Citrus Sinensis ID: 019747

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330------
Protein Sequence
METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDRLMD
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHHccEEEEEcccccccccccEEEEEEccHHHHHHHHHHHHHHHHHHHccccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHcccEEEEEEccccccccccEEEEEEccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccEEEEcccccHHHHHHHcccEEEEEccccccccccEEEEEEEccHHHHHHHHHHHHHHHHcHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccEEEEEEEEHHHHHHHHcHHHHHHHHHHHHHccEEEEcccccEcccccEEEEEEEccHHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEEcccccEEEEccccccHHHHHHHcccEEEEEcccccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHccccccccccccccccccccEEEEEEEEHHHHHHHHcHHHHHHHHHHHHHccEEEEcccccEcccccEEEEEEEccHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
metnessyvpspdvhgkrstapvkslssdptekptyirflvsnplagavigkggstindfqsqsgariqlsrsheffpgttdRIIMISGTIDEILRAVDLVIDKLLTELhaedqaddvgtktklrlivpnsscgsiigKAGATIKSFMDDSQAVIKISRldhsyyglnDRLVTLTGTLDEQMRALELILLKLSEdtlysqtmtvpytyagvffsgfhgmpygavpppvpavphntaahygpnmggrkfqnnkddrtnsltigvadehigfvvgrggrnIMEISQISgarikvsdrgdffsgtserkvtisgpqrsIRTAESMIMQKVAYASDRLMD
Flexible Loop (DISEMBL)
metnessyvpspdvhgkrstapvkslssdptekpTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGAriqlsrsheffpgttDRIIMISGTIDEILRAVDLVIDKLLTELhaedqaddvgtktklrlivpnsscgsIIGKAGATIKSFMDDSQAVIKISrldhsyygLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISqisgarikvsdrgdffsgtserkvtisgpqrsirtaesmIMQKVAYASDRLMD
Low Complexity Region (SEG)
METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGavpppvpavpHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDRLMD
Disordered region (IsUnstruct)
**********************************TYIRFLVSNPLAGAVIGKGGSTINDF******RIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPV*****************************SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVS*******************************************
Disordered Region (DISOPRED)
*************************************RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVID**********************LIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL*******************************************************************TIGVADEHIGFVVGRGGRNIMEISQISGARIKV*********TSERKVTISGPQRSIRTAESMIMQKV**A******
Disordered Region (DISEMBL)
*******************************EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDRLMD
Disordered Region (DISPRO)
*******************************EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH*******VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDRLMD
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	336	2.2.26 [Sep-21-2011]
Q80WA4	474	RNA-binding protein Nova-	yes	no	0.544	0.386	0.353	2e-25
Q2PFW9	483	RNA-binding protein Nova-	N/A	no	0.5	0.347	0.353	3e-25
Q9UNW9	492	RNA-binding protein Nova-	no	no	0.553	0.378	0.351	3e-24
Q9JKN6	507	RNA-binding protein Nova-	no	no	0.547	0.362	0.316	2e-23
P57722	371	Poly(rC)-binding protein	no	no	0.812	0.735	0.274	6e-23
P57721	371	Poly(rC)-binding protein	no	no	0.812	0.735	0.274	6e-23
O19048	356	Poly(rC)-binding protein	no	no	0.827	0.780	0.270	1e-22
P60335	356	Poly(rC)-binding protein	no	no	0.827	0.780	0.270	1e-22
Q15365	356	Poly(rC)-binding protein	no	no	0.827	0.780	0.270	1e-22
Q5E9A3	356	Poly(rC)-binding protein	no	no	0.827	0.780	0.270	1e-22

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

 Score =  116 bits (291), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 71/201 (35%), Positives = 115/201 (57%), Gaps = 18/201 (8%)

Query: 36  YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEIL 95
           +++ L+ +  AG++IGKGG TI   Q ++GA I+LS+S +F+PGTT+R+ +I GTI E L
Sbjct: 50  FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI-EAL 108

Query: 96  RAVDLVIDKLLTE-------------LHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGA 142
            AV   I + + E             L  +   +    K ++++IVPNS+ G IIGK GA
Sbjct: 109 NAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRIK-QVKIIVPNSTAGLIIGKGGA 167

Query: 143 TIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTM 202
           T+K+ M+ S A +++S+       L +R+VT++G  ++  +A+ELI+ K+ ED      +
Sbjct: 168 TVKAIMEQSGAWVQLSQKPDG-INLQERVVTVSGEPEQNRKAVELIIQKIQEDPQSGSCL 226

Query: 203 TVPYT--YAGVFFSGFHGMPY 221
            + Y      V  S   G PY
Sbjct: 227 NISYANVTGPVANSNPTGFPY 247

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 =  115 bits (289), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 65/184 (35%), Positives = 110/184 (59%), Gaps = 16/184 (8%)

Query: 36  YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEIL 95
           +++ L+ +  AG++IGKGG TI   Q ++GA I+LS+S +F+PGTT+R+ +I GT+ E L
Sbjct: 51  FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTV-EAL 109

Query: 96  RAVDLVIDKLLTE-------------LHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGA 142
            AV   I + + E             L  +   +    K ++++IVPNS+ G IIGK GA
Sbjct: 110 NAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRIK-QVKIIVPNSTAGLIIGKGGA 168

Query: 143 TIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTM 202
           T+K+ M+ S A +++S+       L +R+VT++G  ++  +A+ELI+ K+ ED      +
Sbjct: 169 TVKAIMEQSGAWVQLSQKPDG-INLQERVVTVSGEPEQNRKAVELIIQKIQEDPQSGSCL 227

Query: 203 TVPY 206
            + Y
Sbjct: 228 NISY 231

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

Macaca fascicularis (taxid: 9541)

>sp|Q9UNW9|NOVA2_HUMAN RNA-binding protein Nova-2 OS=Homo sapiens GN=NOVA2 PE=1 SV=1

 Score =  112 bits (281), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 71/202 (35%), Positives = 116/202 (57%), Gaps = 16/202 (7%)

Query: 36  YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEIL 95
           +++ L+ +  AG++IGKGG TI   Q ++GA I+LS+S +F+PGTT+R+ ++ GT  E L
Sbjct: 34  FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLVQGT-AEAL 92

Query: 96  RAVDLVIDKLLTEL-HAEDQADDVGT-----------KTKLRLIVPNSSCGSIIGKAGAT 143
            AV   I + + E+  A  + + V               + +LIVPNS+ G IIGK GAT
Sbjct: 93  NAVHSFIAEKVREIPQAMTKPEVVNILQPQTTMNPDRAKQAKLIVPNSTAGLIIGKGGAT 152

Query: 144 IKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMT 203
           +K+ M+ S A +++S+       L +R+VT++G  ++  +A+  I+ K+ ED   S  + 
Sbjct: 153 VKAVMEQSGAWVQLSQKPEG-INLQERVVTVSGEPEQVHKAVSAIVQKVQEDPQSSSCLN 211

Query: 204 VPYT-YAG-VFFSGFHGMPYGA 223
           + Y   AG V  S   G PY +
Sbjct: 212 ISYANVAGPVANSNPTGSPYAS 233

May regulate RNA splicing or metabolism in a specific subset of developing neurons (By similarity). Binds single strand RNA.

Homo sapiens (taxid: 9606)

>sp|Q9JKN6|NOVA1_MOUSE RNA-binding protein Nova-1 OS=Mus musculus GN=Nova1 PE=1 SV=2

 Score =  109 bits (273), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 71/224 (31%), Positives = 116/224 (51%), Gaps = 40/224 (17%)

Query: 36  YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEIL 95
           +++ L+ +  AG++IGKGG TI   Q ++GA I+LS+S +F+PGTT+R+ +I GTI E L
Sbjct: 51  FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI-EAL 109

Query: 96  RAVDLVIDKLLTEL----------------------------------HAEDQADDVGTK 121
            AV   I + + E+                                       +D + T 
Sbjct: 110 NAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRIKQTLPSSPTTTKSSPSDPMTTS 169

Query: 122 --TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD 179
              ++++IVPNS+ G IIGK GAT+K+ M+ S A +++S+       L +R+VT++G  +
Sbjct: 170 RANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDG-INLQERVVTVSGEPE 228

Query: 180 EQMRALELILLKLSEDTLYSQTMTVPYT--YAGVFFSGFHGMPY 221
           +  +A+ELI+ K+ ED      + + Y      V  S   G PY
Sbjct: 229 QNRKAVELIIQKIQEDPQSGSCLNISYANVTGPVANSNPTGSPY 272

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. Most likely acts to activate the inclusion of exon E3A in the glycine receptor alpha-2 chain and of exon E9 in gamma-aminobutyric-acid receptor gamma-2 subunit via a distal downstream UCAU-rich intronic splicing enhancer.

Mus musculus (taxid: 10090)

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

 Score =  108 bits (270), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 89/324 (27%), Positives = 156/324 (48%), Gaps = 51/324 (15%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           IR L+     G++IGK G T+   + +SGARI +S  +       +RI+ I+G  D I +
Sbjct: 48  IRLLMHGKEVGSIIGKKGETVKKMREESGARINISEGN-----CPERIVTITGPTDAIFK 102

Query: 97  AVDLVIDKLLTELHAEDQADDVGTK--TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV 154
           A  ++  K   ++          +K    LRL+VP S CGS+IGK G+ IK   + + A 
Sbjct: 103 AFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQ 162

Query: 155 IKIS--RLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPY----TY 208
           ++++   L +S     +R VT++GT D  ++ ++ I + + E     +  T+PY      
Sbjct: 163 VQVAGDMLPNS----TERAVTISGTPDAIIQCVKQICVVMLESP--PKGATIPYRPKPAS 216

Query: 209 AGVFFSG--------------------FHGMPYGAVP-PPV----PAVPHNT----AAHY 239
             V F+G                     H +     P PP+    PA P       ++  
Sbjct: 217 TPVIFAGGQAYTIQGQYAIPHPDQLTKLHQLAMQQTPFPPLGQTNPAFPGEKLPLHSSEE 276

Query: 240 GPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFF 299
             N+ G+    +     ++  + + ++ IG ++GR G  I EI Q+SGA+IK+++  +  
Sbjct: 277 AQNLMGQSSGLDASPPASTHELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATE-- 334

Query: 300 SGTSERKVTISGPQRSIRTAESMI 323
            G+SER++TI+G   +I  A+ +I
Sbjct: 335 -GSSERQITITGTPANISLAQYLI 357

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

Mus musculus (taxid: 10090)

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

 Score =  108 bits (270), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 89/324 (27%), Positives = 156/324 (48%), Gaps = 51/324 (15%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           IR L+     G++IGK G T+   + +SGARI +S  +       +RI+ I+G  D I +
Sbjct: 48  IRLLMHGKEVGSIIGKKGETVKKMREESGARINISEGN-----CPERIVTITGPTDAIFK 102

Query: 97  AVDLVIDKLLTELHAEDQADDVGTK--TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV 154
           A  ++  K   ++          +K    LRL+VP S CGS+IGK G+ IK   + + A 
Sbjct: 103 AFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQ 162

Query: 155 IKIS--RLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPY----TY 208
           ++++   L +S     +R VT++GT D  ++ ++ I + + E     +  T+PY      
Sbjct: 163 VQVAGDMLPNS----TERAVTISGTPDAIIQCVKQICVVMLESP--PKGATIPYRPKPAS 216

Query: 209 AGVFFSG--------------------FHGMPYGAVP-PPV----PAVPHNT----AAHY 239
             V F+G                     H +     P PP+    PA P       ++  
Sbjct: 217 TPVIFAGGQAYTIQGQYAIPHPDQLTKLHQLAMQQTPFPPLGQTNPAFPGEKLPLHSSEE 276

Query: 240 GPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFF 299
             N+ G+    +     ++  + + ++ IG ++GR G  I EI Q+SGA+IK+++  +  
Sbjct: 277 AQNLMGQSSGLDASPPASTHELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATE-- 334

Query: 300 SGTSERKVTISGPQRSIRTAESMI 323
            G+SER++TI+G   +I  A+ +I
Sbjct: 335 -GSSERQITITGTPANISLAQYLI 357

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

Homo sapiens (taxid: 9606)

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

 Score =  107 bits (268), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 94/347 (27%), Positives = 163/347 (46%), Gaps = 69/347 (19%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           IR L+     G++IGK G ++   + +SGARI +S  +       +RII ++G  + I +
Sbjct: 16  IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN-----CPERIITLTGPTNAIFK 70

Query: 97  AVDLVIDKLLTELHAEDQADDVGTK--TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV 154
           A  ++IDKL  ++++        ++    LRL+VP + CGS+IGK G  IK   + + A 
Sbjct: 71  AFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQ 130

Query: 155 IKIS--RLDHSYYGLNDRLVTLTG---TLDEQMRALELILLKLSEDTLYSQTMTVPY--- 206
           ++++   L +S     +R +T+ G   ++ E ++ + L++L+    +   + MT+PY   
Sbjct: 131 VQVAGDMLPNS----TERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPM 186

Query: 207 -TYAGVFFSGFH-------GMPYGA----VPP-------------PVPAVPHNTAA---- 237
              + V  +G         G P+       PP             P+     N  A    
Sbjct: 187 PASSPVICAGGQDRCSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQS 246

Query: 238 HYGPNMGGRKFQ----------------NNKDDRTNSLTIGVADEHIGFVVGRGGRNIME 281
           H+    GG  F                 +     T+ LTI   +  IG ++GR G NI E
Sbjct: 247 HFAMMHGGTGFAGIDSSSPEVKGYWASLDASTQTTHELTI--PNNLIGCIIGRQGANINE 304

Query: 282 ISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVA 328
           I Q+SGA+IK+++      G+S R+VTI+G   SI  A+ +I  +++
Sbjct: 305 IRQMSGAQIKIANP---VEGSSGRQVTITGSAASISLAQYLINARLS 348

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

Oryctolagus cuniculus (taxid: 9986)

>sp|P60335|PCBP1_MOUSE Poly(rC)-binding protein 1 OS=Mus musculus GN=Pcbp1 PE=1 SV=1

 Score =  107 bits (268), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 94/347 (27%), Positives = 163/347 (46%), Gaps = 69/347 (19%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           IR L+     G++IGK G ++   + +SGARI +S  +       +RII ++G  + I +
Sbjct: 16  IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN-----CPERIITLTGPTNAIFK 70

Query: 97  AVDLVIDKLLTELHAEDQADDVGTK--TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV 154
           A  ++IDKL  ++++        ++    LRL+VP + CGS+IGK G  IK   + + A 
Sbjct: 71  AFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQ 130

Query: 155 IKIS--RLDHSYYGLNDRLVTLTG---TLDEQMRALELILLKLSEDTLYSQTMTVPY--- 206
           ++++   L +S     +R +T+ G   ++ E ++ + L++L+    +   + MT+PY   
Sbjct: 131 VQVAGDMLPNS----TERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPM 186

Query: 207 -TYAGVFFSGFH-------GMPYGA----VPP-------------PVPAVPHNTAA---- 237
              + V  +G         G P+       PP             P+     N  A    
Sbjct: 187 PASSPVICAGGQDRCSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQS 246

Query: 238 HYGPNMGGRKFQ----------------NNKDDRTNSLTIGVADEHIGFVVGRGGRNIME 281
           H+    GG  F                 +     T+ LTI   +  IG ++GR G NI E
Sbjct: 247 HFAMMHGGTGFAGIDSSSPEVKGYWASLDASTQTTHELTI--PNNLIGCIIGRQGANINE 304

Query: 282 ISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVA 328
           I Q+SGA+IK+++      G+S R+VTI+G   SI  A+ +I  +++
Sbjct: 305 IRQMSGAQIKIANP---VEGSSGRQVTITGSAASISLAQYLINARLS 348

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

Mus musculus (taxid: 10090)

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

 Score =  107 bits (268), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 94/347 (27%), Positives = 163/347 (46%), Gaps = 69/347 (19%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           IR L+     G++IGK G ++   + +SGARI +S  +       +RII ++G  + I +
Sbjct: 16  IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN-----CPERIITLTGPTNAIFK 70

Query: 97  AVDLVIDKLLTELHAEDQADDVGTK--TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV 154
           A  ++IDKL  ++++        ++    LRL+VP + CGS+IGK G  IK   + + A 
Sbjct: 71  AFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQ 130

Query: 155 IKIS--RLDHSYYGLNDRLVTLTG---TLDEQMRALELILLKLSEDTLYSQTMTVPY--- 206
           ++++   L +S     +R +T+ G   ++ E ++ + L++L+    +   + MT+PY   
Sbjct: 131 VQVAGDMLPNS----TERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPM 186

Query: 207 -TYAGVFFSGFH-------GMPYGA----VPP-------------PVPAVPHNTAA---- 237
              + V  +G         G P+       PP             P+     N  A    
Sbjct: 187 PASSPVICAGGQDRCSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQS 246

Query: 238 HYGPNMGGRKFQ----------------NNKDDRTNSLTIGVADEHIGFVVGRGGRNIME 281
           H+    GG  F                 +     T+ LTI   +  IG ++GR G NI E
Sbjct: 247 HFAMMHGGTGFAGIDSSSPEVKGYWASLDASTQTTHELTI--PNNLIGCIIGRQGANINE 304

Query: 282 ISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVA 328
           I Q+SGA+IK+++      G+S R+VTI+G   SI  A+ +I  +++
Sbjct: 305 IRQMSGAQIKIANP---VEGSSGRQVTITGSAASISLAQYLINARLS 348

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

Homo sapiens (taxid: 9606)

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

 Score =  107 bits (268), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 94/347 (27%), Positives = 163/347 (46%), Gaps = 69/347 (19%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           IR L+     G++IGK G ++   + +SGARI +S  +       +RII ++G  + I +
Sbjct: 16  IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN-----CPERIITLTGPTNAIFK 70

Query: 97  AVDLVIDKLLTELHAEDQADDVGTK--TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV 154
           A  ++IDKL  ++++        ++    LRL+VP + CGS+IGK G  IK   + + A 
Sbjct: 71  AFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQ 130

Query: 155 IKIS--RLDHSYYGLNDRLVTLTG---TLDEQMRALELILLKLSEDTLYSQTMTVPY--- 206
           ++++   L +S     +R +T+ G   ++ E ++ + L++L+    +   + MT+PY   
Sbjct: 131 VQVAGDMLPNS----TERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPM 186

Query: 207 -TYAGVFFSGFH-------GMPYGA----VPP-------------PVPAVPHNTAA---- 237
              + V  +G         G P+       PP             P+     N  A    
Sbjct: 187 PASSPVICAGGQDRCSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQS 246

Query: 238 HYGPNMGGRKFQ----------------NNKDDRTNSLTIGVADEHIGFVVGRGGRNIME 281
           H+    GG  F                 +     T+ LTI   +  IG ++GR G NI E
Sbjct: 247 HFAMMHGGTGFAGIDSSSPEVKGYWASLDASTQTTHELTI--PNNLIGCIIGRQGANINE 304

Query: 282 ISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVA 328
           I Q+SGA+IK+++      G+S R+VTI+G   SI  A+ +I  +++
Sbjct: 305 IRQMSGAQIKIANP---VEGSSGRQVTITGSAASISLAQYLINARLS 348

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

Bos taurus (taxid: 9913)

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	336
356535513	337	PREDICTED: RNA-binding protein Nova-1-li	0.985	0.982	0.686	1e-126
356576359	337	PREDICTED: RNA-binding protein Nova-1-li	0.985	0.982	0.674	1e-124
146336943	334	putative KH-domain containing protein [M	0.982	0.988	0.658	1e-121
224113143	334	predicted protein [Populus trichocarpa]	0.994	1.0	0.657	1e-120
297810533	334	hypothetical protein ARALYDRAFT_487225 [	0.994	1.0	0.619	1e-118
30680512	334	binding to TOMV RNA 1L (long form) prote	0.994	1.0	0.613	1e-117
359486525	309	PREDICTED: RNA-binding protein Nova-1-li	0.919	1.0	0.648	1e-116
296085941	357	unnamed protein product [Vitis vinifera]	0.919	0.865	0.648	1e-116
255583738	314	Far upstream element-binding protein, pu	0.931	0.996	0.635	1e-114
449449385	326	PREDICTED: RNA-binding protein Nova-2-li	0.934	0.963	0.626	1e-110

>gi|356535513|ref|XP_003536289.1| PREDICTED: RNA-binding protein Nova-1-like [Glycine max]

 Score =  456 bits (1172), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 230/335 (68%), Positives = 276/335 (82%), Gaps = 4/335 (1%)

Query: 1   METNESSYVPSPDVHGKRSTAPV-KSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTIND 59
           ME+ ESSYV SP+   K + +P  KS S D  EKPTYIRFLVSN  AG+VIGKGGSTI D
Sbjct: 1   MESTESSYVSSPEGPRKHAASPPPKSPSLDSEEKPTYIRFLVSNSAAGSVIGKGGSTITD 60

Query: 60  FQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVG 119
           FQSQSGARIQLSR+HEFFPGTTDRIIM+SG I+EI RAV+L++ KLL+ELH+ED  +D  
Sbjct: 61  FQSQSGARIQLSRNHEFFPGTTDRIIMVSGAINEIQRAVELILSKLLSELHSEDD-NDAE 119

Query: 120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD 179
            KTK+RL+VPN SCG IIGK GATI+SF++DSQA IKIS  D++YYG NDRLVTLTG+ D
Sbjct: 120 PKTKVRLVVPNGSCGGIIGKGGATIRSFIEDSQAGIKISPQDNNYYGQNDRLVTLTGSFD 179

Query: 180 EQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHY 239
           EQMRA+ELI+ KLSED  Y+Q+M  P++Y GV+FSG+ G+PY  V P V A P   A +Y
Sbjct: 180 EQMRAIELIVSKLSEDPHYAQSMNSPFSYPGVYFSGYQGVPYTYVLPSV-APPAYNAVNY 238

Query: 240 GPN-MGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDF 298
            PN   G K QN+K++R+NSLT+GVADEHIG VVGRGGRNIMEISQ SGARIK+SDRGD+
Sbjct: 239 RPNGAAGGKLQNSKEERSNSLTMGVADEHIGLVVGRGGRNIMEISQASGARIKISDRGDY 298

Query: 299 FSGTSERKVTISGPQRSIRTAESMIMQKVAYASDR 333
            SGT++RKVTI+G QR+IRTAESMI+QKVAYA++R
Sbjct: 299 VSGTTDRKVTITGSQRAIRTAESMILQKVAYATER 333

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576359|ref|XP_003556300.1| PREDICTED: RNA-binding protein Nova-1-like [Glycine max]

 Score =  449 bits (1155), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 226/335 (67%), Positives = 273/335 (81%), Gaps = 4/335 (1%)

Query: 1   METNESSYVPSPDVHGKRSTAPVKSLSS-DPTEKPTYIRFLVSNPLAGAVIGKGGSTIND 59
           ME+ ESSYV SP+   K + +P     S D  EKPTYIRFLVSN  AG+VIGKGGSTI D
Sbjct: 1   MESTESSYVSSPEGPRKHAASPPPKPPSLDSEEKPTYIRFLVSNSAAGSVIGKGGSTITD 60

Query: 60  FQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVG 119
           FQSQSGARIQLSR+HEFFPGTTDRIIM+SG I+EI RAV+L++ KLL+ELH+ED  +D  
Sbjct: 61  FQSQSGARIQLSRNHEFFPGTTDRIIMVSGAINEIQRAVELILSKLLSELHSEDD-NDAE 119

Query: 120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD 179
            KTK+RL+VPN SCG IIGK G TI+SF++DSQA IKIS  D++YYG NDRLV LTGT D
Sbjct: 120 PKTKVRLVVPNGSCGGIIGKGGVTIRSFIEDSQAGIKISPQDNNYYGQNDRLVMLTGTFD 179

Query: 180 EQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHY 239
           EQMRA+ELI+ KL+ED  Y+Q+M  P++Y GV+FSG+ G+PY  V P V A P   A +Y
Sbjct: 180 EQMRAIELIVSKLAEDPHYAQSMNSPFSYPGVYFSGYQGVPYTYVLPSV-APPAYNAVNY 238

Query: 240 GPN-MGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDF 298
            PN   G K QN+K++R+NSLT+GVADEHIG VVGRGGRNIMEISQ+SGARIK+SDRGD+
Sbjct: 239 RPNGTAGGKLQNSKEERSNSLTMGVADEHIGLVVGRGGRNIMEISQVSGARIKISDRGDY 298

Query: 299 FSGTSERKVTISGPQRSIRTAESMIMQKVAYASDR 333
            SGT++RKVTI+G QR+IRTAESMI+QKVAYA++R
Sbjct: 299 ISGTTDRKVTITGSQRAIRTAESMILQKVAYATER 333

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|146336943|gb|ABQ23585.1| putative KH-domain containing protein [Medicago truncatula]

 Score =  440 bits (1131), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 222/337 (65%), Positives = 273/337 (81%), Gaps = 7/337 (2%)

Query: 1   METNESSYVPSPDVHGKRSTAPVKSLSSDP---TEKPTYIRFLVSNPLAGAVIGKGGSTI 57
           ME+ ESSYV SP+  G R  A      S      EKPTY+RFLVSN  AG+VIGKGGSTI
Sbjct: 1   MESPESSYVSSPE--GPRKHASSPPPDSPSQDSVEKPTYVRFLVSNSAAGSVIGKGGSTI 58

Query: 58  NDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADD 117
            DFQSQSGARIQLSR++EFFPGTTDRIIM+SG I+E+LRAV+L++ KLL+ELH+ED  +D
Sbjct: 59  TDFQSQSGARIQLSRNNEFFPGTTDRIIMVSGAINEVLRAVELILSKLLSELHSEDD-ND 117

Query: 118 VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177
           V  KTK+RLIVPN SCG IIGK GATI+SF+++SQA IKIS  D+SYYG NDR+VT+TGT
Sbjct: 118 VEPKTKVRLIVPNGSCGGIIGKGGATIRSFIEESQAGIKISPQDNSYYGQNDRIVTVTGT 177

Query: 178 LDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAA 237
           LDEQMR ++LI+ KL+ED  YS +M+ P+TY+G + SG+ G+PY  V P V A P     
Sbjct: 178 LDEQMRGIDLIVSKLAEDPHYSHSMSSPFTYSGAYVSGYQGVPYTYVLPSV-APPAYNGV 236

Query: 238 HYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGD 297
           +Y PN  G KFQN+K+DR+NS+TIGVADEHIG VVGRGGRNI +ISQ SGA+IK+SDRGD
Sbjct: 237 NYRPNGTGAKFQNSKEDRSNSMTIGVADEHIGLVVGRGGRNISDISQTSGAKIKISDRGD 296

Query: 298 FFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDRL 334
           + SGT++RKVTI+G QR+IRTAESMI+QKVAYA++R+
Sbjct: 297 YISGTTDRKVTITGSQRAIRTAESMILQKVAYATERV 333

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224113143|ref|XP_002316405.1| predicted protein [Populus trichocarpa] gi|222865445|gb|EEF02576.1| predicted protein [Populus trichocarpa]

 Score =  437 bits (1123), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 221/336 (65%), Positives = 270/336 (80%), Gaps = 2/336 (0%)

Query: 1   METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDF 60
           ME+ ESSYV SP+   KRS  P  S  SD  EKPTY RFLVSN  AG+VIGKGG+TI DF
Sbjct: 1   MESTESSYVSSPEQPQKRSPPPPASPPSDSEEKPTYTRFLVSNAAAGSVIGKGGATITDF 60

Query: 61  QSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGT 120
           QSQSGARIQLSR++EFFPGT+DRIIM+SG ID++L+AV+L+I KLL+E+ AED  D+   
Sbjct: 61  QSQSGARIQLSRNYEFFPGTSDRIIMVSGGIDDVLKAVELIIAKLLSEIPAED-GDEAEP 119

Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE 180
           + ++RL+VPNS+CGSIIGK G+ IKSF+++S A IKIS LD  ++GL DRLVT+TGTL+E
Sbjct: 120 RMRVRLVVPNSACGSIIGKGGSIIKSFIEESHAGIKISPLDTKFFGLTDRLVTVTGTLEE 179

Query: 181 QMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYG 240
           QM A++LIL KL++D  YSQTM  P++YAGVFFSGF G+ Y  V P V    +N+  H G
Sbjct: 180 QMHAIDLILSKLTDDPHYSQTMHAPFSYAGVFFSGFDGIQYACVLPYVATAAYNSMNH-G 238

Query: 241 PNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFS 300
           PN    KFQ+NKDD TNS+TIGVADEHIG VVGRGGRNIMEISQ SGAR+K+SDRGDF S
Sbjct: 239 PNGAAVKFQHNKDDITNSVTIGVADEHIGLVVGRGGRNIMEISQTSGARLKISDRGDFMS 298

Query: 301 GTSERKVTISGPQRSIRTAESMIMQKVAYASDRLMD 336
           GT++RK+TI+G QR+IR AE MIMQKV+YAS+R  D
Sbjct: 299 GTTDRKITITGSQRAIRAAEDMIMQKVSYASERETD 334

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297810533|ref|XP_002873150.1| hypothetical protein ARALYDRAFT_487225 [Arabidopsis lyrata subsp. lyrata] gi|297318987|gb|EFH49409.1| hypothetical protein ARALYDRAFT_487225 [Arabidopsis lyrata subsp. lyrata]

 Score =  431 bits (1108), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 208/336 (61%), Positives = 270/336 (80%), Gaps = 2/336 (0%)

Query: 1   METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDF 60
           ME+ ES    SP+   KRS  P  S  +D  EKPT+IRFLVSN  AG+VIGKGGSTI +F
Sbjct: 1   MESTESYAAASPEELAKRSPEPHDSSEADSAEKPTHIRFLVSNAAAGSVIGKGGSTITEF 60

Query: 61  QSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGT 120
           Q++SGARIQLSR+ EFFPGTTDRIIMISG+I E++  ++L++DKL +ELHAED  ++V  
Sbjct: 61  QAKSGARIQLSRNQEFFPGTTDRIIMISGSIKEVINGLELILDKLHSELHAED-GNEVEP 119

Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE 180
           + ++RL+VPNSSCG IIGK GATIKSF+++S+A IKIS LD+++YGL+DRLVTL+GT +E
Sbjct: 120 RRRIRLVVPNSSCGGIIGKGGATIKSFIEESKAGIKISPLDNTFYGLSDRLVTLSGTFEE 179

Query: 181 QMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYG 240
           QMRA++LIL KL+ED  YSQ +  PY+YAG+F+SGFHG PY    P V    +N+  +Y 
Sbjct: 180 QMRAIDLILAKLTEDDHYSQNVHSPYSYAGLFYSGFHGPPYAYALPSVATAGYNS-VNYA 238

Query: 241 PNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFS 300
           PN  G K+QN+KD+ + ++TIGVADEHIG V+GRGGRNIMEI+QI+GARIK+SDRGDF S
Sbjct: 239 PNGSGGKYQNHKDEASTTVTIGVADEHIGLVLGRGGRNIMEITQITGARIKISDRGDFMS 298

Query: 301 GTSERKVTISGPQRSIRTAESMIMQKVAYASDRLMD 336
           GT++RKV+I+GPQR+I+ AE+MI QKV  A++R  D
Sbjct: 299 GTTDRKVSITGPQRAIQQAETMIKQKVDSATERATD 334

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30680512|ref|NP_850764.1| binding to TOMV RNA 1L (long form) protein [Arabidopsis thaliana] gi|332003360|gb|AED90743.1| binding to TOMV RNA 1L (long form) protein [Arabidopsis thaliana]

 Score =  427 bits (1098), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 206/336 (61%), Positives = 270/336 (80%), Gaps = 2/336 (0%)

Query: 1   METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDF 60
           ME+ ES    SP+   KRS  P  S  +D  EKPT+IRFLVSN  AG+VIGKGGSTI +F
Sbjct: 1   MESTESYAAGSPEELAKRSPEPHDSSEADSAEKPTHIRFLVSNAAAGSVIGKGGSTITEF 60

Query: 61  QSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGT 120
           Q++SGARIQLSR+ EFFPGTTDRIIMISG+I E++  ++L++DKL +ELHAED  ++V  
Sbjct: 61  QAKSGARIQLSRNQEFFPGTTDRIIMISGSIKEVVNGLELILDKLHSELHAED-GNEVEP 119

Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE 180
           + ++RL+VPNSSCG IIGK GATIKSF+++S+A IKIS LD+++YGL+DRLVTL+GT +E
Sbjct: 120 RRRIRLVVPNSSCGGIIGKGGATIKSFIEESKAGIKISPLDNTFYGLSDRLVTLSGTFEE 179

Query: 181 QMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYG 240
           QMRA++LIL KL+ED  YSQ +  PY+YAG+F+SGFHG PY    P V    +N+  +Y 
Sbjct: 180 QMRAIDLILAKLTEDDHYSQNVHSPYSYAGLFYSGFHGPPYAYALPSVATAGYNS-VNYA 238

Query: 241 PNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFS 300
           PN  G K+QN+K++ + ++TIGVADEHIG V+GRGGRNIMEI+Q++GARIK+SDRGDF S
Sbjct: 239 PNGSGGKYQNHKEEASTTVTIGVADEHIGLVLGRGGRNIMEITQMTGARIKISDRGDFMS 298

Query: 301 GTSERKVTISGPQRSIRTAESMIMQKVAYASDRLMD 336
           GT++RKV+I+GPQR+I+ AE+MI QKV  A++R  D
Sbjct: 299 GTTDRKVSITGPQRAIQQAETMIKQKVDSATERTTD 334

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359486525|ref|XP_002264331.2| PREDICTED: RNA-binding protein Nova-1-like [Vitis vinifera]

 Score =  425 bits (1093), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 216/333 (64%), Positives = 263/333 (78%), Gaps = 24/333 (7%)

Query: 1   METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDF 60
           ME+ ES+YV SP+V  KRS+ P +S +SD  EK TYIRFLVSN  AG+VIGKGGSTINDF
Sbjct: 1   MESPESAYVSSPEVPPKRSSPP-RSPTSDFMEKSTYIRFLVSNAAAGSVIGKGGSTINDF 59

Query: 61  QSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGT 120
           QSQSGARIQLSR+HEFFPGT+DRIIMISG  +EI++A++L++ KLL+E+H ED  D+   
Sbjct: 60  QSQSGARIQLSRNHEFFPGTSDRIIMISGATNEIIKAMELILAKLLSEMHTED-GDEADP 118

Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE 180
           ++K+RLIVPNSSCG IIGK G+TIKSF++DSQA IKIS  D++Y GL DRLVTL G+L+E
Sbjct: 119 RSKVRLIVPNSSCGGIIGKGGSTIKSFIEDSQASIKISPQDNNYLGLTDRLVTLMGSLEE 178

Query: 181 QMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYG 240
           QMRA++LIL KL+ED  Y+Q M  P++YA  + S                       +YG
Sbjct: 179 QMRAIDLILSKLTEDPHYTQFMNAPFSYAAAYNS----------------------MNYG 216

Query: 241 PNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFS 300
           PN  G KFQNNK+DR+NS+TIGVADEHIG VVGRGGRNIM+ISQ SGARIK+SDRGDF S
Sbjct: 217 PNGAGGKFQNNKEDRSNSVTIGVADEHIGLVVGRGGRNIMDISQASGARIKISDRGDFMS 276

Query: 301 GTSERKVTISGPQRSIRTAESMIMQKVAYASDR 333
           GT++RKVTI+G QR+IR AESMIMQKVA AS+R
Sbjct: 277 GTTDRKVTITGSQRAIRAAESMIMQKVASASER 309

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296085941|emb|CBI31382.3| unnamed protein product [Vitis vinifera]

 Score =  425 bits (1093), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 216/333 (64%), Positives = 263/333 (78%), Gaps = 24/333 (7%)

Query: 1   METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDF 60
           ME+ ES+YV SP+V  KRS+ P +S +SD  EK TYIRFLVSN  AG+VIGKGGSTINDF
Sbjct: 49  MESPESAYVSSPEVPPKRSSPP-RSPTSDFMEKSTYIRFLVSNAAAGSVIGKGGSTINDF 107

Query: 61  QSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGT 120
           QSQSGARIQLSR+HEFFPGT+DRIIMISG  +EI++A++L++ KLL+E+H ED  D+   
Sbjct: 108 QSQSGARIQLSRNHEFFPGTSDRIIMISGATNEIIKAMELILAKLLSEMHTED-GDEADP 166

Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE 180
           ++K+RLIVPNSSCG IIGK G+TIKSF++DSQA IKIS  D++Y GL DRLVTL G+L+E
Sbjct: 167 RSKVRLIVPNSSCGGIIGKGGSTIKSFIEDSQASIKISPQDNNYLGLTDRLVTLMGSLEE 226

Query: 181 QMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYG 240
           QMRA++LIL KL+ED  Y+Q M  P++YA  + S                       +YG
Sbjct: 227 QMRAIDLILSKLTEDPHYTQFMNAPFSYAAAYNS----------------------MNYG 264

Query: 241 PNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFS 300
           PN  G KFQNNK+DR+NS+TIGVADEHIG VVGRGGRNIM+ISQ SGARIK+SDRGDF S
Sbjct: 265 PNGAGGKFQNNKEDRSNSVTIGVADEHIGLVVGRGGRNIMDISQASGARIKISDRGDFMS 324

Query: 301 GTSERKVTISGPQRSIRTAESMIMQKVAYASDR 333
           GT++RKVTI+G QR+IR AESMIMQKVA AS+R
Sbjct: 325 GTTDRKVTITGSQRAIRAAESMIMQKVASASER 357

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255583738|ref|XP_002532622.1| Far upstream element-binding protein, putative [Ricinus communis] gi|223527642|gb|EEF29753.1| Far upstream element-binding protein, putative [Ricinus communis]

 Score =  418 bits (1075), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 214/337 (63%), Positives = 264/337 (78%), Gaps = 24/337 (7%)

Query: 1   METNESSYVPSPDVHGKRSTAPVKSL-SSDPTEKPTYIRFLVSNPLAGAVIGKGGSTIND 59
           ME+ ESSYV SP+   ++ + P     +SD  EKPTY+RFLVSN  AG+VIGKGG+TI D
Sbjct: 1   MESTESSYVSSPEAPPRKRSPPPPKSPTSDSVEKPTYVRFLVSNAAAGSVIGKGGATITD 60

Query: 60  FQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVG 119
           FQSQSGARIQLSR++EFFPGT+DRII+ISG +D++L+ V+LV+ KLL+ELH ED  DDV 
Sbjct: 61  FQSQSGARIQLSRNYEFFPGTSDRIILISGILDDVLKGVELVLAKLLSELHTED-GDDVD 119

Query: 120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD 179
            +TK+RL+VPNSSCGSIIGK G+ IKSF+++SQA IKIS  D+++YGLNDRLVT+TGTL+
Sbjct: 120 PRTKVRLVVPNSSCGSIIGKGGSIIKSFIEESQAGIKISPQDNNFYGLNDRLVTVTGTLE 179

Query: 180 EQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHY 239
           EQMRA++LIL KL +D  Y QTM  P++YA                     V +N+  +Y
Sbjct: 180 EQMRAIDLILSKLYDDPHYVQTMHAPFSYA---------------------VAYNSM-NY 217

Query: 240 GPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFF 299
           G N  G KFQNNK+DRTNS+TIGVAD HIG VVGRGGRNIMEISQ+SGARIK+SDRGDF 
Sbjct: 218 GANGAGGKFQNNKEDRTNSVTIGVADAHIGLVVGRGGRNIMEISQVSGARIKISDRGDFM 277

Query: 300 SGTSERKVTISGPQRSIRTAESMIMQKVAYASDRLMD 336
           SGT++RK+ I+G QR+IRTAE MIMQKVAYAS+R  D
Sbjct: 278 SGTNDRKIIITGSQRAIRTAEGMIMQKVAYASERGSD 314

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449449385|ref|XP_004142445.1| PREDICTED: RNA-binding protein Nova-2-like [Cucumis sativus] gi|449527683|ref|XP_004170839.1| PREDICTED: RNA-binding protein Nova-2-like [Cucumis sativus]

 Score =  403 bits (1036), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 216/345 (62%), Positives = 263/345 (76%), Gaps = 31/345 (8%)

Query: 1   METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDF 60
           ME+ ESSYV SP+   KRS  P KS +SD  EK TYIRFLVSN  AG+VIGKGGSTINDF
Sbjct: 1   MESTESSYVSSPEAPAKRSPPPPKSPNSDNMEKATYIRFLVSNAAAGSVIGKGGSTINDF 60

Query: 61  QSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGT 120
           QSQSGARIQLSR+HEFFPGTTDRIIM+SG+I+EIL+A++LV+ KLL+ELHAE + DDV  
Sbjct: 61  QSQSGARIQLSRNHEFFPGTTDRIIMVSGSINEILKAMELVLAKLLSELHAE-EGDDVEP 119

Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE 180
           +TK+RLIVP+SSCG+IIGK G+TIKSF++DSQA IKIS  D++Y    DRLVTL+GT++E
Sbjct: 120 RTKVRLIVPHSSCGAIIGKGGSTIKSFIEDSQAGIKISPQDNNYMASTDRLVTLSGTIEE 179

Query: 181 QMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYG 240
           QMRA +LI+ KLSED  Y+Q+M  P++Y     + F+ M YG+                 
Sbjct: 180 QMRATDLIVSKLSEDPHYTQSMNYPFSYP----TSFNAMNYGSNGGGTGG---------- 225

Query: 241 PNMGGRKFQNNKDD----------RTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARI 290
                 +FQNNK D          R NSLTIGV+D HIG VVGRGGRNI+EISQ SGARI
Sbjct: 226 ------RFQNNKPDTRSSEIVQEERNNSLTIGVSDGHIGLVVGRGGRNILEISQASGARI 279

Query: 291 KVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDRLM 335
           K+SDRGDF SGT++RKVTI+G QR+IR AESMI+QKVAYAS+R++
Sbjct: 280 KISDRGDFMSGTTDRKVTITGSQRAIRAAESMILQKVAYASERVL 324

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	336
TAIR|locus:2184362	334	BTR1L "AT5G04430" [Arabidopsis	0.994	1.0	0.607	1.9e-106
RGD|621345	474	Nova1 "neuro-oncological ventr	0.619	0.438	0.346	6.1e-40
UNIPROTKB|F1LMZ7	474	Nova1 "RNA-binding protein Nov	0.619	0.438	0.346	8.1e-40
UNIPROTKB|D3DS81	483	NOVA1 "Neuro-oncological ventr	0.619	0.430	0.342	1.7e-39
ZFIN|ZDB-GENE-060526-113	495	nova1 "neuro-oncological ventr	0.535	0.363	0.328	3.4e-39
UNIPROTKB|F1PUD6	502	NOVA2 "Uncharacterized protein	0.565	0.378	0.362	2.4e-38
UNIPROTKB|F1MS84	464	NOVA2 "Uncharacterized protein	0.547	0.396	0.36	4.4e-38
UNIPROTKB|Q9UNW9	492	NOVA2 "RNA-binding protein Nov	0.574	0.392	0.354	5.8e-38
ZFIN|ZDB-GENE-080211-1	473	nova2 "neuro-oncological ventr	0.550	0.391	0.336	9.8e-38
UNIPROTKB|F1RM28	554	NOVA2 "Uncharacterized protein	0.574	0.348	0.354	1.4e-37

TAIR|locus:2184362 BTR1L "AT5G04430" [Arabidopsis thaliana (taxid:3702)]

 Score = 1053 (375.7 bits), Expect = 1.9e-106, P = 1.9e-106
 Identities = 204/336 (60%), Positives = 268/336 (79%)

Query:     1 METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDF 60
             ME+ ES    SP+   KRS  P  S  +D  EKPT+IRFLVSN  AG+VIGKGGSTI +F
Sbjct:     1 MESTESYAAGSPEELAKRSPEPHDSSEADSAEKPTHIRFLVSNAAAGSVIGKGGSTITEF 60

Query:    61 QSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGT 120
             Q++SGARIQLSR+ EFFPGTTDRIIMISG+I E++  ++L++DKL +ELHAED  ++V  
Sbjct:    61 QAKSGARIQLSRNQEFFPGTTDRIIMISGSIKEVVNGLELILDKLHSELHAED-GNEVEP 119

Query:   121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE 180
             + ++RL+VPNSSCG IIGK GATIKSF+++S+A IKIS LD+++YGL+DRLVTL+GT +E
Sbjct:   120 RRRIRLVVPNSSCGGIIGKGGATIKSFIEESKAGIKISPLDNTFYGLSDRLVTLSGTFEE 179

Query:   181 QMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGXXXXXXXXXXHNTAAHYG 240
             QMRA++LIL KL+ED  YSQ +  PY+YAG+F+SGFHG PY           +N+  +Y 
Sbjct:   180 QMRAIDLILAKLTEDDHYSQNVHSPYSYAGLFYSGFHGPPYAYALPSVATAGYNSV-NYA 238

Query:   241 PNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFS 300
             PN  G K+QN+K++ + ++TIGVADEHIG V+GRGGRNIMEI+Q++GARIK+SDRGDF S
Sbjct:   239 PNGSGGKYQNHKEEASTTVTIGVADEHIGLVLGRGGRNIMEITQMTGARIKISDRGDFMS 298

Query:   301 GTSERKVTISGPQRSIRTAESMIMQKVAYASDRLMD 336
             GT++RKV+I+GPQR+I+ AE+MI QKV  A++R  D
Sbjct:   299 GTTDRKVSITGPQRAIQQAETMIKQKVDSATERTTD 334

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008380 "RNA splicing" evidence=NAS

GO:0003727 "single-stranded RNA binding" evidence=IPI

GO:0046719 "regulation of viral protein levels in host cell" evidence=IMP

RGD|621345 Nova1 "neuro-oncological ventral antigen 1" [Rattus norvegicus (taxid:10116)]

 Score = 290 (107.1 bits), Expect = 6.1e-40, Sum P(2) = 6.1e-40
 Identities = 79/228 (34%), Positives = 128/228 (56%)

Query:    12 PDVHGKRSTAPVKSLSSDPT---EKPTY-IRFLVSNPLAGAVIGKGGSTINDFQSQSGAR 67
             PD   +   AP ++ S+  T   E   Y ++ L+ +  AG++IGKGG TI   Q ++GA 
Sbjct:    22 PDSRKRPLEAPPEAGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGAT 81

Query:    68 IQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAE----DQADDVGTKT- 122
             I+LS+S +F+PGTT+R+ +I GTI E L AV   I + + E+       +    +  +T 
Sbjct:    82 IKLSKSKDFYPGTTERVCLIQGTI-EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTT 140

Query:   123 -------KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT 175
                    ++++IVPNS+ G IIGK GAT+K+ M+ S A +++S+       L +R+VT++
Sbjct:   141 VNPDRIKQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGI-NLQERVVTVS 199

Query:   176 GTLDEQMRALELILLKLSEDTLYSQTMTVPYT-YAG-VFFSGFHGMPY 221
             G  ++  +A+ELI+ K+ ED      + + Y    G V  S   G PY
Sbjct:   200 GEPEQNRKAVELIIQKIQEDPQSGSCLNISYANVTGPVANSNPTGFPY 247

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISO

GO:0003723 "RNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0007399 "nervous system development" evidence=IDA

UNIPROTKB|F1LMZ7 Nova1 "RNA-binding protein Nova-1" [Rattus norvegicus (taxid:10116)]

 Score = 289 (106.8 bits), Expect = 8.1e-40, Sum P(2) = 8.1e-40
 Identities = 79/228 (34%), Positives = 128/228 (56%)

Query:    12 PDVHGKRSTAPVKSLSSDPT---EKPTY-IRFLVSNPLAGAVIGKGGSTINDFQSQSGAR 67
             PD   +   AP ++ S+  T   E   Y ++ L+ +  AG++IGKGG TI   Q ++GA 
Sbjct:    22 PDSRKRPLEAPPEAGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGAT 81

Query:    68 IQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAE----DQADDVGTKT- 122
             I+LS+S +F+PGTT+R+ +I GTI E L AV   I + + E+       +    +  +T 
Sbjct:    82 IKLSKSKDFYPGTTERVCLIQGTI-EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTT 140

Query:   123 -------KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT 175
                    ++++IVPNS+ G IIGK GAT+K+ M+ S A +++S+       L +R+VT++
Sbjct:   141 VNPDRIKQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGI-NLQERVVTVS 199

Query:   176 GTLDEQMRALELILLKLSEDTLYSQTMTVPYT-YAG-VFFSGFHGMPY 221
             G  ++  +A+ELI+ K+ ED      + + Y    G V  S   G PY
Sbjct:   200 GEPEQNRKAVELIIQKIQEDPQSGSCLNISYANVTGPVANSNPTGSPY 247

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|D3DS81 NOVA1 "Neuro-oncological ventral antigen 1, isoform CRA_a" [Homo sapiens (taxid:9606)]

 Score = 287 (106.1 bits), Expect = 1.7e-39, Sum P(2) = 1.7e-39
 Identities = 78/228 (34%), Positives = 128/228 (56%)

Query:    12 PDVHGKRSTAPVKSLSSDPT---EKPTY-IRFLVSNPLAGAVIGKGGSTINDFQSQSGAR 67
             PD   +   AP ++ S+  T   E   Y ++ L+ +  AG++IGKGG TI   Q ++GA 
Sbjct:    23 PDSRKRPLEAPPEAGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGAT 82

Query:    68 IQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAE----DQADDVGTKT- 122
             I+LS+S +F+PGTT+R+ +I GT+ E L AV   I + + E+       +    +  +T 
Sbjct:    83 IKLSKSKDFYPGTTERVCLIQGTV-EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTT 141

Query:   123 -------KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT 175
                    ++++IVPNS+ G IIGK GAT+K+ M+ S A +++S+       L +R+VT++
Sbjct:   142 VNPDRIKQVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGI-NLQERVVTVS 200

Query:   176 GTLDEQMRALELILLKLSEDTLYSQTMTVPYT-YAG-VFFSGFHGMPY 221
             G  ++  +A+ELI+ K+ ED      + + Y    G V  S   G PY
Sbjct:   201 GEPEQNRKAVELIIQKIQEDPQSGSCLNISYANVTGPVANSNPTGSPY 248

GO:0003723 "RNA binding" evidence=IEA

ZFIN|ZDB-GENE-060526-113 nova1 "neuro-oncological ventral antigen 1" [Danio rerio (taxid:7955)]

 Score = 288 (106.4 bits), Expect = 3.4e-39, Sum P(2) = 3.4e-39
 Identities = 63/192 (32%), Positives = 115/192 (59%)

Query:    27 SSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIM 86
             S+   E   +++ L+ +  AG++IGKGG TI   Q ++GA I+LS+S +F+PGTT+R+ +
Sbjct:    49 SNTGEEGEYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCL 108

Query:    87 ISGTIDEILRAVDLVIDKLLTELHAEDQADDVGT---KTKL--------RLIVPNSSCGS 135
             I GT++ +    + + +K+     +  + + V     +T +        +LIVPNS+ G 
Sbjct:   109 IQGTVEALNGVHNFIAEKVREMPQSSQKTEPVSILQPQTTVNPDRIKQAKLIVPNSTAGL 168

Query:   136 IIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED 195
             IIGK GAT+K+ M+ S A +++S+       L +R+VT++G  ++  +A+E+I+ K+ ED
Sbjct:   169 IIGKGGATVKAVMEQSGAWVQLSQKPEGI-NLQERVVTVSGEPEQNRKAVEIIVQKIQED 227

Query:   196 TLYSQTMTVPYT 207
                S  + + Y+
Sbjct:   228 PQSSSCLNISYS 239

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1PUD6 NOVA2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 283 (104.7 bits), Expect = 2.4e-38, Sum P(2) = 2.4e-38
 Identities = 75/207 (36%), Positives = 120/207 (57%)

Query:    30 PTEKPTY-IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMIS 88
             P E+  Y ++ L+ +  AG++IGKGG TI   Q ++GA I+LS+S +F+PGTT+R+ ++ 
Sbjct:    37 PAEEGEYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLVQ 96

Query:    89 GTIDEILRAVDLVIDKLLTEL-HAEDQADDVGT---KTKL--------RLIVPNSSCGSI 136
             GT  E L AV   I + + E+  A  + + V     +T +        +LIVPNS+ G I
Sbjct:    97 GTA-EALNAVHSFIAEKVREIPQAMTKPEVVNILQPQTTMNPDRAKQAKLIVPNSTAGLI 155

Query:   137 IGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDT 196
             IGK GAT+K+ M+ S A +++S+       L +R+VT++G  ++  +A+  I+ K+ ED 
Sbjct:   156 IGKGGATVKAVMEQSGAWVQLSQKPEGI-NLQERVVTVSGEPEQVHKAVSAIVQKVQEDP 214

Query:   197 LYSQTMTVPYT-YAG-VFFSGFHGMPY 221
               S  + + Y   AG V  S   G PY
Sbjct:   215 QSSSCLNISYANVAGPVANSNPTGSPY 241

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1MS84 NOVA2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 278 (102.9 bits), Expect = 4.4e-38, Sum P(2) = 4.4e-38
 Identities = 72/200 (36%), Positives = 117/200 (58%)

