sbjct: 56  TNAIFKAFAMIIDKLEE 72

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

 Score = 82.4 bits (204), Expect = 2e-19
 Identities = 27/83 (32%), Positives = 47/83 (56%), Gaps = 4/83 (4%)

Query: 287 ATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERI 346
           +     G     ++ +P +  G IIG+GG+ IK ++  SGA I+ I + L    GS++RI
Sbjct: 5   SYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIK-IDEPLE---GSEDRI 60

Query: 347 VRVTGDMRQIEIAQEMIKEVLSQ 369
           + +TG   QI+ AQ +++  + Q
Sbjct: 61  ITITGTQDQIQNAQYLLQNSVKQ 83

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

 Score = 78.9 bits (195), Expect = 4e-18
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 3/76 (3%)

Query: 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTL 256
              ++ ++ +P +  G +IGK G  I+ +++ SGA I+I    +    +  R + I GT 
Sbjct: 11  GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQ 67

Query: 257 SNIDKAEKLINAVIAE 272
             I  A+ L+   + +
Sbjct: 68  DQIQNAQYLLQNSVKQ 83

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

 Score = 82.0 bits (203), Expect = 2e-19
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD 352
                 E+ +PN+ +G IIGR G  I  ++  SGA+I++        +GS +R V +TG 
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPV----EGSTDRQVTITGS 57

Query: 353 MRQIEIAQEMIKEVLSQ 369
              I +AQ +I   LS 
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 = 80.0 bits (198), Expect = 1e-18
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 3/75 (4%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLS 257
            T S ++ +PN+ +G +IG+ G  I  ++  SGA+I+I   A+    +  R V I G+ +
Sbjct: 3   QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKI---ANPVEGSTDRQVTITGSAA 59

Query: 258 NIDKAEKLINAVIAE 272
           +I  A+ LIN  ++ 
Sbjct: 60  SISLAQYLINVRLSS 74

>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 = 78.5 bits (193), Expect = 2e-17
 Identities = 33/174 (18%), Positives = 57/174 (32%), Gaps = 37/174 (21%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGA-KIQITRDADADPHAATRPVEIIGTL 256
           S    +  V  + +G+ IG  G  I+  +   G   I +  D        T    I G  
Sbjct: 2   SRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDED--------TCTFHIYGED 53

Query: 257 SNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGE 316
            +  K                           A++     +  I+VP   VG +IG+ G+
Sbjct: 54  QDAVKK--------------------------ARSFLEFAEDVIQVPRNLVGKVIGKNGK 87

Query: 317 TIKGLQTRSGARIQLIPQHLPEGDGSKERIVRV--TGDMRQIEIAQEMIKEVLS 368
            I+ +  +SG     I     +    +E +V     G    I  A  ++   L+
Sbjct: 88  LIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLN 141

>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 = 57.3 bits (138), Expect = 6e-10
 Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 3/76 (3%)

Query: 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGA---KIQITRDADADPHAATRPVEIIGTL 256
               I+VP N VG +IGK G  I+ +   SG    +I+   + +        P   +GT 
Sbjct: 67  AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTK 126

Query: 257 SNIDKAEKLINAVIAE 272
            +I  A  L++  +  
Sbjct: 127 DSIANATVLLDYHLNY 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 = 56.6 bits (136), Expect = 1e-09
 Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 9/81 (11%)

Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMR-QIE 357
           +  V  + +GL IG  G  I+  +   G     + +              + G+ +  ++
Sbjct: 7   QFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE--------DTCTFHIYGEDQDAVK 58

Query: 358 IAQEMIKEVLSQTVRPSTLSG 378
            A+  ++        P  L G
Sbjct: 59  KARSFLEFAEDVIQVPRNLVG 79

>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 = 76.3 bits (188), Expect = 4e-17
 Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 6/82 (7%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
             + +P E    +IG+ GE ++ L+ ++  +IQ IP+            +++TG    IE
Sbjct: 19  ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQ-IPR-----PDDPSNQIKITGTKEGIE 72

Query: 358 IAQEMIKEVLSQTVRPSTLSGG 379
            A+  +  + ++  + S  S G
Sbjct: 73  KARHEVLLISAEQDKRSGPSSG 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 = 72.1 bits (177), Expect = 1e-15
 Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 5/95 (5%)

Query: 186 NSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHA 245
           +  S D  +   +  S  + +P      +IGK G+ ++ L+  +  KIQI R  D     
Sbjct: 3   SGSSGDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPS--- 59

Query: 246 ATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPS 280
               ++I GT   I+KA   +  + AE D    PS
Sbjct: 60  --NQIKITGTKEGIEKARHEVLLISAEQDKRSGPS 92

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

 Score = 71.6 bits (176), Expect = 9e-16
 Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
           VEI + ++    +IG+ G  I  ++ +    ++ IP      D  K  ++R+ GD + ++
Sbjct: 7   VEINIDHKFHRHLIGKSGANINRIKDQYKVSVR-IPP-----DSEKSNLIRIEGDPQGVQ 60

Query: 358 IAQEMIKEVLS 368
            A+  + E+ S
Sbjct: 61  QAKRELLELAS 71

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

 Score = 55.4 bits (134), Expect = 5e-10
 Identities = 12/69 (17%), Positives = 30/69 (43%), Gaps = 5/69 (7%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
           +I + +     LIGK+G  I  ++      ++I  D++         + I G    + +A
Sbjct: 8   EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKS-----NLIRIEGDPQGVQQA 62

Query: 263 EKLINAVIA 271
           ++ +  + +
Sbjct: 63  KRELLELAS 71

>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 = 68.4 bits (167), Expect = 1e-14
 Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 7/79 (8%)

Query: 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQI 356
            ++++VP   VGL++G  G TIK +Q R+   I             KE +  VTG    +
Sbjct: 11  TIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTP-------GRDKEPVFAVTGMPENV 63

Query: 357 EIAQEMIKEVLSQTVRPST 375
           + A+E I+  ++    PS+
Sbjct: 64  DRAREEIEAHITLRSGPSS 82

>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 = 58.0 bits (140), Expect = 7e-11
 Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 6/87 (6%)

Query: 192 PSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVE 251
            S +     + ++ VP   VG+++G  G TI+ +Q  +   I +T   D +P        
Sbjct: 2   SSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYI-VTPGRDKEP-----VFA 55

Query: 252 IIGTLSNIDKAEKLINAVIAEADAGGS 278
           + G   N+D+A + I A I       S
Sbjct: 56  VTGMPENVDRAREEIEAHITLRSGPSS 82

>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 = 66.8 bits (163), Expect = 1e-13
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 3/83 (3%)

Query: 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQI 356
           ++ + V  +    IIGR G  I  ++      IQ  P    +     +  + +TG  +  
Sbjct: 18  KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQ-FPD--KDDGNQPQDQITITGYEKNT 74

Query: 357 EIAQEMIKEVLSQTVRPSTLSGG 379
           E A++ I  ++ +  + S  S G
Sbjct: 75  EAARDAILRIVGELEQMSGPSSG 97

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 59.1 bits (143), Expect = 5e-11
 Identities = 16/80 (20%), Positives = 27/80 (33%), Gaps = 2/80 (2%)

Query: 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNID 260
              + V       +IG+ G  I  ++      IQ       D +     + I G   N +
Sbjct: 18  KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPD--KDDGNQPQDQITITGYEKNTE 75

Query: 261 KAEKLINAVIAEADAGGSPS 280
            A   I  ++ E +    PS
Sbjct: 76  AARDAILRIVGELEQMSGPS 95

>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 = 66.4 bits (162), Expect = 2e-13
 Identities = 13/72 (18%), Positives = 31/72 (43%), Gaps = 6/72 (8%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
           +E++VP +    +IG+ G  I+ +       I +           +  I+ +TG    ++
Sbjct: 19  IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP------ELQSDIIAITGLAANLD 72

Query: 358 IAQEMIKEVLSQ 369
            A+  + E + +
Sbjct: 73  RAKAGLLERVKE 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 = 55.2 bits (133), Expect = 1e-09
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNI 259
           ++ ++EVP +    +IG+ G  IR +       I +       P   +  + I G  +N+
Sbjct: 17  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV-----PAPELQSDIIAITGLAANL 71

Query: 260 DKAEKLINAVIAEADA 275
           D+A+  +   + E  A
Sbjct: 72  DRAKAGLLERVKELQA 87

>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 = 72.6 bits (177), Expect = 3e-13
 Identities = 30/181 (16%), Positives = 42/181 (23%), Gaps = 2/181 (1%)

Query: 512 GHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGH-SNSQPVYSQGGLQSGYHQHQYGKPPY 570
            H +   +   Q  YG        P Q       + +   Y Q G+         G+  +
Sbjct: 2   SHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQF 61

Query: 571 GMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPS 630
             PAQ    Q                   V       P VP Q   P           P+
Sbjct: 62  LTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMA-APA 120

Query: 631 YGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQA 690
           YG   A    N  P +         +  P          P            + +N    
Sbjct: 121 YGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPD 180

Query: 691 Y 691
           Y
Sbjct: 181 Y 181

>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 = 3e-12
 Identities = 32/194 (16%), Positives = 43/194 (22%), Gaps = 10/194 (5%)

Query: 543 GHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPS 602
            H   + VY Q  LQ G +     +P   MP Q          + G P            
Sbjct: 2   SHHKKR-VYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQ 60

Query: 603 AQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYP 662
             +      HQQ     TS      +      P      Q P       Q          
Sbjct: 61  FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQ---------Q 111

Query: 663 QPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYA 722
           Q     AP+YGQ +   G       Q    +                P            
Sbjct: 112 QQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVP 171

Query: 723 APTGQPGYAQPAAT 736
           +           +T
Sbjct: 172 SELSNASPDYIRST 185

>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 = 67.2 bits (163), Expect = 1e-11
 Identities = 29/197 (14%), Positives = 44/197 (22%), Gaps = 11/197 (5%)

Query: 558 SGYHQHQY--GKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQ 615
           S + +  Y   +  YG  A   Q  +   P P  P        Q+            QQQ
Sbjct: 2   SHHKKRVYPQAQLQYGQNATPLQQPAQFMP-PQDPAAAGMSYGQMGMPPQGAVPSMGQQQ 60

Query: 616 YPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQV 675
           +         Q      ++      +  P   P    Q        PQ   Q      Q 
Sbjct: 61  FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQ--------PQVPVQMGTPLQQQ 112

Query: 676 APTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAA 735
                   Y     A  +     N  Y      +     +            P      +
Sbjct: 113 QQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPS 172

Query: 736 TQPSYDQSASQSTAYGV 752
              +      +ST   V
Sbjct: 173 ELSNASPDYIRSTLNAV 189

>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 = 64.1 bits (155), Expect = 1e-10
 Identities = 27/173 (15%), Positives = 39/173 (22%), Gaps = 12/173 (6%)

Query: 481 GHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHP 540
            +P    Q      P  Q          +  G         PQ           +  Q  
Sbjct: 8   VYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAV-------PSMGQQQ 60

Query: 541 YGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQV 600
           +   +  Q         +  +       P   P    QPQ      P Q G     Q Q 
Sbjct: 61  FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQV-----PVQMGTPLQQQQQP 115

Query: 601 PSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQ 653
            +A +YG       Q     +        +    P  D    PP       + 
Sbjct: 116 MAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERM 168

>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 = 62.9 bits (152), Expect = 3e-10
 Identities = 28/167 (16%), Positives = 37/167 (22%), Gaps = 2/167 (1%)

Query: 611 PHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAP 670
             ++ YP A     Q   P     PA     Q PA+A     Q G          GQQ  
Sbjct: 4   HKKRVYPQAQLQYGQNATP--LQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQF 61

Query: 671 SYGQVAPTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGY 730
                           T                             P      P   P Y
Sbjct: 62  LTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAY 121

Query: 731 AQPAATQPSYDQSASQSTAYGVAQGTAAAGYGKTVSPQPGYPQYDST 777
            QP+A      +  +Q     +           T+ P P     +  
Sbjct: 122 GQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERM 168

>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 = 4e-10
 Identities = 23/185 (12%), Positives = 35/185 (18%), Gaps = 4/185 (2%)

Query: 595 PYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQA 654
             +   P AQ          Q P     P            +      PP  A     Q 
Sbjct: 4   HKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAA----GMSYGQMGMPPQGAVPSMGQQ 59

Query: 655 GQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQDPSYGS 714
               P   Q   Q   +   +     +        AY +       G   Q  Q P    
Sbjct: 60  QFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAP 119

Query: 715 SAPGSAYAAPTGQPGYAQPAATQPSYDQSASQSTAYGVAQGTAAAGYGKTVSPQPGYPQY 774
           +    + A         Q        +     +                 V  +      
Sbjct: 120 AYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASP 179

Query: 775 DSTQM 779
           D  + 
Sbjct: 180 DYIRS 184

>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 = 62.2 bits (150), Expect = 5e-10
 Identities = 33/242 (13%), Positives = 53/242 (21%), Gaps = 15/242 (6%)

Query: 411 YPQRGPYPSQNPHYPHLPYGNYPPQQMAPRSNYGGPPNMQGAAGGYDYYGGQGGHVSDRP 470
           + ++  YP     Y         P Q         PP    AA      G   G +   P
Sbjct: 3   HHKKRVYPQAQLQYGQNATPLQQPAQ-------FMPPQDPAAA------GMSYGQMGMPP 49

Query: 471 VSVSHSTSIPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGY 530
                S       +   +        +  + N    H         Y         G   
Sbjct: 50  QGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPL 109

Query: 531 DDNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQP 590
                P+  P  G  ++    +   +   Y      + P  +      P     P     
Sbjct: 110 QQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERML 169

Query: 591 GDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGY 650
                  +     +S    VP        +  P       Y      D  + PP +  G 
Sbjct: 170 VPSELSNASPDYIRSTLNAVPKNSSLLKKSKLPFGLVIRPY--QHLYDDIDPPPLNEDGL 227

Query: 651 PQ 652
             
Sbjct: 228 IV 229

>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 = 58.7 bits (141), Expect = 5e-09
 Identities = 22/151 (14%), Positives = 39/151 (25%), Gaps = 6/151 (3%)

Query: 378 GGFNQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQM 437
               ++ Y    P    Q+G   +   QP  +  PQ       +     +P     P   
Sbjct: 2   SHHKKRVY----PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMG 57

Query: 438 APRSNYGGPPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPS 497
             +        +               H+ + P+   ++   P  P            P 
Sbjct: 58  QQQFLTPAQEQLHQQIDQA-TTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQP- 115

Query: 498 QANYNYGQPHTSEYGHQQPYAHAAPQQGYGH 528
            A   YGQP  +   + +P     P      
Sbjct: 116 MAAPAYGQPSAAMGQNMRPMNQLYPIDLLTE 146

>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 = 55.6 bits (133), Expect = 5e-08
 Identities = 26/181 (14%), Positives = 31/181 (17%), Gaps = 19/181 (10%)

Query: 476 STSIPGHPSVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHA 535
             + P         P        +    G P               P Q   H       
Sbjct: 18  QNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLH------- 70

Query: 536 PVQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPP 595
                       Q +       +  H H           Q   P   G P   Q   +  
Sbjct: 71  ------------QQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAA 118

Query: 596 YQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAG 655
                PSA       P  Q YP                 P P          P     A 
Sbjct: 119 PAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNAS 178

Query: 656 Q 656
            
Sbjct: 179 P 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 = 53.3 bits (127), Expect = 2e-07
 Identities = 20/153 (13%), Positives = 27/153 (17%), Gaps = 20/153 (13%)

Query: 621 SGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAG 680
           S   ++ YP    A      N  P   P                G    P  G V     
Sbjct: 2   SHHKKRVYPQ---AQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQ 58

Query: 681 YGQYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAATQPSY 740
               T  Q+   +Q   +                             P     A  QP  
Sbjct: 59  QQFLTPAQEQLHQQIDQATTSMNDMHLH-----------------NVPLVDPNAYMQPQV 101

Query: 741 DQSASQSTAYGVAQGTAAAGYGKTVSPQPGYPQ 773
                           A A    + +       
Sbjct: 102 PVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRP 134

>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 = 47.1 bits (111), Expect = 2e-05
 Identities = 14/140 (10%), Positives = 23/140 (16%), Gaps = 1/140 (0%)

Query: 382 QQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNYPPQQMAPRS 441
                      PPQ         Q +     Q      Q     +  + +  P       
Sbjct: 37  AAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAY 96

Query: 442 NYGGPPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQANY 501
                P   G                    ++  +         P       PPP     
Sbjct: 97  MQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLY-PIDLLTELPPPITDLT 155

Query: 502 NYGQPHTSEYGHQQPYAHAA 521
               P           +  +
Sbjct: 156 LPPPPLVIPPERMLVPSELS 175

>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 = 46.7 bits (110), Expect = 3e-05
 Identities = 17/150 (11%), Positives = 30/150 (20%), Gaps = 3/150 (2%)

Query: 382 QQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPY-PSQNPHYPHLPYGNYPPQQMAPR 440
            Q   P+ P        +   P Q       Q+    P+Q   +  +         M   
Sbjct: 27  AQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLH 86

Query: 441 SNYGGPPN--MQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGPPPSQ 498
           +     PN  MQ           Q         +    ++  G    P          ++
Sbjct: 87  NVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTE 146

Query: 499 ANYNYGQPHTSEYGHQQPYAHAAPQQGYGH 528
                            P           +
Sbjct: 147 LPPPITDLTLPPPPLVIPPERMLVPSELSN 176

>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 = 62.9 bits (153), Expect = 2e-12
 Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 5/82 (6%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
            ++ + +     IIG  G+ I+ +       I       P+        V VTG    +E
Sbjct: 19  EDVPLDHRVHARIIGARGKAIRKIMDEFKVDI-----RFPQSGAPDPNCVTVTGLPENVE 73

Query: 358 IAQEMIKEVLSQTVRPSTLSGG 379
            A + I  +  + +  S  S G
Sbjct: 74  EAIDHILNLEEEYLADSGPSSG 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 = 57.1 bits (138), Expect = 2e-10
 Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 4/84 (4%)

Query: 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTL 256
           +  +S  + + +     +IG  G  IR +       I+  +    DP      V + G  
Sbjct: 14  EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDP----NCVTVTGLP 69

Query: 257 SNIDKAEKLINAVIAEADAGGSPS 280
            N+++A   I  +  E  A   PS
Sbjct: 70  ENVEEAIDHILNLEEEYLADSGPS 93

>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 = 70.1 bits (171), Expect = 2e-12
 Identities = 55/264 (20%), Positives = 87/264 (32%), Gaps = 24/264 (9%)

Query: 516  PYAHAAPQQGYGHGYDDNHAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQ 575
            PY++ +      +   D    +       S S    + G    G   +     P+G   +
Sbjct: 1472 PYSNESGLV---NADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGE 1528

Query: 576  GTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQYPYATSGPTQQTYPSYGSAP 635
                  +G   PG     P Y    P++ +Y P  P        TS     T PSY    
Sbjct: 1529 APTSPGFGVSSPGFSPTSPTY---SPTSPAYSPTSP----SYSPTSPSYSPTSPSY---- 1577

Query: 636  APDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQP 695
            +P S +  P S    P     + P  P      +PSY   +P      Y+ T  +Y    
Sbjct: 1578 SPTSPSYSPTSPSYSPTSPSYS-PTSPSYSPT-SPSYSPTSP-----SYSPTSPSYSPTS 1630

Query: 696  ATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYAQPAATQPSYDQSASQSTAYGVAQG 755
             + +          PSY  ++P  +  +P   P     + T PSY  ++   +    +  
Sbjct: 1631 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1690

Query: 756  TAAAGYGKTVSPQ--PGYPQYDST 777
              +  Y  T SP   P  P Y   
Sbjct: 1691 PTSPNYSPT-SPSYSPTSPGYSPG 1713

>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 = 68.2 bits (166), Expect = 9e-12
 Identities = 65/317 (20%), Positives = 101/317 (31%), Gaps = 39/317 (12%)

Query: 435  QQMAPRSNYGGPPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGHPSVPAQAPAGGP 494
            + M  +          G    Y    G      D    +  S   P   S    A AGG 
Sbjct: 1452 KYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFS---PLVDSGSNDAMAGGF 1508

Query: 495  PPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPY-GGHSNSQPVYS- 552
                          ++YG       A  +     G+    +P   P    +S + P YS 
Sbjct: 1509 TAYGG---------ADYGEATSPFGAYGEAPTSPGFG-VSSPGFSPTSPTYSPTSPAYSP 1558

Query: 553  QGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPH 612
                 S          P   P       SY P  P      P Y    P++ SY P  P 
Sbjct: 1559 TSPSYSPTSPSYSPTSPSYSPTS----PSYSPTSPSYSPTSPSYS---PTSPSYSPTSP- 1610

Query: 613  QQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQPGGQQAPSY 672
                   +  PT  +Y     + +P S +  P S P Y   +    P  P      +P+Y
Sbjct: 1611 -------SYSPTSPSYSPTSPSYSPTSPSYSPTS-PSYSPTSPSYSPTSPSYS-PTSPAY 1661

Query: 673  GQVAPTAGYGQYTNTQQAY-PEQPATSNAGYGYQGTQDPSYGSSAPGSAYAAPTGQPGYA 731
               +P+     Y+ T  +Y P  P+ S     Y  T  P+Y  ++P  +  +P   PG  
Sbjct: 1662 SPTSPS-----YSPTSPSYSPTSPSYSPTSPSYSPTS-PNYSPTSPSYSPTSPGYSPGSP 1715

Query: 732  QPAATQPSYDQSASQST 748
              +  Q     + ++++
Sbjct: 1716 AYSPKQDEQKHNENENS 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 = 50.5 bits (120), Expect = 2e-06
 Identities = 54/283 (19%), Positives = 85/283 (30%), Gaps = 48/283 (16%)

Query: 367  LSQTVRPSTLSGGFNQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGP--YPSQNPHY 424
            L  +     ++GGF   AY            P G++   P +  +    P   P+   + 
Sbjct: 1495 LVDSGSNDAMAGGFT--AYGGADYGEAT--SPFGAYGEAPTSPGFGVSSPGFSPTSPTYS 1550

Query: 425  PHLPYGNYPPQQMAPRSNYGGPPNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGH-P 483
            P  P  +      +P S    P +   +     Y           P S S+S + P + P
Sbjct: 1551 PTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSY----------SPTSPSYSPTSPSYSP 1600

Query: 484  SVPAQAPAGGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGG 543
            + P+ +P   P  S  + +Y  P +  Y    P             Y             
Sbjct: 1601 TSPSYSPT-SPSYSPTSPSY-SPTSPSYSPTSPS------------YSPTSPSYSPTSPS 1646

Query: 544  HSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSA 603
            +S + P YS               P Y   +    P S     P  P   P   S  P++
Sbjct: 1647 YSPTSPSYS------------PTSPAYSPTSPSYSPTSPS-YSPTSPSYSPTSPSYSPTS 1693

Query: 604  QSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPAS 646
             +Y P  P        TS       P+Y        +N+   S
Sbjct: 1694 PNYSPTSPSYSP----TSPGYSPGSPAYSPKQDEQKHNENENS 1732

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 68.6 bits (167), Expect = 6e-12
 Identities = 64/318 (20%), Positives = 92/318 (28%), Gaps = 34/318 (10%)

