Citrus Sinensis ID: 022837

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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-
Protein Sequence
METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNEC
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHHcccEEEEcccccccccccEEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccEEEEEEEEcccccEEEccccHHHHHHHHHcccEEEEEEccccccccccEEEEEEccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccccEEccccccHHHHHHHHHcccEEEEccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccEEEEEEEEcccHHHHHccccHHHHHHHHHHccEEEEcccccccccccEEEEEEEEcHHHHHHHHHHHHHHHHHccccccccccccccccEEEEEccccccEEEccccccHHHHHHHcccEEEEccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
metnessyvpspdvhgkrstapvkslssdptekptyirflvsnplagavigkggstindfqsqsgariqlsrsheffpgttdRIIMISGTIDEILRAVDLVIDKLLTELhaedqaddvgtktklrlivpnsscgsiigKAGATIKSFMDDSQAVIKISRldhsyyglnDRLVTLTGTLDEQMRALELILLKLSEdtlysqtmtvpytyagvffsgfhgmpygavpppvpavphntaahygpnmggrkfqnnkvllpwplnpvGMLLIILIAQPIICHFSLSIYEEIRLNEC
Flexible Loop (DISEMBL)
metnessyvpspdvhgkrstapvkslssdptekpTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGAriqlsrsheffpgttDRIIMISGTIDEILRAVDLVIDKLLTELhaedqaddvgtktklrlivpnsscgsIIGKAGATIKSFMDDSQAVIKISrldhsyygLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNEC
Low Complexity Region (SEG)
METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGavpppvpavpHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNEC
Disordered region (IsUnstruct)
**********************************TYIRFLVSNPLAGAVIGKGGSTINDF******RIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIR****
Disordered Region (DISOPRED)
*************************************RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDK********************RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLD****GLNDRLVTLTGTLDEQMRALELILLKL**************************************************************LPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNEC
Disordered Region (DISEMBL)
*******************************EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNEC
Disordered Region (DISPRO)
*******************************EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTEL**********TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNEC
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhoooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
METNESSYVPSPDVHGKRSTAPVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNEC
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	291	2.2.26 [Sep-21-2011]
Q80WA4	474	RNA-binding protein Nova-	yes	no	0.621	0.381	0.344	6e-25
Q2PFW9	483	RNA-binding protein Nova-	N/A	no	0.570	0.343	0.344	9e-25
Q9UNW9	492	RNA-binding protein Nova-	no	no	0.639	0.378	0.351	4e-24
Q9JKN6	507	RNA-binding protein Nova-	no	no	0.580	0.333	0.318	6e-23
P51513	510	RNA-binding protein Nova-	no	no	0.580	0.331	0.309	4e-21
O19048	356	Poly(rC)-binding protein	no	no	0.553	0.452	0.288	6e-16
P60335	356	Poly(rC)-binding protein	no	no	0.553	0.452	0.288	6e-16
Q15365	356	Poly(rC)-binding protein	no	no	0.553	0.452	0.288	6e-16
Q5E9A3	356	Poly(rC)-binding protein	no	no	0.553	0.452	0.288	6e-16
P57722	371	Poly(rC)-binding protein	no	no	0.546	0.428	0.304	2e-14

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

 Score =  115 bits (287), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 70/203 (34%), Positives = 114/203 (56%), Gaps = 22/203 (10%)

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  RAVDLVIDKLLTEL---------------HAEDQADDVGTKTKLRLIVPNSSCGSIIGKA 140
            AV   I + + E+                     D +    ++++IVPNS+ G IIGK 
Sbjct: 109 NAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRI---KQVKIIVPNSTAGLIIGKG 165

Query: 141 GATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQ 200
           GAT+K+ M+ S A +++S+       L +R+VT++G  ++  +A+ELI+ K+ ED     
Sbjct: 166 GATVKAIMEQSGAWVQLSQKPDG-INLQERVVTVSGEPEQNRKAVELIIQKIQEDPQSGS 224

Query: 201 TMTVPYT--YAGVFFSGFHGMPY 221
            + + Y      V  S   G PY
Sbjct: 225 CLNISYANVTGPVANSNPTGFPY 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 =  114 bits (285), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 64/186 (34%), Positives = 109/186 (58%), Gaps = 20/186 (10%)

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  RAVDLVIDKLLTEL---------------HAEDQADDVGTKTKLRLIVPNSSCGSIIGKA 140
            AV   I + + E+                     D +    ++++IVPNS+ G IIGK 
Sbjct: 110 NAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRI---KQVKIIVPNSTAGLIIGKG 166

Query: 141 GATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQ 200
           GAT+K+ M+ S A +++S+       L +R+VT++G  ++  +A+ELI+ K+ ED     
Sbjct: 167 GATVKAIMEQSGAWVQLSQKPDG-INLQERVVTVSGEPEQNRKAVELIIQKIQEDPQSGS 225

Query: 201 TMTVPY 206
            + + Y
Sbjct: 226 CLNISY 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 (280), Expect = 4e-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  FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLVQGTA-EAL 92

Query: 96  RAVDLVIDKLLTEL-HAEDQADDVG-----------TKTKLRLIVPNSSCGSIIGKAGAT 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 =  108 bits (269), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 66/207 (31%), Positives = 111/207 (53%), Gaps = 38/207 (18%)

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 EQMRALELILLKLSEDTLYSQTMTVPY 206
           +  +A+ELI+ K+ ED      + + Y
Sbjct: 229 QNRKAVELIIQKIQEDPQSGSCLNISY 255

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|P51513|NOVA1_HUMAN RNA-binding protein Nova-1 OS=Homo sapiens GN=NOVA1 PE=1 SV=1

 Score =  102 bits (254), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 65/210 (30%), Positives = 111/210 (52%), Gaps = 41/210 (19%)

Query: 36  YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSR---SHEFFPGTTDRIIMISGTID 92
           +++ L+ +  AG++IGKGG TI   Q ++GA I+LS+   S +F+PGTT+R+ +I GT+ 
Sbjct: 51  FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKLSKSKDFYPGTTERVCLIQGTV- 109

Query: 93  EILRAVDLVIDKLLTEL----------------------------------HAEDQADDV 118
           E L AV   I + + E+                                       +D +
Sbjct: 110 EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRIKQTLPSSPTTTKSSPSDPM 169

Query: 119 GTK--TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG 176
            T    ++++IVPNS+ G IIGK GAT+K+ M+ S A +++S+       L +R+VT++G
Sbjct: 170 TTSRANQVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDG-INLQERVVTVSG 228

Query: 177 TLDEQMRALELILLKLSEDTLYSQTMTVPY 206
             ++  +A+ELI+ K+ ED      + + Y
Sbjct: 229 EPEQNRKAVELIIQKIQEDPQSGSCLNISY 258

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

Homo sapiens (taxid: 9606)

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

 Score = 84.7 bits (208), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 51/177 (28%), Positives = 97/177 (54%), Gaps = 16/177 (9%)

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----TERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPY 183

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 = 84.7 bits (208), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 51/177 (28%), Positives = 97/177 (54%), Gaps = 16/177 (9%)

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----TERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPY 183

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 = 84.7 bits (208), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 51/177 (28%), Positives = 97/177 (54%), Gaps = 16/177 (9%)

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----TERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPY 183

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 = 84.7 bits (208), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 51/177 (28%), Positives = 97/177 (54%), Gaps = 16/177 (9%)

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----TERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPY 183

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

Bos taurus (taxid: 9913)

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

 Score = 80.1 bits (196), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 53/174 (30%), Positives = 91/174 (52%), Gaps = 15/174 (8%)

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 206
           ++++   L +S     +R VT++GT D  ++ ++ I + + E     +  T+PY
Sbjct: 163 VQVAGDMLPNS----TERAVTISGTPDAIIQCVKQICVVMLESP--PKGATIPY 210

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

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	291
356535513	337	PREDICTED: RNA-binding protein Nova-1-li	0.859	0.741	0.653	2e-85
356576359	337	PREDICTED: RNA-binding protein Nova-1-li	0.859	0.741	0.637	7e-83
297810533	334	hypothetical protein ARALYDRAFT_487225 [	0.859	0.748	0.599	5e-82
30680512	334	binding to TOMV RNA 1L (long form) prote	0.859	0.748	0.599	1e-81
146336943	334	putative KH-domain containing protein [M	0.852	0.742	0.627	2e-81
224113143	334	predicted protein [Populus trichocarpa]	0.859	0.748	0.619	1e-79
359486525	309	PREDICTED: RNA-binding protein Nova-1-li	0.783	0.737	0.599	1e-76
296085941	357	unnamed protein product [Vitis vinifera]	0.783	0.638	0.599	2e-76
255583738	314	Far upstream element-binding protein, pu	0.786	0.729	0.584	1e-73
449449385	326	PREDICTED: RNA-binding protein Nova-2-li	0.742	0.662	0.660	2e-73

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

 Score =  321 bits (823), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 166/254 (65%), Positives = 199/254 (78%), Gaps = 4/254 (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-MGGRKFQNNK 252
            PN   G K QN+K
Sbjct: 239 RPNGAAGGKLQNSK 252

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 =  313 bits (801), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 162/254 (63%), Positives = 195/254 (76%), Gaps = 4/254 (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-MGGRKFQNNK 252
            PN   G K QN+K
Sbjct: 239 RPNGTAGGKLQNSK 252

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  310 bits (793), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 151/252 (59%), Positives = 196/252 (77%), Gaps = 2/252 (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 PNMGGRKFQNNK 252
           PN  G K+QN+K
Sbjct: 239 PNGSGGKYQNHK 250

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 =  309 bits (791), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 151/252 (59%), Positives = 196/252 (77%), Gaps = 2/252 (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 PNMGGRKFQNNK 252
           PN  G K+QN+K
Sbjct: 239 PNGSGGKYQNHK 250

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  308 bits (790), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 160/255 (62%), Positives = 196/255 (76%), Gaps = 7/255 (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 HYGPNMGGRKFQNNK 252
           +Y PN  G KFQN+K
Sbjct: 237 NYRPNGTGAKFQNSK 251

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 =  302 bits (774), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 156/252 (61%), Positives = 195/252 (77%), Gaps = 2/252 (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 PNMGGRKFQNNK 252
           PN    KFQ+NK
Sbjct: 239 PNGAAVKFQHNK 250

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  292 bits (747), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 151/252 (59%), Positives = 188/252 (74%), Gaps = 24/252 (9%)

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 PNMGGRKFQNNK 252
           PN  G KFQNNK
Sbjct: 217 PNGAGGKFQNNK 228

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 =  291 bits (745), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 151/252 (59%), Positives = 188/252 (74%), Gaps = 24/252 (9%)

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 PNMGGRKFQNNK 252
           PN  G KFQNNK
Sbjct: 265 PNGAGGKFQNNK 276

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 =  282 bits (722), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 148/253 (58%), Positives = 188/253 (74%), Gaps = 24/253 (9%)

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++Y                     AV +N+  +Y
Sbjct: 180 EQMRAIDLILSKLYDDPHYVQTMHAPFSY---------------------AVAYNS-MNY 217

Query: 240 GPNMGGRKFQNNK 252
           G N  G KFQNNK
Sbjct: 218 GANGAGGKFQNNK 230

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 =  281 bits (719), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 146/221 (66%), Positives = 180/221 (81%), Gaps = 5/221 (2%)

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 QMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPY 221
           QMRA +LI+ KLSED  Y+Q+M  P++Y     + F+ M Y
Sbjct: 180 QMRATDLIVSKLSEDPHYTQSMNYPFSYP----TSFNAMNY 216

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	291
TAIR|locus:2184362	334	BTR1L "AT5G04430" [Arabidopsis	0.859	0.748	0.591	2.1e-75
FB|FBgn0261552	605	ps "pasilla" [Drosophila melan	0.845	0.406	0.292	9.5e-27
ZFIN|ZDB-GENE-080211-1	473	nova2 "neuro-oncological ventr	0.635	0.391	0.336	6.8e-26
UNIPROTKB|F1NP95	345	NOVA1 "Uncharacterized protein	0.714	0.602	0.342	2.2e-25
RGD|621345	474	Nova1 "neuro-oncological ventr	0.714	0.438	0.346	3.3e-25
UNIPROTKB|F1LMZ7	474	Nova1 "RNA-binding protein Nov	0.714	0.438	0.346	4.3e-25
ZFIN|ZDB-GENE-060526-113	495	nova1 "neuro-oncological ventr	0.618	0.363	0.328	7e-25
UNIPROTKB|D3DS81	483	NOVA1 "Neuro-oncological ventr	0.714	0.430	0.342	8e-25
UNIPROTKB|F1PUD6	502	NOVA2 "Uncharacterized protein	0.652	0.378	0.362	2.7e-24
UNIPROTKB|F1MS84	464	NOVA2 "Uncharacterized protein	0.632	0.396	0.36	6.7e-24