Query:    36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEIL 95
             +++ L+ +  AG++IGKGG TI   Q ++GA I+LS+S +F+PGTT+R+ ++ GT  E L
Sbjct:     6 FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLVQGTA-EAL 64

Query:    96 RAVDLVIDKLLTEL-HAEDQADDVGT---KTKL--------RLIVPNSSCGSIIGKAGAT 143
              AV   I + + E+  A  + + V     +T +        +LIVPNS+ G IIGK GAT
Sbjct:    65 NAVHSFIAEKVREIPQAMTKPEVVNILQPQTTMNPDRAKQAKLIVPNSTAGLIIGKGGAT 124

Query:   144 IKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMT 203
             +K+ M+ S A +++S+       L +R+VT++G  ++  +A+  I+ K+ ED   S  + 
Sbjct:   125 VKAVMEQSGAWVQLSQKPEGI-NLQERVVTVSGEPEQVHKAVSAIVQKVQEDPQSSSCLN 183

Query:   204 VPYT-YAG-VFFSGFHGMPY 221
             + Y   AG V  S   G PY
Sbjct:   184 ISYANVAGPVANSNPTGSPY 203

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q9UNW9 NOVA2 "RNA-binding protein Nova-2" [Homo sapiens (taxid:9606)]

 Score = 279 (103.3 bits), Expect = 5.8e-38, Sum P(2) = 5.8e-38
 Identities = 74/209 (35%), Positives = 120/209 (57%)

Query:    27 SSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIM 86
             S+   E   +++ L+ +  AG++IGKGG TI   Q ++GA I+LS+S +F+PGTT+R+ +
Sbjct:    25 SNTGEEGEYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCL 84

Query:    87 ISGTIDEILRAVDLVIDKLLTEL-HAEDQADDVGT---KTKL--------RLIVPNSSCG 134
             + GT  E L AV   I + + E+  A  + + V     +T +        +LIVPNS+ G
Sbjct:    85 VQGTA-EALNAVHSFIAEKVREIPQAMTKPEVVNILQPQTTMNPDRAKQAKLIVPNSTAG 143

Query:   135 SIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194
              IIGK GAT+K+ M+ S A +++S+       L +R+VT++G  ++  +A+  I+ K+ E
Sbjct:   144 LIIGKGGATVKAVMEQSGAWVQLSQKPEGI-NLQERVVTVSGEPEQVHKAVSAIVQKVQE 202

Query:   195 DTLYSQTMTVPYT-YAG-VFFSGFHGMPY 221
             D   S  + + Y   AG V  S   G PY
Sbjct:   203 DPQSSSCLNISYANVAGPVANSNPTGSPY 231

GO:0003723 "RNA binding" evidence=NAS

GO:0005634 "nucleus" evidence=IDA

ZFIN|ZDB-GENE-080211-1 nova2 "neuro-oncological ventral antigen 2" [Danio rerio (taxid:7955)]

 Score = 296 (109.3 bits), Expect = 9.8e-38, Sum P(2) = 9.8e-38
 Identities = 67/199 (33%), Positives = 119/199 (59%)

Query:    36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEIL 95
             +++ L+ +  AG++IGKGG TI   Q ++GA I+LS+S +F+PGTT+R+ +I GT++ + 
Sbjct:    64 FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTVEALN 123

Query:    96 RAVDLVIDKLLTELHAEDQADDVGT---KTKL--------RLIVPNSSCGSIIGKAGATI 144
                D + +K+     +  + + V     +T +        +L+VPNS+ G IIGK GAT+
Sbjct:   124 NVHDFIAEKVREMPQSAQKTEPVSILQPQTTVNPDRVKQAKLVVPNSTAGLIIGKGGATV 183

Query:   145 KSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTV 204
             K+ M+ S A +++S+       L +R+VT++G  ++  +A+E+I+ K+ ED   S  + +
Sbjct:   184 KAVMEQSGAWVQLSQKPDGI-NLQERVVTISGEPEQNRKAVEIIVQKIQEDPQSSSCLNI 242

Query:   205 PYT-YAG-VFFSGFHGMPY 221
              Y+  +G V  S   G PY
Sbjct:   243 SYSNISGPVANSNPTGSPY 261

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1RM28 NOVA2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 279 (103.3 bits), Expect = 1.4e-37, Sum P(2) = 1.4e-37
 Identities = 74/209 (35%), Positives = 120/209 (57%)

Query:    27 SSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIM 86
             S+   E   +++ L+ +  AG++IGKGG TI   Q ++GA I+LS+S +F+PGTT+R+ +
Sbjct:    87 SNTGEEGEYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCL 146

Query:    87 ISGTIDEILRAVDLVIDKLLTEL-HAEDQADDVGT---KTKL--------RLIVPNSSCG 134
             + GT  E L AV   I + + E+  A  + + V     +T +        +LIVPNS+ G
Sbjct:   147 VQGTA-EALNAVHSFIAEKVREIPQAMTKPEVVNILQPQTTMNPDRAKQAKLIVPNSTAG 205

Query:   135 SIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194
              IIGK GAT+K+ M+ S A +++S+       L +R+VT++G  ++  +A+  I+ K+ E
Sbjct:   206 LIIGKGGATVKAVMEQSGAWVQLSQKPEGI-NLQERVVTVSGEPEQVHKAVSAIVQKVQE 264

Query:   195 DTLYSQTMTVPYT-YAG-VFFSGFHGMPY 221
             D   S  + + Y   AG V  S   G PY
Sbjct:   265 DPQSSSCLNISYANVAGPVANSNPTGSPY 293

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: estExt_fgenesh4_pg.C_LG_X2076 hypothetical protein (335 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	336
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	4e-19
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	2e-17
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	3e-13
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	4e-13
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-12
pfam00013	59	pfam00013, KH_1, KH domain	4e-11
smart00322	68	smart00322, KH, K homology RNA-binding domain	3e-10
pfam00013	59	pfam00013, KH_1, KH domain	4e-10
smart00322	68	smart00322, KH, K homology RNA-binding domain	1e-09
pfam13014	42	pfam13014, KH_3, KH domain	1e-09
smart00322	68	smart00322, KH, K homology RNA-binding domain	2e-09
pfam00013	59	pfam00013, KH_1, KH domain	3e-09
pfam13014	42	pfam13014, KH_3, KH domain	1e-08
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	4e-08
pfam13014	42	pfam13014, KH_3, KH domain	8e-07
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	5e-06
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	3e-04
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	5e-04
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.001
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	0.003

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

 Score = 79.4 bits (197), Expect = 4e-19
 Identities = 27/66 (40%), Positives = 48/66 (72%), Gaps = 2/66 (3%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           +R LV +  AG++IGKGGSTI + + ++GA+I++S+S    PG+T+R++ ISG    + +
Sbjct: 2   LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSAVQK 59

Query: 97  AVDLVI 102
           A+ L++
Sbjct: 60  ALLLIL 65

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

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

 Score = 74.8 bits (185), Expect = 2e-17
 Identities = 29/66 (43%), Positives = 43/66 (65%), Gaps = 2/66 (3%)

Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
           LRL+VP+S  GSIIGK G+TIK   +++ A I++S+      G  +R+VT++G      +
Sbjct: 2   LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLP--GSTERVVTISGKPSAVQK 59

Query: 184 ALELIL 189
           AL LIL
Sbjct: 60  ALLLIL 65

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

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

 Score = 63.7 bits (156), Expect = 3e-13
 Identities = 25/65 (38%), Positives = 43/65 (66%), Gaps = 3/65 (4%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
            R LV + L G +IGKGGSTI + + ++GA+I++  S     G+ +RI+ I+GT + + +
Sbjct: 2   ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVEK 58

Query: 97  AVDLV 101
           A +L+
Sbjct: 59  AKELI 63

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

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

 Score = 63.3 bits (155), Expect = 4e-13
 Identities = 23/67 (34%), Positives = 40/67 (59%), Gaps = 3/67 (4%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           +  + V    +G ++G+GG  I EI + +GA+IK+ D G    G+ ER VTI+G   ++ 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVE 57

Query: 318 TAESMIM 324
            A+ +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|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 61.4 bits (150), Expect = 1e-12
 Identities = 29/66 (43%), Positives = 41/66 (62%), Gaps = 3/66 (4%)

Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
            R++VP+S  G IIGK G+TIK   +++ A IKI        G  +R+VT+TGT +   +
Sbjct: 2   ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG---SGSEERIVTITGTPEAVEK 58

Query: 184 ALELIL 189
           A ELIL
Sbjct: 59  AKELIL 64

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

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

 Score = 57.2 bits (139), Expect = 4e-11
 Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 7/66 (10%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           +  I +  + +G ++G+GG NI EI + +G +I++ D  D         VTISG    + 
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDRD-------DTVTISGTPEQVE 53

Query: 318 TAESMI 323
            A+ +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|197652 smart00322, KH, K homology RNA-binding domain

 Score = 55.4 bits (134), Expect = 3e-10
 Identities = 17/70 (24%), Positives = 39/70 (55%), Gaps = 5/70 (7%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           ++ + +  + +G ++G+GG  I +I + +G +I +        G+ ER V I+GP  ++ 
Sbjct: 4   TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG-----PGSEERVVEITGPPENVE 58

Query: 318 TAESMIMQKV 327
            A  +I++ +
Sbjct: 59  KAAELILEIL 68

Length = 68

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

 Score = 54.5 bits (132), Expect = 4e-10
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 7/65 (10%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
            R L+     G +IGKGGS I + + ++G +I+        P   D  + ISGT +++ +
Sbjct: 2   ERILIPPDKVGRIIGKGGSNIKEIREETGVKIR-------IPDDRDDTVTISGTPEQVEK 54

Query: 97  AVDLV 101
           A +L+
Sbjct: 55  AKELI 59

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

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

 Score = 53.5 bits (129), Expect = 1e-09
 Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 33  KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTID 92
            P  I  L+     G +IGKGGSTI   + ++G +I +       PG+ +R++ I+G  +
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG-----PGSEERVVEITGPPE 55

Query: 93  EILRAVDLVIDKL 105
            + +A +L+++ L
Sbjct: 56  NVEKAAELILEIL 68

Length = 68

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

 Score = 52.9 bits (128), Expect = 1e-09
 Identities = 20/45 (44%), Positives = 32/45 (71%), Gaps = 3/45 (6%)

Query: 45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG 89
          L GA+IGKGG TI + + ++GA+IQ+ +     PG+ +RI+ I+G
Sbjct: 1  LVGAIIGKGGETIKEIREETGAKIQIPKPE---PGSGERIVTITG 42

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

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

 Score = 52.7 bits (127), Expect = 2e-09
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD 179
               + +++P    G IIGK G+TIK   +++   I I        G  +R+V +TG  +
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG-----PGSEERVVEITGPPE 55

Query: 180 EQMRALELILLKL 192
              +A ELIL  L
Sbjct: 56  NVEKAAELILEIL 68

Length = 68

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

 Score = 52.2 bits (126), Expect = 3e-09
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 7/66 (10%)

Query: 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQM 182
             R+++P    G IIGK G+ IK   +++   I+I           D  VT++GT ++  
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR-------DDTVTISGTPEQVE 53

Query: 183 RALELI 188
           +A ELI
Sbjct: 54  KAKELI 59

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

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

 Score = 49.9 bits (120), Expect = 1e-08
 Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 3/45 (6%)

Query: 267 HIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG 311
            +G ++G+GG  I EI + +GA+I++        G+ ER VTI+G
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPEP---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 = 49.4 bits (119), Expect = 4e-08
 Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 2/61 (3%)

Query: 263 VADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESM 322
           V     G ++G+GG  I EI + +GA+I+VS       G++ER VTISG   +++ A  +
Sbjct: 6   VPSSQAGSIIGKGGSTIKEIREETGAKIRVSK--SVLPGSTERVVTISGKPSAVQKALLL 63

Query: 323 I 323
           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|221895 pfam13014, KH_3, KH domain

 Score = 44.9 bits (107), Expect = 8e-07
 Identities = 18/44 (40%), Positives = 28/44 (63%), Gaps = 3/44 (6%)

Query: 133 CGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG 176
            G+IIGK G TIK   +++ A I+I + +    G  +R+VT+TG
Sbjct: 2   VGAIIGKGGETIKEIREETGAKIQIPKPEP---GSGERIVTITG 42

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

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

 Score = 42.9 bits (102), Expect = 5e-06
 Identities = 16/67 (23%), Positives = 35/67 (52%), Gaps = 5/67 (7%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           +  + +  +   F++G+ G NI +I + +G +I+  D G          +TI+GP+ ++ 
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGS-----KSDTITITGPKENVE 55

Query: 318 TAESMIM 324
            A+  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|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 37.9 bits (89), Expect = 3e-04
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 5/53 (9%)

Query: 49  VIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV 101
           +IGK GS I     ++G +I+        PG+    I I+G  + + +A + +
Sbjct: 14  IIGKKGSNIRKIMEETGVKIRFPD-----PGSKSDTITITGPKENVEKAKEEI 61

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

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

 Score = 37.5 bits (88), Expect = 5e-04
 Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 5/66 (7%)

Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
             + +P      IIGK G+ I+  M+++   I+         G     +T+TG  +   +
Sbjct: 2   EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPD-----PGSKSDTITITGPKENVEK 56

Query: 184 ALELIL 189
           A E IL
Sbjct: 57  AKEEIL 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|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 40.2 bits (95), Expect = 0.001
 Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 10/71 (14%)

Query: 259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP-QRSIR 317
            TI +  + I  V+G GG+ I EI++ +GA+I + D G          V I+     +  
Sbjct: 553 ETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDDG---------TVKIAASDGEAAE 603

Query: 318 TAESMIMQKVA 328
            A  MI    A
Sbjct: 604 AAIKMIEGITA 614

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

 Score = 35.2 bits (82), Expect = 0.003
 Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 10/67 (14%)

Query: 259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQR-SIR 317
            T+ +  + I  V+G GG+ I +I + +G +I + D G          V I+   + +  
Sbjct: 4   ETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDG---------TVYIAASDKEAAE 54

Query: 318 TAESMIM 324
            A+ MI 
Sbjct: 55  KAKKMIE 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	336
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	100.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	100.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.97
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.93
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.8
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.78
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.72
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.7
PRK13763	180	putative RNA-processing protein; Provisional	99.7
PRK13763	180	putative RNA-processing protein; Provisional	99.67
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.52
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.52
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.51
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.4
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.39
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.35
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.34
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.32
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.31
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.26
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.24
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	99.16
PF13014	43	KH_3: KH domain	99.09
PF13014	43	KH_3: KH domain	99.08
COG1094	194	Predicted RNA-binding protein (contains KH domains	99.05
smart00322	69	KH K homology RNA-binding domain.	99.05
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	99.04
smart00322	69	KH K homology RNA-binding domain.	99.0
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.96
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.72
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.59
KOG2113	394	consensus Predicted RNA binding protein, contains	98.58
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.56
PRK08406	140	transcription elongation factor NusA-like protein;	98.38
KOG2113	394	consensus Predicted RNA binding protein, contains	98.38
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.12
PRK08406	140	transcription elongation factor NusA-like protein;	98.11
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.1
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.82
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.81
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.74
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.7
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.66
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	97.63
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.49
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.45
PRK00106	535	hypothetical protein; Provisional	97.31
KOG2814	345	consensus Transcription coactivator complex, P50 c	97.29
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.29
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.28
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	97.28
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	97.24
PRK12704	520	phosphodiesterase; Provisional	97.23
COG0195	190	NusA Transcription elongation factor [Transcriptio	97.22
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	97.2
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.18
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.17
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.08
KOG2814	345	consensus Transcription coactivator complex, P50 c	97.05
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.99
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.96
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.94
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.92
PRK00106	535	hypothetical protein; Provisional	96.91
PRK12704	520	phosphodiesterase; Provisional	96.84
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.8
PRK00468	75	hypothetical protein; Provisional	96.61
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.61
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.57
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.57
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.55
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	96.54
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.54
TIGR01953	341	NusA transcription termination factor NusA. This m	96.49
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.49
PRK02821	77	hypothetical protein; Provisional	96.43
PRK12705	508	hypothetical protein; Provisional	96.36
COG1837	76	Predicted RNA-binding protein (contains KH domain)	96.21
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.16
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.12
PRK01064	78	hypothetical protein; Provisional	96.08
TIGR01953	341	NusA transcription termination factor NusA. This m	96.02
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.93
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	95.86
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.76
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.64
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.63
PRK00468	75	hypothetical protein; Provisional	95.53
PRK12705	508	hypothetical protein; Provisional	95.52
PRK02821	77	hypothetical protein; Provisional	95.35
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.32
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	94.98
COG1837	76	Predicted RNA-binding protein (contains KH domain)	94.65
PRK01064	78	hypothetical protein; Provisional	94.42
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	94.41
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	93.9
KOG2874	356	consensus rRNA processing protein [Translation, ri	93.79
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	93.38
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	93.05
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	92.98
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	92.95
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	92.86
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	92.81
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	92.57
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	92.52
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	92.3
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	92.03
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	91.97
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	91.79
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	91.52
COG1855	604	ATPase (PilT family) [General function prediction	90.69
KOG2874	356	consensus rRNA processing protein [Translation, ri	90.28
COG5166	657	Uncharacterized conserved protein [Function unknow	90.21
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	90.2
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	89.81
PRK06418	166	transcription elongation factor NusA-like protein;	89.12
COG1855	604	ATPase (PilT family) [General function prediction	88.95
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	88.39
COG1782	637	Predicted metal-dependent RNase, consists of a met	87.85
PRK13764	602	ATPase; Provisional	87.31
PRK13764	602	ATPase; Provisional	87.11
COG5166	657	Uncharacterized conserved protein [Function unknow	86.64
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	85.89
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	85.13
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	82.57
PRK06418	166	transcription elongation factor NusA-like protein;	82.39
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	82.16
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	81.39

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

Probab=100.00  E-value=3.9e-40  Score=278.86  Aligned_cols=285  Identities=27%  Similarity=0.439  Sum_probs=224.6

Q ss_pred             CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhcc
Q 019747           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH  110 (336)
Q Consensus        31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~  110 (336)
                      ....+.++||+.+..+|+||||+|++||.|+.+++++|+|++++     .++|+|+|+.+.+.|...++.|+-.|.+.+ 
T Consensus        44 k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~-----~peri~tisad~~ti~~ilk~iip~lee~f-  117 (390)
T KOG2192|consen   44 KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS-----GPERILTISADIETIGEILKKIIPTLEEGF-  117 (390)
T ss_pred             hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCCC-----CCceeEEEeccHHHHHHHHHHHhhhhhhCC-
Confidence            44579999999999999999999999999999999999999876     579999999999999888887776655543 


Q ss_pred             ccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 019747          111 AEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILL  190 (336)
Q Consensus       111 ~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~  190 (336)
                            ...+.+.++|+|..+.+|.|||++|++||+|++++.++++|..  +.|+++++|+|.+.|.+.+|..+++.|++
T Consensus       118 ------~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift--~c~p~stdrv~l~~g~~k~v~~~i~~il~  189 (390)
T KOG2192|consen  118 ------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT--ECCPHSTDRVVLIGGKPKRVVECIKIILD  189 (390)
T ss_pred             ------CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh--ccCCCCcceEEEecCCcchHHHHHHHHHH
Confidence                  2346799999999999999999999999999999999999987  78999999999999999999999999999


Q ss_pred             HhhcCcC------CCCCc-CCCccCCCccccCC--CCCCCCCCCCC----CCCCCCCC----------------------
Q 019747          191 KLSEDTL------YSQTM-TVPYTYAGVFFSGF--HGMPYGAVPPP----VPAVPHNT----------------------  235 (336)
Q Consensus       191 ~l~~~~~------~~~~~-~~~~~~~g~~~~~~--~~~p~~~~~~~----~~~~~~~~----------------------  235 (336)
                      ++.+.+.      |.+.. ...+.|+|..+...  .+.|. +.|++    +++++...                      
T Consensus       190 ~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pg-papqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~  268 (390)
T KOG2192|consen  190 LISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPG-PAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSA  268 (390)
T ss_pred             HhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCC-CCCCCCCCCCCCCCccccceeccCCCCCccccccccccc
Confidence            9988654      33332 23355666544322  11111 11111    11111101                      


Q ss_pred             ----------------CCCCCCCCCCCCccCCC---------CCCceEEEEEeccCcccceeccCCchHHHHHhHhCCeE
Q 019747          236 ----------------AAHYGPNMGGRKFQNNK---------DDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARI  290 (336)
Q Consensus       236 ----------------~~~~~~~g~~~~~~~~~---------~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I  290 (336)
                                      .|.|.+.++.....+++         ..+..+.+|.||+++-|.||||+|+.|++|++++||.|
T Consensus       269 detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~I  348 (390)
T KOG2192|consen  269 DETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASI  348 (390)
T ss_pred             cccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceE
Confidence                            12333332222111111         35678899999999999999999999999999999999


Q ss_pred             EEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhhc
Q 019747          291 KVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDR  333 (336)
Q Consensus       291 ~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~  333 (336)
                      +|..   |..++.+|+++|+||.+|++.|+.|++..++.+.+|
T Consensus       349 kide---pleGsedrIitItGTqdQIqnAQYLlQn~Vkq~rer  388 (390)
T KOG2192|consen  349 KIDE---PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYRER  388 (390)
T ss_pred             EecC---cCCCCCceEEEEeccHHHHhhHHHHHHHHHHhhhcc
Confidence            9987   577899999999999999999999999999987765

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

Probab=100.00  E-value=1.5e-37  Score=290.58  Aligned_cols=260  Identities=29%  Similarity=0.388  Sum_probs=214.0

Q ss_pred             CCCCCCCCCCCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHH
Q 019747           21 APVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDL  100 (336)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~  100 (336)
                      ++..|+.+.+ ...++.+|+||++.+|+||||+|+|||+|++++||++.+..+..... ...+.+.|+|+++.|+.|..+
T Consensus       126 ~~~~~~~~q~-~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~-~~~KplritGdp~~ve~a~~l  203 (600)
T KOG1676|consen  126 PPGGFPDNQG-SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT-GADKPLRITGDPDKVEQAKQL  203 (600)
T ss_pred             CCCCccccCC-ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC-CCCCceeecCCHHHHHHHHHH
Confidence            4555555544 67899999999999999999999999999999999999988765433 378899999999999999999


Q ss_pred             HHHHHHhhcccc-----ccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEE
Q 019747          101 VIDKLLTELHAE-----DQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT  175 (336)
Q Consensus       101 I~~~i~~~~~~~-----~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~  175 (336)
                      +.|.|.++....     ..+.+.-...++++.||.+.+|.|||++|++||+|+.+||++|+|.++++  +.+.+|.+.|.
T Consensus       204 V~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~--p~speR~~~Ii  281 (600)
T KOG1676|consen  204 VADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD--PSSPERPAQII  281 (600)
T ss_pred             HHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC--CCCccceeeee
Confidence            999888652211     01122233458999999999999999999999999999999999999665  47789999999


Q ss_pred             cCHHHHHHHHHHHHHHhhcCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCC
Q 019747          176 GTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDR  255 (336)
Q Consensus       176 G~~~~v~~A~~~i~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  255 (336)
                      |+.+.|+.|.++|.++|.+.....                  +.+..+..                           ...
T Consensus       282 G~~d~ie~Aa~lI~eii~~~~~~~------------------~~~~~~G~---------------------------P~~  316 (600)
T KOG1676|consen  282 GTVDQIEHAAELINEIIAEAEAGA------------------GGGMGGGA---------------------------PGL  316 (600)
T ss_pred             cCHHHHHHHHHHHHHHHHHHhccC------------------CCCcCCCC---------------------------ccc
Confidence            999999999999999998743211                  00000000                           011


Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  330 (336)
                      ...+++.||.+++|+||||+|++||.|..+|||++.+++. .+..+..+++++|+|.+.+|+.|++||.+++...
T Consensus       317 ~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~-~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~  390 (600)
T KOG1676|consen  317 VAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ-PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDI  390 (600)
T ss_pred             eeeEEEeccccccccccCCCccchhhhcccCCccccccCC-CCCCCccceEEEEecCcccchHHHHHHHHHhccc
Confidence            1278999999999999999999999999999999999997 4566678999999999999999999999998763

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

Probab=100.00  E-value=2.9e-35  Score=256.10  Aligned_cols=308  Identities=31%  Similarity=0.449  Sum_probs=246.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCC
Q 019747            2 ETNESSYVPSPDVHGKRSTAPVKSLSSDPTEK-PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGT   80 (336)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~   80 (336)
                      ...|+-..-++.++..+++.|-.....+.-++ .+++|||||+..+|.||||+|++|.+|+++|||+|++++..+++||.
T Consensus         5 ~~~d~~~~~s~kr~~~a~pe~~~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGT   84 (402)
T KOG2191|consen    5 VPIDSDAPDSRKRPLEAPPEPGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGT   84 (402)
T ss_pred             CcccCCCCCCccccccCCCCccccccccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCc
Confidence            34455566666777777776665444444444 49999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEEeeHHHHHHHHHHHHHHHHhhccccccCCC------CCCceeEEEEEecCccceeecCCChHHHHHHHhcCCE
Q 019747           81 TDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADD------VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV  154 (336)
Q Consensus        81 ~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~------~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~  154 (336)
                      +||+|.|+|+.+++...++.|.|+|++..+......+      .+....+++++|++.+|.||||+|.+||.|++++||.
T Consensus        85 TeRvcli~Gt~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~  164 (402)
T KOG2191|consen   85 TERVCLIQGTVEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAW  164 (402)
T ss_pred             cceEEEEeccHHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcc
Confidence            9999999999999999999999999998765422111      2333568999999999999999999999999999999


Q ss_pred             EEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCC
Q 019747          155 IKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHN  234 (336)
Q Consensus       155 I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~  234 (336)
                      |+|.+..+..-+..+|+|++.|++++..+|+.+|+.++.+++++..+++.++.+..+...                    
T Consensus       165 iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpva--------------------  224 (402)
T KOG2191|consen  165 IQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPVA--------------------  224 (402)
T ss_pred             eEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCccc--------------------
Confidence            999976565556789999999999999999999999999999999888877665533111                    


Q ss_pred             CCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChH
Q 019747          235 TAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQR  314 (336)
Q Consensus       235 ~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~  314 (336)
                         .+++.|.......+...........++....|..-|.+|.++..|...+|+.+.+....+...+...+ .-+.|.+-
T Consensus       225 ---NsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~g~gy~-~n~~g~~l  300 (402)
T KOG2191|consen  225 ---NSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMAGYGYN-TNILGLGL  300 (402)
T ss_pred             ---ccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccccceeeccccccccccccc-ccccchhh
Confidence               12222222222222233335566778899999999999999999999999999999876654455555 78889999


Q ss_pred             hHHHHHHHHHHHHHhhhhc
Q 019747          315 SIRTAESMIMQKVAYASDR  333 (336)
Q Consensus       315 ~v~~A~~~I~~~i~~~~~~  333 (336)
                      ++..|-.+|...+....++
T Consensus       301 s~~aa~g~L~~~~~~a~t~  319 (402)
T KOG2191|consen  301 SILAAEGVLAAKVASANTA  319 (402)
T ss_pred             hhhhhhhHHHHhhcccCcc
Confidence            9999999998887765544

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

Probab=100.00  E-value=8.3e-37  Score=273.17  Aligned_cols=281  Identities=25%  Similarity=0.430  Sum_probs=217.1

Q ss_pred             CCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhc
Q 019747           30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTEL  109 (336)
Q Consensus        30 ~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~  109 (336)
                      .....+.+|++||..+||.||||.|+|||.|-++|.|+|.|.+.++  .|..|++++|.|+++...+|+++|++.|..+.
T Consensus       194 ~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken--~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA  271 (584)
T KOG2193|consen  194 QQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN--AGAAEKIITVHSTPEGTSKACKMILEIMQKEA  271 (584)
T ss_pred             ccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc--CCcccCceEEecCccchHHHHHHHHHHHHHhh
Confidence            3456678999999999999999999999999999999999998765  48899999999999999999999999998884


Q ss_pred             cccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 019747          110 HAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL  189 (336)
Q Consensus       110 ~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~  189 (336)
                      ...    .......++++..+.++|+||||.|.+||+|+.+||++|.|.+--+......+|.+++.|+-++|..|..+|+
T Consensus       272 ~~~----k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eIm  347 (584)
T KOG2193|consen  272 VDD----KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIM  347 (584)
T ss_pred             hcc----chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHH
Confidence            332    2235688899999999999999999999999999999999998444444457999999999999999999999


Q ss_pred             HHhhcCcCCCCC---cCCCccCCCcc------ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEE
Q 019747          190 LKLSEDTLYSQT---MTVPYTYAGVF------FSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLT  260 (336)
Q Consensus       190 ~~l~~~~~~~~~---~~~~~~~~g~~------~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~  260 (336)
                      .+|++....+..   +-.++ ..|..      ++..++++++..||.    +......|.      .+..  ........
T Consensus       348 kKlre~yEnDl~a~s~q~~l-~P~l~~~~l~~f~ssS~~~~Ph~~Ps----~v~~a~p~~------~~hq--~pe~e~V~  414 (584)
T KOG2193|consen  348 KKLRECYENDLAAMSLQCHL-PPGLNLPALGLFPSSSAVSPPHFPPS----PVTFASPYP------LFHQ--NPEQEQVR  414 (584)
T ss_pred             HHHHHHHhhhHHHhhccCCC-CcccCccccCCCCcccccCCCCCCCC----ccccCCCch------hhhc--Ccchhhee
Confidence            999886332210   00000 00100      111111111111111    110000000      0000  12446788


Q ss_pred             EEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          261 IGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       261 v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      +.||...+|.|||++|.+||+|.+.+||.|+|.+++  .++..+|.|+|+|++++..+|+..|+.+|+++.
T Consensus       415 ~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE--~pdvseRMViItGppeaqfKAQgrifgKikEen  483 (584)
T KOG2193|consen  415 MFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE--IPDVSERMVIITGPPEAQFKAQGRIFGKIKEEN  483 (584)
T ss_pred             eeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC--CCCcceeEEEecCChHHHHhhhhhhhhhhhhhc
Confidence            999999999999999999999999999999999875  566889999999999999999999999999875

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

Probab=100.00  E-value=1e-33  Score=264.92  Aligned_cols=255  Identities=25%  Similarity=0.387  Sum_probs=207.9

Q ss_pred             CCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhc
Q 019747           30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTEL  109 (336)
Q Consensus        30 ~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~  109 (336)
                      +....++-+..||...||+||||+|+.|..|+.++||+|++....   .+..+|.+.+.|.+++|+.|+.+|.+.+.+..
T Consensus        49 ~s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~---s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~  125 (600)
T KOG1676|consen   49 PSDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADP---SGIGYRSVDLTGSPENVEVAKQLIGEVVSRGR  125 (600)
T ss_pred             CcccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCC---CCcccccccccCCcccHHHHHHhhhhhhhccC
Confidence            334567889999999999999999999999999999999986544   34578999999999999999999997655543


Q ss_pred             ccc-ccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 019747          110 HAE-DQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELI  188 (336)
Q Consensus       110 ~~~-~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i  188 (336)
                      ... ...+......+..++||.+.+|.||||+|++||.|++.+||++.+..+.... ...++.+.|+|++++|+.|..+|
T Consensus       126 ~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~-~~~~KplritGdp~~ve~a~~lV  204 (600)
T KOG1676|consen  126 PPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIA-TGADKPLRITGDPDKVEQAKQLV  204 (600)
T ss_pred             CCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcC-CCCCCceeecCCHHHHHHHHHHH
Confidence            111 1122234678999999999999999999999999999999999999854433 33678999999999999999999


Q ss_pred             HHHhhcCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcc
Q 019747          189 LLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHI  268 (336)
Q Consensus       189 ~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~v  268 (336)
                      .++|.+........                                 ..++++.          .....+.+|.||...|
T Consensus       205 ~dil~e~~~~~~g~---------------------------------~~~~g~~----------~g~~~~~~V~VPr~~V  241 (600)
T KOG1676|consen  205 ADILREEDDEVPGS---------------------------------GGHAGVR----------GGGSATREVKVPRSKV  241 (600)
T ss_pred             HHHHHhcccCCCcc---------------------------------ccccCcC----------ccccceeEEeccccce
Confidence            99999642211000                                 0011111          1122589999999999


Q ss_pred             cceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhhc
Q 019747          269 GFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDR  333 (336)
Q Consensus       269 g~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~  333 (336)
                      |.||||+|++||+|+.+||++|.|.+++++  .+.+|.+.|.|+.++|+.|.+||.++|+.....
T Consensus       242 G~IIGkgGE~IKklq~etG~KIQfkpDd~p--~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~  304 (600)
T KOG1676|consen  242 GIIIGKGGEMIKKLQNETGAKIQFKPDDDP--SSPERPAQIIGTVDQIEHAAELINEIIAEAEAG  304 (600)
T ss_pred             eeEEecCchHHHHHhhccCceeEeecCCCC--CCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence            999999999999999999999999998654  577999999999999999999999999987654

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

Probab=100.00  E-value=1.5e-30  Score=247.29  Aligned_cols=291  Identities=26%  Similarity=0.400  Sum_probs=211.7

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEe---------eHHHHHHHHHHHHHH
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG---------TIDEILRAVDLVIDK  104 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G---------~~~~v~~A~~~I~~~  104 (336)
                      ..++|+||+...+|.||||+|..||+|++++.++|+|..   ..++|.+|+++|+|         ..+++.+|..+|...
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            344999999999999999999999999999999999975   36889999999999         999999999999977


Q ss_pred             HHhhccccccCC-CCCC-ceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHH
Q 019747          105 LLTELHAEDQAD-DVGT-KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQM  182 (336)
Q Consensus       105 i~~~~~~~~~~~-~~~~-~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~  182 (336)
                      +.++.....+.. ..+. ..+++|+||.+++|.||||+|+.||+|+++|||+|++.++  ..+.+++|.|+|.|.+++|.
T Consensus       119 ~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~lP~ster~V~IsG~~~av~  196 (485)
T KOG2190|consen  119 LEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD--MLPNSTERAVTISGEPDAVK  196 (485)
T ss_pred             ccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC--CCCcccceeEEEcCchHHHH
Confidence            664433332222 1222 4789999999999999999999999999999999999984  77889999999999999999


Q ss_pred             HHHHHHHHHhhcCcCCCCC-cCC-----C-ccCCCccccCCCCCCCCCCCCCCCCC----------C-----------C-
Q 019747          183 RALELILLKLSEDTLYSQT-MTV-----P-YTYAGVFFSGFHGMPYGAVPPPVPAV----------P-----------H-  233 (336)
Q Consensus       183 ~A~~~i~~~l~~~~~~~~~-~~~-----~-~~~~g~~~~~~~~~p~~~~~~~~~~~----------~-----------~-  233 (336)
                      +|+..|...|.+.....+. ...     | ..+.+............+++.....+          |           + 
T Consensus       197 ~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~  276 (485)
T KOG2190|consen  197 KALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGL  276 (485)
T ss_pred             HHHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCc
Confidence            9999999999986432111 111     1 11111111111110000000000000          0           0 


Q ss_pred             -------------C-C---------CCCCCCCCC----------------CCCccCCCCCCceEEEEEeccCcccceecc
Q 019747          234 -------------N-T---------AAHYGPNMG----------------GRKFQNNKDDRTNSLTIGVADEHIGFVVGR  274 (336)
Q Consensus       234 -------------~-~---------~~~~~~~g~----------------~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk  274 (336)
                                   . +         .........                ........ ...++.++.||++++|+||||
T Consensus       277 ~i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk  355 (485)
T KOG2190|consen  277 VIRALRNETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGK  355 (485)
T ss_pred             cchhhhhhcCCceEeccccCcceeeeccccCcccccccchhhhhhccccccccccccc-cceeeeeeccCccccceeecc
Confidence                         0 0         000000000                00000011 445789999999999999999


Q ss_pred             CCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          275 GGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       275 ~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      +|.+|.+||+.|||.|.|....+ .....++.++|+|+..+...|+.++..++....
T Consensus       356 ~G~~iseir~~tgA~I~I~~~~~-~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~  411 (485)
T KOG2190|consen  356 GGAKISEIRQRTGASISILNKEE-VSGVREALVQITGMLREDLLAQYLIRARLSAPK  411 (485)
T ss_pred             cccchHHHHHhcCCceEEccccc-cCCcceeEEEecchhHHHHhhhhhcccccccCc
Confidence            99999999999999999998643 125679999999999999999999988776644

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

Probab=99.97  E-value=3.2e-31  Score=237.47  Aligned_cols=251  Identities=24%  Similarity=0.385  Sum_probs=212.0

Q ss_pred             CCCCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           28 SDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        28 ~~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      .+....++.++++-++.++|.+|||.|.+||+|+.+||++|.|+.-.+..-=.+||.|++.|+.++|..|-.+|+.+|.+
T Consensus       273 ~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre  352 (584)
T KOG2193|consen  273 DDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRE  352 (584)
T ss_pred             ccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHH
Confidence            35556789999999999999999999999999999999999998766543335699999999999999999999998887


Q ss_pred             hccccc-----------c-------------CC-------------C-------CCCceeEEEEEecCccceeecCCChH
Q 019747          108 ELHAED-----------Q-------------AD-------------D-------VGTKTKLRLIVPNSSCGSIIGKAGAT  143 (336)
Q Consensus       108 ~~~~~~-----------~-------------~~-------------~-------~~~~~~~~l~ip~~~~g~iIG~~G~~  143 (336)
                      -+.++-           .             ..             .       .......+++||...+|.|||++|..
T Consensus       353 ~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~h  432 (584)
T KOG2193|consen  353 CYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQH  432 (584)
T ss_pred             HHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchh
Confidence            654320           0             00             0       02446778999999999999999999


Q ss_pred             HHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCCcCCCccCCCccccCCCCCCCCC
Q 019747          144 IKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGA  223 (336)
Q Consensus       144 Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~  223 (336)
                      ||.|.+.+|+.|+|.+  ...++..+|.|+|+|++++..+|.-.|..+|.+..++.+.                      
T Consensus       433 IKql~RfagASiKIap--pE~pdvseRMViItGppeaqfKAQgrifgKikEenf~~Pk----------------------  488 (584)
T KOG2193|consen  433 IKQLSRFAGASIKIAP--PEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFLPK----------------------  488 (584)
T ss_pred             HHHHHHhccceeeecC--CCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccCCch----------------------
Confidence            9999999999999998  3456778999999999999999999999999887554322                      


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCc
Q 019747          224 VPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTS  303 (336)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~  303 (336)
                                                   ........+.||...+|+||||||.++++|+..|+|.|.|+++..+. ..+
T Consensus       489 -----------------------------eevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpd-End  538 (584)
T KOG2193|consen  489 -----------------------------EEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPD-END  538 (584)
T ss_pred             -----------------------------hhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCC-ccc
Confidence                                         23345678899999999999999999999999999999999987433 345


Q ss_pred             ceEEEEEcChHhHHHHHHHHHHHHHhhhh
Q 019747          304 ERKVTISGPQRSIRTAESMIMQKVAYASD  332 (336)
Q Consensus       304 ~r~v~I~G~~~~v~~A~~~I~~~i~~~~~  332 (336)
                      .-+|.|.|..-..+.|+..|.++|..++.
T Consensus       539 ~vivriiGhfyatq~aQrki~~iv~qvkq  567 (584)
T KOG2193|consen  539 QVIVRIIGHFYATQNAQRKIAHIVNQVKQ  567 (584)
T ss_pred             eeeeeeechhhcchHHHHHHHHHHHHHHH
Confidence            67899999999999999999999988763

>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=6.5e-25  Score=191.61  Aligned_cols=170  Identities=30%  Similarity=0.431  Sum_probs=143.9

Q ss_pred             ceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCC
Q 019747          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQ  200 (336)
Q Consensus       121 ~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~  200 (336)
                      .+.++++||+..+|.||||+|++|.+|++++||+|++.+..++.|+.+||+|.|.|+.+++....+.|.++|++.+....
T Consensus        38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~  117 (402)
T KOG2191|consen   38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVA  117 (402)
T ss_pred             ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhc
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999998755321


Q ss_pred             CcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHH
Q 019747          201 TMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIM  280 (336)
Q Consensus       201 ~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~  280 (336)
                      ....-+.            |.                              ...+....++.||+...|.||||+|.+||
T Consensus       118 k~v~~~~------------pq------------------------------t~~r~kqikivvPNstag~iigkggAtiK  155 (402)
T KOG2191|consen  118 KPVDILQ------------PQ------------------------------TPDRIKQIKIVVPNSTAGMIIGKGGATIK  155 (402)
T ss_pred             CCccccC------------CC------------------------------CccccceeEEeccCCcccceecCCcchHH
Confidence            1100000            00                              01233558999999999999999999999


Q ss_pred             HHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhh
Q 019747          281 EISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASD  332 (336)
Q Consensus       281 ~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~  332 (336)
                      .|++++||+|+|++.....-.-.+|+|+++|++++..+|..+|.++|.++..
T Consensus       156 ~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq  207 (402)
T KOG2191|consen  156 AIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ  207 (402)
T ss_pred             HHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence            9999999999999643223445689999999999999999999999988754

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

Probab=99.80  E-value=1.7e-18  Score=165.13  Aligned_cols=158  Identities=29%  Similarity=0.491  Sum_probs=134.2

Q ss_pred             eeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEc---------CHHHHHHHHHHHHHHh
Q 019747          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG---------TLDEQMRALELILLKL  192 (336)
Q Consensus       122 ~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G---------~~~~v~~A~~~i~~~l  192 (336)
                      .++|++++...+|.+||++|..+++|+.++.++|++..   .+++..+|+++|+|         ..+++.+|..+|...+
T Consensus        43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~---~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~  119 (485)
T KOG2190|consen   43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNE---SLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKL  119 (485)
T ss_pred             ceEEEEeccccceeEEccCcHHHHHHhhcccccceeec---CCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcc
Confidence            44899999999999999999999999999999999986   35677899999999         8999999999999887


Q ss_pred             hcCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCccccee
Q 019747          193 SEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVV  272 (336)
Q Consensus       193 ~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~II  272 (336)
                      .++.....+....                                              .....+++++.||..++|+||
T Consensus       120 ~~d~~~~~d~~~~----------------------------------------------~~~~~v~~RLlVp~sq~GslI  153 (485)
T KOG2190|consen  120 EEDDEAAEDNGED----------------------------------------------ASGPEVTCRLLVPSSQVGSLI  153 (485)
T ss_pred             cccccccccCCcc----------------------------------------------ccCCceEEEEEechhheeeee
Confidence            6433222110000                                              011137899999999999999


Q ss_pred             ccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747          273 GRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       273 Gk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  330 (336)
                      ||+|+.||+|++.|||+|.+.++  ..|.+.+|.|+|+|.++.|.+|...|..+|.+.
T Consensus       154 GK~G~~Ik~Ire~TgA~I~v~~~--~lP~ster~V~IsG~~~av~~al~~Is~~L~~~  209 (485)
T KOG2190|consen  154 GKGGSLIKEIREETGAKIRVSSD--MLPNSTERAVTISGEPDAVKKALVQISSRLLEN  209 (485)
T ss_pred             ccCcHHHHHHHHhcCceEEecCC--CCCcccceeEEEcCchHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999987  477889999999999999999999999998774

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

Probab=99.78  E-value=1.9e-18  Score=147.23  Aligned_cols=159  Identities=31%  Similarity=0.536  Sum_probs=134.4

Q ss_pred             CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhcc
Q 019747           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH  110 (336)
Q Consensus        31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~  110 (336)
                      ..+.+.+||||+.+++|.|||++|+.||+|++++.+++++-.  +..|++++|++.+.|.+.+|..+++.|++.|.+.--
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            344578999999999999999999999999999999999964  567899999999999999999999999976654410


Q ss_pred             cc--------------c-----cCC-C-----------------------------------------------------
Q 019747          111 AE--------------D-----QAD-D-----------------------------------------------------  117 (336)
Q Consensus       111 ~~--------------~-----~~~-~-----------------------------------------------------  117 (336)
                      +.              +     +.. +                                                     
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            00              0     000 0                                                     


Q ss_pred             ----------------------------------CCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCC
Q 019747          118 ----------------------------------VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHS  163 (336)
Q Consensus       118 ----------------------------------~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~  163 (336)
                                                        .....+.++.||.++-|.|||++|..|++|+.++|+.|++..   +
T Consensus       277 dtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide---p  353 (390)
T KOG2192|consen  277 DTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE---P  353 (390)
T ss_pred             CCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC---c
Confidence                                              022367789999999999999999999999999999999985   5


Q ss_pred             CCCCCceEEEEEcCHHHHHHHHHHHHHHhhc
Q 019747          164 YYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (336)
Q Consensus       164 ~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~  194 (336)
                      ..++.+|+++|+|+.++++.|..++...+..
T Consensus       354 leGsedrIitItGTqdQIqnAQYLlQn~Vkq  384 (390)
T KOG2192|consen  354 LEGSEDRIITITGTQDQIQNAQYLLQNSVKQ  384 (390)
T ss_pred             CCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence            6678999999999999999999999988764

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.72  E-value=4.4e-17  Score=136.33  Aligned_cols=139  Identities=22%  Similarity=0.284  Sum_probs=107.4

Q ss_pred             EEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEE---EcCHHHHHHHHHHHHHHhhcCcCCCCCc
Q 019747          126 LIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL---TGTLDEQMRALELILLKLSEDTLYSQTM  202 (336)
Q Consensus       126 l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I---~G~~~~v~~A~~~i~~~l~~~~~~~~~~  202 (336)
                      +.||.+.++.|||++|++|+.|+++||++|.+..        .+..|.|   +++++++.+|.++|..+........ ..
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~   72 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS--------ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEK-AL   72 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc--------CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHH-HH
Confidence            5689999999999999999999999999999996        2346777   7889999999999999776411000 00


Q ss_pred             CCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEecc---------Ccccceec
Q 019747          203 TVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVAD---------EHIGFVVG  273 (336)
Q Consensus       203 ~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~---------~~vg~IIG  273 (336)
                          ...                                           ........+.|+.         ...|+|||
T Consensus        73 ----~l~-------------------------------------------gd~y~~~Vi~I~~~~~~~~~~~~~~griIG  105 (172)
T TIGR03665        73 ----KLL-------------------------------------------DDDYMLEVIDLKEYGKSPNALRRIKGRIIG  105 (172)
T ss_pred             ----Hhc-------------------------------------------CCcceEEEEEhhhccCCHHHHHHHHhhhcC
Confidence                000                                           0000111223332         37899999


Q ss_pred             cCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747          274 RGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       274 k~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  330 (336)
                      ++|++++.|+..|||+|.|+          +..|.|.|++++++.|+.+|.++++..
T Consensus       106 ~~G~t~~~ie~~t~~~i~i~----------~~~v~i~G~~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665       106 EGGKTRRIIEELTGVSISVY----------GKTVGIIGDPEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             CCcHHHHHHHHHHCCeEEEc----------CCEEEEECCHHHHHHHHHHHHHHHcCC
Confidence            99999999999999999994          268999999999999999999988553

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.