Query: 435  QQMAPRSNYGGPPNMQGAAGGYDYYGGQGGH--VSDRPVSVSHSTSIPGHPSV-PAQAPA 491
            Q M    + G        +G       +G        P+  S     P   +  P     
Sbjct: 1453 QDMLMNYSLGTAVPTLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDAAAFSPLVQGG 1512

Query: 492  GGPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDN------HAPVQHPYGGHS 545
                    +Y      +   G Q P   +        GY          +P       + 
Sbjct: 1513 SEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYM 1572

Query: 546  NSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQS--YGPPRPGQPGDIPPYQSQVPSA 603
             S P YS       Y       P Y   +    P S  Y    P      P   S  P++
Sbjct: 1573 PSSPSYS--PTSPSYSP---TSPSYSPTSPSYSPTSPSYSATSPSYS---PTSPSYSPTS 1624

Query: 604  QSYGPNVPHQQQYPYATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQAVPNYPQ 663
             SY P  P       + S PT  +Y S  S     +      ++P Y   +    P  P 
Sbjct: 1625 PSYSPTSPSYSPTSPSYS-PTSPSY-SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1682

Query: 664  PGGQQAPSYGQVAPTAGYGQYTNTQQAYPEQPATSNAGYGYQGTQDPSYGSSAPGSAYAA 723
                  PSY    PT+     T+        P+ S     Y  T  PSY  ++P  +  +
Sbjct: 1683 YSPTS-PSYS---PTSPSYSPTS--------PSYSPTSPSYSPTS-PSYSPTSPSYSPTS 1729

Query: 724  PTGQPGYAQPAATQPSYD 741
            P+  P     + T PSY 
Sbjct: 1730 PSYSPTSPSYSPTSPSYS 1747

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 60.1 bits (145), Expect = 3e-09
 Identities = 55/222 (24%), Positives = 78/222 (35%), Gaps = 24/222 (10%)

Query: 572  MPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQS--YGPNVP--HQQQYPYATSGPTQQT 627
                       G   P +    P Y S   SA S  YG   P        Y+TS     +
Sbjct: 1515 GREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPS 1574

Query: 628  YPSYGSAPAPDSYNQPPASAPGY-PQQAG--QAVPNYPQPGGQQAPSYGQVAPTAGYGQY 684
             PSY     P S +  P S P Y P         P+Y       +P+    +PT+    Y
Sbjct: 1575 SPSYS----PTSPSYSPTS-PSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTS--PSY 1627

Query: 685  TNTQQAY-PEQPATSNAGYGYQGT------QDPSYGSSAPGSAYAAPTGQPGYAQPAATQ 737
            + T  +Y P  P+ S     Y  T        PSY  ++P  +  +P+  P     + T 
Sbjct: 1628 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1687

Query: 738  PSYDQSASQSTAYGVAQGTAAAGYGKTVSPQ--PGYPQYDST 777
            PSY  ++   +    +    +  Y  T SP   P  P Y  T
Sbjct: 1688 PSYSPTSPSYSPTSPSYSPTSPSYSPT-SPSYSPTSPSYSPT 1728

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 51.6 bits (123), Expect = 9e-07
 Identities = 54/284 (19%), Positives = 82/284 (28%), Gaps = 50/284 (17%)

Query: 373  PSTLSGGFNQQAYRPRVPTGPPQWGPRGSHPSQPMAYDYPQRGPYPSQNPHYPHLPYGNY 432
            P    G   ++ +      G          P     +       Y   +P Y     G  
Sbjct: 1507 PLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYS 1566

Query: 433  PPQQMAPRSNYGGP--PNMQGAAGGYDYYGGQGGHVSDRPVSVSHSTSIPGH-PSVPAQA 489
                  P S    P  P+                     P S S+S + P + P+ P+ +
Sbjct: 1567 TSPAYMPSSPSYSPTSPSYS-------------------PTSPSYSPTSPSYSPTSPSYS 1607

Query: 490  PAG-GPPPSQANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGHSNSQ 548
                   P+  +Y+   P  S       Y+  +P           ++P    Y   S + 
Sbjct: 1608 ATSPSYSPTSPSYSPTSPSYS--PTSPSYSPTSPS----------YSPTSPSY---SPTS 1652

Query: 549  PVYSQGGLQSGYHQHQYGK--PPYGMPAQGTQPQS--YGPPRPGQPGDIPPYQSQVPSAQ 604
            P YS            Y    P Y   +    P S  Y P  P      P Y    P++ 
Sbjct: 1653 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS---PTSP 1709

Query: 605  SYGPNVPHQQQYPYATSG--PTQQTYPSYGSAPAPDSYNQPPAS 646
            SY P  P    Y   +    PT  +Y     + +P S +  P S
Sbjct: 1710 SYSPTSP---SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1750

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 62.6 bits (151), Expect = 4e-10
 Identities = 45/283 (15%), Positives = 89/283 (31%), Gaps = 75/283 (26%)

Query: 127 VDNQQISVKEETKEVLFSTEEAFI------DVKEETKEVTVKEE--ETVKEEESVE---- 174
           +D +    + + K++L   E+AF+      DV++  K +  KEE    +  +++V     
Sbjct: 7   MDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLR 66

Query: 175 --------PSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQ 226
                      +V Q+ V+     +        MS                +  T  Y++
Sbjct: 67  LFWTLLSKQEEMV-QKFVEEVLRINY----KFLMSPIKTEQR-------QPSMMTRMYIE 114

Query: 227 -----YNSG---AKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAG-G 277
                YN     AK  ++R     P+   R       L  +  A+     V+ +   G G
Sbjct: 115 QRDRLYNDNQVFAKYNVSR---LQPYLKLRQA-----LLELRPAKN----VLIDGVLGSG 162

Query: 278 SPSLVARGLATAQASGAAEQVEIKVPNE----KVGLIIGRGGETIKGLQTRSGARIQLIP 333
              +             + +V+ K+  +     +          ++ LQ       Q+ P
Sbjct: 163 KTWVALDVC-------LSYKVQCKMDFKIFWLNLKN-CNSPETVLEMLQKLL---YQIDP 211

Query: 334 QHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPSTL 376
                 D S    +R       I   Q  ++ +L      + L
Sbjct: 212 NWTSRSDHSSNIKLR-------IHSIQAELRRLLKSKPYENCL 247

>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 = 53.3 bits (128), Expect = 5e-09
 Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 7/83 (8%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGA-RIQLIPQHLPEGDGSKERIVRVTGDMRQI 356
           VE+ +P +    +IG  G  I+ +    G   I   P      +GS    V + G    +
Sbjct: 19  VEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIH-FPV-----EGSGSDTVVIRGPSSDV 72

Query: 357 EIAQEMIKEVLSQTVRPSTLSGG 379
           E A++ +  +  +    S  S G
Sbjct: 73  EKAKKQLLHLAEEKQTKSGPSSG 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 = 46.3 bits (110), Expect = 1e-06
 Identities = 20/96 (20%), Positives = 33/96 (34%), Gaps = 6/96 (6%)

Query: 186 NSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGA-KIQITRDADADPH 244
           +  S        +    ++ +P      LIG  G  IR +    G   I    +      
Sbjct: 3   SGSSGSIQKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGS-- 60

Query: 245 AATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPS 280
                V I G  S+++KA+K +  +  E      PS
Sbjct: 61  ---DTVVIRGPSSDVEKAKKQLLHLAEEKQTKSGPS 93

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

 Score = 50.6 bits (122), Expect = 2e-06
 Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 11/68 (16%)

Query: 300 IKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEI 358
           ++VP  K    +G GG  +K LQ  +G  I          +        V       +  
Sbjct: 571 VQVPLSKRAKFVGPGGYNLKKLQAETGVTISQ------VDEE----TFSVFAPTPSAMHE 620

Query: 359 AQEMIKEV 366
           A++ I E+
Sbjct: 621 ARDFITEI 628

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

 Score = 50.2 bits (121), Expect = 2e-06
 Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 11/68 (16%)

Query: 300 IKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEI 358
           I +P +K+  +IG GG+ I+ +   +GA++ +        DG    +V+V+  D  +I+ 
Sbjct: 574 INIPTDKIREVIGSGGKVIREIVATTGAKVDI------NDDG----VVKVSASDGAKIKA 623

Query: 359 AQEMIKEV 366
           A + IK +
Sbjct: 624 AIDWIKSI 631

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

 Score = 45.6 bits (109), Expect = 5e-05
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 10/75 (13%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT-LSNIDK 261
            I +P +K+  +IG  G  IR +   +GAK+ I  D           V++  +  + I  
Sbjct: 573 TINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGV---------VKVSASDGAKIKA 623

Query: 262 AEKLINAVIAEADAG 276
           A   I ++  EA+ G
Sbjct: 624 AIDWIKSITDEAEVG 638

>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 = 44.5 bits (105), Expect = 6e-06
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 8/82 (9%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
             +  P+     IIG+ G+ +  +  +   ++ +      EG    E  + + G    + 
Sbjct: 29  SSVAAPSWLHRFIIGKKGQNLAKITQQMP-KVHI---EFTEG----EDKITLEGPTEDVS 80

Query: 358 IAQEMIKEVLSQTVRPSTLSGG 379
           +AQE I+ ++   +  S  S G
Sbjct: 81  VAQEQIEGMVKDLINRSGPSSG 102

>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 = 41.8 bits (98), Expect = 5e-05
 Identities = 14/86 (16%), Positives = 30/86 (34%), Gaps = 9/86 (10%)

Query: 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN-SGAKIQITRDADADPHAATRPVEIIG 254
            +S     +  P+     +IGK G  +  +        I+ T   D         + + G
Sbjct: 23  ANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDK--------ITLEG 74

Query: 255 TLSNIDKAEKLINAVIAEADAGGSPS 280
              ++  A++ I  ++ +      PS
Sbjct: 75  PTEDVSVAQEQIEGMVKDLINRSGPS 100

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

 Score = 48.6 bits (117), Expect = 6e-06
 Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 11/68 (16%)

Query: 300 IKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEI 358
           IK+  +K+  +IG+GG  I+ L   +G  I++      E DG     V++   D  + + 
Sbjct: 564 IKINPDKIKDVIGKGGSVIRALTEETGTTIEI------EDDG----TVKIAATDGEKAKH 613

Query: 359 AQEMIKEV 366
           A   I+E+
Sbjct: 614 AIRRIEEI 621

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

 Score = 44.0 bits (105), Expect = 2e-04
 Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 10/74 (13%)

Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT-LSNIDKA 262
           I++  +K+  +IGK G  IR L   +G  I+I  D           V+I  T       A
Sbjct: 564 IKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDDGT---------VKIAATDGEKAKHA 614

Query: 263 EKLINAVIAEADAG 276
            + I  + AE + G
Sbjct: 615 IRRIEEITAEIEVG 628

>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 = 48.0 bits (115), Expect = 1e-05
 Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 11/68 (16%)

Query: 300 IKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEI 358
           +K+P +K+G +IG   + I  +Q  +GA I +      E DG+    + +   D    E 
Sbjct: 602 VKIPVDKIGEVIGPKRQMINQIQEDTGAEITI------EDDGT----IYIGAADGPAAEA 651

Query: 359 AQEMIKEV 366
           A+  I  +
Sbjct: 652 ARATINGI 659

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score = 46.1 bits (108), Expect = 3e-05
 Identities = 13/78 (16%), Positives = 31/78 (39%), Gaps = 5/78 (6%)

Query: 298 VEIKVPNEKVGLIIGRGG--ETIKGLQTRSGARIQLIPQHLPEGDGSKE--RIVRVTGDM 353
           + ++  ++   L+    G  E +  +   +   IQ +P     G       + V +TG  
Sbjct: 32  LNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQ-LPDRSVGGTTPDPFAQQVTITGYF 90

Query: 354 RQIEIAQEMIKEVLSQTV 371
             ++ A+ +++     TV
Sbjct: 91  GDVDRARMLMRRNCHFTV 108

>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 = 45.1 bits (106), Expect = 7e-05
 Identities = 21/156 (13%), Positives = 40/156 (25%), Gaps = 20/156 (12%)

Query: 499 ANYNYGQPHTSEYGHQQPYAHAAPQQGYGHGYDDNHAPVQHPYGGHSNSQPVYSQGGLQS 558
           A++++      +         +        G     AP  HP  G     P         
Sbjct: 2   AHHHHHHVDDDDKMFSTQVNSSLTSP---TGRGSMAAPSLHPSLGPGIGSP--------- 49

Query: 559 GYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDIPPYQSQVPSAQSYGPNVPHQQQY-P 617
                  G+    +    +     GPP       + P+   VP+  + G +    Q   P
Sbjct: 50  -------GQLHSPISTLSSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSP 102

Query: 618 YATSGPTQQTYPSYGSAPAPDSYNQPPASAPGYPQQ 653
                 ++   P  G          P  +   + + 
Sbjct: 103 MNPVSSSEDIKPPLGLNGVLKVPAHPSGNMASFTKH 138

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A Length = 144

 Score = 42.3 bits (100), Expect = 8e-05
 Identities = 22/117 (18%), Positives = 37/117 (31%), Gaps = 29/117 (24%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
              V   + G  IG+ G  I+ L+   G  I++   +                    D  
Sbjct: 39  IFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSS-------------------DLE 79

Query: 263 EKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIK 319
             + N              +       +     +QV IKV  +  G  IG+GG+ +K
Sbjct: 80  RIVKNLF--------PGVKIES--INVRERNGVKQVVIKVSEDDKGAAIGKGGKNVK 126

>1c1g_A Tropomyosin; contractIle protein; 7.00A {Sus scrofa} SCOP: h.1.5.1 PDB: 2tma_A 2w49_A 2w4u_A Length = 284

 Score = 43.5 bits (102), Expect = 2e-04
 Identities = 32/173 (18%), Positives = 66/173 (38%), Gaps = 19/173 (10%)

Query: 2   AEEEVLAPASAAAADLKRKLDDLEPDEALEHAEGMRDDEAKNSDEVEKNVDGFAEAHGSE 61
           A E+           L++KL   E  + L+       D  +  +  EK     AEA  + 
Sbjct: 31  AAEDRSKQLEDELVSLQKKLKATE--DELDKYSEALKDAQEKLELAEKKATD-AEADVAS 87

Query: 62  VKRPRLDDDKTEKPDGPVNVNGLKEEKPDEVVDAEQLTEDTTKEEELESAEVKTEQHSSV 121
           + R R+   + E            +   + +  A Q  E+  K  +     +K  +  + 
Sbjct: 88  LNR-RIQLFEEEL-----------DRAQERLATALQKLEEAEKAADESERGMKVIESRAQ 135

Query: 122 EEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVE 174
           +++  ++ Q+I +KE         E+A    +E  +++ + E +  + EE  E
Sbjct: 136 KDEEKMEIQEIQLKEAKHIA----EDADRKYEEVARKLVIIESDLERAEERAE 184

>1c1g_A Tropomyosin; contractIle protein; 7.00A {Sus scrofa} SCOP: h.1.5.1 PDB: 2tma_A 2w49_A 2w4u_A Length = 284

 Score = 41.2 bits (96), Expect = 9e-04
 Identities = 33/175 (18%), Positives = 71/175 (40%), Gaps = 6/175 (3%)

Query: 4   EEVLAPASAAAADLKRKLDDLEP--DEALEHAEGMRDDEAKNSDEVEKNVDGFAEA-HGS 60
           EE L  A    A   +KL++ E   DE+    + +     K+ +++E       EA H +
Sbjct: 96  EEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIA 155

Query: 61  EVKRPRLDDDKTEKPDGPVNVNGLKEEKPDEVVDAEQLTED-TTKEEELESAEVKTEQHS 119
           E    + ++   +      ++   +E          +L E+  T    L+S E + E++S
Sbjct: 156 EDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEEIKTVTNNLKSLEAQAEKYS 215

Query: 120 SVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVE 174
             +++   + +   + ++ KE     E A   V +  K +   E+E   ++   +
Sbjct: 216 --QKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLKYK 268

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 41.7 bits (97), Expect = 3e-04
 Identities = 14/87 (16%), Positives = 34/87 (39%), Gaps = 15/87 (17%)

Query: 92  VVDAEQLTEDTTKEEELESA-EVKTEQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFI 150
           +  A++LT+      E ES  + + EQ   ++E  +        ++E +E      E + 
Sbjct: 74  IAQADRLTQ------EPESIRKWREEQRKRLQELDAASKVM---EQEWREKAKKDLEEWN 124

Query: 151 DVKEETKEVTVK-----EEETVKEEES 172
             + E  E         ++   ++ ++
Sbjct: 125 QRQSEQVEKNKINNRIADKAFYQQPDA 151

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448

 Score = 42.6 bits (100), Expect = 4e-04
 Identities = 25/80 (31%), Positives = 28/80 (35%), Gaps = 5/80 (6%)

Query: 534 HAPVQHPYGGHSNSQPVYSQGGLQSGYHQHQYGKPPYGMPAQGTQPQSYGPPRPGQPGDI 593
            A         +  Q +  Q   Q+ Y    Y  PP G P QG  PQ Y P      G  
Sbjct: 365 SADAAQMKEMMAMMQKMQQQ---QAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGYP 421

Query: 594 PPYQSQVPSAQSYGPNVPHQ 613
           PP Q   P  Q   P  P Q
Sbjct: 422 PPPQGAPP--QGAPPAAPPQ 439

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448

 Score = 41.4 bits (97), Expect = 9e-04
 Identities = 26/93 (27%), Positives = 29/93 (31%), Gaps = 12/93 (12%)

Query: 569 PYGMPAQGTQPQSYGPPRPGQPGDIPPYQ----SQVPSAQSYGPNVPHQQQYPYATSGPT 624
           P    AQ  +  +       Q    PP       Q    Q Y P     Q YP     P 
Sbjct: 364 PSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGYPPP 423

Query: 625 QQTYPSYGSAPAPDSYNQPPASAPGYPQQAGQA 657
            Q  P  G+ PA      PP    G   QA QA
Sbjct: 424 PQGAPPQGAPPA-----APPQ---GVDNQAYQA 448

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	784
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.94
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.94
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.93
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.93
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.93
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.87
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.86
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.86
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.86
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.85
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.85
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.8
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.76
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.69
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.65
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.57
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.5
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.49
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.49
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.48
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.47
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.47
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.47
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.47
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.47
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.46
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.46
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.44
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.44
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.44
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.43
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.42
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.42
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.42
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.41
1we8_A	104	Tudor and KH domain containing protein; structural	99.41
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.4
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.39
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.39
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.38
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.38
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.37
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.36
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.35
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.34
1we8_A	104	Tudor and KH domain containing protein; structural	99.34
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.32
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.31
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.3
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.3
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.29
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.27
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.25
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.24
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.23
2ctm_A	95	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
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.2
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	98.99
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.96
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.83
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.8
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.76
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.74
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.73
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.41
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.37
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.25
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.04
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.95
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.9
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.77
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.54
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.37
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.2
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.91
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.85
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	96.78
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.62
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	96.48
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	96.37
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.15
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	96.09
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	95.57
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	94.35
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	87.63
4hhu_A	170	OR280; engineered protein, PSI-biology, structural	86.91
3gku_A	225	Probable RNA-binding protein; APC21302, clostridiu	81.17

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

Probab=99.94  E-value=2.7e-27  Score=235.69  Aligned_cols=171  Identities=32%  Similarity=0.468  Sum_probs=136.5

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCC
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGG  277 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g  277 (784)
                      ..++++|+||.+++|+||||+|++||+|+++|||+|+|.++.+..+++.+|+|+|+|+.++|.+|+.+|.+++.+.....
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            46899999999999999999999999999999999999876555677889999999999999999999999998753211


Q ss_pred             CCcccccccch--hhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHH
Q 003942          278 SPSLVARGLAT--AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ  355 (784)
Q Consensus       278 ~p~~~~~g~~~--~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~q  355 (784)
                      .......-+.+  ........+++|+||.+++|+||||+|++||+|+++|||+|+|..+.  ....+.+|+|+|+|+.++
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            00000000000  00112347889999999999999999999999999999999997643  223467899999999999


Q ss_pred             HHHHHHHHHHHHhcc
Q 003942          356 IEIAQEMIKEVLSQT  370 (784)
Q Consensus       356 V~~Ak~lI~~~L~~~  370 (784)
                      |++|+.||.++|.+.
T Consensus       162 v~~A~~~I~~~i~e~  176 (178)
T 2anr_A          162 NRKAVELIIQKIQED  176 (178)
T ss_dssp             HHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHhC
Confidence            999999999999753

>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=99.94  E-value=2.2e-26  Score=225.75  Aligned_cols=157  Identities=28%  Similarity=0.441  Sum_probs=134.4

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCC
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSP  279 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p  279 (784)
                      .+++|+||.+++|+||||+|++||+|+++|||+|+|..+.  .+++.+|+|+|+|+.++|.+|+.+|+++|.+...... 
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            5899999999999999999999999999999999998742  4577899999999999999999999999988632110 


Q ss_pred             cccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHH
Q 003942          280 SLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIA  359 (784)
Q Consensus       280 ~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~A  359 (784)
                                 ......+.+|.||.+++|+||||+|++||+|+++|||+|.|.++.++  ....++.|+|+|+.++|++|
T Consensus        80 -----------~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~--~~~~~~~v~I~G~~~~v~~A  146 (163)
T 3krm_A           80 -----------KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTP--DENDQVIVKIIGHFYASQMA  146 (163)
T ss_dssp             -----------SCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCC--CTTSEEEEEEEECHHHHHHH
T ss_pred             -----------ccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCC--CCCCceEEEEEeCHHHHHHH
Confidence                       01234567999999999999999999999999999999999876533  23445689999999999999


Q ss_pred             HHHHHHHHhcccC
Q 003942          360 QEMIKEVLSQTVR  372 (784)
Q Consensus       360 k~lI~~~L~~~~r  372 (784)
                      +.||+++|++..+
T Consensus       147 ~~~I~~~i~~~~~  159 (163)
T 3krm_A          147 QRKIRDILAQVKQ  159 (163)
T ss_dssp             HHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999987554

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

Probab=99.93  E-value=2.2e-26  Score=225.58  Aligned_cols=160  Identities=31%  Similarity=0.554  Sum_probs=132.8

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCC
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSP  279 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p  279 (784)
                      ++++|+||.+++|+||||+|++||+|+++|||+|+|..+. ..+.+.+|+|+|+|+.++|.+|+.+|+++|.+....+..
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 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG-SQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQGGFG   80 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCT-TSSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSSSCCCS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCC-CCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhccCCCCC
Confidence            6889999999999999999999999999999999998653 234567899999999999999999999999876432211


Q ss_pred             cccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHH
Q 003942          280 SLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIA  359 (784)
Q Consensus       280 ~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~A  359 (784)
                      .....+      .....+++|.||.+++|+||||+|++||+|+++|||+|.|.+..    +.+.+|+|+|+|+.++|++|
T Consensus        81 ~~~~~~------~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~----~~~~~~~v~I~G~~~~v~~A  150 (164)
T 2jvz_A           81 DRNEYG------SRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD----GTGPEKIAHIMGPPDRCEHA  150 (164)
T ss_dssp             SCSSCT------TSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC----TTSSEEEEEEESCHHHHHHH
T ss_pred             CccccC------CCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC----CCCCcEEEEEEcCHHHHHHH
Confidence            110000      01124578999999999999999999999999999999997642    34568999999999999999