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

 Score = 760 (272.6 bits), Expect = 2.1e-75, P = 2.1e-75
 Identities = 149/252 (59%), Positives = 194/252 (76%)

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 PNMGGRKFQNNK 252
             PN  G K+QN+K
Sbjct:   239 PNGSGGKYQNHK 250

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

FB|FBgn0261552 ps "pasilla" [Drosophila melanogaster (taxid:7227)]

 Score = 308 (113.5 bits), Expect = 9.5e-27, P = 9.5e-27
 Identities = 76/260 (29%), Positives = 133/260 (51%)

Query:    22 PVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTT 81
             P   L     E   +++ LV    +GA+IGKGG TI   Q  +GAR+++S+SH+F+PGTT
Sbjct:    86 PAFQLQQSFCETTYHMKILVPAVASGAIIGKGGETIASLQKDTGARVKMSKSHDFYPGTT 145

Query:    82 DRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKT------KLRLIVPNSSCGS 135
             +R+ +I+G+ + I+  ++ ++DK+  +    ++  D  +K       +++++VPNS+ G 
Sbjct:   146 ERVCLITGSTEAIMVVMEFIMDKIREKPDLTNKIVDTDSKQTQERDKQVKILVPNSTAGM 205

Query:   136 IIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED 195
             IIGK GA IK   ++S + ++IS+       L +R +T+ G  +    A ++IL K+ ED
Sbjct:   206 IIGKGGAFIKQIKEESGSYVQISQKPTDV-SLQERCITIIGDKENNKNACKMILSKIVED 264

Query:   196 TLYSQTMTVPYTYAGVFFSGFH--GMPYGXXXXXXXXXXHNTAAHYGPNMGGRKFQNNKV 253
                   + V Y       + F+  G PY            +  +  G  +GG    N+  
Sbjct:   265 PQSGTCLNVSYADVSGPVANFNPTGSPYATNQNAINSSTASLNSTLGTTIGGA---NSAA 321

Query:   254 LLPWPLNPVGMLLIILIAQP 273
              L   +N  G+ L I +  P
Sbjct:   322 SLL--VNGTGINLSINLGSP 339

GO:0003729 "mRNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

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

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

 Score = 296 (109.3 bits), Expect = 6.8e-26, P = 6.8e-26
 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|F1NP95 NOVA1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 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:     6 PDSRKRPLEAPPEAGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGAT 65

Query:    68 IQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAE----DQADDVGTKT- 122
             I+LS+S +F+PGTT+R+ +I GT+ E L AV   I + + E+       +    +  +T 
Sbjct:    66 IKLSKSKDFYPGTTERVCLIQGTV-EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTT 124

Query:   123 -------KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT 175
                    ++++IVPNS+ G IIGK GAT+K+ M+ S A +++S+       L +R+VT++
Sbjct:   125 VNPDRIKQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGI-NLQERVVTVS 183

Query:   176 GTLDEQMRALELILLKLSEDTLYSQTMTVPYT-YAG-VFFSGFHGMPY 221
             G  ++  +A+ELI+ K+ ED      + + Y    G V  S   G PY
Sbjct:   184 GEPEQNRKAVELIIQKIQEDPQSGSCLNISYANVTGPVANSNPTGSPY 231

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 290 (107.1 bits), Expect = 3.3e-25, P = 3.3e-25
 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 = 4.3e-25, P = 4.3e-25
 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

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

 Score = 288 (106.4 bits), Expect = 7.0e-25, P = 7.0e-25
 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|D3DS81 NOVA1 "Neuro-oncological ventral antigen 1, isoform CRA_a" [Homo sapiens (taxid:9606)]

 Score = 287 (106.1 bits), Expect = 8.0e-25, P = 8.0e-25
 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

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

 Score = 283 (104.7 bits), Expect = 2.7e-24, P = 2.7e-24
 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 = 6.7e-24, P = 6.7e-24
 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

---

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: fgenesh2_kg.6__359__AT5G04430.2 annotation not avaliable (334 aa) (Arabidopsis lyrata)

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	291
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	6e-20
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	3e-18
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	5e-14
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	3e-13
pfam00013	59	pfam00013, KH_1, KH domain	8e-11
pfam13014	42	pfam13014, KH_3, KH domain	2e-10
smart00322	68	smart00322, KH, K homology RNA-binding domain	4e-10
pfam00013	59	pfam00013, KH_1, KH domain	5e-10
smart00322	68	smart00322, KH, K homology RNA-binding domain	8e-10
pfam13014	42	pfam13014, KH_3, KH domain	2e-07
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	2e-04
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	2e-04

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

 Score = 81.0 bits (201), Expect = 6e-20
 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 = 76.4 bits (189), Expect = 3e-18
 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 = 65.3 bits (160), Expect = 5e-14
 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 = 63.0 bits (154), Expect = 3e-13
 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 = 56.4 bits (137), Expect = 8e-11
 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|221895 pfam13014, KH_3, KH domain

 Score = 54.9 bits (133), Expect = 2e-10
 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 = 54.6 bits (132), Expect = 4e-10
 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|215657 pfam00013, KH_1, KH domain

 Score = 54.1 bits (131), Expect = 5e-10
 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|197652 smart00322, KH, K homology RNA-binding domain

 Score = 53.8 bits (130), Expect = 8e-10
 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|221895 pfam13014, KH_3, KH domain

 Score = 46.4 bits (111), Expect = 2e-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 = 38.6 bits (91), Expect = 2e-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 = 38.3 bits (90), Expect = 2e-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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	291
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	100.0
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.97
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.96
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.9
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.87
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.85
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.79
PRK13763	180	putative RNA-processing protein; Provisional	99.76
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.57
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.56
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.52
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.4
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.4
PRK13763	180	putative RNA-processing protein; Provisional	99.39
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.38
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.37
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.36
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.34
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.34
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.31
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.28
PF13014	43	KH_3: KH domain	99.15
PF13014	43	KH_3: KH domain	99.13
COG1094	194	Predicted RNA-binding protein (contains KH domains	99.1
smart00322	69	KH K homology RNA-binding domain.	99.1
smart00322	69	KH K homology RNA-binding domain.	99.05
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.77
KOG2113	394	consensus Predicted RNA binding protein, contains	98.77
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.77
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.65
PRK08406	140	transcription elongation factor NusA-like protein;	98.64
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.57
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.49
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.43
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.24
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	98.18
KOG0119	554	consensus Splicing factor 1/branch point binding p	98.09
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.94
KOG2113	394	consensus Predicted RNA binding protein, contains	97.91
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.86
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.8
COG0195	190	NusA Transcription elongation factor [Transcriptio	97.71
PRK08406	140	transcription elongation factor NusA-like protein;	97.7
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	97.68
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.68
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	97.61
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.58
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.57
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.47
PRK00106	535	hypothetical protein; Provisional	97.39
KOG2814	345	consensus Transcription coactivator complex, P50 c	97.38
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	97.37
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	97.37
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	97.36
PRK12704	520	phosphodiesterase; Provisional	97.35
COG1094	194	Predicted RNA-binding protein (contains KH domains	97.3
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	97.19
TIGR01953	341	NusA transcription termination factor NusA. This m	97.12
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.11
PRK12327	362	nusA transcription elongation factor NusA; Provisi	97.1
KOG2814	345	consensus Transcription coactivator complex, P50 c	97.06
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	97.05
PRK00468	75	hypothetical protein; Provisional	97.03
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.9
PRK02821	77	hypothetical protein; Provisional	96.86
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.86
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.83
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.72
COG1837	76	Predicted RNA-binding protein (contains KH domain)	96.72
PRK09202	470	nusA transcription elongation factor NusA; Validat	96.61
PRK12705	508	hypothetical protein; Provisional	96.6
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.55
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	96.54
PRK01064	78	hypothetical protein; Provisional	96.5
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.43
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	96.41
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.33
PRK02821	77	hypothetical protein; Provisional	96.33
PRK00468	75	hypothetical protein; Provisional	96.32
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.92
PRK12704	520	phosphodiesterase; Provisional	95.63
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.55
PRK01064	78	hypothetical protein; Provisional	95.5
PRK00106	535	hypothetical protein; Provisional	95.48
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	95.48
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	95.01
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	94.48
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	94.42
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	94.37
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	94.12
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	93.81
COG1855	604	ATPase (PilT family) [General function prediction	93.69
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	93.54
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	93.43
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	93.1
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	93.08
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	93.08
KOG2874	356	consensus rRNA processing protein [Translation, ri	92.93
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	92.88
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	92.8
PRK13764	602	ATPase; Provisional	92.6
COG1782	637	Predicted metal-dependent RNase, consists of a met	92.41
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	92.02
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	92.01
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	91.95
PRK12705	508	hypothetical protein; Provisional	91.78
COG0195	190	NusA Transcription elongation factor [Transcriptio	90.61
COG1855	604	ATPase (PilT family) [General function prediction	90.58
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	90.57
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	90.56
KOG2874	356	consensus rRNA processing protein [Translation, ri	90.28
PRK12328	374	nusA transcription elongation factor NusA; Provisi	90.02
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	89.82
PRK06418	166	transcription elongation factor NusA-like protein;	89.81
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	89.71
TIGR01953	341	NusA transcription termination factor NusA. This m	89.41
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	89.08
COG5166	657	Uncharacterized conserved protein [Function unknow	89.07
PRK13764	602	ATPase; Provisional	89.0
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	87.52
PRK12327	362	nusA transcription elongation factor NusA; Provisi	86.46
PRK06418	166	transcription elongation factor NusA-like protein;	86.18
PRK09202	470	nusA transcription elongation factor NusA; Validat	86.09
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	85.19
TIGR00436	270	era GTP-binding protein Era. Era is an essential G	84.69
PRK12329	449	nusA transcription elongation factor NusA; Provisi	84.19
PRK15494	339	era GTPase Era; Provisional	84.18
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	84.14
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	82.12
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	81.65
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	81.59
COG1159	298	Era GTPase [General function prediction only]	80.88
KOG1423	379	consensus Ras-like GTPase ERA [Cell cycle control,	80.39

>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=3.6e-40  Score=287.50  Aligned_cols=268  Identities=28%  Similarity=0.429  Sum_probs=217.9

Q ss_pred             CCCCCCCCCCcCCCCCCCCCCCCCCCCCCCc-EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCc
Q 022837            4 NESSYVPSPDVHGKRSTAPVKSLSSDPTEKP-TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTD   82 (291)
Q Consensus         4 ~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~e   82 (291)
                      .++...-++.++.++++.+....+.+..++. +++|||||+..+|.||||+|++|.+||++|||+|++++..|++|+++|
T Consensus         7 ~d~~~~~s~kr~~~a~pe~~~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTe   86 (402)
T KOG2191|consen    7 IDSDAPDSRKRPLEAPPEPGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTE   86 (402)
T ss_pred             ccCCCCCCccccccCCCCccccccccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccc
Confidence            4555555667777777766666666665555 999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCC------CCceEEEEEecCCccceeeccCChhHHHHHHhccceEE
Q 022837           83 RIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDV------GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIK  156 (291)
Q Consensus        83 r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~------~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~  156 (291)
                      |+|.|+|+.+++....+.|.|+|++..+..+...+.      +....++++||+..+|.||||+|.+||.|++++||+|+
T Consensus        87 Rvcli~Gt~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iq  166 (402)
T KOG2191|consen   87 RVCLIQGTVEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQ  166 (402)
T ss_pred             eEEEEeccHHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceE
Confidence            999999999999999999999999986654321211      22245999999999999999999999999999999999


Q ss_pred             EecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCC
Q 022837          157 ISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTA  236 (291)
Q Consensus       157 i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~  236 (291)
                      |++.++...+..+|+|++.|++++..+|..+|+++|.|||++..++|.+|.|...        |..-..|        .+
T Consensus       167 isPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsG--------pvaNsnP--------tG  230 (402)
T KOG2191|consen  167 ISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSG--------PVANSNP--------TG  230 (402)
T ss_pred             ecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccC--------cccccCC--------CC
Confidence            9986665667789999999999999999999999999999999999977665421        1111111        01