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.70  E-value=9.4e-17  Score=134.32  Aligned_cols=138  Identities=17%  Similarity=0.216  Sum_probs=106.5

Q ss_pred             EEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEE---EeeHHHHHHHHHHHHHHHHhhccccccC
Q 019747           39 FLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMI---SGTIDEILRAVDLVIDKLLTELHAEDQA  115 (336)
Q Consensus        39 i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I---~G~~~~v~~A~~~I~~~i~~~~~~~~~~  115 (336)
                      |.||.+.+|.|||++|++|+.|+++|||+|++...        +..|.|   +++++++.+|..+|...... ...++..
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~--------~g~V~I~~~t~d~~~i~kA~~~I~~i~~g-f~~e~A~   72 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE--------TGEVKIEEEDEDPLAVMKAREVVKAIGRG-FSPEKAL   72 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--------CceEEEecCCCCHHHHHHHHHHHHHHHcC-CCHHHHH
Confidence            56899999999999999999999999999999642        245777   78899999999999864332 1111000


Q ss_pred             -CCCCCceeEEEEEec---------CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHH
Q 019747          116 -DDVGTKTKLRLIVPN---------SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRAL  185 (336)
Q Consensus       116 -~~~~~~~~~~l~ip~---------~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~  185 (336)
                       .-.+......+.|+.         ...|+|||++|.+++.|+..|||+|.|..          ..|.|.|++++++.|+
T Consensus        73 ~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~  142 (172)
T TIGR03665        73 KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----------KTVGIIGDPEQVQIAR  142 (172)
T ss_pred             HhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC----------CEEEEECCHHHHHHHH
Confidence             000111222234443         36899999999999999999999999974          5799999999999999


Q ss_pred             HHHHHHhhcC
Q 019747          186 ELILLKLSED  195 (336)
Q Consensus       186 ~~i~~~l~~~  195 (336)
                      ++|.+++...
T Consensus       143 ~~i~~li~~~  152 (172)
T TIGR03665       143 EAIEMLIEGA  152 (172)
T ss_pred             HHHHHHHcCC
Confidence            9999999664

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=99.70  E-value=3.2e-16  Score=132.02  Aligned_cols=141  Identities=19%  Similarity=0.246  Sum_probs=109.1

Q ss_pred             eeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEE----cCHHHHHHHHHHHHHHhhcCcC
Q 019747          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT----GTLDEQMRALELILLKLSEDTL  197 (336)
Q Consensus       122 ~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~----G~~~~v~~A~~~i~~~l~~~~~  197 (336)
                      ....+.||.+.++.|||++|.+|+.|+++||++|++..        .+..|.|.    ++++++.+|+++|..++.....
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 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS--------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSP   74 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC--------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCH
Confidence            46789999999999999999999999999999999996        23567785    8899999999999998764110


Q ss_pred             CCC--CcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEe---------ccC
Q 019747          198 YSQ--TMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGV---------ADE  266 (336)
Q Consensus       198 ~~~--~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~v---------p~~  266 (336)
                      ...  ....  .|                                                ....+.|         ...
T Consensus        75 e~A~~l~gd--~y------------------------------------------------~~~Vi~i~~~~~~~~~~~r  104 (180)
T PRK13763         75 EKALRLLDD--DY------------------------------------------------VLEVIDLSDYGDSPNALRR  104 (180)
T ss_pred             HHHHHHhCC--Cc------------------------------------------------eEEEEEhhhccCChhHHHH
Confidence            000  0000  00                                                0001111         113


Q ss_pred             cccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747          267 HIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       267 ~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  330 (336)
                      .+|+|||++|++++.|++.|||+|.|..          ..|.|.|++++++.|+..|.++++..
T Consensus       105 ~~griIG~~G~~~k~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        105 IKGRIIGEGGKTRRIIEELTGVDISVYG----------KTVAIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             HhhheeCCCcHHHHHHHHHHCcEEEEcC----------CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence            7899999999999999999999999953          34999999999999999999988553

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.67  E-value=6.3e-16  Score=130.22  Aligned_cols=143  Identities=18%  Similarity=0.226  Sum_probs=108.8

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEE----eeHHHHHHHHHHHHHHHHhhc
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMIS----GTIDEILRAVDLVIDKLLTEL  109 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~----G~~~~v~~A~~~I~~~i~~~~  109 (336)
                      .+...+.||.+.+|.|||++|++|+.|+++|||+|++...        +..|.|.    ++++.+.+|+.+|.+.+... 
T Consensus         2 ~~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~--------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf-   72 (180)
T PRK13763          2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE--------TGEVIIEPTDGEDPLAVLKARDIVKAIGRGF-   72 (180)
T ss_pred             CceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC--------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCC-
Confidence            3578899999999999999999999999999999999642        2456774    88999999999999655421 


Q ss_pred             cccccCCCCCCceeEE-EEEec---------CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHH
Q 019747          110 HAEDQADDVGTKTKLR-LIVPN---------SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD  179 (336)
Q Consensus       110 ~~~~~~~~~~~~~~~~-l~ip~---------~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~  179 (336)
                      ..++...-..+.+... +.+..         ..+|+|||++|.+++.|+..|||+|.|..          +.|.|.|+++
T Consensus        73 ~~e~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~----------~~v~i~G~~~  142 (180)
T PRK13763         73 SPEKALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG----------KTVAIIGDPE  142 (180)
T ss_pred             CHHHHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----------CEEEEEeCHH
Confidence            1000000000111211 11111         36899999999999999999999999975          3489999999


Q ss_pred             HHHHHHHHHHHHhhcC
Q 019747          180 EQMRALELILLKLSED  195 (336)
Q Consensus       180 ~v~~A~~~i~~~l~~~  195 (336)
                      ++..|.+.|.+++...
T Consensus       143 ~~~~A~~~I~~li~g~  158 (180)
T PRK13763        143 QVEIAREAIEMLIEGA  158 (180)
T ss_pred             HHHHHHHHHHHHHcCC
Confidence            9999999999999654

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.52  E-value=4.3e-14  Score=98.96  Aligned_cols=64  Identities=42%  Similarity=0.772  Sum_probs=59.1

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHH
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV  101 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I  101 (336)
                      ++||+||.+.+|.|||++|++|++|+++|||+|++.+...  ++..+|++.|.|+++++.+|+.+|
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--CCCCceEEEEEeCHHHHHHHHHhh
Confidence            4799999999999999999999999999999999987543  567899999999999999999887

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=99.52  E-value=3.9e-14  Score=99.19  Aligned_cols=63  Identities=38%  Similarity=0.592  Sum_probs=58.1

Q ss_pred             EEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHH
Q 019747          259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMI  323 (336)
Q Consensus       259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I  323 (336)
                      .++.||..++|+|||++|++|++|+++|||+|.+.++.+  ++..+|+|+|+|++++++.|+.||
T Consensus         2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--CCCCceEEEEEeCHHHHHHHHHhh
Confidence            689999999999999999999999999999999998643  356789999999999999999987

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

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

Probab=99.51  E-value=7.6e-14  Score=130.36  Aligned_cols=278  Identities=22%  Similarity=0.272  Sum_probs=190.4

Q ss_pred             CCCCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           28 SDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        28 ~~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      .....+++.+++.||...+-+++||.|++|+.|++.++++|.+...+-    ..++...+.|-+..+-.|...+++++..
T Consensus        61 e~e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~----g~e~~~~~~~~p~~v~~a~a~~~~~~~~  136 (608)
T KOG2279|consen   61 EQKPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV----GDERVLLISGFPVQVCKAKAAIHQILTE  136 (608)
T ss_pred             ecCchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC----CcccchhhccCCCCCChHHHHHHHHHhc
Confidence            445558899999999999999999999999999999999999976441    3567777777888888888888877666


Q ss_pred             hccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHH
Q 019747          108 ELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALEL  187 (336)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~  187 (336)
                      .           ..+...+.+|...+++++|++|.+++.|+..++++|.+..+  . -....+...|.|.......|..+
T Consensus       137 ~-----------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n--g-r~g~~~~~~i~~qqk~~~~a~~~  202 (608)
T KOG2279|consen  137 N-----------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN--G-RLGLSRLIKISGQQKEVAAAKHL  202 (608)
T ss_pred             C-----------Ccccccccchhhhcccccccchhhhcchhcccccccccccc--c-ccccccceecccccchHHHHHhh
Confidence            4           34677889999999999999999999999999999999873  1 12245788888888888899999


Q ss_pred             HHHHhhcCcCCCCC----------cCCCccCCCccc--cCCCCCCCCCCCCCCCCCCCCCCCCCCC-CC--C---CCCc-
Q 019747          188 ILLKLSEDTLYSQT----------MTVPYTYAGVFF--SGFHGMPYGAVPPPVPAVPHNTAAHYGP-NM--G---GRKF-  248 (336)
Q Consensus       188 i~~~l~~~~~~~~~----------~~~~~~~~g~~~--~~~~~~p~~~~~~~~~~~~~~~~~~~~~-~g--~---~~~~-  248 (336)
                      +.+.+.++......          +..+....+..+  .+..+.+.-+.--.....++..+.+.++ ..  +   .+.| 
T Consensus       203 ~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~  282 (608)
T KOG2279|consen  203 ILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWE  282 (608)
T ss_pred             hhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccC
Confidence            98888765331110          111111111111  0001111100000000011100000000 00  0   0011 


Q ss_pred             ----cC-CCCCCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCC--cceEEEEEcChHhHHHHHH
Q 019747          249 ----QN-NKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGT--SERKVTISGPQRSIRTAES  321 (336)
Q Consensus       249 ----~~-~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~--~~r~v~I~G~~~~v~~A~~  321 (336)
                          +. .........+|.+|...+|.|||+.|++++.+...+++.+.|.-..  ..+.  ...++.+.|+..-++.|..
T Consensus       283 ~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~p--yt~~v~~~qic~~egkqh~~n~vl~  360 (608)
T KOG2279|consen  283 KPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQP--YTSRVLQLQICVNEGKQHYENSVLE  360 (608)
T ss_pred             CccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEecc--ccchhhhhhhheecchhHHHHHHHh
Confidence                11 1234566789999999999999999999999999999998887642  1111  1267889999999999999


Q ss_pred             HHHH
Q 019747          322 MIMQ  325 (336)
Q Consensus       322 ~I~~  325 (336)
                      |+..
T Consensus       361 ml~~  364 (608)
T KOG2279|consen  361 MLTV  364 (608)
T ss_pred             hhhc
Confidence            9973

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.40  E-value=5.7e-13  Score=92.46  Aligned_cols=61  Identities=26%  Similarity=0.583  Sum_probs=56.0

Q ss_pred             EEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHH
Q 019747          259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIM  324 (336)
Q Consensus       259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~  324 (336)
                      .++.||.+++++|||++|++|++|+++|||+|.+++..     +.++.|+|+|+++++..|+.+|+
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            57899999999999999999999999999999998753     46899999999999999999873

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=99.39  E-value=4.5e-13  Score=92.35  Aligned_cols=60  Identities=33%  Similarity=0.570  Sum_probs=55.1

Q ss_pred             EEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHH
Q 019747          258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMI  323 (336)
Q Consensus       258 ~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I  323 (336)
                      |.+|.||.+++|+|||++|++|++|+++|||+|.++++     + ....|+|+|++++++.|+.+|
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            57899999999999999999999999999999999764     2 456999999999999999986

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

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

Probab=99.35  E-value=2.6e-12  Score=88.43  Aligned_cols=59  Identities=27%  Similarity=0.471  Sum_probs=53.9

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcC-hHhHHHHHHHHH
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP-QRSIRTAESMIM  324 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~  324 (336)
                      .+..+.||.+++|+|||++|++|++|+++|||+|.+++         ++.|.|+|+ +++++.|+.+|+
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            56789999999999999999999999999999999964         467999998 999999999873

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.34  E-value=1.4e-12  Score=89.84  Aligned_cols=60  Identities=30%  Similarity=0.577  Sum_probs=54.6

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHH
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV  101 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I  101 (336)
                      |.+|.||.+++|+|||++|++|++|+++|||+|+|++.     + .+..+.|.|+.+++.+|+++|
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            67999999999999999999999999999999999763     2 355999999999999999876

; 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=99.32  E-value=6e-12  Score=87.82  Aligned_cols=63  Identities=37%  Similarity=0.683  Sum_probs=56.9

Q ss_pred             EEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHH
Q 019747          259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIM  324 (336)
Q Consensus       259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~  324 (336)
                      .++.||.+++++|||++|++|++|++.|||+|.|++...   +..++.|+|.|+.++++.|+.+|.
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~~v~~a~~~i~   64 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVEKAKELIL   64 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHHHHHHHHHHhC
Confidence            578999999999999999999999999999999988532   356899999999999999999873

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.31  E-value=3.1e-12  Score=88.72  Aligned_cols=61  Identities=21%  Similarity=0.415  Sum_probs=55.8

Q ss_pred             EEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHH
Q 019747           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI  102 (336)
Q Consensus        37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~  102 (336)
                      .+|.||.++++.|||++|++|++|+++|||+|.|++..     ..++.|.|.|+.+++..|+.+|+
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            67999999999999999999999999999999998643     56889999999999999998873

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=99.26  E-value=2.8e-11  Score=84.41  Aligned_cols=62  Identities=40%  Similarity=0.756  Sum_probs=56.2

Q ss_pred             EEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHH
Q 019747           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV  101 (336)
Q Consensus        37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I  101 (336)
                      .+|.||.+++++|||++|++|++|+++|||.|.|+...+   ...++.+.|.|..+++..|..+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHHHHHHHHHHh
Confidence            689999999999999999999999999999999986542   35789999999999999998876

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=99.24  E-value=3.9e-11  Score=82.59  Aligned_cols=58  Identities=21%  Similarity=0.388  Sum_probs=52.5

Q ss_pred             EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEee-HHHHHHHHHHH
Q 019747           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLV  101 (336)
Q Consensus        35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~-~~~v~~A~~~I  101 (336)
                      .+..|.||.+++|.|||++|++|++|+++|||+|.+++         ++.|.|.|. .++++.|..+|
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---------~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---------DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---------CCEEEEEeCCHHHHHHHHHHh
Confidence            46789999999999999999999999999999999964         357999998 89999998876

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.

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=99.16  E-value=2.2e-10  Score=115.79  Aligned_cols=226  Identities=21%  Similarity=0.271  Sum_probs=162.4

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCC--CCceEEEEEeeHHHHHHHHHHHHHHHHhh---
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPG--TTDRIIMISGTIDEILRAVDLVIDKLLTE---  108 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~--~~~r~i~I~G~~~~v~~A~~~I~~~i~~~---  108 (336)
                      -+..++.+....+.++||++|.+++.++.++.+.++|+..+...+.  ...+...+....-++..++.++...+...   
T Consensus       200 ~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~~  279 (753)
T KOG2208|consen  200 SVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEII  279 (753)
T ss_pred             eEEEEeeccccchhhhccccccccccccccceeEEEcccccccchhhhhccccccceehhhhhHHHHHHhcChhhhhhhh
Confidence            4889999999999999999999999999999999999876643221  11122233333344444444443211111   


Q ss_pred             ---cccc-----------------------cc---C-------------------------CCCCCceeEEEEEecCccc
Q 019747          109 ---LHAE-----------------------DQ---A-------------------------DDVGTKTKLRLIVPNSSCG  134 (336)
Q Consensus       109 ---~~~~-----------------------~~---~-------------------------~~~~~~~~~~l~ip~~~~g  134 (336)
                         ++..                       ..   .                         ..........+.+-...+.
T Consensus       280 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~~  359 (753)
T KOG2208|consen  280 YRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEELK  359 (753)
T ss_pred             hccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhhh
Confidence               0000                       00   0                         0003446777888889999


Q ss_pred             eeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCCcCCCccCCCcccc
Q 019747          135 SIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFS  214 (336)
Q Consensus       135 ~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~~~~~~~~~g~~~~  214 (336)
                      .++|++|.++.+|++++.|.+.+..     .++.+..+.+.|...++.+|.+.+.....+....                
T Consensus       360 ~v~GK~~~ni~ki~e~~~~~i~~~~-----~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~----------------  418 (753)
T KOG2208|consen  360 FVIGKKGANIEKIREESQVKIDLPK-----QGSNNKKVVITGVSANDEKAVEDVEKIIAEILNS----------------  418 (753)
T ss_pred             hhcCCCCccHHHHHHhhhhceeccc-----ccCCCCCeEEeccccchhHHHHHHHHHHHhhhcc----------------
Confidence            9999999999999999999999987     3446788999999999999999999998774321                


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHHHHhHhC-CeEEEc
Q 019747          215 GFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISG-ARIKVS  293 (336)
Q Consensus       215 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sg-a~I~i~  293 (336)
                                                               .....+.+|...+.+|||.+|..|.+|...++ .+|+.+
T Consensus       419 -----------------------------------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~  457 (753)
T KOG2208|consen  419 -----------------------------------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQ  457 (753)
T ss_pred             -----------------------------------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecC
Confidence                                                     14567899999999999999999999999999 566665


Q ss_pred             cCCCCCCCCcceEEEEEcChHhHHHHHHHHHHH
Q 019747          294 DRGDFFSGTSERKVTISGPQRSIRTAESMIMQK  326 (336)
Q Consensus       294 ~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~  326 (336)
                      +..     .....+++.|....+..++.++..+
T Consensus       458 ~~~-----~~~~~~~~~~~~~dv~~~~~~~~~~  485 (753)
T KOG2208|consen  458 NNN-----NSSDMVTIRGISKDVEKSVSLLKAL  485 (753)
T ss_pred             CCC-----cccccceEeccccccchhHHHHHhh
Confidence            542     4456677777766666655555444

>PF13014 KH_3: KH domain

Probab=99.09  E-value=1.9e-10  Score=73.43  Aligned_cols=43  Identities=40%  Similarity=0.723  Sum_probs=38.7

Q ss_pred             cccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc
Q 019747          267 HIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG  311 (336)
Q Consensus       267 ~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G  311 (336)
                      +||+|||++|++|++|+++|||+|.|++.  ..++..++.|+|+|
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            58999999999999999999999999982  35567899999998

>PF13014 KH_3: KH domain

Probab=99.08  E-value=3.2e-10  Score=72.35  Aligned_cols=43  Identities=44%  Similarity=0.890  Sum_probs=38.8

Q ss_pred             ccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEe
Q 019747           45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG   89 (336)
Q Consensus        45 ~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G   89 (336)
                      ++|+|||++|++|++|+++|+|+|+|++  +..+...++.|+|+|
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            5899999999999999999999999988  345678899999987

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

Probab=99.05  E-value=1.1e-09  Score=90.86  Aligned_cols=144  Identities=18%  Similarity=0.232  Sum_probs=107.1

Q ss_pred             eeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEc-----CHHHHHHHHHHHHHHhhcCc
Q 019747          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG-----TLDEQMRALELILLKLSEDT  196 (336)
Q Consensus       122 ~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G-----~~~~v~~A~~~i~~~l~~~~  196 (336)
                      ....+.||.+..+.++|+.|...+.|++.++++|.++.+        +..|.|..     ++-.+.+|.+.|..+-....
T Consensus         8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~--------~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~   79 (194)
T COG1094           8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK--------TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFP   79 (194)
T ss_pred             ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC--------CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCC
Confidence            456789999999999999999999999999999999972        34455543     58899999999998865421


Q ss_pred             CCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEe------cc----C
Q 019747          197 LYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGV------AD----E  266 (336)
Q Consensus       197 ~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~v------p~----~  266 (336)
                      ...   .-.+.                                             ........+.+      +.    .
T Consensus        80 pe~---A~~LL---------------------------------------------~d~~~levIdi~~~~~~~~~~l~R  111 (194)
T COG1094          80 PEK---ALKLL---------------------------------------------EDDYYLEVIDLKDVVTLSGDHLRR  111 (194)
T ss_pred             HHH---HHHHh---------------------------------------------cCCcEEEEEEHHHhccCchhhhhH
Confidence            100   00000                                             00001111111      11    2


Q ss_pred             cccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          267 HIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       267 ~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      ..|+|||++|.+.+.|++.|||+|.|.          ..+|.|-|.+++++.|+..|..++....
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~----------g~tVaiiG~~~~v~iAr~AVemli~G~~  166 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVY----------GKTVAIIGGFEQVEIAREAVEMLINGAP  166 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEe----------CcEEEEecChhhhHHHHHHHHHHHcCCC
Confidence            569999999999999999999999996          4789999999999999999999887643

>smart00322 KH K homology RNA-binding domain

Probab=99.05  E-value=1.2e-09  Score=76.82  Aligned_cols=66  Identities=26%  Similarity=0.668  Sum_probs=59.9

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHH
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKV  327 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  327 (336)
                      .+..+.||..+++++||++|++|++|++.||++|.+....     .....+.|.|+++++..|+.+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-----~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-----SEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-----CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            6788999999999999999999999999999999997642     25789999999999999999998876

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=99.04  E-value=4.3e-10  Score=113.72  Aligned_cols=217  Identities=19%  Similarity=0.224  Sum_probs=160.8

Q ss_pred             EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhcccccc
Q 019747           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQ  114 (336)
Q Consensus        35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~  114 (336)
                      ..+.+.+-...+..++||+|.+|.+|+++++|.+.++...     ..+..+.++|...++.+|...+...+.+....   
T Consensus       347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~-----~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~---  418 (753)
T KOG2208|consen  347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQG-----SNNKKVVITGVSANDEKAVEDVEKIIAEILNS---  418 (753)
T ss_pred             eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccccc-----CCCCCeEEeccccchhHHHHHHHHHHHhhhcc---
Confidence            6678888889999999999999999999999999998743     67888999999999999999999655554221   


Q ss_pred             CCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcC-CEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhh
Q 019747          115 ADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQ-AVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLS  193 (336)
Q Consensus       115 ~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tg-a~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~  193 (336)
                            .....+.+|...+.+++|.+|..|..|..+++ ++|++...     ......+++.|....+..+...+..+..
T Consensus       419 ------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-----~~~~~~~~~~~~~~dv~~~~~~~~~~~~  487 (753)
T KOG2208|consen  419 ------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-----NNSSDMVTIRGISKDVEKSVSLLKALKA  487 (753)
T ss_pred             ------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-----CcccccceEeccccccchhHHHHHhhhh
Confidence                  24567999999999999999999999999999 77766652     2244557777877777776665555543


Q ss_pred             cCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceec
Q 019747          194 EDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVG  273 (336)
Q Consensus       194 ~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIG  273 (336)
                      ......                                                     .....+.....|..+.+..+|
T Consensus       488 ~a~~~~-----------------------------------------------------~~~~~~~d~~~~~~~~~~~~g  514 (753)
T KOG2208|consen  488 DAKNLK-----------------------------------------------------FRDVVTKDKLLPVKYIGKEIG  514 (753)
T ss_pred             hhhcch-----------------------------------------------------hhhhhhccccchHHhhccccc
Confidence            221100                                                     011134455566677777777


Q ss_pred             cCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          274 RGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       274 k~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      +.|..+...++..    .+....    +.++..++|.|..+.|..|+..+...+....
T Consensus       515 ~~~~i~d~~~~~~----i~~~~~----~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~~  564 (753)
T KOG2208|consen  515 KNGTIRDSLGDKS----IFPPNE----DEDHEKITIEGKLELVLEAPAELKALIEALI  564 (753)
T ss_pred             CceeeeccCCcee----eccccc----ccccceeeecccccchhhhHHHHHhcchhhh
Confidence            7766555554444    444322    2468999999999999999999988876644

>smart00322 KH K homology RNA-binding domain

Probab=99.00  E-value=3.7e-09  Score=74.18  Aligned_cols=67  Identities=30%  Similarity=0.658  Sum_probs=59.5

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHH
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL  105 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i  105 (336)
                      .++.+|.||.+.++.+||++|++|++|+++++++|.+....     .....+.|.|..+++..|..+|.+.+
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            46789999999999999999999999999999999997533     25788999999999999999998654

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

Probab=98.96  E-value=1.5e-08  Score=84.22  Aligned_cols=144  Identities=17%  Similarity=0.255  Sum_probs=105.6

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEe-----eHHHHHHHHHHHHHHHHhh
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-----TIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G-----~~~~v~~A~~~I~~~i~~~  108 (336)
                      ..+..+.||.+..+.+||+.|++.+.|++.+++++.+..        .+..+.|..     ++-.+.+|...|. .+-..
T Consensus         7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~--------~~~~V~i~~~~~t~Dp~~~~ka~d~Vk-AIgrG   77 (194)
T COG1094           7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS--------KTGSVTIRTTRKTEDPLALLKARDVVK-AIGRG   77 (194)
T ss_pred             cceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC--------CCCeEEEEecCCCCChHHHHHHHHHHH-HHhcC
Confidence            456779999999999999999999999999999999953        345566654     4567777877776 34333


Q ss_pred             ccccccCCCCCCceeEE------EEE-ec----CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcC
Q 019747          109 LHAEDQADDVGTKTKLR------LIV-PN----SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT  177 (336)
Q Consensus       109 ~~~~~~~~~~~~~~~~~------l~i-p~----~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~  177 (336)
                      ++.+....-.++...+.      +.- +.    ...|+|||++|.+.+.|++-|+|.|.+..          ..|.|-|.
T Consensus        78 F~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG~  147 (194)
T COG1094          78 FPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIGG  147 (194)
T ss_pred             CCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEecC
Confidence            32210000001111111      111 11    34689999999999999999999999986          57999999


Q ss_pred             HHHHHHHHHHHHHHhhcCc
Q 019747          178 LDEQMRALELILLKLSEDT  196 (336)
Q Consensus       178 ~~~v~~A~~~i~~~l~~~~  196 (336)
                      ++++..|+++|..++....
T Consensus       148 ~~~v~iAr~AVemli~G~~  166 (194)
T COG1094         148 FEQVEIAREAVEMLINGAP  166 (194)
T ss_pred             hhhhHHHHHHHHHHHcCCC
Confidence            9999999999999997653

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

Probab=98.72  E-value=9.2e-09  Score=96.80  Aligned_cols=145  Identities=28%  Similarity=0.465  Sum_probs=122.1

Q ss_pred             CceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCC
Q 019747          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS  199 (336)
Q Consensus       120 ~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~  199 (336)
                      ......+.++...+.+++|+.|.+|+.|+..++++|.+..++-    ..++.-.+.|-+.++..|..++..++.+..   
T Consensus        66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~---  138 (608)
T KOG2279|consen   66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV----GDERVLLISGFPVQVCKAKAAIHQILTENT---  138 (608)
T ss_pred             hheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC----CcccchhhccCCCCCChHHHHHHHHHhcCC---
Confidence            4577889999999999999999999999999999999987322    134555566688899999998888876532   


Q ss_pred             CCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchH
Q 019747          200 QTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNI  279 (336)
Q Consensus       200 ~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I  279 (336)
                                                                              .+...+.+|...+++|+|++|.++
T Consensus       139 --------------------------------------------------------pvk~~lsvpqr~~~~i~grgget~  162 (608)
T KOG2279|consen  139 --------------------------------------------------------PVSEQLSVPQRSVGRIIGRGGETI  162 (608)
T ss_pred             --------------------------------------------------------cccccccchhhhcccccccchhhh
Confidence                                                                    256778899999999999999999


Q ss_pred             HHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747          280 MEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       280 ~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  330 (336)
                      ..|+..++|+|.+..++.   ....+.+.|.|...-++.|+.++.+.+++.
T Consensus       163 ~si~~ss~aki~~d~ngr---~g~~~~~~i~~qqk~~~~a~~~~~~~~~ed  210 (608)
T KOG2279|consen  163 RSICKSSGAKITCDKNGR---LGLSRLIKISGQQKEVAAAKHLILEKVSED  210 (608)
T ss_pred             cchhcccccccccccccc---cccccceecccccchHHHHHhhhhccccch
Confidence            999999999999998742   345788999999999999999999998764

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

Probab=98.59  E-value=1.7e-07  Score=73.26  Aligned_cols=65  Identities=18%  Similarity=0.375  Sum_probs=52.8

Q ss_pred             CcccceeccCCchHHHHHhHhCCeEEEccCCCCCC--------------CCcceEEEEEcC---hHhHHHHHHHHHHHHH
Q 019747          266 EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFS--------------GTSERKVTISGP---QRSIRTAESMIMQKVA  328 (336)
Q Consensus       266 ~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~--------------~~~~r~v~I~G~---~~~v~~A~~~I~~~i~  328 (336)
                      +++|.|||++|++||+|+++|||+|.|..++....              ..++-.|.|++.   .++++.|..+|..++.
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            68899999999999999999999999988632111              123367889994   5999999999999887


Q ss_pred             hh
Q 019747          329 YA  330 (336)
Q Consensus       329 ~~  330 (336)
                      ..
T Consensus        95 ~~   96 (120)
T cd02395          95 PA   96 (120)
T ss_pred             cC
Confidence            54

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

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

Probab=98.58  E-value=8.7e-08  Score=84.28  Aligned_cols=154  Identities=21%  Similarity=0.269  Sum_probs=113.1

Q ss_pred             CceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCC
Q 019747          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS  199 (336)
Q Consensus       120 ~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~  199 (336)
                      +..+..+.+|...++.++|++|.+||.|+.+|.+.|+-+...      .+-++.++|..+.|..|++.|...-+.-   .
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~------eePiF~vTg~~edv~~aRrei~saaeH~---~   94 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG------EEPIFPVTGRHEDVRRARREIPSAAEHF---G   94 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC------CCCcceeccCchhHHHHhhcCcccccee---e
Confidence            567888999999999999999999999999999999887632      3468999999999999998776633221   0


Q ss_pred             CCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchH
Q 019747          200 QTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNI  279 (336)
Q Consensus       200 ~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I  279 (336)
                      .-.     |-+.   +.++.|. +                            ....+.+.++.+|...+|.|+|..|.+|
T Consensus        95 l~~-----~s~s---~Sgg~~~-~----------------------------s~s~qt~sy~svP~rvvglvv~~~~~ti  137 (394)
T KOG2113|consen   95 LIR-----ASRS---FSGGTNG-A----------------------------SASGQTTSYVSVPLRVVGLVVGPKGATI  137 (394)
T ss_pred             eee-----eccc---ccCCCcc-c----------------------------cccCCCceeeeccceeeeeccccccCcc
Confidence            000     0000   0000000 0                            0223467788899999999999999999


Q ss_pred             HHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHh-HHHHH-HHHHH
Q 019747          280 MEISQISGARIKVSDRGDFFSGTSERKVTISGPQRS-IRTAE-SMIMQ  325 (336)
Q Consensus       280 ~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~-v~~A~-~~I~~  325 (336)
                      +.|++.+...|.-.-+      ..+.++-++|.+++ +++|+ .-|++
T Consensus       138 ~~iqq~tnt~I~T~v~------~~~~Vf~Vtg~~~nC~kra~s~eie~  179 (394)
T KOG2113|consen  138 KRIQQFTNTYIATPVR------CGEPVFCVTGAPKNCVKRARSCEIEQ  179 (394)
T ss_pred             chheecccceEeeecc------CCCceEEEecCCcchhhhccccchhh
Confidence            9999999999887543      36899999998888 55566 34433

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

Probab=98.56  E-value=3.5e-07  Score=71.56  Aligned_cols=69  Identities=16%  Similarity=0.360  Sum_probs=51.2

Q ss_pred             EEEEecC------ccceeecCCChHHHHHHHHhCCeEEEcCCCCCC--------------CCCCceEEEEEee---HHHH
Q 019747           38 RFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFF--------------PGTTDRIIMISGT---IDEI   94 (336)
Q Consensus        38 ~i~ip~~------~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~--------------~~~~~r~i~I~G~---~~~v   94 (336)
                      +|+||.+      ++|.|||++|++||+|+++|||+|.|.......              .....--|.|.+.   .+.+
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            5666664      689999999999999999999999997642100              0112245777775   4889


Q ss_pred             HHHHHHHHHHHH
Q 019747           95 LRAVDLVIDKLL  106 (336)
Q Consensus        95 ~~A~~~I~~~i~  106 (336)
                      .+|+.+|...+.
T Consensus        83 ~~A~~~I~~ll~   94 (120)
T cd02395          83 AKAVEAIEELLK   94 (120)
T ss_pred             HHHHHHHHHHhc
Confidence            999999985554

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

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.38  E-value=9.4e-07  Score=71.20  Aligned_cols=104  Identities=20%  Similarity=0.279  Sum_probs=72.4

Q ss_pred             EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhcccccc
Q 019747           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQ  114 (336)
Q Consensus        35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~  114 (336)
                      =.+.++|+...+|..||++|++|+.|++..|-+|.+-..++                    .+...|...+...-...-.
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~--------------------d~~~fI~n~l~Pa~V~~v~   91 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD--------------------DPEEFIKNIFAPAAVRSVT   91 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC--------------------CHHHHHHHHcCCCEEEEEE
Confidence            46888999999999999999999999999999998854331                    1222222222111000000


Q ss_pred             CCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEe
Q 019747          115 ADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKIS  158 (336)
Q Consensus       115 ~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~  158 (336)
                      -...+......+.|+.+..+.+||++|.+++.++.-++-.+.+.
T Consensus        92 I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         92 IKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             EEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            00112234566779999999999999999999999998877664

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

Probab=98.38  E-value=8.3e-07  Score=78.22  Aligned_cols=140  Identities=17%  Similarity=0.252  Sum_probs=109.5

Q ss_pred             CcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhcc--
Q 019747           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH--  110 (336)
Q Consensus        33 ~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~--  110 (336)
                      +.++..+.+|..+++.|+|++|.+||.|+.+|...|.-+-..      .+.+..++|..+.+..|++.|.. -.+.+.  
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~------eePiF~vTg~~edv~~aRrei~s-aaeH~~l~   96 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG------EEPIFPVTGRHEDVRRARREIPS-AAEHFGLI   96 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC------CCCcceeccCchhHHHHhhcCcc-ccceeeee
Confidence            789999999999999999999999999999999999886432      45788999999999999999873 111110  


Q ss_pred             -------ccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHH-HH
Q 019747          111 -------AEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE-QM  182 (336)
Q Consensus       111 -------~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~-v~  182 (336)
                             ................-+|-..++.++|.+|.+|+.++..++..|...-.      ..+.++-++|-+++ ++
T Consensus        97 ~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~------~~~~Vf~Vtg~~~nC~k  170 (394)
T KOG2113|consen   97 RASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR------CGEPVFCVTGAPKNCVK  170 (394)
T ss_pred             eecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc------CCCceEEEecCCcchhh
Confidence                   00011122445667788888899999999999999999999988887752      14578889998888 45


Q ss_pred             HHH
Q 019747          183 RAL  185 (336)
Q Consensus       183 ~A~  185 (336)
                      +|.
T Consensus       171 ra~  173 (394)
T KOG2113|consen  171 RAR  173 (394)
T ss_pred             hcc
Confidence            555

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.12  E-value=1.3e-05  Score=80.04  Aligned_cols=64  Identities=28%  Similarity=0.396  Sum_probs=57.8

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  329 (336)
                      ....+.||.+++|.|||+||++||.|.++||++|.|.+         +..|.|.+ ..+.+++|+.+|...+..
T Consensus       578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            67789999999999999999999999999999999954         57888888 789999999999988773

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

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.11  E-value=1.2e-05  Score=64.77  Aligned_cols=104  Identities=20%  Similarity=0.361  Sum_probs=74.9

Q ss_pred             eeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCC
Q 019747          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQT  201 (336)
Q Consensus       122 ~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~  201 (336)
                      ....++|+...+|..||++|++|+.|++..|-+|.+-.-              .-      .+.+.|...+.......-.
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~--------------s~------d~~~fI~n~l~Pa~V~~v~   91 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY--------------SD------DPEEFIKNIFAPAAVRSVT   91 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc--------------CC------CHHHHHHHHcCCCEEEEEE
Confidence            567789999999999999999999999999988888751              11      2344555554331110000


Q ss_pred             cCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHH
Q 019747          202 MTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIME  281 (336)
Q Consensus       202 ~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~  281 (336)
                      ..                                                .........+.|+.+..|..|||+|++|+.
T Consensus        92 I~------------------------------------------------~~~~~~~~~V~V~~~d~g~aIGK~G~ni~l  123 (140)
T PRK08406         92 IK------------------------------------------------KKNGDKVAYVEVAPEDKGIAIGKNGKNIER  123 (140)
T ss_pred             EE------------------------------------------------ecCCcEEEEEEECccccchhhCCCCHHHHH
Confidence            00                                                011124567889999999999999999999


Q ss_pred             HHhHhCCeEEEc
Q 019747          282 ISQISGARIKVS  293 (336)
Q Consensus       282 I~~~sga~I~i~  293 (336)
                      ++..++-.+.|.
T Consensus       124 a~~L~~~~~di~  135 (140)
T PRK08406        124 AKDLAKRHFDID  135 (140)
T ss_pred             HHHHhCCccCCe
Confidence            999999988774

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.10  E-value=2.3e-05  Score=78.35  Aligned_cols=91  Identities=18%  Similarity=0.191  Sum_probs=75.3

Q ss_pred             HHHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEE
Q 019747           94 ILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVT  173 (336)
Q Consensus        94 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~  173 (336)
                      ..+++..|++.+.+.+... ...+...+....+.||.+.++.|||++|.+||.|.++||++|.|..         +..|.
T Consensus       551 A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------~G~V~  620 (719)
T TIGR02696       551 ARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------DGTVY  620 (719)
T ss_pred             HHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---------CcEEE
Confidence            3455666777777776655 4455566788899999999999999999999999999999999985         46788


Q ss_pred             EEcC-HHHHHHHHHHHHHHhhc
Q 019747          174 LTGT-LDEQMRALELILLKLSE  194 (336)
Q Consensus       174 I~G~-~~~v~~A~~~i~~~l~~  194 (336)
                      |.+. .+++++|+++|..+...
T Consensus       621 I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       621 IGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             EEeCCHHHHHHHHHHHHHhhCc
Confidence            8886 79999999999999874

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

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.82  E-value=4.6e-05  Score=61.22  Aligned_cols=103  Identities=24%  Similarity=0.329  Sum_probs=70.8

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccccC
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQA  115 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~  115 (336)
                      .+-++|....+|..||++|++|+.|++..|-+|.+-..+              .++...      |...+....-..-..
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys--------------~D~~~f------I~N~l~PA~V~~V~i   93 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYS--------------ENLEEF------VANKLAPAEVKNVTV   93 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcC--------------CCHHHH------HHHcCCCceEEEEEE
Confidence            788899999999999999999999999989888885432              112211      111111110000000


Q ss_pred             CCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEe
Q 019747          116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKIS  158 (336)
Q Consensus       116 ~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~  158 (336)
                      ...++.....+.||.+..+..||++|.+++...+-++-++.+.
T Consensus        94 ~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        94 SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            0112345677889999999999999999999999988777665

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

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

Probab=97.81  E-value=0.00014  Score=68.32  Aligned_cols=73  Identities=18%  Similarity=0.299  Sum_probs=56.1

Q ss_pred             eEEEEEecc------CcccceeccCCchHHHHHhHhCCeEEEccCCCCCC------------CC-cceEEEEEc-ChHhH
Q 019747          257 NSLTIGVAD------EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFS------------GT-SERKVTISG-PQRSI  316 (336)
Q Consensus       257 ~~~~v~vp~------~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~------------~~-~~r~v~I~G-~~~~v  316 (336)
                      .+.+|.||-      ++||+|||..|.++|+|+++|||+|.|-.++...+            +. ++=.+.|++ +.|.|
T Consensus       138 ~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki  217 (554)
T KOG0119|consen  138 LHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKI  217 (554)
T ss_pred             cccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHH
Confidence            445666663      58999999999999999999999999987422111            11 223466777 89999


Q ss_pred             HHHHHHHHHHHHh
Q 019747          317 RTAESMIMQKVAY  329 (336)
Q Consensus       317 ~~A~~~I~~~i~~  329 (336)
                      ++|..+|+.+|.+
T Consensus       218 ~~Ai~vienli~~  230 (554)
T KOG0119|consen  218 KKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999886

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.74  E-value=0.00014  Score=73.70  Aligned_cols=90  Identities=12%  Similarity=0.138  Sum_probs=70.0

Q ss_pred             HHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEE
Q 019747           95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL  174 (336)
Q Consensus        95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I  174 (336)
                      .++...|++.+.+.+.......+...+....+.||.+.++.|||++|.+||.|+++|||+|.|..         +..|.|
T Consensus       524 ~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---------dG~V~i  594 (684)
T TIGR03591       524 KEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---------DGTVKI  594 (684)
T ss_pred             HHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---------CeEEEE
Confidence            34455566666666555434444556778889999999999999999999999999999999985         355667


Q ss_pred             EcC-HHHHHHHHHHHHHHhh
Q 019747          175 TGT-LDEQMRALELILLKLS  193 (336)
Q Consensus       175 ~G~-~~~v~~A~~~i~~~l~  193 (336)
                      .+. .+.+.+|.+.|..+..
T Consensus       595 ~~~~~~~~~~a~~~I~~~~~  614 (684)
T TIGR03591       595 AASDGEAAEAAIKMIEGITA  614 (684)
T ss_pred             EECcHHHHHHHHHHHHhhhc
Confidence            665 7888999999888865

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).

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.70  E-value=0.00011  Score=74.65  Aligned_cols=64  Identities=31%  Similarity=0.421  Sum_probs=55.4

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  329 (336)
                      ....+.||.++++.|||++|++||+|.++|||+|.|.+         +..|.|.+ ..+.++.|+.+|..+...
T Consensus       551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---------dG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---------DGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            67789999999999999999999999999999999954         35566665 788999999999887653

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

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

Probab=97.66  E-value=0.00038  Score=65.50  Aligned_cols=74  Identities=19%  Similarity=0.193  Sum_probs=57.3

Q ss_pred             ceeEEEEEec------CccceeecCCChHHHHHHHhcCCEEEEeccC------------CCCCCC-CceEEEEEcC-HHH
Q 019747          121 KTKLRLIVPN------SSCGSIIGKAGATIKSFMDDSQAVIKISRLD------------HSYYGL-NDRLVTLTGT-LDE  180 (336)
Q Consensus       121 ~~~~~l~ip~------~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~------------~~~~~~-~~r~v~I~G~-~~~  180 (336)
                      .++-++.||.      +++|.|||.+|.+.|+|+++|||+|.|-.+.            ....+. .+=-|.|+++ .+.
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            5667787774      5689999999999999999999999998621            111122 2345778887 688


Q ss_pred             HHHHHHHHHHHhhc
Q 019747          181 QMRALELILLKLSE  194 (336)
Q Consensus       181 v~~A~~~i~~~l~~  194 (336)
                      |++|.+.|..+|.+
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999986

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=97.63  E-value=0.004  Score=54.02  Aligned_cols=129  Identities=16%  Similarity=0.150  Sum_probs=97.5

Q ss_pred             eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCCc
Q 019747          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTM  202 (336)
Q Consensus       123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~~  202 (336)
                      ...+.++......|+..+|..+++|-...|++|.+..        ....+.|+|+...+..+...|.+.+..-       
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--------~~~~i~I~g~k~~~~~i~~~i~~~l~~i-------   91 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--------SENRIRITGTKSTAEYIEASINEILSNI-------   91 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec--------CCcEEEEEccHHHHHHHHHHHHHHHhhc-------
Confidence            4445556788889999999999999888899999987        5578999999999999999998888652       


Q ss_pred             CCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceec----cCCch
Q 019747          203 TVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVG----RGGRN  278 (336)
Q Consensus       203 ~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIG----k~G~~  278 (336)
                                                                            .+..+.++.-.--.-.+    .....
T Consensus        92 ------------------------------------------------------~~~~i~l~~~~~~~~~~~~~~~~~~~  117 (210)
T PF14611_consen   92 ------------------------------------------------------RTEEIDLSPIISKHSEKKNSQFTPDL  117 (210)
T ss_pred             ------------------------------------------------------EEEEEecchhhhhhcccccccccHHH
Confidence                                                                  45556555432211111    13667


Q ss_pred             HHHHHhHhCCeEEEccCCCCCCCCcceEEEEE-----cChHhHHHHHHHHHHHHH
Q 019747          279 IMEISQISGARIKVSDRGDFFSGTSERKVTIS-----GPQRSIRTAESMIMQKVA  328 (336)
Q Consensus       279 I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~-----G~~~~v~~A~~~I~~~i~  328 (336)
                      |+.|++.|++.|...+.        ...+.|+     -.+..++.|+.++.-.+.
T Consensus       118 l~~i~~~t~~~ie~~~~--------~~~~~i~~~~~~~~~~~~~~a~RlL~~a~~  164 (210)
T PF14611_consen  118 LEEIQKLTNVYIEKNPD--------GNKLKISWLASPENEKRADRAKRLLLWALD  164 (210)
T ss_pred             HHHHHHHHcEEEEECCC--------CCeEEEEEEeeccccchHHHHHHHHHHhcc
Confidence            99999999999999764        2233333     578999999999988774

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.49  E-value=0.00042  Score=55.73  Aligned_cols=103  Identities=19%  Similarity=0.375  Sum_probs=71.7

Q ss_pred             eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCCc
Q 019747          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTM  202 (336)
Q Consensus       123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~~  202 (336)
                      ..-|+|....+|..+|++|.+|+.|++..|-+|.+-.              ...+++      +.|...+....-..-..
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe--------------ys~D~~------~fI~N~l~PA~V~~V~i   93 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE--------------YSENLE------EFVANKLAPAEVKNVTV   93 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE--------------cCCCHH------HHHHHcCCCceEEEEEE
Confidence            6778999999999999999999999988888887764              222222      22333322110000000


Q ss_pred             CCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHHH
Q 019747          203 TVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEI  282 (336)
Q Consensus       203 ~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I  282 (336)
                                                                     .+ ........+.||.+..+..|||+|++++..
T Consensus        94 -----------------------------------------------~~-~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la  125 (141)
T TIGR01952        94 -----------------------------------------------SE-FNGKKVAYVEVHPRDKGIAIGKGGKNIERA  125 (141)
T ss_pred             -----------------------------------------------Ec-CCCCEEEEEEEChhhhhhhhCCCchhHHHH
Confidence                                                           00 011255778899999999999999999999


Q ss_pred             HhHhCCeEEEc
Q 019747          283 SQISGARIKVS  293 (336)
Q Consensus       283 ~~~sga~I~i~  293 (336)
                      .+.+|-++.|.
T Consensus       126 ~~l~~~~~dI~  136 (141)
T TIGR01952       126 KELAKRHHDID  136 (141)
T ss_pred             HHHhcCccCCe
Confidence            99999988774

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.45  E-value=0.00032  Score=72.00  Aligned_cols=91  Identities=14%  Similarity=0.127  Sum_probs=73.4

Q ss_pred             HHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCE-EEEeccCCCCCCCCceEEE
Q 019747           95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV-IKISRLDHSYYGLNDRLVT  173 (336)
Q Consensus        95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~-I~i~~~~~~~~~~~~r~v~  173 (336)
                      .+|+..|++.|.+.+...+...+...+....+.||.+.++.|||.+|.+|+.|.++||+. |.+..         +-.|.
T Consensus       658 ~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---------dg~V~  728 (891)
T PLN00207        658 KDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---------DGTVK  728 (891)
T ss_pred             HHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---------CeeEE
Confidence            445556676777776665555555667888999999999999999999999999999998 88864         45688


Q ss_pred             EEcC-HHHHHHHHHHHHHHhhc
Q 019747          174 LTGT-LDEQMRALELILLKLSE  194 (336)
Q Consensus       174 I~G~-~~~v~~A~~~i~~~l~~  194 (336)
                      |.+. .+.+++|+++|..++..
T Consensus       729 I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        729 ITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             EEeCCHHHHHHHHHHHHHHhcC
Confidence            8886 79999999999988763

>PRK00106 hypothetical protein; Provisional

Probab=97.31  E-value=0.0014  Score=64.05  Aligned_cols=67  Identities=22%  Similarity=0.370  Sum_probs=57.3

Q ss_pred             CceEEEEEecc-CcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747          255 RTNSLTIGVAD-EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       255 ~~~~~~v~vp~-~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  329 (336)
                      ...+..|.+|+ ++-|+|||+.|.||+.+...||+.|.|++        ++..|+|+| .|=--+.|+.-+..+|..
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--------tp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD--------TPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC--------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            34667889998 67799999999999999999999999976        467888999 888888898888877764

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

Probab=97.29  E-value=0.00038  Score=62.51  Aligned_cols=70  Identities=19%  Similarity=0.306  Sum_probs=58.3

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHhhh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~~~  331 (336)
                      ....+.+++.+.|.|||++|.+.+.|+++|++.|.++.+     +++...|+|+| ..++|..|...|...|.+.-
T Consensus        57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p-----~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP-----NTNKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC-----CCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            556788999999999999999999999999999999774     33445555555 89999999999988877654

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

Probab=97.29  E-value=0.00099  Score=65.68  Aligned_cols=101  Identities=18%  Similarity=0.172  Sum_probs=80.1

Q ss_pred             EEEEeeHH--------HHHHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEE
Q 019747           85 IMISGTID--------EILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIK  156 (336)
Q Consensus        85 i~I~G~~~--------~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~  156 (336)
                      +.|.|-..        +...|+..|+..+.+.+...+...+...+....+.|+.+.++-+||++|.+|++|.++||++|.
T Consensus       507 iKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Id  586 (692)
T COG1185         507 IKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKID  586 (692)
T ss_pred             eeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEE
Confidence            66667533        3355667788777777766544455556778889999999999999999999999999999999


Q ss_pred             EeccCCCCCCCCceEEEEEcCH-HHHHHHHHHHHHHhhc
Q 019747          157 ISRLDHSYYGLNDRLVTLTGTL-DEQMRALELILLKLSE  194 (336)
Q Consensus       157 i~~~~~~~~~~~~r~v~I~G~~-~~v~~A~~~i~~~l~~  194 (336)
                      +..         +..|.|.++. +.+.+|++.|..+..+
T Consensus       587 ied---------dGtv~i~~s~~~~~~~ak~~I~~i~~e  616 (692)
T COG1185         587 IED---------DGTVKIAASDGESAKKAKERIEAITRE  616 (692)
T ss_pred             ecC---------CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence            984         3568888884 8889999999999855

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.28  E-value=0.00058  Score=70.14  Aligned_cols=64  Identities=20%  Similarity=0.393  Sum_probs=56.5

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCe-EEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGAR-IKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~-I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  329 (336)
                      ....+.||.++++.|||.||.+||.|.++||+. |.+.+         +-.|.|.+ ..+.++.|+.+|.+++..
T Consensus       685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---------dg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---------DGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---------CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            677899999999999999999999999999999 99854         56777777 899999999999888653

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=97.28  E-value=0.0014  Score=64.23  Aligned_cols=67  Identities=22%  Similarity=0.395  Sum_probs=56.9

Q ss_pred             CceEEEEEecc-CcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747          255 RTNSLTIGVAD-EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       255 ~~~~~~v~vp~-~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  329 (336)
                      ...+..|.+|+ ++-|+|||+.|.||+.+...||+.|.|++        ++..|+|+| .|=--+.|+.-+..+|..
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC--------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            34667889998 67799999999999999999999999975        467888999 888888888888877764

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

Probab=97.24  E-value=0.00042  Score=60.51  Aligned_cols=44  Identities=16%  Similarity=0.387  Sum_probs=38.7

Q ss_pred             CCCCCcEEEEEEEecC------ccceeecCCChHHHHHHHHhCCeEEEcC
Q 019747           29 DPTEKPTYIRFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSR   72 (336)
Q Consensus        29 ~~~~~~~~~~i~ip~~------~vg~iIGk~G~~Ik~I~~~tg~~I~i~~   72 (336)
                      +...-.++.+|+||..      +||.|+|++|.++|+|+++|||+|.|.-
T Consensus        86 ~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG  135 (259)
T KOG1588|consen   86 SGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG  135 (259)
T ss_pred             cCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence            3455568899999988      7999999999999999999999999964

>PRK12704 phosphodiesterase; Provisional

Probab=97.23  E-value=0.0016  Score=63.97  Aligned_cols=66  Identities=24%  Similarity=0.395  Sum_probs=55.2

Q ss_pred             ceEEEEEecc-CcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747          256 TNSLTIGVAD-EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       256 ~~~~~v~vp~-~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  329 (336)
                      ..+..|.+|+ ++-|+|||+.|.||+.+...||+.|.|++        ++..|+|+| .|---+.|+..+...+..
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence            4567888998 67799999999999999999999999975        467888999 777777888877766653

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=97.22  E-value=0.00091  Score=56.54  Aligned_cols=102  Identities=22%  Similarity=0.248  Sum_probs=69.3

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeH-HHHHHHHHHHHHHHHhhcccccc
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTI-DEILRAVDLVIDKLLTELHAEDQ  114 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~-~~v~~A~~~I~~~i~~~~~~~~~  114 (336)
                      .+-+.+-.+.+|..||++|++|+.|.++.|=+|.+-...+              ++ +-+..|+.-.  .+..-...   
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~--------------d~~~fI~nal~Pa--~v~~V~~~---  137 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE--------------DPAEFIKNALAPA--EVLSVNIK---  137 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCC--------------CHHHHHHHhcCcc--eEeEEEEE---
Confidence            3444555567899999999999999999998888754321              11 1122222100  00000000   


Q ss_pred             CCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEec
Q 019747          115 ADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (336)
Q Consensus       115 ~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~  159 (336)
                        ..+. ....+.||.+..+..||++|.+++-+.+-||-++.|..
T Consensus       138 --~~d~-~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         138 --EDDG-HVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             --eCCC-cEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence              0012 26778899999999999999999999999999999976

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

Probab=97.20  E-value=0.00072  Score=46.30  Aligned_cols=37  Identities=27%  Similarity=0.451  Sum_probs=34.5

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEE
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQL   70 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i   70 (336)
                      ...+.+.|+.+..|..|||+|.+|+.+++.++-+|.+
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            4689999999999999999999999999999988876

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

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

Probab=97.18  E-value=0.00071  Score=62.74  Aligned_cols=66  Identities=30%  Similarity=0.402  Sum_probs=55.3

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHH
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKV  327 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  327 (336)
                      .....+.|-+.+||.|||++|++|+.||..|.++|+|.+-      ..+..|+|-|.-+--.+|+..|...+
T Consensus        46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~------~~e~kv~ifg~~~m~~kaka~id~~~  111 (629)
T KOG0336|consen   46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC------DLEVKVTIFGINHMRKKAKASIDRGQ  111 (629)
T ss_pred             CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc------CceeEEEEechHHHHHHHHhhHhhhh
Confidence            3456777889999999999999999999999999999874      45788999998777777777765544

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

Probab=97.17  E-value=0.00052  Score=63.62  Aligned_cols=66  Identities=24%  Similarity=0.343  Sum_probs=53.7

Q ss_pred             CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHH
Q 019747           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI  102 (336)
Q Consensus        31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~  102 (336)
                      -.+++.+.+.|-+++||.|||++|++||.|+..|+++|++.+.      ..+-.++|.|...--.+|...|.
T Consensus        43 g~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~------~~e~kv~ifg~~~m~~kaka~id  108 (629)
T KOG0336|consen   43 GGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC------DLEVKVTIFGINHMRKKAKASID  108 (629)
T ss_pred             CCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc------CceeEEEEechHHHHHHHHhhHh
Confidence            3456788899999999999999999999999999999999753      35677889998665555555554

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

Probab=97.08  E-value=0.0016  Score=64.19  Aligned_cols=65  Identities=26%  Similarity=0.399  Sum_probs=56.9

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcC-hHhHHHHHHHHHHHHHhh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP-QRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~~~  330 (336)
                      ...++.|+.+.++.+||++|.+|++|.++||++|.|.+         +-+|.|.++ .+.+..|+..|.+++++.
T Consensus       552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied---------dGtv~i~~s~~~~~~~ak~~I~~i~~e~  617 (692)
T COG1185         552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED---------DGTVKIAASDGESAKKAKERIEAITREV  617 (692)
T ss_pred             ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC---------CCcEEEEecchHHHHHHHHHHHHHHhhc
Confidence            56788899999999999999999999999999999953         567888885 589999999999888654

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

Probab=97.05  E-value=0.00096  Score=60.01  Aligned_cols=71  Identities=20%  Similarity=0.333  Sum_probs=57.5

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      ....-++++....+.|||++|.|-++|+++|+|+|.++++.+    ..+.++.+.+..++|.+|.++|...|...
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~----n~~~i~i~~~~~~~V~~a~~Ri~~~ids~  126 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT----NKEEIKIIGISRNCVIQALERIAKLIDSD  126 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC----CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence            467788999999999999999999999999999999987652    33444555567888999999998444443

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.99  E-value=0.0018  Score=57.17  Aligned_cols=63  Identities=19%  Similarity=0.241  Sum_probs=53.5

Q ss_pred             EEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHhh
Q 019747          259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~~  330 (336)
                      ..+.||.++++.+||++|.+|+.|.+.+++.|.+-.         +-.|-|.+ +.+.++.|..+|+..-++.
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~---------NG~VwI~~~~~~~~~~a~~~I~~~e~~~  210 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ---------NGRIWIKGPDEEDEEIAIEAIKKIEREA  210 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC---------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence            578899999999999999999999999999999943         56777888 5669999999997655443

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

Probab=96.96  E-value=0.0045  Score=54.22  Aligned_cols=42  Identities=19%  Similarity=0.399  Sum_probs=36.3

Q ss_pred             CceEEEEEecc------CcccceeccCCchHHHHHhHhCCeEEEccCC
Q 019747          255 RTNSLTIGVAD------EHIGFVVGRGGRNIMEISQISGARIKVSDRG  296 (336)
Q Consensus       255 ~~~~~~v~vp~------~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~  296 (336)
                      ...+.+|.||-      ++||+|+|.+|.++|+|+++|||+|.|-.++
T Consensus        90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrg  137 (259)
T KOG1588|consen   90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRG  137 (259)
T ss_pred             eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCC
Confidence            34667777775      4999999999999999999999999998764

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

Probab=96.94  E-value=0.0014  Score=44.89  Aligned_cols=36  Identities=28%  Similarity=0.674  Sum_probs=33.9

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEE
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKV  292 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i  292 (336)
                      ....+.|+.+..|..|||+|.+|+.+++.+|-+|.+
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            678999999999999999999999999999988876

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

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.92  E-value=0.0018  Score=66.02  Aligned_cols=91  Identities=19%  Similarity=0.180  Sum_probs=70.3

Q ss_pred             HHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEE
Q 019747           95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL  174 (336)
Q Consensus        95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I  174 (336)
                      .+++..|++.|.+.+...+.......+....+.||.+.++.+||.+|.+|++|.++||+.|.+..         +..|.|
T Consensus       527 ~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d---------~G~v~i  597 (693)
T PRK11824        527 KEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED---------DGTVKI  597 (693)
T ss_pred             HHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC---------CceEEE
Confidence            45566677777777665544344445566778889999999999999999999999999877753         356788