Q ss_pred             HHHHHHHHhcc
Q 003942          360 QEMIKEVLSQT  370 (784)
Q Consensus       360 k~lI~~~L~~~  370 (784)
                      +.||+++|++.
T Consensus       151 ~~~I~~~i~~~  161 (164)
T 2jvz_A          151 ARIINDLLQSL  161 (164)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHhhh
Confidence            99999999753

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

Probab=99.93  E-value=4.2e-26  Score=226.36  Aligned_cols=165  Identities=30%  Similarity=0.536  Sum_probs=130.5

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCC
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGS  278 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~  278 (784)
                      ..+++|+||.+++|+||||+|++||+|+++|||+|+|..+   ...+.+|+|+|+|+.++|.+|+++|+++|.+...+..
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~---~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~   78 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD---DGTTPERIAQITGPPDRAQHAAEIITDLLRSVQAGNP   78 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECC---TTSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC----
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecC---CCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcccCCC
Confidence            4689999999999999999999999999999999999853   2356789999999999999999999999988743211


Q ss_pred             Cc--ccccccchh------hccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEE
Q 003942          279 PS--LVARGLATA------QASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVT  350 (784)
Q Consensus       279 p~--~~~~g~~~~------~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~  350 (784)
                      ..  ...+++...      .......+++|.||.+++|+||||+|++||+|+++|||+|+|.++.. ...++.+|+|+|+
T Consensus        79 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~-~~~~~~~~~v~I~  157 (174)
T 1j4w_A           79 GGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPP-PNADPNMKLFTIR  157 (174)
T ss_dssp             -------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT-TTSCTTEEEEEEE
T ss_pred             CCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCC-CCCCCCceEEEEE
Confidence            00  000000000      00123468899999999999999999999999999999999986542 3445778999999


Q ss_pred             cCHHHHHHHHHHHHHHH
Q 003942          351 GDMRQIEIAQEMIKEVL  367 (784)
Q Consensus       351 Gt~~qV~~Ak~lI~~~L  367 (784)
                      |+.++|++|++||+++|
T Consensus       158 G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          158 GTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             CCHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHhC
Confidence            99999999999999875

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

Probab=99.93  E-value=3.4e-26  Score=223.78  Aligned_cols=157  Identities=27%  Similarity=0.438  Sum_probs=133.3

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCC
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGG  277 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g  277 (784)
                      ..++++|+||.+++|+||||+|++||+|+++|||+|+|...     ++.+|.|+|+|+.++|.+|+.+|+++|.+.....
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~-----~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~~~   77 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKLEEDISSS   77 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC-----TTTEEEEEEEEEHHHHHHHHHHHHHHHHHHHTSC
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC-----CCCceEEEEEeCHHHHHHHHHHHHHHHHhhcccc
Confidence            45799999999999999999999999999999999999864     3568999999999999999999999998864321


Q ss_pred             CCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHH
Q 003942          278 SPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE  357 (784)
Q Consensus       278 ~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~  357 (784)
                      ...    ..   .......+++|.||.+++|+||||+|++||+|+++|||+|+|..+.++   .+.+|+|+|+|+.++|+
T Consensus        78 ~~~----~~---~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~---~~~~~~v~I~G~~~~v~  147 (160)
T 2jzx_A           78 MTN----ST---AASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLP---NSTERAITIAGIPQSII  147 (160)
T ss_dssp             CCS----SS---CCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCST---TCCEEEEEEEECHHHHH
T ss_pred             CCC----Cc---cCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCC---CCCceEEEEEcCHHHHH
Confidence            100    00   011234689999999999999999999999999999999999765433   46799999999999999


Q ss_pred             HHHHHHHHHHhc
Q 003942          358 IAQEMIKEVLSQ  369 (784)
Q Consensus       358 ~Ak~lI~~~L~~  369 (784)
                      +|+++|.++|.+
T Consensus       148 ~A~~~I~~~i~e  159 (160)
T 2jzx_A          148 ECVKQICVVMLE  159 (160)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhc
Confidence            999999998865

>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=99.87  E-value=1.1e-22  Score=201.65  Aligned_cols=154  Identities=19%  Similarity=0.287  Sum_probs=129.1

Q ss_pred             cceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCC---
Q 003942          117 QHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPS---  193 (784)
Q Consensus       117 ~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~---  193 (784)
                      .+.+++||.++++.||||+|++|++|+++++++|+|.+....+.+|.+.|+|..++|++|+.+|.+++.+.......   
T Consensus         3 ~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~~~~~   82 (174)
T 1j4w_A            3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQAGNPGGPG   82 (174)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC--------
T ss_pred             eEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcccCCCCCCC
Confidence            46789999999999999999999999999999999987666677899999999999999999999998744311100   


Q ss_pred             ---------------CCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhh
Q 003942          194 ---------------STDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN  258 (784)
Q Consensus       194 ---------------~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~  258 (784)
                                     ......++++|+||.+++|+||||+|++||+|+++|||+|+|.++......+.+|.|+|+|+.++
T Consensus        83 p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~  162 (174)
T 1j4w_A           83 PGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQ  162 (174)
T ss_dssp             ---------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHH
T ss_pred             CCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHH
Confidence                           00123468999999999999999999999999999999999987543333467899999999999


Q ss_pred             HHHHHHHHHHHH
Q 003942          259 IDKAEKLINAVI  270 (784)
Q Consensus       259 V~kA~~~I~elI  270 (784)
                      |++|+.+|+++|
T Consensus       163 v~~A~~~I~~~i  174 (174)
T 1j4w_A          163 IDYARQLIEEKI  174 (174)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhC
Confidence            999999999875

>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=99.86  E-value=1.4e-22  Score=201.65  Aligned_cols=157  Identities=21%  Similarity=0.203  Sum_probs=131.9

Q ss_pred             ccceeeeccccccccccCCCchhhhhhhcccCceeeeccccc---ccccceeeecCchhchhhhhhhhhHhhhcCCCCCC
Q 003942          116 EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETK---EVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDP  192 (784)
Q Consensus       116 ~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~---~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~  192 (784)
                      +.+.+++||.++++.||||+|++|+.|+++++++|+|.+...   .+.+|.+.|+|+.++|++|+.+|.+++.+......
T Consensus         5 ~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~   84 (178)
T 2anr_A            5 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQNVA   84 (178)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCCCC--
T ss_pred             CEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhccCCccc
Confidence            567899999999999999999999999999999999987542   46679999999999999999999999975432111


Q ss_pred             C------------CCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHH
Q 003942          193 S------------STDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNID  260 (784)
Q Consensus       193 ~------------~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~  260 (784)
                      .            ......++++|+||.+++|+||||+|++||+|+++|||+|+|.++. ..+.+.+|.|+|+|+.++|.
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~-~~~~~~~~~v~I~G~~~~v~  163 (178)
T 2anr_A           85 KTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKP-DGINLQNRVVTVSGEPEQNR  163 (178)
T ss_dssp             ---------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC-----CCEEEEEEESSHHHHH
T ss_pred             cCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCC-CCCCCCceEEEEEcCHHHHH
Confidence            0            0112357899999999999999999999999999999999998753 23456789999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 003942          261 KAEKLINAVIAEA  273 (784)
Q Consensus       261 kA~~~I~elI~e~  273 (784)
                      +|+.+|+++|+++
T Consensus       164 ~A~~~I~~~i~e~  176 (178)
T 2anr_A          164 KAVELIIQKIQED  176 (178)
T ss_dssp             HHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHhC
Confidence            9999999999874

>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=99.86  E-value=4.4e-22  Score=195.16  Aligned_cols=154  Identities=21%  Similarity=0.238  Sum_probs=132.9

Q ss_pred             cceeeeccccccccccCCCchhhhhhhcccCceeeecccc-cccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCC
Q 003942          117 QHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEET-KEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSST  195 (784)
Q Consensus       117 ~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~-~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~  195 (784)
                      ...+++||.+.++.||||+|++|+.|+++++++|+|.+.. ..+.+|.+.|+|+.+++.+|+.+|.+++.......+.  
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~~~~~--   80 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFGPK--   80 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTSSCSS--
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccccccc--
Confidence            3578999999999999999999999999999999999874 3677899999999999999999999988755332221  


Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCC-CcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAAT-RPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~e-R~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      ....++.+|+||.+++|+||||+|++||+|+++|||+|+|.++.  .+++.+ +.|+|+|+.++|++|+++|+++|++..
T Consensus        81 ~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~--~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~  158 (163)
T 3krm_A           81 EEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQ--TPDENDQVIVKIIGHFYASQMAQRKIRDILAQVK  158 (163)
T ss_dssp             CCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTC--CCCTTSEEEEEEEECHHHHHHHHHHHHHHHHHHT
T ss_pred             cCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCC--CCCCCCceEEEEEeCHHHHHHHHHHHHHHHHHHH
Confidence            23457889999999999999999999999999999999998653  334444 489999999999999999999999863

>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=99.86  E-value=8.3e-22  Score=193.00  Aligned_cols=155  Identities=17%  Similarity=0.241  Sum_probs=130.4

Q ss_pred             cceeeeccccccccccCCCchhhhhhhcccCceeeeccccc--ccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCC
Q 003942          117 QHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETK--EVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSS  194 (784)
Q Consensus       117 ~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~--~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~  194 (784)
                      +..+++||.+.++.||||+|++|+.|+++++++|+|..+..  .+.+|.+.|.|+.++|++|+.+|.+++.+........
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~~~~~~   81 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQGGFGD   81 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSSSCCCSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhccCCCCCC
Confidence            35689999999999999999999999999999999976542  4557899999999999999999999997543211100


Q ss_pred             ----CCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHH
Q 003942          195 ----TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVI  270 (784)
Q Consensus       195 ----~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI  270 (784)
                          .....++++|+||.+++|+||||+|++||+|+++|||+|+|.++.   ..+.+|.|+|+|+.++|++|+.+|+++|
T Consensus        82 ~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~---~~~~~~~v~I~G~~~~v~~A~~~I~~~i  158 (164)
T 2jvz_A           82 RNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD---GTGPEKIAHIMGPPDRCEHAARIINDLL  158 (164)
T ss_dssp             CSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC---TTSSEEEEEEESCHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC---CCCCcEEEEEEcCHHHHHHHHHHHHHHH
Confidence                011135689999999999999999999999999999999998653   3456799999999999999999999999


Q ss_pred             Hhhh
Q 003942          271 AEAD  274 (784)
Q Consensus       271 ~e~~  274 (784)
                      ++.+
T Consensus       159 ~~~~  162 (164)
T 2jvz_A          159 QSLR  162 (164)
T ss_dssp             HHHH
T ss_pred             hhhh
Confidence            8864

>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=99.85  E-value=3.6e-22  Score=195.15  Aligned_cols=154  Identities=19%  Similarity=0.256  Sum_probs=132.3

Q ss_pred             cccceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCC---
Q 003942          115 TEQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDD---  191 (784)
Q Consensus       115 ~~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~---  191 (784)
                      .....+++||..+++.||||+|++|+.|+++++++|+|.+.  .+.+|.+.|.|..++|++|+.+|.+++.+.....   
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~~~~~~   80 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEEDISSSMTN   80 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHHHHHHHHHHHHHHHHHHHTSCCCS
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHHHHHHHHHHHHHHHHhhccccCCC
Confidence            35677999999999999999999999999999999999876  3557899999999999999999988876421110   


Q ss_pred             CCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHH
Q 003942          192 PSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIA  271 (784)
Q Consensus       192 ~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~  271 (784)
                      ........++++|+||.+++|+||||+|++||+|+++|||+|+|.++  ..+++.++.|+|+|+.++|.+|+++|+++|.
T Consensus        81 ~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~--~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~  158 (160)
T 2jzx_A           81 STAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD--MLPNSTERAITIAGIPQSIIECVKQICVVML  158 (160)
T ss_dssp             SSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCC--CSTTCCEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             CccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCC--CCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Confidence            11112346899999999999999999999999999999999999864  3567789999999999999999999999998


Q ss_pred             h
Q 003942          272 E  272 (784)
Q Consensus       272 e  272 (784)
                      |
T Consensus       159 e  159 (160)
T 2jzx_A          159 E  159 (160)
T ss_dssp             H
T ss_pred             c
Confidence            7

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

Probab=99.85  E-value=1.6e-21  Score=212.97  Aligned_cols=223  Identities=9%  Similarity=0.087  Sum_probs=168.1

Q ss_pred             cccceeeeccccccccccCCCc--hhhhhhhcccCceeeecccc--c---ccccceeeecCchhchhhhhhhhhHhhhcC
Q 003942          115 TEQHSSVEEQASVDNQQISVKE--ETKEVLFSTEEAFIDVKEET--K---EVTVKEEETVKEEESVEPSNVVPQQVVDNS  187 (784)
Q Consensus       115 ~~~~~ki~iP~~~vg~iIGk~G--e~Ik~iq~~s~a~I~I~~~~--~---~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~  187 (784)
                      +.++.++.|+...+..||||+|  ++|++|+++++++|++.+.+  .   ......+.|+|..++|++|+..|.+++   
T Consensus        28 ~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l~---  104 (376)
T 3n89_A           28 TRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNC---  104 (376)
T ss_dssp             TEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHSC---
T ss_pred             CEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhcC---
Confidence            3677899999999999999999  99999999999999998876  1   245578999999999999999998866   


Q ss_pred             CCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHH
Q 003942          188 KSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN  267 (784)
Q Consensus       188 ~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~  267 (784)
                                 .+++.|.++...+..  .+...+|++ ++..+++|.|....+.. ......|+|+|...+|++|++.+.
T Consensus       105 -----------Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~-~~~sd~V~IrG~~~nv~~akeA~~  169 (376)
T 3n89_A          105 -----------HFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKN-GIVTTYLRITAREKNQHELIEAAK  169 (376)
T ss_dssp             -----------EEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC------CEEEEEEEEEGGGHHHHHHHHH
T ss_pred             -----------CceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCccccc-CCCCCEEEEEcChhhHHHHHHHHH
Confidence                       356777777655443  222345655 67899999986542211 112457999999999988888877


Q ss_pred             HHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCc--hHHHHHHHHhCCeEEeccCCCCCCCCCCce
Q 003942          268 AVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGG--ETIKGLQTRSGARIQLIPQHLPEGDGSKER  345 (784)
Q Consensus       268 elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG--~~IK~Iq~~SGarIqI~~~~~p~~~~~~er  345 (784)
                      .+++......            .......+++|.|+...+.+||||+|  ..|++|+++|||+|.|.+............
T Consensus       170 ~Ll~~l~~~e------------~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~  237 (376)
T 3n89_A          170 RLNEILFRES------------PAPENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIY  237 (376)
T ss_dssp             HHHHHHCC--------------CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEE
T ss_pred             HHHHHHHhhh------------cccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCce
Confidence            7776642210            01124578899999999999999999  677999999999999965321111112356


Q ss_pred             EEEEEcCHHHHHHHHHHHHHHH
Q 003942          346 IVRVTGDMRQIEIAQEMIKEVL  367 (784)
Q Consensus       346 ~V~I~Gt~~qV~~Ak~lI~~~L  367 (784)
                      .|+|+|+.++|+.|+++|+++|
T Consensus       238 ~ItItGs~e~V~~Ark~I~~lL  259 (376)
T 3n89_A          238 EIKVVGNIDNVLKARRYIMDLL  259 (376)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTS
T ss_pred             EEEEEeCHHHHHHHHHHHHhhC
Confidence            8999999999999999999987

>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=99.80  E-value=7.3e-20  Score=176.42  Aligned_cols=137  Identities=19%  Similarity=0.258  Sum_probs=106.3

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCC
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGS  278 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~  278 (784)
                      .++++|+||...||++||++|++||.|++++|++|....+      ..++.+...++++.|.+|+.+|.     .     
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~~------~~~~~i~~~~~p~~v~~~~~~l~-----~-----   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE------DTCTFHIYGEDQDAVKKARSFLE-----F-----   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEET------TTTEEEEEESSHHHHHHHHHHHC-----E-----
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccCC------CchheeeccCCHHHHHHHHHhhh-----c-----
Confidence            4789999999999999999999999999999955444322      12334444447888888765331     1     


Q ss_pred             CcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCC-eEEeccCCCCCCCCCCc--eEEEEEcCHHH
Q 003942          279 PSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGA-RIQLIPQHLPEGDGSKE--RIVRVTGDMRQ  355 (784)
Q Consensus       279 p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGa-rIqI~~~~~p~~~~~~e--r~V~I~Gt~~q  355 (784)
                                       ...+|.||.+++|++|||+|+|||.|++.||| +|.|..+..... ..++  +.|+|+|+.++
T Consensus        67 -----------------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~-~~~~~~~~vtI~G~~~~  128 (144)
T 2qnd_A           67 -----------------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV-PQEEGMVPFVFVGTKDS  128 (144)
T ss_dssp             -----------------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC-CCCTTEEEEEEEEEHHH
T ss_pred             -----------------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc-cccCCeeEEEEEeCHHH
Confidence                             13789999999999999999999999999997 999986431111 1223  45899999999


Q ss_pred             HHHHHHHHHHHHhc
Q 003942          356 IEIAQEMIKEVLSQ  369 (784)
Q Consensus       356 V~~Ak~lI~~~L~~  369 (784)
                      |+.|+.||+++|++
T Consensus       129 v~~Ak~li~~~l~~  142 (144)
T 2qnd_A          129 IANATVLLDYHLNY  142 (144)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999974

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.76  E-value=1.5e-18  Score=177.85  Aligned_cols=144  Identities=27%  Similarity=0.351  Sum_probs=111.9

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecc-----hhhHHHHHHHHHHHHHh
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT-----LSNIDKAEKLINAVIAE  272 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~-----~e~V~kA~~~I~elI~e  272 (784)
                      ...+++|.||.+++|.|||++|++||.|+++|||+|.|..+        ++.|+|.++     .+.|.+|+++|++++..
T Consensus        32 aP~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~--------~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg  103 (219)
T 2e3u_A           32 FKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE--------TGEVWITSTKETEDPLAVWKARDIVLAIGRG  103 (219)
T ss_dssp             -CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT--------TCEEEEEECTTCCSHHHHHHHHHHHHHHHTT
T ss_pred             CCEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC--------CCEEEEecCCCCCCHHHHHHHHHHHHHHhcc
Confidence            34577999999999999999999999999999999999743        467888875     59999999999998842


Q ss_pred             hhcCCCCcccccccchhhccCCccEEEEEec-----C------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCC
Q 003942          273 ADAGGSPSLVARGLATAQASGAAEQVEIKVP-----N------EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDG  341 (784)
Q Consensus       273 ~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP-----~------~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~  341 (784)
                      .+......+.         ........|.|.     +      +.+|+||||+|+|||.|++.|||+|.|.         
T Consensus       104 ~~~e~g~~ll---------~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~---------  165 (219)
T 2e3u_A          104 FSPERAFRLL---------NEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY---------  165 (219)
T ss_dssp             CCHHHHGGGG---------STTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE---------
T ss_pred             CCccccceec---------cCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC---------
Confidence            2100000000         011112223332     1      3689999999999999999999999994         


Q ss_pred             CCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          342 SKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       342 ~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                        +++|+|.|+.++|+.|+++|+++|..
T Consensus       166 --~~~v~i~G~~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          166 --GKTVAIIGNPIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             --TTEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             --CeEEEEEeCHHHHHHHHHHHHHHHcC
Confidence              46799999999999999999999965

>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=99.69  E-value=4.6e-17  Score=163.12  Aligned_cols=141  Identities=19%  Similarity=0.264  Sum_probs=112.5

Q ss_pred             EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEe-----cchhhHHHHHHHHHHHHHhhhc
Q 003942          201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEII-----GTLSNIDKAEKLINAVIAEADA  275 (784)
Q Consensus       201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~-----G~~e~V~kA~~~I~elI~e~~~  275 (784)
                      .++|+||.+.+|.|||++|+++|.|+++++++|.|...        ++.|+|.     +++..|.+|+++|.+++..+..
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~~--------~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf~~   76 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE--------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPP   76 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT--------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCH
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEcC--------CCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCH
Confidence            47999999999999999999999999999999999742        6788888     8889999999999998874321


Q ss_pred             CCCCcccccccchhhccCCccEEEEEec----------CCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCce
Q 003942          276 GGSPSLVARGLATAQASGAAEQVEIKVP----------NEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKER  345 (784)
Q Consensus       276 ~g~p~~~~~g~~~~~~~~~~~~~~i~VP----------~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er  345 (784)
                      .....+.         .+......|.|.          .+.+|+||||+|+|||.|++.|||+|.|.           ++
T Consensus        77 e~A~~Ll---------~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~-----------~~  136 (191)
T 1tua_A           77 EKAFRLL---------EEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG-----------EY  136 (191)
T ss_dssp             HHHGGGG---------STTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC-----------SS
T ss_pred             HHhhhcc---------cCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc-----------CC
Confidence            0000000         011122334343          23689999999999999999999999994           35


Q ss_pred             EEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          346 IVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       346 ~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      +|+|.|+.+.|+.|+..|+++|..
T Consensus       137 ~v~i~G~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          137 EVAIIGDYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             EEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             EEEEEeChHHHHHHHHHHHHHHcC
Confidence            899999999999999999999964

>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=99.65  E-value=1.7e-16  Score=152.88  Aligned_cols=137  Identities=18%  Similarity=0.244  Sum_probs=107.3

Q ss_pred             cceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCC
Q 003942          117 QHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTD  196 (784)
Q Consensus       117 ~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~  196 (784)
                      .+.+++||.+.+|.+||++|++|+.|+++++  |++.... .+..+.+....+++.|.+|+.++. +.            
T Consensus         4 ~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~-~~~~~~i~~~~~p~~v~~~~~~l~-~~------------   67 (144)
T 2qnd_A            4 FHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLD-EDTCTFHIYGEDQDAVKKARSFLE-FA------------   67 (144)
T ss_dssp             CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEE-TTTTEEEEEESSHHHHHHHHHHHC-EE------------
T ss_pred             eEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccC-CCchheeeccCCHHHHHHHHHhhh-cc------------
Confidence            4568999999999999999999999998887  5443332 233344444456788888876431 11            


Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCC-EEEEccCCCCCCCCCCC--cEEEecchhhHHHHHHHHHHHHHhh
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGA-KIQITRDADADPHAATR--PVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGa-kI~V~~~~~~~p~s~eR--~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                          ..+|.||.+.+|++|||+|+|||.|++.||| +|.|..+.+......++  .|+|+|+.++|++|+.+|+++|.+.
T Consensus        68 ----e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~l  143 (144)
T 2qnd_A           68 ----EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNYL  143 (144)
T ss_dssp             ----EEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHHHTC
T ss_pred             ----eEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence                3899999999999999999999999999997 99998765432222333  4899999999999999999999863

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.57  E-value=7.8e-16  Score=157.73  Aligned_cols=147  Identities=19%  Similarity=0.214  Sum_probs=114.0

Q ss_pred             ccceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCC-
Q 003942          116 EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSS-  194 (784)
Q Consensus       116 ~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~-  194 (784)
                      ....++.||..+++.|||++|++|+.|+++++++|+|..++.....+....+++.+++++|+.+|..++..+....... 
T Consensus        33 P~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg~~~e~g~~l  112 (219)
T 2e3u_A           33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPERAFRL  112 (219)
T ss_dssp             CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTTTCEEEEEECTTCCSHHHHHHHHHHHHHHHTTCCHHHHGGG
T ss_pred             CEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcCCCEEEEecCCCCCCHHHHHHHHHHHHHHhccCCcccccee
Confidence            4456899999999999999999999999999999999855444434444455667999999999999885332211100 