Q ss_pred             CCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehccccccceEEeec
Q 022837          237 AHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNE  290 (291)
Q Consensus       237 ~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tga~i~~~~  290 (291)
                      .+|+.. .+..+...+.++.+|+.++|..-|.  |+.++-.+...+|+.|.+.+
T Consensus       231 spya~~-~~~~~astas~~sva~~~iG~a~ga--G~~~~a~l~~~~G~l~~itq  281 (402)
T KOG2191|consen  231 SPYAYQ-AHVLPASTASTISVAAGLIGGANGA--GGAFGAALSGFTGALIAITQ  281 (402)
T ss_pred             CCCCCC-Cccccccchhhcccccccccccccc--ccccceeeecccccceeecc
Confidence            111111 1224445568889999999999999  99999999999999887754

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

Probab=100.00  E-value=6.6e-36  Score=279.30  Aligned_cols=215  Identities=27%  Similarity=0.335  Sum_probs=177.1

Q ss_pred             CCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhc
Q 022837           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH  110 (291)
Q Consensus        31 ~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~  110 (291)
                      ....++.+|+||.+.+|+||||+|++||+|++++||++.+..++....+ ..+.+.|+|.++.|+.|+.++.+.|.++..
T Consensus       135 ~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-~~KplritGdp~~ve~a~~lV~dil~e~~~  213 (600)
T KOG1676|consen  135 GSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-ADKPLRITGDPDKVEQAKQLVADILREEDD  213 (600)
T ss_pred             CccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-CCCceeecCCHHHHHHHHHHHHHHHHhccc
Confidence            3678999999999999999999999999999999999999987654333 678999999999999999999999986522


Q ss_pred             ccc-----ccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHH
Q 022837          111 AED-----QADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRAL  185 (291)
Q Consensus       111 ~~~-----~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~  185 (291)
                      ...     .........+.++.||...||.||||+|++||+|+.+||++|+|.++++  +.+.||.+.|.|++++|++|.
T Consensus       214 ~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~--p~speR~~~IiG~~d~ie~Aa  291 (600)
T KOG1676|consen  214 EVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD--PSSPERPAQIIGTVDQIEHAA  291 (600)
T ss_pred             CCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC--CCCccceeeeecCHHHHHHHH
Confidence            110     1122234458999999999999999999999999999999999999765  367899999999999999999


Q ss_pred             HHHHHHHhcCcccCCCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCccee
Q 022837          186 ELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGML  265 (291)
Q Consensus       186 ~~I~~~l~e~~~~~~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~i  265 (291)
                      ++|.++|++.......        +|    ..|.|.                           .....+|.||++++|.|
T Consensus       292 ~lI~eii~~~~~~~~~--------~~----~~G~P~---------------------------~~~~fy~~VPa~KcGLv  332 (600)
T KOG1676|consen  292 ELINEIIAEAEAGAGG--------GM----GGGAPG---------------------------LVAQFYMKVPADKCGLV  332 (600)
T ss_pred             HHHHHHHHHHhccCCC--------Cc----CCCCcc---------------------------ceeeEEEeccccccccc
Confidence            9999999985432100        00    001110                           00158999999999999


Q ss_pred             EEeecCccceehccccccceEEee
Q 022837          266 LIILIAQPIICHFSLSIYEEIRLN  289 (291)
Q Consensus       266 IG~~~gg~~ik~~~~~tga~i~~~  289 (291)
                      |||  ||++||+|.+++||.+.+.
T Consensus       333 IGr--GGEtIK~in~qSGA~~el~  354 (600)
T KOG1676|consen  333 IGR--GGETIKQINQQSGARCELS  354 (600)
T ss_pred             cCC--CccchhhhcccCCcccccc
Confidence            999  9999999999999999874

>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=5.8e-37  Score=274.72  Aligned_cols=245  Identities=23%  Similarity=0.321  Sum_probs=189.9

Q ss_pred             CCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhh
Q 022837           30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTEL  109 (291)
Q Consensus        30 ~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~  109 (291)
                      .....+++|+|||..++|.||||.|.|||.|.+.|.|+|+|.+..+  .|..|+.++|-|+++...+|+++|++.|.++.
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            3456789999999999999999999999999999999999998765  47889999999999999999999999999884


Q ss_pred             ccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 022837          110 HAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL  189 (291)
Q Consensus       110 ~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~  189 (291)
                      ...    +...++.++++.++++||+||||.|.+||+|+.+||++|.|++-.+...-..||+++++|+.++|..|..+|+
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    2235688999999999999999999999999999999999998444333346999999999999999999999


Q ss_pred             HHHhcCcccC-CCCC-CCccCCCcccC------CCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCeEEEeecCC
Q 022837          190 LKLSEDTLYS-QTMT-VPYTYAGVFFS------GFHGMPYGAVPPPVPAVPHNTAAHYGPNM-GGRKFQNNKVLLPWPLN  260 (291)
Q Consensus       190 ~~l~e~~~~~-~~~~-~~~~~~g~~~~------~~~g~p~~~~~p~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~iP~~  260 (291)
                      .+|+++.+.+ ..++ ....-+++..+      +.++++++..+|.+   .+|    .++.. .+..+....+.|+||+.
T Consensus       348 kKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~---v~~----a~p~~~~hq~pe~e~V~~fiP~~  420 (584)
T KOG2193|consen  348 KKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSP---VTF----ASPYPLFHQNPEQEQVRMFIPAQ  420 (584)
T ss_pred             HHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCc---ccc----CCCchhhhcCcchhheeeeccHH
Confidence            9999986544 2222 12122333222      12222222111111   111    11111 12344566799999999


Q ss_pred             CcceeEEeecCccceehccccccceEEee
Q 022837          261 PVGMLLIILIAQPIICHFSLSIYEEIRLN  289 (291)
Q Consensus       261 ~vG~iIG~~~gg~~ik~~~~~tga~i~~~  289 (291)
                      .||+|||+  .|.+||+|.+++||.|+|.
T Consensus       421 ~vGAiIGk--kG~hIKql~RfagASiKIa  447 (584)
T KOG2193|consen  421 AVGAIIGK--KGQHIKQLSRFAGASIKIA  447 (584)
T ss_pred             HHHHHHhh--cchhHHHHHHhccceeeec
Confidence            99999999  9999999999999999985

>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=2.3e-32  Score=232.74  Aligned_cols=241  Identities=24%  Similarity=0.332  Sum_probs=183.7

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccc
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAE  112 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~  112 (291)
                      ..+.+|+|+.+..+|+||||+|++||.|+.++++.|+|++.+     ..+|+++|+...+.|.+-++.|+-.|.+.+.  
T Consensus        46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~-----~peri~tisad~~ti~~ilk~iip~lee~f~--  118 (390)
T KOG2192|consen   46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS-----GPERILTISADIETIGEILKKIIPTLEEGFQ--  118 (390)
T ss_pred             cceeEEEEEecccccceeccccccHHHHhhhccceeeccCCC-----CCceeEEEeccHHHHHHHHHHHhhhhhhCCC--
Confidence            358999999999999999999999999999999999998764     5799999999999888888877766655432  


Q ss_pred             cccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 022837          113 DQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL  192 (291)
Q Consensus       113 ~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l  192 (291)
                           ....+.++|+|+.+++|.|||++|+.||+|+++..|+++|...  .++.+++|+|.|.|.+..|..+++.|++.|
T Consensus       119 -----~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~--c~p~stdrv~l~~g~~k~v~~~i~~il~~i  191 (390)
T KOG2192|consen  119 -----LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE--CCPHSTDRVVLIGGKPKRVVECIKIILDLI  191 (390)
T ss_pred             -----CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc--cCCCCcceEEEecCCcchHHHHHHHHHHHh
Confidence                 2455899999999999999999999999999999999999863  568899999999999999999999999999


Q ss_pred             hcCcccC------CC-CCCCccCCCccc--CCCCCCCCCCCCCC-C--CCCCC---------------------------
Q 022837          193 SEDTLYS------QT-MTVPYTYAGVFF--SGFHGMPYGAVPPP-V--PAVPH---------------------------  233 (291)
Q Consensus       193 ~e~~~~~------~~-~~~~~~~~g~~~--~~~~g~p~~~~~p~-~--~~~~~---------------------------  233 (291)
                      .|.|.+.      +. ....+.|+|..+  ....+.|.+.+.+. +  |++++                           
T Consensus       192 ~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~det  271 (390)
T KOG2192|consen  192 SESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADET  271 (390)
T ss_pred             hcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCcccccccccccccc
Confidence            9987533      11 123456776532  22222222111110 0  01100                           


Q ss_pred             ----------------CC---CCC--------CCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehccccccceE
Q 022837          234 ----------------NT---AAH--------YGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEI  286 (291)
Q Consensus       234 ----------------~~---~~~--------~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tga~i  286 (291)
                                      |.   +..        ||+.+.. ...-.+.++.||.++-|.||||  ||..||||++++||+|
T Consensus       272 w~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdl-GGPitTaQvtip~dlggsiigk--ggqri~~ir~esGA~I  348 (390)
T KOG2192|consen  272 WPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDL-GGPITTAQVTIPKDLGGSIIGK--GGQRIKQIRHESGASI  348 (390)
T ss_pred             CCCcCCCcCccccccccCCCCCCCCCccccccccccCCC-CCceeeeeEecccccCcceecc--cchhhhhhhhccCceE
Confidence                            00   000        1111111 1223458999999999999999  9999999999999999


Q ss_pred             Eeec
Q 022837          287 RLNE  290 (291)
Q Consensus       287 ~~~~  290 (291)
                      +|.+
T Consensus       349 kide  352 (390)
T KOG2192|consen  349 KIDE  352 (390)
T ss_pred             EecC
Confidence            9976

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

Probab=100.00  E-value=3.4e-32  Score=254.45  Aligned_cols=214  Identities=23%  Similarity=0.319  Sum_probs=171.4

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccc
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAE  112 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~  112 (291)
                      ..++.+..||...||+||||+|+.|..|+.++||+|++.....   +..+|.+.++|.+++|+.|+.||-+++.+.....
T Consensus        52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s---~~~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~  128 (600)
T KOG1676|consen   52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPS---GIGYRSVDLTGSPENVEVAKQLIGEVVSRGRPPG  128 (600)
T ss_pred             cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCC---CcccccccccCCcccHHHHHHhhhhhhhccCCCC
Confidence            4467889999999999999999999999999999999876542   4578999999999999999999987765542111


Q ss_pred             -cccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 022837          113 -DQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLK  191 (291)
Q Consensus       113 -~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~  191 (291)
                       -..+.....++.+|+||++.||+||||+|++||+|++++||++.+..+.....+ .++.+.|+|++++|+.|..||.++
T Consensus       129 ~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-~~KplritGdp~~ve~a~~lV~di  207 (600)
T KOG1676|consen  129 GFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-ADKPLRITGDPDKVEQAKQLVADI  207 (600)
T ss_pred             CccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-CCCceeecCCHHHHHHHHHHHHHH
Confidence             011122456899999999999999999999999999999999999885543333 789999999999999999999999


Q ss_pred             HhcCcccCCCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecC
Q 022837          192 LSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIA  271 (291)
Q Consensus       192 l~e~~~~~~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~g  271 (291)
                      |+|.-.....     +                       ..+|++         +.....+.+|.||...||.||||  |
T Consensus       208 l~e~~~~~~g-----~-----------------------~~~~g~---------~~g~~~~~~V~VPr~~VG~IIGk--g  248 (600)
T KOG1676|consen  208 LREEDDEVPG-----S-----------------------GGHAGV---------RGGGSATREVKVPRSKVGIIIGK--G  248 (600)
T ss_pred             HHhcccCCCc-----c-----------------------ccccCc---------CccccceeEEeccccceeeEEec--C
Confidence            9973211100     0                       001111         01122369999999999999999  9


Q ss_pred             ccceehccccccceEEee
Q 022837          272 QPIICHFSLSIYEEIRLN  289 (291)
Q Consensus       272 g~~ik~~~~~tga~i~~~  289 (291)
                      |++||.|+.+||++|||-
T Consensus       249 GE~IKklq~etG~KIQfk  266 (600)
T KOG1676|consen  249 GEMIKKLQNETGAKIQFK  266 (600)
T ss_pred             chHHHHHhhccCceeEee
Confidence            999999999999999984