Q ss_pred             EcC-HHHHHHHHHHHHHHhhc
Q 019747          175 TGT-LDEQMRALELILLKLSE  194 (336)
Q Consensus       175 ~G~-~~~v~~A~~~i~~~l~~  194 (336)
                      .+. .+.+.+|.+.|..+..+
T Consensus       598 ~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        598 AATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             EcccHHHHHHHHHHHHHhccc
Confidence            885 78899999999888753

>PRK00106 hypothetical protein; Provisional

Probab=96.91  E-value=0.0052  Score=60.24  Aligned_cols=68  Identities=19%  Similarity=0.242  Sum_probs=56.0

Q ss_pred             CCceeEEEEEec-CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHhhc
Q 019747          119 GTKTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSE  194 (336)
Q Consensus       119 ~~~~~~~l~ip~-~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~i~~~l~~  194 (336)
                      .......+.+|+ ++-|+|||+.|.+|+.++..||+.+.|+.        +...|+++|. |---+-|+..+..++.+
T Consensus       222 ~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--------tp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        222 TEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD--------TPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             hhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC--------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            345666788998 67799999999999999999999999987        5567889984 77777788877777765

>PRK12704 phosphodiesterase; Provisional

Probab=96.84  E-value=0.0053  Score=60.38  Aligned_cols=67  Identities=21%  Similarity=0.207  Sum_probs=53.3

Q ss_pred             CceeEEEEEec-CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHhhc
Q 019747          120 TKTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSE  194 (336)
Q Consensus       120 ~~~~~~l~ip~-~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~i~~~l~~  194 (336)
                      ......+.+|+ +.-|+|||+.|.+|+.++..||+.|.|+.        +...|.++|. +-.-+.|+..+..++.+
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence            44566788897 66799999999999999999999999987        5678889984 55555677766666654

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.80  E-value=0.0072  Score=59.37  Aligned_cols=68  Identities=21%  Similarity=0.220  Sum_probs=55.2

Q ss_pred             CCceeEEEEEec-CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHhhc
Q 019747          119 GTKTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSE  194 (336)
Q Consensus       119 ~~~~~~~l~ip~-~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~i~~~l~~  194 (336)
                      .......+.+|+ ++-|+|||+.|.+|+.++..||+.+.|+.        +...|+|++- |---+-|+..+..++.+
T Consensus       201 ~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       201 AETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             hhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC--------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            344666788897 66799999999999999999999999987        5567888884 66667777777777754

>PRK00468 hypothetical protein; Provisional

Probab=96.61  E-value=0.0026  Score=45.28  Aligned_cols=36  Identities=22%  Similarity=0.307  Sum_probs=30.9

Q ss_pred             CCCCcEEEEEEEecCccceeecCCChHHHHHHHHhC
Q 019747           30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSG   65 (336)
Q Consensus        30 ~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg   65 (336)
                      ..++.+.+++.+..+.+|.||||+|.+|+.||.--.
T Consensus        25 ~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~   60 (75)
T PRK00468         25 EGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK   60 (75)
T ss_pred             eCCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence            345668999999999999999999999999996443

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.61  E-value=0.0036  Score=63.80  Aligned_cols=64  Identities=30%  Similarity=0.428  Sum_probs=54.3

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  329 (336)
                      ....+.||.+.++.+||.||.+||.|.++||+.|.+.+         +-.|.|.+ ..+.++.|+.+|......
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            45567779999999999999999999999999888843         46677777 789999999999887753

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.57  E-value=0.0044  Score=54.65  Aligned_cols=64  Identities=27%  Similarity=0.345  Sum_probs=52.4

Q ss_pred             EEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEee-HHHHHHHHHHHHHHHHhhcc
Q 019747           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLVIDKLLTELH  110 (336)
Q Consensus        37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~-~~~v~~A~~~I~~~i~~~~~  110 (336)
                      +.+.||.++++.+||++|.+|+.|.++|++.|.+-.         +-.|-|.+. .+.+.+|..+|. .+.++.|
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~---------NG~VwI~~~~~~~~~~a~~~I~-~~e~~~~  211 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ---------NGRIWIKGPDEEDEEIAIEAIK-KIEREAH  211 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC---------CcEEEEeeCCHHHHHHHHHHHH-HHHhhhh
Confidence            568899999999999999999999999999999943         345777765 567888888887 6666644

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.57  E-value=0.0074  Score=51.10  Aligned_cols=37  Identities=24%  Similarity=0.526  Sum_probs=34.7

Q ss_pred             EEEEEeccCcccceeccCCchHHHHHhHhCCeEEEcc
Q 019747          258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSD  294 (336)
Q Consensus       258 ~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~  294 (336)
                      ...+.||.+..+..|||+|.+++.+.+.||-++.|..
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            6788899999999999999999999999999999965

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

Probab=96.55  E-value=0.005  Score=51.72  Aligned_cols=41  Identities=24%  Similarity=0.387  Sum_probs=35.4

Q ss_pred             CcEEEEEEEecC------ccceeecCCChHHHHHHHHhCCeEEEcCC
Q 019747           33 KPTYIRFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSRS   73 (336)
Q Consensus        33 ~~~~~~i~ip~~------~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~   73 (336)
                      ..++-++.||.+      +||+|||+.|+|+|+|++.++|+|-|...
T Consensus       146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            346678888865      79999999999999999999999999643

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=96.54  E-value=0.11  Score=45.08  Aligned_cols=129  Identities=13%  Similarity=0.113  Sum_probs=90.9

Q ss_pred             EEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccccCC
Q 019747           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQAD  116 (336)
Q Consensus        37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~  116 (336)
                      +.+.++....-++...+|..++.|-...|++|.+..        .+..+.|+|+...+..+...|.+.+..-        
T Consensus        28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--------~~~~i~I~g~k~~~~~i~~~i~~~l~~i--------   91 (210)
T PF14611_consen   28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--------SENRIRITGTKSTAEYIEASINEILSNI--------   91 (210)
T ss_pred             eEEEecchheeeeecCCchHHHHHHHhcCceEEEec--------CCcEEEEEccHHHHHHHHHHHHHHHhhc--------
Confidence            344445788899999999999999888899999964        3467999999999988888888544443        


Q ss_pred             CCCCceeEEEEEecCccceee----cCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEE-----cCHHHHHHHHHH
Q 019747          117 DVGTKTKLRLIVPNSSCGSII----GKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT-----GTLDEQMRALEL  187 (336)
Q Consensus       117 ~~~~~~~~~l~ip~~~~g~iI----G~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~-----G~~~~v~~A~~~  187 (336)
                           .+..+.++.-....-.    -.....++.|++.|++.|...++        ...+.|.     -....+..|..+
T Consensus        92 -----~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~--------~~~~~i~~~~~~~~~~~~~~a~Rl  158 (210)
T PF14611_consen   92 -----RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD--------GNKLKISWLASPENEKRADRAKRL  158 (210)
T ss_pred             -----EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC--------CCeEEEEEEeeccccchHHHHHHH
Confidence                 2334444422111111    12356789999999999998862        2233333     457788889988


Q ss_pred             HHHHhhc
Q 019747          188 ILLKLSE  194 (336)
Q Consensus       188 i~~~l~~  194 (336)
                      +...+..
T Consensus       159 L~~a~~~  165 (210)
T PF14611_consen  159 LLWALDY  165 (210)
T ss_pred             HHHhccC
Confidence            8888753

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.54  E-value=0.0054  Score=57.06  Aligned_cols=92  Identities=20%  Similarity=0.199  Sum_probs=64.4

Q ss_pred             ccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHH-HHHHHHHHHHHHHHhhccccccCCCCCCce
Q 019747           45 LAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTID-EILRAVDLVIDKLLTELHAEDQADDVGTKT  122 (336)
Q Consensus        45 ~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~-~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~  122 (336)
                      -+|..||++|++|+.|.++. |=+|.+-..++              ++. =+..|+.-.  .+..      -..+ +...
T Consensus       252 PvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~--------------D~~~fI~Nal~Pa--~V~~------V~i~-~~~~  308 (374)
T PRK12328        252 PIGATVGVKGVRINAVSKELNGENIDCIEYSN--------------VPEIFIARALAPA--IISS------VKIE-EEEK  308 (374)
T ss_pred             hHHhhcCCCcchHHHHHHHhCCCeEEEEEcCC--------------CHHHHHHHhCCCc--eeeE------EEEc-CCCc
Confidence            58999999999999999998 88888854432              011 111111100  0000      0000 2235


Q ss_pred             eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEec
Q 019747          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (336)
Q Consensus       123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~  159 (336)
                      ...+.||.++.+..||++|.+++-..+-||.+|.|..
T Consensus       309 ~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s  345 (374)
T PRK12328        309 KAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE  345 (374)
T ss_pred             EEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence            6788999999999999999999999999999999987

>TIGR01953 NusA transcription termination factor NusA

Probab=96.49  E-value=0.0065  Score=56.40  Aligned_cols=93  Identities=20%  Similarity=0.304  Sum_probs=64.7

Q ss_pred             ccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHH-HHHHHHHHHHHHHHhhccccccCCCCCCce
Q 019747           45 LAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTID-EILRAVDLVIDKLLTELHAEDQADDVGTKT  122 (336)
Q Consensus        45 ~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~-~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~  122 (336)
                      -+|..||++|++|+.|.++. |=+|.+-..++              ++. -+..|+.-..  +..-     .-.+ ....
T Consensus       244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~--------------d~~~fi~nal~Pa~--v~~v-----~i~~-~~~~  301 (341)
T TIGR01953       244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSD--------------DPAEFIANALSPAK--VISV-----EVLD-EDKH  301 (341)
T ss_pred             cceeeECCCCchHHHHHHHhCCCeEEEEEcCC--------------CHHHHHHHhcCCce--EEEE-----EEEc-CCCc
Confidence            48999999999999999998 88888854432              111 1111111100  0000     0001 1225


Q ss_pred             eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEec
Q 019747          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (336)
Q Consensus       123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~  159 (336)
                      ...+.||.++.+..||++|.+++-..+-||.+|.|..
T Consensus       302 ~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       302 SAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             EEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            7789999999999999999999999999999999976

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.49  E-value=0.0056  Score=57.18  Aligned_cols=94  Identities=21%  Similarity=0.301  Sum_probs=65.3

Q ss_pred             ccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHH-HHHHHHHHHHHHHHhhccccccCCCCCCce
Q 019747           45 LAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTID-EILRAVDLVIDKLLTELHAEDQADDVGTKT  122 (336)
Q Consensus        45 ~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~-~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~  122 (336)
                      -+|+.||++|.+|+.|.++. |=+|.+-..++              ++. -+..|+.-..  +..-     .-.+ +...
T Consensus       246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~--------------d~~~fi~nal~Pa~--v~~v-----~i~~-~~~~  303 (362)
T PRK12327        246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSE--------------DPAEFVANALSPAK--VVSV-----EVDD-EEEK  303 (362)
T ss_pred             chheeECCCChhHHHHHHHhCCCeEEEEEcCC--------------CHHHHHHHhCCCce--EEEE-----EEEc-CCCc
Confidence            58999999999999999998 88888854432              111 1111111100  0000     0001 2235


Q ss_pred             eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEecc
Q 019747          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL  160 (336)
Q Consensus       123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~  160 (336)
                      ...+.||.++.+..||++|.+++-..+-||.+|.|...
T Consensus       304 ~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        304 AARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             EEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            67899999999999999999999999999999999873

>PRK02821 hypothetical protein; Provisional

Probab=96.43  E-value=0.0031  Score=45.06  Aligned_cols=36  Identities=25%  Similarity=0.377  Sum_probs=30.9

Q ss_pred             CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCC
Q 019747           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGA   66 (336)
Q Consensus        31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~   66 (336)
                      .++.+.+++.+..+.+|.||||+|.+|+.||.--.+
T Consensus        27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            445588999999999999999999999999966543

>PRK12705 hypothetical protein; Provisional

Probab=96.36  E-value=0.01  Score=57.80  Aligned_cols=66  Identities=21%  Similarity=0.316  Sum_probs=52.1

Q ss_pred             ceEEEEEecc-CcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747          256 TNSLTIGVAD-EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       256 ~~~~~v~vp~-~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~  329 (336)
                      .....|.+|+ ++-|+|||+.|.||+.+...||+.|.|++        ....|+|++ .|.--+.|+..+..+|..
T Consensus       197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--------tp~~V~ls~fdp~rreia~~~l~~Li~d  264 (508)
T PRK12705        197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD--------TPEAVVISSFNPIRREIARLTLEKLLAD  264 (508)
T ss_pred             heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC--------CccchhhcccCccchHHHHHHHHHHHhc
Confidence            3567788897 56699999999999999999999999976        345677777 666666777776666543

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

Probab=96.21  E-value=0.007  Score=42.98  Aligned_cols=34  Identities=35%  Similarity=0.418  Sum_probs=30.4

Q ss_pred             CCCcEEEEEEEecCccceeecCCChHHHHHHHHh
Q 019747           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQS   64 (336)
Q Consensus        31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~t   64 (336)
                      .+..+.+++-+.....|.||||+|.+|+.||.--
T Consensus        26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             cCCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            3677889999999999999999999999999543

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.16  E-value=0.017  Score=53.89  Aligned_cols=40  Identities=20%  Similarity=0.383  Sum_probs=36.7

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCC
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRG  296 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~  296 (336)
                      ....+.||.+..+..|||+|.|++-..+.||.+|.|..-+
T Consensus       308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~  347 (374)
T PRK12328        308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG  347 (374)
T ss_pred             cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence            4678899999999999999999999999999999998854

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.12  E-value=0.0078  Score=57.01  Aligned_cols=93  Identities=23%  Similarity=0.262  Sum_probs=64.2

Q ss_pred             ccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHH-HHHHHHHHHHHHHHhhccccccCCCCCCce
Q 019747           45 LAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTID-EILRAVDLVIDKLLTELHAEDQADDVGTKT  122 (336)
Q Consensus        45 ~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~-~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~  122 (336)
                      -+|..||++|++|+.|.++. |=+|.|-..++              ++. =|..|+.-.  .+..-     ...+ ....
T Consensus       278 PvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~--------------Dp~~fI~NaLsPA--~V~~V-----~i~~-~~~k  335 (449)
T PRK12329        278 PVGACIGARGSRIQAVVNELRGEKIDVIRWSP--------------DPATYIANALSPA--RVDEV-----RLVD-PEGR  335 (449)
T ss_pred             hhhccCCCCcchHHHHHHHhCCCeEEEEEcCC--------------CHHHHHHHhcCCc--eeeEE-----EEEc-CCCc
Confidence            58999999999999999998 88888854431              111 111111110  00000     0001 1224


Q ss_pred             eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEec
Q 019747          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (336)
Q Consensus       123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~  159 (336)
                      ...+.||.++.+..||++|.+++-..+-||.+|.|..
T Consensus       336 ~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        336 HAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             EEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            5789999999999999999999999999999999976

>PRK01064 hypothetical protein; Provisional

Probab=96.08  E-value=0.0077  Score=43.20  Aligned_cols=34  Identities=26%  Similarity=0.420  Sum_probs=30.3

Q ss_pred             CCCcEEEEEEEecCccceeecCCChHHHHHHHHh
Q 019747           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQS   64 (336)
Q Consensus        31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~t   64 (336)
                      .++.+.+++.|.....|.+|||+|.+|+.|+.-.
T Consensus        26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            3567899999999999999999999999999643

>TIGR01953 NusA transcription termination factor NusA

Probab=96.02  E-value=0.022  Score=52.90  Aligned_cols=38  Identities=29%  Similarity=0.593  Sum_probs=35.6

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEcc
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSD  294 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~  294 (336)
                      ....+.||.+..+..|||+|.|++-..+.||.+|.|..
T Consensus       301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            56789999999999999999999999999999999975

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.

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

Probab=95.93  E-value=0.01  Score=49.84  Aligned_cols=31  Identities=26%  Similarity=0.644  Sum_probs=28.9

Q ss_pred             CcccceeccCCchHHHHHhHhCCeEEEccCC
Q 019747          266 EHIGFVVGRGGRNIMEISQISGARIKVSDRG  296 (336)
Q Consensus       266 ~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~  296 (336)
                      ++||.|||+.|.++|+|++.|+|+|-|-..+
T Consensus       163 NFVGLliGPRG~Tlk~le~~s~akIaIRG~g  193 (269)
T COG5176         163 NFVGLLIGPRGSTLKQLERISRAKIAIRGSG  193 (269)
T ss_pred             ceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence            6999999999999999999999999997753

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

Probab=95.86  E-value=0.025  Score=54.57  Aligned_cols=93  Identities=16%  Similarity=0.166  Sum_probs=75.0

Q ss_pred             HHHHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEE
Q 019747           93 EILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLV  172 (336)
Q Consensus        93 ~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v  172 (336)
                      +...|...|++.+.+.++..+.......+....+.++.+....+||++|...|+|..+||+.-.++          +..+
T Consensus       568 ~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD----------e~t~  637 (760)
T KOG1067|consen  568 KAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD----------EGTF  637 (760)
T ss_pred             hhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec----------CceE
Confidence            445677788888888877776566666778889999999999999999999999999999655554          3567


Q ss_pred             EEEcC-HHHHHHHHHHHHHHhhcC
Q 019747          173 TLTGT-LDEQMRALELILLKLSED  195 (336)
Q Consensus       173 ~I~G~-~~~v~~A~~~i~~~l~~~  195 (336)
                      .|... ..+.++|++.|..++...
T Consensus       638 ~i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  638 SIFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             EEEecCHHHHHHHHHHHHHHhcCc
Confidence            77776 778899999999987653

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.76  E-value=0.03  Score=52.41  Aligned_cols=39  Identities=18%  Similarity=0.438  Sum_probs=36.1

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccC
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDR  295 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~  295 (336)
                      ....+.||.+..+.-|||+|.|++--...||.+|.|...
T Consensus       303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            567899999999999999999999999999999999764

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.64  E-value=0.027  Score=54.61  Aligned_cols=39  Identities=23%  Similarity=0.534  Sum_probs=36.2

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccC
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDR  295 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~  295 (336)
                      ....+.||.+..+.-|||+|.|++...+.||.+|.|...
T Consensus       302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            467899999999999999999999999999999999764

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.63  E-value=0.028  Score=54.47  Aligned_cols=91  Identities=19%  Similarity=0.275  Sum_probs=64.2

Q ss_pred             ccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccc-cC-CCCCCc
Q 019747           45 LAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAED-QA-DDVGTK  121 (336)
Q Consensus        45 ~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~-~~-~~~~~~  121 (336)
                      -+|..||++|++|+.|.++. |=+|.|-..++              ++..          .+...+.... .. .-....
T Consensus       246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~--------------d~~~----------fi~nal~pa~v~~v~~~~~~  301 (470)
T PRK09202        246 PVGACVGMRGSRIQAISNELGGEKIDIILWSD--------------DPAQ----------FIINALSPAEVSSVVVDEDE  301 (470)
T ss_pred             hhHccCCCCCchHHHHHHHhCCCeEEEEEcCC--------------CHHH----------HHHHhCCCCEEEEEEEeCCC
Confidence            48999999999999999998 78888854431              1111          1111111100 00 000112


Q ss_pred             eeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEec
Q 019747          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (336)
Q Consensus       122 ~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~  159 (336)
                      ....+.||..+.+..||++|.+++-..+-||.+|.|..
T Consensus       302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            47789999999999999999999999999999999986

>PRK00468 hypothetical protein; Provisional

Probab=95.53  E-value=0.016  Score=41.30  Aligned_cols=33  Identities=30%  Similarity=0.460  Sum_probs=28.5

Q ss_pred             CceEEEEEeccCcccceeccCCchHHHHHhHhC
Q 019747          255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISG  287 (336)
Q Consensus       255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sg  287 (336)
                      ....+.+.+.++-+|+||||+|.+|+.||..-.
T Consensus        28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~   60 (75)
T PRK00468         28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK   60 (75)
T ss_pred             CeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence            346788999999999999999999999987654

>PRK12705 hypothetical protein; Provisional

Probab=95.52  E-value=0.033  Score=54.35  Aligned_cols=66  Identities=18%  Similarity=0.185  Sum_probs=46.0

Q ss_pred             CceeEEEEEec-CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHhh
Q 019747          120 TKTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLS  193 (336)
Q Consensus       120 ~~~~~~l~ip~-~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~i~~~l~  193 (336)
                      ......+.+|+ +.-|+|||+.|.+|+.++..||+.+.|+.        +...|++.+. +..-+.|...+..++.
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--------tp~~V~ls~fdp~rreia~~~l~~Li~  263 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD--------TPEAVVISSFNPIRREIARLTLEKLLA  263 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC--------CccchhhcccCccchHHHHHHHHHHHh
Confidence            44556678887 66799999999999999999999999986        3334555544 3333344444444443

>PRK02821 hypothetical protein; Provisional

Probab=95.35  E-value=0.019  Score=41.06  Aligned_cols=34  Identities=29%  Similarity=0.567  Sum_probs=29.7

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCe
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGAR  289 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~  289 (336)
                      ...+.+.+.++-+|+||||+|.+|+.||..-.+-
T Consensus        30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~   63 (77)
T PRK02821         30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI   63 (77)
T ss_pred             cEEEEEEEChhhCcceeCCCCchHHHHHHHHHHh
Confidence            3678899999999999999999999999876653

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.32  E-value=0.038  Score=52.44  Aligned_cols=38  Identities=18%  Similarity=0.490  Sum_probs=35.3

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEcc
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSD  294 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~  294 (336)
                      ....+.||.+..+.-|||+|.|++--...||.+|.|..
T Consensus       335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            45689999999999999999999999999999999976

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

Probab=94.98  E-value=0.073  Score=51.51  Aligned_cols=64  Identities=22%  Similarity=0.214  Sum_probs=54.1

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHhh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~~  330 (336)
                      ....+.|+.+....+||.+|.+.|+|..+||+.-.+          ++.++.|-. +++..+.|+.+|...+...
T Consensus       597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v----------De~t~~i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV----------DEGTFSIFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             eeeEEeecchhhheeecCccceeeeEeeeccceeee----------cCceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence            667888999999999999999999999999955554          356777776 8999999999999887653

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

Probab=94.65  E-value=0.042  Score=39.03  Aligned_cols=32  Identities=34%  Similarity=0.581  Sum_probs=27.9

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhC
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISG  287 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sg  287 (336)
                      ....++.+.+.-.|.||||+|.+|+.||-.-.
T Consensus        29 ~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~   60 (76)
T COG1837          29 TVTIELRVAPEDMGKVIGKQGRTIQAIRTLLS   60 (76)
T ss_pred             eEEEEEEECcccccceecCCChhHHHHHHHHH
Confidence            46688899999999999999999999987654

>PRK01064 hypothetical protein; Provisional

Probab=94.42  E-value=0.041  Score=39.46  Aligned_cols=33  Identities=30%  Similarity=0.444  Sum_probs=28.5

Q ss_pred             CceEEEEEeccCcccceeccCCchHHHHHhHhC
Q 019747          255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISG  287 (336)
Q Consensus       255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sg  287 (336)
                      ....+.+.|.+.-.|.+|||+|.+|+.||....
T Consensus        28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~   60 (78)
T PRK01064         28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV   60 (78)
T ss_pred             CEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence            346788999999999999999999999988644

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=94.41  E-value=0.02  Score=40.66  Aligned_cols=35  Identities=34%  Similarity=0.385  Sum_probs=29.4

Q ss_pred             CCcEEEEEEEecCccceeecCCChHHHHHHHHhCC
Q 019747           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGA   66 (336)
Q Consensus        32 ~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~   66 (336)
                      .+...+.+.+..+..|.+|||+|.+++.||.-.+.
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            45567888889999999999999999999965543

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

Probab=93.90  E-value=0.023  Score=59.08  Aligned_cols=70  Identities=24%  Similarity=0.162  Sum_probs=58.5

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHH
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKV  327 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  327 (336)
                      ....++.+|-....+|||++|.+|+.++..|||.|+|.+-+  ..+..+|.+.+.|.++.+..|...|.-.+
T Consensus      1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq--~~Nqaers~~~kg~p~~~r~a~~~I~~~i 1408 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--PDNQAERSKAPKGRPPSQRVATSPIGLPI 1408 (2131)
T ss_pred             ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--CccchhhhcccCCCChhhhhhhcccccee
Confidence            34567788888899999999999999999999999998832  12356899999999999999988775544

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

Probab=93.79  E-value=0.13  Score=45.41  Aligned_cols=51  Identities=14%  Similarity=0.325  Sum_probs=46.8

Q ss_pred             cceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747          269 GFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       269 g~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  329 (336)
                      .++||.+|++++.|+-.|.|.|-++          ..+|.+.|+...+..++..+.+.+.+
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            6789999999999999999999995          36899999999999999999998865

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

Probab=93.38  E-value=0.17  Score=34.69  Aligned_cols=35  Identities=29%  Similarity=0.337  Sum_probs=28.5

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeE
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARI   68 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I   68 (336)
                      .....+.+.....|.+||++|.+|+.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            45666667666789999999999999999988544

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

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

Probab=93.05  E-value=0.066  Score=44.88  Aligned_cols=55  Identities=25%  Similarity=0.491  Sum_probs=49.2

Q ss_pred             cCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747          265 DEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       265 ~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  329 (336)
                      +..+|+|+||+|.+--.|.+.|.++|.+.          +..|.|-|+.+++..|+..|..+|..
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVla----------d~kIHiLG~~~niriAR~avcsLIlG  231 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA----------DSKIHILGAFQNIRIARDAVCSLILG  231 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEec----------CceEEEeecchhhHHHHHhhHhhhcc
Confidence            34789999999999999999999999994          47899999999999999999887654

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

Probab=92.98  E-value=0.076  Score=55.41  Aligned_cols=73  Identities=19%  Similarity=0.130  Sum_probs=59.9

Q ss_pred             CCCCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHH
Q 019747           28 SDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI  102 (336)
Q Consensus        28 ~~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~  102 (336)
                      +.+.......++.+|......|||++|.+|..++.-||+.|++.+-..  ....||.+.+.|.++....|...|.
T Consensus      1333 ~ss~~~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~--~Nqaers~~~kg~p~~~r~a~~~I~ 1405 (2131)
T KOG4369|consen 1333 DSSQVPANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQP--DNQAERSKAPKGRPPSQRVATSPIG 1405 (2131)
T ss_pred             ccccCcccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCC--ccchhhhcccCCCChhhhhhhcccc
Confidence            344445566788999999999999999999999999999999975221  1146899999999999998887776

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=92.95  E-value=0.056  Score=38.29  Aligned_cols=36  Identities=14%  Similarity=0.425  Sum_probs=30.3

Q ss_pred             CceEEEEEeccCcccceeccCCchHHHHHhHhCCeE
Q 019747          255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARI  290 (336)
Q Consensus       255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I  290 (336)
                      ......+.+..+..|.||||+|.+|+.||...+.-+
T Consensus        27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~   62 (73)
T PF13083_consen   27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA   62 (73)
T ss_dssp             TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence            346788889999999999999999999988766443

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

Probab=92.86  E-value=0.12  Score=36.15  Aligned_cols=39  Identities=28%  Similarity=0.491  Sum_probs=30.7

Q ss_pred             eEEEEEeccCc-----ccceeccCCchHHHHHhHh-CCeEEEccC
Q 019747          257 NSLTIGVADEH-----IGFVVGRGGRNIMEISQIS-GARIKVSDR  295 (336)
Q Consensus       257 ~~~~v~vp~~~-----vg~IIGk~G~~I~~I~~~s-ga~I~i~~~  295 (336)
                      ....+.|-...     +|..||++|.+|+.|.++. |-+|++-.-
T Consensus         3 ~r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen    3 NRTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             TEEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             ceEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            34566677766     8999999999999999999 999998763

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

Probab=92.81  E-value=0.26  Score=42.89  Aligned_cols=61  Identities=23%  Similarity=0.334  Sum_probs=45.8

Q ss_pred             EEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHH-HHHHHHHHHHHHHhh
Q 019747           38 RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDE-ILRAVDLVIDKLLTE  108 (336)
Q Consensus        38 ~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~-v~~A~~~I~~~i~~~  108 (336)
                      -+.||...|..+||++|+.++.|.++++|.|-+-.         +-.|-|.+..+. ...|.+.|. .+..+
T Consensus       149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~---------NG~IWV~~~~~~~e~~~~~aI~-~ie~e  210 (239)
T COG1097         149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ---------NGRIWVDGENESLEELAIEAIR-KIERE  210 (239)
T ss_pred             EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec---------CCEEEecCCCcchHHHHHHHHH-HHhhh
Confidence            46889999999999999999999999999999953         334667776553 444555555 44444

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

Probab=92.57  E-value=0.1  Score=36.52  Aligned_cols=38  Identities=29%  Similarity=0.417  Sum_probs=30.1

Q ss_pred             EEEEEEecCc-----cceeecCCChHHHHHHHHh-CCeEEEcCC
Q 019747           36 YIRFLVSNPL-----AGAVIGKGGSTINDFQSQS-GARIQLSRS   73 (336)
Q Consensus        36 ~~~i~ip~~~-----vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~   73 (336)
                      ..++.|-...     +|..||++|.+|+.|.++. |-+|++-..
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            3567777777     9999999999999999999 899988544

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

Probab=92.52  E-value=0.36  Score=42.07  Aligned_cols=47  Identities=15%  Similarity=0.357  Sum_probs=40.2

Q ss_pred             EEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChH
Q 019747          259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQR  314 (336)
Q Consensus       259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~  314 (336)
                      .-+.|++..|-++||++|++++.|.+.++|+|.+-.         +-.|=|.|..+
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~---------NG~IWV~~~~~  194 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ---------NGRIWVDGENE  194 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec---------CCEEEecCCCc
Confidence            567899999999999999999999999999999954         45666777655

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

Probab=92.30  E-value=0.096  Score=43.94  Aligned_cols=149  Identities=11%  Similarity=0.067  Sum_probs=88.3

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh-cccc
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE-LHAE  112 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~-~~~~  112 (336)
                      .-+-++.||.+....+=--==..---|-+..+.+|.+.-...   ...-|.+.-+-++.+++++...|...+... +...
T Consensus        73 ~e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK~r---~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DA  149 (252)
T KOG3273|consen   73 IETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLKAR---SVELRTCKDTEDPSALQKGADFVRAFILGFDIDDA  149 (252)
T ss_pred             cceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecccc---eeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhH
Confidence            456778888887643321111112234567777887742211   011233333345667777776666444332 0000


Q ss_pred             ------cc--CCCC--CCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHH
Q 019747          113 ------DQ--ADDV--GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQM  182 (336)
Q Consensus       113 ------~~--~~~~--~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~  182 (336)
                            ++  ....  .+..+++=.=-+..+|+|.|++|.+--.|+..|.++|.+..          ..+.|-|..+++.
T Consensus       150 iALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVlad----------~kIHiLG~~~nir  219 (252)
T KOG3273|consen  150 IALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLAD----------SKIHILGAFQNIR  219 (252)
T ss_pred             HHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEecC----------ceEEEeecchhhH
Confidence                  00  0000  01111111111356899999999999999999999999974          5799999999999


Q ss_pred             HHHHHHHHHhhcC
Q 019747          183 RALELILLKLSED  195 (336)
Q Consensus       183 ~A~~~i~~~l~~~  195 (336)
                      .|+..|..++-..
T Consensus       220 iAR~avcsLIlGs  232 (252)
T KOG3273|consen  220 IARDAVCSLILGS  232 (252)
T ss_pred             HHHHhhHhhhccC
Confidence            9999999998654

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

Probab=92.03  E-value=0.49  Score=37.99  Aligned_cols=39  Identities=28%  Similarity=0.475  Sum_probs=34.2

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccC
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDR  295 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~  295 (336)
                      .+.++.|-...-|.+||++|.++++|...||-.-.+-+.
T Consensus        76 ~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          76 DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence            456788888899999999999999999999988887664

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.

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=91.97  E-value=0.2  Score=35.92  Aligned_cols=34  Identities=24%  Similarity=0.352  Sum_probs=27.2

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEE
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQ   69 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~   69 (336)
                      .+.+.|..+..|.+|||+|.++..||--.+.-++
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            4567777888999999999999999976664443

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.

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

Probab=91.79  E-value=0.32  Score=33.24  Aligned_cols=34  Identities=26%  Similarity=0.447  Sum_probs=27.2

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeE
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARI  290 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I  290 (336)
                      ....+.+.....|.+||++|++|+.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            4455566655679999999999999999998554

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.

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=91.52  E-value=0.1  Score=37.39  Aligned_cols=34  Identities=26%  Similarity=0.462  Sum_probs=29.0

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEE
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQ   69 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~   69 (336)
                      .+.+.+...+-|.|||++|++|++|....+-.+.
T Consensus        26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            4678899999999999999999999977765553

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

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

Probab=90.69  E-value=0.31  Score=46.54  Aligned_cols=66  Identities=20%  Similarity=0.222  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEecc
Q 019747           94 ILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL  160 (336)
Q Consensus        94 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~  160 (336)
                      ...|..+|...+...++.. ............+.+|..+++.+||++|.+|++|+++.|.+|.+...
T Consensus       459 ~~~a~~~i~~~i~r~~p~~-~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~  524 (604)
T COG1855         459 LKLAEEEIEREIKRYLPGD-VEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL  524 (604)
T ss_pred             hHHHHHHHHHHHHHhCCCC-ceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence            4556666665566554421 11111223456789999999999999999999999999999999873

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

Probab=90.28  E-value=0.59  Score=41.39  Aligned_cols=51  Identities=16%  Similarity=0.221  Sum_probs=46.2

Q ss_pred             ceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhc
Q 019747          134 GSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (336)
Q Consensus       134 g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~  194 (336)
                      .+|||++|.+++.|+--|.|.|-+.+          ..|.+.|....+..+.+.+.+.+..
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG----------~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQG----------NTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeC----------cEEEeecCcchHHHHHHHHHHHHhc
Confidence            47999999999999999999999976          5699999999999999999988865

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=90.21  E-value=0.87  Score=43.88  Aligned_cols=152  Identities=18%  Similarity=0.223  Sum_probs=103.0

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccccC
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQA  115 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~  115 (336)
                      .+-+.||...|..|||.||..|.+++.+.++-|.+...-+ .+.+                        .+.        
T Consensus       450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~-~~qs------------------------~~~--------  496 (657)
T COG5166         450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYK-FGQS------------------------QWH--------  496 (657)
T ss_pred             heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhh-cchh------------------------hhh--------
Confidence            4778999999999999999999999999999999964221 0100                        111        


Q ss_pred             CCCCCceeEEEEEecCccceeecCCChHHHHHHHhc----CCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 019747          116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDS----QAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLK  191 (336)
Q Consensus       116 ~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~t----ga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~  191 (336)
                            --+-+..|..-.+.|+|++......+++..    ...|.|.      +++. +++++-|-...+.+..+. ...
T Consensus       497 ------dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~------~~~~-sI~~v~~~~~~I~rv~kn-e~v  562 (657)
T COG5166         497 ------DNVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFC------PQST-SIFTVDIYSDEIERVIKN-ETV  562 (657)
T ss_pred             ------cceEEECCccCccchhcccccHHHHHhhhcccccccceEEc------CCce-EEEEEcccccHHHHHhhc-cce
Confidence                  124567788888999999888877777543    3444444      3333 588888877665544330 111


Q ss_pred             hhcCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccce
Q 019747          192 LSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFV  271 (336)
Q Consensus       192 l~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~I  271 (336)
                      +-.                                                            -....-+.+|++.++..
T Consensus       563 ~~~------------------------------------------------------------~p~~~~~y~~se~h~~g  582 (657)
T COG5166         563 LLE------------------------------------------------------------FPAEMHFYVPSEIHKKG  582 (657)
T ss_pred             EEe------------------------------------------------------------cccccccccchhhhhcc
Confidence            100                                                            11334566788899999


Q ss_pred             ec---cCCchHHHHHhHhCCeEEEcc
Q 019747          272 VG---RGGRNIMEISQISGARIKVSD  294 (336)
Q Consensus       272 IG---k~G~~I~~I~~~sga~I~i~~  294 (336)
                      +|   -+|++|..+.....-.|...-
T Consensus       583 ~gena~R~~ni~~~t~~y~~~ie~~~  608 (657)
T COG5166         583 IGENAFRGENIQRVTKLYNSYIEFST  608 (657)
T ss_pred             CCcccccccchhhhhhhhhccceeec
Confidence            99   788888888888777776654

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

Probab=90.20  E-value=0.44  Score=34.53  Aligned_cols=35  Identities=17%  Similarity=0.347  Sum_probs=30.1

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEE
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQL   70 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i   70 (336)
                      .+++.|....-|.|||++|+.|++|+++-.-.+.+
T Consensus        31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~   65 (81)
T cd02413          31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF   65 (81)
T ss_pred             eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence            48889999999999999999999999877665555

S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=89.81  E-value=0.39  Score=34.35  Aligned_cols=36  Identities=11%  Similarity=0.517  Sum_probs=29.2

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEE
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKV  292 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i  292 (336)
                      ....+.|..+..|.+|||+|++|..||-.....+.-
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~   59 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR   59 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence            446677778889999999999999999887755543

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.

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=89.12  E-value=0.67  Score=38.34  Aligned_cols=37  Identities=22%  Similarity=0.428  Sum_probs=31.8

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCC
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS   73 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~   73 (336)
                      .+-++|-... |.-|||+|.+|+++++..|-+|.+-..
T Consensus        62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~   98 (166)
T PRK06418         62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK   98 (166)
T ss_pred             EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence            3567777777 999999999999999999999999653

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

Probab=88.95  E-value=0.27  Score=46.89  Aligned_cols=39  Identities=26%  Similarity=0.406  Sum_probs=35.5

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCC
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSH   74 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~   74 (336)
                      ...+.||...++.+|||+|.+|++|++..|.+|.|...+
T Consensus       487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e  525 (604)
T COG1855         487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE  525 (604)
T ss_pred             eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence            477899999999999999999999999999999996544

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=88.39  E-value=0.31  Score=34.88  Aligned_cols=35  Identities=23%  Similarity=0.444  Sum_probs=28.6

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEE
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIK  291 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~  291 (336)
                      ....+.+....-|.|||++|++|++|++..+-.+.
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            44677788899999999999999999877665553

; 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 ....

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

Probab=87.85  E-value=2.1  Score=41.50  Aligned_cols=97  Identities=21%  Similarity=0.252  Sum_probs=67.8

Q ss_pred             ceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCCcCCCccCCCccc
Q 019747          134 GSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFF  213 (336)
Q Consensus       134 g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~~~~~~~~~g~~~  213 (336)
                      ..++-+.|..|++|-++..-+|.+-++...           .-   .-+.|.+.|.+++-+...-..     +       
T Consensus        41 P~~~~~~~dlik~lAk~lrKRI~iR~dPsv-----------l~---~~e~A~~~I~eivP~ea~i~~-----i-------   94 (637)
T COG1782          41 PELFAKDGDLIKDLAKDLRKRIIIRPDPSV-----------LK---PPEEARKIILEIVPEEAGITD-----I-------   94 (637)
T ss_pred             HHHhccchhHHHHHHHHHhhceEeccCchh-----------cC---CHHHHHHHHHHhCccccCcee-----E-------
Confidence            345567889999999999888888763111           11   224688888888754321100     0       


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEc
Q 019747          214 SGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVS  293 (336)
Q Consensus       214 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~  293 (336)
                                                             .-...+.++.|-.+.=|.+|||+|+++++|.+++|-.-.|-
T Consensus        95 ---------------------------------------~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~iv  135 (637)
T COG1782          95 ---------------------------------------YFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIV  135 (637)
T ss_pred             ---------------------------------------EecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceee
Confidence                                                   11225567888889999999999999999999999777766


Q ss_pred             cC
Q 019747          294 DR  295 (336)
Q Consensus       294 ~~  295 (336)
                      +.
T Consensus       136 R~  137 (637)
T COG1782         136 RT  137 (637)
T ss_pred             ec
Confidence            54

>PRK13764 ATPase; Provisional

Probab=87.31  E-value=0.44  Score=47.74  Aligned_cols=40  Identities=25%  Similarity=0.336  Sum_probs=36.0

Q ss_pred             EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCC
Q 019747           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSH   74 (336)
Q Consensus        35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~   74 (336)
                      -...+.||.+.++.+|||+|.+|++|+++.|.+|.|...+
T Consensus       481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~  520 (602)
T PRK13764        481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD  520 (602)
T ss_pred             CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence            3567899999999999999999999999999999996544

>PRK13764 ATPase; Provisional

Probab=87.11  E-value=0.87  Score=45.69  Aligned_cols=65  Identities=22%  Similarity=0.218  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEecc
Q 019747           95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL  160 (336)
Q Consensus        95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~  160 (336)
                      ..|..+|.+.+...+... ............+.||...++.+|||+|.+|++|+++.|..|.+...
T Consensus       455 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~  519 (602)
T PRK13764        455 RLAEKEIEREIKRYLPGP-VEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL  519 (602)
T ss_pred             HHHHHHHHHHHHHhcCCc-eEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence            445566665555543211 11111234567789999999999999999999999999999999874

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=86.64  E-value=0.59  Score=44.95  Aligned_cols=127  Identities=15%  Similarity=0.074  Sum_probs=79.6

Q ss_pred             ceeecCCChHHHHHHHHhCCeEE--EcCCCCCCCCCCceEEE-EEeeHHHHHHHHHHHHHHHHhhccccccCCCCCCcee
Q 019747           47 GAVIGKGGSTINDFQSQSGARIQ--LSRSHEFFPGTTDRIIM-ISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTK  123 (336)
Q Consensus        47 g~iIGk~G~~Ik~I~~~tg~~I~--i~~~~~~~~~~~~r~i~-I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~  123 (336)
                      -.+=||+.-.+.+|++...|.+.  +....      ..++.. +.|..-.-.+++..+.    .+           -...
T Consensus       392 dFl~gkkngK~TrIm~~v~c~~~~~i~~~~------gs~~~~~~~g~~~~F~k~~~~~~----~E-----------Fpae  450 (657)
T COG5166         392 DFLRGKKNGKATRIMKGVSCSELSSIVSST------GSIVETNGIGEKMSFSKKLSIPP----TE-----------FPAE  450 (657)
T ss_pred             HHhccccCcchhhhhhhcccceeeEEEecC------CcEEEEeccCcchhhHHHhcCCc----cc-----------Cchh
Confidence            37788888889999999999844  43322      234433 3455444455444333    22           2345


Q ss_pred             EEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcC---HHHHHHHHHHHHHHhhc
Q 019747          124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT---LDEQMRALELILLKLSE  194 (336)
Q Consensus       124 ~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~---~~~v~~A~~~i~~~l~~  194 (336)
                      ..+.||+..+..|||.+|..|++...++++.|.+...-+.....--.-|.|.-+   ..++.-++.-+.+++.+
T Consensus       451 ~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~  524 (657)
T COG5166         451 IAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ  524 (657)
T ss_pred             eEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhh
Confidence            789999999999999999999999999999999875211111111122555544   23444455555555554

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

Probab=85.89  E-value=0.87  Score=34.98  Aligned_cols=29  Identities=21%  Similarity=0.460  Sum_probs=25.5

Q ss_pred             EEEEEecCccceeecCCChHHHHHHHHhC
Q 019747           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSG   65 (336)
Q Consensus        37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg   65 (336)
                      +++.|....-|.|||++|++|++|+....
T Consensus        63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~   91 (109)
T cd02412          63 VEVTIHTARPGIIIGKKGAGIEKLRKELQ   91 (109)
T ss_pred             EEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence            77888888999999999999999986654

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

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

Probab=85.13  E-value=1.2  Score=32.43  Aligned_cols=28  Identities=25%  Similarity=0.485  Sum_probs=24.0

Q ss_pred             EEEEEecCccceeecCCChHHHHHHHHh
Q 019747           37 IRFLVSNPLAGAVIGKGGSTINDFQSQS   64 (336)
Q Consensus        37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~t   64 (336)
                      +++.|....-|.+||++|.+|++|+..-
T Consensus        40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l   67 (85)
T cd02411          40 TQITIYAERPGMVIGRGGKNIRELTEIL   67 (85)
T ss_pred             EEEEEEECCCCceECCCchhHHHHHHHH
Confidence            6677777899999999999999998654

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

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

Probab=82.57  E-value=2.1  Score=34.38  Aligned_cols=37  Identities=30%  Similarity=0.524  Sum_probs=31.1

Q ss_pred             EEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCC
Q 019747           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS   73 (336)
Q Consensus        37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~   73 (336)
                      =++.|-...-|.+||++|.++++|..+||-.-.+.+.
T Consensus        78 GEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          78 GEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             cEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence            3556666777999999999999999999988888653

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

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=82.39  E-value=2  Score=35.60  Aligned_cols=38  Identities=18%  Similarity=0.427  Sum_probs=32.3

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccC
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDR  295 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~  295 (336)
                      ...-+.|.... |.-|||+|.+++.+++..|-+|.+-..
T Consensus        61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~   98 (166)
T PRK06418         61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK   98 (166)
T ss_pred             CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence            45566666666 999999999999999999999999774

>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]

Probab=82.16  E-value=1.5  Score=38.20  Aligned_cols=31  Identities=32%  Similarity=0.506  Sum_probs=26.4

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHh
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQS   64 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~t   64 (336)
                      ...+++.|....-|.|||++|+.|++|++..
T Consensus        50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l   80 (233)
T COG0092          50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKEL   80 (233)
T ss_pred             CCceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence            3457889999999999999999999987543

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

Probab=81.39  E-value=2.1  Score=30.94  Aligned_cols=37  Identities=22%  Similarity=0.334  Sum_probs=29.8

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEc
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVS  293 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~  293 (336)
                      ...++.|-...-|.|||++|+.|++|++.-.....+.
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~   66 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP   66 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence            3467777788889999999999999988876665553

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	336
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		4e-26
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		4e-11
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		4e-25
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		1e-10
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		5e-14
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		2e-09
1ec6_A	87	Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Bind		2e-10
1dtj_A	76	Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Bind		4e-10
1dt4_A	73	Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Bind		2e-09
1j4w_A	174	Complex Of The Kh3 And Kh4 Domains Of Fbp With A Si		3e-08
1wvn_A	82	Crsytal Structure Of Domain 3 Of Human Alpha Polyc		5e-06
3vke_A	76	Contribution Of The First K-Homology Domain Of Poly		1e-05
3vke_A	76	Contribution Of The First K-Homology Domain Of Poly		8e-05
1ztg_A	74	Human Alpha Polyc Binding Protein Kh1 Length = 74		2e-05
1ztg_A	74	Human Alpha Polyc Binding Protein Kh1 Length = 74		1e-04
2p2r_A	76	Crystal Structure Of The Third Kh Domain Of Human P		2e-05
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		6e-05
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		9e-05
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		6e-05
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		8e-05
1we8_A	104	Solution Structure Of Kh Domain In Protein Bab28342		8e-05
2axy_A	73	Crystal Structure Of Kh1 Domain Of Human Poly(C)-Bi		1e-04
2opu_A	89	Solution Nmr Structure Of The First Domain Of Ksrp		3e-04
2jvz_A	164	Solution Nmr Structure Of The Second And Third Kh D		3e-04
3krm_A	163	Imp1 Kh34 Length = 163		4e-04
1khm_A	89	C-Terminal Kh Domain Of Hnrnp K (Kh3) Length = 89		5e-04
1khm_A	89	C-Terminal Kh Domain Of Hnrnp K (Kh3) Length = 89		7e-04
1x4n_A	92	Solution Structure Of Kh Domain In Fuse Binding Pro		6e-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 =  115 bits (287), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 66/178 (37%), Positives = 107/178 (60%), Gaps = 26/178 (14%)
Query: 36  YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEIL 95
           +++ L+ +  AG++IGKGG TI   Q ++GA I+LS+S +F+PGTT+R+ +I GTI E L
Sbjct: 7   FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI-EAL 65
Query: 96  RAVDLVIDKLLTELHAE------------------DQADDVGTKTKLRLIVPNSSCGSII 137
            AV   I + + E+                     D+A+ V      ++IVPNS+ G II
Sbjct: 66  NAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQV------KIIVPNSTAGLII 119
Query: 138 GKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED 195
           GK GAT+K+ M+ S A +++S+       L +R+VT++G  ++  +A+ELI+ K+ ED
Sbjct: 120 GKGGATVKAIMEQSGAWVQLSQKPDG-INLQNRVVTVSGEPEQNRKAVELIIQKIQED 176

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 53/210 (25%), Positives = 89/210 (42%), Gaps = 38/210 (18%)
Query: 118 VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177
           +G++  L++++P+ + GSIIGK G TI     ++ A IK+S+    Y G  +R+  + GT
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61
Query: 178 LDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGXXXXXXXXXXHNTAA 237
           + E + A+                        G        MP                A
Sbjct: 62  I-EALNAVH-----------------------GFIAEKIREMP-------------QNVA 84
Query: 238 HYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGD 297
              P    +       DR N + I V +   G ++G+GG  +  I + SGA +++S + D
Sbjct: 85  KTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD 144
Query: 298 FFSGTSERKVTISGPQRSIRTAESMIMQKV 327
             +    R VT+SG     R A  +I+QK+
Sbjct: 145 GIN-LQNRVVTVSGEPEQNRKAVELIIQKI 173

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

Iteration: 1
 Score =  112 bits (279), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 58/171 (33%), Positives = 103/171 (60%), Gaps = 12/171 (7%)
Query: 36  YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEIL 95
           +++ L+ +  AG++IGKGG TI   Q ++GA I+LS+S +F+PGTT+R+ +I GTI+ + 
Sbjct: 7   FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALN 66
Query: 96  RAVDLVIDKLLTELHAEDQADDVGT-----------KTKLRLIVPNSSCGSIIGKAGATI 144
                + +K+        + + V               ++++IVPNS+ G IIGK GAT+
Sbjct: 67  AVHGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATV 126
Query: 145 KSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED 195
           K+  + S A +++S+       L +R+VT++G  ++  +A+ELI+ K+ ED
Sbjct: 127 KAIXEQSGAWVQLSQKPDG-INLQNRVVTVSGEPEQNRKAVELIIQKIQED 176

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 51/210 (24%), Positives = 92/210 (43%), Gaps = 38/210 (18%)
Query: 118 VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177
           +G++  L++++P+ + GSIIGK G TI     ++ A IK+S+    Y G  +R+  + GT
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61
Query: 178 LDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGXXXXXXXXXXHNTAA 237
           + E + A+   + +   +   +   T P +                           T  
Sbjct: 62  I-EALNAVHGFIAEKIREXPQNVAKTEPVSI----------------------LQPQTTV 98
Query: 238 HYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGD 297
           +               DR N + I V +   G ++G+GG  +  I + SGA +++S + D
Sbjct: 99  N--------------PDRANQVKIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQKPD 144
Query: 298 FFSGTSERKVTISGPQRSIRTAESMIMQKV 327
             +    R VT+SG     R A  +I+QK+
Sbjct: 145 GIN-LQNRVVTVSGEPEQNRKAVELIIQKI 173

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 47/162 (29%), Positives = 89/162 (54%), Gaps = 16/162 (9%)
Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           IR L+     G++IGK G ++   + +SGARI +S  +       +RII ++G  + I +
Sbjct: 7   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-----CPERIITLAGPTNAIFK 61
Query: 97  AVDLVIDKLLTELHAEDQADDVGTK--TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV 154
           A  ++IDKL  ++ +        ++    LRL+VP S CGS+IGK G  IK   + + A 
Sbjct: 62  AFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQ 121
Query: 155 IKIS--RLDHSYYGLNDRLVTLTG---TLDEQMRALELILLK 191
           ++++   L +S     +R +T+ G   ++ E ++ + +++L+
Sbjct: 122 VQVAGDMLPNS----TERAITIAGIPQSIIECVKQICVVMLE 159

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 52/193 (26%), Positives = 87/193 (45%), Gaps = 53/193 (27%)
Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
           +RL++     GSIIGK G ++K   ++S A     R++ S     +R++TL G  +   +
Sbjct: 7   IRLLMHGKEVGSIIGKKGESVKKMREESGA-----RINISEGNCPERIITLAGPTNAIFK 61
Query: 184 ALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGXXXXXXXXXXHNTAAHYGPNM 243
           A  +I+ KL ED   S +MT                             ++TAA   P  
Sbjct: 62  AFAMIIDKLEED--ISSSMT-----------------------------NSTAASRPP-- 88
Query: 244 GGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTS 303
                         +L + V     G ++G+GG  I EI + +GA+++V+  GD    ++
Sbjct: 89  -------------VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVA--GDMLPNST 133
Query: 304 ERKVTISGPQRSI 316
           ER +TI+G  +SI
Sbjct: 134 ERAITIAGIPQSI 146

>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 = 63.2 bits (152), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 26/69 (37%), Positives = 48/69 (69%)
Query: 261 IGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAE 320
           I V +  +G ++G+GG+ ++E  +++GARI++S +G+F  GT  R+VTI+G   + + A+
Sbjct: 7   IAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQ 66
Query: 321 SMIMQKVAY 329
            +I Q+V Y
Sbjct: 67  YLISQRVTY 75