Q ss_pred             CCCCCeEEEEEecCC-----------ccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHH
Q 003942          195 TDDSTMSRKIEVPNN-----------KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAE  263 (784)
Q Consensus       195 ~~~~~~t~rI~VP~~-----------~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~  263 (784)
                      ..+......|.|...           .+|+||||+|+|||.|++.|||+|.|.          ++.|+|+|+.++|+.|+
T Consensus       113 l~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~----------~~~v~i~G~~~~i~~A~  182 (219)
T 2e3u_A          113 LNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY----------GKTVAIIGNPIQIEIAK  182 (219)
T ss_dssp             GSTTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE----------TTEEEEEECHHHHHHHH
T ss_pred             ccCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC----------CeEEEEEeCHHHHHHHH
Confidence            012223334444422           689999999999999999999999997          25799999999999999


Q ss_pred             HHHHHHHHh
Q 003942          264 KLINAVIAE  272 (784)
Q Consensus       264 ~~I~elI~e  272 (784)
                      ++|+++|..
T Consensus       183 ~~i~~li~g  191 (219)
T 2e3u_A          183 TAIEKLARG  191 (219)
T ss_dssp             HHHHHHHTT
T ss_pred             HHHHHHHcC
Confidence            999999965

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

Probab=99.50  E-value=1.9e-14  Score=131.70  Aligned_cols=76  Identities=28%  Similarity=0.568  Sum_probs=66.8

Q ss_pred             cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccC
Q 003942          296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVR  372 (784)
Q Consensus       296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~r  372 (784)
                      .+++|+||.++||+||||+|++||+|+++|||+|+|.++..+ ..+..+|+|+|+|+.++|++|++||+++|++...
T Consensus         7 ~~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~-~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~~   82 (107)
T 2hh2_A            7 GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPP-NGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLC   82 (107)
T ss_dssp             CCEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCT-TCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCCC
T ss_pred             CeEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCC-CCCCCceEEEEECCHHHHHHHHHHHHHHHhcccc
Confidence            378999999999999999999999999999999999875432 2345789999999999999999999999987543

>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=99.49  E-value=3.5e-14  Score=123.72  Aligned_cols=73  Identities=36%  Similarity=0.568  Sum_probs=65.0

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      ...+++|.||.+++|+||||+|++||+|+++|||+|+|.+.    .+.+.+|+|+|+|+.++|++|+.||.++|++.
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~----~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP----VEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC----CTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC----CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            45788999999999999999999999999999999999753    24567999999999999999999999999765

>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=99.49  E-value=5.5e-14  Score=122.45  Aligned_cols=72  Identities=33%  Similarity=0.597  Sum_probs=65.0

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ...+++|.||.+++|+||||+|++||+|+++|||+|+|.+.    ...+.+|+|+|+|+.++|++|+.||+++|++
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~----~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   76 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   76 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT----TSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC----CCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            45788999999999999999999999999999999999753    2346789999999999999999999999975

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

Probab=99.48  E-value=3.1e-14  Score=130.03  Aligned_cols=73  Identities=32%  Similarity=0.563  Sum_probs=64.7

Q ss_pred             cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccC
Q 003942          296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVR  372 (784)
Q Consensus       296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~r  372 (784)
                      .+++|+||.+++++||||+|++||+|+++|||+|+|.++.    ..+.+|+|+|+|+.++|++|++||+++|++...
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~----~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~~   83 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD----GTGPEKIAHIMGPPDRCEHAARIINDLLQSLRS   83 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC----SSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC-
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC----CCCceeEEEEEeCHHHHHHHHHHHHHHHhcccc
Confidence            4789999999999999999999999999999999997542    345689999999999999999999999987543

>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=99.47  E-value=6e-14  Score=120.25  Aligned_cols=73  Identities=36%  Similarity=0.515  Sum_probs=64.0

Q ss_pred             cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ++++|.||.+++|+||||+|++||+|+++|||+|+|.++.. ....+.+|.|+|+|+.++|++|+.||.++|++
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            57899999999999999999999999999999999986421 12356789999999999999999999999864

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

Probab=99.47  E-value=4.3e-14  Score=120.52  Aligned_cols=69  Identities=32%  Similarity=0.507  Sum_probs=63.8

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ...++|+||.+++|+||||+|++||+|+++|||+|+|.++      ...+|+|+|+|+.++|++|+.||.++|++
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~------~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG------NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC------CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            4678999999999999999999999999999999999754      35699999999999999999999999976

>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=4.3e-14  Score=121.30  Aligned_cols=71  Identities=37%  Similarity=0.598  Sum_probs=64.8

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ..+++|.||.+++|+||||+|++||+|+++|||+|+|.+.    ...+.+|+|+|+|+.++|++|+.||.++|++
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~----~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   74 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP----VEGSTDRQVTITGSAASISLAQYLINVRLSS   74 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC----CTTCSEEEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC----CCCCCeEEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            4678999999999999999999999999999999999752    3456899999999999999999999999975

>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=99.47  E-value=3.5e-14  Score=121.68  Aligned_cols=73  Identities=32%  Similarity=0.461  Sum_probs=67.1

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE  272 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e  272 (784)
                      ++++|+||.+++|+||||+|++||+|+++|||+|+|.++.+..+++.+|.|+|+|+.++|.+|+.+|+++|.+
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            6889999999999999999999999999999999999875556677889999999999999999999999875

>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=99.47  E-value=6e-14  Score=124.92  Aligned_cols=74  Identities=35%  Similarity=0.618  Sum_probs=66.7

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccc
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTV  371 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~  371 (784)
                      ...+++|.||.+++|+||||+|++||+|+++|||+|+|.++.    +...+|+|+|+|+.++|++|+.||+++|++..
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            457899999999999999999999999999999999997643    34578999999999999999999999998654

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

Probab=99.46  E-value=1.3e-13  Score=120.89  Aligned_cols=73  Identities=37%  Similarity=0.640  Sum_probs=65.2

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ....+|.||.+++|+||||+|++||+|+++|||+|.|..+..  ...+.+|.|+|+|++++|++|++||+++|.+
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 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS--QNTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSC--SSTTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCC--CCCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            467899999999999999999999999999999999987542  2356799999999999999999999999864

>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=99.46  E-value=1.9e-14  Score=144.25  Aligned_cols=145  Identities=16%  Similarity=0.179  Sum_probs=116.9

Q ss_pred             ceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCC-C
Q 003942          118 HSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSST-D  196 (784)
Q Consensus       118 ~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~-~  196 (784)
                      ..++.||...++.|||+.|++++.|++.+++++++...+.....+.+..+++..++.+|+.+|..+...+........ .
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf~~e~A~~Ll~   84 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPEKAFRLLE   84 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCHHHHGGGGS
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEcCCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCHHHhhhccc
Confidence            458999999999999999999999999899999997665544445555669999999999999998876654332221 1


Q ss_pred             CCCeEEEEEecC----------CccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHH
Q 003942          197 DSTMSRKIEVPN----------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLI  266 (784)
Q Consensus       197 ~~~~t~rI~VP~----------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I  266 (784)
                      +..+...|.|..          ..+|+||||+|.|||.|++.|||+|.|..          +.|+|.|+.++|+.|+..|
T Consensus        85 Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~~----------~~v~i~G~~~~i~~Ar~~i  154 (191)
T 1tua_A           85 EDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGE----------YEVAIIGDYERAMAAKQAI  154 (191)
T ss_dssp             TTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEECS----------SEEEEEEEHHHHHHHHHHH
T ss_pred             CcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEcC----------CEEEEEeChHHHHHHHHHH
Confidence            223444454552          24899999999999999999999999973          4899999999999999999


Q ss_pred             HHHHHh
Q 003942          267 NAVIAE  272 (784)
Q Consensus       267 ~elI~e  272 (784)
                      +++|..
T Consensus       155 ~~li~g  160 (191)
T 1tua_A          155 EMLAEG  160 (191)
T ss_dssp             HHHHTT
T ss_pred             HHHHcC
Confidence            999964

>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=6.6e-14  Score=125.14  Aligned_cols=76  Identities=36%  Similarity=0.620  Sum_probs=67.1

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccc
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTV  371 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~  371 (784)
                      ...+++|+||.+++|+||||+|++||+|+++|||+|.|.++..  .....+|+|+|+|+.++|++|++||+++|++..
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            5678899999999999999999999999999999999986542  124578999999999999999999999997643

>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=99.44  E-value=6.6e-14  Score=119.35  Aligned_cols=71  Identities=27%  Similarity=0.469  Sum_probs=65.2

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      ..++++|+||.+++|.||||+|++||+|+++|||+|+|.++     ++.+|+|+|+|+.++|.+|+.+|+++|+|+
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~-----~~~er~v~I~G~~~~v~~A~~~I~~~l~ed   73 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKLEED   73 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-----CCSEEEEEEEECHHHHHHHHHHHHHHHHC-
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-----CCCcEEEEEEeCHHHHHHHHHHHHHHHhcC
Confidence            35899999999999999999999999999999999999864     356899999999999999999999999863

>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=99.44  E-value=7.7e-14  Score=123.44  Aligned_cols=73  Identities=33%  Similarity=0.581  Sum_probs=65.6

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      ...+++|.||.+++|+||||+|++||+|+++|||+|+|.+.    ...+.+|+|+|+|+.++|++|++||+++|++.
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            45788999999999999999999999999999999999753    23467899999999999999999999999753

>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=5.9e-14  Score=122.59  Aligned_cols=68  Identities=31%  Similarity=0.493  Sum_probs=61.9

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS  368 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~  368 (784)
                      ...+++|.||.+++|+||||+|++||+|+++|||+|+|....       ++++|+|+|+.++|++|++||+++|+
T Consensus         8 ~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~-------~~~~v~ItG~~e~v~~A~~~I~~~i~   75 (83)
T 2dgr_A            8 GQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD-------KEPVFAVTGMPENVDRAREEIEAHIT   75 (83)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS-------SCCEEEEEECTTTHHHHHHHHHHHHH
T ss_pred             CceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC-------CCCeEEEEcCHHHHHHHHHHHHHHHh
Confidence            457889999999999999999999999999999999996422       36899999999999999999999876

>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=99.42  E-value=1.3e-13  Score=121.35  Aligned_cols=74  Identities=36%  Similarity=0.514  Sum_probs=65.1

Q ss_pred             cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      .+++|.||.+++|+||||+|++||+|+++|||+|.|.++.. ....+.+|.|+|+|+.++|++|+.||.++|++.
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~-~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGE-FLPGTRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTC-BSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCC-CCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            57899999999999999999999999999999999986421 123457899999999999999999999999764

>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=99.42  E-value=2.7e-13  Score=118.05  Aligned_cols=74  Identities=26%  Similarity=0.482  Sum_probs=67.5

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      ...++++|+||.+++|+||||+|++||+|+++|||+|+|.+.   .+++.+|.|+|+|+.++|++|+++|+++|++.
T Consensus         4 g~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~---~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            4 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT---TSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC---CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            346899999999999999999999999999999999999853   34567899999999999999999999999986

>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=99.42  E-value=9.9e-14  Score=122.15  Aligned_cols=75  Identities=32%  Similarity=0.460  Sum_probs=69.1

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      ++++|+||.+++|+||||+|++||+|+++|||+|+|.++.+..+++.+|.|+|+|+.++|.+|+.+|+++|.+..
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            588999999999999999999999999999999999986555567788999999999999999999999998863

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

Probab=99.41  E-value=1.5e-13  Score=125.84  Aligned_cols=74  Identities=24%  Similarity=0.464  Sum_probs=66.4

Q ss_pred             EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      +++|+||.++||+||||+|++||+|+++|||+|+|.++.+......+|+|+|+|+.++|++|+++|+++|.+..
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~   81 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhccc
Confidence            78999999999999999999999999999999999976433334568999999999999999999999998753

>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=2.6e-13  Score=123.52  Aligned_cols=75  Identities=33%  Similarity=0.564  Sum_probs=65.3

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      ...+++|.||.+++|+||||+|++||+|+++|||+|+|.+..  ......+|+|+|+|+.++|++|++||+++|.+.
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 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES--EGTLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSS--CCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCC--CCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            346789999999999999999999999999999999997643  122346899999999999999999999999653

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

Probab=99.40  E-value=1.6e-13  Score=117.71  Aligned_cols=73  Identities=32%  Similarity=0.527  Sum_probs=66.9

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      ..++++|+||.+++|+||||+|++||+|+++|||+|+|.+.   .+++.+|.|+|+|+.++|++|+.+|+++|.++
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~---~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP---VEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC---CTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC---CCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            45789999999999999999999999999999999999863   45677999999999999999999999999764

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

Probab=99.39  E-value=5.7e-13  Score=116.80  Aligned_cols=76  Identities=28%  Similarity=0.554  Sum_probs=67.2

Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE  272 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e  272 (784)
                      .....+++|+||.+++|+||||+|++||+|+++|||+|.|.++.. ...+.+|.|+|+|+.++|++|+++|+++++|
T Consensus        10 g~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~-~~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           10 GQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SCSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSC-SSTTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCC-CCCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            345678999999999999999999999999999999999997532 2356789999999999999999999999864

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

Probab=99.39  E-value=2.8e-13  Score=120.55  Aligned_cols=74  Identities=31%  Similarity=0.585  Sum_probs=67.7

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      ..++++|+||.+++|+||||+|++||+|+++|||+|+|.++.   .+..+|.|+|+|+.++|++|+++|+++|++..
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            458999999999999999999999999999999999999753   35568999999999999999999999999864

>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=99.38  E-value=2.9e-13  Score=117.88  Aligned_cols=73  Identities=33%  Similarity=0.538  Sum_probs=65.6

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      ..++++|+||.+++|+||||+|++||+|+++|||+|+|.+.   .+++.+|.|+|+|+.++|++|+.+|+++|.++
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~---~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP---VEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC---CTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC---CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            45789999999999999999999999999999999999864   34667999999999999999999999999875

>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=99.38  E-value=3.8e-13  Score=120.24  Aligned_cols=78  Identities=27%  Similarity=0.535  Sum_probs=69.0

Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      ....++++|+||.+++|+||||+|++||+|+++|||+|+|.++... ....+|+|+|+|+.++|++|+++|+++|++..
T Consensus        11 ~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~-~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   88 (94)
T 1x4m_A           11 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQ-NTGADKPLRITGDPYKVQQAKEMVLELIRDQG   88 (94)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCC-SSCSCEEEEEEECTTTHHHHHHHHHHHHCCCS
T ss_pred             CCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCC-CCCCceEEEEEeCHHHHHHHHHHHHHHHhccC
Confidence            3567899999999999999999999999999999999999976432 23468999999999999999999999998754

>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=99.37  E-value=3e-13  Score=119.63  Aligned_cols=74  Identities=26%  Similarity=0.482  Sum_probs=67.8

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      ...++++|+||.+++|+||||+|++||+|+++|||+|+|.+.   .+++.+|.|+|+|+.++|++|+++|+++|++.
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~---~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC---CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC---CCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            456899999999999999999999999999999999999853   34667899999999999999999999999985

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

Probab=99.36  E-value=4.7e-13  Score=122.20  Aligned_cols=74  Identities=27%  Similarity=0.555  Sum_probs=65.7

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcC
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAG  276 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~  276 (784)
                      .+++|+||.+++++||||+|++||+|+++|+|+|+|.++.   ..+.+|+|+|+|+.++|++|+++|+++|.+...+
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            4789999999999999999999999999999999998653   2456899999999999999999999999987643

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

Probab=99.35  E-value=7e-13  Score=144.98  Aligned_cols=143  Identities=14%  Similarity=0.236  Sum_probs=101.6

Q ss_pred             CCCCeEEEEEecCCccceeeccCc--chHhhHHhhcCCEEEEccCC--CCCCCCCCCcEEEecchhhHHHHHHHHHHHHH
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAG--DTIRYLQYNSGAKIQITRDA--DADPHAATRPVEIIGTLSNIDKAEKLINAVIA  271 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG--~tIK~Iq~~TGakI~V~~~~--~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~  271 (784)
                      ....++++|.||..+++.||||+|  ++|++|+++|+|+|+|...+  ...+......|+|+|..++|++|+++|++++.
T Consensus        26 ~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l~P  105 (376)
T 3n89_A           26 NPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNCH  105 (376)
T ss_dssp             CTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHSCE
T ss_pred             cCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhcCC
Confidence            356799999999999999999999  99999999999999998654  22223456789999999999999999998432


Q ss_pred             hhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEc
Q 003942          272 EADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG  351 (784)
Q Consensus       272 e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~G  351 (784)
                                              .++.+.++...+..  .+...+|.+ ++..+++|.|....  .........|+|+|
T Consensus       106 ------------------------l~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~--~~~~~~sd~V~IrG  156 (376)
T 3n89_A          106 ------------------------FTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAP--EKNGIVTTYLRITA  156 (376)
T ss_dssp             ------------------------EEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC-------CEEEEEEEE
T ss_pred             ------------------------ceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCcc--cccCCCCCEEEEEc
Confidence                                    24556666543332  112345554 56789999885421  11112367899999


Q ss_pred             CHHHHHHHHHHHHHHH
Q 003942          352 DMRQIEIAQEMIKEVL  367 (784)
Q Consensus       352 t~~qV~~Ak~lI~~~L  367 (784)
                      ....|+.|++.+..+|
T Consensus       157 ~~~nv~~akeA~~~Ll  172 (376)
T 3n89_A          157 REKNQHELIEAAKRLN  172 (376)
T ss_dssp             EGGGHHHHHHHHHHHH
T ss_pred             ChhhHHHHHHHHHHHH
Confidence            9876666655555444

>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=99.34  E-value=4.9e-13  Score=116.77  Aligned_cols=71  Identities=24%  Similarity=0.361  Sum_probs=64.0

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      ...++++|.||.+++|+||||+|++||+|+++|||+|+|.+..      .+++|+|+|+.++|++|+.+|++++...
T Consensus         7 ~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~------~~~~v~ItG~~e~v~~A~~~I~~~i~~r   77 (83)
T 2dgr_A            7 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD------KEPVFAVTGMPENVDRAREEIEAHITLR   77 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS------SCCEEEEEECTTTHHHHHHHHHHHHHSC
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC------CCCeEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            4568999999999999999999999999999999999998642      2689999999999999999999987754

>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=99.34  E-value=1.7e-12  Score=118.11  Aligned_cols=78  Identities=29%  Similarity=0.536  Sum_probs=67.8

Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      ....++++|+||.+++|+||||+|++||+|+++|||+|+|.+..+.. ...+|.|+|+|+.++|++|+++|+++|.+..
T Consensus        11 ~~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~-~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T 1we8_A           11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT-LLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS-SSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCC-CCCcceEEEEcCHHHHHHHHHHHHHHHhhCh
Confidence            34568899999999999999999999999999999999998753221 2358999999999999999999999998753

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

Probab=99.32  E-value=1.6e-12  Score=110.10  Aligned_cols=68  Identities=21%  Similarity=0.434  Sum_probs=61.1

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVL  367 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L  367 (784)
                      ...+.+|.||.+++|.|||++|++||+|+++|||+|.|.++.      ..+|.|+|+|+.+.|++|+++|++++
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g------~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC------CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            346789999999999999999999999999999999996532      36789999999999999999999875

>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=2.1e-12  Score=115.36  Aligned_cols=75  Identities=19%  Similarity=0.403  Sum_probs=65.5

Q ss_pred             CCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccC
Q 003942          293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVR  372 (784)
Q Consensus       293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~r  372 (784)
                      ....+.+|.||.+++|+||||+|++||+|+++|||+|.|.+..      ..++.|+|+|+.++|++|+.+|++++++..+
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~------~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~~   87 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD------DPSNQIKITGTKEGIEKARHEVLLISAEQDK   87 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT------SSCCEEEEEECHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC------CCCCeEEEEECHHHHHHHHHHHHHHhhcccc
Confidence            3457889999999999999999999999999999999996422      2468999999999999999999999987654


Q ss_pred             C
Q 003942          373 P  373 (784)
Q Consensus       373 ~  373 (784)
                      .
T Consensus        88 ~   88 (94)
T 2cte_A           88 R   88 (94)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.30  E-value=3.6e-12  Score=114.57  Aligned_cols=75  Identities=19%  Similarity=0.272  Sum_probs=65.4

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccc
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTV  371 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~  371 (784)
                      ...+++|.||.+++++||||+|++||+|+++|||+|.|.++..   ....+|.|+|+|+.++|++|+.+|+.++.+..
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~---~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~e   89 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD---GNQPQDQITITGYEKNTEAARDAILRIVGELE   89 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT---CSSCSSEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHHHHH
Confidence            3468899999999999999999999999999999999976431   22367999999999999999999999987643

>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=3.5e-12  Score=114.19  Aligned_cols=75  Identities=17%  Similarity=0.203  Sum_probs=66.0

Q ss_pred             CCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccC
Q 003942          293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVR  372 (784)
Q Consensus       293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~r  372 (784)
                      ....+.+|.||.+++++|||++|++||+|+++|||+|+|.++.     ...+|+|+|+|+.++|++|+++|++++++...
T Consensus        14 ~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g-----~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~~   88 (95)
T 2ctm_A           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-----APDPNCVTVTGLPENVEEAIDHILNLEEEYLA   88 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-----CSCTTEEEEESCHHHHHHHHHHHHHHHHHHHT
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC-----CCCCcEEEEEcCHHHHHHHHHHHHHHHHHHHH
Confidence            4567899999999999999999999999999999999996532     23578999999999999999999999987544

>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=99.29  E-value=1.9e-12  Score=117.32  Aligned_cols=90  Identities=13%  Similarity=0.217  Sum_probs=80.0

Q ss_pred             eecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhh-cCCEEEEccCCCCCC
Q 003942          165 ETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN-SGAKIQITRDADADP  243 (784)
Q Consensus       165 ~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~-TGakI~V~~~~~~~p  243 (784)
                      .|+|..++|++|+.+|.+++..            .++.+|.||..+++.|||++|++||+|+++ ++++|.|.++     
T Consensus         4 ~i~G~~~~V~~A~~~i~~~~~~------------~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~~-----   66 (102)
T 2ctf_A            4 GSSGEPEKLGQALTEVYAKANS------------FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG-----   66 (102)
T ss_dssp             CCCCCCCCCCCSCCCCCCCCCC------------CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS-----
T ss_pred             ccCcCHHHHHHHHHHHHHHhcC------------eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCCC-----
Confidence            4689999999999999877731            278999999999999999999999999997 5899999852     


Q ss_pred             CCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          244 HAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       244 ~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                         ++.|+|.|.++.|++|+.+|..++++..
T Consensus        67 ---~~~ItI~G~~~~V~~a~~~I~~~v~el~   94 (102)
T 2ctf_A           67 ---EDKITLEGPTEDVSVAQEQIEGMVKDLI   94 (102)
T ss_dssp             ---SCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             ---CCEEEEECCHHHHHHHHHHHHHHHHHHH
Confidence               5699999999999999999999998864

>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=99.27  E-value=6.1e-12  Score=113.05  Aligned_cols=75  Identities=19%  Similarity=0.308  Sum_probs=67.1

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      ..++++|.||..++++||||+|++||+|+++|||+|+|.++.+  +...+|.|+|+|+.++|.+|+.+|+.++.+..
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~--~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~e   89 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQITITGYEKNTEAARDAILRIVGELE   89 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT--CSSCSSEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC--CCCCccEEEEEeCHHHHHHHHHHHHHHHHHHH
Confidence            3479999999999999999999999999999999999987542  34467999999999999999999999998764