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

Probab=99.97  E-value=1.3e-30  Score=246.49  Aligned_cols=241  Identities=26%  Similarity=0.372  Sum_probs=180.8

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec---------CHHHHHHHHHHHHH
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG---------TIDEILRAVDLVID  103 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G---------~~~~v~~A~~~I~~  103 (291)
                      ...++|+||+...+|.||||+|.+||+|+++|.++|+|...   .+++.+|+++|+|         ..+++.+|.++|..
T Consensus        41 ~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~---~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~  117 (485)
T KOG2190|consen   41 ETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNES---LPGCPERIITITGNRVELNLSPATDALFKAFDMIVF  117 (485)
T ss_pred             CcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecC---CCCCCcceEEEecccccccCCchHHHHHHHHHHHhh
Confidence            33449999999999999999999999999999999999754   5799999999999         99999999999997


Q ss_pred             HHhhhhccccccC-CCCC-ceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHH
Q 022837          104 KLLTELHAEDQAD-DVGT-KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQ  181 (291)
Q Consensus       104 ~i~~~~~~~~~~~-~~~~-~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v  181 (291)
                      .+.++.....+.. +.+. .++++|+||.+++|+||||+|+.||+|+++|||+|++.++  .+|...+|.|+|.|.+++|
T Consensus       118 ~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~lP~ster~V~IsG~~~av  195 (485)
T KOG2190|consen  118 KLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD--MLPNSTERAVTISGEPDAV  195 (485)
T ss_pred             cccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC--CCCcccceeEEEcCchHHH
Confidence            7664433332222 2222 4899999999999999999999999999999999999985  6788899999999999999


Q ss_pred             HHHHHHHHHHHhcCcccCCCCC-CCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCeEEEeecC
Q 022837          182 MRALELILLKLSEDTLYSQTMT-VPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAH-YGPNMGGRKFQNNKVLLPWPL  259 (291)
Q Consensus       182 ~~A~~~I~~~l~e~~~~~~~~~-~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~-~~~~~~~~~~~~~~~~i~iP~  259 (291)
                      .+|+..|..+|.+++...+... ....|..   +..++.|.-   |     ..+..+. +...+........-..+.+|.
T Consensus       196 ~~al~~Is~~L~~~~~~~~~~~~st~~y~P---~~~~~~~~~---~-----s~~~~~~~~~~~~~~~~~~e~~~~~~~p~  264 (485)
T KOG2190|consen  196 KKALVQISSRLLENPPRSPPPLVSTIPYRP---SASQGGPVL---P-----STAQTSPDAHPFGGIVPEEELVFKLICPS  264 (485)
T ss_pred             HHHHHHHHHHHHhcCCcCCCCCCCcccCCC---cccccCccc---c-----ccccCCcccccccccccchhhhhhhcCch
Confidence            9999999999999764421100 0111110   000000000   0     0000000 001111112222336789999


Q ss_pred             CCcceeEEeecCccceehccccccceEEeecC
Q 022837          260 NPVGMLLIILIAQPIICHFSLSIYEEIRLNEC  291 (291)
Q Consensus       260 ~~vG~iIG~~~gg~~ik~~~~~tga~i~~~~~  291 (291)
                      +.++.|||+  +|..|+.+++++|+.|.++++
T Consensus       265 ~~~~~v~g~--~~~~i~~l~~~~~~~i~v~~~  294 (485)
T KOG2190|consen  265 DKVGSVIGK--GGLVIRALRNETGASISVGDS  294 (485)
T ss_pred             hhceeeecC--CCccchhhhhhcCCceEeccc
Confidence            999999999  999999999999999999874

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

Probab=99.96  E-value=5.7e-30  Score=229.89  Aligned_cols=213  Identities=22%  Similarity=0.361  Sum_probs=181.1

Q ss_pred             CCCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           29 DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        29 ~~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      +....++++|++..+..||++|||.|.+||+|+++||++|.|++-.+..-...||.|+|.|+.++|.+|..+|+.+|.+.
T Consensus       274 ~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~  353 (584)
T KOG2193|consen  274 DKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLREC  353 (584)
T ss_pred             cchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHH
Confidence            44567899999999999999999999999999999999999998777655668999999999999999999999999887


Q ss_pred             hccccc-------------------------cC-------------------CCCCceEEEEEecCCccceeeccCChhH
Q 022837          109 LHAEDQ-------------------------AD-------------------DVGTKTKLRLIVPNSSCGSIIGKAGATI  144 (291)
Q Consensus       109 ~~~~~~-------------------------~~-------------------~~~~~~~~~i~VP~~~vg~IIGk~G~~I  144 (291)
                      ++.+-.                         ..                   .......++|+||...+|+|||++|.+|
T Consensus       354 yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hI  433 (584)
T KOG2193|consen  354 YENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHI  433 (584)
T ss_pred             HhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhH
Confidence            554300                         00                   0124467899999999999999999999


Q ss_pred             HHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCCCCCCccCCCcccCCCCCCCCCCC
Q 022837          145 KSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAV  224 (291)
Q Consensus       145 k~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~~g~~~~~~~g~p~~~~  224 (291)
                      |.|.+.+||.|+|.+.+  .++..+|.|+|+|++++..+|.-.|..+|.|...+.+.-.                     
T Consensus       434 Kql~RfagASiKIappE--~pdvseRMViItGppeaqfKAQgrifgKikEenf~~Pkee---------------------  490 (584)
T KOG2193|consen  434 KQLSRFAGASIKIAPPE--IPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFLPKEE---------------------  490 (584)
T ss_pred             HHHHHhccceeeecCCC--CCCcceeEEEecCChHHHHhhhhhhhhhhhhhccCCchhh---------------------
Confidence            99999999999998844  3567899999999999999999999999998543321100                     


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehccccccceEEeec
Q 022837          225 PPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNE  290 (291)
Q Consensus       225 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tga~i~~~~  290 (291)
                                              =--.+.+.||...+|.||||  ||.+++.|+.-|+|.+.|++
T Consensus       491 ------------------------vklethirVPs~~aGRvIGK--GGktVnELQnlt~AeV~vPr  530 (584)
T KOG2193|consen  491 ------------------------VKLETHIRVPSSAAGRVIGK--GGKTVNELQNLTSAEVVVPR  530 (584)
T ss_pred             ------------------------heeeeeeeccchhhhhhhcc--ccccHHHHhccccceEEccc
Confidence                                    00127889999999999999  99999999999999999986

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

Probab=99.90  E-value=2.4e-23  Score=197.22  Aligned_cols=201  Identities=26%  Similarity=0.414  Sum_probs=153.7

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcccc
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAED  113 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~  113 (291)
                      ++++|||||..++|.||||+|+.||+|+++|||+|++..+  .+|.+++|.|+|.|.++.|.+|+..|...|.+......
T Consensus       137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~  214 (485)
T KOG2190|consen  137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD--MLPNSTERAVTISGEPDAVKKALVQISSRLLENPPRSP  214 (485)
T ss_pred             ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC--CCCcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCC
Confidence            6899999999999999999999999999999999999985  78999999999999999999999999999988531110


Q ss_pred             c--------------cC-------------------CCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837          114 Q--------------AD-------------------DVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL  160 (291)
Q Consensus       114 ~--------------~~-------------------~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  160 (291)
                      .              ..                   ....+...++..|.+.++.|||++|..|+.|+.++|+.|.+...
T Consensus       215 ~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~  294 (485)
T KOG2190|consen  215 PPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDS  294 (485)
T ss_pred             CCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccc
Confidence            0              00                   00123346788999999999999999999999999999999763


Q ss_pred             CCCCCCCCceEEEEEcC--HHHH----HHHHHHHHHHHhcCcccCCCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCC
Q 022837          161 DHSYYGLNDRLVTLTGT--LDEQ----MRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHN  234 (291)
Q Consensus       161 ~~~~~~~~er~V~I~G~--~~~v----~~A~~~I~~~l~e~~~~~~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~  234 (291)
                      .      .+++|+++..  ++..    ..|..++...+.+.                                       
T Consensus       295 ~------~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~---------------------------------------  329 (485)
T KOG2190|consen  295 R------TDRIVTISARENPEDRYSMAQEALLLVQPRISEN---------------------------------------  329 (485)
T ss_pred             c------CcceeeeccccCcccccccchhhhhhcccccccc---------------------------------------
Confidence            2      2277777653  1110    11111111111110                                       


Q ss_pred             CCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehccccccceEEeecC
Q 022837          235 TAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNEC  291 (291)
Q Consensus       235 ~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tga~i~~~~~  291 (291)
                             .+... ....+.+|+||++.+|+||||  +|.+|..|++.|||.|+|.++
T Consensus       330 -------~~~~~-~~~v~~~l~vps~~igciiGk--~G~~iseir~~tgA~I~I~~~  376 (485)
T KOG2190|consen  330 -------AGDDL-TQTVTQRLLVPSDLIGCIIGK--GGAKISEIRQRTGASISILNK  376 (485)
T ss_pred             -------ccccc-cceeeeeeccCccccceeecc--cccchHHHHHhcCCceEEccc
Confidence                   00011 334568999999999999999  999999999999999999753

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

Probab=99.87  E-value=1.8e-21  Score=166.32  Aligned_cols=160  Identities=31%  Similarity=0.540  Sum_probs=136.7

Q ss_pred             CCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhh
Q 022837           30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTEL  109 (291)
Q Consensus        30 ~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~  109 (291)
                      ....++.+||||+.+++|.|||++|+.||+|++++.+++++..  +..|++++|+|.+.|.+.+|..+++.|++.|.+..
T Consensus       118 ~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift--~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~p  195 (390)
T KOG2192|consen  118 QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT--ECCPHSTDRVVLIGGKPKRVVECIKIILDLISESP  195 (390)
T ss_pred             CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh--ccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCC
Confidence            3445689999999999999999999999999999999999975  67899999999999999999999999998775441


Q ss_pred             ccc--------------c---------c---------------------------------c------------------
Q 022837          110 HAE--------------D---------Q---------------------------------A------------------  115 (291)
Q Consensus       110 ~~~--------------~---------~---------------------------------~------------------  115 (291)
                      -..              +         +                                 .                  
T Consensus       196 ikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~sa  275 (390)
T KOG2192|consen  196 IKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSA  275 (390)
T ss_pred             cCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCc
Confidence            000              0         0                                 0                  


Q ss_pred             ---------------------------------CCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCC
Q 022837          116 ---------------------------------DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDH  162 (291)
Q Consensus       116 ---------------------------------~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~  162 (291)
                                                       .......+.++.||.+.-|.||||+|+.|++|+.++||.|++..   
T Consensus       276 idtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide---  352 (390)
T KOG2192|consen  276 IDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE---  352 (390)
T ss_pred             CCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC---
Confidence                                             00134568899999999999999999999999999999999976   


Q ss_pred             CCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          163 SYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       163 ~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      .+.++.||+++|+|+.++++.|..+++..++.
T Consensus       353 pleGsedrIitItGTqdQIqnAQYLlQn~Vkq  384 (390)
T KOG2192|consen  353 PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ  384 (390)
T ss_pred             cCCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence            44577899999999999999999999988874

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

Probab=99.85  E-value=8.3e-21  Score=166.49  Aligned_cols=132  Identities=23%  Similarity=0.293  Sum_probs=112.6

Q ss_pred             CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccC
Q 022837          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS  199 (291)
Q Consensus       120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~  199 (291)
                      ....++++||+..+|.||||+|++|.+|+.+|||+|++++..++.|+.+||+|.|+|+.+++....+.|.++|+|.+...
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~  116 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAV  116 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhh
Confidence            34899999999999999999999999999999999999999999999999999999999999999999999999976543


Q ss_pred             CCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehcc
Q 022837          200 QTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFS  279 (291)
Q Consensus       200 ~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~  279 (291)
                      ......+            -|+                        ...+...+.|.||+...|.||||  ||.+||.++
T Consensus       117 ~k~v~~~------------~pq------------------------t~~r~kqikivvPNstag~iigk--ggAtiK~~~  158 (402)
T KOG2191|consen  117 AKPVDIL------------QPQ------------------------TPDRIKQIKIVVPNSTAGMIIGK--GGATIKAIQ  158 (402)
T ss_pred             cCCcccc------------CCC------------------------CccccceeEEeccCCcccceecC--CcchHHHHH
Confidence            2211000            000                        01122348999999999999999  999999999