>pdb|1DTJ|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding Domain Length = 76

Iteration: 1
 Score = 62.0 bits (149), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 25/69 (36%), Positives = 48/69 (69%)
Query: 261 IGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAE 320
           + V +  +G ++G+GG+ ++E  +++GARI++S +G+F  GT  R+VTI+G   + + A+
Sbjct: 7   MAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQ 66
Query: 321 SMIMQKVAY 329
            +I Q+V Y
Sbjct: 67  YLISQRVTY 75

>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding Domain Length = 73

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 24/67 (35%), Positives = 46/67 (68%)
Query: 261 IGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAE 320
           I V +  +G ++G+GG+ ++E  +++G RI++S +G+F  GT  RKVTI+G   + + A+
Sbjct: 7   IAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAAQ 66
Query: 321 SMIMQKV 327
            +I Q++
Sbjct: 67  YLITQRI 73

>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 = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 54/174 (31%), Positives = 72/174 (41%), Gaps = 29/174 (16%)
Query: 38  RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTT-DRIIMISGTIDEILR 96
           RF V     G VIG+ G  I   Q+ +G RIQ         GTT +RI  I+G  D    
Sbjct: 11  RFAV-----GIVIGRNGEMIKKIQNDAGVRIQFKPDD----GTTPERIAQITGPPDRAQH 61
Query: 97  AVDLVIDKLLTELHAEDQADDV------------------GTKTKLRLIVPNSSCGSIIG 138
           A +++ D LL  + A +                       G   +   IVP    G IIG
Sbjct: 62  AAEIITD-LLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIG 120
Query: 139 KAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL 192
           K G TIKS    S A I++ R        N +L T+ GT  +   A +LI  K+
Sbjct: 121 KGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 47/73 (64%), Gaps = 5/73 (6%)
Query: 256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRS 315
           T+ LTI   +  IG ++GR G NI EI Q+SGA+IK+++      G+S R+VTI+G   S
Sbjct: 7   THELTI--PNNLIGCIIGRQGANINEIRQMSGAQIKIANP---VEGSSGRQVTITGSAAS 61
Query: 316 IRTAESMIMQKVA 328
           I  A+ +I  +++
Sbjct: 62  ISLAQYLINARLS 74

>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 = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 45/75 (60%), Gaps = 5/75 (6%)
Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           IR L+     G++IGK G ++   + +SGARI +S  +     + +RII ++G  + I +
Sbjct: 5   IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN-----SPERIITLTGPTNAIFK 59
Query: 97  AVDLVIDKLLTELHA 111
           A  ++IDKL  ++++
Sbjct: 60  AFAMIIDKLEEDINS 74

>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 = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
           +RL++     GSIIGK G ++K   ++S A I IS  +       +R++TLTG  +   +
Sbjct: 5   IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNSP-----ERIITLTGPTNAIFK 59
Query: 184 ALELILLKLSED 195
           A  +I+ KL ED
Sbjct: 60  AFAMIIDKLEED 71

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 5/75 (6%)
Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           IR L+     G++IGK G ++   + +SGARI +S  +       +RII ++G  + I +
Sbjct: 5   IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN-----CPERIITLTGPTNAIFK 59
Query: 97  AVDLVIDKLLTELHA 111
           A  ++IDKL  ++++
Sbjct: 60  AFAMIIDKLEEDINS 74

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
           +RL++     GSIIGK G ++K   ++S A     R++ S     +R++TLTG  +   +
Sbjct: 5   IRLLMHGKEVGSIIGKKGESVKRIREESGA-----RINISEGNCPERIITLTGPTNAIFK 59
Query: 184 ALELILLKLSED 195
           A  +I+ KL ED
Sbjct: 60  AFAMIIDKLEED 71

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 44/69 (63%), Gaps = 3/69 (4%)
Query: 255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQR 314
           +T S  + + ++ IG ++GR G  I EI Q SGA+IK+++      G+++R+VTI+G   
Sbjct: 3   QTTSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANP---VEGSTDRQVTITGSAA 59
Query: 315 SIRTAESMI 323
           SI  A+ +I
Sbjct: 60  SISLAQYLI 68

>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A Single_stranded 10mer Dna Oligonucleotide Length = 89

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/61 (42%), Positives = 37/61 (60%), Gaps = 3/61 (4%)
Query: 41  VSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDL 100
           +   LAG++IGKGG  I   + +SGA I++    E   G+ DRII I+GT D+I  A  L
Sbjct: 20  IPKDLAGSIIGKGGQRIKQIRHESGASIKID---EPLEGSEDRIITITGTQDQIQNAQYL 76
Query: 101 V 101
           +
Sbjct: 77  L 77

>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A Single_stranded 10mer Dna Oligonucleotide Length = 89

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 26/64 (40%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRA 184
           ++ +P    GSIIGK G  IK    +S A IKI   D    G  DR++T+TGT D+   A
Sbjct: 17  QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNA 73
Query: 185 LELI 188
             L+
Sbjct: 74  QYLL 77

>pdb|1ZZI|A Chain A, Crystal Structure Analysis Of The Third Kh Domain Of Hnrnp K In Complex With Ssdna Length = 82

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/61 (42%), Positives = 37/61 (60%), Gaps = 3/61 (4%)
Query: 41  VSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDL 100
           +   LAG++IGKGG  I   + +SGA I++    E   G+ DRII I+GT D+I  A  L
Sbjct: 13  IPKDLAGSIIGKGGQRIKQIRHESGASIKID---EPLEGSEDRIITITGTQDQIQNAQYL 69
Query: 101 V 101
           +
Sbjct: 70  L 70

>pdb|1ZZI|A Chain A, Crystal Structure Analysis Of The Third Kh Domain Of Hnrnp K In Complex With Ssdna Length = 82

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/64 (40%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRA 184
           ++ +P    GSIIGK G  IK    +S A IKI   D    G  DR++T+TGT D+   A
Sbjct: 10  QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNA 66
Query: 185 LELI 188
             L+
Sbjct: 67  QYLL 70

>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342 Length = 104

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRA 184
           +L VP  S G IIG+ G TI+S    S A I   +       L  RL+ ++GT  E   A
Sbjct: 18  QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTL-LLSRLIKISGTQKEVAAA 76
Query: 185 LELILLKLSED 195
             LIL K+SED
Sbjct: 77  KHLILEKVSED 87

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           IR L      G++IGK G ++   + +SGARI +S  +       +RII ++G  + I +
Sbjct: 7   IRLLXHGKEVGSIIGKKGESVKKXREESGARINISEGN-----CPERIITLAGPTNAIFK 61
Query: 97  AVDLVIDKL 105
           A   +IDKL
Sbjct: 62  AFAXIIDKL 70

>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp Length = 89

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 38/62 (61%), Gaps = 5/62 (8%)
Query: 263 VADEHIGFVVGRGGRNIMEISQISGARIKVS-DRGDFFSGTSERKVTISGPQRSIRTAES 321
           V D  +G ++GRGG  I +I Q SG ++++S D G    G  ER V+++G   S++ A+ 
Sbjct: 22  VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSG----GLPERSVSLTGAPESVQKAKM 77
Query: 322 MI 323
           M+
Sbjct: 78  ML 79

>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains Of Ksrp Length = 164

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 36/134 (26%), Positives = 64/134 (47%), Gaps = 12/134 (8%)
Query: 35  TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEI 94
           T    ++    AG VIGKGG TI   Q ++G ++ L +         D+ + I G   ++
Sbjct: 2   TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNT-NVDKPLRIIGDPYKV 60
Query: 95  LRAVDLVIDKLLTELHAEDQA-----DDVGTKT--KLRLIVPNSSCGSIIGKAGATIKSF 147
            +A ++V+D     L   DQ      ++ G++    + + VP  S G +IG++G  IK  
Sbjct: 61  QQACEMVMDI----LRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKI 116
Query: 148 MDDSQAVIKISRLD 161
            +D+   I+  + D
Sbjct: 117 QNDAGVRIQFKQDD 130

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 31/123 (25%), Positives = 59/123 (47%), Gaps = 5/123 (4%)
Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           ++  +     GA+IGK G  I      + A I+++      P +  R+++I+G  +   +
Sbjct: 5   VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPET--PDSKVRMVIITGPPEAQFK 62
Query: 97  AVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIK 156
           A   +  KL  E +     ++V  +T +R  VP S+ G +IGK G T+    + + A + 
Sbjct: 63  AQGRIYGKLKEE-NFFGPKEEVKLETHIR--VPASAAGRVIGKGGKTVNELQNLTAAEVV 119
Query: 157 ISR 159
           + R
Sbjct: 120 VPR 122

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 35/57 (61%), Gaps = 3/57 (5%)
Query: 45  LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV 101
           LA ++IGKGG  I   + +SGA I++    E   G+ DRII I+GT D+I  A  L+
Sbjct: 24  LARSIIGKGGQRIKQIRHESGASIKID---EPLEGSEDRIITITGTQDQIQNAQYLL 77

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRA 184
           ++ +P     SIIGK G  IK    +S A IKI   D    G  DR++T+TGT D+   A
Sbjct: 17  QVTIPKDLARSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNA 73
Query: 185 LELI 188
             L+
Sbjct: 74  QYLL 77

>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1 Length = 92

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 39/66 (59%), Gaps = 5/66 (7%)
Query: 263 VADEHIGFVVGRGGRNIMEISQISGARIKVS-DRGDFFSGTSERKVTISGPQRSIRTAES 321
           V D  +GF++GRGG  I  I Q SG +I+++ D G    G  ER   ++G   S+++A+ 
Sbjct: 21  VPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG----GLPERSCMLTGTPESVQSAKR 76
Query: 322 MIMQKV 327
           ++ Q V
Sbjct: 77  LLDQIV 82

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	336
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-47
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	5e-33
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-18
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-14
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-42
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-30
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-15
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-41
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-27
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	9e-18
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-12
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	5e-40
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-29
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	9e-16
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-12
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	6e-40
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-37
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-17
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-23
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-21
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-18
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	2e-23
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	7e-21
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	3e-18
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-20
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	8e-17
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-14
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	4e-20
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	4e-17
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-15
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	7e-20
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-17
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-15
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	9e-20
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	3e-17
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	7e-16
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	1e-17
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-15
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	9e-19
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-18
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-17
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	2e-18
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	3e-15
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-13
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	7e-18
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	1e-17
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	1e-16
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	5e-17
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-14
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	3e-13
1we8_A	104	Tudor and KH domain containing protein; structural	6e-17
1we8_A	104	Tudor and KH domain containing protein; structural	2e-15
1we8_A	104	Tudor and KH domain containing protein; structural	2e-15
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	8e-17
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	1e-16
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	5e-15
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	8e-13
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	3e-09
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	5e-08
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	7e-12
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	7e-07
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	4e-04
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	1e-11
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-09
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-08
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	1e-10
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	1e-06
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	3e-10
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	2e-09
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	1e-06
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	7e-10
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	3e-08
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	3e-06
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	4e-09
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	6e-08
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	6e-07
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	3e-08
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	1e-05
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	1e-05
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	9e-08
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	4e-05
1tua_A	191	Hypothetical protein APE0754; structural genomics,	5e-06
1tua_A	191	Hypothetical protein APE0754; structural genomics,	2e-05
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	9e-04

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

 Score =  157 bits (399), Expect = 1e-47
 Identities = 60/177 (33%), Positives = 105/177 (59%), Gaps = 12/177 (6%)

Query: 30  PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG 89
           P     +++ L+ +  AG++IGKGG TI   Q ++GA I+LS+S +F+PGTT+R+ +I G
Sbjct: 1   PLGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQG 60

Query: 90  TIDEILRAVDLVIDKLLTELHAEDQADDV-----------GTKTKLRLIVPNSSCGSIIG 138
           TI+ +      + +K+        + + V               ++++IVPNS+ G IIG
Sbjct: 61  TIEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIG 120

Query: 139 KAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED 195
           K GAT+K+ M+ S A +++S+       L +R+VT++G  ++  +A+ELI+ K+ ED
Sbjct: 121 KGGATVKAIMEQSGAWVQLSQ-KPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176

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

 Score =  119 bits (300), Expect = 5e-33
 Identities = 51/211 (24%), Positives = 87/211 (41%), Gaps = 38/211 (18%)

Query: 118 VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177
           +G++  L++++P+ + GSIIGK G TI     ++ A IK+S+    Y G  +R+  + GT
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61

Query: 178 LDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAA 237
           ++        I  K+ E                                          A
Sbjct: 62  IEALNAVHGFIAEKIREM-------------------------------------PQNVA 84

Query: 238 HYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGD 297
              P    +       DR N + I V +   G ++G+GG  +  I + SGA +++S + D
Sbjct: 85  KTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD 144

Query: 298 FFSGTSERKVTISGPQRSIRTAESMIMQKVA 328
             +    R VT+SG     R A  +I+QK+ 
Sbjct: 145 GINLQ-NRVVTVSGEPEQNRKAVELIIQKIQ 174

>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 = 80.3 bits (198), Expect = 2e-18
 Identities = 26/98 (26%), Positives = 54/98 (55%), Gaps = 1/98 (1%)

Query: 11  SPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQL 70
             +V      + ++  ++   ++   ++ +V N  AG +IGKGG+T+     QSGA +QL
Sbjct: 80  PQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQL 139

Query: 71  SRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE 108
           S+  +      +R++ +SG  ++  +AV+L+I K+  +
Sbjct: 140 SQKPD-GINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176

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

 Score = 69.9 bits (171), Expect = 1e-14
 Identities = 21/81 (25%), Positives = 40/81 (49%)

Query: 256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRS 315
              L + +     G ++G+GG+ I+++ + +GA IK+S   DF+ GT+ER   I G   +
Sbjct: 5   QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEA 64

Query: 316 IRTAESMIMQKVAYASDRLMD 336
           +      I +K+      +  
Sbjct: 65  LNAVHGFIAEKIREMPQNVAK 85

>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 =  143 bits (362), Expect = 3e-42
 Identities = 35/159 (22%), Positives = 66/159 (41%), Gaps = 6/159 (3%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           ++  +     GA+IGK G  I      + A I+++      P +  R+++I+G  +   +
Sbjct: 5   VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPET--PDSKVRMVIITGPPEAQFK 62

Query: 97  AVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIK 156
           A   +  KL  E            K +  + VP S+ G +IGK G T+    + + A + 
Sbjct: 63  AQGRIYGKLKEE---NFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVV 119

Query: 157 ISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED 195
           + R D +    +  +V + G       A   I   L++ 
Sbjct: 120 VPR-DQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQV 157

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

 Score =  112 bits (281), Expect = 3e-30
 Identities = 42/212 (19%), Positives = 72/212 (33%), Gaps = 54/212 (25%)

Query: 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQ 181
             +++ +P  + G+IIGK G  IK     + A IKI+  +        R+V +TG  + Q
Sbjct: 3   EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETP--DSKVRMVIITGPPEAQ 60

Query: 182 MRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGP 241
            +A   I  KL E+                                              
Sbjct: 61  FKAQGRIYGKLKEE---------------------------------------------- 74

Query: 242 NMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSG 301
                 F   K++      I V     G V+G+GG+ + E+  ++ A + V  R      
Sbjct: 75  -----NFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVP-RDQTPDE 128

Query: 302 TSERKVTISGPQRSIRTAESMIMQKVAYASDR 333
             +  V I G   + + A+  I   +A    +
Sbjct: 129 NDQVIVKIIGHFYASQMAQRKIRDILAQVKQQ 160

>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 = 71.7 bits (176), Expect = 2e-15
 Identities = 21/91 (23%), Positives = 32/91 (35%), Gaps = 1/91 (1%)

Query: 24  KSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDR 83
           ++      E        V    AG VIGKGG T+N+ Q+ + A + + R           
Sbjct: 74  ENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQT-PDENDQV 132

Query: 84  IIMISGTIDEILRAVDLVIDKLLTELHAEDQ 114
           I+ I G       A   + D L        +
Sbjct: 133 IVKIIGHFYASQMAQRKIRDILAQVKQQHQK 163

>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 =  140 bits (355), Expect = 3e-41
 Identities = 45/165 (27%), Positives = 80/165 (48%), Gaps = 9/165 (5%)

Query: 32  EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTI 91
                IR L+     G++IGK G ++   + +SGARI +S          +RII ++G  
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE-----GNCPERIITLAGPT 56

Query: 92  DEILRAVDLVIDKLLTELHAE--DQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMD 149
           + I +A  ++IDKL  ++ +   +          LRL+VP S CGS+IGK G  IK   +
Sbjct: 57  NAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRE 116

Query: 150 DSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194
            + A ++++          +R +T+ G     +  ++ I + + E
Sbjct: 117 STGAQVQVAG--DMLPNSTERAITIAGIPQSIIECVKQICVVMLE 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 =  104 bits (261), Expect = 2e-27
 Identities = 49/204 (24%), Positives = 82/204 (40%), Gaps = 53/204 (25%)

Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
           +RL++     GSIIGK G ++K   ++S A I IS  +       +R++TL G  +   +
Sbjct: 7   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP-----ERIITLAGPTNAIFK 61

Query: 184 ALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNM 243
           A  +I+ KL ED   S T +                                        
Sbjct: 62  AFAMIIDKLEEDISSSMTNS---------------------------------------- 81

Query: 244 GGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTS 303
                         +L + V     G ++G+GG  I EI + +GA+++V+  GD    ++
Sbjct: 82  ------TAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVA--GDMLPNST 133

Query: 304 ERKVTISGPQRSIRTAESMIMQKV 327
           ER +TI+G  +SI      I   +
Sbjct: 134 ERAITIAGIPQSIIECVKQICVVM 157

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

 Score = 78.3 bits (193), Expect = 9e-18
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 2/80 (2%)

Query: 27  SSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIM 86
           S+  +  P  +R +V     G++IGKGG  I + +  +GA++Q++   +  P +T+R I 
Sbjct: 81  STAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG--DMLPNSTERAIT 138

Query: 87  ISGTIDEILRAVDLVIDKLL 106
           I+G    I+  V  +   +L
Sbjct: 139 IAGIPQSIIECVKQICVVML 158

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

 Score = 62.9 bits (153), Expect = 3e-12
 Identities = 20/74 (27%), Positives = 44/74 (59%), Gaps = 5/74 (6%)

Query: 254 DRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQ 313
           + T ++ + +  + +G ++G+ G ++ ++ + SGARI +S+         ER +T++GP 
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE-----GNCPERIITLAGPT 56

Query: 314 RSIRTAESMIMQKV 327
            +I  A +MI+ K+
Sbjct: 57  NAIFKAFAMIIDKL 70

>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 =  137 bits (347), Expect = 5e-40
 Identities = 38/163 (23%), Positives = 68/163 (41%), Gaps = 7/163 (4%)

Query: 35  TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEI 94
           T    ++    AG VIGKGG TI   Q ++G ++ L +         D+ + I G   ++
Sbjct: 2   TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRIIGDPYKV 60

Query: 95  LRAVDLVIDKLLTELHAEDQADDVGTK---TKLRLIVPNSSCGSIIGKAGATIKSFMDDS 151
            +A ++V+D L           +         + + VP  S G +IG++G  IK   +D+
Sbjct: 61  QQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDA 120

Query: 152 QAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194
              I+  + D       +++  + G  D    A  +I   L  
Sbjct: 121 GVRIQFKQDDG---TGPEKIAHIMGPPDRCEHAARIINDLLQS 160

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

 Score =  110 bits (276), Expect = 1e-29
 Identities = 36/207 (17%), Positives = 63/207 (30%), Gaps = 49/207 (23%)

Query: 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQ 181
           T   +++P    G +IGK G TIK   + +   + + + D S     D+ + + G   + 
Sbjct: 2   TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQ-DGSQNTNVDKPLRIIGDPYKV 60

Query: 182 MRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGP 241
            +A E+++  L E                                               
Sbjct: 61  QQACEMVMDILRER-------------------------------------DQGGFGDRN 83

Query: 242 NMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSG 301
             G              + + V    +G V+GR G  I +I   +G RI+          
Sbjct: 84  EYGS--------RIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG---T 132

Query: 302 TSERKVTISGPQRSIRTAESMIMQKVA 328
             E+   I GP      A  +I   + 
Sbjct: 133 GPEKIAHIMGPPDRCEHAARIINDLLQ 159

>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 = 72.9 bits (179), Expect = 9e-16
 Identities = 22/93 (23%), Positives = 34/93 (36%), Gaps = 3/93 (3%)

Query: 13  DVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSR 72
           D+  +R        +   +     I   V     G VIG+ G  I   Q+ +G RIQ  +
Sbjct: 69  DILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQ 128

Query: 73  SHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL 105
                    ++I  I G  D    A  ++ D L
Sbjct: 129 DD---GTGPEKIAHIMGPPDRCEHAARIINDLL 158

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

 Score = 62.9 bits (153), Expect = 3e-12
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 1/79 (1%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
              I +     G V+G+GG  I ++ + +G ++ +   G   +   ++ + I G    ++
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNV-DKPLRIIGDPYKVQ 61

Query: 318 TAESMIMQKVAYASDRLMD 336
            A  M+M  +         
Sbjct: 62  QACEMVMDILRERDQGGFG 80

>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 =  137 bits (347), Expect = 6e-40
 Identities = 48/175 (27%), Positives = 67/175 (38%), Gaps = 20/175 (11%)

Query: 35  TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEI 94
             I   +     G VIG+ G  I   Q+ +G RIQ          T +RI  I+G  D  
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD---GTTPERIAQITGPPDRA 59

Query: 95  LRAVDLVIDKLLTELHAEDQADDVGTK-----------------TKLRLIVPNSSCGSII 137
             A +++ D L +           G +                  +   IVP    G II
Sbjct: 60  QHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLII 119

Query: 138 GKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL 192
           GK G TIKS    S A I++ R        N +L T+ GT  +   A +LI  K+
Sbjct: 120 GKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 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 =  130 bits (329), Expect = 3e-37
 Identities = 42/209 (20%), Positives = 70/209 (33%), Gaps = 35/209 (16%)

Query: 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTL 178
           G+   + + +P  + G +IG+ G  IK   +D+   I+    D +     +R+  +TG  
Sbjct: 1   GSHM-IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTT---PERIAQITGPP 56

Query: 179 DEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAH 238
           D    A E+I   L                                              
Sbjct: 57  DRAQHAAEIITDLLRSV-------------------------------QAGNPGGPGPGG 85

Query: 239 YGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDF 298
            G   G   +              V     G ++G+GG  I  ISQ SGARI++      
Sbjct: 86  RGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPP 145

Query: 299 FSGTSERKVTISGPQRSIRTAESMIMQKV 327
            +  + +  TI G  + I  A  +I +K+
Sbjct: 146 NADPNMKLFTIRGTPQQIDYARQLIEEKI 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 = 77.6 bits (191), Expect = 2e-17
 Identities = 28/105 (26%), Positives = 45/105 (42%)

Query: 1   METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDF 60
           + + ++     P   G+       + +  P        F+V     G +IGKGG TI   
Sbjct: 70  LRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSI 129

Query: 61  QSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL 105
             QSGARI+L R+         ++  I GT  +I  A  L+ +K+
Sbjct: 130 SQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

>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 = 91.2 bits (227), Expect = 1e-23
 Identities = 24/72 (33%), Positives = 48/72 (66%)

Query: 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSI 316
             + + V +  +G ++G+GG+ ++E  +++GARI++S +G+F  GT  R+VTI+G   + 
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62

Query: 317 RTAESMIMQKVA 328
           + A+ +I Q+V 
Sbjct: 63  QAAQYLISQRVT 74

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

 Score = 86.2 bits (214), Expect = 1e-21
 Identities = 27/72 (37%), Positives = 43/72 (59%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           +   V   L GA++GKGG T+ ++Q  +GARIQ+S+  EF PGT +R + I+G+      
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64

Query: 97  AVDLVIDKLLTE 108
           A  L+  ++  E
Sbjct: 65  AQYLISQRVTYE 76

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

 Score = 77.7 bits (192), Expect = 2e-18
 Identities = 22/74 (29%), Positives = 39/74 (52%)

Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE 180
           K  + + VP +  G+I+GK G T+  + + + A I+IS+      G  +R VT+TG+   
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

Query: 181 QMRALELILLKLSE 194
              A  LI  +++ 
Sbjct: 62  TQAAQYLISQRVTY 75

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

 Score = 91.2 bits (227), Expect = 2e-23
 Identities = 26/77 (33%), Positives = 49/77 (63%)

Query: 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSI 316
             + I V +  +G ++G+GG+ ++E  +++GARI++S +G+F  GT  R+VTI+G   + 
Sbjct: 3   ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62

Query: 317 RTAESMIMQKVAYASDR 333
           + A+ +I Q+V Y    
Sbjct: 63  QAAQYLISQRVTYEQGV 79

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

 Score = 84.3 bits (209), Expect = 7e-21
 Identities = 27/72 (37%), Positives = 43/72 (59%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           +   V   L GA++GKGG T+ ++Q  +GARIQ+S+  EF PGT +R + I+G+      
Sbjct: 5   VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64

Query: 97  AVDLVIDKLLTE 108
           A  L+  ++  E
Sbjct: 65  AQYLISQRVTYE 76

>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 = 77.8 bits (192), Expect = 3e-18
 Identities = 22/75 (29%), Positives = 40/75 (53%)

Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE 180
           K  + + VP +  G+I+GK G T+  + + + A I+IS+      G  +R VT+TG+   
Sbjct: 2   KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

Query: 181 QMRALELILLKLSED 195
              A  LI  +++ +
Sbjct: 62  TQAAQYLISQRVTYE 76

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

 Score = 83.5 bits (207), Expect = 1e-20
 Identities = 26/77 (33%), Positives = 50/77 (64%), Gaps = 3/77 (3%)

Query: 255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQR 314
           +T S  + + ++ IG ++GR G  I EI Q+SGA+IK+++  +   G+++R+VTI+G   
Sbjct: 3   QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVE---GSTDRQVTITGSAA 59

Query: 315 SIRTAESMIMQKVAYAS 331
           SI  A+ +I  +++  +
Sbjct: 60  SISLAQYLINVRLSSET 76

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

 Score = 73.1 bits (180), Expect = 8e-17
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 3/77 (3%)

Query: 32  EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTI 91
            + T     + N L G +IG+ G+ IN+ +  SGA+I+++       G+TDR + I+G+ 
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPV---EGSTDRQVTITGSA 58

Query: 92  DEILRAVDLVIDKLLTE 108
             I  A  L+  +L +E
Sbjct: 59  ASISLAQYLINVRLSSE 75

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

 Score = 67.3 bits (165), Expect = 1e-14
 Identities = 29/78 (37%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTL 178
              T   L +PN   G IIG+ GA I      S A IKI+       G  DR VT+TG+ 
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIAN---PVEGSTDRQVTITGSA 58

Query: 179 DEQMRALELILLKLSEDT 196
                A  LI ++LS +T
Sbjct: 59  ASISLAQYLINVRLSSET 76

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

 Score = 82.3 bits (204), Expect = 4e-20
 Identities = 26/73 (35%), Positives = 46/73 (63%), Gaps = 3/73 (4%)

Query: 256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRS 315
             +  + + +  IG ++GR G NI EI Q+SGA+IK+++  +   G+S R+VTI+G   S
Sbjct: 5   QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE---GSSGRQVTITGSAAS 61

Query: 316 IRTAESMIMQKVA 328
           I  A+ +I  +++
Sbjct: 62  ISLAQYLINARLS 74

>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 = 74.2 bits (183), Expect = 4e-17
 Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 30  PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG 89
           P    T     + N L G +IG+ G+ IN+ +  SGA+I+++       G++ R + I+G
Sbjct: 1   PLGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV---EGSSGRQVTITG 57

Query: 90  TIDEILRAVDLVIDKLLTE 108
           +   I  A  L+  +L +E
Sbjct: 58  SAASISLAQYLINARLSSE 76

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

 Score = 69.6 bits (171), Expect = 2e-15
 Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 3/78 (3%)

Query: 118 VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177
           +G++T   L +PN+  G IIG+ GA I      S A IKI+       G + R VT+TG+
Sbjct: 2   LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIAN---PVEGSSGRQVTITGS 58

Query: 178 LDEQMRALELILLKLSED 195
                 A  LI  +LS +
Sbjct: 59  AASISLAQYLINARLSSE 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 = 81.6 bits (202), Expect = 7e-20
 Identities = 21/76 (27%), Positives = 42/76 (55%), Gaps = 3/76 (3%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           +  + +  +  G ++G+GG+ I +I   SGA IK+ +  +   G+ +R +TI+G Q  I+
Sbjct: 8   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE---GSEDRIITITGTQDQIQ 64

Query: 318 TAESMIMQKVAYASDR 333
            A+ ++   V   S +
Sbjct: 65  NAQYLLQNSVKQYSGK 80

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

 Score = 75.0 bits (185), Expect = 2e-17
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
            +  +   LAG++IGKGG  I   + +SGA I++        G+ DRII I+GT D+I  
Sbjct: 9   TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL---EGSEDRIITITGTQDQIQN 65

Query: 97  AVDLVIDKLLTE 108
           A  L+ + +   
Sbjct: 66  AQYLLQNSVKQY 77

>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 = 69.2 bits (170), Expect = 2e-15
 Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTL 178
           G     ++ +P    GSIIGK G  IK    +S A IKI        G  DR++T+TGT 
Sbjct: 4   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE---PLEGSEDRIITITGTQ 60

Query: 179 DEQMRALELILLKLSEDT 196
           D+   A  L+   + + +
Sbjct: 61  DQIQNAQYLLQNSVKQYS 78

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

 Score = 81.6 bits (202), Expect = 9e-20
 Identities = 22/90 (24%), Positives = 44/90 (48%), Gaps = 3/90 (3%)

Query: 244 GGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTS 303
           G      +      +  + +  +  G ++G+GG+ I +I   SGA IK+ +  +   G+ 
Sbjct: 1   GSHMSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE---GSE 57

Query: 304 ERKVTISGPQRSIRTAESMIMQKVAYASDR 333
           +R +TI+G Q  I+ A+ ++   V   S +
Sbjct: 58  DRIITITGTQDQIQNAQYLLQNSVKQYSGK 87

>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 = 75.1 bits (185), Expect = 3e-17
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
            +  +   LAG++IGKGG  I   + +SGA I++        G+ DRII I+GT D+I  
Sbjct: 16  TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL---EGSEDRIITITGTQDQIQN 72

Query: 97  AVDLVIDKLLTE 108
           A  L+ + +   
Sbjct: 73  AQYLLQNSVKQY 84

>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 = 70.8 bits (174), Expect = 7e-16
 Identities = 27/82 (32%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 115 ADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL 174
            D  G     ++ +P    GSIIGK G  IK    +S A IKI        G  DR++T+
Sbjct: 7   GDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE---PLEGSEDRIITI 63

Query: 175 TGTLDEQMRALELILLKLSEDT 196
           TGT D+   A  L+   + + +
Sbjct: 64  TGTQDQIQNAQYLLQNSVKQYS 85

>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 = 81.2 bits (201), Expect = 1e-19
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           IR L+     G++IGK G ++   + +SGARI +S          +RII ++G  + I +
Sbjct: 7   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISE-----GNCPERIITLAGPTNAIFK 61

Query: 97  AVDLVIDKLLTE 108
           A  ++IDKL  +
Sbjct: 62  AFAMIIDKLEED 73

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

 Score = 75.4 bits (186), Expect = 1e-17
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
           +RL++     GSIIGK G ++K   ++S A I IS          +R++TL G  +   +
Sbjct: 7   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFK 61

Query: 184 ALELILLKLSED 195
           A  +I+ KL ED
Sbjct: 62  AFAMIIDKLEED 73

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

 Score = 69.6 bits (171), Expect = 1e-15
 Identities = 20/75 (26%), Positives = 44/75 (58%), Gaps = 5/75 (6%)

Query: 253 DDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP 312
            + T ++ + +  + +G ++G+ G ++ ++ + SGARI +S+         ER +T++GP
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE-----GNCPERIITLAGP 55

Query: 313 QRSIRTAESMIMQKV 327
             +I  A +MI+ K+
Sbjct: 56  TNAIFKAFAMIIDKL 70

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

 Score = 79.5 bits (196), Expect = 9e-19
 Identities = 18/72 (25%), Positives = 34/72 (47%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           + F +     G VIG+GG  +     Q+GA +++SR          ++ +I G+  +I  
Sbjct: 9   MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDH 68

Query: 97  AVDLVIDKLLTE 108
           A  L+ +K+   
Sbjct: 69  AKQLIEEKIEGP 80

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

 Score = 79.1 bits (195), Expect = 1e-18
 Identities = 19/72 (26%), Positives = 36/72 (50%)

Query: 256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRS 315
              +T  +     G V+GRGG N+  I+Q +GA +++S +       + +   I G  + 
Sbjct: 6   GGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQ 65

Query: 316 IRTAESMIMQKV 327
           I  A+ +I +K+
Sbjct: 66  IDHAKQLIEEKI 77

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

 Score = 76.5 bits (188), Expect = 1e-17
 Identities = 22/103 (21%), Positives = 40/103 (38%), Gaps = 1/103 (0%)

Query: 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTL 178
               ++   +P   CG +IG+ G  +K+    + A ++ISR        N +L  + G+ 
Sbjct: 4   APGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSP 63

Query: 179 DEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPY 221
            +   A +LI  K+                AG     F+  P+
Sbjct: 64  QQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAGP-MGPFNPGPF 105

>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 = 77.9 bits (192), Expect = 2e-18
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRS 315
             +    V D  +GF++GRGG  I  I Q SG +I+++       G  ER   ++G   S
Sbjct: 14  VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG---GLPERSCMLTGTPES 70

Query: 316 IRTAESMIMQKVA 328
           +++A+ ++ Q V 
Sbjct: 71  VQSAKRLLDQIVE 83

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

 Score = 69.4 bits (170), Expect = 3e-15
 Identities = 19/82 (23%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 27  SSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIM 86
                       + V + + G +IG+GG  I+  Q +SG +IQ++       G  +R  M
Sbjct: 7   GHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCM 63

Query: 87  ISGTIDEILRAVDLVIDKLLTE 108
           ++GT + +  A  L+   +   
Sbjct: 64  LTGTPESVQSAKRLLDQIVEKG 85

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

 Score = 65.1 bits (159), Expect = 1e-13
 Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 3/77 (3%)

Query: 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTL 178
            +       VP+   G IIG+ G  I     +S   I+I+       GL +R   LTGT 
Sbjct: 12  RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG---GLPERSCMLTGTP 68

Query: 179 DEQMRALELILLKLSED 195
           +    A  L+   + + 
Sbjct: 69  ESVQSAKRLLDQIVEKG 85

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

 Score = 76.2 bits (188), Expect = 7e-18
 Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 3/84 (3%)

Query: 247 KFQNNKDDRTNSLT--IGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSE 304
           +F +N +   N     I +     G V+G+GG  I ++ + +G ++ +   G   +   +
Sbjct: 2   QFHDNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVD 60

Query: 305 RKVTISGPQRSIRTAESMIMQKVA 328
           + + I G    ++ A  M+M  + 
Sbjct: 61  KPLRIIGDPYKVQQACEMVMDILR 84

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

 Score = 75.5 bits (186), Expect = 1e-17
 Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 27  SSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIM 86
           +++  +  T    ++    AG VIGKGG TI   Q ++G ++ L +         D+ + 
Sbjct: 6   NANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLR 64

Query: 87  ISGTIDEILRAVDLVIDKL 105
           I G   ++ +A ++V+D L
Sbjct: 65  IIGDPYKVQQACEMVMDIL 83

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

 Score = 73.2 bits (180), Expect = 1e-16
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 1/85 (1%)

Query: 110 HAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLND 169
              D A+     T   +++P    G +IGK G TIK   + +   + + + D S     D
Sbjct: 2   QFHDNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQ-DGSQNTNVD 60

Query: 170 RLVTLTGTLDEQMRALELILLKLSE 194
           + + + G   +  +A E+++  L E
Sbjct: 61  KPLRIIGDPYKVQQACEMVMDILRE 85

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

 Score = 74.8 bits (184), Expect = 5e-17
 Identities = 24/103 (23%), Positives = 36/103 (34%), Gaps = 10/103 (9%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           I   V     G VIG+ G  I   Q+ +G RIQ  +         ++I  I G  D    
Sbjct: 13  IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD---GTGPEKIAHIMGPPDRCEH 69

Query: 97  AVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGK 139
           A  ++ D L        ++   G        +P    G   G+
Sbjct: 70  AARIINDLL-----QSLRSGPPGPPG--GPGMPPGGRGRGRGQ 105

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

 Score = 66.7 bits (163), Expect = 4e-14
 Identities = 17/78 (21%), Positives = 27/78 (34%), Gaps = 3/78 (3%)

Query: 256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRS 315
              + + V    +G V+GR G  I +I   +G RI+            E+   I GP   
Sbjct: 10  GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG---TGPEKIAHIMGPPDR 66

Query: 316 IRTAESMIMQKVAYASDR 333
              A  +I   +      
Sbjct: 67  CEHAARIINDLLQSLRSG 84

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

 Score = 64.0 bits (156), Expect = 3e-13
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 3/76 (3%)

Query: 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTL 178
                + + VP  S G +IG++G  IK   +D+   I+  + D       +++  + G  
Sbjct: 8   RIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD---GTGPEKIAHIMGPP 64

Query: 179 DEQMRALELILLKLSE 194
           D    A  +I   L  
Sbjct: 65  DRCEHAARIINDLLQS 80

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

 Score = 74.5 bits (183), Expect = 6e-17
 Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 1/85 (1%)

Query: 244 GGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTS 303
                    ++      + V    +G ++GRGG  I  I + SGA+I      +  +   
Sbjct: 2   SSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE-GTLLL 60

Query: 304 ERKVTISGPQRSIRTAESMIMQKVA 328
            R + ISG Q+ +  A+ +I++KV+
Sbjct: 61  SRLIKISGTQKEVAAAKHLILEKVS 85

>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 = 70.2 bits (172), Expect = 2e-15
 Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 1/84 (1%)

Query: 125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRA 184
           +L VP  S G IIG+ G TI+S    S A I   + +     L  RL+ ++GT  E   A
Sbjct: 18  QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDK-ESEGTLLLSRLIKISGTQKEVAAA 76

Query: 185 LELILLKLSEDTLYSQTMTVPYTY 208
             LIL K+SED    + +    + 
Sbjct: 77  KHLILEKVSEDEELRKRIAHSASG 100

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

 Score = 70.2 bits (172), Expect = 2e-15
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 34  PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDE 93
           P + +  V     G +IG+GG TI      SGA+I   +  E       R+I ISGT  E
Sbjct: 14  PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE-GTLLLSRLIKISGTQKE 72

Query: 94  ILRAVDLVIDKL 105
           +  A  L+++K+
Sbjct: 73  VAAAKHLILEKV 84

>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 = 73.6 bits (181), Expect = 8e-17
 Identities = 14/85 (16%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 244 GGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTS 303
                 +          I +     G V+G+GG  I ++ + +G ++ +   G   +G  
Sbjct: 2   SSGSSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGA- 60

Query: 304 ERKVTISGPQRSIRTAESMIMQKVA 328
           ++ + I+G    ++ A+ M+++ + 
Sbjct: 61  DKPLRITGDPYKVQQAKEMVLELIR 85

>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 = 73.2 bits (180), Expect = 1e-16
 Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
              ++    AG VIGKGG TI   Q ++G ++ + +         D+ + I+G   ++ +
Sbjct: 17  QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGP-QNTGADKPLRITGDPYKVQQ 75

Query: 97  AVDLVIDKLLTE 108
           A ++V++ +  +
Sbjct: 76  AKEMVLELIRDQ 87

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

 Score = 68.6 bits (168), Expect = 5e-15
 Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
             +++P S  G +IGK G TIK   + +   + + + D       D+ + +TG   +  +
Sbjct: 17  QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQ-DGPQNTGADKPLRITGDPYKVQQ 75

Query: 184 ALELILLKLSED 195
           A E++L  + + 
Sbjct: 76  AKEMVLELIRDQ 87

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 62.9 bits (153), Expect = 8e-13
 Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 2/85 (2%)

Query: 249 QNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVT 308
           Q ++  R+  L++ V  ++   ++GR G  I +I       I+  D+ D      + ++T
Sbjct: 9   QEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQIT 66

Query: 309 ISGPQRSIRTAESMIMQKVAYASDR 333
           I+G +++   A   I++ V      
Sbjct: 67  ITGYEKNTEAARDAILRIVGELEQM 91

>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 = 52.9 bits (127), Expect = 3e-09
 Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 3/84 (3%)

Query: 29  DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMIS 88
           D   +   +   V       +IG+ G+ I   + +    IQ     +         I I+
Sbjct: 11  DRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQITIT 68

Query: 89  GTIDEILRAVDLVIDKLLTELHAE 112
           G       A D  I +++ EL   
Sbjct: 69  GYEKNTEAARDA-ILRIVGELEQM 91

>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 = 49.1 bits (117), Expect = 5e-08
 Identities = 22/93 (23%), Positives = 33/93 (35%), Gaps = 6/93 (6%)

Query: 113 DQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLV 172
           +Q D      KL + V       IIG+ GA I     +    I+    D          +
Sbjct: 8   EQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG--NQPQDQI 65

Query: 173 TLTGTLDEQMRALELILLKLSEDTLYSQTMTVP 205
           T+TG       A + IL  + E     + M+ P
Sbjct: 66  TITGYEKNTEAARDAILRIVGE----LEQMSGP 94

>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 = 61.6 bits (149), Expect = 7e-12
 Identities = 32/159 (20%), Positives = 48/159 (30%), Gaps = 29/159 (18%)

Query: 34  PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGA-RIQLSRSHEFFPGTTDRIIMISGTID 92
             + +F+V   L G  IG  G+ I   +   G   I L                I G   
Sbjct: 3   RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDED--------TCTFHIYGEDQ 54

Query: 93  EILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQ 152
           +                 A  +A       +  + VP +  G +IGK G  I+  +D S 
Sbjct: 55  D-----------------AVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSG 97

Query: 153 AV---IKISRLDHSYYGLNDRLVTLTGTLDEQMRALELI 188
            V   I+     +             GT D    A  L+
Sbjct: 98  VVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLL 136

>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 = 47.3 bits (112), Expect = 7e-07
 Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 3/72 (4%)

Query: 261 IGVADEHIGFVVGRGGRNIMEISQISGA---RIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           I V    +G V+G+ G+ I EI   SG    RI+  +  +             G + SI 
Sbjct: 71  IQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIA 130

Query: 318 TAESMIMQKVAY 329
            A  ++   + Y
Sbjct: 131 NATVLLDYHLNY 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 = 39.2 bits (91), Expect = 4e-04
 Identities = 22/80 (27%), Positives = 28/80 (35%), Gaps = 4/80 (5%)

Query: 33  KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGA---RIQLSRSHEFFPGTTDRIIMISG 89
           +       V   L G VIGK G  I +   +SG    RI+                +  G
Sbjct: 65  EFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVG 124

Query: 90  TIDEILRAVDLVIDKLLTEL 109
           T D I  A  L +D  L  L
Sbjct: 125 TKDSIANATVL-LDYHLNYL 143

>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 = 59.4 bits (144), Expect = 1e-11
 Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           S T+ +  EH  FV+G+ G  + ++   +  +I++    D        ++ I+G +  I 
Sbjct: 18  SATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD-----PSNQIKITGTKEGIE 72

Query: 318 TAESMIMQKVAYASDR 333
            A   ++   A    R
Sbjct: 73  KARHEVLLISAEQDKR 88

>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 = 52.8 bits (127), Expect = 2e-09
 Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 6/76 (7%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
               +       VIGK G  + D + ++  +IQ+ R     P      I I+GT + I +
Sbjct: 19  ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR-----PDDPSNQIKITGTKEGIEK 73

Query: 97  AVDLVIDKLLTELHAE 112
           A    +  +  E    
Sbjct: 74  ARHE-VLLISAEQDKR 88

>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 = 50.1 bits (120), Expect = 2e-08
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 5/75 (6%)

Query: 120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD 179
           T+    + +P      +IGK G  ++     +   I+I R            + +TGT +
Sbjct: 15  TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-----DDPSNQIKITGTKE 69

Query: 180 EQMRALELILLKLSE 194
              +A   +LL  +E
Sbjct: 70  GIEKARHEVLLISAE 84

>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 = 59.3 bits (143), Expect = 1e-10
 Identities = 24/153 (15%), Positives = 47/153 (30%), Gaps = 24/153 (15%)

Query: 47  GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVID--- 103
             +IGK G T  + + ++  +I +                 +     + +A D+V+    
Sbjct: 46  AVLIGKKGQTKKEIEKRTKTKITIDSETGEVW---ITSTKETEDPLAVWKARDIVLAIGR 102

Query: 104 --------KLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVI 155
                   +LL E    +  +                 G IIG+ G T +   + S A +
Sbjct: 103 GFSPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASV 162

Query: 156 KISRLDHSYYGLNDRLVTLTGTLDEQMRALELI 188
            +            + V + G   +   A   I
Sbjct: 163 SVY----------GKTVAIIGNPIQIEIAKTAI 185

>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 = 47.4 bits (112), Expect = 1e-06
 Identities = 33/197 (16%), Positives = 54/197 (27%), Gaps = 50/197 (25%)

Query: 128 VPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALEL 187
           +P      +IGK G T K     ++  I I       +         T       +A ++
Sbjct: 40  IPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVW---ITSTKETEDPLAVWKARDI 96

Query: 188 ILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRK 247
           +L                                G  P     + +        N+    
Sbjct: 97  VLAIG----------------------------RGFSPERAFRLLNEGEYLEIINLTDII 128

Query: 248 FQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKV 307
             N K+               G ++GR GR    I ++SGA + V            + V
Sbjct: 129 IGNEKN---------ALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG----------KTV 169

Query: 308 TISGPQRSIRTAESMIM 324
            I G    I  A++ I 
Sbjct: 170 AIIGNPIQIEIAKTAIE 186

>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 = 55.6 bits (134), Expect = 3e-10
 Identities = 22/81 (27%), Positives = 30/81 (37%), Gaps = 6/81 (7%)

Query: 32  EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTI 91
             P  I   V   L   VIG+ GS I     +    I +       P     II I+G  
Sbjct: 14  LVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA-----PELQSDIIAITGLA 68

Query: 92  DEILRAVDLVIDKLLTELHAE 112
             + RA    + + + EL AE
Sbjct: 69  ANLDRAKAG-LLERVKELQAE 88

>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 = 53.3 bits (128), Expect = 2e-09
 Identities = 11/71 (15%), Positives = 30/71 (42%), Gaps = 5/71 (7%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           ++ + V  +   +V+G+ G  I ++       I V              + I+G   ++ 
Sbjct: 18  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL-----QSDIIAITGLAANLD 72

Query: 318 TAESMIMQKVA 328
            A++ ++++V 
Sbjct: 73  RAKAGLLERVK 83

>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 = 45.6 bits (108), Expect = 1e-06
 Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 5/67 (7%)

Query: 128 VPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALEL 187
           VP      +IG+ G+ I+  MD+ +  I +         L   ++ +TG      RA   
Sbjct: 23  VPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA-----PELQSDIIAITGLAANLDRAKAG 77

Query: 188 ILLKLSE 194
           +L ++ E
Sbjct: 78  LLERVKE 84

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

 Score = 53.5 bits (129), Expect = 7e-10
 Identities = 10/75 (13%), Positives = 30/75 (40%), Gaps = 5/75 (6%)

Query: 254 DRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQ 313
           +R + + I +  +    ++G+ G NI  I       +++              + I G  
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPP-----DSEKSNLIRIEGDP 56

Query: 314 RSIRTAESMIMQKVA 328
           + ++ A+  +++  +
Sbjct: 57  QGVQQAKRELLELAS 71

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

 Score = 49.3 bits (118), Expect = 3e-08
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 5/72 (6%)

Query: 32  EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTI 91
            +  Y+   + +     +IGK G+ IN  + Q    +++    E        +I I G  
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE-----KSNLIRIEGDP 56

Query: 92  DEILRAVDLVID 103
             + +A   +++
Sbjct: 57  QGVQQAKRELLE 68

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

 Score = 43.5 bits (103), Expect = 3e-06
 Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 5/72 (6%)

Query: 118 VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177
           +     + + + +     +IGK+GA I    D  +  ++I             L+ + G 
Sbjct: 1   INRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE-----KSNLIRIEGD 55

Query: 178 LDEQMRALELIL 189
                +A   +L
Sbjct: 56  PQGVQQAKRELL 67

>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 = 51.9 bits (124), Expect = 4e-09
 Identities = 15/71 (21%), Positives = 25/71 (35%), Gaps = 6/71 (8%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           ++ + V    +G VVG  G  I  I Q +   I    R        E    ++G   ++ 
Sbjct: 11  TIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDK------EPVFAVTGMPENVD 64

Query: 318 TAESMIMQKVA 328
            A   I   + 
Sbjct: 65  RAREEIEAHIT 75

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 48.8 bits (116), Expect = 6e-08
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 27  SSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIM 86
           SS  +   T I+  V   + G V+G  G+TI   Q ++   I      +      + +  
Sbjct: 2   SSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDK------EPVFA 55

Query: 87  ISGTIDEILRAVDLVIDKLLTE 108
           ++G  + + RA + +   +   
Sbjct: 56  VTGMPENVDRAREEIEAHITLR 77

>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 = 45.7 bits (108), Expect = 6e-07
 Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 114 QADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVT 173
            +   G +T +++ VP    G ++G  GATIK     +   I     D       + +  
Sbjct: 2   SSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD------KEPVFA 55

Query: 174 LTGTLDEQMRALELILLKLSEDT 196
           +TG  +   RA E I   ++  +
Sbjct: 56  VTGMPENVDRAREEIEAHITLRS 78

>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 = 49.8 bits (119), Expect = 3e-08
 Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 4/78 (5%)

Query: 251 NKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTIS 310
            + ++  S  + +       ++G  G+ I +I       I+    G          VT++
Sbjct: 11  GELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVT 66

Query: 311 GPQRSIRTAESMIMQKVA 328
           G   ++  A   I+    
Sbjct: 67  GLPENVEEAIDHILNLEE 84

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 4/74 (5%)

Query: 116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT 175
            ++       + + +     IIG  G  I+  MD+ +  I+  +        +   VT+T
Sbjct: 11  GELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP----DPNCVTVT 66

Query: 176 GTLDEQMRALELIL 189
           G  +    A++ IL
Sbjct: 67  GLPENVEEAIDHIL 80

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 5/81 (6%)

Query: 32  EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTI 91
           E+       + + +   +IG  G  I     +    I+  +S           + ++G  
Sbjct: 14  EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLP 69

Query: 92  DEILRAVDLVIDKLLTELHAE 112
           + +  A+D  I  L  E  A+
Sbjct: 70  ENVEEAIDH-ILNLEEEYLAD 89

>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 = 48.6 bits (116), Expect = 9e-08
 Identities = 14/83 (16%), Positives = 28/83 (33%), Gaps = 7/83 (8%)

Query: 247 KFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEI-SQISGARIKVSDRGDFFSGTSER 305
             Q +  +    + + +  +    ++G  GR I  I  +  G  I          G+   
Sbjct: 8   SIQKDLANIA-EVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV-----EGSGSD 61

Query: 306 KVTISGPQRSIRTAESMIMQKVA 328
            V I GP   +  A+  ++    
Sbjct: 62  TVVIRGPSSDVEKAKKQLLHLAE 84

>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 = 40.9 bits (96), Expect = 4e-05
 Identities = 16/97 (16%), Positives = 32/97 (32%), Gaps = 12/97 (12%)

Query: 17  KRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGA-RIQLSRSHE 75
             S +  K L++    +       +   L  ++IG  G  I     + G   I       
Sbjct: 4   GSSGSIQKDLANIAEVE-----VSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-- 56

Query: 76  FFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAE 112
              G+    ++I G   ++ +A    +  L  E   +
Sbjct: 57  ---GSGSDTVVIRGPSSDVEKAKKQ-LLHLAEEKQTK 89

>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 = 45.4 bits (107), Expect = 5e-06
 Identities = 23/149 (15%), Positives = 44/149 (29%), Gaps = 17/149 (11%)

Query: 47  GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDR-------IIMISGTIDEILRAVD 99
           GAVIG  G    +   ++G  I +   +       +        ++  +  +  I     
Sbjct: 16  GAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFP 75

Query: 100 LVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR 159
                 L E        D+               G IIG+ G   ++  + +   I +  
Sbjct: 76  PEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG- 134

Query: 160 LDHSYYGLNDRLVTLTGTLDEQMRALELI 188
                    +  V + G  +  M A + I
Sbjct: 135 ---------EYEVAIIGDYERAMAAKQAI 154

>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 = 43.5 bits (102), Expect = 2e-05
 Identities = 31/206 (15%), Positives = 55/206 (26%), Gaps = 51/206 (24%)