>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=99.25  E-value=2.1e-12  Score=117.55  Aligned_cols=84  Identities=20%  Similarity=0.275  Sum_probs=71.5

Q ss_pred             chhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEE
Q 003942          172 SVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVE  251 (784)
Q Consensus       172 ~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~  251 (784)
                      +|++|+..|.+++              .++.+|.||.+++|+|||++|++||+|+++|||+|+|.++.+     ..+.|+
T Consensus         3 ~~~~Ak~~i~~~a--------------p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~-----~~~~V~   63 (104)
T 2ctk_A            3 SGSSGKEALEALV--------------PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL-----QSDIIA   63 (104)
T ss_dssp             CCCCCCCCCCCSS--------------CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT-----TCCEEE
T ss_pred             hHHHHHHHHHhhC--------------CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCC-----CcceEE
Confidence            4556666665544              378999999999999999999999999999999999986532     346999


Q ss_pred             EecchhhHHHHHHHHHHHHHhhh
Q 003942          252 IIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       252 I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      |+|+.++|++|+.+|++++++..
T Consensus        64 I~G~~e~v~~A~~~I~~i~~e~e   86 (104)
T 2ctk_A           64 ITGLAANLDRAKAGLLERVKELQ   86 (104)
T ss_dssp             EEECHHHHHHHHHHHHHHHHHHH
T ss_pred             EEcCHHHHHHHHHHHHHHHhhHH
Confidence            99999999999999999998753

>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=99.24  E-value=1.1e-11  Score=110.79  Aligned_cols=74  Identities=28%  Similarity=0.484  Sum_probs=65.9

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhc
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA  275 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~  275 (784)
                      ...++++|.||.+++|+|||++|++||+|+++|||+|+|.+..     ..++.|+|+|+.++|++|+.+|++++.+...
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-----~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~~   87 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-----DPSNQIKITGTKEGIEKARHEVLLISAEQDK   87 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-----SSCCEEEEEECHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-----CCCCeEEEEECHHHHHHHHHHHHHHhhcccc
Confidence            3458999999999999999999999999999999999998542     2357999999999999999999999988643

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

Probab=99.23  E-value=5.7e-12  Score=106.75  Aligned_cols=68  Identities=18%  Similarity=0.268  Sum_probs=61.6

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHH
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVI  270 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI  270 (784)
                      ..++.+|.||.+++|.|||++|++||+|+++|||+|+|.++.     ..+|.|+|+|+.++|++|+++|++++
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-----~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-----EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-----SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-----CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            357899999999999999999999999999999999998653     25689999999999999999999864

>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=99.22  E-value=2e-11  Score=109.29  Aligned_cols=74  Identities=18%  Similarity=0.235  Sum_probs=66.5

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      ...++++|.||..++++|||++|++||+|+++|+|+|+|.++.+    ..+|.|+|+|..++|++|+++|++++++..
T Consensus        14 ~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~----~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~   87 (95)
T 2ctm_A           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLPENVEEAIDHILNLEEEYL   87 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC----SCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC----CCCcEEEEEcCHHHHHHHHHHHHHHHHHHH
Confidence            44689999999999999999999999999999999999986532    346899999999999999999999998864

>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=5.1e-13  Score=121.15  Aligned_cols=90  Identities=17%  Similarity=0.283  Sum_probs=76.3

Q ss_pred             EEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHH-hCCeE
Q 003942          251 EIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTR-SGARI  329 (784)
Q Consensus       251 ~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~-SGarI  329 (784)
                      .|+|+.++|.+|+++|.+++.+                      ..+.+|.||..++++|||++|++||+|+++ ++|+|
T Consensus         4 ~i~G~~~~V~~A~~~i~~~~~~----------------------~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I   61 (102)
T 2ctf_A            4 GSSGEPEKLGQALTEVYAKANS----------------------FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHI   61 (102)
T ss_dssp             CCCCCCCCCCCSCCCCCCCCCC----------------------CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEE
T ss_pred             ccCcCHHHHHHHHHHHHHHhcC----------------------eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEE
Confidence            4678888888888887765432                      267899999999999999999999999997 59999


Q ss_pred             EeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccc
Q 003942          330 QLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTV  371 (784)
Q Consensus       330 qI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~  371 (784)
                      .|.+         .++.|+|+|+.+.|++|+.+|+.++++..
T Consensus        62 ~fp~---------~~~~ItI~G~~~~V~~a~~~I~~~v~el~   94 (102)
T 2ctf_A           62 EFTE---------GEDKITLEGPTEDVSVAQEQIEGMVKDLI   94 (102)
T ss_dssp             EECS---------SSCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             EeCC---------CCCEEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            9853         36799999999999999999999987644

>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=99.20  E-value=1.4e-11  Score=112.12  Aligned_cols=69  Identities=19%  Similarity=0.325  Sum_probs=61.9

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ....+|.||.+++|+|||++|++||+|+++|||+|.|.++.      ...+.|+|+|+.++|++|+.+|++++++
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g------~~~~~V~I~G~~e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE------LQSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT------TTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC------CCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            46789999999999999999999999999999999996532      2356999999999999999999998876

>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=7e-11  Score=105.71  Aligned_cols=75  Identities=20%  Similarity=0.362  Sum_probs=66.2

Q ss_pred             cCCccEEEEEecCCceeeeecCCchHHHHHHHHh-CCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          292 SGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS-GARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       292 ~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~S-GarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      .....+..|.||.++++.|||++|++||+|+++| ||+|.|.++      .+..+.|+|+|+.++|++|+++|++++++.
T Consensus        13 ~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~------g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~   86 (95)
T 2ctj_A           13 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   86 (95)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT------TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             HhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC------CCCcceEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            4567889999999999999999999999999999 999999643      345779999999999999999999999865


Q ss_pred             cC
Q 003942          371 VR  372 (784)
Q Consensus       371 ~r  372 (784)
                      ..
T Consensus        87 e~   88 (95)
T 2ctj_A           87 QT   88 (95)
T ss_dssp             SC
T ss_pred             hh
Confidence            43

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

Probab=98.99  E-value=4.7e-10  Score=100.35  Aligned_cols=74  Identities=23%  Similarity=0.348  Sum_probs=66.3

Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      .+..++..|.||..+++.|||++|++||+|+++| ||+|.|.++     ++..+.|+|+|..+.|++|+++|++++.+..
T Consensus        13 ~~~~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           13 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-----GSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   87 (95)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-----TTTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             HhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC-----CCCcceEEEEcCHHHHHHHHHHHHHHHhhhh
Confidence            3556799999999999999999999999999999 999999865     2446799999999999999999999998864

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.96  E-value=2.4e-10  Score=100.97  Aligned_cols=75  Identities=25%  Similarity=0.308  Sum_probs=64.2

Q ss_pred             CCccEEEEEecCCceeeeecCCchHHHHHHHHhCCe-EEeccCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcc
Q 003942          293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGAR-IQLIPQHLPEGDGSKERIVRVTG-DMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGar-IqI~~~~~p~~~~~~er~V~I~G-t~~qV~~Ak~lI~~~L~~~  370 (784)
                      .......|.|+.+++|.|||++|++||+|+++|||+ |.|..         ++++|+|.| +.+++++|+.||+.+.+..
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e---------ddG~V~I~g~~~ea~~~A~~~I~~ie~~~   82 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE---------DTGTFRIYGESADAVKKARGFLEFVEDFI   82 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET---------TTTEEEEEESSHHHHHHHHHHHSCCCCCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc---------CCCEEEEEECCHHHHHHHHHHHHhhheEE
Confidence            456788999999999999999999999999999998 99953         258999999 6999999999999877655


Q ss_pred             cCCCCC
Q 003942          371 VRPSTL  376 (784)
Q Consensus       371 ~r~~~~  376 (784)
                      ..++.+
T Consensus        83 ~vp~~~   88 (91)
T 2cpq_A           83 QVPSGP   88 (91)
T ss_dssp             CCCSSC
T ss_pred             ecChhh
Confidence            555543

>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=98.83  E-value=7.7e-10  Score=97.72  Aligned_cols=66  Identities=23%  Similarity=0.394  Sum_probs=58.9

Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCE-EEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHH
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAK-IQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAV  269 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGak-I~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~el  269 (784)
                      ....+...|.|+.+++|.|||++|++||+|+++|||+ |.|..+        +..|+|.| +.+.+++|+++|+.+
T Consensus        11 ~~~~~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           11 LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED--------TGTFRIYGESADAVKKARGFLEFV   78 (91)
T ss_dssp             SSCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT--------TTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             ccCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEcC--------CCEEEEEECCHHHHHHHHHHHHhh
Confidence            3456899999999999999999999999999999998 999742        47899999 899999999998774

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.80  E-value=7.7e-09  Score=96.01  Aligned_cols=75  Identities=13%  Similarity=0.162  Sum_probs=58.0

Q ss_pred             cEEEEEecC-------CceeeeecCCchHHHHHHHHhCCeEEeccCCC------CCCCCCCceEEEEEcC-HHHHHHHHH
Q 003942          296 EQVEIKVPN-------EKVGLIIGRGGETIKGLQTRSGARIQLIPQHL------PEGDGSKERIVRVTGD-MRQIEIAQE  361 (784)
Q Consensus       296 ~~~~i~VP~-------~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~------p~~~~~~er~V~I~Gt-~~qV~~Ak~  361 (784)
                      .+.+|.||-       +++|+|||.+|.+||+|+++|||+|.|..+..      ...+..++..|.|++. .+.|++|++
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            455665554       58999999999999999999999999974321      1112334567888876 899999999


Q ss_pred             HHHHHHhcc
Q 003942          362 MIKEVLSQT  370 (784)
Q Consensus       362 lI~~~L~~~  370 (784)
                      ||+++|...
T Consensus        92 ~Ie~Ll~~v  100 (119)
T 2yqr_A           92 LCENLLQTV  100 (119)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHhhch
Confidence            999999753

>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=98.76  E-value=1.4e-08  Score=95.87  Aligned_cols=78  Identities=24%  Similarity=0.379  Sum_probs=62.6

Q ss_pred             CccEEEEEecCC------ceeeeecCCchHHHHHHHHhCCeEEeccCCCC------------CCCCCCceEEEEEcC-HH
Q 003942          294 AAEQVEIKVPNE------KVGLIIGRGGETIKGLQTRSGARIQLIPQHLP------------EGDGSKERIVRVTGD-MR  354 (784)
Q Consensus       294 ~~~~~~i~VP~~------~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p------------~~~~~~er~V~I~Gt-~~  354 (784)
                      ...+.+|.||-+      ++|+|||.+|.+||+|+++|||+|.|.....-            ..+...+-.|.|+++ .+
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e   84 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTME   84 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHH
Confidence            346778889876      99999999999999999999999999753210            012234678999996 88


Q ss_pred             HHHHHHHHHHHHHhccc
Q 003942          355 QIEIAQEMIKEVLSQTV  371 (784)
Q Consensus       355 qV~~Ak~lI~~~L~~~~  371 (784)
                      .|++|+++|+++|...+
T Consensus        85 ~~~~A~~~I~~ll~~~~  101 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQGI  101 (131)
T ss_dssp             HHHHHHHHHHHHHTTTT
T ss_pred             HHHHHHHHHHHHHhccC
Confidence            99999999999997643

>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=98.74  E-value=1.1e-08  Score=96.74  Aligned_cols=76  Identities=25%  Similarity=0.443  Sum_probs=62.6

Q ss_pred             CCeEEEEEecCC------ccceeeccCcchHhhHHhhcCCEEEEccCCCCC-------------CCCCCCcEEEec-chh
Q 003942          198 STMSRKIEVPNN------KVGVLIGKAGDTIRYLQYNSGAKIQITRDADAD-------------PHAATRPVEIIG-TLS  257 (784)
Q Consensus       198 ~~~t~rI~VP~~------~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~-------------p~s~eR~V~I~G-~~e  257 (784)
                      ..++.+|.||.+      ++|+|||.+|.|||+|+++|||+|.|.......             ....+..|.|++ +.+
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e   84 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTME   84 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHH
Confidence            457899999988      899999999999999999999999998742110             012255788888 789


Q ss_pred             hHHHHHHHHHHHHHhh
Q 003942          258 NIDKAEKLINAVIAEA  273 (784)
Q Consensus       258 ~V~kA~~~I~elI~e~  273 (784)
                      .|++|+++|+++|.+.
T Consensus        85 ~~~~A~~~I~~ll~~~  100 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQG  100 (131)
T ss_dssp             HHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhcc
Confidence            9999999999999763

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.73  E-value=1.8e-08  Score=93.46  Aligned_cols=76  Identities=14%  Similarity=0.125  Sum_probs=60.4

Q ss_pred             CCeEEEEEecCC-------ccceeeccCcchHhhHHhhcCCEEEEccCCCCC-------CCCCCCcEEEec-chhhHHHH
Q 003942          198 STMSRKIEVPNN-------KVGVLIGKAGDTIRYLQYNSGAKIQITRDADAD-------PHAATRPVEIIG-TLSNIDKA  262 (784)
Q Consensus       198 ~~~t~rI~VP~~-------~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~-------p~s~eR~V~I~G-~~e~V~kA  262 (784)
                      ..++.+|.||.+       ++|+|||++|.|||+|+++|||+|.|..+....       ....+..|.|++ +.+.|++|
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A   89 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA   89 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHH
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHH
Confidence            457888988864       799999999999999999999999998542110       011234677877 89999999


Q ss_pred             HHHHHHHHHhh
Q 003942          263 EKLINAVIAEA  273 (784)
Q Consensus       263 ~~~I~elI~e~  273 (784)
                      +++|++||.+.
T Consensus        90 ~~~Ie~Ll~~v  100 (119)
T 2yqr_A           90 KKLCENLLQTV  100 (119)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHhhch
Confidence            99999999875

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.41  E-value=2e-07  Score=88.66  Aligned_cols=73  Identities=26%  Similarity=0.314  Sum_probs=55.7

Q ss_pred             EEEEEecC------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCC--------------CCCCceEEEEEcC-H--
Q 003942          297 QVEIKVPN------EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEG--------------DGSKERIVRVTGD-M--  353 (784)
Q Consensus       297 ~~~i~VP~------~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~--------------~~~~er~V~I~Gt-~--  353 (784)
                      +.+|.||-      |++|+|||.+|.+||+|+++|||+|.|..+.+-..              ...++..|.|++. .  
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            45666664      67999999999999999999999999986442110              1234457889985 3  


Q ss_pred             ---HHHHHHHHHHHHHHhc
Q 003942          354 ---RQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       354 ---~qV~~Ak~lI~~~L~~  369 (784)
                         ..|++|+++|+++|..
T Consensus        83 ~~~~~l~~A~~~I~~lL~p  101 (140)
T 2bl5_A           83 RAELKLKRAVEEVKKLLVP  101 (140)
T ss_dssp             HHHHHHHHHHHHHHHHSSC
T ss_pred             hHHHHHHHHHHHHHHHCCC
Confidence               2799999999999864

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.37  E-value=3.1e-07  Score=87.40  Aligned_cols=73  Identities=21%  Similarity=0.300  Sum_probs=56.9

Q ss_pred             eEEEEEecCC------ccceeeccCcchHhhHHhhcCCEEEEccCCCCC---------------CCCCCCcEEEec-chh
Q 003942          200 MSRKIEVPNN------KVGVLIGKAGDTIRYLQYNSGAKIQITRDADAD---------------PHAATRPVEIIG-TLS  257 (784)
Q Consensus       200 ~t~rI~VP~~------~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~---------------p~s~eR~V~I~G-~~e  257 (784)
                      ++.+|.||.+      ++|+|||.+|.|||+|+++|||+|.|..+....               -.+.+..|.|++ +.+
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            5788999864      599999999999999999999999999764211               012234678888 443


Q ss_pred             -----hHHHHHHHHHHHHHh
Q 003942          258 -----NIDKAEKLINAVIAE  272 (784)
Q Consensus       258 -----~V~kA~~~I~elI~e  272 (784)
                           .|.+|+++|+++|..
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p  101 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVP  101 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSC
T ss_pred             hhHHHHHHHHHHHHHHHCCC
Confidence                 789999999998864

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

Probab=98.25  E-value=8.6e-07  Score=103.55  Aligned_cols=63  Identities=25%  Similarity=0.387  Sum_probs=55.5

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHH
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVL  367 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L  367 (784)
                      .....|.||.++++.|||+||++||.|+++|||+|.|.+          +.+|.|.++ .+.+++|+++|+.++
T Consensus       566 p~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d----------~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          566 PVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD----------EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             CEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS----------SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             CeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC----------CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            457889999999999999999999999999999999952          568999998 789999999998876

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

Probab=98.04  E-value=2.5e-06  Score=99.72  Aligned_cols=66  Identities=20%  Similarity=0.382  Sum_probs=56.5

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHH
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIA  271 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~  271 (784)
                      .....+.|.|+.++++.|||++|++||.|+++|||+|.|.+         +..|+|.+ +.+.+++|+++|+++++
T Consensus       564 ~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d---------~G~V~I~~~~~~~~~~A~~~I~~i~~  630 (630)
T 3u1k_A          564 NGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD---------EETFSVFAPTPSAMHEARDFITEICK  630 (630)
T ss_dssp             TCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS---------SSEEEEEESSHHHHHHHHHHTTC---
T ss_pred             cCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC---------CcEEEEEeCCHHHHHHHHHHHHHHhC
Confidence            34678899999999999999999999999999999999984         35889998 57899999999988763

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.95  E-value=1.2e-05  Score=75.32  Aligned_cols=67  Identities=13%  Similarity=0.176  Sum_probs=59.8

Q ss_pred             EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942          297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS  368 (784)
Q Consensus       297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~  368 (784)
                      -+.|.|..++++.|||++|+.|++|+..|.+.|+|+.-     +.+..-.|+|.|+...=.+|+.||..+++
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~-----~s~g~tEVtIfG~~~~Q~rak~MI~sLA~  123 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVW-----GPERRAEIWIFGPPPFRRDVDRMLTDLAH  123 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECC-----CTTSCEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEecc-----CCCCcEEEEEECCHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999999853     33467889999999999999999998775

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.90  E-value=4.6e-06  Score=79.76  Aligned_cols=104  Identities=19%  Similarity=0.285  Sum_probs=77.0

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCC
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSP  279 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p  279 (784)
                      -...|+|....+|..||++|++|+.|+++.|-+|.|...++      +                  +.++|.+..   +|
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~------d------------------~~~fI~naL---sP   88 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSS------D------------------LERIVKNLF---PG   88 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCS------S------------------HHHHHHHHS---TT
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCC------C------------------HHHHHHHhc---CC
Confidence            47789999999999999999999999999999999986542      1                  223333321   12


Q ss_pred             cccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEec
Q 003942          280 SLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLI  332 (784)
Q Consensus       280 ~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~  332 (784)
                      ..+..-..  ...+......+.|+.+..++.|||+|.||+-..+.||.+|.|.
T Consensus        89 A~V~~V~i--~~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           89 VKIESINV--RERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             SCEEEEEE--EEETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             ceEEEEEE--eecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            21110000  0002446778899999999999999999999999999998875

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

Probab=97.77  E-value=1.1e-05  Score=95.26  Aligned_cols=68  Identities=24%  Similarity=0.490  Sum_probs=12.8

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcccC
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQTVR  372 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~~~r  372 (784)
                      .....|.|+.++++.|||+||.+||.|+++|||+|.|..          +.+|.|.+. .+.+++|+++|+.++.+...
T Consensus       569 p~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d----------dG~v~I~~~~~~~~~~A~~~i~~i~~~~~v  637 (726)
T 4aid_A          569 PKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND----------DGVVKVSASDGAKIKAAIDWIKSITDEAEV  637 (726)
T ss_dssp             CC-----------------------------------------------------CCSCHHHHHHHHHC----------
T ss_pred             CeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC----------CceEEEEeCCHHHHHHHHHHHHHHhhhhcC
Confidence            346788999999999999999999999999999999852          467888887 88999999999998876433

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

Probab=97.54  E-value=3.1e-05  Score=91.55  Aligned_cols=68  Identities=28%  Similarity=0.462  Sum_probs=13.3

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhhh
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~~  274 (784)
                      ......|.|+.++++.|||++|++||.|.++||++|.|..+         ..|.|.+ +.+.+++|+++|+.++.+..
T Consensus       568 ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~dd---------G~v~I~~~~~~~~~~A~~~i~~i~~~~~  636 (726)
T 4aid_A          568 APKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDD---------GVVKVSASDGAKIKAAIDWIKSITDEAE  636 (726)
T ss_dssp             CCC----------------------------------------------------CCSCHHHHHHHHHC---------
T ss_pred             CCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEECC---------ceEEEEeCCHHHHHHHHHHHHHHhhhhc
Confidence            35578899999999999999999999999999999999743         4677777 78999999999999987653

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.37  E-value=0.00023  Score=66.61  Aligned_cols=70  Identities=13%  Similarity=0.186  Sum_probs=60.5

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      .-+.|.|...+++.|||++|+.|+.|+..|.+.|+|..-.    .+..-.|+|.|+...=.+|+.+|..+..-.
T Consensus        56 dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~----s~g~tEVtIfG~~~~Q~rak~MI~sLA~~h  125 (140)
T 3v69_A           56 DPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWG----PERRAEIWIFGPPPFRRDVDRMLTDLAHYC  125 (140)
T ss_dssp             SCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC----TTSCEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC----CCCcEEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            3567899999999999999999999999999999998642    235678999999999999999999887654

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.20  E-value=1.6e-05  Score=76.11  Aligned_cols=104  Identities=13%  Similarity=0.151  Sum_probs=73.5

Q ss_pred             ccceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCC-C
Q 003942          116 EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPS-S  194 (784)
Q Consensus       116 ~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~-~  194 (784)
                      .....+.+....+|..||++|.+|+.|.++.+.+|+|-.-+...                 +.+|...|.-.....-. .
T Consensus        35 ~dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~d~-----------------~~fI~naLsPA~V~~V~i~   97 (144)
T 2cxc_A           35 NNRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSSDL-----------------ERIVKNLFPGVKIESINVR   97 (144)
T ss_dssp             GTEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCSSH-----------------HHHHHHHSTTSCEEEEEEE
T ss_pred             CCEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCCCH-----------------HHHHHHhcCCceEEEEEEe
Confidence            34557888888999999999999999997778888776655432                 12222222211110000 0


Q ss_pred             CCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEc
Q 003942          195 TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT  236 (784)
Q Consensus       195 ~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~  236 (784)
                      ..+......+.|+....+++|||+|.|+|-+.+-||.+|.|.
T Consensus        98 ~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           98 ERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             EETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             ecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            002346788999999999999999999999999999888775

>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=96.91  E-value=0.00078  Score=69.77  Aligned_cols=104  Identities=26%  Similarity=0.395  Sum_probs=72.2