Q ss_pred             ccccceEEee
Q 022837          280 LSIYEEIRLN  289 (291)
Q Consensus       280 ~~tga~i~~~  289 (291)
                      +++||.|||.
T Consensus       159 Eqsga~iqis  168 (402)
T KOG2191|consen  159 EQSGAWIQIS  168 (402)
T ss_pred             HhhCcceEec
Confidence            9999999986

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.79  E-value=6.6e-19  Score=146.84  Aligned_cols=139  Identities=17%  Similarity=0.227  Sum_probs=107.4

Q ss_pred             EEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEE---ecCHHHHHHHHHHHHHHHhhhhcccccc
Q 022837           39 FLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMI---SGTIDEILRAVDLVIDKLLTELHAEDQA  115 (291)
Q Consensus        39 ilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I---~G~~~~v~~A~~~I~~~i~~~~~~~~~~  115 (291)
                      |.||.+.+|.|||++|++|+.|+++||++|++.++        +..|.|   +++++++.+|+++|....... ..++..
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 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE--------TGEVKIEEEDEDPLAVMKAREVVKAIGRGF-SPEKAL   72 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--------CceEEEecCCCCHHHHHHHHHHHHHHHcCC-CHHHHH
Confidence            56899999999999999999999999999999753        245777   789999999999998644321 111000


Q ss_pred             CCCCCceE-EEEEecC---------CccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHH
Q 022837          116 DDVGTKTK-LRLIVPN---------SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRAL  185 (291)
Q Consensus       116 ~~~~~~~~-~~i~VP~---------~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~  185 (291)
                      ....+... ..+.|+.         ..+|+|||++|++++.|++.|||+|.|..          +.|.|.|++++++.|+
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            00011112 2233433         36899999999999999999999999963          6799999999999999


Q ss_pred             HHHHHHHhcCc
Q 022837          186 ELILLKLSEDT  196 (291)
Q Consensus       186 ~~I~~~l~e~~  196 (291)
                      .+|.+++.+.+
T Consensus       143 ~~i~~li~~~~  153 (172)
T TIGR03665       143 EAIEMLIEGAP  153 (172)
T ss_pred             HHHHHHHcCCC
Confidence            99999997654

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=99.76  E-value=7.8e-18  Score=141.30  Aligned_cols=142  Identities=18%  Similarity=0.222  Sum_probs=109.1

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEe----cCHHHHHHHHHHHHHHHhh-hh
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMIS----GTIDEILRAVDLVIDKLLT-EL  109 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~----G~~~~v~~A~~~I~~~i~~-~~  109 (291)
                      +...+.||.+.+|.|||++|++|+.|+++||++|++..+        +..|.|.    ++++++.+|+++|.+.+.. ..
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~--------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~   74 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE--------TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSP   74 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC--------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCH
Confidence            467899999999999999999999999999999999753        2557774    8999999999999865542 11


Q ss_pred             ccccccCCCCCceEEEE-Eec---------CCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHH
Q 022837          110 HAEDQADDVGTKTKLRL-IVP---------NSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD  179 (291)
Q Consensus       110 ~~~~~~~~~~~~~~~~i-~VP---------~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~  179 (291)
                      +..  .....+....++ .+.         ...+|+|||++|++++.|++.|||+|.|..          +.|.|.|+++
T Consensus        75 e~A--~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~----------~~v~i~G~~~  142 (180)
T PRK13763         75 EKA--LRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG----------KTVAIIGDPE  142 (180)
T ss_pred             HHH--HHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----------CEEEEEeCHH
Confidence            100  000011112121 111         136899999999999999999999999964          3499999999


Q ss_pred             HHHHHHHHHHHHHhcCc
Q 022837          180 EQMRALELILLKLSEDT  196 (291)
Q Consensus       180 ~v~~A~~~I~~~l~e~~  196 (291)
                      +++.|...|..+++...
T Consensus       143 ~~~~A~~~I~~li~g~~  159 (180)
T PRK13763        143 QVEIAREAIEMLIEGAP  159 (180)
T ss_pred             HHHHHHHHHHHHHcCCC
Confidence            99999999999997653

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.57  E-value=8.3e-15  Score=102.62  Aligned_cols=64  Identities=42%  Similarity=0.772  Sum_probs=59.2

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHH
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV  101 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I  101 (291)
                      ++||+||.+.+|+||||+|.+|++|+++|||+|++.+..+  ++..+|+|+|.|+++++.+|+.+|
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            4799999999999999999999999999999999987653  467899999999999999999987

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=99.56  E-value=1.2e-14  Score=101.86  Aligned_cols=65  Identities=45%  Similarity=0.671  Sum_probs=58.8

Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL  189 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~  189 (291)
                      +++|+||.+++|+|||++|++|++|+++|||+|++.+...  ++..+|.|+|+|+++++.+|+.+|.
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--CCCCceEEEEEeCHHHHHHHHHhhC
Confidence            3689999999999999999999999999999999987543  3567899999999999999999873

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=99.52  E-value=2.8e-14  Score=133.19  Aligned_cols=241  Identities=24%  Similarity=0.285  Sum_probs=168.7

Q ss_pred             CCCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           29 DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        29 ~~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      ....+++.+++.|+...|-+++||.|.+|+.|++.++++|.+..++-    ..++..++.|-+..+..|+..+++++.+.
T Consensus        62 ~e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~  137 (608)
T KOG2279|consen   62 QKPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV----GDERVLLISGFPVQVCKAKAAIHQILTEN  137 (608)
T ss_pred             cCchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC----CcccchhhccCCCCCChHHHHHHHHHhcC
Confidence            44557799999999999999999999999999999999999976542    35677778888999999999998777654


Q ss_pred             hccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 022837          109 LHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELI  188 (291)
Q Consensus       109 ~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I  188 (291)
                                 ..+...+-+|...+++|+|++|.+++.|+.-++|+|.+...-   .....+...|.|...-+..|..++
T Consensus       138 -----------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng---r~g~~~~~~i~~qqk~~~~a~~~~  203 (608)
T KOG2279|consen  138 -----------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG---RLGLSRLIKISGQQKEVAAAKHLI  203 (608)
T ss_pred             -----------Ccccccccchhhhcccccccchhhhcchhccccccccccccc---ccccccceecccccchHHHHHhhh
Confidence                       346778889999999999999999999999999999998742   233578889999988899999999


Q ss_pred             HHHHhcCcccCCCC----------CCCccC--CCcccCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCC---C-CCCCC-
Q 022837          189 LLKLSEDTLYSQTM----------TVPYTY--AGVFFSGFHGMPYGAVPPPVPAVPHNTAAH--YGPNM---G-GRKFQ-  249 (291)
Q Consensus       189 ~~~l~e~~~~~~~~----------~~~~~~--~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~--~~~~~---~-~~~~~-  249 (291)
                      .+.+.++......+          ..+.+-  .++..+...+.|.--..-.....++.++..  .++..   . .+.++ 
T Consensus       204 ~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~  283 (608)
T KOG2279|consen  204 LEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEK  283 (608)
T ss_pred             hccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCC
Confidence            99988763211111          011111  111112222222111100001111111111  11110   0 00111 


Q ss_pred             --CC---------eEEEeecCCCcceeEEeecCccceehccccccceEEee
Q 022837          250 --NN---------KVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLN  289 (291)
Q Consensus       250 --~~---------~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tga~i~~~  289 (291)
                        ..         ..+|.+|.-.+|.+||+  .|+.++.++..+++.++|-
T Consensus       284 ~~d~s~~k~~~l~i~e~e~p~~lsg~lig~--~gey~s~yssasn~~~hi~  332 (608)
T KOG2279|consen  284 PSDDSFQKSEALAIPEMEMPEILSGDLIGH--AGEYLSVYSSASNHPNHIW  332 (608)
T ss_pred             ccccccccccccccceeecCcccccchhhh--hhhhhhhhhhccCccceEE
Confidence              11         17889999999999999  9999999999999999874

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.40  E-value=1.1e-13  Score=115.38  Aligned_cols=111  Identities=14%  Similarity=0.078  Sum_probs=84.6

Q ss_pred             EEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEE---EcCHHHHHHHHHHHHHHHhcC-cccCC-
Q 022837          126 LIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL---TGTLDEQMRALELILLKLSED-TLYSQ-  200 (291)
Q Consensus       126 i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I---~G~~~~v~~A~~~I~~~l~e~-~~~~~-  200 (291)
                      +.||.+.+|.|||++|++||+|+++|||+|++..        ++..|.|   +++++++.+|+.+|..+.... +.... 
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~~   73 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS--------ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALK   73 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc--------CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence            5689999999999999999999999999999986        2357888   789999999999999987752 11000 


Q ss_pred             CCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeec---------CCCcceeEEeecC
Q 022837          201 TMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWP---------LNPVGMLLIILIA  271 (291)
Q Consensus       201 ~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP---------~~~vG~iIG~~~g  271 (291)
                      .+..  .|.+                                          .-+.|+         ...+|.|||+  |
T Consensus        74 l~gd--~y~~------------------------------------------~Vi~I~~~~~~~~~~~~~~griIG~--~  107 (172)
T TIGR03665        74 LLDD--DYML------------------------------------------EVIDLKEYGKSPNALRRIKGRIIGE--G  107 (172)
T ss_pred             hcCC--cceE------------------------------------------EEEEhhhccCCHHHHHHHHhhhcCC--C
Confidence            0000  0000                                          001111         1369999999  9


Q ss_pred             ccceehccccccceEEeec
Q 022837          272 QPIICHFSLSIYEEIRLNE  290 (291)
Q Consensus       272 g~~ik~~~~~tga~i~~~~  290 (291)
                      |.+++.|+..|||+|.|.+
T Consensus       108 G~t~~~ie~~t~~~i~i~~  126 (172)
T TIGR03665       108 GKTRRIIEELTGVSISVYG  126 (172)
T ss_pred             cHHHHHHHHHHCCeEEEcC
Confidence            9999999999999999975

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.

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.40  E-value=4.8e-13  Score=92.72  Aligned_cols=61  Identities=26%  Similarity=0.404  Sum_probs=55.8

Q ss_pred             EEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 022837          124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL  189 (291)
Q Consensus       124 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~  189 (291)
                      .++.||..++++|||++|++|++|+++|||+|.|++..     ..++.|+|+|+.++|..|+.+|.
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            57899999999999999999999999999999999743     36789999999999999999873

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.

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.39  E-value=3.7e-13  Score=113.07  Aligned_cols=124  Identities=13%  Similarity=0.075  Sum_probs=88.5

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEE----cCHHHHHHHHHHHHHHHhc-Cc
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT----GTLDEQMRALELILLKLSE-DT  196 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~----G~~~~v~~A~~~I~~~l~e-~~  196 (291)
                      ....+.||.+.+|.|||++|++||.|+++|||+|++..        ++..|.|.    ++++++++|+++|..++.. ++
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            46789999999999999999999999999999999986        23678885    8999999999999998875 22


Q ss_pred             ccCC-CCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccce
Q 022837          197 LYSQ-TMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPII  275 (291)
Q Consensus       197 ~~~~-~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~i  275 (291)
                      .... ....  .|.+-...                ...|     +.+.       +     .....+|.|||+  ||.++
T Consensus        75 e~A~~l~gd--~y~~~Vi~----------------i~~~-----~~~~-------~-----~~~r~~griIG~--~G~~~  117 (180)
T PRK13763         75 EKALRLLDD--DYVLEVID----------------LSDY-----GDSP-------N-----ALRRIKGRIIGE--GGKTR  117 (180)
T ss_pred             HHHHHHhCC--CceEEEEE----------------hhhc-----cCCh-------h-----HHHHHhhheeCC--CcHHH
Confidence            2000 0000  01100000                0000     0000       0     011369999999  99999


Q ss_pred             ehccccccceEEeec
Q 022837          276 CHFSLSIYEEIRLNE  290 (291)
Q Consensus       276 k~~~~~tga~i~~~~  290 (291)
                      +.|++.|||+|+|.+
T Consensus       118 k~ie~~t~~~i~i~~  132 (180)
T PRK13763        118 RIIEELTGVDISVYG  132 (180)
T ss_pred             HHHHHHHCcEEEEcC
Confidence            999999999999976

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.38  E-value=4e-13  Score=92.49  Aligned_cols=60  Identities=32%  Similarity=0.520  Sum_probs=54.9

Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELI  188 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I  188 (291)
                      |.+|.||.+++|+|||++|++|++|+++|||+|+|+++     + .+..|+|+|++++|++|+.+|
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            57899999999999999999999999999999999863     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 ....