Query: 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTL 178
             K ++ + V     G++IG  G      M  +  VI +   D     +           
Sbjct: 1   AMKPRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITV---DTENSMVIVEPEAEGIPP 57

Query: 179 DEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAH 238
              M+A E++                          GF         PP  A        
Sbjct: 58  VNLMKAAEVVKA---------------------ISLGF---------PPEKAFRLLEEDQ 87

Query: 239 YGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDF 298
               +  ++   +  +              G ++G GGR    I +++   I V +    
Sbjct: 88  ILVVVDLKQVVGDSQNHLK--------RIKGRIIGEGGRARRTIEEMTDTYINVGE---- 135

Query: 299 FSGTSERKVTISGPQRSIRTAESMIM 324
                  +V I G       A+  I 
Sbjct: 136 ------YEVAIIGDYERAMAAKQAIE 155

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

 Score = 40.2 bits (95), Expect = 9e-04
 Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 10/71 (14%)

Query: 259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP-QRSIR 317
            TI +  + I  V+G GG+ I EI   +GA++ ++D G          V +S      I+
Sbjct: 572 ETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDG---------VVKVSASDGAKIK 622

Query: 318 TAESMIMQKVA 328
            A   I     
Sbjct: 623 AAIDWIKSITD 633

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	336
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.95
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.95
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.95
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.95
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.94
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.94
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.94
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.94
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.94
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.94
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.94
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.82
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.8
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.75
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.72
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.68
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.65
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.64
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.63
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.63
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.63
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.63
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.63
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.62
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.62
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.61
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.61
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.58
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.58
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.58
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.57
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.56
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.56
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.56
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.55
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.54
1we8_A	104	Tudor and KH domain containing protein; structural	99.54
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.54
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.53
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.51
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.5
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.49
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.49
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.49
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.49
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.49
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.47
1we8_A	104	Tudor and KH domain containing protein; structural	99.46
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.46
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.43
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.42
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.42
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.41
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.41
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.4
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.4
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.31
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.3
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.26
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.23
2cpq_A	91	FragIle X mental retardation syndrome related prot	99.03
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.81
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.77
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.69
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.68
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.66
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.32
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.29
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	98.28
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.13
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.1
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.8
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.66
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.58
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.55
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.43
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.49
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.22
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.06
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.83
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.79
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.68
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	95.19
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	95.0
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	94.74
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	93.85
4hhu_A	170	OR280; engineered protein, PSI-biology, structural	92.11
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	83.45
1wh9_A	92	40S ribosomal protein S3; KH domain, structural ge	81.24

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

Probab=99.95  E-value=2.9e-28  Score=205.38  Aligned_cols=165  Identities=35%  Similarity=0.626  Sum_probs=138.5

Q ss_pred             CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhcc
Q 019747           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH  110 (336)
Q Consensus        31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~  110 (336)
                      .+++++++|+||.+++|.||||+|++|++|+++|||+|+|++..+..+++.+|+|.|+|+.+++.+|+.+|.+.+.+...
T Consensus         2 l~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~~   81 (178)
T 2anr_A            2 LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQ   81 (178)
T ss_dssp             -CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhccCC
Confidence            46789999999999999999999999999999999999998876677889999999999999999999999977655421


Q ss_pred             ccc-----------cCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHH
Q 019747          111 AED-----------QADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD  179 (336)
Q Consensus       111 ~~~-----------~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~  179 (336)
                      ...           .....+...+.+|.||.+++|+|||++|.+|++|+++|||+|+|.+.. .++...++.|+|+|+++
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~-~~~~~~~~~v~I~G~~~  160 (178)
T 2anr_A           82 NVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKP-DGINLQNRVVTVSGEPE  160 (178)
T ss_dssp             C-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC-----CCEEEEEEESSHH
T ss_pred             ccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCC-CCCCCCceEEEEEcCHH
Confidence            110           001122357889999999999999999999999999999999998742 24556789999999999


Q ss_pred             HHHHHHHHHHHHhhcCc
Q 019747          180 EQMRALELILLKLSEDT  196 (336)
Q Consensus       180 ~v~~A~~~i~~~l~~~~  196 (336)
                      ++.+|+.+|.+++.+++
T Consensus       161 ~v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          161 QNRKAVELIIQKIQEDP  177 (178)
T ss_dssp             HHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHHhCC
Confidence            99999999999998753

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

Probab=99.95  E-value=3.7e-27  Score=195.79  Aligned_cols=160  Identities=24%  Similarity=0.358  Sum_probs=134.6

Q ss_pred             ceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCC
Q 019747          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQ  200 (336)
Q Consensus       121 ~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~  200 (336)
                      ..+++|+||.+.+|.|||++|++|++|+++|||+|+|...  ..+++.+|.|+|+|+++++.+|+.+|.+++.+...+.+
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~--~~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~~~~   79 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPP--ETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFGP   79 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCC--SSTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTSSCS
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCC--CCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccccccc
Confidence            3578999999999999999999999999999999999873  34677899999999999999999999999887532211


Q ss_pred             CcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHH
Q 019747          201 TMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIM  280 (336)
Q Consensus       201 ~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~  280 (336)
                      .                                                   .....+.++.||.+++|+|||++|++|+
T Consensus        80 ~---------------------------------------------------~~~~~~~~i~vp~~~~g~iIGkgG~~I~  108 (163)
T 3krm_A           80 K---------------------------------------------------EEVKLETHIRVPASAAGRVIGKGGKTVN  108 (163)
T ss_dssp             S---------------------------------------------------CCCCEEEEEEEETTTHHHHHCGGGHHHH
T ss_pred             c---------------------------------------------------cCCceEEEEEcChhheeeEEcCCChHHH
Confidence            0                                                   1223677999999999999999999999


Q ss_pred             HHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhhcc
Q 019747          281 EISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDRL  334 (336)
Q Consensus       281 ~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~  334 (336)
                      +|++.|||+|.|++...+ ...+.+.|+|+|++++|+.|+.+|.+++.+..+..
T Consensus       109 ~i~~~tga~I~i~~~~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~~~  161 (163)
T 3krm_A          109 ELQNLTAAEVVVPRDQTP-DENDQVIVKIIGHFYASQMAQRKIRDILAQVKQQH  161 (163)
T ss_dssp             HHHHHHCCEEECCTTCCC-CTTSEEEEEEEECHHHHHHHHHHHHHHHHHHTC--
T ss_pred             HHHHHhCCeEEECCCCCC-CCCCceEEEEEeCHHHHHHHHHHHHHHHHHHHHhh
Confidence            999999999999876432 22344589999999999999999999999876543

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

Probab=99.95  E-value=2.4e-27  Score=217.05  Aligned_cols=237  Identities=11%  Similarity=0.083  Sum_probs=169.5

Q ss_pred             CCCCCCCCCCCCCcEEEEEEEecCccceeecCCC--hHHHHHHHHhCCeEEEcCCC--CCCCCCCceEEEEEeeHHHHHH
Q 019747           21 APVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGG--STINDFQSQSGARIQLSRSH--EFFPGTTDRIIMISGTIDEILR   96 (336)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~i~ip~~~vg~iIGk~G--~~Ik~I~~~tg~~I~i~~~~--~~~~~~~~r~i~I~G~~~~v~~   96 (336)
                      -|.+.+--+.....+++++.||..+|+.||||+|  ++|++|+++|||+|+|++.+  ..-+......|+|+|..++|++
T Consensus        16 ~~~~~~~le~~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~   95 (376)
T 3n89_A           16 LPSNIPMIEINPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDR   95 (376)
T ss_dssp             BCCCSCCCCCCTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHH
T ss_pred             CCccceEEEecCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHH
Confidence            4555667788899999999999999999999999  99999999999999998765  2222345678999999999999


Q ss_pred             HHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEc
Q 019747           97 AVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG  176 (336)
Q Consensus        97 A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G  176 (336)
                      |+.+|.+. .              +....+.+|...+..  ..-+..|.+ ++.++++|.|..... ..+.....|+|+|
T Consensus        96 AR~~I~~l-~--------------Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~-~~~~~sd~V~IrG  156 (376)
T 3n89_A           96 ARMLMRRN-C--------------HFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPE-KNGIVTTYLRITA  156 (376)
T ss_dssp             HHHHHHHS-C--------------EEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC------CEEEEEEEE
T ss_pred             HHHHHHhc-C--------------CceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCccc-ccCCCCCEEEEEc
Confidence            99999852 1              234555555433221  111234444 567899999976321 1111356899999


Q ss_pred             CHHHHHHHHHHHHHHhhcCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCc
Q 019747          177 TLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRT  256 (336)
Q Consensus       177 ~~~~v~~A~~~i~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  256 (336)
                      ...++..|.+++..++.........                                                   ....
T Consensus       157 ~~~nv~~akeA~~~Ll~~l~~~e~~---------------------------------------------------~~~~  185 (376)
T 3n89_A          157 REKNQHELIEAAKRLNEILFRESPA---------------------------------------------------PENN  185 (376)
T ss_dssp             EGGGHHHHHHHHHHHHHHHCC--CC---------------------------------------------------CSSC
T ss_pred             ChhhHHHHHHHHHHHHHHHHhhhcc---------------------------------------------------cccc
Confidence            9977766666655554331110000                                                   1233


Q ss_pred             eEEEEEeccCcccceeccCC--chHHHHHhHhCCeEEEccCCCCCC-CCcceEEEEEcChHhHHHHHHHHHHHH
Q 019747          257 NSLTIGVADEHIGFVVGRGG--RNIMEISQISGARIKVSDRGDFFS-GTSERKVTISGPQRSIRTAESMIMQKV  327 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G--~~I~~I~~~sga~I~i~~~~~~~~-~~~~r~v~I~G~~~~v~~A~~~I~~~i  327 (336)
                      .+..+.|+..+|.+|||++|  ..|++|+++|||+|.+++.++..+ ......|+|+|+.++|..|+++|+++|
T Consensus       186 ~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lL  259 (376)
T 3n89_A          186 FTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLL  259 (376)
T ss_dssp             EEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTS
T ss_pred             eEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhC
Confidence            78899999999999999999  556999999999999987543211 124578999999999999999999875

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

Probab=99.95  E-value=5.2e-27  Score=194.33  Aligned_cols=156  Identities=29%  Similarity=0.537  Sum_probs=135.8

Q ss_pred             CCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccc
Q 019747           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHA  111 (336)
Q Consensus        32 ~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~  111 (336)
                      +..++++|+||.+.+|.||||+|++|++|+++|||+|+|++.     ++.+|.|.|.|+.+++.+|+.+|.+.+.+.+..
T Consensus         2 ~~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~-----~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~~   76 (160)
T 2jzx_A            2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKLEEDISS   76 (160)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC-----TTTEEEEEEEEEHHHHHHHHHHHHHHHHHHHTS
T ss_pred             CccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC-----CCCceEEEEEeCHHHHHHHHHHHHHHHHhhccc
Confidence            356899999999999999999999999999999999999864     367999999999999999999999888876543


Q ss_pred             cccC--CCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 019747          112 EDQA--DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL  189 (336)
Q Consensus       112 ~~~~--~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~  189 (336)
                      ....  .......+.++.||.+++|+|||++|.+|++|++.|||+|.+.+  +..++..++.|+|.|+++++.+|+.+|.
T Consensus        77 ~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~--~~~~~~~~~~v~I~G~~~~v~~A~~~I~  154 (160)
T 2jzx_A           77 SMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG--DMLPNSTERAITIAGIPQSIIECVKQIC  154 (160)
T ss_dssp             CCCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCC--CCSTTCCEEEEEEEECHHHHHHHHHHHH
T ss_pred             cCCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECC--CCCCCCCceEEEEEcCHHHHHHHHHHHH
Confidence            2111  11234588999999999999999999999999999999999986  3456778999999999999999999999


Q ss_pred             HHhhc
Q 019747          190 LKLSE  194 (336)
Q Consensus       190 ~~l~~  194 (336)
                      +++.+
T Consensus       155 ~~i~e  159 (160)
T 2jzx_A          155 VVMLE  159 (160)
T ss_dssp             HHHHH
T ss_pred             HHHhc
Confidence            98865

>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=2.1e-26  Score=191.28  Aligned_cols=155  Identities=23%  Similarity=0.350  Sum_probs=132.4

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccc
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAED  113 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~  113 (336)
                      .-+++|+||.+.+|.||||+|++|++|+++|||+|+|++..  .+++.+|+|.|+|+++++.+|+.+|.+.+.+....  
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~--~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~~--   77 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPE--TPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFF--   77 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCS--STTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTSS--
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCC--CCCCCceEEEEEcCHHHHHHHHHHHHHHHhccccc--
Confidence            35899999999999999999999999999999999998743  47789999999999999999999999887765111  


Q ss_pred             cCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCc-eEEEEEcCHHHHHHHHHHHHHHh
Q 019747          114 QADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLND-RLVTLTGTLDEQMRALELILLKL  192 (336)
Q Consensus       114 ~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~-r~v~I~G~~~~v~~A~~~i~~~l  192 (336)
                       ..........+|.||.+++|+|||++|.+|++|++.|||+|.|.++.  .++.++ +.|+|.|+++++..|+.+|.+++
T Consensus        78 -~~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~--~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  154 (163)
T 3krm_A           78 -GPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQ--TPDENDQVIVKIIGHFYASQMAQRKIRDIL  154 (163)
T ss_dssp             -CSSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTC--CCCTTSEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             -ccccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCC--CCCCCCceEEEEEeCHHHHHHHHHHHHHHH
Confidence             11123456779999999999999999999999999999999998632  233344 58999999999999999999999


Q ss_pred             hcC
Q 019747          193 SED  195 (336)
Q Consensus       193 ~~~  195 (336)
                      .+.
T Consensus       155 ~~~  157 (163)
T 3krm_A          155 AQV  157 (163)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            763

>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=7e-27  Score=196.91  Aligned_cols=173  Identities=29%  Similarity=0.468  Sum_probs=136.3

Q ss_pred             CceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCC
Q 019747          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS  199 (336)
Q Consensus       120 ~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~  199 (336)
                      ..++++|+||.+++|.|||++|++|++|+++|||+|+|.+..+..++..+|.|+|+|+.+++.+|+.+|.+++.+.....
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            45889999999999999999999999999999999999875555677889999999999999999999999997653221


Q ss_pred             CCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchH
Q 019747          200 QTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNI  279 (336)
Q Consensus       200 ~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I  279 (336)
                      .. ..+               ....+|.                     .........+.++.||.+++|+|||++|++|
T Consensus        84 ~~-~~~---------------~~~~~~~---------------------~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~I  126 (178)
T 2anr_A           84 AK-TEP---------------VSILQPQ---------------------TTVNPDRANQVKIIVPNSTAGLIIGKGGATV  126 (178)
T ss_dssp             -----------------------------------------------------CGGGGEEEEEEEHHHHHHHHCGGGHHH
T ss_pred             cc-CCc---------------ccccCCc---------------------cCCCCCCceEEEEEEchhheeeeECCCcHHH
Confidence            00 000               0000000                     0000223478899999999999999999999


Q ss_pred             HHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747          280 MEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       280 ~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  330 (336)
                      ++|++.|||+|.|.+..+ .++..++.|+|+|++++++.|+.+|.++|.+.
T Consensus       127 k~i~~~tga~I~i~~~~~-~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~  176 (178)
T 2anr_A          127 KAIMEQSGAWVQLSQKPD-GINLQNRVVTVSGEPEQNRKAVELIIQKIQED  176 (178)
T ss_dssp             HHHHHHSSCEEEECCCC-----CCEEEEEEESSHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHCCEEEEeCCCC-CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhC
Confidence            999999999999987532 23456899999999999999999999999864

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

Probab=99.94  E-value=3.6e-26  Score=191.83  Aligned_cols=156  Identities=31%  Similarity=0.407  Sum_probs=129.6

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccc
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAED  113 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~  113 (336)
                      ..+++|+||.+++|.||||+|++|++|+++|||+|+|.+..   +++.+|+|.|+|+.+++.+|+.+|.+.+.+......
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~   78 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD---GTTPERIAQITGPPDRAQHAAEIITDLLRSVQAGNP   78 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT---TSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC----
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHHhcccCCC
Confidence            57899999999999999999999999999999999997532   457899999999999999999999977765421100


Q ss_pred             c-----------------CCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEc
Q 019747          114 Q-----------------ADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG  176 (336)
Q Consensus       114 ~-----------------~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G  176 (336)
                      .                 ........+.+|.||.+++|.|||++|.+|++|++.|||+|+|.++...+.+..++.|+|.|
T Consensus        79 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G  158 (174)
T 1j4w_A           79 GGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRG  158 (174)
T ss_dssp             -------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEEC
T ss_pred             CCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEEC
Confidence            0                 00011246889999999999999999999999999999999999754445567889999999


Q ss_pred             CHHHHHHHHHHHHHHh
Q 019747          177 TLDEQMRALELILLKL  192 (336)
Q Consensus       177 ~~~~v~~A~~~i~~~l  192 (336)
                      +++++.+|+.+|.+++
T Consensus       159 ~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          159 TPQQIDYARQLIEEKI  174 (174)
T ss_dssp             CHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHhC
Confidence            9999999999999874

>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=99.94  E-value=6.1e-26  Score=188.66  Aligned_cols=161  Identities=22%  Similarity=0.330  Sum_probs=131.0

Q ss_pred             eeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCC
Q 019747          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQT  201 (336)
Q Consensus       122 ~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~  201 (336)
                      ++.+|+||.+++|.|||++|++|++|+++|||+|++.++. ..++..++.|+|+|+++++.+|+.+|.+++.+.....  
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~-~~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~~~--   78 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG-SQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQGG--   78 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCT-TSSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSSSCC--
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCC-CCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhccCCC--
Confidence            5789999999999999999999999999999999998632 3355678999999999999999999999987642110  


Q ss_pred             cCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHH
Q 019747          202 MTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIME  281 (336)
Q Consensus       202 ~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~  281 (336)
                                           +.+.          ..|++            ....+.++.||.+++|+|||++|++|++
T Consensus        79 ---------------------~~~~----------~~~~~------------~~~~~~~i~vp~~~~g~iIGk~G~~I~~  115 (164)
T 2jvz_A           79 ---------------------FGDR----------NEYGS------------RIGGGIDVPVPRHSVGVVIGRSGEMIKK  115 (164)
T ss_dssp             ---------------------CSSC----------SSCTT------------SCSSSBCCEEETTTHHHHHCSSSHHHHH
T ss_pred             ---------------------CCCc----------cccCC------------CCCceEEEEEChhhccccCCCCcHhHHH
Confidence                                 0000          00110            0014468889999999999999999999


Q ss_pred             HHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          282 ISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       282 I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      |++.|||+|.|++..   +...++.|+|+|++++++.|+.+|.+++++..
T Consensus       116 i~~~tg~~I~i~~~~---~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~  162 (164)
T 2jvz_A          116 IQNDAGVRIQFKQDD---GTGPEKIAHIMGPPDRCEHAARIINDLLQSLR  162 (164)
T ss_dssp             HHHHTCCEEEECCCC---TTSSEEEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCeEEEeCCC---CCCCcEEEEEEcCHHHHHHHHHHHHHHHhhhh
Confidence            999999999998753   33558999999999999999999999987653

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

Probab=99.94  E-value=3.5e-26  Score=191.85  Aligned_cols=172  Identities=25%  Similarity=0.347  Sum_probs=129.2

Q ss_pred             eeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCC
Q 019747          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQT  201 (336)
Q Consensus       122 ~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~  201 (336)
                      .+.+|+||.+++|.|||++|++|++|+++|||+|+|.+.+   ++..+|.|+|+|+++++.+|+.+|.+++.+.....  
T Consensus         3 ~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~~--   77 (174)
T 1j4w_A            3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD---GTTPERIAQITGPPDRAQHAAEIITDLLRSVQAGN--   77 (174)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT---TSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC-----
T ss_pred             eEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHHhcccCC--
Confidence            5789999999999999999999999999999999998632   35578999999999999999999999987642100  


Q ss_pred             cCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHH
Q 019747          202 MTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIME  281 (336)
Q Consensus       202 ~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~  281 (336)
                            +.     +  ..|.+         +.   +..+    ...|...+.....+.++.||.+++|+|||++|++|++
T Consensus        78 ------~~-----~--~~p~~---------~~---~~~~----~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~  128 (174)
T 1j4w_A           78 ------PG-----G--PGPGG---------RG---RGRG----QGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKS  128 (174)
T ss_dssp             -------------------------------------------------------CEEEEEEETTTHHHHHCGGGHHHHH
T ss_pred             ------CC-----C--CCCCC---------CC---CCCC----CCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHH
Confidence                  00     0  00000         00   0000    0000001112346889999999999999999999999


Q ss_pred             HHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHH
Q 019747          282 ISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKV  327 (336)
Q Consensus       282 I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  327 (336)
                      |++.|||+|.|.+..++..++.++.|+|+|++++++.|+.+|.++|
T Consensus       129 I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          129 ISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             HHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             HHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            9999999999998654444567899999999999999999998864

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

Probab=99.94  E-value=3.2e-26  Score=189.58  Aligned_cols=157  Identities=30%  Similarity=0.464  Sum_probs=132.0

Q ss_pred             CceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCC
Q 019747          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS  199 (336)
Q Consensus       120 ~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~  199 (336)
                      ....++|+||.+.+|.|||++|.+|++|+++|||+|+|...     +..+|.|+|.|+.+++.+|+.+|.+++.+.....
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            35788999999999999999999999999999999999873     3468999999999999999999999887642211


Q ss_pred             CCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchH
Q 019747          200 QTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNI  279 (336)
Q Consensus       200 ~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I  279 (336)
                      ..                   ....                           ......+.++.||.+++|+|||++|++|
T Consensus        78 ~~-------------------~~~~---------------------------~~~~~~~~~i~vp~~~~g~iIGkgG~~I  111 (160)
T 2jzx_A           78 MT-------------------NSTA---------------------------ASRPPVTLRLVVPASQCGSLIGKGGCKI  111 (160)
T ss_dssp             CC-------------------SSSC---------------------------CCCCSEEEEEEEEHHHHHHHHCGGGHHH
T ss_pred             CC-------------------CCcc---------------------------CCCCCEEEEEEEChhheeeEECCCCHHH
Confidence            00                   0000                           0112378999999999999999999999


Q ss_pred             HHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747          280 MEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       280 ~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  329 (336)
                      ++|++.|||+|.+++.  ..+++.++.|+|+|++++++.|+.+|.+++.+
T Consensus       112 k~i~~~tga~I~i~~~--~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          112 KEIRESTGAQVQVAGD--MLPNSTERAITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             HHHHHHHSSEECCCCC--CSTTCCEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCeEEECCC--CCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            9999999999999864  34567799999999999999999999998865

>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=99.94  E-value=7.8e-26  Score=188.01  Aligned_cols=156  Identities=24%  Similarity=0.336  Sum_probs=130.2

Q ss_pred             EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhcccccc
Q 019747           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQ  114 (336)
Q Consensus        35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~  114 (336)
                      ++++|+||.+++|.||||+|++|++|+++|||+|++.+.. ..+++.+|.|.|+|+++++.+|+.+|.+.+.+.......
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            6899999999999999999999999999999999997643 345678999999999999999999999766554211100


Q ss_pred             CCC---CCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 019747          115 ADD---VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLK  191 (336)
Q Consensus       115 ~~~---~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~  191 (336)
                      ..+   .....+.++.||.+++|+|||++|.+|++|+++|||+|.|.+..   +...++.|+|+|+++++..|+.+|.++
T Consensus        81 ~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~---~~~~~~~v~I~G~~~~v~~A~~~I~~~  157 (164)
T 2jvz_A           81 DRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD---GTGPEKIAHIMGPPDRCEHAARIINDL  157 (164)
T ss_dssp             SCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC---TTSSEEEEEEESCHHHHHHHHHHHHHH
T ss_pred             CccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC---CCCCcEEEEEEcCHHHHHHHHHHHHHH
Confidence            000   01124578999999999999999999999999999999998742   345689999999999999999999999


Q ss_pred             hhc
Q 019747          192 LSE  194 (336)
Q Consensus       192 l~~  194 (336)
                      +.+
T Consensus       158 i~~  160 (164)
T 2jvz_A          158 LQS  160 (164)
T ss_dssp             HHH
T ss_pred             Hhh
Confidence            865

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

Probab=99.82  E-value=3.9e-20  Score=149.43  Aligned_cols=138  Identities=20%  Similarity=0.227  Sum_probs=108.2

Q ss_pred             ceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCC
Q 019747          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQ  200 (336)
Q Consensus       121 ~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~  200 (336)
                      .++.+|+||.+.+|.+||++|++|+.|++++|+.+....+      ..+..+...++++++.+|..++    .-      
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~~------~~~~~i~~~~~p~~v~~~~~~l----~~------   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE------DTCTFHIYGEDQDAVKKARSFL----EF------   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEET------TTTEEEEEESSHHHHHHHHHHH----CE------
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccCC------CchheeeccCCHHHHHHHHHhh----hc------
Confidence            4678999999999999999999999999999954443331      1334555556789988886532    11      


Q ss_pred             CcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHH
Q 019747          201 TMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIM  280 (336)
Q Consensus       201 ~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~  280 (336)
                                                                              ...++.||.+.+|++|||+|++|+
T Consensus        67 --------------------------------------------------------~e~~v~Vp~~~~g~~IGK~G~nIr   90 (144)
T 2qnd_A           67 --------------------------------------------------------AEDVIQVPRNLVGKVIGKNGKLIQ   90 (144)
T ss_dssp             --------------------------------------------------------EEEEEEEEGGGHHHHHCGGGHHHH
T ss_pred             --------------------------------------------------------ceEEEEECHHHcCeeECCCCHHHH
Confidence                                                                    236889999999999999999999


Q ss_pred             HHHhHhCC-eEEEccCCCCCCCCcc--eEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747          281 EISQISGA-RIKVSDRGDFFSGTSE--RKVTISGPQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       281 ~I~~~sga-~I~i~~~~~~~~~~~~--r~v~I~G~~~~v~~A~~~I~~~i~~~  330 (336)
                      .|++.||| +|.|.+..+......+  ..|+|+|++++++.|+.||+++|.+-
T Consensus        91 ~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~l  143 (144)
T 2qnd_A           91 EIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNYL  143 (144)
T ss_dssp             HHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            99999997 9999885432211223  46999999999999999999999763

>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=1.9e-19  Score=145.46  Aligned_cols=137  Identities=22%  Similarity=0.267  Sum_probs=107.9

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccc
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAED  113 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~  113 (336)
                      .++.+|+||.+.+|++||++|++|++|++++|+.|....  +    .+++.+...++++.+.+|..++.     .     
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~--~----~~~~~i~~~~~p~~v~~~~~~l~-----~-----   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLD--E----DTCTFHIYGEDQDAVKKARSFLE-----F-----   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEE--T----TTTEEEEEESSHHHHHHHHHHHC-----E-----
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccC--C----CchheeeccCCHHHHHHHHHhhh-----c-----
Confidence            467899999999999999999999999999994443322  1    34555555567898888765321     1     


Q ss_pred             cCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCC-EEEEeccCCCCCCCCc--eEEEEEcCHHHHHHHHHHHHH
Q 019747          114 QADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQA-VIKISRLDHSYYGLND--RLVTLTGTLDEQMRALELILL  190 (336)
Q Consensus       114 ~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga-~I~i~~~~~~~~~~~~--r~v~I~G~~~~v~~A~~~i~~  190 (336)
                              ....+.||.+++|.+|||+|.+|+.+++.||+ +|.|.++++.....++  ..|+|+|++++|+.|..+|..
T Consensus        67 --------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~  138 (144)
T 2qnd_A           67 --------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDY  138 (144)
T ss_dssp             --------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             --------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHH
Confidence                    13789999999999999999999999999997 9999985443212233  358999999999999999999


Q ss_pred             Hhhc
Q 019747          191 KLSE  194 (336)
Q Consensus       191 ~l~~  194 (336)
                      ++.+
T Consensus       139 ~l~~  142 (144)
T 2qnd_A          139 HLNY  142 (144)
T ss_dssp             HHHT
T ss_pred             HHHh
Confidence            9875

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.75  E-value=4.9e-18  Score=145.66  Aligned_cols=145  Identities=22%  Similarity=0.229  Sum_probs=111.5

Q ss_pred             CCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcC-----HHHHHHHHHHHHHHhh
Q 019747          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-----LDEQMRALELILLKLS  193 (336)
Q Consensus       119 ~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~-----~~~v~~A~~~i~~~l~  193 (336)
                      ..+....+.||.+.++.|||++|.+|+.|+++|||+|.++.        .++.|.|.|+     ++++.+|+++|..+..
T Consensus        31 ~aP~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~--------~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~r  102 (219)
T 2e3u_A           31 FFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS--------ETGEVWITSTKETEDPLAVWKARDIVLAIGR  102 (219)
T ss_dssp             --CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT--------TTCEEEEEECTTCCSHHHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc--------CCCEEEEecCCCCCCHHHHHHHHHHHHHHhc
Confidence            34567799999999999999999999999999999999985        2467888876     6999999999999874


Q ss_pred             cCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEec---------
Q 019747          194 EDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVA---------  264 (336)
Q Consensus       194 ~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp---------  264 (336)
                      ....   .....+.                                             ........+.++         
T Consensus       103 g~~~---e~g~~ll---------------------------------------------~dd~~~e~i~i~~~~v~~~~~  134 (219)
T 2e3u_A          103 GFSP---ERAFRLL---------------------------------------------NEGEYLEIINLTDIIIGNEKN  134 (219)
T ss_dssp             TCCH---HHHGGGG---------------------------------------------STTCEEEEEEGGGCC------
T ss_pred             cCCc---cccceec---------------------------------------------cCCccceeEEcccccccCCch
Confidence            3110   0000000                                             000011123332         


Q ss_pred             --cCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747          265 --DEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       265 --~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  329 (336)
                        ...+|+|||++|++|+.|++.|||+|.|++          +.|+|.|++++++.|+.+|.++|.+
T Consensus       135 ~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~~----------~~v~i~G~~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          135 ALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG----------KTVAIIGNPIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEET----------TEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             hhhhhhheeECCCchHHHHHHHHhCceEEECC----------eEEEEEeCHHHHHHHHHHHHHHHcC
Confidence              236899999999999999999999999953          5799999999999999999999965

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.72  E-value=2e-17  Score=141.92  Aligned_cols=142  Identities=17%  Similarity=0.121  Sum_probs=109.7

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEee-----HHHHHHHHHHHHHHHHhhcc
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-----IDEILRAVDLVIDKLLTELH  110 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~-----~~~v~~A~~~I~~~i~~~~~  110 (336)
                      +.++.||.+.+|.|||++|++|+.|+++|||+|++..        .+..+.|.++     ++.+.+|..+|.+.+... .
T Consensus        35 i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~--------~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg~-~  105 (219)
T 2e3u_A           35 EEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS--------ETGEVWITSTKETEDPLAVWKARDIVLAIGRGF-S  105 (219)
T ss_dssp             EEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT--------TTCEEEEEECTTCCSHHHHHHHHHHHHHHHTTC-C
T ss_pred             EEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc--------CCCEEEEecCCCCCCHHHHHHHHHHHHHHhccC-C
Confidence            5699999999999999999999999999999999963        3466888876     599999999999655211 0


Q ss_pred             ccc-cCCCCCCceeEEEEEec-----------CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCH
Q 019747          111 AED-QADDVGTKTKLRLIVPN-----------SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTL  178 (336)
Q Consensus       111 ~~~-~~~~~~~~~~~~l~ip~-----------~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~  178 (336)
                      .+. ...-.++.....+.++.           ..+|+|||++|.+|+.|+..|||+|.|..          +.|+|.|+.
T Consensus       106 ~e~g~~ll~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~~----------~~v~i~G~~  175 (219)
T 2e3u_A          106 PERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG----------KTVAIIGNP  175 (219)
T ss_dssp             HHHHGGGGSTTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEET----------TEEEEEECH
T ss_pred             ccccceeccCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEECC----------eEEEEEeCH
Confidence            000 00000111222233332           26889999999999999999999999974          569999999


Q ss_pred             HHHHHHHHHHHHHhhcCc
Q 019747          179 DEQMRALELILLKLSEDT  196 (336)
Q Consensus       179 ~~v~~A~~~i~~~l~~~~  196 (336)
                      ++++.|+.+|.+++....
T Consensus       176 ~~i~~A~~~i~~li~g~~  193 (219)
T 2e3u_A          176 IQIEIAKTAIEKLARGSP  193 (219)
T ss_dssp             HHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHcCCC
Confidence            999999999999997643

>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=99.68  E-value=7.8e-17  Score=115.76  Aligned_cols=73  Identities=34%  Similarity=0.772  Sum_probs=67.3

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  329 (336)
                      .+.++.||.+++|+|||++|++|++|++.|||+|.|++.+++.+++.++.|+|+|++++++.|+.+|.+++.+
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            6789999999999999999999999999999999999876666777899999999999999999999998765

>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=99.65  E-value=1.8e-16  Score=116.87  Aligned_cols=77  Identities=34%  Similarity=0.731  Sum_probs=70.4

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhhc
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDR  333 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~  333 (336)
                      .+.++.||.+++|+|||++|++|++|++.|||+|.|++.+++.+++.++.|+|+|++++++.|+.+|.+++.+...+
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~   79 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQGV   79 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhccccc
Confidence            67899999999999999999999999999999999998765567778999999999999999999999999886543

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

Probab=99.64  E-value=8.4e-16  Score=111.86  Aligned_cols=74  Identities=28%  Similarity=0.530  Sum_probs=67.3

Q ss_pred             CceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      ...+.++.||.+++|+|||++|++|++|+++|||+|.|++.   .+++.++.|+|+|++++++.|+.+|.+++.+..
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~---~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~   78 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQYS   78 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT---TSCSSEEEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC---CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            34889999999999999999999999999999999999863   446678999999999999999999999998754

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

Probab=99.63  E-value=3.3e-16  Score=112.37  Aligned_cols=72  Identities=36%  Similarity=0.622  Sum_probs=66.5

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  330 (336)
                      ..+.++.||.+++|+|||++|++|++|++.|||+|.|.+.   .+++.++.|+|+|++++++.|+.+|.+++.++
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~---~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP---VEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC---CTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC---CCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            4788999999999999999999999999999999999873   45678999999999999999999999998764

>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=99.63  E-value=7.4e-16  Score=110.62  Aligned_cols=74  Identities=35%  Similarity=0.627  Sum_probs=67.5

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      .++++|+||.+.+|.|||++|++|++|+++|||+|+|.+..++.+++.++.|.|.|+++++.+|+.+|.+.+.+
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            46899999999999999999999999999999999999876677888999999999999999999999976543

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=99.63  E-value=7.9e-16  Score=128.70  Aligned_cols=141  Identities=18%  Similarity=0.249  Sum_probs=111.5

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEE-----eeHHHHHHHHHHHHHHHHhhcc
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMIS-----GTIDEILRAVDLVIDKLLTELH  110 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~-----G~~~~v~~A~~~I~~~i~~~~~  110 (336)
                      .++++||.+.+|+|||++|++++.|++++|++|++..        .++.+.|.     |++..+.+|..+|.+... .+.
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~--------~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~r-gf~   75 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT--------ENSMVIVEPEAEGIPPVNLMKAAEVVKAISL-GFP   75 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET--------TTTEEEEEESSTTSCHHHHHHHHHHHHHHHH-TCC
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc--------CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHc-CCC
Confidence            3699999999999999999999999999999999953        46677888     889999999999985443 222


Q ss_pred             ccccCCC-CCCceeEEEEEec----------CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHH
Q 019747          111 AEDQADD-VGTKTKLRLIVPN----------SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD  179 (336)
Q Consensus       111 ~~~~~~~-~~~~~~~~l~ip~----------~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~  179 (336)
                      .++...- .++.+...+.++.          ...|+|||++|.+++.|+..|||+|.|..          ..|.|.|+.+
T Consensus        76 ~e~A~~Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~~----------~~v~i~G~~~  145 (191)
T 1tua_A           76 PEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGE----------YEVAIIGDYE  145 (191)
T ss_dssp             HHHHGGGGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEECS----------SEEEEEEEHH
T ss_pred             HHHhhhcccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEcC----------CEEEEEeChH
Confidence            1111100 1122333344442          35799999999999999999999999975          4799999999


Q ss_pred             HHHHHHHHHHHHhhcC
Q 019747          180 EQMRALELILLKLSED  195 (336)
Q Consensus       180 ~v~~A~~~i~~~l~~~  195 (336)
                      +++.|+..|..++...
T Consensus       146 ~i~~Ar~~i~~li~g~  161 (191)
T 1tua_A          146 RAMAAKQAIEMLAEGR  161 (191)
T ss_dssp             HHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHcCC
Confidence            9999999999999754

>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=99.63  E-value=5.8e-16  Score=112.76  Aligned_cols=73  Identities=36%  Similarity=0.597  Sum_probs=65.8

Q ss_pred             CceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747          255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  330 (336)
                      ...+.++.||.+++|.|||++|++|++|+++|||+|.|.+.   .+++.++.|+|+|++++++.|+.+|.+++.+.
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            34889999999999999999999999999999999999874   35577999999999999999999999998876

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=99.63  E-value=9.3e-16  Score=128.25  Aligned_cols=140  Identities=18%  Similarity=0.246  Sum_probs=112.5

Q ss_pred             eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEE-----cCHHHHHHHHHHHHHHhhcCcC
Q 019747          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT-----GTLDEQMRALELILLKLSEDTL  197 (336)
Q Consensus       123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~-----G~~~~v~~A~~~i~~~l~~~~~  197 (336)
                      ..++.||.+.++.|||++|++++.|++.+|++|.++.        .++.++|.     |++.++.+|.++|.++......
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 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT--------ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPP   76 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET--------TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCH
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc--------CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCH
Confidence            4689999999999999999999999999999999986        46678888     9999999999999998765321


Q ss_pred             CCC-CcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEec----------cC
Q 019747          198 YSQ-TMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVA----------DE  266 (336)
Q Consensus       198 ~~~-~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp----------~~  266 (336)
                      ... .+.                                                 ........+.++          ..
T Consensus        77 e~A~~Ll-------------------------------------------------~Dd~~~e~i~i~~~~~~~~~~~~r  107 (191)
T 1tua_A           77 EKAFRLL-------------------------------------------------EEDQILVVVDLKQVVGDSQNHLKR  107 (191)
T ss_dssp             HHHGGGG-------------------------------------------------STTEEEEEEETHHHHTTCHHHHHH
T ss_pred             HHhhhcc-------------------------------------------------cCcceeEEEEcccccccCchhHHH
Confidence            000 000                                                 001122233343          24


Q ss_pred             cccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747          267 HIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       267 ~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  329 (336)
                      ..|+|||++|.+|+.|+..|||+|.|++          ..|.|.|++++++.|+..|.++|..
T Consensus       108 ~~GrIIGk~G~tik~iE~~Tg~~I~v~~----------~~v~i~G~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          108 IKGRIIGEGGRARRTIEEMTDTYINVGE----------YEVAIIGDYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS----------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhhheeCCCccHHHHHHHHHCceEEEcC----------CEEEEEeChHHHHHHHHHHHHHHcC
Confidence            6899999999999999999999999953          4899999999999999999999865

>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=99.62  E-value=7.5e-16  Score=109.43  Aligned_cols=71  Identities=34%  Similarity=0.628  Sum_probs=65.4

Q ss_pred             CCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        32 ~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      ...++++|+||.+.+|.||||+|++|++|+++|||+|++++.     ++++|++.|.|+++++.+|+.+|.++|.+
T Consensus         2 ~~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~-----~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-----CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             CceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-----CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            356899999999999999999999999999999999999864     36799999999999999999999987765

>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=99.62  E-value=7.7e-16  Score=109.37  Aligned_cols=69  Identities=29%  Similarity=0.540  Sum_probs=64.4

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  329 (336)
                      ..+.++.||.+++|.|||++|++|++|+++|||+|.|++.     +..+|+|+|+|++++++.|+.+|.++|++
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            3789999999999999999999999999999999999875     35689999999999999999999999976

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

Probab=99.61  E-value=9.1e-16  Score=113.43  Aligned_cols=75  Identities=28%  Similarity=0.523  Sum_probs=68.0

Q ss_pred             CCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          254 DRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       254 ~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      ....+.++.||.+++|+|||++|++|++|+++|||+|+|++.   .+++.++.|+|+|++++++.|+.+|.+++.+.+
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~---~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~~   85 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQYS   85 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC---CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHC
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC---CCCCCccEEEEEcCHHHHHHHHHHHHHHHHhhh
Confidence            455889999999999999999999999999999999999863   456779999999999999999999999998754

>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=99.61  E-value=2.3e-15  Score=111.92  Aligned_cols=74  Identities=30%  Similarity=0.540  Sum_probs=67.2

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhh
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASD  332 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~  332 (336)
                      ..+.+|.||.+++|+|||++|++|++|+++|||+|.|.+..   ++..++.|+|+|++++++.|+.+|.+++++...
T Consensus        14 ~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~---~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~~   87 (92)
T 1x4n_A           14 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCMLTGTPESVQSAKRLLDQIVEKGRS   87 (92)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC---TTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTC
T ss_pred             CEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHHhccc
Confidence            47899999999999999999999999999999999998752   346789999999999999999999999987643

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

Probab=99.58  E-value=2.6e-15  Score=114.78  Aligned_cols=74  Identities=26%  Similarity=0.425  Sum_probs=66.5

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  330 (336)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|.+..++..+..+++|+|+|++++|+.|+.+|.++|.+.
T Consensus         7 ~~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            7 GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CCEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             CeEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            46899999999999999999999999999999999998654444567899999999999999999999998764

>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=99.58  E-value=2.5e-15  Score=110.68  Aligned_cols=75  Identities=36%  Similarity=0.632  Sum_probs=69.0

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      .++++|+||.+.+|.|||++|++|++|+++|||+|+|.+..++.|++.++.|.|.|+++++..|+.+|.+.+.+.
T Consensus         2 k~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (87)
T 1ec6_A            2 KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             CSEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            467899999999999999999999999999999999998766678889999999999999999999999877654

>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=99.58  E-value=2.8e-15  Score=108.72  Aligned_cols=69  Identities=22%  Similarity=0.341  Sum_probs=62.5

Q ss_pred             CceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747          255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  329 (336)
                      ...+.+|.||.+++|+||||+|++||+|+++|||+|+|++.+      +++.|+|+|++++++.|+.+|.+++..
T Consensus         8 ~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~------~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            8 GQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD------KEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS------SCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC------CCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            448899999999999999999999999999999999998642      368999999999999999999997654

>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=99.57  E-value=1.4e-14  Score=105.39  Aligned_cols=74  Identities=34%  Similarity=0.544  Sum_probs=66.6

Q ss_pred             CCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        32 ~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      ...++++|+||.+++|.||||+|++|++|+++|||+|++++.   .+++.+|.|.|+|+++++.+|+.+|.+.+.+.
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            356899999999999999999999999999999999999763   35678999999999999999999999776653

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

Probab=99.56  E-value=4.5e-15  Score=106.39  Aligned_cols=73  Identities=33%  Similarity=0.540  Sum_probs=66.6

Q ss_pred             CcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        33 ~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      ..++++|+||.+++|.|||++|++|++|+++|||+|++.+.   .+++.++.|.|.|+++++.+|+.+|.+.+.++
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            56899999999999999999999999999999999999863   46788999999999999999999999876553

>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=99.56  E-value=8.8e-15  Score=109.21  Aligned_cols=75  Identities=17%  Similarity=0.399  Sum_probs=66.7

Q ss_pred             CceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747          255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  330 (336)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|.|.++..+. ...+|.|+|+|++++++.|+.+|.+++.+.
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~-~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           13 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN-TGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS-SCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCC-CCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            348899999999999999999999999999999999999865322 346899999999999999999999998764

>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=99.56  E-value=6.9e-15  Score=107.03  Aligned_cols=75  Identities=29%  Similarity=0.496  Sum_probs=66.4

Q ss_pred             CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      ....++++|+||.+++|.||||+|++|++|+++|||+|+|.+.   .++..++.|.|+|+++++.+|+.+|.+.+.++
T Consensus         2 ~g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~---~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            2 LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP---VEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             CTTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC---CTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CCCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC---CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            3467899999999999999999999999999999999999863   36678999999999999999999999776554

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

Probab=99.55  E-value=1.5e-14  Score=105.90  Aligned_cols=72  Identities=19%  Similarity=0.410  Sum_probs=64.8

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHH
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVA  328 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~  328 (336)
                      ..+.+|.||.+++|.|||++|++|++|+++|||+|.|.+++. .+.+.+|.|+|+|++++++.|+.+|.+++.
T Consensus        13 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~-~~~~~er~v~I~G~~~~v~~A~~~I~~i~~   84 (85)
T 2opv_A           13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRIIGDPYKVQQACEMVMDILR   84 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSC-SSTTSCEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCC-CCCCCceEEEEEeCHHHHHHHHHHHHHHhc
Confidence            377899999999999999999999999999999999998643 234578999999999999999999999875

>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=99.54  E-value=2.3e-14  Score=106.46  Aligned_cols=74  Identities=26%  Similarity=0.441  Sum_probs=66.8

Q ss_pred             CCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        32 ~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      ...++++|+||.+++|.||||+|++|++|+++|||+|+|.+..   ++..+|.|.|+|+.+++.+|+.+|.+.+.+.
T Consensus        12 ~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~---~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~   85 (92)
T 1x4n_A           12 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC---TTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            3579999999999999999999999999999999999998643   4578999999999999999999999776654

>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=99.54  E-value=3e-14  Score=108.33  Aligned_cols=75  Identities=28%  Similarity=0.463  Sum_probs=66.1

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      ..+.+|.||.+++|+|||++|++|++|+++|||+|.|.+..+. ....++.|+|+|++++++.|+.+|.+++.+..
T Consensus        14 p~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~-~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T 1we8_A           14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG-TLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             EEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC-SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCC-CCCCcceEEEEcCHHHHHHHHHHHHHHHhhCh
Confidence            4788999999999999999999999999999999999875421 12358999999999999999999999997654

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

Probab=99.54  E-value=1.4e-14  Score=110.06  Aligned_cols=73  Identities=23%  Similarity=0.399  Sum_probs=64.7

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASD  332 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~  332 (336)
                      .+.+|.||.+++++||||+|++|++|+++|||+|+|.++.   ++..+|.|+|+|+++++++|+.+|.+++.+...
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            5789999999999999999999999999999999998742   345689999999999999999999999887543

>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=99.53  E-value=1.4e-14  Score=106.96  Aligned_cols=77  Identities=34%  Similarity=0.529  Sum_probs=68.0

Q ss_pred             CCCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           29 DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        29 ~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      +.....++++|+||.+++|.||||+|++|++|+++|||+|+|.+.   .+++.++.|.|+|+++++.+|+.+|.+.+.+.
T Consensus         8 ~~~~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~---~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A            8 DLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             --CCCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC---CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC---CCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            345668999999999999999999999999999999999999753   35678999999999999999999999777654

>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=99.51  E-value=6.7e-14  Score=104.32  Aligned_cols=74  Identities=16%  Similarity=0.203  Sum_probs=66.2

Q ss_pred             CCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          254 DRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       254 ~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      ...++..+.||.+++|.|||++|++|++|+++|||+|+|+++++    ..++.|+|+|++++++.|+.+|..++++..
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            44588999999999999999999999999999999999987542    347899999999999999999999987754

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

Probab=99.50  E-value=3.4e-14  Score=108.54  Aligned_cols=73  Identities=25%  Similarity=0.408  Sum_probs=64.8

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      +++|+||.+++|.||||+|++||+|+++|||+|+|.+..++..+..++.|+|+|+.+++.+|+.+|.+.+.+.
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            6899999999999999999999999999999999987654334457899999999999999999999766554

>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=99.49  E-value=7.5e-14  Score=104.54  Aligned_cols=75  Identities=21%  Similarity=0.348  Sum_probs=66.5

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhh
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASD  332 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~  332 (336)
                      ..+..|.||.++++.|||++|++|++|+++|||+|.|+++++  ++..++.|+|+|++++++.|+.+|..++....+
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~--~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~e~   90 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQITITGYEKNTEAARDAILRIVGELEQ   90 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT--CSSCSSEEEEESCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC--CCCCccEEEEEeCHHHHHHHHHHHHHHHHHHHh
Confidence            468999999999999999999999999999999999988653  223679999999999999999999999876543

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

Probab=99.49  E-value=1.6e-13  Score=100.39  Aligned_cols=72  Identities=29%  Similarity=0.447  Sum_probs=64.4

Q ss_pred             CcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHH
Q 019747           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL  105 (336)
Q Consensus        33 ~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i  105 (336)
                      ...+.+|.||.+++|.||||+|++||+|+++|||+|.+.+.. ..+...+|.|.|+|+++++.+|+.+|.+.+
T Consensus        12 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~-~~~~~~er~v~I~G~~~~v~~A~~~I~~i~   83 (85)
T 2opv_A           12 NGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG-SQNTNVDKPLRIIGDPYKVQQACEMVMDIL   83 (85)
T ss_dssp             SSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSS-CSSTTSCEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCC-CCCCCCceEEEEEeCHHHHHHHHHHHHHHh
Confidence            457899999999999999999999999999999999998743 235578999999999999999999998654

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

Probab=99.49  E-value=3.1e-14  Score=100.39  Aligned_cols=67  Identities=13%  Similarity=0.332  Sum_probs=60.8

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHH
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKV  327 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  327 (336)
                      ..+..+.||.+++|.|||++|++|++|+++|||+|.|++++     ..++.|+|+|++++++.|+.+|.+++
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-----~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-----EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-----SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-----CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            37789999999999999999999999999999999998754     35789999999999999999998753

>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=99.49  E-value=6.6e-14  Score=104.42  Aligned_cols=77  Identities=22%  Similarity=0.390  Sum_probs=67.4

Q ss_pred             CCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        30 ~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      .....++++|+||.+++|.||||+|++||+|+++|||+|+|.+.... ....+|.|.|.|+++++.+|+.+|.+.+.+
T Consensus        10 ~~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~-~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   86 (94)
T 1x4m_A           10 DGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQ-NTGADKPLRITGDPYKVQQAKEMVLELIRD   86 (94)
T ss_dssp             CCCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCC-SSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CCCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCC-CCCCceEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            35678999999999999999999999999999999999999875432 234789999999999999999999976654

>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=99.49  E-value=6.1e-14  Score=104.56  Aligned_cols=75  Identities=20%  Similarity=0.434  Sum_probs=66.8

Q ss_pred             CCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhhc
Q 019747          254 DRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDR  333 (336)
Q Consensus       254 ~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~  333 (336)
                      ..+.+.+|.||.+++|+|||++|++|++|+++|||+|.|++.+     ..++.|+|+|++++++.|+.+|.+++.+....
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-----~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~~~   88 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-----DPSNQIKITGTKEGIEKARHEVLLISAEQDKR   88 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-----SSCCEEEEEECHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-----CCCCeEEEEECHHHHHHHHHHHHHHhhccccc
Confidence            4568899999999999999999999999999999999997642     24589999999999999999999999876654

>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=99.47  E-value=3.2e-14  Score=103.10  Aligned_cols=71  Identities=20%  Similarity=0.308  Sum_probs=63.3

Q ss_pred             CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      ....++++|.||.+++|+||||+|++||+|+++|||+|++++.+      .++++.|+|+++++.+|+.+|.+.+..
T Consensus         6 ~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~------~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            6 SGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD------KEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             SCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS------SCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC------CCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            34678999999999999999999999999999999999998533      368999999999999999999975443

>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=99.46  E-value=4e-13  Score=102.13  Aligned_cols=75  Identities=32%  Similarity=0.509  Sum_probs=65.2

Q ss_pred             CcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        33 ~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      -.++++|+||.+++|.||||+|++|++|+++|||+|+|.+..+. ....++.|.|.|+.+++.+|+.+|.+.+.+.
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 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG-TLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC-SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCC-CCCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            45789999999999999999999999999999999999865421 1236899999999999999999999877654

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

Probab=99.46  E-value=1.3e-13  Score=104.70  Aligned_cols=71  Identities=28%  Similarity=0.391  Sum_probs=63.3

Q ss_pred             EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      .+++|+||.++++.||||+|++||+|+++|+|+|+|.++.   +...+|.|+|+|+++++.+|+.+|.+.+.+.
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~---~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD---GTGPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC---SSSSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC---CCCceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            3689999999999999999999999999999999998643   3467899999999999999999999776654

>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=99.43  E-value=6.3e-15  Score=111.26  Aligned_cols=69  Identities=23%  Similarity=0.421  Sum_probs=62.3

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhH-hCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhhc
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQI-SGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDR  333 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~-sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~  333 (336)
                      ++..|.||.++|++|||++|++|++|+++ ++++|.+++        .++.|+|+|++++|++|+.+|..++++..++
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~--------~~~~ItI~G~~~~V~~a~~~I~~~v~el~~~   96 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE--------GEDKITLEGPTEDVSVAQEQIEGMVKDLINR   96 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS--------SSCEEEEEECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC--------CCCEEEEECCHHHHHHHHHHHHHHHHHHHhh
Confidence            78999999999999999999999999997 599999975        3579999999999999999999999876543