Q ss_pred             EEEEEecC-----CccceeeccCcchHhhH-HhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          201 SRKIEVPN-----NKVGVLIGKAGDTIRYL-QYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       201 t~rI~VP~-----~~vG~IIGkgG~tIK~I-q~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      ..+|.|-+     +-||..||++|.+|+.| ++-.|-+|.|...++      +              ...+|...|.   
T Consensus       113 R~KiAV~s~d~~iDpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~------d--------------p~~fi~nals---  169 (251)
T 2asb_A          113 RSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYDD------D--------------PARFVANALS---  169 (251)
T ss_dssp             EEEEEEEESSTTCCHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS------S--------------HHHHHHHHTT---
T ss_pred             eeEEEEEcCCCCCCHHHHHhCCCchHHHHHHHHhCCCeEEEEEecC------C--------------HHHHHHhccC---
Confidence            34555544     35999999999999999 777889999986542      1              1222322222   


Q ss_pred             cCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 003942          275 AGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQ  334 (784)
Q Consensus       275 ~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~  334 (784)
                          |..+..-..   .......+.+.|+.+..++.|||+|.||+-..+.||.+|.|...
T Consensus       170 ----PA~V~~V~i---~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  222 (251)
T 2asb_A          170 ----PAKVVSVSV---IDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  222 (251)
T ss_dssp             ----TSCCSEEEE---EETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             ----CcceEEEEE---EcCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEH
Confidence                211110000   01123578899999999999999999999999999999999754

>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=96.85  E-value=0.00089  Score=72.95  Aligned_cols=105  Identities=28%  Similarity=0.355  Sum_probs=74.6

Q ss_pred             eEEEEEecC-----CccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          200 MSRKIEVPN-----NKVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       200 ~t~rI~VP~-----~~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      ...+|.|-+     +-||..||++|.+|+.|.++. |-+|.|...++      +                  +..+|.+.
T Consensus       235 ~RaKIAV~s~d~~iDpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~------d------------------p~~fi~na  290 (366)
T 1k0r_A          235 HRSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYDD------D------------------PARFVANA  290 (366)
T ss_dssp             TEEEEEEEESSTTCCHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS------S------------------HHHHHHHH
T ss_pred             CeEEEEEEeCCCCCCCcccccCCcchHHHHHHHHhCCCeEEEEEcCC------C------------------HHHHHHHh
Confidence            344666654     469999999999999999998 89999986532      1                  22233332


Q ss_pred             hcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 003942          274 DAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQ  334 (784)
Q Consensus       274 ~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~  334 (784)
                      .   +|..+..-.   ..........+.|+.+..++.|||+|.||+-..+.||++|.|..+
T Consensus       291 l---sPA~V~~V~---~~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          291 L---SPAKVVSVS---VIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             T---TTSCCSEEE---EEETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             c---CCcceeEEE---EEcCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            1   121111000   001234678999999999999999999999999999999999754

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

Probab=96.78  E-value=0.00042  Score=82.19  Aligned_cols=66  Identities=23%  Similarity=0.425  Sum_probs=0.0

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~~  370 (784)
                      .....|.|+.++++.|||++|.+||.|.++||++|.|..          +..|+|.+. .+.+++|+++|+.++.+.
T Consensus       559 p~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~----------dg~v~I~~~~~~~~~~a~~~i~~i~~~~  625 (723)
T 3cdi_A          559 PRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED----------DGTVKIAATDGEKAKHAIRRIEEITAEI  625 (723)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             ceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC----------CccEEEecCCHHHHHHHHHHHHHHhhhh
Confidence            346778999999999999999999999999999998842          567888876 678889999998877653

>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=96.62  E-value=0.00082  Score=69.58  Aligned_cols=97  Identities=19%  Similarity=0.231  Sum_probs=66.4

Q ss_pred             cccccccCCCchhhhhh-hcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEE
Q 003942          126 SVDNQQISVKEETKEVL-FSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKI  204 (784)
Q Consensus       126 ~~vg~iIGk~Ge~Ik~i-q~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI  204 (784)
                      +-+|..||++|.+|+.| ++..+.+|+|-.-+...                 ..+|...|.-.....-...+....+..+
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~dp-----------------~~fi~nalsPA~V~~V~i~~~~~~~a~V  188 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDDP-----------------ARFVANALSPAKVVSVSVIDQTARAARV  188 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSSH-----------------HHHHHHHTTTSCCSEEEEEETTTTEEEE
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecCCH-----------------HHHHHhccCCcceEEEEEEcCCCcEEEE
Confidence            34568999999999998 56777777776554432                 1222222221111100000112257899


Q ss_pred             EecCCccceeeccCcchHhhHHhhcCCEEEEccCC
Q 003942          205 EVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDA  239 (784)
Q Consensus       205 ~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~  239 (784)
                      .|+....++.|||+|.|||...+-||.+|.|....
T Consensus       189 ~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  223 (251)
T 2asb_A          189 VVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  223 (251)
T ss_dssp             EECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             EEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHH
Confidence            99999999999999999999999999999998654

>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=96.48  E-value=0.0003  Score=83.76  Aligned_cols=62  Identities=23%  Similarity=0.406  Sum_probs=22.7

Q ss_pred             cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHH
Q 003942          296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVL  367 (784)
Q Consensus       296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L  367 (784)
                      ....|.||.++++.|||++|.+||.|++++|++|.|..          +..|+|+.. ...+++|+++|+.++
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            34568899999999999999999999999999998842          567888887 678888888888776

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

Probab=96.37  E-value=0.00074  Score=80.10  Aligned_cols=67  Identities=27%  Similarity=0.382  Sum_probs=0.0

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhh
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~  273 (784)
                      ......|.|+.++++.|||++|.+||.|.++||+.|.|..         +..|.|.+ +.+.+++|+++|+.++.+.
T Consensus       558 ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~---------dg~v~I~~~~~~~~~~a~~~i~~i~~~~  625 (723)
T 3cdi_A          558 APRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED---------DGTVKIAATDGEKAKHAIRRIEEITAEI  625 (723)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             CceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC---------CccEEEecCCHHHHHHHHHHHHHHhhhh
Confidence            3567788999999999999999999999999999998874         34667766 6778888988888877654

>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=96.15  E-value=0.0018  Score=70.48  Aligned_cols=97  Identities=20%  Similarity=0.247  Sum_probs=66.9

Q ss_pred             cccccccCCCchhhhhhhccc-CceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEE
Q 003942          126 SVDNQQISVKEETKEVLFSTE-EAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKI  204 (784)
Q Consensus       126 ~~vg~iIGk~Ge~Ik~iq~~s-~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI  204 (784)
                      +-+|..||++|.+|+.|..+. +.+|+|-.-+...                 ..+|...|.-.....-...+.......+
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~dp-----------------~~fi~nalsPA~V~~V~~~~~~~~~a~V  311 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDDP-----------------ARFVANALSPAKVVSVSVIDQTARAARV  311 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSSH-----------------HHHHHHHTTTSCCSEEEEEETTTTEEEE
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhcCCcceeEEEEEcCCCcEEEE
Confidence            456799999999999998555 6677766544321                 1223333322221111000112457899


Q ss_pred             EecCCccceeeccCcchHhhHHhhcCCEEEEccCC
Q 003942          205 EVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDA  239 (784)
Q Consensus       205 ~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~  239 (784)
                      .|+....++.|||+|.|||...+-||.+|.|....
T Consensus       312 ~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  346 (366)
T 1k0r_A          312 VVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  346 (366)
T ss_dssp             EECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESS
T ss_pred             EEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHH
Confidence            99999999999999999999999999999998654

>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=96.09  E-value=0.0058  Score=66.28  Aligned_cols=95  Identities=24%  Similarity=0.412  Sum_probs=68.2

Q ss_pred             CccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccc
Q 003942          209 NKVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLA  287 (784)
Q Consensus       209 ~~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~  287 (784)
                      +-+|..||.+|.+|+.|.++. |-+|.|..-++.                        ..++|.+..   +|..+..-.-
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s~d------------------------~~~fi~nal---~Pa~v~~v~~  297 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWSDD------------------------PKQLIANAL---APATVIEVEI  297 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECCSS------------------------HHHHHHHHT---CSSCCSEEEE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecCCC------------------------HHHHHHHhc---CccEEEEEEE
Confidence            359999999999999999998 788888764321                        222333321   1211110000


Q ss_pred             hhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942          288 TAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP  333 (784)
Q Consensus       288 ~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~  333 (784)
                         .........+.|+.+..++.|||+|.||+--.+.||.+|.|..
T Consensus       298 ---~d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          298 ---LDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             ---EETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             ---EcCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence               0123467899999999999999999999999999999999964

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

Probab=95.57  E-value=0.0016  Score=77.70  Aligned_cols=64  Identities=23%  Similarity=0.352  Sum_probs=22.8

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHH
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVI  270 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI  270 (784)
                      ......|.||.++++.|||++|++||.|+++||+.|.|..         +..|+|+. +.+.+++|+++|..++
T Consensus       596 ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~---------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          596 APRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED---------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             SCBCCCC------------------CTTCCCCCSCC-----------------CCCBSSHHHHCC---------
T ss_pred             CceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC---------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            3445678899999999999999999999999999999874         34677776 6677777877777765

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=94.35  E-value=0.017  Score=62.61  Aligned_cols=96  Identities=16%  Similarity=0.164  Sum_probs=63.1

Q ss_pred             cccccccCCCchhhhhhhccc-CceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEE
Q 003942          126 SVDNQQISVKEETKEVLFSTE-EAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKI  204 (784)
Q Consensus       126 ~~vg~iIGk~Ge~Ik~iq~~s-~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI  204 (784)
                      +-+|..||.+|.+|+.+..+. +.+|.|-.-....                 ..+|...|.-.....-...+....+..+
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s~d~-----------------~~fi~nal~Pa~v~~v~~~d~~~~~~~v  307 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWSDDP-----------------KQLIANALAPATVIEVEILDKENKAARV  307 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECCSSH-----------------HHHHHHHTCSSCCSEEEEEETTTTEEEE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecCCCH-----------------HHHHHHhcCccEEEEEEEEcCCCCEEEE
Confidence            345688999999999997544 5555554433221                 1222222221111000000122457899


Q ss_pred             EecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942          205 EVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD  238 (784)
Q Consensus       205 ~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~  238 (784)
                      .|+....++.|||+|.|||...+-||.+|.|...
T Consensus       308 ~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          308 LVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             EECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            9999999999999999999999999999999754

>2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori}

Probab=87.63  E-value=0.12  Score=49.58  Aligned_cols=94  Identities=14%  Similarity=0.032  Sum_probs=55.3

Q ss_pred             chhhhhhhhhHhhhcCCCCCC-CCC-CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCc
Q 003942          172 SVEPSNVVPQQVVDNSKSDDP-SST-DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRP  249 (784)
Q Consensus       172 ~Ve~A~~lI~~ii~~~~~~~~-~~~-~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~  249 (784)
                      .++.++..|.+++....++.. ... .....++.|.|-...+|+||||.|.|++.|+--+.  +++.+..     ...-.
T Consensus         3 ~~~~~~~~L~~il~~m~~~~~~i~v~~~~~~~i~i~i~ged~glLIGK~G~TL~ALQyL~~--~~vn~~~-----~~~V~   75 (152)
T 2pt7_G            3 KLHEIKQELKDLFSHLPYKINKVEVSLYEPGVLLIDIDGEDSALLIGEKGYRYKALSYLLF--NWIHPTY-----GYSIR   75 (152)
T ss_dssp             CHHHHHHHHHHHTTTTTCCEEEEEEEEEETTEEEEEEEEGGGTTTTCGGGHHHHHHHHHHH--HHHHHHH-----SCEEE
T ss_pred             HHHHHHHHHHHHHHHcCCCceEEEEEEecCCEEEEEEecCCcceEECCCCcchHHHHHHHH--HHhhhcC-----CceEE
Confidence            356677788888875555321 110 11233567777888999999999999999987542  2222210     00112


Q ss_pred             EEEecchhhHHHHHHHHHHHHHh
Q 003942          250 VEIIGTLSNIDKAEKLINAVIAE  272 (784)
Q Consensus       250 V~I~G~~e~V~kA~~~I~elI~e  272 (784)
                      |.|.+-.+.-++.++.+...|++
T Consensus        76 LDve~YRerReetL~~lA~~~A~   98 (152)
T 2pt7_G           76 LEISTFLQNQEKVMDTQLQSVIM   98 (152)
T ss_dssp             EEETTHHHHHHHHHHHHHHHHHH
T ss_pred             EEhHHhHHHHHHHHHHHHHHHHH
Confidence            34445566666666555555554

>4hhu_A OR280; engineered protein, PSI-biology, structural genomi unknown function; HET: AE4 PG4; 2.00A {Synthetic construct}

Probab=86.91  E-value=9.8  Score=34.58  Aligned_cols=46  Identities=13%  Similarity=0.057  Sum_probs=28.4

Q ss_pred             hHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          221 TIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       221 tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      .|++.|+-.|+-.....       .++.+|.|+|.+++|.+-+..-.+.++.+
T Consensus        23 mirqarkfagtvtytl~-------gn~l~i~itgvpeqvrkelakeaerl~~e   68 (170)
T 4hhu_A           23 MIRQARKFAGTVTYTLS-------GNRLVIVITGVPEQVRKELAKEAERLKAE   68 (170)
T ss_dssp             HHHHHHHTTCEEEEEEE-------TTEEEEEEESCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhcceEEEEEe-------CCEEEEEEeCCcHHHHHHHHHHHHHHHHh
Confidence            45555665554332221       22568899999999998776655555543

>3gku_A Probable RNA-binding protein; APC21302, clostridium symbiosum ATCC 14 structural genomics, PSI-2, protein structure initiative; 2.95A {Clostridium symbiosum atcc 14940}

Probab=81.17  E-value=0.25  Score=50.40  Aligned_cols=59  Identities=24%  Similarity=0.360  Sum_probs=41.1

Q ss_pred             hhhhhhhhhHhhhcCCCCCCCCCC--CCCeEEEEEecCCccceeeccCcchHhhHHhhcCC
Q 003942          173 VEPSNVVPQQVVDNSKSDDPSSTD--DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGA  231 (784)
Q Consensus       173 Ve~A~~lI~~ii~~~~~~~~~~~~--~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGa  231 (784)
                      .+.|...|.++|....++......  ...-++.|.|.....|+||||+|.+|+.|+.-+..
T Consensus        63 ~~~a~~~L~~ll~~m~~~~~i~~~~~~~~~~i~i~i~g~d~g~LIGk~G~tLdALQyL~~~  123 (225)
T 3gku_A           63 QDKAIEFLEQVFDAMNMAVDISVEYNETEKEMNVNLKGDDMGILIGKRGQTLDSLQYLVSL  123 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCCCEEEEEEETTTTEEEEEEECHHHHHCSTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCeEEEEEEecCCCEEEEEEcCCccceeecCCCeEhHHHHHHHHH
Confidence            456788888888766654332211  11235566677778999999999999999886653

---

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	784
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	5e-21
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	6e-18
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	5e-21
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	5e-20
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	6e-19
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-18
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	9e-19
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	6e-16
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-18
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-18
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	6e-17
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	5e-16
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	7e-17
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	9e-16
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-16
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-15
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	3e-16
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	7e-15
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	4e-16
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	8e-14
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	9e-16
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	9e-15
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-15
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-14
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-15
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	7e-14
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	5e-15
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	1e-14
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	6e-13
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	4e-12
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	3e-11
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	6e-12
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	5e-10
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	2e-11
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	6e-11
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	4e-11
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	2e-10
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	2e-08
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	2e-07
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	3e-07
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	1e-04
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	8e-07
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	3e-06
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	8e-07
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	1e-06

>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 = 85.3 bits (211), Expect = 5e-21
 Identities = 26/72 (36%), Positives = 45/72 (62%), Gaps = 1/72 (1%)

Query: 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ 355
           ++    VP  K GLIIG+GGETIK +  +SGARI+ + ++ P       ++  + G  +Q
Sbjct: 1   QEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIE-LQRNPPPNADPNMKLFTIRGTPQQ 59

Query: 356 IEIAQEMIKEVL 367
           I+ A+++I+E +
Sbjct: 60  IDYARQLIEEKI 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 = 76.5 bits (188), Expect = 6e-18
 Identities = 24/68 (35%), Positives = 36/68 (52%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
              VP  K G++IGK G+TI+ +   SGA+I++ R+   +     +   I GT   ID A
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYA 63

Query: 263 EKLINAVI 270
            +LI   I
Sbjct: 64  RQLIEEKI 71

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 85.3 bits (211), Expect = 5e-21
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ 355
           E VE+ VP   VG I+G+GG+T+   Q  +GARIQ I +      G++ R V +TG    
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQ-ISKKGEFLPGTRNRRVTITGSPAA 61

Query: 356 IEIAQEMIKEVLS 368
            + AQ +I + ++
Sbjct: 62  TQAAQYLISQRVT 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 = 82.6 bits (204), Expect = 5e-20
 Identities = 23/69 (33%), Positives = 38/69 (55%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
           ++ VP N VG ++GK G T+   Q  +GA+IQI++  +  P    R V I G+ +    A
Sbjct: 6   EMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAA 65

Query: 263 EKLINAVIA 271
           + 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 = 79.4 bits (196), Expect = 6e-19
 Identities = 19/76 (25%), Positives = 41/76 (53%), Gaps = 5/76 (6%)

Query: 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTL 256
           + T++ ++ +   +VG +IGK G++++ ++  SGA+I I+     +     R + + G  
Sbjct: 1   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPE-----RIITLAGPT 55

Query: 257 SNIDKAEKLINAVIAE 272
           + I KA  +I   + E
Sbjct: 56  NAIFKAFAMIIDKLEE 71

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 78.3 bits (193), Expect = 1e-18
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
           + + +  ++VG IIG+ GE++K ++  SGARI +            ERI+ + G    I 
Sbjct: 6   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISE------GNCPERIITLAGPTNAIF 59

Query: 358 IAQEMIKEVLSQ 369
            A  MI + L +
Sbjct: 60  KAFAMIIDKLEE 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 = 79.1 bits (195), Expect = 9e-19
 Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 4/74 (5%)

Query: 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ 355
             +++ +P   VG++IGR GE IK +Q  +G RI    Q  P+   + ERI ++TG   +
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRI----QFKPDDGTTPERIAQITGPPDR 58

Query: 356 IEIAQEMIKEVLSQ 369
            + A E+I ++L  
Sbjct: 59  AQHAAEIITDLLRS 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 = 70.7 bits (173), Expect = 6e-16
 Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
            + +P   VG++IG+ G+ I+ +Q ++G +IQ   D   D     R  +I G       A
Sbjct: 6   DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD---DGTTPERIAQITGPPDRAQHA 62

Query: 263 EKLINAVIAEA 273
            ++I  ++   
Sbjct: 63  AEIITDLLRSV 73

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 78.7 bits (194), Expect = 1e-18
 Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 3/76 (3%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLS 257
           S M+ + +VP+  VG +IG+ G+ I  +Q  SG KIQI  D+   P    R   + GT  
Sbjct: 6   SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPE---RSCMLTGTPE 62

Query: 258 NIDKAEKLINAVIAEA 273
           ++  A++L++ ++ + 
Sbjct: 63  SVQSAKRLLDQIVEKG 78

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 77.9 bits (192), Expect = 2e-18
 Identities = 27/80 (33%), Positives = 43/80 (53%), Gaps = 4/80 (5%)

Query: 290 QASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRV 349
           Q   +    E KVP+  VG IIGRGGE I  +Q  SG +IQ+     P+  G  ER   +
Sbjct: 2   QQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIA----PDSGGLPERSCML 57

Query: 350 TGDMRQIEIAQEMIKEVLSQ 369
           TG    ++ A+ ++ +++ +
Sbjct: 58  TGTPESVQSAKRLLDQIVEK 77

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.0 bits (182), Expect = 6e-17
 Identities = 14/75 (18%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
             + +P E    +IG+ GE ++ L+ ++  +IQ+               +++TG    IE
Sbjct: 12  ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR------PDDPSNQIKITGTKEGIE 65

Query: 358 IAQEMIKEVLSQTVR 372
            A+  +  + ++  +
Sbjct: 66  KARHEVLLISAEQDK 80

>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 = 71.3 bits (175), Expect = 5e-16
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTL 256
            +  S  + +P      +IGK G+ ++ L+  +  KIQI R  D         ++I GT 
Sbjct: 7   QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPS-----NQIKITGTK 61

Query: 257 SNIDKAEKLINAVIAEAD 274
             I+KA   +  + AE D
Sbjct: 62  EGIEKARHEVLLISAEQD 79

>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 = 73.3 bits (180), Expect = 7e-17
 Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 4/71 (5%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
            E+ +PN  +G IIGR G  I  ++  SGA+I++        +GS  R V +TG    I 
Sbjct: 4   HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV----EGSSGRQVTITGSAASIS 59

Query: 358 IAQEMIKEVLS 368
           +AQ +I   LS
Sbjct: 60  LAQYLINARLS 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 = 70.2 bits (172), Expect = 9e-16
 Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 3/71 (4%)

Query: 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNID 260
           + ++ +PNN +G +IG+ G  I  ++  SGA+I+I    +       R V I G+ ++I 
Sbjct: 3   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSG---RQVTITGSAASIS 59

Query: 261 KAEKLINAVIA 271
            A+ LINA ++
Sbjct: 60  LAQYLINARLS 70

>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 = 72.2 bits (177), Expect = 2e-16
 Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 4/77 (5%)

Query: 293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD 352
           G     ++ +P +  G IIG+GG+ IK ++  SGA I++        +GS++RI+ +TG 
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP----LEGSEDRIITITGT 56

Query: 353 MRQIEIAQEMIKEVLSQ 369
             QI+ AQ +++  + Q
Sbjct: 57  QDQIQNAQYLLQNSVKQ 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 = 70.3 bits (172), Expect = 1e-15
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLS 257
             ++ ++ +P +  G +IGK G  I+ +++ SGA I+I         +  R + I GT  
Sbjct: 2   PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQD 58

Query: 258 NIDKAEKLINAVIAE 272
            I  A+ L+   + +
Sbjct: 59  QIQNAQYLLQNSVKQ 73

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.2 bits (177), Expect = 3e-16
 Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 3/73 (4%)

Query: 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQI 356
           ++ + V  +    IIGR G  I  ++      IQ   +         +  + +TG  +  
Sbjct: 11  KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG---NQPQDQITITGYEKNT 67

Query: 357 EIAQEMIKEVLSQ 369
           E A++ I  ++ +
Sbjct: 68  EAARDAILRIVGE 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 = 67.9 bits (166), Expect = 7e-15
 Identities = 14/72 (19%), Positives = 25/72 (34%), Gaps = 2/72 (2%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
            + V       +IG+ G  I  ++      IQ       D +     + I G   N + A
Sbjct: 13  SVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPD--KDDGNQPQDQITITGYEKNTEAA 70

Query: 263 EKLINAVIAEAD 274
              I  ++ E +
Sbjct: 71  RDAILRIVGELE 82

>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 = 71.3 bits (175), Expect = 4e-16
 Identities = 17/73 (23%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ 355
           + VEI + ++    +IG+ G  I  ++ +    ++ IP      D  K  ++R+ GD + 
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVR-IPP-----DSEKSNLIRIEGDPQG 58

Query: 356 IEIAQEMIKEVLS 368
           ++ A+  + E+ S
Sbjct: 59  VQQAKRELLELAS 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 = 64.8 bits (158), Expect = 8e-14
 Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTL 256
           +     +I + +     LIGK+G  I  ++      ++I  D++         + I G  
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKS-----NLIRIEGDP 56

Query: 257 SNIDKAEKLINAVIA 271
             + +A++ +  + +
Sbjct: 57  QGVQQAKRELLELAS 71

>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 = 70.9 bits (174), Expect = 9e-16
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 9/74 (12%)

Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAE 263
           + +   +V  +IGK G  I+ L+     +I + ++           + + G    +  AE
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQN---------GLIWVNGDRRKVSIAE 55

Query: 264 KLINAVIAEADAGG 277
           + I  +  EA   G
Sbjct: 56  EAIYLIEQEAHTEG 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 = 67.8 bits (166), Expect = 9e-15
 Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 10/70 (14%)

Query: 300 IKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIA 359
           + +   +V  +IG+ G  IK L++    +I +           +  ++ V GD R++ IA
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVV----------GQNGLIWVNGDRRKVSIA 54

Query: 360 QEMIKEVLSQ 369
           +E I  +  +
Sbjct: 55  EEAIYLIEQE 64

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 70.0 bits (171), Expect = 1e-15
 Identities = 27/72 (37%), Positives = 46/72 (63%), Gaps = 2/72 (2%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
            EI +P  K GL+IG+GGETIK LQ R+G ++ +I       +   ++ +R+TGD  +++
Sbjct: 10  QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQD--GPQNTGADKPLRITGDPYKVQ 67

Query: 358 IAQEMIKEVLSQ 369
            A+EM+ E++  
Sbjct: 68  QAKEMVLELIRD 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 = 67.7 bits (165), Expect = 1e-14
 Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTL 256
                ++I +P +K G++IGK G+TI+ LQ  +G K+ + +D       A +P+ I G  
Sbjct: 5   PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGP-QNTGADKPLRITGDP 63

Query: 257 SNIDKAEKLINAVIAE 272
             + +A++++  +I +
Sbjct: 64  YKVQQAKEMVLELIRD 79

>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 = 69.8 bits (171), Expect = 2e-15
 Identities = 13/72 (18%), Positives = 31/72 (43%), Gaps = 6/72 (8%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
           +E++VP +    +IG+ G  I+ +       I +           +  I+ +TG    ++
Sbjct: 12  IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA------PELQSDIIAITGLAANLD 65

Query: 358 IAQEMIKEVLSQ 369
            A+  + E + +
Sbjct: 66  RAKAGLLERVKE 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 = 65.6 bits (160), Expect = 7e-14
 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNI 259
           ++ ++EVP +    +IG+ G  IR +       I +              + I G  +N+
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQS-----DIIAITGLAANL 64

Query: 260 DKAEKLINAVIAEADA 275
           D+A+  +   + E  A
Sbjct: 65  DRAKAGLLERVKELQA 80

>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 = 5e-15
 Identities = 24/81 (29%), Positives = 46/81 (56%), Gaps = 1/81 (1%)

Query: 195 TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG 254
           T+++ +  ++ VP   VG +IG+ G+TIR +   SGAKI   ++++      +R ++I G
Sbjct: 10  TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTL-LLSRLIKISG 68

Query: 255 TLSNIDKAEKLINAVIAEADA 275
           T   +  A+ LI   ++E + 
Sbjct: 69  TQKEVAAAKHLILEKVSEDEE 89

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.5 bits (167), Expect = 1e-14
 Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 2/85 (2%)

Query: 285 GLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKE 344
           G +           ++ VP   VG IIGRGGETI+ +   SGA+I    +   EG     
Sbjct: 4   GSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKE--SEGTLLLS 61

Query: 345 RIVRVTGDMRQIEIAQEMIKEVLSQ 369
           R+++++G  +++  A+ +I E +S+
Sbjct: 62  RLIKISGTQKEVAAAKHLILEKVSE 86

>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 = 62.5 bits (152), Expect = 6e-13
 Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 9/75 (12%)

Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357
            ++ + +     IIG  G+ I+ +       I+      P+        V VTG    +E
Sbjct: 12  EDVPLDHRVHARIIGARGKAIRKIMDEFKVDIR-----FPQSGAPDPNCVTVTGLPENVE 66

Query: 358 IAQEMI----KEVLS 368
            A + I    +E L+
Sbjct: 67  EAIDHILNLEEEYLA 81

>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 = 60.2 bits (146), Expect = 4e-12
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 4/76 (5%)

Query: 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTL 256
           +  +S  + + +     +IG  G  IR +       I+  +    DP      V + G  
Sbjct: 7   EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDP----NCVTVTGLP 62

Query: 257 SNIDKAEKLINAVIAE 272
            N+++A   I  +  E
Sbjct: 63  ENVEEAIDHILNLEEE 78

>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 = 61.3 bits (149), Expect = 2e-12
 Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 6/71 (8%)

Query: 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGS-KERIVRVTGDMRQ 355
           ++ +KV  E++G +IG  GE    +  R+G  I +  +     +                
Sbjct: 4   RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE-----NSMVIVEPEAEGIPPVN 58

Query: 356 IEIAQEMIKEV 366
           +  A E++K +
Sbjct: 59  LMKAAEVVKAI 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 = 57.9 bits (140), Expect = 3e-11
 Identities = 12/66 (18%), Positives = 28/66 (42%), Gaps = 3/66 (4%)

Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAE 263
           ++V   ++G +IG  G+    +   +G  I +  +   +      P        N+ KA 
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE---NSMVIVEPEAEGIPPVNLMKAA 63

Query: 264 KLINAV 269
           +++ A+
Sbjct: 64  EVVKAI 69

>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 = 59.9 bits (145), Expect = 6e-12
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 7/74 (9%)

Query: 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRS-GARIQLIPQHLPEGDGSKERIVRVTGDMRQ 355
           +VE+ +P +    +IG  G  I+ +     G  I          +GS    V + G    
Sbjct: 11  EVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV------EGSGSDTVVIRGPSSD 64

Query: 356 IEIAQEMIKEVLSQ 369
           +E A++ +  +  +
Sbjct: 65  VEKAKKQLLHLAEE 78

>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 = 54.5 bits (131), Expect = 5e-10
 Identities = 17/80 (21%), Positives = 29/80 (36%), Gaps = 6/80 (7%)

Query: 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGT 255
            +    ++ +P      LIG  G  IR +     G  I    +           V I G 
Sbjct: 7   ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGS-----DTVVIRGP 61

Query: 256 LSNIDKAEKLINAVIAEADA 275
            S+++KA+K +  +  E   
Sbjct: 62  SSDVEKAKKQLLHLAEEKQT 81

>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 = 57.8 bits (140), Expect = 2e-11
 Identities = 12/71 (16%), Positives = 23/71 (32%), Gaps = 10/71 (14%)

Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT-LSNIDKA 262
           I++   KV  +IGK       L   SG  I +  +           +        + +  
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGR---------IWATCPSRFSEEIL 55

Query: 263 EKLINAVIAEA 273
            + I  +  E+
Sbjct: 56  IEAIRKIENES 66

>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 = 56.3 bits (136), Expect = 6e-11
 Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 11/71 (15%)

Query: 300 IKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEI 358
           I +   KV  +IG+     + L ++SG  I +          +    +  T       EI
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFV----------ANNGRIWATCPSRFSEEI 54

Query: 359 AQEMIKEVLSQ 369
             E I+++ ++
Sbjct: 55  LIEAIRKIENE 65

>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 = 57.4 bits (139), Expect = 4e-11
 Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 13/85 (15%)

Query: 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT-LSNI 259
            + +E+   KV  +IG+    ++ L+  +  KI + R+           + +        
Sbjct: 2   GKIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNGR---------IHLECPNEDLE 52

Query: 260 DKAEKLINAVIAEADAGGSPSLVAR 284
             A   I  +  EA   G   L  R
Sbjct: 53  AIAVMAIKIIDEEAYTSG---LTKR 74

>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 = 55.9 bits (135), Expect = 2e-10
 Identities = 13/68 (19%), Positives = 28/68 (41%), Gaps = 11/68 (16%)

Query: 300 IKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEI 358
           +++   KV  +IGR    +K L+ ++  +I +        +G     + +   +     I
Sbjct: 5   VEISPAKVPRVIGRKMSMLKTLEEKTECKIFV------ARNG----RIHLECPNEDLEAI 54

Query: 359 AQEMIKEV 366
           A   IK +
Sbjct: 55  AVMAIKII 62

>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 = 49.9 bits (119), Expect = 2e-08
 Identities = 11/68 (16%), Positives = 22/68 (32%), Gaps = 7/68 (10%)

Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEI 358
           E  V  + +GL IG  G  I+  +   G     + +                     ++ 
Sbjct: 11  EFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED-------TGTFRIYGESADAVKK 63

Query: 359 AQEMIKEV 366
           A+  ++ V
Sbjct: 64  ARGFLEFV 71

>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 = 13/76 (17%), Positives = 23/76 (30%), Gaps = 8/76 (10%)

Query: 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TL 256
           +    +  V  + +G+ IG  G  I+  +   G                T    I G + 
Sbjct: 6   AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIE-------LDEDTGTFRIYGESA 58

Query: 257 SNIDKAEKLINAVIAE 272
             + KA   +  V   
Sbjct: 59  DAVKKARGFLEFVEDF 74

>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 = 46.8 bits (111), Expect = 3e-07
 Identities = 17/96 (17%), Positives = 37/96 (38%), Gaps = 13/96 (13%)

Query: 277 GSPSLVARGLAT--AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTR-SGARIQLIP 333
           G P  + + L    A+A+       +  P+     IIG+ G+ +  +  +     I+   
Sbjct: 1   GEPEKLGQALTEVYAKANSFTV-SSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIE-FT 58

Query: 334 QHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369
           +         E  + + G    + +AQE I+ ++  
Sbjct: 59  EG--------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 = 39.1 bits (91), Expect = 1e-04
 Identities = 11/77 (14%), Positives = 27/77 (35%), Gaps = 9/77 (11%)

Query: 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN-SGAKIQITRDADADPHAATRPVEIIGT 255
           +S     +  P+     +IGK G  +  +        I+ T             + + G 
Sbjct: 18  NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG--------EDKITLEGP 69

Query: 256 LSNIDKAEKLINAVIAE 272
             ++  A++ I  ++ +
Sbjct: 70  TEDVSVAQEQIEGMVKD 86

>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 = 44.3 bits (105), Expect = 8e-07
 Identities = 11/31 (35%), Positives = 19/31 (61%)

Query: 300 IKVPNEKVGLIIGRGGETIKGLQTRSGARIQ 330
           +K+P +K+G +IG   + I  +Q  +GA I 
Sbjct: 7   VKIPVDKIGEVIGPKRQMINQIQEDTGAEIT 37

>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 = 42.7 bits (101), Expect = 3e-06
 Identities = 12/36 (33%), Positives = 22/36 (61%)

Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238
            +++P +K+G +IG     I  +Q ++GA+I I  D
Sbjct: 6   TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDD 41

>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 = 45.9 bits (109), Expect = 8e-07
 Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 11/61 (18%)

Query: 307 VGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEV 366
            G IIG GG   + ++  +   I +               V + GD  +   A++ I+ +
Sbjct: 24  KGRIIGEGGRARRTIEEMTDTYINV------GEYE-----VAIIGDYERAMAAKQAIEML 72

Query: 367 L 367
            
Sbjct: 73  A 73

>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 = 45.5 bits (108), Expect = 1e-06
 Identities = 12/66 (18%), Positives = 21/66 (31%), Gaps = 10/66 (15%)

Query: 211 VGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVI 270
            G +IG+ G   R ++  +   I +              V IIG       A++ I  + 
Sbjct: 24  KGRIIGEGGRARRTIEEMTDTYINVGEY----------EVAIIGDYERAMAAKQAIEMLA 73

Query: 271 AEADAG 276
                 
Sbjct: 74  EGRMHS 79

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	784
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.56
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.55
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.54
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.53
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.53
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.51
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.5
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.5
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.49
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.48
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.48
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.47
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.46
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.45
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.45
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.43
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.41
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.39
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.32
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.31
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.3
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.28
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.27
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.24
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.24
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.23
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.22
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.22
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.18
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.17
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.1
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.06
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.89
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.88
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.79
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.77
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.71
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.69
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.64
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.47
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.43
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.35
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.34
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.3
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.15
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.09
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.16
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.13
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.29
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	93.93
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	92.04
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	89.31
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	88.35
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	84.84
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	80.68

>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=99.56  E-value=1.8e-15  Score=126.27  Aligned_cols=70  Identities=37%  Similarity=0.642  Sum_probs=63.2

Q ss_pred             EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 003942          297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVL  367 (784)
Q Consensus       297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L  367 (784)
                      +++|.||++++|+||||+|++||+|+++|||+|+|..+.. ....+.+|+|+|+|++++|++|++||.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~-~~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPP-PNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT-TTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCC-CCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            5789999999999999999999999999999999987553 334567899999999999999999999875

>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=99.55  E-value=2.1e-15  Score=126.88  Aligned_cols=71  Identities=35%  Similarity=0.659  Sum_probs=64.6

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ...++|.||.+++|+||||+|++||+|+++|||+|+|....    +...+|+|+|+|+.++|++|++||.++|++
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~----~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   72 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD----GTTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT----TSCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCC----CCCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            35789999999999999999999999999999999997642    456789999999999999999999999975

>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=99.54  E-value=4.8e-15  Score=124.69  Aligned_cols=72  Identities=36%  Similarity=0.529  Sum_probs=64.0

Q ss_pred             cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942          296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS  368 (784)
Q Consensus       296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~  368 (784)
                      +.++|.||++++|+||||+|++||+|+++|||+|+|.++.. ....+.+|+|+|+|+.++|++|++||+++|+
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~-~~~~~~~r~v~I~G~~~~v~~A~~~I~~~is   74 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGE-FLPGTRNRRVTITGSPAATQAAQYLISQRVT   74 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTC-CSTTCCEEEEEEEESHHHHHHHHHHHHHHCC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCC-CCCCCCceEEEEEeCHHHHHHHHHHHHHHcC
Confidence            46899999999999999999999999999999999976442 2345679999999999999999999999873

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=3.8e-15  Score=123.97  Aligned_cols=69  Identities=38%  Similarity=0.596  Sum_probs=62.8

Q ss_pred             cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942          296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS  368 (784)
Q Consensus       296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~  368 (784)
                      .+.+|.||++++|+||||+|++||+|+++|||+|.|.+.    .+++.+|+|+|+|++++|++|+.||+++|+
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            478999999999999999999999999999999999653    345678999999999999999999999873

>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=6.3e-15  Score=124.10  Aligned_cols=71  Identities=34%  Similarity=0.604  Sum_probs=64.8

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ..+.+|.||.+++|+||||+|++||+|+++|||+|+|...    .+.+.+|+|+|+|+.++|++|+.||.++|++
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            4578999999999999999999999999999999999653    3457899999999999999999999999975

>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=99.51  E-value=5.8e-15  Score=126.34  Aligned_cols=74  Identities=36%  Similarity=0.660  Sum_probs=66.7

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ...+.+|+||.+++|+||||+|++||+|+++|||+|+|.++.  ....+.+|+|+|+|++++|++|+.||.++|++
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            467889999999999999999999999999999999997643  33456799999999999999999999999965

>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=8e-15  Score=122.32  Aligned_cols=69  Identities=32%  Similarity=0.507  Sum_probs=63.3

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ..+++|+||.+++|+||||+|++||+|+++|||+|+|.+.      ...+|+|+|+|++++|++|+.||.++|++
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            4678999999999999999999999999999999999653      34589999999999999999999999975

>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=99.50  E-value=8.1e-15  Score=122.27  Aligned_cols=70  Identities=34%  Similarity=0.565  Sum_probs=64.3

Q ss_pred             EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHH
Q 003942          201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVI  270 (784)
Q Consensus       201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI  270 (784)
                      +++|+||.++||+||||+|++||+|+++|||+|+|..+.+....+.+|+|+|+|+.++|++|+++|.++|
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            5789999999999999999999999999999999987765556677899999999999999999999875

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=1.1e-14  Score=122.36  Aligned_cols=71  Identities=32%  Similarity=0.484  Sum_probs=66.5

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHH
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVI  270 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI  270 (784)
                      .+++|+||.++||+||||+|++||+|+++|||+|.|.++.+..+++.+|+|+|+|+.++|++|+++|+++|
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            46899999999999999999999999999999999998776677788999999999999999999999876

>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=1.9e-14  Score=122.42  Aligned_cols=74  Identities=35%  Similarity=0.625  Sum_probs=66.8

Q ss_pred             CCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      ....+.+|.||.+++|+|||++|++|++|+++|||+|.|.+.    .+++.+|+|+|+|+.++|++|+.||.++|++.
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~----~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD----SGGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSC----CTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCC----CCCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            346788999999999999999999999999999999999753    34567899999999999999999999999864

>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=99.48  E-value=9.6e-15  Score=121.85  Aligned_cols=70  Identities=27%  Similarity=0.477  Sum_probs=64.6

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE  272 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e  272 (784)
                      ..++++|+||.+++|+||||+|++||+|+++|||+|+|.++     .+.+|+|+|+|+.++|.+|+.+|.++|+|
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~-----~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-----CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC-----CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            35799999999999999999999999999999999999864     35589999999999999999999999975

>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=99.47  E-value=3.5e-14  Score=119.42  Aligned_cols=72  Identities=26%  Similarity=0.493  Sum_probs=66.2

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      .++++|+||.++||+||||+|++||+|+++|||+|.|...   .+++.+|+|+|+|+.++|++|+++|.++|++.
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            4789999999999999999999999999999999999754   34567899999999999999999999999875

>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=99.46  E-value=2.3e-14  Score=122.52  Aligned_cols=76  Identities=28%  Similarity=0.554  Sum_probs=68.5

Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE  272 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e  272 (784)
                      ....++++|+||..++|+||||+|++||+|+++|||+|.|.++.+ .+.+.+|+|+|+|+.++|.+|+++|+++|+|
T Consensus         4 ~~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~-~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           4 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGP-QNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCC-CSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CCccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCC-CCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            345789999999999999999999999999999999999987533 3456789999999999999999999999976

>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=99.45  E-value=2.4e-14  Score=120.27  Aligned_cols=72  Identities=24%  Similarity=0.479  Sum_probs=65.9

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      ..+++|.||.+++|+||||+|+|||+|+++|||+|+|....   ..+.+|+|+|+|+.++|.+|+++|+++|++.
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            46899999999999999999999999999999999998653   3566899999999999999999999999874

>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=4.8e-14  Score=126.15  Aligned_cols=75  Identities=33%  Similarity=0.564  Sum_probs=66.2

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      ...+.+|.||.+++|+||||+|++||+|+++|||+|.|.+..  ......+|+|+|+|+.++|++|+.||.++|++.
T Consensus        13 ~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~--~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES--EGTLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSS--CCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCC--CCCCCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            456788999999999999999999999999999999997643  233457899999999999999999999999753

>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=99.43  E-value=4.3e-14  Score=117.50  Aligned_cols=68  Identities=34%  Similarity=0.560  Sum_probs=62.7

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHH
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVI  270 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI  270 (784)
                      ++.+|+||.++||+||||+|++||+|+++|||+|+|.+.   ..++.+|+|+|+|+.++|++|+.+|.++|
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            689999999999999999999999999999999999754   34567899999999999999999999876

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=1.4e-13  Score=123.05  Aligned_cols=78  Identities=29%  Similarity=0.536  Sum_probs=68.9

Q ss_pred             CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      ....++++|+||..+||+||||+|.+||+|+++|||+|.|.++.+. ....+|+|+|+|+.++|.+|+++|.++|++..
T Consensus        11 ~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~-~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T d1we8a_          11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG-TLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC-SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC-CCCCccEEEEEeCHHHHHHHHHHHHHHHhCcH
Confidence            4556889999999999999999999999999999999999876432 24467999999999999999999999998764

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.39  E-value=1.1e-13  Score=117.50  Aligned_cols=74  Identities=31%  Similarity=0.582  Sum_probs=67.4

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      ...++.+|+||..++|+|||++|.+||+|+++|||+|.|.+.   ..++.+|.|+|+|+.++|++|+.+|.++|.+.
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~---~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD---SGGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSC---CTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCC---CCCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            346899999999999999999999999999999999999864   33567899999999999999999999999874

>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=99.34  E-value=4.1e-13  Score=111.81  Aligned_cols=68  Identities=21%  Similarity=0.437  Sum_probs=61.6

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVL  367 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L  367 (784)
                      ....++|.||.+++++|||++|++|++|+++|||+|+|.++      .+.++.|+|+|+.++|++|+++|++++
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~------~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD------SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC------CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC------CCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            45678999999999999999999999999999999999543      356789999999999999999999875

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=5.5e-13  Score=113.83  Aligned_cols=73  Identities=18%  Similarity=0.203  Sum_probs=64.0

Q ss_pred             CCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      ....+.+|.||.+++++|||++|++|++|+++|||+|+|.+..     +...++|+|+|+.++|++|+++|++++++.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-----~~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG-----APDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT-----CSCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCcc-----CCCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            3456789999999999999999999999999999999996532     234678999999999999999999999864

>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=4.8e-13  Score=114.19  Aligned_cols=71  Identities=20%  Similarity=0.433  Sum_probs=64.2

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      ...+.+|.||..++|+|||++|++|++|+++|||+|.|.+.      ++.++.|+|+|+.++|++|+.+|+++|++.
T Consensus         8 ~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~------~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           8 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP------DDPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT------TSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC------CCCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            45688999999999999999999999999999999999542      356789999999999999999999999764

>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=99.34  E-value=8.1e-13  Score=113.49  Aligned_cols=72  Identities=19%  Similarity=0.320  Sum_probs=64.3

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ..+++|.||..++++||||+|++||+|+++|||+|+|.+..   .....+++|+|+|+.++|++|+.+|.++|++
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~---~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKD---DGNQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTT---TCSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCC---CCCCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            35689999999999999999999999999999999997543   2356788999999999999999999999875

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=1.1e-12  Score=112.75  Aligned_cols=74  Identities=19%  Similarity=0.313  Sum_probs=66.8

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      .++++|.||..++++|||++|++||+|+++|||+|+|.+..  ..+..++.|+|+|+.++|.+|+.+|+++|.+.+
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~--~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~e   82 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKD--DGNQPQDQITITGYEKNTEAARDAILRIVGELE   82 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTT--TCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCC--CCCCCcceEEEECCHHHHHHHHHHHHHHHHhHh
Confidence            46889999999999999999999999999999999997642  345678899999999999999999999999863

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.31  E-value=8.5e-13  Score=112.85  Aligned_cols=72  Identities=21%  Similarity=0.396  Sum_probs=63.5

Q ss_pred             CCccEEEEEecCCceeeeecCCchHHHHHHHH-hCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTR-SGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~-SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      .+..+.+|.||.+++|+||||+|++|++|+++ ++|+|+|.+.      ++.+++|+|+|+.++|++|+.+|++++++.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~------~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT------TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC------CCCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            35678899999999999999999999999987 5999998542      356799999999999999999999999753

>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=99.30  E-value=1.6e-12  Score=110.98  Aligned_cols=73  Identities=18%  Similarity=0.256  Sum_probs=65.3

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      ...++.+|.||..++++|||++|++||+|+++|||+|+|....+    ...+.|+|+|+.++|.+|+++|+++++|.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~----~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC----SCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC----CCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            44578999999999999999999999999999999999986532    23578999999999999999999999986

>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=99.28  E-value=1.7e-12  Score=110.79  Aligned_cols=73  Identities=29%  Similarity=0.496  Sum_probs=66.1