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.37  E-value=7.4e-13  Score=91.12  Aligned_cols=60  Identities=30%  Similarity=0.577  Sum_probs=54.6

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHH
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV  101 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I  101 (291)
                      +.+|+||.+++|+|||++|.+|++|+++|||+|+|+++     + .+..|+|+|++++|.+|+++|
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 345999999999999999886

; 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=99.36  E-value=2.7e-12  Score=88.54  Aligned_cols=58  Identities=22%  Similarity=0.396  Sum_probs=53.2

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHH
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELI  188 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I  188 (291)
                      ....+.||.+++|+||||+|++||+|+++|||+|.++.         ++.|.|+|+ .+++++|+++|
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            46778999999999999999999999999999999975         357999999 99999999987

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.34  E-value=1.8e-12  Score=89.82  Aligned_cols=61  Identities=21%  Similarity=0.415  Sum_probs=55.8

Q ss_pred             EEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHH
Q 022837           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI  102 (291)
Q Consensus        37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~  102 (291)
                      .+|.||..++|.|||++|++|++|+++|||+|.|++..     ..++.|+|+|+.++|..|+.+|+
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     46789999999999999998873

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=99.34  E-value=5.9e-12  Score=87.51  Aligned_cols=62  Identities=45%  Similarity=0.663  Sum_probs=56.3

Q ss_pred             EEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 022837          124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELI  188 (291)
Q Consensus       124 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I  188 (291)
                      .++.||.+++++|||++|++|++|+++|||+|.|.+...   ...++.|+|.|+.+++..|+.+|
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            579999999999999999999999999999999987432   34789999999999999999887

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.

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

Probab=99.31  E-value=9.9e-12  Score=86.37  Aligned_cols=62  Identities=40%  Similarity=0.756  Sum_probs=56.6

Q ss_pred             EEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHH
Q 022837           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV  101 (291)
Q Consensus        37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I  101 (291)
                      .+|.||..++++|||++|++|++|+++|||+|.|+...+   ...++.|.|.|+.+++..|+.+|
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            689999999999999999999999999999999987543   45789999999999999998876

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=99.28  E-value=1.6e-11  Score=84.71  Aligned_cols=58  Identities=21%  Similarity=0.388  Sum_probs=52.8

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecC-HHHHHHHHHHH
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLV  101 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~-~~~v~~A~~~I  101 (291)
                      ....|.||.+.+|+||||+|++|++|+++|||+|++++         ++.|.|+|+ .++++.|+++|
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         356999998 89999999887

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

>PF13014 KH_3: KH domain

Probab=99.15  E-value=8.5e-11  Score=75.21  Aligned_cols=43  Identities=44%  Similarity=0.661  Sum_probs=38.4

Q ss_pred             ccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEc
Q 022837          132 SCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG  176 (291)
Q Consensus       132 ~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G  176 (291)
                      ++|+|||++|++|++|+++|||+|+|++  ...++..++.|+|+|
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            5899999999999999999999999998  234566899999998

>PF13014 KH_3: KH domain

Probab=99.13  E-value=1.2e-10  Score=74.47  Aligned_cols=43  Identities=44%  Similarity=0.890  Sum_probs=38.8

Q ss_pred             ccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec
Q 022837           45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG   89 (291)
Q Consensus        45 ~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G   89 (291)
                      ++|+||||+|.+|++|+++|||+|+|++  +..++..+|.|+|+|
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            5899999999999999999999999998  344677899999987

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

Probab=99.10  E-value=1.9e-09  Score=89.77  Aligned_cols=146  Identities=16%  Similarity=0.234  Sum_probs=107.8

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec-----CHHHHHHHHHHHHHHHhh
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-----TIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G-----~~~~v~~A~~~I~~~i~~  107 (291)
                      ......+.||.+..+.+||+.|++.+.|++.++++|.+..        .+..|.|.-     .|-.+.+|.+.|. .+..
T Consensus         6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~--------~~~~V~i~~~~~t~Dp~~~~ka~d~Vk-AIgr   76 (194)
T COG1094           6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS--------KTGSVTIRTTRKTEDPLALLKARDVVK-AIGR   76 (194)
T ss_pred             ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC--------CCCeEEEEecCCCCChHHHHHHHHHHH-HHhc
Confidence            3456779999999999999999999999999999999964        345666654     4678888988885 3333


Q ss_pred             hhccccccCCCCCceEEEE-E-----e-cC----CccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEc
Q 022837          108 ELHAEDQADDVGTKTKLRL-I-----V-PN----SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG  176 (291)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~i-~-----V-P~----~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G  176 (291)
                      -+..+....-..+...+.+ .     - +.    ...|+|||++|.+.+.|++-|||.|.|..          .+|.|-|
T Consensus        77 GF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG  146 (194)
T COG1094          77 GFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIG  146 (194)
T ss_pred             CCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEec
Confidence            2221100000000111111 1     1 11    24589999999999999999999999975          5899999


Q ss_pred             CHHHHHHHHHHHHHHHhcCcc
Q 022837          177 TLDEQMRALELILLKLSEDTL  197 (291)
Q Consensus       177 ~~~~v~~A~~~I~~~l~e~~~  197 (291)
                      .+++|+.|++.|..++...++
T Consensus       147 ~~~~v~iAr~AVemli~G~~h  167 (194)
T COG1094         147 GFEQVEIAREAVEMLINGAPH  167 (194)
T ss_pred             ChhhhHHHHHHHHHHHcCCCc
Confidence            999999999999999988664

>smart00322 KH K homology RNA-binding domain

Probab=99.10  E-value=7.1e-10  Score=77.27  Aligned_cols=67  Identities=33%  Similarity=0.547  Sum_probs=60.2

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLS  193 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~  193 (291)
                      .+.++.||..+++.+||++|++|++|++.||++|.+.....     ....|+|.|+.+++..|..+|.+.++
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~-----~~~~v~i~g~~~~v~~a~~~i~~~~~   69 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS-----EERVVEITGPPENVEKAAELILEILE   69 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC-----CccEEEEEcCHHHHHHHHHHHHHHhC
Confidence            57899999999999999999999999999999999976321     56889999999999999999998763

>smart00322 KH K homology RNA-binding domain

Probab=99.05  E-value=1.8e-09  Score=75.23  Aligned_cols=67  Identities=30%  Similarity=0.658  Sum_probs=59.6

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHH
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL  105 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i  105 (291)
                      .+..+|.||...+|.+||++|.+|++|++.||++|.+....     .....+.|.|..+++..|..+|.+.+
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            46789999999999999999999999999999999997543     25688999999999999999998654

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.77  E-value=2.4e-08  Score=100.47  Aligned_cols=201  Identities=19%  Similarity=0.230  Sum_probs=148.1

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCC--CCceEEEEecCHHHHHHHHHHHHHHHhhh-
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPG--TTDRIIMISGTIDEILRAVDLVIDKLLTE-  108 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~--~~er~v~I~G~~~~v~~A~~~I~~~i~~~-  108 (291)
                      ..-+..++.+......++||++|.+++.++.++.+.+.++..++..+.  ...+...+....-++..+..++..-+..+ 
T Consensus       198 ~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~  277 (753)
T KOG2208|consen  198 ERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDE  277 (753)
T ss_pred             ceeEEEEeeccccchhhhccccccccccccccceeEEEcccccccchhhhhccccccceehhhhhHHHHHHhcChhhhhh
Confidence            344889999999999999999999999999999999999865542111  12233334444445555555442211000 


Q ss_pred             -----hc-------------------cc----cc---c-------------------------CCCCCceEEEEEecCCc
Q 022837          109 -----LH-------------------AE----DQ---A-------------------------DDVGTKTKLRLIVPNSS  132 (291)
Q Consensus       109 -----~~-------------------~~----~~---~-------------------------~~~~~~~~~~i~VP~~~  132 (291)
                           ++                   ..    ..   .                         .-........+.+-...
T Consensus       278 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~  357 (753)
T KOG2208|consen  278 IIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEE  357 (753)
T ss_pred             hhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHh
Confidence                 00                   00    00   0                         00123367788889999


Q ss_pred             cceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCCCCCCccCCCcc
Q 022837          133 CGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVF  212 (291)
Q Consensus       133 vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~~g~~  212 (291)
                      +..++||+|.+|.+|++++.|.|.+...     +..+..|.++|....+.+|...+...+.+-.+-              
T Consensus       358 ~~~v~GK~~~ni~ki~e~~~~~i~~~~~-----~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~--------------  418 (753)
T KOG2208|consen  358 LKFVIGKKGANIEKIREESQVKIDLPKQ-----GSNNKKVVITGVSANDEKAVEDVEKIIAEILNS--------------  418 (753)
T ss_pred             hhhhcCCCCccHHHHHHhhhhceecccc-----cCCCCCeEEeccccchhHHHHHHHHHHHhhhcc--------------
Confidence            9999999999999999999999999873     346788999999999999999999998884321              


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehcccccc-ceEEeec
Q 022837          213 FSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIY-EEIRLNE  290 (291)
Q Consensus       213 ~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tg-a~i~~~~  290 (291)
                                                           ...-.+.+|...+..+||.  ||..|..|+.+.| -+|++.+
T Consensus       419 -------------------------------------~~~~~~~iP~k~~~~iig~--~g~~i~~I~~k~~~v~i~f~~  458 (753)
T KOG2208|consen  419 -------------------------------------IVKEEVQIPTKSHKRIIGT--KGALINYIMGKHGGVHIKFQN  458 (753)
T ss_pred             -------------------------------------cccceeecCccchhhhhcc--ccccHHHHHhhcCcEEEecCC
Confidence                                                 0125678999999999999  9999999999999 7777654

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

Probab=98.77  E-value=1.3e-08  Score=89.66  Aligned_cols=140  Identities=17%  Similarity=0.254  Sum_probs=111.2

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhc--
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH--  110 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~--  110 (291)
                      +.++..+.||..+++.|.|++|.+||.|+.+|.+.|+-+...      .+.++.++|..++|..|++.|... .+.+.  
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~------eePiF~vTg~~edv~~aRrei~sa-aeH~~l~   96 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG------EEPIFPVTGRHEDVRRARREIPSA-AEHFGLI   96 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC------CCCcceeccCchhHHHHhhcCccc-cceeeee
Confidence            788899999999999999999999999999999999998654      468899999999999999998641 11111  


Q ss_pred             -------cccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHH-HH
Q 022837          111 -------AEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE-QM  182 (291)
Q Consensus       111 -------~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~-v~  182 (291)
                             ..........+.+...-+|...+|.|.|..|++|+.|++.+...|.-.-.      ..+.++.++|-+.. ++
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                   00011123456778888999999999999999999999999988876642      25678889998887 45


Q ss_pred             HHH
Q 022837          183 RAL  185 (291)
Q Consensus       183 ~A~  185 (291)
                      +|.
T Consensus       171 ra~  173 (394)
T KOG2113|consen  171 RAR  173 (394)
T ss_pred             hcc
Confidence            555

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

Probab=98.77  E-value=3.3e-08  Score=77.32  Aligned_cols=67  Identities=22%  Similarity=0.180  Sum_probs=53.5

Q ss_pred             CCccceeeccCChhHHHHHHhccceEEEecCCCCC--------------CCCCceEEEEEcCH---HHHHHHHHHHHHHH
Q 022837          130 NSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSY--------------YGLNDRLVTLTGTL---DEQMRALELILLKL  192 (291)
Q Consensus       130 ~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~--------------~~~~er~V~I~G~~---~~v~~A~~~I~~~l  192 (291)
                      .+++|.|||++|.+||+|+++|||+|.|..+....              ...++-.|.|++..   +++.+|+.+|..++
T Consensus        14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll   93 (120)
T cd02395          14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL   93 (120)
T ss_pred             CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence            46889999999999999999999999998742110              11233579999975   99999999999999


Q ss_pred             hcCc
Q 022837          193 SEDT  196 (291)
Q Consensus       193 ~e~~  196 (291)
                      ....
T Consensus        94 ~~~~   97 (120)
T cd02395          94 KPAI   97 (120)
T ss_pred             ccCC
Confidence            8643

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

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.65  E-value=6.6e-08  Score=97.34  Aligned_cols=146  Identities=23%  Similarity=0.324  Sum_probs=118.9