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

Probab=99.42  E-value=3.8e-13  Score=123.27  Aligned_cols=144  Identities=12%  Similarity=0.151  Sum_probs=104.8

Q ss_pred             CCceeEEEEEecCccceeecCCC--hHHHHHHHhcCCEEEEeccC--CCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhc
Q 019747          119 GTKTKLRLIVPNSSCGSIIGKAG--ATIKSFMDDSQAVIKISRLD--HSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (336)
Q Consensus       119 ~~~~~~~l~ip~~~~g~iIG~~G--~~Ik~I~~~tga~I~i~~~~--~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~  194 (336)
                      .+.++..+.||..+++.|||++|  ++|++|+++|||+|+|+..+  ...+......|+|+|.+++|++|+.+|.+++- 
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l~P-  105 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNCH-  105 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHSCE-
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhcCC-
Confidence            56799999999999999999999  99999999999999998643  11223455789999999999999999988531 


Q ss_pred             CcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceecc
Q 019747          195 DTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGR  274 (336)
Q Consensus       195 ~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk  274 (336)
                                                                                    .+..+.+|...++.  ..
T Consensus       106 --------------------------------------------------------------l~i~~elp~~~i~~--~~  121 (376)
T 3n89_A          106 --------------------------------------------------------------FTVFMALSKMKMPL--HE  121 (376)
T ss_dssp             --------------------------------------------------------------EEEEEECTTCSSCH--HH
T ss_pred             --------------------------------------------------------------ceEEEEccccccCc--ch
Confidence                                                                          44566666543332  11


Q ss_pred             CCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747          275 GGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       275 ~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  329 (336)
                      .+..|.+ ++..+++|.++...+ ..+.....|+|+|++.+++.|+..+.+++..
T Consensus       122 l~~~I~q-q~~y~V~I~Fp~~~~-~~~~~sd~V~IrG~~~nv~~akeA~~~Ll~~  174 (376)
T 3n89_A          122 LQAHVRQ-NPIQNVEMSFVDAPE-KNGIVTTYLRITAREKNQHELIEAAKRLNEI  174 (376)
T ss_dssp             HHHHHHH-CCCTTCEEEEEEEC------CEEEEEEEEEGGGHHHHHHHHHHHHHH
T ss_pred             hhhhhcc-ceeCceEEEeCCccc-ccCCCCCEEEEEcChhhHHHHHHHHHHHHHH
Confidence            1234444 567899998865321 1112367899999999888877776666654

>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=99.42  E-value=3.1e-13  Score=100.71  Aligned_cols=74  Identities=22%  Similarity=0.302  Sum_probs=64.8

Q ss_pred             CCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        30 ~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      ..+..++.+|.||.+++|.|||++|++|++|+++|||+|+|++.+     ..++.|.|+|+.+++.+|+.+|.+.+.+.
T Consensus        12 ~l~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-----~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           12 RLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-----DPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             CCCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-----SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             HhCCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-----CCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            345679999999999999999999999999999999999997643     34678999999999999999999665544

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

Probab=99.41  E-value=3.7e-13  Score=94.85  Aligned_cols=66  Identities=18%  Similarity=0.389  Sum_probs=60.4

Q ss_pred             CcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHH
Q 019747           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVID  103 (336)
Q Consensus        33 ~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~  103 (336)
                      ...+.+|.||.+++|.|||++|++|++|+++|||+|+|+++.     ..++.|.|+|..+++.+|+.+|.+
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-----~~~~~V~I~G~~~~v~~A~~~I~~   68 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-----EKSNLIRIEGDPQGVQQAKRELLE   68 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-----SSSEEEEEEESSHHHHHHHHHHHH
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-----CcccEEEEEcCHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999999998744     467899999999999999999984

>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=99.41  E-value=4.2e-13  Score=100.43  Aligned_cols=76  Identities=16%  Similarity=0.222  Sum_probs=65.6

Q ss_pred             CCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        30 ~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      .....++++|.||.++++.|||++|++|++|+++|||+|+|++..+  ++..++.|.|+|..+++.+|+.+|.+.+.+
T Consensus        12 ~~~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~--~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           12 RALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             HHHTTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT--CSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hhccceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC--CCCCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            3345689999999999999999999999999999999999987543  334679999999999999999999955433

>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=99.40  E-value=4.2e-13  Score=100.00  Aligned_cols=75  Identities=13%  Similarity=0.230  Sum_probs=65.4

Q ss_pred             CCCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           29 DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        29 ~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      .+.+..++.+|.||.++++.|||++|++|++|+++|||+|+|++..+    ..++.|.|+|..+++.+|+.+|.+.+.+
T Consensus        11 ~~l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~----~~~~~V~I~G~~e~v~~A~~~I~~i~~e   85 (95)
T 2ctm_A           11 GELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLPENVEEAIDHILNLEEE   85 (95)
T ss_dssp             CCTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC----SCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             HhhcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC----CCCcEEEEEcCHHHHHHHHHHHHHHHHH
Confidence            34577899999999999999999999999999999999999986532    3468999999999999999999965443

>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=99.40  E-value=3.7e-13  Score=102.04  Aligned_cols=70  Identities=16%  Similarity=0.266  Sum_probs=63.5

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      .+..|.||.+++|+|||++|++|++|+++|||+|.|++.+     ...+.|+|+|++++++.|+.+|.+++++..
T Consensus        17 ~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g-----~~~~~V~I~G~~e~v~~A~~~I~~i~~e~e   86 (104)
T 2ctk_A           17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-----LQSDIIAITGLAANLDRAKAGLLERVKELQ   86 (104)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-----TTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-----CCcceEEEEcCHHHHHHHHHHHHHHHhhHH
Confidence            7889999999999999999999999999999999998754     245799999999999999999999887643

>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=99.31  E-value=2.5e-12  Score=95.57  Aligned_cols=75  Identities=17%  Similarity=0.310  Sum_probs=66.4

Q ss_pred             CCCceEEEEEeccCcccceeccCCchHHHHHhHh-CCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          253 DDRTNSLTIGVADEHIGFVVGRGGRNIMEISQIS-GARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       253 ~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~s-ga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      ....++..|.||.++++.|||++|++|++|+++| ||+|.|++.+     +..+.|+|+|+.+++++|+.+|++++.+..
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 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-----SGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   87 (95)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-----TTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             HhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC-----CCcceEEEEcCHHHHHHHHHHHHHHHhhhh
Confidence            3456789999999999999999999999999999 9999997643     457799999999999999999999988654


Q ss_pred             h
Q 019747          332 D  332 (336)
Q Consensus       332 ~  332 (336)
                      .
T Consensus        88 ~   88 (95)
T 2ctj_A           88 T   88 (95)
T ss_dssp             C
T ss_pred             h
Confidence            3

>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=99.30  E-value=3.6e-12  Score=96.52  Aligned_cols=68  Identities=24%  Similarity=0.295  Sum_probs=60.8

Q ss_pred             EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      ++..|.||.+++|.|||+||++|++|+++|||+|+|++..     ...+.|.|+|..+++.+|+.+|.+.+.+
T Consensus        17 ~~~~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           17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-----LQSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-----TTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-----CCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            8899999999999999999999999999999999998744     3456899999999999999999965543

>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=99.26  E-value=1.3e-11  Score=91.79  Aligned_cols=75  Identities=13%  Similarity=0.253  Sum_probs=66.5

Q ss_pred             CCCCCCcEEEEEEEecCccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHH
Q 019747           28 SDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL  106 (336)
Q Consensus        28 ~~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~  106 (336)
                      ....++.++..|.||.++++.|||++|++|++|+++| ||+|+|+++.     ...+.|.|.|..+++.+|+.+|.+.+.
T Consensus        10 ~~e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g-----~~~~~V~I~G~~~~v~~A~~~I~~iv~   84 (95)
T 2ctj_A           10 QKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-----SGSDTVVIRGPSSDVEKAKKQLLHLAE   84 (95)
T ss_dssp             CCCCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-----TTCCEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC-----CCcceEEEEcCHHHHHHHHHHHHHHHh
Confidence            4567888999999999999999999999999999999 9999998643     557789999999999999999996554


Q ss_pred             h
Q 019747          107 T  107 (336)
Q Consensus       107 ~  107 (336)
                      +
T Consensus        85 e   85 (95)
T 2ctj_A           85 E   85 (95)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.23  E-value=3.2e-13  Score=101.85  Aligned_cols=88  Identities=22%  Similarity=0.230  Sum_probs=72.4

Q ss_pred             EEeeHHHHHHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhc-CCEEEEeccCCCCC
Q 019747           87 ISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDS-QAVIKISRLDHSYY  165 (336)
Q Consensus        87 I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~t-ga~I~i~~~~~~~~  165 (336)
                      |+|.+++|.+|+.+|.+.+             ....+..+.||..+++.|||++|++|++|++++ +++|+|++      
T Consensus         5 i~G~~~~V~~A~~~i~~~~-------------~~~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~------   65 (102)
T 2ctf_A            5 SSGEPEKLGQALTEVYAKA-------------NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE------   65 (102)
T ss_dssp             CCCCCCCCCCSCCCCCCCC-------------CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS------
T ss_pred             cCcCHHHHHHHHHHHHHHh-------------cCeEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC------
Confidence            4566777777766665321             123778999999999999999999999999974 99999986      


Q ss_pred             CCCceEEEEEcCHHHHHHHHHHHHHHhhcC
Q 019747          166 GLNDRLVTLTGTLDEQMRALELILLKLSED  195 (336)
Q Consensus       166 ~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~  195 (336)
                        .++.|+|+|+++.|.+|+..|..++.+.
T Consensus        66 --~~~~ItI~G~~~~V~~a~~~I~~~v~el   93 (102)
T 2ctf_A           66 --GEDKITLEGPTEDVSVAQEQIEGMVKDL   93 (102)
T ss_dssp             --SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             --CCCEEEEECCHHHHHHHHHHHHHHHHHH
Confidence              3568999999999999999999998763

>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=99.03  E-value=2.8e-10  Score=82.98  Aligned_cols=64  Identities=17%  Similarity=0.361  Sum_probs=57.5

Q ss_pred             CceEEEEEeccCcccceeccCCchHHHHHhHhCCe-EEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHH
Q 019747          255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISGAR-IKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQK  326 (336)
Q Consensus       255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~-I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~  326 (336)
                      ......+.||.+++|.|||++|++|++|+++||++ |.|.+        ++.+|+|.| +.+++++|+.+|...
T Consensus        13 ~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e--------ddG~V~I~g~~~ea~~~A~~~I~~i   78 (91)
T 2cpq_A           13 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE--------DTGTFRIYGESADAVKKARGFLEFV   78 (91)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET--------TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             CceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc--------CCCEEEEEECCHHHHHHHHHHHHhh
Confidence            34788999999999999999999999999999998 99964        358999999 899999999999643

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.81  E-value=1.7e-08  Score=77.71  Aligned_cols=75  Identities=16%  Similarity=0.091  Sum_probs=57.5

Q ss_pred             eEEEEEeccC-------cccceeccCCchHHHHHhHhCCeEEEccCCCC-------CCCCcceEEEEEc-ChHhHHHHHH
Q 019747          257 NSLTIGVADE-------HIGFVVGRGGRNIMEISQISGARIKVSDRGDF-------FSGTSERKVTISG-PQRSIRTAES  321 (336)
Q Consensus       257 ~~~~v~vp~~-------~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~-------~~~~~~r~v~I~G-~~~~v~~A~~  321 (336)
                      .+.+|.||-+       ++|.|||++|.+||+|+++|||+|.|..++..       ....++-.|.|++ +++++++|+.
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            5667777754       78999999999999999999999999754210       0011344677776 7999999999


Q ss_pred             HHHHHHHhhh
Q 019747          322 MIMQKVAYAS  331 (336)
Q Consensus       322 ~I~~~i~~~~  331 (336)
                      +|.+++....
T Consensus        92 ~Ie~Ll~~v~  101 (119)
T 2yqr_A           92 LCENLLQTVH  101 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHhhchH
Confidence            9999987643

>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=98.77  E-value=1.7e-08  Score=79.28  Aligned_cols=75  Identities=13%  Similarity=0.278  Sum_probs=61.6

Q ss_pred             CceEEEEEeccC------cccceeccCCchHHHHHhHhCCeEEEccCCCCC-------------CCCcceEEEEEc-ChH
Q 019747          255 RTNSLTIGVADE------HIGFVVGRGGRNIMEISQISGARIKVSDRGDFF-------------SGTSERKVTISG-PQR  314 (336)
Q Consensus       255 ~~~~~~v~vp~~------~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~-------------~~~~~r~v~I~G-~~~  314 (336)
                      ...+.+|.||.+      ++|.|||++|.+||+|+++|||+|.|...+...             ...++-.|.|++ +.+
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            347889999987      889999999999999999999999998743111             112356788888 799


Q ss_pred             hHHHHHHHHHHHHHh
Q 019747          315 SIRTAESMIMQKVAY  329 (336)
Q Consensus       315 ~v~~A~~~I~~~i~~  329 (336)
                      .++.|+.+|..+|..
T Consensus        85 ~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999865

>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=98.69  E-value=5.6e-08  Score=76.30  Aligned_cols=76  Identities=14%  Similarity=0.298  Sum_probs=58.9

Q ss_pred             CcEEEEEEEecC------ccceeecCCChHHHHHHHHhCCeEEEcCCCCCC-------------CCCCceEEEEEe-eHH
Q 019747           33 KPTYIRFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFF-------------PGTTDRIIMISG-TID   92 (336)
Q Consensus        33 ~~~~~~i~ip~~------~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~-------------~~~~~r~i~I~G-~~~   92 (336)
                      ..++.+|.||.+      ++|.|||++|.+||+|+++|||+|.+....-..             ....+-.|.|++ +.+
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            468899999999      788999999999999999999999996522000             012245677777 578


Q ss_pred             HHHHHHHHHHHHHHhh
Q 019747           93 EILRAVDLVIDKLLTE  108 (336)
Q Consensus        93 ~v~~A~~~I~~~i~~~  108 (336)
                      .+.+|+++|.+.+...
T Consensus        85 ~~~~A~~~I~~ll~~~  100 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQG  100 (131)
T ss_dssp             HHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhcc
Confidence            8999999999766543

>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=98.68  E-value=1.8e-08  Score=73.35  Aligned_cols=66  Identities=15%  Similarity=0.220  Sum_probs=57.7

Q ss_pred             CCceeEEEEEecCccceeecCCChHHHHHHHhcCCE-EEEeccCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHh
Q 019747          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV-IKISRLDHSYYGLNDRLVTLTG-TLDEQMRALELILLKL  192 (336)
Q Consensus       119 ~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~-I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~i~~~l  192 (336)
                      ...+...|.||.+.++.+||++|.+|++|+++||++ |.|..        .+..|+|.| +.+++.+|+.+|..+-
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e--------ddG~V~I~g~~~ea~~~A~~~I~~ie   79 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE--------DTGTFRIYGESADAVKKARGFLEFVE   79 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET--------TTTEEEEEESSHHHHHHHHHHHSCCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc--------CCCEEEEEECCHHHHHHHHHHHHhhh
Confidence            455888999999999999999999999999999998 99974        347899999 6899999998876643

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.66  E-value=1.2e-07  Score=72.92  Aligned_cols=75  Identities=23%  Similarity=0.209  Sum_probs=55.8

Q ss_pred             CcEEEEEEEecC-------ccceeecCCChHHHHHHHHhCCeEEEcCCCCCC--C-----CCCceEEEEE-eeHHHHHHH
Q 019747           33 KPTYIRFLVSNP-------LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFF--P-----GTTDRIIMIS-GTIDEILRA   97 (336)
Q Consensus        33 ~~~~~~i~ip~~-------~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~--~-----~~~~r~i~I~-G~~~~v~~A   97 (336)
                      ..+.-+|.||.+       ++|.|||++|.+||+|+++|||+|.|.......  +     ...+-.|.|. .+.+.+.+|
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            468889999986       689999999999999999999999996331000  0     0123346665 468899999


Q ss_pred             HHHHHHHHHh
Q 019747           98 VDLVIDKLLT  107 (336)
Q Consensus        98 ~~~I~~~i~~  107 (336)
                      +++|.+.+..
T Consensus        90 ~~~Ie~Ll~~   99 (119)
T 2yqr_A           90 KKLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHhhc
Confidence            9999865543

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.32  E-value=7.2e-07  Score=70.31  Aligned_cols=72  Identities=21%  Similarity=0.340  Sum_probs=52.9

Q ss_pred             EEEEEEEecCc------cceeecCCChHHHHHHHHhCCeEEEcCCCCCC--------CC-------CCceEEEEEee-HH
Q 019747           35 TYIRFLVSNPL------AGAVIGKGGSTINDFQSQSGARIQLSRSHEFF--------PG-------TTDRIIMISGT-ID   92 (336)
Q Consensus        35 ~~~~i~ip~~~------vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~--------~~-------~~~r~i~I~G~-~~   92 (336)
                      ++-+|.||.+.      +|.|||++|.++|+|+++|||+|.|.......        .|       ...--|.|++. .+
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            67789999876      89999999999999999999999997543110        00       11235778874 32


Q ss_pred             -----HHHHHHHHHHHHHH
Q 019747           93 -----EILRAVDLVIDKLL  106 (336)
Q Consensus        93 -----~v~~A~~~I~~~i~  106 (336)
                           .+.+|+++|.+.+.
T Consensus        82 ~~~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             hhHHHHHHHHHHHHHHHCC
Confidence                 68888888885543

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.29  E-value=9.4e-07  Score=69.65  Aligned_cols=73  Identities=15%  Similarity=0.222  Sum_probs=55.0

Q ss_pred             eEEEEEeccC------cccceeccCCchHHHHHhHhCCeEEEccCCCCCC---------------CCcceEEEEEcC-hH
Q 019747          257 NSLTIGVADE------HIGFVVGRGGRNIMEISQISGARIKVSDRGDFFS---------------GTSERKVTISGP-QR  314 (336)
Q Consensus       257 ~~~~v~vp~~------~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~---------------~~~~r~v~I~G~-~~  314 (336)
                      .+.+|.||-+      ++|.|||++|.++|+|+++|||+|.|..++...+               ..++=.|.|++. ++
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            3567777754      5999999999999999999999999998652110               011237888883 43


Q ss_pred             -----hHHHHHHHHHHHHHh
Q 019747          315 -----SIRTAESMIMQKVAY  329 (336)
Q Consensus       315 -----~v~~A~~~I~~~i~~  329 (336)
                           .++.|+.+|..+|..
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                 799999999988763

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=98.28  E-value=1.5e-06  Score=67.09  Aligned_cols=73  Identities=18%  Similarity=0.292  Sum_probs=63.6

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhhc
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDR  333 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~  333 (336)
                      .-..+.|..+.++.|+|++|+.|+.|+..|.+.|+|..-.    .+....|+|.|++..-..|+.+|..+.+.....
T Consensus        56 dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~----s~g~tEVtIfG~~~~Q~rak~MI~sLA~~hr~~  128 (140)
T 3v69_A           56 DPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWG----PERRAEIWIFGPPPFRRDVDRMLTDLAHYCRMK  128 (140)
T ss_dssp             SCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC----TTSCEEEEEESCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC----CCCcEEEEEECCHHHHHHHHHHHHHHHHHHHHH
Confidence            3467888999999999999999999999999999998742    246889999999999999999999888776443

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

Probab=98.13  E-value=2.8e-06  Score=83.54  Aligned_cols=62  Identities=23%  Similarity=0.329  Sum_probs=54.2

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcC-hHhHHHHHHHHHHHH
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP-QRSIRTAESMIMQKV  327 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i  327 (336)
                      ....+.||.+++|.|||++|++||+|+++|||+|.|.+         +-.|.|.|+ .+.+++|+.+|.+++
T Consensus       567 ~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d---------~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          567 VVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD---------EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS---------SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             eEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC---------CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            67889999999999999999999999999999999953         578888885 788999999997654

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

Probab=98.10  E-value=4.3e-06  Score=82.16  Aligned_cols=89  Identities=11%  Similarity=0.113  Sum_probs=69.0

Q ss_pred             HHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEE
Q 019747           95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL  174 (336)
Q Consensus        95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I  174 (336)
                      .+++..|.+.+.+.+...+...+...+....+.||.+.++.|||++|.+||.|+++|||+|.|..         +..|.|
T Consensus       540 ~~g~~~I~~~m~~al~~~~~~~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d---------~G~V~I  610 (630)
T 3u1k_A          540 SVAKKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD---------EETFSV  610 (630)
T ss_dssp             HHHHHHHHHHHHHHCSSCCSSCCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS---------SSEEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC---------CcEEEE
Confidence            34455566666666655444444556778899999999999999999999999999999999974         357889


Q ss_pred             EcC-HHHHHHHHHHHHHHh
Q 019747          175 TGT-LDEQMRALELILLKL  192 (336)
Q Consensus       175 ~G~-~~~v~~A~~~i~~~l  192 (336)
                      .|. .+.+.+|+++|..++
T Consensus       611 ~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          611 FAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EESSHHHHHHHHHHTTC--
T ss_pred             EeCCHHHHHHHHHHHHHHh
Confidence            988 688899998887654

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.80  E-value=4.1e-06  Score=66.46  Aligned_cols=101  Identities=21%  Similarity=0.324  Sum_probs=73.6

Q ss_pred             EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccc-
Q 019747           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAED-  113 (336)
Q Consensus        35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~-  113 (336)
                      -.+.++|+...+|..||++|++|+.|+++.|-+|.+-..++      +        +..          .+...+.... 
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~------d--------~~~----------fI~naLsPA~V   91 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSS------D--------LER----------IVKNLFPGVKI   91 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCS------S--------HHH----------HHHHHSTTSCE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCC------C--------HHH----------HHHHhcCCceE
Confidence            46889999999999999999999999999999999965432      1        111          1111111110 


Q ss_pred             ---cCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEec
Q 019747          114 ---QADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (336)
Q Consensus       114 ---~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~  159 (336)
                         .....+......+.||.+..+..||++|.+++-..+-||.++.|..
T Consensus        92 ~~V~i~~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~~  140 (144)
T 2cxc_A           92 ESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVEK  140 (144)
T ss_dssp             EEEEEEEETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEEE
T ss_pred             EEEEEeecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCceE
Confidence               0000023467788999999999999999999999999988877753

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.66  E-value=0.00011  Score=56.68  Aligned_cols=65  Identities=22%  Similarity=0.176  Sum_probs=56.9

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHH
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDK  104 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~  104 (336)
                      .+.|.|.+..++.|+|++|+.|+.|+..|++.|++..-+   + +..-.|+|.|++..-.+|+.+|...
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~---s-~g~tEVtIfG~~~~Q~rak~MI~sL  121 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWG---P-ERRAEIWIFGPPPFRRDVDRMLTDL  121 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC---T-TSCEEEEEESCHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC---C-CCcEEEEEECCHHHHHHHHHHHHHH
Confidence            367889999999999999999999999999999997643   2 4678899999999999999999843

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

Probab=97.58  E-value=4.5e-05  Score=75.87  Aligned_cols=65  Identities=29%  Similarity=0.426  Sum_probs=11.8

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHhh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~~  330 (336)
                      ....+.||.++++.|||+||++||+|.++||++|.|.+         +-.|.|.+ ..+.++.|+.+|..++...
T Consensus       570 ~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d---------dG~v~I~~~~~~~~~~A~~~i~~i~~~~  635 (726)
T 4aid_A          570 KIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND---------DGVVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             C----------------------------------------------------CCSCHHHHHHHHHC--------
T ss_pred             eEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC---------CceEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence            45688899999999999999999999999999999953         45667777 5889999999998877543

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

Probab=97.55  E-value=5.1e-05  Score=75.51  Aligned_cols=91  Identities=14%  Similarity=0.199  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEE
Q 019747           95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL  174 (336)
Q Consensus        95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I  174 (336)
                      .+++..|.+.+.+.+...+...+...+....+.||.+.++.+||++|.+|+.|.++||++|.+..         +..|.|
T Consensus       543 ~~g~~~I~~~m~~al~~~r~~~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d---------dG~v~I  613 (726)
T 4aid_A          543 KEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND---------DGVVKV  613 (726)
T ss_dssp             HHHHHHHHHHHHTTCSSCCSSCCSSCCC----------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHhhhhhhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC---------CceEEE
Confidence            33455566566665554433344455677889999999999999999999999999999999974         345777


Q ss_pred             EcC-HHHHHHHHHHHHHHhhc
Q 019747          175 TGT-LDEQMRALELILLKLSE  194 (336)
Q Consensus       175 ~G~-~~~v~~A~~~i~~~l~~  194 (336)
                      .+. .+++.+|+..|..++.+
T Consensus       614 ~~~~~~~~~~A~~~i~~i~~~  634 (726)
T 4aid_A          614 SASDGAKIKAAIDWIKSITDE  634 (726)
T ss_dssp             CCSCHHHHHHHHHC-------
T ss_pred             EeCCHHHHHHHHHHHHHHhhh
Confidence            776 78899999999888754

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.43  E-value=7.2e-05  Score=59.26  Aligned_cols=104  Identities=18%  Similarity=0.340  Sum_probs=75.3

Q ss_pred             eeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCC
Q 019747          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQT  201 (336)
Q Consensus       122 ~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~  201 (336)
                      -...+.|+...+|..||++|.+++.|+++.|-+|.+-..++              ++      ...|...|....-..-.
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~--------------d~------~~fI~naLsPA~V~~V~   95 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSS--------------DL------ERIVKNLFPGVKIESIN   95 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCS--------------SH------HHHHHHHSTTSCEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCC--------------CH------HHHHHHhcCCceEEEEE
Confidence            57789999999999999999999999999999999876211              11      23344443321000000


Q ss_pred             cCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHH
Q 019747          202 MTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIME  281 (336)
Q Consensus       202 ~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~  281 (336)
                      .                                                ..........+.||.+..+..|||+|.+++-
T Consensus        96 i------------------------------------------------~~~~~~~~~~V~V~~~q~slAIGk~G~NvrL  127 (144)
T 2cxc_A           96 V------------------------------------------------RERNGVKQVVIKVSEDDKGAAIGKGGKNVKR  127 (144)
T ss_dssp             E------------------------------------------------EEETTEEEEEEEECTTTHHHHHCGGGHHHHH
T ss_pred             E------------------------------------------------eecCCcEEEEEEEChHHhhhccCCCCHHHHH
Confidence            0                                                0001235678899999999999999999999


Q ss_pred             HHhHhCCeEEEc
Q 019747          282 ISQISGARIKVS  293 (336)
Q Consensus       282 I~~~sga~I~i~  293 (336)
                      ..+.||.+|.|.
T Consensus       128 a~~Ltg~~idI~  139 (144)
T 2cxc_A          128 ARLVLSKLFGVE  139 (144)
T ss_dssp             HHHHHHHHHCEE
T ss_pred             HHHHhCCeeCce
Confidence            999999988774

>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=96.49  E-value=0.0014  Score=56.37  Aligned_cols=97  Identities=22%  Similarity=0.225  Sum_probs=66.1

Q ss_pred             ccceeecCCChHHHHH-HHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccccCCCCCCcee
Q 019747           45 LAGAVIGKGGSTINDF-QSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTK  123 (336)
Q Consensus        45 ~vg~iIGk~G~~Ik~I-~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~  123 (336)
                      -+|..||++|++|+.| ++-.|=+|.+-..++      +        +.      ..|...|...-... .....+....
T Consensus       127 pvGacIG~~G~rI~~i~~eL~gekIDIi~~s~------d--------p~------~fi~nalsPA~V~~-V~i~~~~~~~  185 (251)
T 2asb_A          127 AKGACIGPMGQRVRNVMSELSGEKIDIIDYDD------D--------PA------RFVANALSPAKVVS-VSVIDQTARA  185 (251)
T ss_dssp             HHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS------S--------HH------HHHHHHTTTSCCSE-EEEEETTTTE
T ss_pred             HHHHHhCCCchHHHHHHHHhCCCeEEEEEecC------C--------HH------HHHHhccCCcceEE-EEEEcCCCcE
Confidence            4899999999999999 677789999865432      1        11      11111111110000 0000112357


Q ss_pred             EEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCC
Q 019747          124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDH  162 (336)
Q Consensus       124 ~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~  162 (336)
                      ..+.||..+.+.-||++|.+++-..+-||.+|.|....+
T Consensus       186 a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  224 (251)
T 2asb_A          186 ARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  224 (251)
T ss_dssp             EEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESSC
T ss_pred             EEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHHH
Confidence            789999999999999999999999999999999987433

>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=96.22  E-value=0.0083  Score=51.66  Aligned_cols=41  Identities=20%  Similarity=0.406  Sum_probs=37.3

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCC
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGD  297 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~  297 (336)
                      ....+.||.+..+.-|||+|+|++--.+.||.+|.|....+
T Consensus       184 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  224 (251)
T 2asb_A          184 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  224 (251)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESSC
T ss_pred             cEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHHH
Confidence            46789999999999999999999999999999999987543

>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=96.06  E-value=0.0034  Score=57.16  Aligned_cols=97  Identities=22%  Similarity=0.227  Sum_probs=67.4

Q ss_pred             CccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccccCCCCCCce
Q 019747           44 PLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKT  122 (336)
Q Consensus        44 ~~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~  122 (336)
                      +-+|..||++|++|+.|.++. |=+|.|-..++      +        +.      ..|...|...-...-... .+...
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~------d--------p~------~fi~nalsPA~V~~V~~~-~~~~~  307 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDD------D--------PA------RFVANALSPAKVVSVSVI-DQTAR  307 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS------S--------HH------HHHHHHTTTSCCSEEEEE-ETTTT
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcCC------C--------HH------HHHHHhcCCcceeEEEEE-cCCCc
Confidence            458999999999999999999 89999865432      1        11      111111111100000000 11245


Q ss_pred             eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccC
Q 019747          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLD  161 (336)
Q Consensus       123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~  161 (336)
                      ...+.||..+.+..||++|.+++-..+-||.+|.|....
T Consensus       308 ~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  346 (366)
T 1k0r_A          308 AARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  346 (366)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESS
T ss_pred             EEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHH
Confidence            788999999999999999999999999999999998743

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

Probab=95.83  E-value=0.0035  Score=62.57  Aligned_cols=89  Identities=16%  Similarity=0.183  Sum_probs=8.2

Q ss_pred             HHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEE
Q 019747           96 RAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT  175 (336)
Q Consensus        96 ~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~  175 (336)
                      ++...|.+.+.+.+.......+...+....+.||.+.++.+||++|.+|+.|.++||+.|.+..         +..+.|.
T Consensus       534 ~~~~~I~~~m~~al~~~~~~~~~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~---------dg~v~I~  604 (723)
T 3cdi_A          534 GARLHILGVMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED---------DGTVKIA  604 (723)
T ss_dssp             HHHHHHHHHHHHHCC-----------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHhhhcchhccccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC---------CccEEEe
Confidence            3444566566665554423333445667788999999999999999999999999999998874         3456666


Q ss_pred             cC-HHHHHHHHHHHHHHhh
Q 019747          176 GT-LDEQMRALELILLKLS  193 (336)
Q Consensus       176 G~-~~~v~~A~~~i~~~l~  193 (336)
                      +. .+.+.+|.+.+..++.
T Consensus       605 ~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          605 ATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             -------------------
T ss_pred             cCCHHHHHHHHHHHHHHhh
Confidence            65 5677778777766553

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=95.79  E-value=0.02  Score=52.16  Aligned_cols=40  Identities=20%  Similarity=0.422  Sum_probs=36.9

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCC
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRG  296 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~  296 (336)
                      ....+.||.+..+..|||+|.|++-..+.||.+|.|....
T Consensus       307 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  346 (366)
T 1k0r_A          307 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  346 (366)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESS
T ss_pred             cEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHH
Confidence            5688999999999999999999999999999999997753

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

Probab=95.68  E-value=0.0034  Score=62.70  Aligned_cols=63  Identities=25%  Similarity=0.386  Sum_probs=0.0

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHH
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVA  328 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~  328 (336)
                      ....+.||.++++.|||++|.+|+.|.+++|+.|.|.+         +..|.|.+ ..+.++.|+.+|...+.
T Consensus       560 ~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~---------dg~v~I~~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          560 RIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED---------DGTVKIAATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             -------------------------------------------------------------------------
T ss_pred             eEEEEEECHHHhcccccccceeeeeeehhhCceEEecC---------CccEEEecCCHHHHHHHHHHHHHHhh
Confidence            55678899999999999999999999999999998853         45666666 56677888887776654

>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=95.19  E-value=0.0023  Score=64.14  Aligned_cols=87  Identities=16%  Similarity=0.181  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEE
Q 019747           96 RAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT  175 (336)
Q Consensus        96 ~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~  175 (336)
                      ++...|.+.+.+.+... .......+....+.||.+.++.+||++|.+|+.|.+++|+.|.|..         +..|.|.
T Consensus       573 ~~~~~I~~~m~~al~~~-~~~~~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~---------dG~v~Is  642 (757)
T 1e3p_A          573 DARLHILDVMMEAIDTP-DEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED---------DGTIYIG  642 (757)
T ss_dssp             HHHHHHHHHHHHHCSSC-CCCCTTSCBCCCC------------------CTTCCCCCSCC-----------------CCC
T ss_pred             HHHHHHHHHHHHHhccc-ccccccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC---------CceEEEe
Confidence            34455665666655444 3333444566678999999999999999999999999999998874         3456666


Q ss_pred             cC-HHHHHHHHHHHHHHh
Q 019747          176 GT-LDEQMRALELILLKL  192 (336)
Q Consensus       176 G~-~~~v~~A~~~i~~~l  192 (336)
                      +. .....+|.+.|..+.
T Consensus       643 ~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          643 AADGPAAEAARATINGIA  660 (757)
T ss_dssp             BSSHHHHCC---------
T ss_pred             cCCHHHHHHHHHHHHHhc
Confidence            65 566667766666554

>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=95.00  E-value=0.0023  Score=64.18  Aligned_cols=62  Identities=23%  Similarity=0.340  Sum_probs=20.8

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHH
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKV  327 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i  327 (336)
                      ....+.||.+++|.+||++|++|+.|.+.+|+.|.|.+         +..|.|++ ..+..+.|+.+|..+.
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            33467799999999999999999999999999999953         46677777 4566667777776654

>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=94.74  E-value=0.016  Score=52.56  Aligned_cols=91  Identities=21%  Similarity=0.256  Sum_probs=65.0

Q ss_pred             ccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccc-ccc--CCCCCC
Q 019747           45 LAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHA-EDQ--ADDVGT  120 (336)
Q Consensus        45 ~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~-~~~--~~~~~~  120 (336)
                      -+|+.||.+|.+|+.+.++. |=+|.+-..++              ++.      .    .+...+.. .-.  ....+.
T Consensus       246 pvGacvg~~G~ri~~i~~el~ge~Idii~~s~--------------d~~------~----fi~nal~Pa~v~~v~~~d~~  301 (344)
T 1hh2_P          246 PIGACIGEGGSRIAAILKELKGEKLDVLKWSD--------------DPK------Q----LIANALAPATVIEVEILDKE  301 (344)
T ss_dssp             HHHHHHCTTSTTHHHHHHHTTTCEEEEEECCS--------------SHH------H----HHHHHTCSSCCSEEEEEETT
T ss_pred             ccceeeccCCcEeHHHHHHhCCCeeeEEecCC--------------CHH------H----HHHHhcCccEEEEEEEEcCC
Confidence            58999999999999999998 78888855432              111      1    11121111 100  000123


Q ss_pred             ceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEec
Q 019747          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (336)
Q Consensus       121 ~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~  159 (336)
                      .....+.||..+.+.-||++|.+++--.+-||.+|.|..
T Consensus       302 ~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          302 NKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             TTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            457889999999999999999999999999999999976

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=93.85  E-value=0.065  Score=48.53  Aligned_cols=39  Identities=18%  Similarity=0.434  Sum_probs=35.9

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccC
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDR  295 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~  295 (336)
                      ....+.||.+..+.-|||+|.|++--.+.||.+|.|...
T Consensus       303 ~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          303 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             CEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            568899999999999999999999999999999999653

>4hhu_A OR280; engineered protein, PSI-biology, structural genomi unknown function; HET: AE4 PG4; 2.00A {Synthetic construct}

Probab=92.11  E-value=1.3  Score=32.94  Aligned_cols=48  Identities=10%  Similarity=0.127  Sum_probs=31.8

Q ss_pred             chHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          277 RNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       277 ~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      +.|++-+...|+--.--+       .+.-.|.|+|-|+||.+-...=.+++..+.
T Consensus       103 emirqarkfagtvtytl~-------gn~l~i~itgvpeqvrkelakeaerl~~ef  150 (170)
T 4hhu_A          103 EMIRQARKFAGTVTYTLS-------GNRLVIVITGVPEQVRKELAKEAERLKAEF  150 (170)
T ss_dssp             HHHHHHHHTTCEEEEEEC-------SSEEEEEEESCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcceEEEEEe-------CCEEEEEEeCCcHHHHHHHHHHHHHHHHhc
Confidence            456666666775433322       356789999999999886666666665544

>2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori}

Probab=83.45  E-value=0.47  Score=37.59  Aligned_cols=66  Identities=11%  Similarity=0.079  Sum_probs=41.0

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      ++.+.+..+..|.+|||.|.|++.|+--+...++-.  .     .-.-.+-+.+..+.-.+.+..+...+.+.
T Consensus        34 ~i~i~i~ged~glLIGK~G~TL~ALQyL~~~~vn~~--~-----~~~V~LDve~YRerReetL~~lA~~~A~k   99 (152)
T 2pt7_G           34 VLLIDIDGEDSALLIGEKGYRYKALSYLLFNWIHPT--Y-----GYSIRLEISTFLQNQEKVMDTQLQSVIMT   99 (152)
T ss_dssp             EEEEEEEEGGGTTTTCGGGHHHHHHHHHHHHHHHHH--H-----SCEEEEEETTHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEecCCcceEECCCCcchHHHHHHHHHHhhhc--C-----CceEEEEhHHhHHHHHHHHHHHHHHHHHH
Confidence            466777788999999999999999995543222211  0     01112334455566666666666665555

>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens} SCOP: d.52.3.1

Probab=81.24  E-value=0.54  Score=33.88  Aligned_cols=28  Identities=14%  Similarity=0.328  Sum_probs=24.2

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHH
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQ   63 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~   63 (336)
                      .+++.|....-|.|||++|..|++|+.+
T Consensus        36 ~i~I~I~tarPg~vIGkkG~~Ie~L~~~   63 (92)
T 1wh9_A           36 RTEIIILATRTQNVLGEKGRRIRELTAV   63 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHH
T ss_pred             eEEEEEEeCCCceEEcCCcHHHHHHHHH
Confidence            4788888899999999999999988754

---

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	336
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-18
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	7e-18
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	6e-16
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	6e-18
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	7e-17
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-14
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-16
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-12
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	4e-11
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-16
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	5e-15
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-14
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-15
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-14
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-12
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-15
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-14
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	5e-13
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	9e-15
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	6e-12
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-11
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	1e-14
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	6e-14
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	2e-11
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	2e-13
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	3e-13
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	2e-12
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-13
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	5e-12
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	4e-09
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	3e-13
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-11
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-11
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	5e-13
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	4e-11
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	2e-07
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-12
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	2e-12
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	2e-11
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-10
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-08
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-07
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	5e-10
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-07
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	9e-06
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	1e-09
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	2e-07
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	2e-07
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	2e-06
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	1e-04
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.001
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	2e-06
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	1e-04
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	1e-04
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	4e-06
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	3e-04
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	6e-05
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	2e-04
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	0.004
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	7e-05
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	0.001
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	8e-05
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	6e-04
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	8e-04
d1hh2p3	68	d.52.3.1 (P:277-344) Transcription factor NusA, C-	0.002
d2asba3	67	d.52.3.1 (A:263-329) Transcription factor NusA, C-	0.004

>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 = 76.8 bits (189), Expect = 1e-18
 Identities = 24/72 (33%), Positives = 48/72 (66%)

Query: 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSI 316
             + + V +  +G ++G+GG+ ++E  +++GARI++S +G+F  GT  R+VTI+G   + 
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62

Query: 317 RTAESMIMQKVA 328
           + A+ +I Q+V 
Sbjct: 63  QAAQYLISQRVT 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 = 74.9 bits (184), Expect = 7e-18
 Identities = 26/69 (37%), Positives = 42/69 (60%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           +   V   L GA++GKGG T+ ++Q  +GARIQ+S+  EF PGT +R + I+G+      
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64

Query: 97  AVDLVIDKL 105
           A  L+  ++
Sbjct: 65  AQYLISQRV 73

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.5 bits (170), Expect = 6e-16
 Identities = 22/73 (30%), Positives = 39/73 (53%)

Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE 180
           K  + + VP +  G+I+GK G T+  + + + A I+IS+      G  +R VT+TG+   
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

Query: 181 QMRALELILLKLS 193
              A  LI  +++
Sbjct: 62  TQAAQYLISQRVT 74

>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 = 74.9 bits (184), Expect = 6e-18
 Identities = 25/69 (36%), Positives = 35/69 (50%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
             F+V     G +IGKGG TI     QSGARI+L R+         ++  I GT  +I  
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDY 62

Query: 97  AVDLVIDKL 105
           A  L+ +K+
Sbjct: 63  ARQLIEEKI 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 = 71.9 bits (176), Expect = 7e-17
 Identities = 21/69 (30%), Positives = 33/69 (47%)

Query: 259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRT 318
               V     G ++G+GG  I  ISQ SGARI++       +  + +  TI G  + I  
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDY 62

Query: 319 AESMIMQKV 327
           A  +I +K+
Sbjct: 63  ARQLIEEKI 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 = 65.3 bits (159), Expect = 2e-14
 Identities = 26/70 (37%), Positives = 34/70 (48%)

Query: 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQM 182
           +   IVP    G IIGK G TIKS    S A I++ R        N +L T+ GT  +  
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQID 61

Query: 183 RALELILLKL 192
            A +LI  K+
Sbjct: 62  YARQLIEEKI 71

>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 = 71.8 bits (176), Expect = 1e-16
 Identities = 18/80 (22%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 249 QNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVT 308
           Q ++  R+  L++ V  ++   ++GR G  I +I       I+  D+ D      + ++T
Sbjct: 2   QEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQIT 59

Query: 309 ISGPQRSIRTAESMIMQKVA 328
           I+G +++   A   I++ V 
Sbjct: 60  ITGYEKNTEAARDAILRIVG 79

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.6 bits (147), Expect = 1e-12
 Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 3/81 (3%)

Query: 29  DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMIS 88
           D   +   +   V       +IG+ G+ I   + +    IQ     +         I I+
Sbjct: 4   DRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQITIT 61

Query: 89  GTIDEILRAVDLVIDKLLTEL 109
           G       A D  I +++ EL
Sbjct: 62  GYEKNTEAARDA-ILRIVGEL 81

>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 = 56.4 bits (136), Expect = 4e-11
 Identities = 20/82 (24%), Positives = 29/82 (35%), Gaps = 2/82 (2%)

Query: 113 DQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLV 172
           +Q D      KL + V       IIG+ GA I     +    I+    D          +
Sbjct: 1   EQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG--NQPQDQI 58

Query: 173 TLTGTLDEQMRALELILLKLSE 194
           T+TG       A + IL  + E
Sbjct: 59  TITGYEKNTEAARDAILRIVGE 80

>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 = 70.6 bits (173), Expect = 3e-16
 Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           IR L+     G++IGK G ++   + +SGARI +S          +RII ++G  + I +
Sbjct: 6   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISE-----GNCPERIITLAGPTNAIFK 60

Query: 97  AVDLVIDKL 105
           A  ++IDKL
Sbjct: 61  AFAMIIDKL 69

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.7 bits (163), Expect = 5e-15
 Identities = 20/74 (27%), Positives = 44/74 (59%), Gaps = 5/74 (6%)

Query: 254 DRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQ 313
           + T ++ + +  + +G ++G+ G ++ ++ + SGARI +S+         ER +T++GP 
Sbjct: 1   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE-----GNCPERIITLAGPT 55

Query: 314 RSIRTAESMIMQKV 327
            +I  A +MI+ K+
Sbjct: 56  NAIFKAFAMIIDKL 69

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.6 bits (160), Expect = 1e-14
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 5/71 (7%)

Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
           +RL++     GSIIGK G ++K   ++S A I IS          +R++TL G  +   +
Sbjct: 6   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISE-----GNCPERIITLAGPTNAIFK 60

Query: 184 ALELILLKLSE 194
           A  +I+ KL E
Sbjct: 61  AFAMIIDKLEE 71

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.7 bits (168), Expect = 1e-15
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           +    V D  +GF++GRGG  I  I Q SG +I+++       G  ER   ++G   S++
Sbjct: 9   TEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG---GLPERSCMLTGTPESVQ 65

Query: 318 TAESMIMQKVA 328
           +A+ ++ Q V 
Sbjct: 66  SAKRLLDQIVE 76

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.6 bits (160), Expect = 2e-14
 Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 32  EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTI 91
                  + V + + G +IG+GG  I+  Q +SG +IQ++       G  +R  M++GT 
Sbjct: 5   RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCMLTGTP 61

Query: 92  DEILRAVDLVIDKL 105
           + +  A  L+   +
Sbjct: 62  ESVQSAKRLLDQIV 75

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.6 bits (147), Expect = 1e-12
 Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 3/71 (4%)

Query: 125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRA 184
              VP+   G IIG+ G  I     +S   I+I+       GL +R   LTGT +    A
Sbjct: 11  EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG---GLPERSCMLTGTPESVQSA 67

Query: 185 LELILLKLSED 195
             L+   + + 
Sbjct: 68  KRLLDQIVEKG 78

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.9 bits (166), Expect = 2e-15
 Identities = 26/71 (36%), Positives = 46/71 (64%), Gaps = 3/71 (4%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           +  + + +  IG ++GR G NI EI Q+SGA+IK+++  +   G+S R+VTI+G   SI 
Sbjct: 3   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE---GSSGRQVTITGSAASIS 59

Query: 318 TAESMIMQKVA 328
            A+ +I  +++
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 = 65.2 bits (159), Expect = 2e-14
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 35  TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEI 94
           T     + N L G +IG+ G+ IN+ +  SGA+I+++       G++ R + I+G+   I
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV---EGSSGRQVTITGSAASI 58

Query: 95  LRAVDLVIDKL 105
             A  L+  +L
Sbjct: 59  SLAQYLINARL 69

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.4 bits (149), Expect = 5e-13
 Identities = 27/73 (36%), Positives = 36/73 (49%), Gaps = 3/73 (4%)

Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE 180
           +T   L +PN+  G IIG+ GA I      S A IKI+       G + R VT+TG+   
Sbjct: 1   QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE---GSSGRQVTITGSAAS 57

Query: 181 QMRALELILLKLS 193
              A  LI  +LS
Sbjct: 58  ISLAQYLINARLS 70

>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 = 66.3 bits (162), Expect = 9e-15
 Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           S T+ +  EH  FV+G+ G  + ++   +  +I++    D        ++ I+G +  I 
Sbjct: 11  SATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD-----PSNQIKITGTKEGIE 65

Query: 318 TAESMIMQKVAYASDR 333
            A   ++   A    R
Sbjct: 66  KARHEVLLISAEQDKR 81

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.6 bits (142), Expect = 6e-12
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 32  EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTI 91
           +        +       VIGK G  + D + ++  +IQ+ R     P      I I+GT 
Sbjct: 7   QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR-----PDDPSNQIKITGTK 61

Query: 92  DEILRAVDLVIDKLLTEL 109
           + I +A    +  +  E 
Sbjct: 62  EGIEKARHE-VLLISAEQ 78

>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 = 56.6 bits (137), Expect = 3e-11
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 5/79 (6%)

Query: 116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT 175
             + T+    + +P      +IGK G  ++     +   I+I R D          + +T
Sbjct: 4   ARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD-----PSNQIKIT 58

Query: 176 GTLDEQMRALELILLKLSE 194
           GT +   +A   +LL  +E
Sbjct: 59  GTKEGIEKARHEVLLISAE 77

>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 = 65.7 bits (160), Expect = 1e-14
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 3/73 (4%)

Query: 256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRS 315
           ++ + + +    +G V+GR G  I +I   +G RI+          T ER   I+GP   
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG---TTPERIAQITGPPDR 58

Query: 316 IRTAESMIMQKVA 328
            + A  +I   + 
Sbjct: 59  AQHAAEIITDLLR 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 = 64.1 bits (156), Expect = 6e-14
 Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 3/69 (4%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
           I   +     G VIG+ G  I   Q+ +G RIQ          T +RI  I+G  D    
Sbjct: 5   IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD---GTTPERIAQITGPPDRAQH 61

Query: 97  AVDLVIDKL 105
           A +++ D L
Sbjct: 62  AAEIITDLL 70

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.8 bits (137), Expect = 2e-11
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 3/73 (4%)

Query: 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQ 181
             + + +P  + G +IG+ G  IK   +D+   I+            +R+  +TG  D  
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQF---KPDDGTTPERIAQITGPPDRA 59

Query: 182 MRALELILLKLSE 194
             A E+I   L  
Sbjct: 60  QHAAEIITDLLRS 72

>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 = 63.8 bits (155), Expect = 2e-13
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
              + V    +G ++GRGG  I  I + SGA+I      +  +    R + ISG Q+ + 
Sbjct: 16  FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE-GTLLLSRLIKISGTQKEVA 74

Query: 318 TAESMIMQKVAYASDR 333
            A+ +I++KV+   + 
Sbjct: 75  AAKHLILEKVSEDEEL 90

>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 = 62.7 bits (152), Expect = 3e-13
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 34  PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDE 93
           P + +  V     G +IG+GG TI      SGA+I   +  E       R+I ISGT  E
Sbjct: 14  PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLL-LSRLIKISGTQKE 72

Query: 94  ILRAVDLVIDKL 105
           +  A  L+++K+
Sbjct: 73  VAAAKHLILEKV 84

>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 = 60.8 bits (147), Expect = 2e-12
 Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
            +L VP  S G IIG+ G TI+S    S A I   + +     L  RL+ ++GT  E   
Sbjct: 17  EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDK-ESEGTLLLSRLIKISGTQKEVAA 75

Query: 184 ALELILLKLSEDTLYSQTM 202
           A  LIL K+SED    + +
Sbjct: 76  AKHLILEKVSEDEELRKRI 94

>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 = 62.9 bits (153), Expect = 2e-13
 Identities = 12/79 (15%), Positives = 31/79 (39%), Gaps = 5/79 (6%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           ++ + V  +   +V+G+ G  I ++       I V              + I+G   ++ 
Sbjct: 11  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL-----QSDIIAITGLAANLD 65

Query: 318 TAESMIMQKVAYASDRLMD 336
            A++ ++++V        D
Sbjct: 66  RAKAGLLERVKELQAEQED 84

>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 = 59.1 bits (143), Expect = 5e-12
 Identities = 22/81 (27%), Positives = 31/81 (38%), Gaps = 6/81 (7%)

Query: 34  PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDE 93
           P  I   V   L   VIG+ GS I     +    I +       P     II I+G    
Sbjct: 9   PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA-----PELQSDIIAITGLAAN 63

Query: 94  ILRAVDLVIDKLLTELHAEDQ 114
           + RA    + + + EL AE +
Sbjct: 64  LDRAKAG-LLERVKELQAEQE 83

>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 = 51.0 bits (122), Expect = 4e-09
 Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 5/71 (7%)

Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
           + + VP      +IG+ G+ I+  MD+ +  I +   +         ++ +TG      R
Sbjct: 12  IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL-----QSDIIAITGLAANLDR 66

Query: 184 ALELILLKLSE 194
           A   +L ++ E
Sbjct: 67  AKAGLLERVKE 77

>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 = 62.2 bits (151), Expect = 3e-13
 Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 3/74 (4%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           +  + +  +  G ++G+GG+ I +I   SGA IK+ +  +   G+ +R +TI+G Q  I+
Sbjct: 5   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE---GSEDRIITITGTQDQIQ 61

Query: 318 TAESMIMQKVAYAS 331
            A+ ++   V   S
Sbjct: 62  NAQYLLQNSVKQYS 75

>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 = 58.0 bits (140), Expect = 1e-11
 Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 3/76 (3%)

Query: 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTL 178
           G     ++ +P    GSIIGK G  IK    +S A IKI        G  DR++T+TGT 
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE---GSEDRIITITGTQ 57

Query: 179 DEQMRALELILLKLSE 194
           D+   A  L+   + +
Sbjct: 58  DQIQNAQYLLQNSVKQ 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 = 57.6 bits (139), Expect = 1e-11
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 3/69 (4%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
            +  +   LAG++IGKGG  I   + +SGA I++        G+ DRII I+GT D+I  
Sbjct: 6   TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL---EGSEDRIITITGTQDQIQN 62