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      ...++.+|.||..++|+|||++|++|++|+++|||+|.|...     .+.++.|+|+|+.++|++|+++|++++++.+
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-----~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~~   79 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-----DDPSNQIKITGTKEGIEKARHEVLLISAEQD   79 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-----TSSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC-----CCCCCEEEEEeCHHHHHHHHHHHHHHHHHHh
Confidence            345799999999999999999999999999999999999764     3457899999999999999999999999863

>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=99.27  E-value=1.7e-12  Score=113.03  Aligned_cols=86  Identities=15%  Similarity=0.241  Sum_probs=73.1

Q ss_pred             CchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCC
Q 003942          168 KEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAA  246 (784)
Q Consensus       168 G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~  246 (784)
                      |..++|.+|++.|.+.+            ...++.+|.||..++++|||++|++||+|++++ +|+|.|..+        
T Consensus         1 G~~~~v~~A~~~~~~~~------------~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~--------   60 (90)
T d2ctfa1           1 GEPEKLGQALTEVYAKA------------NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG--------   60 (90)
T ss_dssp             CCCCCCCCSCCCCCCCC------------CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS--------
T ss_pred             CCHHHHHHHHHHHHHHc------------CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC--------
Confidence            45667777776665433            235899999999999999999999999999995 899999854        


Q ss_pred             CCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          247 TRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       247 eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      +..|+|+|+.++|++|+++|++++++.
T Consensus        61 ~~~v~i~G~~~~ve~Ak~~I~~iv~el   87 (90)
T d2ctfa1          61 EDKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             SCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            468999999999999999999999985

>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=99.24  E-value=8.5e-13  Score=111.83  Aligned_cols=67  Identities=22%  Similarity=0.309  Sum_probs=58.6

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEIAQEMIKEVLS  368 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~G-t~~qV~~Ak~lI~~~L~  368 (784)
                      ...+.+|.||.+++|+|||++|++||+|+++|||+|.+.++        .+++|+|.| +.++|++|++||+.+.+
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~--------~~g~v~I~g~~~eav~~A~~~Ie~~~~   73 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE--------DTGTFRIYGESADAVKKARGFLEFVED   73 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET--------TTTEEEEEESSHHHHHHHHHHHSCCCC
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC--------CCceEEEEECCHHHHHHHHHHHHHhhe
Confidence            44577899999999999999999999999999999998643        357899999 59999999999976554

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=3.3e-12  Score=111.32  Aligned_cols=69  Identities=19%  Similarity=0.319  Sum_probs=62.7

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ..+.+|.||.+++++|||++|++|++|+++|||+|.|.+.      ++.+++|+|+|+.++|++|+.+|+++|.+
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 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP------ELQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT------TTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC------CCCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            5688999999999999999999999999999999999543      34578999999999999999999998865

>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=99.23  E-value=3.4e-12  Score=109.03  Aligned_cols=73  Identities=23%  Similarity=0.372  Sum_probs=65.0

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhh-cCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN-SGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~-TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      .+.++.+|.||..++|+||||+|++|++|+++ ++|+|.|...     +..++.|+|+|+.++|++|+++|++++++..
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~-----~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~~   80 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-----GSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   80 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-----TTTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC-----CCCCceEEEeCCHHHHHHHHHHHHHHHhhhh
Confidence            44678999999999999999999999999987 5899999754     3457899999999999999999999999863

>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=99.22  E-value=3.2e-13  Score=117.64  Aligned_cols=67  Identities=18%  Similarity=0.358  Sum_probs=60.7

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHH-hCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTR-SGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~-SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      ...+.+|.||..++++|||++|++|++|+++ ++|+|.|.+         .++.|+|+|+.++|++|+++|+++|.+
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~---------~~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE---------GEDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS---------SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC---------CCceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            4578999999999999999999999999999 589999953         357899999999999999999999875

>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=99.22  E-value=4.8e-12  Score=105.21  Aligned_cols=68  Identities=18%  Similarity=0.261  Sum_probs=61.5

Q ss_pred             CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHH
Q 003942          198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVI  270 (784)
Q Consensus       198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI  270 (784)
                      ..++.+|.||..++++|||++|++||+|+++|||+|.|.++     ++.++.|+|+|+.++|++|+++|++++
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~-----~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-----SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC-----CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC-----CCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            35788999999999999999999999999999999999854     345689999999999999999999864

>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=99.18  E-value=9e-12  Score=106.85  Aligned_cols=63  Identities=25%  Similarity=0.385  Sum_probs=57.6

Q ss_pred             EEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942          298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       298 ~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~  370 (784)
                      ..+.||.+++|+||||+|++||+|+++|||+|.|.+          ++.|+|+|+.++|+.|+.+|+.++++.
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~----------~g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ----------NGLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT----------TSEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC----------CCEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            358899999999999999999999999999999942          468999999999999999999998764

>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=99.17  E-value=8.7e-12  Score=108.56  Aligned_cols=71  Identities=21%  Similarity=0.325  Sum_probs=64.9

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      .++.+|.||..++++|||++|++||+|+++|||+|.|...     ++.++.|+|+|+.++|++|+++|++++++..
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-----~~~~~~v~I~G~~~~V~~A~~~I~~~v~e~~   79 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-----ELQSDIIAITGLAANLDRAKAGLLERVKELQ   79 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT-----TTTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC-----CCCcceEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999999999999864     3446799999999999999999999998753

>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=7.8e-12  Score=105.80  Aligned_cols=68  Identities=19%  Similarity=0.298  Sum_probs=59.6

Q ss_pred             CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHH
Q 003942          197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIA  271 (784)
Q Consensus       197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~  271 (784)
                      ...++.+|.||.+++|+|||++|++||+|+++|||+|.+..+.       ++.|+|+| +.+.|++|++||+.+.+
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~~-------~g~v~I~g~~~eav~~A~~~Ie~~~~   73 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED-------TGTFRIYGESADAVKKARGFLEFVED   73 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT-------TTEEEEEESSHHHHHHHHHHHSCCCC
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecCC-------CceEEEEECCHHHHHHHHHHHHHhhe
Confidence            3468999999999999999999999999999999999987532       46899999 79999999999975543

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.06  E-value=4.4e-11  Score=102.46  Aligned_cols=64  Identities=23%  Similarity=0.337  Sum_probs=58.7

Q ss_pred             EEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942          202 RKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       202 ~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~  274 (784)
                      ..|.||.+++|+||||+|++||+|+++|||+|+|.+         ++.|+|+|+.++|.+|+++|+.++++..
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            568999999999999999999999999999999974         3579999999999999999999998753

>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=3e-11  Score=99.79  Aligned_cols=63  Identities=22%  Similarity=0.272  Sum_probs=49.2

Q ss_pred             EEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcc
Q 003942          298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQT  370 (784)
Q Consensus       298 ~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~~  370 (784)
                      +.|.||.+++|+||||+|++||.|+++|||+|.|..          +..|+|+|. .+.|++|+++|+.++++.
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 IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN----------NGRIWATCPSRFSEEILIEAIRKIENES   66 (69)
T ss_dssp             CEEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT----------TSEEEC-----CTTCCTHHHHTTTTTTT
T ss_pred             EEEEEChhhccceECCchhHHHHHHHHHCCEEEEcC----------CCEEEEEeCCHHHHHHHHHHHHHHHHhh
Confidence            358899999999999999999999999999999942          457999996 679999999998877654

>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=98.88  E-value=1.8e-10  Score=98.41  Aligned_cols=62  Identities=26%  Similarity=0.359  Sum_probs=51.8

Q ss_pred             EEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEE-----EcCHHHHHHHHHHHHHHHh
Q 003942          298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRV-----TGDMRQIEIAQEMIKEVLS  368 (784)
Q Consensus       298 ~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I-----~Gt~~qV~~Ak~lI~~~L~  368 (784)
                      +.|.||.+++|+||||+|++||+|+++|||+|+|..+         +..|.|     .+...++++|+++|.++..
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d---------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~r   71 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE---------NSMVIVEPEAEGIPPVNLMKAAEVVKAISL   71 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT---------TTEEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC---------CCeEEEecCCccccHHHHHHHHHHHHHHhC
Confidence            5789999999999999999999999999999999643         233444     4568889999999988765

>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=90.48  Aligned_cols=64  Identities=19%  Similarity=0.200  Sum_probs=57.0

Q ss_pred             EEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhccc
Q 003942          298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQTV  371 (784)
Q Consensus       298 ~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~~~  371 (784)
                      ..+.||.++++.|||++|++||.|+++|||+|.|..          +..|.|.|. .+.+..|+.+|+.+.++..
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 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR----------NGRIHLECPNEDLEAIAVMAIKIIDEEAY   67 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET----------TTEEEEECSCHHHHHHHHHHHHHHHHCSC
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC----------CcEEEEEeCCHHHHHHHHHHHHHHHHhch
Confidence            357899999999999999999999999999999953          347999996 8999999999999987653

>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=98.77  E-value=1.6e-10  Score=95.28  Aligned_cols=62  Identities=19%  Similarity=0.169  Sum_probs=49.0

Q ss_pred             EEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhh
Q 003942          203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       203 rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~  273 (784)
                      .|.||.+++|+||||+|++||+|+++|||+|+|.++         ..|+|+| +.+++++|+++|+++++|.
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~---------g~v~I~g~~~~~v~~A~~~I~~i~~ea   66 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN---------GRIWATCPSRFSEEILIEAIRKIENES   66 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT---------SEEEC-----CTTCCTHHHHTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC---------CEEEEEeCCHHHHHHHHHHHHHHHHhh
Confidence            578999999999999999999999999999999642         4689999 5789999999998877764

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.71  E-value=3.5e-09  Score=90.35  Aligned_cols=61  Identities=20%  Similarity=0.328  Sum_probs=47.0

Q ss_pred             EEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-----chhhHHHHHHHHHHHH
Q 003942          202 RKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-----TLSNIDKAEKLINAVI  270 (784)
Q Consensus       202 ~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-----~~e~V~kA~~~I~elI  270 (784)
                      +.|.||.+++|+||||+|++||+|+++|||+|+|..+        +..|.+.+     ...++.+|+++|.++.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d--------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~   70 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE--------NSMVIVEPEAEGIPPVNLMKAAEVVKAIS   70 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT--------TTEEEEEESSTTSCHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC--------CCeEEEecCCccccHHHHHHHHHHHHHHh
Confidence            3689999999999999999999999999999999754        23555554     3455566666665543

>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=98.69  E-value=1.1e-08  Score=87.59  Aligned_cols=64  Identities=20%  Similarity=0.219  Sum_probs=57.0

Q ss_pred             EEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhhh
Q 003942          202 RKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEAD  274 (784)
Q Consensus       202 ~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~~  274 (784)
                      ..|.||.+++++|||++|++||.|+++|||+|.|..+         -.|+|.| +.+.+.+|+++|+.+.++..
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            3588999999999999999999999999999999743         3789999 68999999999999888753

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.64  E-value=8e-09  Score=91.28  Aligned_cols=53  Identities=25%  Similarity=0.352  Sum_probs=48.1

Q ss_pred             ceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942          306 KVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       306 ~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~  369 (784)
                      .+|+|||++|++||.|++.|||+|.|.           +..|+|.|+.++++.|+++|+++|.+
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~-----------d~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVG-----------EYEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEEC-----------SSEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEe-----------CCeEEEEECchhHHHHHHHHHHHHcC
Confidence            479999999999999999999999994           34688889999999999999999975

>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=98.47  E-value=4.6e-09  Score=81.93  Aligned_cols=46  Identities=24%  Similarity=0.496  Sum_probs=14.5

Q ss_pred             EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC
Q 003942          297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD  352 (784)
Q Consensus       297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt  352 (784)
                      ..+|.||.+++|.|||+||++||.|+++|||+|.|.+          +++|+|.|.
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d----------dg~v~I~a~   49 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED----------DGTIYIGAA   49 (54)
T ss_dssp             CC---------------------CHHHHSCCCC------------------CCCCB
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC----------CeEEEEEec
Confidence            3568999999999999999999999999999999953          567888775

>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=98.43  E-value=1.5e-07  Score=85.56  Aligned_cols=75  Identities=28%  Similarity=0.502  Sum_probs=60.0

Q ss_pred             CeEEEEEecCC------ccceeeccCcchHhhHHhhcCCEEEEccCCCC--------C----C-CCCCCcEEEec-chhh
Q 003942          199 TMSRKIEVPNN------KVGVLIGKAGDTIRYLQYNSGAKIQITRDADA--------D----P-HAATRPVEIIG-TLSN  258 (784)
Q Consensus       199 ~~t~rI~VP~~------~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~--------~----p-~s~eR~V~I~G-~~e~  258 (784)
                      .++.+|.||.+      +||+|||.+|.|+|+|+++|||+|.|......        .    . ......|.|++ +.+.
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~   81 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   81 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhh
Confidence            46889999985      59999999999999999999999999875321        0    0 11234677888 7789


Q ss_pred             HHHHHHHHHHHHHhh
Q 003942          259 IDKAEKLINAVIAEA  273 (784)
Q Consensus       259 V~kA~~~I~elI~e~  273 (784)
                      |++|+.+|+++|...
T Consensus        82 ~~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          82 VKKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999764

>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=98.35  E-value=3.5e-07  Score=83.00  Aligned_cols=75  Identities=25%  Similarity=0.392  Sum_probs=57.5

Q ss_pred             cEEEEEecC------CceeeeecCCchHHHHHHHHhCCeEEeccCCCC----------C--CCCCCceEEEEEcC-HHHH
Q 003942          296 EQVEIKVPN------EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLP----------E--GDGSKERIVRVTGD-MRQI  356 (784)
Q Consensus       296 ~~~~i~VP~------~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p----------~--~~~~~er~V~I~Gt-~~qV  356 (784)
                      .+.+|.||-      |+||+|||.+|.++|+|+++|||+|.|.....-          .  ......--|.|++. .+.|
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            345677765      579999999999999999999999999753310          0  01123346888887 7899


Q ss_pred             HHHHHHHHHHHhcc
Q 003942          357 EIAQEMIKEVLSQT  370 (784)
Q Consensus       357 ~~Ak~lI~~~L~~~  370 (784)
                      ++|+.+|+.+|...
T Consensus        83 ~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          83 KKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999653

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.34  E-value=1.2e-07  Score=83.54  Aligned_cols=53  Identities=23%  Similarity=0.327  Sum_probs=47.9

Q ss_pred             cceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942          211 VGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA  273 (784)
Q Consensus       211 vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~  273 (784)
                      .|+|||++|+|||.|++.|||+|.|..          ..|.|.|+.++++.|+++|+.+|.+.
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~d----------~~v~iig~~e~i~~A~~~Ie~li~~~   76 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVGE----------YEVAIIGDYERAMAAKQAIEMLAEGR   76 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEECS----------SEEEEEEEHHHHHHHHHHHHHHHTTC
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEeC----------CeEEEEECchhHHHHHHHHHHHHcCC
Confidence            699999999999999999999999963          25788899999999999999999763

>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=98.30  E-value=2.6e-08  Score=77.59  Aligned_cols=46  Identities=26%  Similarity=0.433  Sum_probs=14.5

Q ss_pred             EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecc
Q 003942          201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT  255 (784)
Q Consensus       201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~  255 (784)
                      .++|.||.+++|.|||++|++||.|+++|||+|.|.+         +..|+|++.
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d---------dg~v~I~a~   49 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED---------DGTIYIGAA   49 (54)
T ss_dssp             CC---------------------CHHHHSCCCC-----------------CCCCB
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC---------CeEEEEEec
Confidence            4679999999999999999999999999999999974         357777774

>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=98.15  E-value=6.5e-07  Score=82.21  Aligned_cols=73  Identities=22%  Similarity=0.314  Sum_probs=55.9

Q ss_pred             eEEEEEecC------CccceeeccCcchHhhHHhhcCCEEEEccCCCC--------C-------CCCCCCcEEEecc-h-
Q 003942          200 MSRKIEVPN------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADA--------D-------PHAATRPVEIIGT-L-  256 (784)
Q Consensus       200 ~t~rI~VP~------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~--------~-------p~s~eR~V~I~G~-~-  256 (784)
                      +..+|.||.      ++||+|||.+|.|+|+|+++|||+|.|......        .       ....+.-|.|++. . 
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            567889985      579999999999999999999999999986421        0       0123456788874 2 


Q ss_pred             ----hhHHHHHHHHHHHHHh
Q 003942          257 ----SNIDKAEKLINAVIAE  272 (784)
Q Consensus       257 ----e~V~kA~~~I~elI~e  272 (784)
                          ..|.+|+.+|..+|..
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                2488899999888754

>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=98.09  E-value=1.3e-06  Score=80.26  Aligned_cols=73  Identities=26%  Similarity=0.299  Sum_probs=55.1

Q ss_pred             EEEEEecC------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCC--------------CCCCCceEEEEEcCH---
Q 003942          297 QVEIKVPN------EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPE--------------GDGSKERIVRVTGDM---  353 (784)
Q Consensus       297 ~~~i~VP~------~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~--------------~~~~~er~V~I~Gt~---  353 (784)
                      +.+|.||-      |+||+|||.+|.|+|+|+++|||+|.|.....-.              ....++--|.|++..   
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            44666664      7999999999999999999999999998654210              012345568888862   


Q ss_pred             ---HHHHHHHHHHHHHHhc
Q 003942          354 ---RQIEIAQEMIKEVLSQ  369 (784)
Q Consensus       354 ---~qV~~Ak~lI~~~L~~  369 (784)
                         ..|.+|+.+|+.+|..
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               3588999999999853

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.16  E-value=0.0055  Score=48.91  Aligned_cols=41  Identities=24%  Similarity=0.408  Sum_probs=37.4

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQ  334 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~  334 (784)
                      ....+.+.|+.+...+.|||+|.|||-..+.||.+|.|..+
T Consensus        24 ~~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          24 TARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             CCcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            34578899999999999999999999999999999999764

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.13  E-value=0.0038  Score=49.85  Aligned_cols=41  Identities=29%  Similarity=0.482  Sum_probs=37.5

Q ss_pred             CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCC
Q 003942          199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDA  239 (784)
Q Consensus       199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~  239 (784)
                      .....|.|+.+...+.|||+|.|||-..+-||.+|.|..++
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~es   65 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA   65 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeCC
Confidence            34788999999999999999999999999999999998754

>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=94.29  E-value=0.012  Score=47.09  Aligned_cols=39  Identities=26%  Similarity=0.532  Sum_probs=36.1

Q ss_pred             ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942          295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP  333 (784)
Q Consensus       295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~  333 (784)
                      ...+.+.|+.+..++.|||+|.|||-..+.||.+|.|..
T Consensus        26 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          26 NKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             TTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CCEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            457889999999999999999999999999999999964

>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=93.93  E-value=0.012  Score=47.00  Aligned_cols=39  Identities=28%  Similarity=0.417  Sum_probs=36.0

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD  238 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~  238 (784)
                      ....+.|+.+..++.|||+|.|||-..+-||.+|.|...
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~   65 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI   65 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEc
Confidence            468899999999999999999999999999999999753

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=92.04  E-value=0.077  Score=44.00  Aligned_cols=60  Identities=17%  Similarity=0.067  Sum_probs=47.6

Q ss_pred             EEEecCCccceeeccCcc-hHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHH
Q 003942          203 KIEVPNNKVGVLIGKAGD-TIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIA  271 (784)
Q Consensus       203 rI~VP~~~vG~IIGkgG~-tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~  271 (784)
                      -|.|+.+++.+|||++++ .|+.|.+.+.+.|.|-.+         -.|.|.+ +.+....+.+.|.++-.
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~N---------GrIWi~~~~~~~~i~i~~aI~~~e~   65 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLN---------GKIWVKCEELSNTLACYRTIMECCQ   65 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETT---------TEEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecC---------cEEEEECCCHHHHHHHHHHHHHHHH
Confidence            467888999999999998 899999999999999753         4789999 56666665666655433

>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=89.31  E-value=0.069  Score=44.96  Aligned_cols=33  Identities=18%  Similarity=0.325  Sum_probs=28.0

Q ss_pred             CccEEEEEecCCceeeeecCCchHHHHHHHHhC
Q 003942          294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSG  326 (784)
Q Consensus       294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SG  326 (784)
                      ....++|.|....-|.||||+|++|++|++.-.
T Consensus        33 t~~~i~I~I~tarPGivIGrkG~~I~~L~~~l~   65 (92)
T d1wh9a_          33 TPTRTEIIILATRTQNVLGEKGRRIRELTAVVQ   65 (92)
T ss_dssp             CSSCEEEEEEESCHHHHHCGGGHHHHHHHHHHH
T ss_pred             CCCeEEEEEEeCCCceeeccCchhHHHHHHHHH
Confidence            345688899999999999999999999986543

>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=88.35  E-value=0.17  Score=41.85  Aligned_cols=59  Identities=12%  Similarity=0.039  Sum_probs=46.1

Q ss_pred             EEEEecCCceeeeecCCch-HHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHH
Q 003942          298 VEIKVPNEKVGLIIGRGGE-TIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEV  366 (784)
Q Consensus       298 ~~i~VP~~~vG~VIGkgG~-~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~  366 (784)
                      +-|.|+-+++.+|||++++ .|+.|.+.++|+|.|-.          ...|-|.|. .+.+.++...|..+
T Consensus         3 ~v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~----------NGrIWi~~~~~~~~i~i~~aI~~~   63 (85)
T d2ja9a2           3 MIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL----------NGKIWVKCEELSNTLACYRTIMEC   63 (85)
T ss_dssp             EEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET----------TTEEEEECSSHHHHHHHHHHHHHH
T ss_pred             EEEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec----------CcEEEEECCCHHHHHHHHHHHHHH
Confidence            4578889999999999998 89999999999999953          557889996 55555555555443

>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=84.84  E-value=0.069  Score=44.94  Aligned_cols=30  Identities=20%  Similarity=0.276  Sum_probs=26.1

Q ss_pred             eEEEEEecCCccceeeccCcchHhhHHhhc
Q 003942          200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNS  229 (784)
Q Consensus       200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~T  229 (784)
                      ..++|.|-..+-|.||||+|++|++|+++.
T Consensus        35 ~~i~I~I~tarPGivIGrkG~~I~~L~~~l   64 (92)
T d1wh9a_          35 TRTEIIILATRTQNVLGEKGRRIRELTAVV   64 (92)
T ss_dssp             SCEEEEEEESCHHHHHCGGGHHHHHHHHHH
T ss_pred             CeEEEEEEeCCCceeeccCchhHHHHHHHH
Confidence            457888999999999999999999998654

>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: GTPase Era C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.68  E-value=0.43  Score=41.38  Aligned_cols=37  Identities=24%  Similarity=0.240  Sum_probs=27.6

Q ss_pred             cEEEEEecC-CceeeeecCCchHHHHHHH--------HhCCeEEec
Q 003942          296 EQVEIKVPN-EKVGLIIGRGGETIKGLQT--------RSGARIQLI  332 (784)
Q Consensus       296 ~~~~i~VP~-~~vG~VIGkgG~~IK~Iq~--------~SGarIqI~  332 (784)
                      ....|.|.. +..+.||||+|++||+|..        ..+|+|.+.
T Consensus        49 I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~ar~~le~~~~~kV~L~   94 (113)
T d1egaa2          49 INGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQEMFEAPVHLE   94 (113)
T ss_dssp             EEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHHHTTSCEEEE
T ss_pred             EEEEEEECCcchhhhhhcccchHHHHHHHHHHHHHHHHhCCCeEEE
Confidence            445677777 6789999999999997754        456666653