Q ss_pred             CCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhc
Q 022837           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH  110 (291)
Q Consensus        31 ~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~  110 (291)
                      .+..+.+.+.+-......|+||+|.+|.+|++++.|.|.++..     +..+..+.++|...++.+|.+.+.....+...
T Consensus       343 ~~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-----~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n  417 (753)
T KOG2208|consen  343 EENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ-----GSNNKKVVITGVSANDEKAVEDVEKIIAEILN  417 (753)
T ss_pred             hccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc-----cCCCCCeEEeccccchhHHHHHHHHHHHhhhc
Confidence            3445888899999999999999999999999999999999873     35678899999999999999999866555421


Q ss_pred             cccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhcc-ceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 022837          111 AEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQ-AVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL  189 (291)
Q Consensus       111 ~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tG-a~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~  189 (291)
                      .         .....+.+|...+.++||.+|..|..|.++++ .+|++...     ......+++.|....+..+..+..
T Consensus       418 ~---------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-----~~~~~~~~~~~~~~dv~~~~~~~~  483 (753)
T KOG2208|consen  418 S---------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-----NNSSDMVTIRGISKDVEKSVSLLK  483 (753)
T ss_pred             c---------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-----CcccccceEeccccccchhHHHHH
Confidence            1         35677999999999999999999999999999 66666553     224556888888888877777776


Q ss_pred             HHHhcC
Q 022837          190 LKLSED  195 (291)
Q Consensus       190 ~~l~e~  195 (291)
                      .+..+.
T Consensus       484 ~~~~~a  489 (753)
T KOG2208|consen  484 ALKADA  489 (753)
T ss_pred             hhhhhh
Confidence            665543

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.64  E-value=8.8e-08  Score=77.05  Aligned_cols=103  Identities=20%  Similarity=0.281  Sum_probs=74.3

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcccccc
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQA  115 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~  115 (291)
                      .+.|+|+...+|..||++|++|+.|++..|-+|.+-..++                    .+..+|...+....-..-..
T Consensus        33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~--------------------d~~~fI~n~l~Pa~V~~v~I   92 (140)
T PRK08406         33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD--------------------DPEEFIKNIFAPAAVRSVTI   92 (140)
T ss_pred             EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC--------------------CHHHHHHHHcCCCEEEEEEE
Confidence            4778899999999999999999999999999998865321                    13344443332211000001


Q ss_pred             CCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEe
Q 022837          116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKIS  158 (291)
Q Consensus       116 ~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~  158 (291)
                      .+........+.|+.+..|..|||+|++++.++.-+|-++.|.
T Consensus        93 ~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         93 KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            1112235677789999999999999999999999999887764

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

Probab=98.57  E-value=2.9e-07  Score=72.03  Aligned_cols=63  Identities=19%  Similarity=0.431  Sum_probs=48.2

Q ss_pred             cccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCC--------------CCceEEEEecC---HHHHHHHHHHHHHHHh
Q 022837           44 PLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPG--------------TTDRIIMISGT---IDEILRAVDLVIDKLL  106 (291)
Q Consensus        44 ~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~--------------~~er~v~I~G~---~~~v~~A~~~I~~~i~  106 (291)
                      +.+|.|||++|.+||+|+++|||+|.|........+              ...-.|.|++.   .+.+.+|+.+|...+.
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            468999999999999999999999999875211100              12245788875   4899999999986665

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

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.49  E-value=8.6e-07  Score=87.94  Aligned_cols=91  Identities=18%  Similarity=0.191  Sum_probs=73.8

Q ss_pred             HHHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEE
Q 022837           94 ILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVT  173 (291)
Q Consensus        94 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~  173 (291)
                      +.+|+..|++.+.+.+... .......+....+.||.+++|.|||+||++||+|+++|||+|.|..         +..|.
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            3455666777777665544 3333345678889999999999999999999999999999999974         46899


Q ss_pred             EEcC-HHHHHHHHHHHHHHHhc
Q 022837          174 LTGT-LDEQMRALELILLKLSE  194 (291)
Q Consensus       174 I~G~-~~~v~~A~~~I~~~l~e  194 (291)
                      |.+. .+++++|+.+|..++..
T Consensus       621 I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       621 IGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             EEeCCHHHHHHHHHHHHHhhCc
Confidence            8885 88999999999999885

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.

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

Probab=98.43  E-value=1.1e-07  Score=89.63  Aligned_cols=113  Identities=23%  Similarity=0.295  Sum_probs=96.7

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCccc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLY  198 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~  198 (291)
                      ...+..++.|+..++-+++||.|.+||.|+..++++|.+..++-    ..++.-.+.|.+.++..|+..+.+++.+++..
T Consensus        65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~pv  140 (608)
T KOG2279|consen   65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV----GDERVLLISGFPVQVCKAKAAIHQILTENTPV  140 (608)
T ss_pred             hhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC----CcccchhhccCCCCCChHHHHHHHHHhcCCcc
Confidence            45678999999999999999999999999999999999987542    25666777779999999999999999885443


Q ss_pred             CCCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehc
Q 022837          199 SQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHF  278 (291)
Q Consensus       199 ~~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~  278 (291)
                      .                                                     .++.+|..++++|+||  ||.++..+
T Consensus       141 k-----------------------------------------------------~~lsvpqr~~~~i~gr--gget~~si  165 (608)
T KOG2279|consen  141 S-----------------------------------------------------EQLSVPQRSVGRIIGR--GGETIRSI  165 (608)
T ss_pred             c-----------------------------------------------------ccccchhhhccccccc--chhhhcch
Confidence            2                                                     5566788999999999  99999999


Q ss_pred             cccccceEEeec
Q 022837          279 SLSIYEEIRLNE  290 (291)
Q Consensus       279 ~~~tga~i~~~~  290 (291)
                      ...++|.|-+.+
T Consensus       166 ~~ss~aki~~d~  177 (608)
T KOG2279|consen  166 CKSSGAKITCDK  177 (608)
T ss_pred             hccccccccccc
Confidence            999999987654

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.24  E-value=4.4e-06  Score=83.79  Aligned_cols=91  Identities=13%  Similarity=0.150  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEE
Q 022837           95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL  174 (291)
Q Consensus        95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I  174 (291)
                      .++...|++.+.+.+...........+....+.||.+.++.|||+||++||+|+++|||+|.|..         +..|.|
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            34445566666555443322223344578889999999999999999999999999999999974         356777


Q ss_pred             EcC-HHHHHHHHHHHHHHHhc
Q 022837          175 TGT-LDEQMRALELILLKLSE  194 (291)
Q Consensus       175 ~G~-~~~v~~A~~~I~~~l~e  194 (291)
                      .+. .+.+++|..+|..+..+
T Consensus       595 ~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       595 AASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             EECcHHHHHHHHHHHHhhhcc
Confidence            774 78899999999988664

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).

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=98.18  E-value=5.3e-06  Score=66.62  Aligned_cols=103  Identities=23%  Similarity=0.329  Sum_probs=72.1

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcccccc
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQA  115 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~  115 (291)
                      .+-|+|....+|..||++|.+|+.|++..|-+|.+-..+              ..+.      ..|...+.-..-..-..
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys--------------~D~~------~fI~N~l~PA~V~~V~i   93 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYS--------------ENLE------EFVANKLAPAEVKNVTV   93 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcC--------------CCHH------HHHHHcCCCceEEEEEE
Confidence            677899999999999999999999999999888885432              1121      22222111110000000


Q ss_pred             CCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEe
Q 022837          116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKIS  158 (291)
Q Consensus       116 ~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~  158 (291)
                      ...++.....+.||.+..+..|||+|.|++...+-+|-++.|.
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            1112345677889999999999999999999999998887664

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=98.09  E-value=3.6e-05  Score=72.12  Aligned_cols=75  Identities=20%  Similarity=0.200  Sum_probs=59.0

Q ss_pred             ceEEEEEec------CCccceeeccCChhHHHHHHhccceEEEecCC------------CCCCCCC-ceEEEEEcC-HHH
Q 022837          121 KTKLRLIVP------NSSCGSIIGKAGATIKSFMDDSQAVIKISRLD------------HSYYGLN-DRLVTLTGT-LDE  180 (291)
Q Consensus       121 ~~~~~i~VP------~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~------------~~~~~~~-er~V~I~G~-~~~  180 (291)
                      ..+.++.||      -++||+|||..|.|.|+|+++|||+|.|-.+.            ...++.. +=.+.|+++ .+.
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            577888888      56899999999999999999999999997611            0112222 334888887 788


Q ss_pred             HHHHHHHHHHHHhcC
Q 022837          181 QMRALELILLKLSED  195 (291)
Q Consensus       181 v~~A~~~I~~~l~e~  195 (291)
                      |++|++.|..+|.+.
T Consensus       217 i~~Ai~vienli~~a  231 (554)
T KOG0119|consen  217 IKKAIAVIENLIQSA  231 (554)
T ss_pred             HHHHHHHHHHHHHhh
Confidence            999999999999864

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.94  E-value=2.1e-05  Score=79.95  Aligned_cols=91  Identities=14%  Similarity=0.127  Sum_probs=70.5

Q ss_pred             HHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccce-EEEecCCCCCCCCCceEEE
Q 022837           95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV-IKISRLDHSYYGLNDRLVT  173 (291)
Q Consensus        95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~-I~i~~~~~~~~~~~er~V~  173 (291)
                      .+|+..|++.|.+.+...........+....+.||.++++.|||.||.+||.|.++||+. |.+..         +-.|.
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            344455666666655433222333456788899999999999999999999999999999 88764         46788


Q ss_pred             EEcC-HHHHHHHHHHHHHHHhc
Q 022837          174 LTGT-LDEQMRALELILLKLSE  194 (291)
Q Consensus       174 I~G~-~~~v~~A~~~I~~~l~e  194 (291)
                      |.+. .+.+++|+++|.++..+
T Consensus       729 I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        729 ITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             EEeCCHHHHHHHHHHHHHHhcC
Confidence            8885 88999999999998874

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

Probab=97.91  E-value=1.4e-05  Score=70.72  Aligned_cols=126  Identities=19%  Similarity=0.190  Sum_probs=92.9

Q ss_pred             CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccC
Q 022837          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS  199 (291)
Q Consensus       120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~  199 (291)
                      ..++..+.||..+++.+.|++|.+||.|+.+|...|.-+...      .+.++.++|.++.|..|+..|..-- |+....
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~------eePiF~vTg~~edv~~aRrei~saa-eH~~l~   96 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG------EEPIFPVTGRHEDVRRARREIPSAA-EHFGLI   96 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC------CCCcceeccCchhHHHHhhcCcccc-ceeeee
Confidence            568889999999999999999999999999999998876532      4678999999999999998775421 111000


Q ss_pred             CCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehcc
Q 022837          200 QTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFS  279 (291)
Q Consensus       200 ~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~  279 (291)
                             .|.+.                         +..+.+++ ..+-+.+.+..+|-..||.|.|-  -|.+||.++
T Consensus        97 -------~~s~s-------------------------~Sgg~~~~-s~s~qt~sy~svP~rvvglvv~~--~~~ti~~iq  141 (394)
T KOG2113|consen   97 -------RASRS-------------------------FSGGTNGA-SASGQTTSYVSVPLRVVGLVVGP--KGATIKRIQ  141 (394)
T ss_pred             -------eeccc-------------------------ccCCCccc-cccCCCceeeeccceeeeecccc--ccCccchhe
Confidence                   01100                         00111111 12334568889999999999999  999999999


Q ss_pred             ccccceEE
Q 022837          280 LSIYEEIR  287 (291)
Q Consensus       280 ~~tga~i~  287 (291)
                      +.+-..|.
T Consensus       142 q~tnt~I~  149 (394)
T KOG2113|consen  142 QFTNTYIA  149 (394)
T ss_pred             ecccceEe
Confidence            99988875

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

Probab=97.86  E-value=4.4e-05  Score=74.62  Aligned_cols=102  Identities=19%  Similarity=0.164  Sum_probs=78.2

Q ss_pred             EEEEecCHHH--------HHHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceE
Q 022837           84 IIMISGTIDE--------ILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVI  155 (291)
Q Consensus        84 ~v~I~G~~~~--------v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I  155 (291)
                      -+.|.|....        ...|.-.|+..+.+.+...........+....+.|+.+.++-+||++|++|++|.++|||+|
T Consensus       506 DiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~I  585 (692)
T COG1185         506 DIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKI  585 (692)
T ss_pred             eeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEE
Confidence            3777775543        34456667777766654432223334456788889999999999999999999999999999