Query: 97  AVDLVIDKL 105
           A  L+ + +
Sbjct: 63  AQYLLQNSV 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 = 61.3 bits (149), Expect = 5e-13
 Identities = 10/75 (13%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 254 DRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQ 313
           +R + + I +  +    ++G+ G NI  I       +++    +         + I G  
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE-----KSNLIRIEGDP 56

Query: 314 RSIRTAESMIMQKVA 328
           + ++ A+  +++  +
Sbjct: 57  QGVQQAKRELLELAS 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 = 55.9 bits (135), Expect = 4e-11
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 5/72 (6%)

Query: 32  EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTI 91
            +  Y+   + +     +IGK G+ IN  + Q    +++    E        +I I G  
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE-----KSNLIRIEGDP 56

Query: 92  DEILRAVDLVID 103
             + +A   +++
Sbjct: 57  QGVQQAKRELLE 68

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (108), Expect = 2e-07
 Identities = 12/65 (18%), Positives = 24/65 (36%), Gaps = 5/65 (7%)

Query: 125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRA 184
            + + +     +IGK+GA I    D  +  ++I             L+ + G      +A
Sbjct: 8   EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE-----KSNLIRIEGDPQGVQQA 62

Query: 185 LELIL 189
              +L
Sbjct: 63  KRELL 67

>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 = 60.7 bits (147), Expect = 1e-12
 Identities = 17/69 (24%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 37  IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
              ++    AG VIGKGG TI   Q ++G ++ + +         D+ + I+G   ++ +
Sbjct: 10  QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGP-QNTGADKPLRITGDPYKVQQ 68

Query: 97  AVDLVIDKL 105
           A ++V++ +
Sbjct: 69  AKEMVLELI 77

>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 = 60.0 bits (145), Expect = 2e-12
 Identities = 14/71 (19%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
              I +     G V+G+GG  I ++ + +G ++ +   G   +G  ++ + I+G    ++
Sbjct: 9   VQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGA-DKPLRITGDPYKVQ 67

Query: 318 TAESMIMQKVA 328
            A+ M+++ + 
Sbjct: 68  QAKEMVLELIR 78

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.3 bits (138), Expect = 2e-11
 Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
             +++P S  G +IGK G TIK   + +   + + + D       D+ + +TG   +  +
Sbjct: 10  QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQ-DGPQNTGADKPLRITGDPYKVQQ 68

Query: 184 ALELILLKLSE 194
           A E++L  + +
Sbjct: 69  AKEMVLELIRD 79

>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 = 54.0 bits (130), Expect = 3e-10
 Identities = 12/71 (16%), Positives = 24/71 (33%), Gaps = 4/71 (5%)

Query: 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIR 317
           S  + +       ++G  G+ I +I       I+    G          VT++G   ++ 
Sbjct: 11  SEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLPENVE 66

Query: 318 TAESMIMQKVA 328
            A   I+    
Sbjct: 67  EAIDHILNLEE 77

>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 = 49.4 bits (118), Expect = 1e-08
 Identities = 10/74 (13%), Positives = 27/74 (36%), Gaps = 4/74 (5%)

Query: 32  EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTI 91
           E+       + + +   +IG  G  I     +    I+  +S           + ++G  
Sbjct: 7   EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLP 62

Query: 92  DEILRAVDLVIDKL 105
           + +  A+D +++  
Sbjct: 63  ENVEEAIDHILNLE 76

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (110), Expect = 1e-07
 Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 4/79 (5%)

Query: 116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT 175
            ++       + + +     IIG  G  I+  MD+ +  I+  +        +   VT+T
Sbjct: 4   GELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP----DPNCVTVT 59

Query: 176 GTLDEQMRALELILLKLSE 194
           G  +    A++ IL    E
Sbjct: 60  GLPENVEEAIDHILNLEEE 78

>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 = 53.2 bits (128), Expect = 5e-10
 Identities = 12/71 (16%), Positives = 24/71 (33%), Gaps = 9/71 (12%)

Query: 260 TIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTA 319
            + +    +  V+G+ G  I  +      +I V              + ++G +R +  A
Sbjct: 4   IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ---------NGLIWVNGDRRKVSIA 54

Query: 320 ESMIMQKVAYA 330
           E  I      A
Sbjct: 55  EEAIYLIEQEA 65

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 46.7 bits (111), Expect = 1e-07
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 10/78 (12%)

Query: 41  VSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDL 100
           ++      VIGK GS I   +S+   +I + +         + +I ++G   ++  A + 
Sbjct: 7   INPARVPRVIGKKGSMIKLLKSELDVQIVVGQ---------NGLIWVNGDRRKVSIAEEA 57

Query: 101 VIDKLLTELHAEDQADDV 118
            I  +  E H E   D V
Sbjct: 58  -IYLIEQEAHTEGLTDRV 74

>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 = 41.3 bits (97), Expect = 9e-06
 Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 9/67 (13%)

Query: 128 VPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALEL 187
           +  +    +IGK G+ IK    +    I + +         + L+ + G   +   A E 
Sbjct: 7   INPARVPRVIGKKGSMIKLLKSELDVQIVVGQ---------NGLIWVNGDRRKVSIAEEA 57

Query: 188 ILLKLSE 194
           I L   E
Sbjct: 58  IYLIEQE 64

>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 = 52.5 bits (126), Expect = 1e-09
 Identities = 14/86 (16%), Positives = 28/86 (32%), Gaps = 7/86 (8%)

Query: 249 QNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQIS-GARIKVSDRGDFFSGTSERKV 307
           Q +  +    + + +  +    ++G  GR I  I +   G  I     G          V
Sbjct: 3   QKDLANIA-EVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS-----GSDTV 56

Query: 308 TISGPQRSIRTAESMIMQKVAYASDR 333
            I GP   +  A+  ++        +
Sbjct: 57  VIRGPSSDVEKAKKQLLHLAEEKQTK 82

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (109), Expect = 2e-07
 Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 6/81 (7%)

Query: 115 ADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV-IKISRLDHSYYGLNDRLVT 173
             D+    ++ + +P     S+IG  G  I+S M++   V I                V 
Sbjct: 3   QKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS-----GSDTVV 57

Query: 174 LTGTLDEQMRALELILLKLSE 194
           + G   +  +A + +L    E
Sbjct: 58  IRGPSSDVEKAKKQLLHLAEE 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 = 45.6 bits (108), Expect = 2e-07
 Identities = 13/82 (15%), Positives = 26/82 (31%), Gaps = 7/82 (8%)

Query: 32  EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGT 90
                +   +   L  ++IG  G  I     +  G  I          G+    ++I G 
Sbjct: 7   ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV-----EGSGSDTVVIRGP 61

Query: 91  IDEILRAVDLVIDKLLTELHAE 112
             ++ +A    +  L  E   +
Sbjct: 62  SSDVEKAKKQ-LLHLAEEKQTK 82

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 42.8 bits (101), Expect = 2e-06
 Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 10/68 (14%)

Query: 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP-QRS 315
           N + I +    +  V+G+       ++  SG  I V++ G         ++  + P + S
Sbjct: 1   NGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNG---------RIWATCPSRFS 51

Query: 316 IRTAESMI 323
                  I
Sbjct: 52  EEILIEAI 59

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 37.4 bits (87), Expect = 1e-04
 Identities = 14/64 (21%), Positives = 21/64 (32%), Gaps = 9/64 (14%)

Query: 47  GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL 106
             VIGK  S      S+SG  I ++          +  I  +         +   I K+ 
Sbjct: 13  PRVIGKNKSMYETLTSKSGCSIFVAN---------NGRIWATCPSRFSEEILIEAIRKIE 63

Query: 107 TELH 110
            E H
Sbjct: 64  NESH 67

>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 = 34.3 bits (79), Expect = 0.001
 Identities = 9/68 (13%), Positives = 21/68 (30%), Gaps = 9/68 (13%)

Query: 128 VPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALEL 187
           +       +IGK  +  ++    S   I ++         N+  +  T         L  
Sbjct: 7   IMPVKVPRVIGKNKSMYETLTSKSGCSIFVA---------NNGRIWATCPSRFSEEILIE 57

Query: 188 ILLKLSED 195
            + K+  +
Sbjct: 58  AIRKIENE 65

>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 = 43.2 bits (102), Expect = 2e-06
 Identities = 13/68 (19%), Positives = 25/68 (36%), Gaps = 5/68 (7%)

Query: 259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKV-SDRGDFFSGTSERKVTISGPQRSIR 317
           + + V  E +G V+G  G    EI + +G  I V ++                 P  ++ 
Sbjct: 5   IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSM----VIVEPEAEGIPPVNLM 60

Query: 318 TAESMIMQ 325
            A  ++  
Sbjct: 61  KAAEVVKA 68

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 12/68 (17%), Positives = 24/68 (35%), Gaps = 3/68 (4%)

Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE 180
           K ++ + V     G++IG  G      M  +  VI +   +     +             
Sbjct: 2   KPRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSM---VIVEPEAEGIPPVN 58

Query: 181 QMRALELI 188
            M+A E++
Sbjct: 59  LMKAAEVV 66

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 10/60 (16%), Positives = 25/60 (41%), Gaps = 13/60 (21%)

Query: 47  GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDE-----ILRAVDLV 101
           GAVIG  G    +   ++G  I +           + ++++    +      +++A ++V
Sbjct: 15  GAVIGPRGEVKAEIMRRTGTVITVDT--------ENSMVIVEPEAEGIPPVNLMKAAEVV 66

>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 = 42.0 bits (99), Expect = 4e-06
 Identities = 10/72 (13%), Positives = 25/72 (34%), Gaps = 10/72 (13%)

Query: 260 TIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP-QRSIRT 318
            + ++   +  V+GR    +  + + +  +I V+  G         ++ +  P +     
Sbjct: 4   IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNG---------RIHLECPNEDLEAI 54

Query: 319 AESMIMQKVAYA 330
           A   I      A
Sbjct: 55  AVMAIKIIDEEA 66

>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 = 36.6 bits (85), Expect = 3e-04
 Identities = 9/72 (12%), Positives = 26/72 (36%), Gaps = 9/72 (12%)

Query: 47  GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL 106
             VIG+  S +   + ++  +I ++R         +  I +    +++     + I  + 
Sbjct: 13  PRVIGRKMSMLKTLEEKTECKIFVAR---------NGRIHLECPNEDLEAIAVMAIKIID 63

Query: 107 TELHAEDQADDV 118
            E +       +
Sbjct: 64  EEAYTSGLTKRI 75

>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 = 38.1 bits (89), Expect = 6e-05
 Identities = 15/57 (26%), Positives = 18/57 (31%), Gaps = 9/57 (15%)

Query: 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT 90
          P  I   +     G VIG     IN  Q  +GA I +           D  I I   
Sbjct: 2  PRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED---------DGTIYIGAA 49

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 36.2 bits (84), Expect = 2e-04
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 9/53 (16%)

Query: 260 TIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP 312
           T+ +  + IG V+G   + I +I + +GA I + D         +  + I   
Sbjct: 6   TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED---------DGTIYIGAA 49

>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 = 32.7 bits (75), Expect = 0.004
 Identities = 10/53 (18%), Positives = 18/53 (33%), Gaps = 9/53 (16%)

Query: 125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177
            + +P    G +IG     I    +D+ A I I          +D  + +   
Sbjct: 6   TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE---------DDGTIYIGAA 49

>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 = 38.3 bits (89), Expect = 7e-05
 Identities = 11/71 (15%), Positives = 23/71 (32%), Gaps = 8/71 (11%)

Query: 260 TIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP-QRSIRT 318
              V ++ +G  +G  G NI +  ++ G      D              I G    +++ 
Sbjct: 11  EFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDT-------GTFRIYGESADAVKK 63

Query: 319 AESMIMQKVAY 329
           A   +     +
Sbjct: 64  ARGFLEFVEDF 74

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.9 bits (80), Expect = 0.001
 Identities = 13/63 (20%), Positives = 20/63 (31%), Gaps = 6/63 (9%)

Query: 39  FLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAV 98
           F+V   L G  IG  GS I   +   G               T    +   + D + +A 
Sbjct: 12  FVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED------TGTFRIYGESADAVKKAR 65

Query: 99  DLV 101
             +
Sbjct: 66  GFL 68

>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 = 38.7 bits (90), Expect = 8e-05
 Identities = 17/84 (20%), Positives = 35/84 (41%), Gaps = 9/84 (10%)

Query: 251 NKDDRTNSLTIGVADEHIGFVVGRGGRNIMEI-SQISGARIKVSDRGDFFSGTSERKVTI 309
            K +     ++        F++G+ G+N+ +I  Q+    I+ ++         E K+T+
Sbjct: 15  AKANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG--------EDKITL 66

Query: 310 SGPQRSIRTAESMIMQKVAYASDR 333
            GP   +  A+  I   V    +R
Sbjct: 67  EGPTEDVSVAQEQIEGMVKDLINR 90

>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 = 36.6 bits (85), Expect = 6e-04
 Identities = 13/56 (23%), Positives = 20/56 (35%), Gaps = 10/56 (17%)

Query: 268 IGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMI 323
            G ++G GGR    I +++   I V +            V I G       A+  I
Sbjct: 24  KGRIIGEGGRARRTIEEMTDTYINVGEYE----------VAIIGDYERAMAAKQAI 69

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 36.2 bits (84), Expect = 8e-04
 Identities = 9/50 (18%), Positives = 18/50 (36%)

Query: 47 GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
          G +IG+GG      +  +   I +        G  +R +     I+ +  
Sbjct: 25 GRIIGEGGRARRTIEEMTDTYINVGEYEVAIIGDYERAMAAKQAIEMLAE 74

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]} Length = 68

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]

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 8/42 (19%), Positives = 20/42 (47%)

Query: 253 DDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSD 294
           D    +  + V    +   +G+GG+N    ++++G +I +  
Sbjct: 23  DKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP 64

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]} Length = 67

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]

 Score = 33.5 bits (77), Expect = 0.004
 Identities = 9/40 (22%), Positives = 20/40 (50%)

Query: 253 DDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKV 292
           D    +  + V D  +   +G+ G+N    ++++G RI +
Sbjct: 22  DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDI 61

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	336
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.71
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.7
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.7
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.69
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.66
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.66
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.65
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.65
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.64
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.64
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.63
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.62
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.62
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.62
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.6
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.6
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.58
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.57
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.57
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.57
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.55
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.53
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.52
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.49
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.48
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.48
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.48
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.45
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.43
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.42
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.38
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.37
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.36
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.27
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.21
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.16
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.02
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.0
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.97
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.83
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.83
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.82
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.78
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.71
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.69
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.53
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.4
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.38
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.89
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.87
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	96.36
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	96.3
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	96.0
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	95.78
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	93.59
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	90.68
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	90.44
d2uubc1	105	Ribosomal protein S3 N-terminal domain {Thermus th	83.83
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	82.41
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	80.58

>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=99.71  E-value=9.5e-18  Score=116.97  Aligned_cols=70  Identities=30%  Similarity=0.463  Sum_probs=64.5

Q ss_pred             EEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHH
Q 019747          258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKV  327 (336)
Q Consensus       258 ~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  327 (336)
                      .++|.||..++|+|||++|++|++|++.|||+|.|++..++.+++.+|.|+|+|++++|+.|+.+|.++|
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            4689999999999999999999999999999999998766666778999999999999999999999874

>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=99.70  E-value=1.2e-17  Score=117.52  Aligned_cols=71  Identities=34%  Similarity=0.754  Sum_probs=66.6

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHH
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKV  327 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  327 (336)
                      .+.++.||.+++|+|||++|++|++|++.|||+|.|++..++.++..+|+|+|+|++++|+.|+.+|.++|
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            56799999999999999999999999999999999998877777788999999999999999999999876

>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=99.70  E-value=3.5e-17  Score=115.53  Aligned_cols=73  Identities=29%  Similarity=0.541  Sum_probs=67.0

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      ..+.++.||.+++|+|||++|++|++|+++|||+|.+.++   .+++.+|.|+|+|++++|+.|+.+|.++|++++
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~---~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~S   75 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQYS   75 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT---TSCSSEEEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccC---CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhcC
Confidence            3788999999999999999999999999999999999764   455778999999999999999999999998763

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=2.3e-17  Score=114.51  Aligned_cols=68  Identities=38%  Similarity=0.645  Sum_probs=63.2

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHH
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKV  327 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  327 (336)
                      .+.+|.||..++|+|||++|.+|++|+++|||+|.|++.   .+++++|.|+|+|++++|+.|+.+|+++|
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            688999999999999999999999999999999999774   45577899999999999999999999876

>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=99.66  E-value=6.6e-17  Score=113.66  Aligned_cols=71  Identities=25%  Similarity=0.416  Sum_probs=65.4

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  330 (336)
                      .+++|.||.+++|+|||++|++|++|+++|||+|.|++.   .++..+|.|+|+|++++|+.|+.+|.++|++.
T Consensus         3 ~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~---~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD---DGTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECC---TTSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccC---CCCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            678999999999999999999999999999999999875   34567899999999999999999999999874

>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=99.66  E-value=1.4e-16  Score=111.90  Aligned_cols=71  Identities=37%  Similarity=0.672  Sum_probs=66.2

Q ss_pred             EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHH
Q 019747           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL  105 (336)
Q Consensus        35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i  105 (336)
                      .+++|+||++++|.|||++|++|++|+++|||+|+|++..+..+++.+|+|.|+|+++++.+|..+|.+.|
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            46899999999999999999999999999999999998877778889999999999999999999998653

>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=99.65  E-value=8.2e-17  Score=112.08  Aligned_cols=70  Identities=34%  Similarity=0.637  Sum_probs=64.1

Q ss_pred             CcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        33 ~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      -.++++|+||++++|+|||++|++|++|+++|||+|++++..     .++|++.|+|+++++.+|..+|.+.|.+
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~-----~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-----CPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC-----CSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCC-----CCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            468999999999999999999999999999999999997643     6789999999999999999999977653

>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=99.65  E-value=1.3e-16  Score=111.02  Aligned_cols=69  Identities=36%  Similarity=0.516  Sum_probs=64.0

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHH
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDK  104 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~  104 (336)
                      .++|+||++.+|.||||+|++|++|+++|||+|+|++..+..++..+|.|.|+|+++++.+|..+|.++
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~   70 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEK   70 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHH
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhh
Confidence            468999999999999999999999999999999998877666778899999999999999999999875

>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=99.64  E-value=1.9e-16  Score=113.23  Aligned_cols=74  Identities=18%  Similarity=0.410  Sum_probs=66.6

Q ss_pred             CceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747          255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  329 (336)
                      ...+.+|.||..++|+|||++|++|++|++.|||+|.|.+.. +.+.+.+|.|+|+|++++|+.|+.+|.++|.+
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            458999999999999999999999999999999999998754 34456789999999999999999999998854

>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=99.64  E-value=1.5e-16  Score=110.69  Aligned_cols=68  Identities=28%  Similarity=0.536  Sum_probs=63.3

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  329 (336)
                      .+.++.||..++|+|||++|++|++|++.|||+|.+++..     ..+|+|+|+|++++|..|+.+|.++|++
T Consensus         4 vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~-----~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           4 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-----CPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC-----CSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             EEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCC-----CCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            7899999999999999999999999999999999998753     4689999999999999999999999874

>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=99.63  E-value=3.1e-16  Score=108.75  Aligned_cols=69  Identities=30%  Similarity=0.524  Sum_probs=63.0

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHH
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL  105 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i  105 (336)
                      +++.+|+||++++|+||||+|++|++|+++|||+|+|++..   +++.+|+|.|+|+++++.+|+.+|.++|
T Consensus         1 q~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           1 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV---EGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCC---TTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCC---CCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            47899999999999999999999999999999999997643   5678999999999999999999998654

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=3.7e-16  Score=111.22  Aligned_cols=73  Identities=30%  Similarity=0.531  Sum_probs=66.9

Q ss_pred             CceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747          255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~  330 (336)
                      ...+.+|.||.+++|+|||++|.+|++|++.|||+|.|++.   .+++.++.|+|+|++++|+.|+.+|.++|++.
T Consensus         6 ~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~---~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           6 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD---SGGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSC---CTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCC---CCCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            34889999999999999999999999999999999999874   44567899999999999999999999999864

>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=99.62  E-value=1e-15  Score=107.82  Aligned_cols=72  Identities=35%  Similarity=0.558  Sum_probs=65.3

Q ss_pred             CcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        33 ~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      ..++.+|.||.+++|+|||++|++|++|+++|||+|+|.+..   +++.+|+|.|.|+++++.+|+.+|.+.+.+
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~---~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL---EGSEDRIITITGTQDQIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT---SCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCC---CCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            357899999999999999999999999999999999997543   567899999999999999999999977665

>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=99.62  E-value=8.3e-16  Score=115.24  Aligned_cols=77  Identities=27%  Similarity=0.459  Sum_probs=68.0

Q ss_pred             CCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          254 DRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       254 ~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      ...++.+|.||..++|+|||++|.+|++|++.|||+|.|.++.+. ....+|+|+|+|++++|+.|+.+|.++|.+..
T Consensus        12 ~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~-~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T d1we8a_          12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG-TLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC-SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC-CCCCccEEEEEeCHHHHHHHHHHHHHHHhCcH
Confidence            345789999999999999999999999999999999999876532 33468999999999999999999999997654

>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=99.60  E-value=6.1e-16  Score=110.52  Aligned_cols=76  Identities=22%  Similarity=0.384  Sum_probs=67.9

Q ss_pred             CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      ....++.+|+||..++|.|||++|++|++|+++|||+|.|++.. ..++..+|.|+|+|++++|.+|..+|.+.|.+
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 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG-PQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSC-CCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CCccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCC-CCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            34679999999999999999999999999999999999998743 44567899999999999999999999977654

>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=99.60  E-value=7.7e-16  Score=108.10  Aligned_cols=71  Identities=30%  Similarity=0.472  Sum_probs=64.5

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      ..+++|.||.+++|+||||+|++|++|+++|||+|+|++..   ++..+|.++|+|+++++.+|..+|.+.+.+
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            56899999999999999999999999999999999998654   456789999999999999999999977654

>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=99.58  E-value=1.6e-15  Score=108.25  Aligned_cols=75  Identities=19%  Similarity=0.395  Sum_probs=67.3

Q ss_pred             CCCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhh
Q 019747          253 DDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASD  332 (336)
Q Consensus       253 ~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~  332 (336)
                      .....+.++.||..++|+|||++|++|++|+++|||+|.+++.     ++.++.|+|+|++++|+.|+.+|++++++...
T Consensus         6 ~~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-----~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~~~   80 (81)
T d2ctea1           6 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-----DDPSNQIKITGTKEGIEKARHEVLLISAEQDK   80 (81)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-----TSSCCEEEEEECHHHHHHHHHHHHHHHHHHHT
T ss_pred             hcCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC-----CCCCCEEEEEeCHHHHHHHHHHHHHHHHHHhc
Confidence            3455889999999999999999999999999999999999764     35679999999999999999999999987654

>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=99.57  E-value=3.1e-15  Score=107.56  Aligned_cols=74  Identities=20%  Similarity=0.307  Sum_probs=66.7

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      ..+.++.||..++++|||++|++|++|++.|||+|.+++.+  ..+..++.|+|+|++++|+.|+.+|.+++.+..
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            36789999999999999999999999999999999998754  345668899999999999999999999998764

>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=99.57  E-value=2.3e-15  Score=107.43  Aligned_cols=74  Identities=16%  Similarity=0.203  Sum_probs=65.8

Q ss_pred             CCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          254 DRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       254 ~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      ....+.++.||..++++|||++|++|++|++.|||+|.+++.++    .+.+.|+|+|++++|++|+.+|+++++++.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~----~~~~~v~I~G~~~~V~~A~~~I~~i~~e~~   80 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLPENVEEAIDHILNLEEEYL   80 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC----SCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC----CCCCEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            34577899999999999999999999999999999999987542    346789999999999999999999998764

>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=99.57  E-value=3.8e-15  Score=105.88  Aligned_cols=74  Identities=26%  Similarity=0.444  Sum_probs=67.2

Q ss_pred             CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      ....++.+|.||.+++|+|||++|.+|++|+++|||+|+|++..   +++.++.|.|+|++++|.+|..+|.+.|.+
T Consensus         4 ~~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   77 (79)
T d1x4na1           4 QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCMLTGTPESVQSAKRLLDQIVEK   77 (79)
T ss_dssp             CCCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC---TTCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cCCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCC---CCCCceEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            45679999999999999999999999999999999999998643   567899999999999999999999977765

>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=99.55  E-value=1.5e-14  Score=108.23  Aligned_cols=77  Identities=31%  Similarity=0.500  Sum_probs=67.8

Q ss_pred             CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      ....++.+|+||..++|+||||+|.+|++|+++|||+|.|++..+. ....+|+|.|+|++++|.+|+.+|.+.|.+.
T Consensus        11 ~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~-~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG-TLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC-SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC-CCCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            4456889999999999999999999999999999999999876533 3356899999999999999999999888654

>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=99.53  E-value=5.6e-15  Score=102.56  Aligned_cols=67  Identities=13%  Similarity=0.332  Sum_probs=60.8

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHH
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKV  327 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i  327 (336)
                      ....++.||..++++|||++|++|++|+++|||+|.++++     ++.++.|+|+|++++|+.|+.+|++++
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~-----~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-----SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC-----CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC-----CCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            3678999999999999999999999999999999999764     356789999999999999999998753

>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=99.52  E-value=5.6e-15  Score=105.70  Aligned_cols=73  Identities=18%  Similarity=0.340  Sum_probs=64.8

Q ss_pred             CceEEEEEeccCcccceeccCCchHHHHHhH-hCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhh
Q 019747          255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQI-SGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASD  332 (336)
Q Consensus       255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~-sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~  332 (336)
                      ..++.+|.||..+||+|||++|++|++|+++ ++++|.+++.     ++.++.|+|+|++++|+.|+.+|++++++...
T Consensus         8 ~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~-----~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~~~   81 (82)
T d2ctja1           8 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-----GSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQT   81 (82)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-----TTTCCEEEEESCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC-----CCCCceEEEeCCHHHHHHHHHHHHHHHhhhhc
Confidence            3478899999999999999999999999987 5899999764     35679999999999999999999999987654

>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=99.49  E-value=2.4e-14  Score=101.99  Aligned_cols=76  Identities=13%  Similarity=0.215  Sum_probs=66.1

Q ss_pred             CCCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           29 DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        29 ~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      +..+..++..|.||..+++.|||++|++|++|+++|||+|+|++.++    ..++.|+|+|++++|.+|.++|.+.+.+.
T Consensus         4 ~e~~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~----~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           4 GELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             CCTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC----SCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hHhhcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC----CCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            45667888999999999999999999999999999999999987542    23578999999999999999999765543

>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=99.48  E-value=2.6e-14  Score=101.80  Aligned_cols=72  Identities=22%  Similarity=0.306  Sum_probs=65.1

Q ss_pred             CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      ....++.+|.||..++|+|||++|.+|++|+++|||+|+|++.+     +.++.++|+|+.++|.+|..+|++.+.+
T Consensus         6 ~~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-----~~~~~v~I~G~~~~v~~A~~~I~~iv~e   77 (81)
T d2ctea1           6 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-----DPSNQIKITGTKEGIEKARHEVLLISAE   77 (81)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-----SSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             hcCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC-----CCCCEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            45668999999999999999999999999999999999997643     6788999999999999999999976554

>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=99.48  E-value=4.1e-14  Score=101.58  Aligned_cols=73  Identities=16%  Similarity=0.212  Sum_probs=64.7

Q ss_pred             CcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        33 ~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      ..++++|.||..+++.|||++|++|++|+++|||+|+|++..  .++..++.|.|.|+.++|.+|..+|.+.+.+
T Consensus         8 ~~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~--~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1           8 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKD--DGNQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTT--TCSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCC--CCCCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            467899999999999999999999999999999999997643  3556788999999999999999999965544

>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=99.48  E-value=1.5e-14  Score=105.57  Aligned_cols=71  Identities=15%  Similarity=0.263  Sum_probs=64.8

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      .++..|.||..+|++|||++|.+|++|+++|||+|.+++.     ++.++.|+|+|++++|+.|+.+|++++.+..
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            4889999999999999999999999999999999999764     3567899999999999999999999987644

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=7.2e-14  Score=96.83  Aligned_cols=67  Identities=18%  Similarity=0.388  Sum_probs=61.2

Q ss_pred             CCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHH
Q 019747           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVID  103 (336)
Q Consensus        32 ~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~  103 (336)
                      +..++.+|.||..++++|||++|++|++|+++|||+|+|++..     ..++.|.|+|++++|.+|..+|++
T Consensus         2 ~~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~-----~~~~~v~I~G~~~~v~~A~~~I~~   68 (71)
T d1viga_           2 NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-----EKSNLIRIEGDPQGVQQAKRELLE   68 (71)
T ss_dssp             CCCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-----SSSEEEEEEESSHHHHHHHHHHHH
T ss_pred             CceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCC-----CCCCEEEEECCHHHHHHHHHHHHH
Confidence            3567899999999999999999999999999999999997643     678899999999999999999985

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=7e-14  Score=99.87  Aligned_cols=75  Identities=13%  Similarity=0.258  Sum_probs=65.4

Q ss_pred             CCCCCcEEEEEEEecCccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           29 DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        29 ~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      ......++.+|.||..++|+|||++|++|++|++++ +|.|+|++.+     ..++.|+|+|++++|.+|..+|++.+.+
T Consensus         4 ~e~~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~-----~~~~~v~I~G~~~~v~~A~~~I~~~v~e   78 (82)
T d2ctja1           4 KDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-----SGSDTVVIRGPSSDVEKAKKQLLHLAEE   78 (82)
T ss_dssp             CCCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-----TTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hhhcCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCC-----CCCceEEEeCCHHHHHHHHHHHHHHHhh
Confidence            345667889999999999999999999999999885 9999997643     5789999999999999999999976655


Q ss_pred             h
Q 019747          108 E  108 (336)
Q Consensus       108 ~  108 (336)
                      .
T Consensus        79 ~   79 (82)
T d2ctja1          79 K   79 (82)
T ss_dssp             H
T ss_pred             h
Confidence            3

>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=99.42  E-value=2.1e-13  Score=98.86  Aligned_cols=72  Identities=22%  Similarity=0.394  Sum_probs=64.6

Q ss_pred             CCceEEEEEeccCcccceeccCCchHHHHHhHh-CCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhh
Q 019747          254 DRTNSLTIGVADEHIGFVVGRGGRNIMEISQIS-GARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASD  332 (336)
Q Consensus       254 ~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~s-ga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~  332 (336)
                      ....+..|.||..+|++|||++|++|++|++++ |++|.+++        ++..|+|+|++++|+.|+.+|++++.+..+
T Consensus        18 ~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~--------~~~~v~i~G~~~~ve~Ak~~I~~iv~el~~   89 (90)
T d2ctfa1          18 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE--------GEDKITLEGPTEDVSVAQEQIEGMVKDLIN   89 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS--------SSCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC--------CCceEEEeCCHHHHHHHHHHHHHHHHHHhc
Confidence            345899999999999999999999999999995 89999965        357899999999999999999999998765


Q ss_pred             c
Q 019747          333 R  333 (336)
Q Consensus       333 ~  333 (336)
                      |
T Consensus        90 r   90 (90)
T d2ctfa1          90 R   90 (90)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.38  E-value=2.9e-13  Score=96.32  Aligned_cols=64  Identities=19%  Similarity=0.243  Sum_probs=57.8

Q ss_pred             EEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747          259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS  331 (336)
Q Consensus       259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~  331 (336)
                      ..+.||.+++|+|||++|++|++|+++|||+|.|.+         +..|+|+|++++++.|+.+|+..+++..
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            467899999999999999999999999999999954         4689999999999999999988887643

>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=99.37  E-value=3.5e-13  Score=98.12  Aligned_cols=69  Identities=25%  Similarity=0.327  Sum_probs=62.7

Q ss_pred             cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      .++..|.||..+++.|||++|.+|++|+++|||+|.|+..+     ..+..|+|+|+.++|.+|..+|.+.+.+
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-----~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-----LQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-----TTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCC-----CCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            58899999999999999999999999999999999997643     5678999999999999999999966654

>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=99.36  E-value=1.9e-13  Score=95.91  Aligned_cols=64  Identities=17%  Similarity=0.302  Sum_probs=57.3

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHH
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQK  326 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~  326 (336)
                      ..+.+|.||.+++|+|||++|++|++|++.|||+|.+.+.       +++.|+|.| +++++++|+.||+.+
T Consensus         7 ~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~-------~~g~v~I~g~~~eav~~A~~~Ie~~   71 (78)
T d2cpqa1           7 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-------DTGTFRIYGESADAVKKARGFLEFV   71 (78)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-------TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             CceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC-------CCceEEEEECCHHHHHHHHHHHHHh
Confidence            3788999999999999999999999999999999998663       457899999 799999999999543

>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=5.8e-12  Score=91.02  Aligned_cols=71  Identities=15%  Similarity=0.219  Sum_probs=62.2

Q ss_pred             CCCCCcEEEEEEEecCccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           29 DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        29 ~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      +..++.++..|.||..++++|||++|++|++|++++ +|+|+|++        .+..++|+|++++|.+|..+|.+.+.+
T Consensus        15 ~~~~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~--------~~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          15 AKANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE--------GEDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCCCCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS--------SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHcCCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC--------CCceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            345567999999999999999999999999999996 79999974        346799999999999999999965544

>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=99.21  E-value=6e-12  Score=89.38  Aligned_cols=62  Identities=21%  Similarity=0.272  Sum_probs=54.7

Q ss_pred             EEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~  108 (336)
                      .-+.||.+.+|.|||++|++|++|+++|||+|+|.+         +..|.|.|+++++..|..+|.. +.++
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~---------~g~v~I~G~~e~v~~A~~~I~~-i~~e   64 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ---------NGLIWVNGDRRKVSIAEEAIYL-IEQE   64 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT---------TSEEEEESCHHHHHHHHHHHHH-HHHC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC---------CCEEEEEeCHHHHHHHHHHHHH-HHHh
Confidence            357899999999999999999999999999999954         3579999999999999999984 4444

>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=99.16  E-value=6.7e-12  Score=87.90  Aligned_cols=64  Identities=22%  Similarity=0.275  Sum_probs=56.6

Q ss_pred             CCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEe-eHHHHHHHHHHHH
Q 019747           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVI  102 (336)
Q Consensus        32 ~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G-~~~~v~~A~~~I~  102 (336)
                      ...++.+|.||.+++|+|||++|++|++|+++|||+|.+.+.       .+..+.|.| +.+++.+|+.+|.
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~-------~~g~v~I~g~~~eav~~A~~~Ie   69 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-------DTGTFRIYGESADAVKKARGFLE   69 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-------TTTEEEEEESSHHHHHHHHHHHS
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC-------CCceEEEEECCHHHHHHHHHHHH
Confidence            345788999999999999999999999999999999998652       356799999 6999999999985

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.02  E-value=5e-12  Score=86.36  Aligned_cols=61  Identities=16%  Similarity=0.167  Sum_probs=47.1

Q ss_pred             EEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcC-hHhHHHHHHHHHHHHHh
Q 019747          260 TIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP-QRSIRTAESMIMQKVAY  329 (336)
Q Consensus       260 ~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~~  329 (336)
                      .+.||.+++|.|||++|++|++|+++|||+|.|.+         +..|+|+|. ++.++.|+.+|....++
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~---------~g~v~I~g~~~~~v~~A~~~I~~i~~e   65 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN---------NGRIWATCPSRFSEEILIEAIRKIENE   65 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT---------TSEEEC-----CTTCCTHHHHTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC---------CCEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            67899999999999999999999999999999954         357999995 78999999999765443

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.00  E-value=2.1e-10  Score=80.97  Aligned_cols=62  Identities=23%  Similarity=0.323  Sum_probs=51.4

Q ss_pred             EEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEE-----cChHhHHHHHHHHHHHHH
Q 019747          259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTIS-----GPQRSIRTAESMIMQKVA  328 (336)
Q Consensus       259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~-----G~~~~v~~A~~~I~~~i~  328 (336)
                      .++.||.+.+|.|||++|++|++|+++|||+|.|+.+        ...+.+.     |.+.+++.|+.+|.+...
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            4689999999999999999999999999999999653        2344443     468889999999987643

>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=98.97  E-value=5.8e-10  Score=78.83  Aligned_cols=63  Identities=13%  Similarity=0.109  Sum_probs=55.3

Q ss_pred             EEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHhh
Q 019747          259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAYA  330 (336)
Q Consensus       259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~~  330 (336)
                      ..+.||.+++|.|||++|++|+.|++.|||+|.|.+         +-.|.|.| ..+.+..|+.+|....++.
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d---------~G~V~I~g~~~~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR---------NGRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET---------TTEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC---------CcEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            367899999999999999999999999999999964         35799999 5899999999998876653

>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=98.83  E-value=3e-10  Score=80.18  Aligned_cols=60  Identities=20%  Similarity=0.331  Sum_probs=47.8

Q ss_pred             EEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEE-----eeHHHHHHHHHHHHHH
Q 019747           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMIS-----GTIDEILRAVDLVIDK  104 (336)
Q Consensus        37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~-----G~~~~v~~A~~~I~~~  104 (336)
                      +.+.||.+.+|.|||++|++||+|+++|||+|+|...+        ..+.+.     +.+.++.+|...|.+.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~--------g~v~i~~~~~~~~~~a~~~a~~iI~aI   69 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTEN--------SMVIVEPEAEGIPPVNLMKAAEVVKAI   69 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTT--------TEEEEEESSTTSCHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCC--------CeEEEecCCccccHHHHHHHHHHHHHH
Confidence            45899999999999999999999999999999996432        234444     3567788888888743

>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=98.83  E-value=4.8e-11  Score=81.35  Aligned_cols=61  Identities=20%  Similarity=0.138  Sum_probs=45.3

Q ss_pred             EEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEee-HHHHHHHHHHHHHHHHhh
Q 019747           38 RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        38 ~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~-~~~v~~A~~~I~~~i~~~  108 (336)
                      -+.||.+++|.|||++|++|++|+++|||+|++.+         +..+.|.|. .+++.+|..+|. .+.++
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~---------~g~v~I~g~~~~~v~~A~~~I~-~i~~e   65 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN---------NGRIWATCPSRFSEEILIEAIR-KIENE   65 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT---------TSEEEC-----CTTCCTHHHHT-TTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC---------CCEEEEEeCCHHHHHHHHHHHH-HHHHh
Confidence            47799999999999999999999999999999953         235889885 678999999987 44443

>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=98.82  E-value=2.7e-09  Score=75.30  Aligned_cols=61  Identities=20%  Similarity=0.162  Sum_probs=52.2

Q ss_pred             EEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEee-HHHHHHHHHHHHHHHHhh
Q 019747           38 RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        38 ~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~-~~~v~~A~~~I~~~i~~~  108 (336)
                      -+.||.+.++.|||++|++|+.|+++|||+|.+.+         +-.|.|.|. .+.+..|..+|. .+.++
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d---------~G~V~I~g~~~~~~~~A~~~I~-~I~~e   65 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR---------NGRIHLECPNEDLEAIAVMAIK-IIDEE   65 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET---------TTEEEEECSCHHHHHHHHHHHH-HHHHC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC---------CcEEEEEeCCHHHHHHHHHHHH-HHHHh
Confidence            47899999999999999999999999999999964         235899995 788899999998 55554

>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=98.78  E-value=1.9e-09  Score=78.83  Aligned_cols=54  Identities=24%  Similarity=0.325  Sum_probs=48.1

Q ss_pred             CcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747          266 EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY  329 (336)
Q Consensus       266 ~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~  329 (336)
                      .+.|+|||++|.+|+.|++.|||.|.|.+          ..|.|.|++++++.|+.+|..++.+
T Consensus        22 R~~GrIIG~gGktik~Ie~~Tg~~I~I~d----------~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          22 RIKGRIIGEGGRARRTIEEMTDTYINVGE----------YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHTCEEEECS----------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HHhcceeCCCcHHHHHHHHHHCCeEEEeC----------CeEEEEECchhHHHHHHHHHHHHcC
Confidence            35799999999999999999999999943          3577889999999999999998865

>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=98.71  E-value=4e-10  Score=72.16  Aligned_cols=47  Identities=26%  Similarity=0.444  Sum_probs=14.8

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcC
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP  312 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~  312 (336)
                      ....+.||.+++|.|||++|++||.|+++|||+|.+.+         +..|+|.|+
T Consensus         3 ~~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d---------dg~v~I~a~   49 (54)
T d1e3ha4           3 RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED---------DGTIYIGAA   49 (54)
T ss_dssp             BCC---------------------CHHHHSCCCC-----------------CCCCB
T ss_pred             eEEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC---------CeEEEEEec
Confidence            34578899999999999999999999999999999953         567777774

>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=98.69  E-value=6.2e-10  Score=71.24  Aligned_cols=46  Identities=30%  Similarity=0.434  Sum_probs=13.8

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEee
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT   90 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~   90 (336)
                      ..+|.||.+++|.|||+||++||+|+++|||+|.+.+         +..|.|.|.
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            3578899999999999999999999999999999953         455666653

>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=98.53  E-value=4.2e-08  Score=71.49  Aligned_cols=52  Identities=17%  Similarity=0.275  Sum_probs=44.9

Q ss_pred             cceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747           46 AGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (336)
Q Consensus        46 vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~  107 (336)
                      .|.|||++|.+|+.|++.|||.|.|.+          ..+.|.|+++++..|..+|.+.+..
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~d----------~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVGE----------YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEECS----------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEeC----------CeEEEEECchhHHHHHHHHHHHHcC
Confidence            689999999999999999999999953          2377789999999999999965543

>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=98.40  E-value=7e-07  Score=67.07  Aligned_cols=76  Identities=17%  Similarity=0.370  Sum_probs=55.8

Q ss_pred             cEEEEEEEecCc------cceeecCCChHHHHHHHHhCCeEEEcCCCC--------C----CCC-CCceEEEEEe-eHHH
Q 019747           34 PTYIRFLVSNPL------AGAVIGKGGSTINDFQSQSGARIQLSRSHE--------F----FPG-TTDRIIMISG-TIDE   93 (336)
Q Consensus        34 ~~~~~i~ip~~~------vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~--------~----~~~-~~~r~i~I~G-~~~~   93 (336)
                      .++-+|+||.+.      +|.|||++|.++|+|+++|||+|.|.-...        .    .+. ...--|.|++ +.+.
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            467899999985      999999999999999999999999953210        0    010 1123355666 4678


Q ss_pred             HHHHHHHHHHHHHhhc
Q 019747           94 ILRAVDLVIDKLLTEL  109 (336)
Q Consensus        94 v~~A~~~I~~~i~~~~  109 (336)
                      +..|+.+|.+.|...+
T Consensus        82 ~~~A~~~i~~ll~~~~   97 (122)
T d1k1ga_          82 VKKAVEQIRNILKQGI   97 (122)
T ss_dssp             HHHHHHHHHHHHTTTT
T ss_pred             HHHHHHHHHHHHHhcC
Confidence            9999999997766543

>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=98.38  E-value=5.5e-07  Score=67.68  Aligned_cols=73  Identities=14%  Similarity=0.287  Sum_probs=57.2

Q ss_pred             eEEEEEeccC------cccceeccCCchHHHHHhHhCCeEEEccCCCCC------------C-CCcceEEEEEc-ChHhH
Q 019747          257 NSLTIGVADE------HIGFVVGRGGRNIMEISQISGARIKVSDRGDFF------------S-GTSERKVTISG-PQRSI  316 (336)
Q Consensus       257 ~~~~v~vp~~------~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~------------~-~~~~r~v~I~G-~~~~v  316 (336)
                      .+.+|.||-+      ++|.|||++|.++|+|+++|||+|.|-..+...            . ...+=.|.|++ +++.+
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            5677888865      589999999999999999999999997653210            0 11233577777 78899


Q ss_pred             HHHHHHHHHHHHh
Q 019747          317 RTAESMIMQKVAY  329 (336)
Q Consensus       317 ~~A~~~I~~~i~~  329 (336)
                      +.|+.+|..+|..
T Consensus        83 ~~A~~~i~~ll~~   95 (122)
T d1k1ga_          83 KKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999853

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=97.89  E-value=7.8e-06  Score=61.93  Aligned_cols=71  Identities=15%  Similarity=0.238  Sum_probs=52.9

Q ss_pred             EEEEEecc------CcccceeccCCchHHHHHhHhCCeEEEccCCCCCC---------------CCcceEEEEEcC-h--
Q 019747          258 SLTIGVAD------EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFS---------------GTSERKVTISGP-Q--  313 (336)
Q Consensus       258 ~~~v~vp~------~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~---------------~~~~r~v~I~G~-~--  313 (336)
                      ..+|.||-      +++|.|||++|.++|+|+++|||+|.|-.++...+               ..++=-|.|++. +  
T Consensus         3 ~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~~   82 (134)
T d2bl5a1           3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQN   82 (134)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCH
T ss_pred             ceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcHH
Confidence            45677774      58899999999999999999999999988753110               123445777774 2  


Q ss_pred             ---HhHHHHHHHHHHHHH
Q 019747          314 ---RSIRTAESMIMQKVA  328 (336)
Q Consensus       314 ---~~v~~A~~~I~~~i~  328 (336)
                         ..++.|..+|..+|.
T Consensus        83 ~a~~kl~~A~~~I~~lL~  100 (134)
T d2bl5a1          83 RAELKLKRAVEEVKKLLV  100 (134)
T ss_dssp             HHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHcC
Confidence               357889999988774

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=97.87  E-value=7.8e-06  Score=61.92  Aligned_cols=71  Identities=20%  Similarity=0.271  Sum_probs=50.6

Q ss_pred             EEEEEEEecC------ccceeecCCChHHHHHHHHhCCeEEEcCCCCC--------CC-------CCCceEEEEEeeH--
Q 019747           35 TYIRFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSRSHEF--------FP-------GTTDRIIMISGTI--   91 (336)
Q Consensus        35 ~~~~i~ip~~------~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~--------~~-------~~~~r~i~I~G~~--   91 (336)
                      +.-+|+||.+      ++|.|||++|.++|+|+++|||+|.|.-....        ..       -..+-=|.|++..  
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            5678999976      58999999999999999999999999653310        00       0123346777642  


Q ss_pred             ----HHHHHHHHHHHHHH
Q 019747           92 ----DEILRAVDLVIDKL  105 (336)
Q Consensus        92 ----~~v~~A~~~I~~~i  105 (336)
                          ..+..|+.+|...|
T Consensus        82 ~~a~~kl~~A~~~I~~lL   99 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLL   99 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHc
Confidence                24777888887554

>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=96.36  E-value=0.00095  Score=43.69  Aligned_cols=39  Identities=23%  Similarity=0.256  Sum_probs=36.0

Q ss_pred             EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCC
Q 019747           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS   73 (336)
Q Consensus        35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~   73 (336)
                      -.+.+.||.++.+..|||+|.+++-..+-||.+|.|...
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            478899999999999999999999999999999999654

>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=96.30  E-value=0.0015  Score=42.71  Aligned_cols=40  Identities=20%  Similarity=0.423  Sum_probs=36.7

Q ss_pred             ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccC
Q 019747          256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDR  295 (336)
Q Consensus       256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~  295 (336)
                      .....+.||.+.....|||+|.+++-..+.||.+|.|...
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            3567889999999999999999999999999999999775

>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=96.00  E-value=0.002  Score=42.25  Aligned_cols=37  Identities=27%  Similarity=0.349  Sum_probs=34.8

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcC
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSR   72 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~   72 (336)
                      .+.+.||.++.+..|||+|.+|+-..+-||.+|.|..
T Consensus        28 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          28 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            5889999999999999999999999999999999964

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=95.78  E-value=0.0033  Score=41.16  Aligned_cols=39  Identities=18%  Similarity=0.434  Sum_probs=35.8

Q ss_pred             eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccC
Q 019747          257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDR  295 (336)
Q Consensus       257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~  295 (336)
                      ....+.||.+..+..|||+|.+++-..+.||.+|.|...
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            467889999999999999999999999999999999753

>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=93.59  E-value=0.051  Score=37.00  Aligned_cols=59  Identities=8%  Similarity=0.019  Sum_probs=47.6

Q ss_pred             EEEEeccCcccceeccCCc-hHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHH
Q 019747          259 LTIGVADEHIGFVVGRGGR-NIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQK  326 (336)
Q Consensus       259 ~~v~vp~~~vg~IIGk~G~-~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~  326 (336)
                      +.+.||..++.+++|++++ .|+.|.+.+++.|.|-         .+-.|-|.| +++..-.+...|.+.
T Consensus         3 ~v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG---------~NGrIWi~~~~~~~~i~i~~aI~~~   63 (85)
T d2ja9a2           3 MIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIG---------LNGKIWVKCEELSNTLACYRTIMEC   63 (85)
T ss_dssp             EEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEE---------TTTEEEEECSSHHHHHHHHHHHHHH
T ss_pred             EEEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEe---------cCcEEEEECCCHHHHHHHHHHHHHH
Confidence            4578899999999999998 8999999999999994         356777888 567776666666443

>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=90.68  E-value=0.1  Score=35.41  Aligned_cols=61  Identities=7%  Similarity=0.084  Sum_probs=46.8

Q ss_pred             EEEEecCccceeecCCCh-HHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEe-eHHHHHHHHHHHHHHHHhh
Q 019747           38 RFLVSNPLAGAVIGKGGS-TINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVIDKLLTE  108 (336)
Q Consensus        38 ~i~ip~~~vg~iIGk~G~-~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G-~~~~v~~A~~~I~~~i~~~  108 (336)
                      -+-||..++..+||++++ .++.|.+.++|.|-|-.         +-.|-|.| +.+....+.+.|. .+.++
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~---------NGrIWi~~~~~~~~i~i~~aI~-~~e~~   66 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL---------NGKIWVKCEELSNTLACYRTIM-ECCQK   66 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET---------TTEEEEECSSHHHHHHHHHHHH-HHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec---------CcEEEEECCCHHHHHHHHHHHH-HHHHh
Confidence            356888899999999998 89999999999999953         34477777 4677666666665 44444

>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=90.44  E-value=0.043  Score=37.94  Aligned_cols=31  Identities=13%  Similarity=0.270  Sum_probs=26.6

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHhCC
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGA   66 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~   66 (336)
                      .++|.|....-|.|||++|..|++|++.-.-
T Consensus        36 ~i~I~I~tarPGivIGrkG~~I~~L~~~l~k   66 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGEKGRRIRELTAVVQK   66 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHHHHH
T ss_pred             eEEEEEEeCCCceeeccCchhHHHHHHHHHH
Confidence            3778999999999999999999999865543

>d2uubc1 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal domain {Thermus thermophilus [TaxId: 274]}

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: Thermus thermophilus [TaxId: 274]

Probab=83.83  E-value=0.12  Score=36.56  Aligned_cols=29  Identities=28%  Similarity=0.469  Sum_probs=25.6

Q ss_pred             EEEEEEecCccceeecCCChHHHHHHHHh
Q 019747           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQS   64 (336)
Q Consensus        36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~t   64 (336)
                      .+++.|....-|.|||++|+.|++|+++-
T Consensus        62 ~i~I~I~tarPG~iIGkkG~~i~~L~~~l   90 (105)
T d2uubc1          62 NVAVTVHVAKPGVVIGRGGERIRVLREEL   90 (105)
T ss_dssp             CEECCEEESCHHHHHCSTTSHHHHHHHHH
T ss_pred             cEEEEEEECCCceEEcCCchhHHHHHHHH
Confidence            37888889999999999999999998764

>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=82.41  E-value=0.18  Score=36.07  Aligned_cols=30  Identities=23%  Similarity=0.240  Sum_probs=24.4

Q ss_pred             cEEEEEEEecC-ccceeecCCChHHHHHHHH
Q 019747           34 PTYIRFLVSNP-LAGAVIGKGGSTINDFQSQ   63 (336)
Q Consensus        34 ~~~~~i~ip~~-~vg~iIGk~G~~Ik~I~~~   63 (336)
                      .+...|.|+.. +-+.|||++|++||+|..+
T Consensus        48 ~I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~   78 (113)
T d1egaa2          48 DINGLILVEREGQKKMVIGNKGAKIKTIGIE   78 (113)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHH
T ss_pred             EEEEEEEECCcchhhhhhcccchHHHHHHHH
Confidence            36677888876 6789999999999998744

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.58  E-value=0.28  Score=33.65  Aligned_cols=30  Identities=23%  Similarity=0.325  Sum_probs=25.2

Q ss_pred             EEEEEeccCcccceeccCCchHHHHHhHhC
Q 019747          258 SLTIGVADEHIGFVVGRGGRNIMEISQISG  287 (336)
Q Consensus       258 ~~~v~vp~~~vg~IIGk~G~~I~~I~~~sg  287 (336)
                      ..+|.|....-|.|||++|+.|++|++.-.
T Consensus        36 ~i~I~I~tarPGivIGrkG~~I~~L~~~l~   65 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGEKGRRIRELTAVVQ   65 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHHHH
T ss_pred             eEEEEEEeCCCceeeccCchhHHHHHHHHH
Confidence            467778888889999999999999876553