Q ss_pred             EEecCCCCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHhc
Q 022837          156 KISRLDHSYYGLNDRLVTLTGTL-DEQMRALELILLKLSE  194 (291)
Q Consensus       156 ~i~~~~~~~~~~~er~V~I~G~~-~~v~~A~~~I~~~l~e  194 (291)
                      ++..         +..|.|.++. +.+.+|+.+|..+.++
T Consensus       586 died---------dGtv~i~~s~~~~~~~ak~~I~~i~~e  616 (692)
T COG1185         586 DIED---------DGTVKIAASDGESAKKAKERIEAITRE  616 (692)
T ss_pred             EecC---------CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence            9973         4579999985 8899999999999966

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

Probab=97.80  E-value=9.7e-05  Score=69.32  Aligned_cols=74  Identities=19%  Similarity=0.368  Sum_probs=54.5

Q ss_pred             cEEEEEEeccc------ccceeeccCChhHHHHHHHhCCcEEEcCCC------------CCCCCC-CceEEEEec-CHHH
Q 022837           34 PTYIRFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSRSH------------EFFPGT-TDRIIMISG-TIDE   93 (291)
Q Consensus        34 ~~~~rilvp~~------~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~------------~~~p~~-~er~v~I~G-~~~~   93 (291)
                      .++-|+.||.+      .||+|||..|.|.|+|+++|||+|.|.-..            ...++. ++--+.|++ +.|.
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            56667777754      699999999999999999999999996521            112222 233477776 4678


Q ss_pred             HHHHHHHHHHHHhh
Q 022837           94 ILRAVDLVIDKLLT  107 (291)
Q Consensus        94 v~~A~~~I~~~i~~  107 (291)
                      |.+|++.|..+|.+
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            89999998866665

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=97.71  E-value=9.2e-05  Score=62.43  Aligned_cols=103  Identities=19%  Similarity=0.251  Sum_probs=70.8

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcccccc
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQA  115 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~  115 (291)
                      .+-+.+-.+.+|..||++|.+|+.|+++.|-+|.|-...+              .      -...|...|....-..-..
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~--------------d------~~~fI~nal~Pa~v~~V~~  136 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE--------------D------PAEFIKNALAPAEVLSVNI  136 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCC--------------C------HHHHHHHhcCcceEeEEEE
Confidence            4455666678999999999999999999998888854321              1      1122222221000000000


Q ss_pred             CCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEec
Q 022837          116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (291)
Q Consensus       116 ~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~  159 (291)
                      ...+. ....+.||.+..+.+|||+|.+++-+.+-||-++.|..
T Consensus       137 ~~~d~-~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         137 KEDDG-HVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EeCCC-cEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            00011 27888899999999999999999999999999999976

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.70  E-value=5.6e-05  Score=60.86  Aligned_cols=104  Identities=14%  Similarity=0.166  Sum_probs=74.5

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCC
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQT  201 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~  201 (291)
                      ..+.++|+...+|..||++|++|+.|++..|-+|.+-.-++                    .+..+|...|.-..-.+-.
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            57889999999999999999999999999999988876211                    1344555544332111100


Q ss_pred             CCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehcccc
Q 022837          202 MTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLS  281 (291)
Q Consensus       202 ~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~  281 (291)
                      ..                                          ....+....+.|+.+..|..|||  +|.|++.++.-
T Consensus        92 I~------------------------------------------~~~~~~~~~V~V~~~d~g~aIGK--~G~ni~la~~L  127 (140)
T PRK08406         92 IK------------------------------------------KKNGDKVAYVEVAPEDKGIAIGK--NGKNIERAKDL  127 (140)
T ss_pred             EE------------------------------------------ecCCcEEEEEEECccccchhhCC--CCHHHHHHHHH
Confidence            00                                          00011336788999999999999  99999999998


Q ss_pred             ccceEEee
Q 022837          282 IYEEIRLN  289 (291)
Q Consensus       282 tga~i~~~  289 (291)
                      +|-.+-|.
T Consensus       128 ~~~~~di~  135 (140)
T PRK08406        128 AKRHFDID  135 (140)
T ss_pred             hCCccCCe
Confidence            88877654

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

Probab=97.68  E-value=0.00052  Score=59.93  Aligned_cols=79  Identities=25%  Similarity=0.282  Sum_probs=56.5

Q ss_pred             CCceEEEEEecC------CccceeeccCChhHHHHHHhccceEEEecCCCCC--------------CCCCc---eEEEEE
Q 022837          119 GTKTKLRLIVPN------SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSY--------------YGLND---RLVTLT  175 (291)
Q Consensus       119 ~~~~~~~i~VP~------~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~--------------~~~~e---r~V~I~  175 (291)
                      ....+.+++||-      ++||+|+|..|.++|+|+++|||+|-|-...-.-              ....+   -.|+..
T Consensus        89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~  168 (259)
T KOG1588|consen   89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE  168 (259)
T ss_pred             ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe
Confidence            345788999994      5999999999999999999999999997632110              01111   246667


Q ss_pred             cCHHHH----HHHHHHHHHHHhcCcc
Q 022837          176 GTLDEQ----MRALELILLKLSEDTL  197 (291)
Q Consensus       176 G~~~~v----~~A~~~I~~~l~e~~~  197 (291)
                      +++..+    ..|++.|.++|.-+.+
T Consensus       169 ~p~~ea~~rl~~AleeI~klL~P~~e  194 (259)
T KOG1588|consen  169 APPAEAYARLAYALEEIKKLLVPDHE  194 (259)
T ss_pred             CCHHHHHHHHHHHHHHHHHhcCCCCC
Confidence            775544    4588888888866544

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.68  E-value=0.00017  Score=71.85  Aligned_cols=66  Identities=24%  Similarity=0.299  Sum_probs=55.7

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHHh
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVIDKLL  106 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G-~~~~v~~A~~~I~~~i~  106 (291)
                      .-+....|.||.+++|.|||+||.+||.|+++||++|.+.+         +-.|.|.+ ..+.+.+|+++|...+.
T Consensus       575 ~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------~G~V~I~a~d~~~~~~A~~~I~~i~~  641 (719)
T TIGR02696       575 YAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------DGTVYIGAADGPSAEAARAMINAIAN  641 (719)
T ss_pred             CCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---------CcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence            34567889999999999999999999999999999999964         34577776 57889999999985554

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=97.61  E-value=0.0001  Score=74.24  Aligned_cols=91  Identities=19%  Similarity=0.180  Sum_probs=68.6

Q ss_pred             HHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEE
Q 022837           95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL  174 (291)
Q Consensus        95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I  174 (291)
                      .+|+..|++.|.+.+................+.||.+.++.+||.||.+||+|.++||+.|.+..         +..|.|
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            45566677777766543322222234456677789999999999999999999999999887742         467888


Q ss_pred             EcC-HHHHHHHHHHHHHHHhc
Q 022837          175 TGT-LDEQMRALELILLKLSE  194 (291)
Q Consensus       175 ~G~-~~~v~~A~~~I~~~l~e  194 (291)
                      .+. .+.+++|+.+|..+..+
T Consensus       598 ~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        598 AATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             EcccHHHHHHHHHHHHHhccc
Confidence            885 88899999999988864

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

Probab=97.58  E-value=0.00011  Score=68.08  Aligned_cols=67  Identities=24%  Similarity=0.340  Sum_probs=56.5

Q ss_pred             CCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHH
Q 022837           30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI  102 (291)
Q Consensus        30 ~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~  102 (291)
                      ....++++.|.|-++.||.|||++|++||.||..|+++|++.+.      ..+-.|+|.|...--.+|+..|-
T Consensus        42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~------~~e~kv~ifg~~~m~~kaka~id  108 (629)
T KOG0336|consen   42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC------DLEVKVTIFGINHMRKKAKASID  108 (629)
T ss_pred             cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc------CceeEEEEechHHHHHHHHhhHh
Confidence            45567889999999999999999999999999999999999763      35778999998776666666664

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

Probab=97.57  E-value=0.00021  Score=66.20  Aligned_cols=74  Identities=26%  Similarity=0.359  Sum_probs=59.7

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCccc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLY  198 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~  198 (291)
                      .....+-+-|-+++||.|||++|++||.||..|.++|++.+.+      .+-.|+|.|...--.+|...|...+..+..+
T Consensus        44 ~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~------~e~kv~ifg~~~m~~kaka~id~~~~k~e~y  117 (629)
T KOG0336|consen   44 GGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD------LEVKVTIFGINHMRKKAKASIDRGQDKDERY  117 (629)
T ss_pred             CCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC------ceeEEEEechHHHHHHHHhhHhhhhhhhhhc
Confidence            4456777888999999999999999999999999999998743      4678999999877777777776655544333

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.47  E-value=0.00024  Score=71.47  Aligned_cols=64  Identities=19%  Similarity=0.335  Sum_probs=52.6

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHH
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVIDKL  105 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G-~~~~v~~A~~~I~~~i  105 (291)
                      -+....+.||.+.+|.|||++|.+||.|+++|||+|.|.++         -.|.|.+ ..+.+.+|+++|....
T Consensus       549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd---------G~V~i~~~~~~~~~~a~~~I~~~~  613 (684)
T TIGR03591       549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD---------GTVKIAASDGEAAEAAIKMIEGIT  613 (684)
T ss_pred             CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC---------eEEEEEECcHHHHHHHHHHHHhhh
Confidence            45678899999999999999999999999999999999652         3355554 5778899988887543

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).

>PRK00106 hypothetical protein; Provisional

Probab=97.39  E-value=0.001  Score=64.70  Aligned_cols=67  Identities=19%  Similarity=0.251  Sum_probs=51.1

Q ss_pred             CceEEEEEecC-CccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 022837          120 TKTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSE  194 (291)
Q Consensus       120 ~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I~~~l~e  194 (291)
                      ......+.+|+ ++-|+||||.|.||+.+...||+.+.|.+        +...|+|+|. |-.-+-|+..+..++.+
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            34566677887 56799999999999999999999999976        4467889994 55555566555555543

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

Probab=97.38  E-value=0.00028  Score=63.33  Aligned_cols=71  Identities=20%  Similarity=0.333  Sum_probs=58.8

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      .+..-++|++...|.|||++|.|.++|+++|+++|.++..++    ..+.++.+.++.++|.+|.+.|...|...
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            467778999999999999999999999999999999998543    24455555668899999999998666544

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=97.37  E-value=0.00097  Score=64.94  Aligned_cols=67  Identities=21%  Similarity=0.221  Sum_probs=50.8

Q ss_pred             CceEEEEEecC-CccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 022837          120 TKTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSE  194 (291)
Q Consensus       120 ~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I~~~l~e  194 (291)
                      ......+.+|+ ++-|+||||.|.|||.++..||+.|.|.+        +...|+|+|. |-.-+-|+..+..++.+
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            34556677887 56699999999999999999999999976        3457889994 55555566655555543

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

Probab=97.37  E-value=0.0013  Score=57.41  Aligned_cols=45  Identities=16%  Similarity=0.377  Sum_probs=38.8

Q ss_pred             CCCCCcEEEEEEeccc------ccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837           29 DPTEKPTYIRFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSRS   73 (291)
Q Consensus        29 ~~~~~~~~~rilvp~~------~vG~IIGk~G~~Ik~I~~~tga~I~v~~~   73 (291)
                      +...-.++.||+||.+      .||+|+|..|.++|+|+++|||+|.|.-.
T Consensus        86 ~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr  136 (259)
T KOG1588|consen   86 SGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR  136 (259)
T ss_pred             cCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence            3445567899999976      69999999999999999999999999653

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

Probab=97.36  E-value=0.00037  Score=47.79  Aligned_cols=37  Identities=27%  Similarity=0.451  Sum_probs=34.5

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEE
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQL   70 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v   70 (291)
                      ...+.+.|+.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3679999999999999999999999999999988876

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

>PRK12704 phosphodiesterase; Provisional

Probab=97.35  E-value=0.0011  Score=64.68  Aligned_cols=65  Identities=22%  Similarity=0.200  Sum_probs=49.1

Q ss_pred             ceEEEEEecC-CccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHh
Q 022837          121 KTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLS  193 (291)
Q Consensus       121 ~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I~~~l~  193 (291)
                      .....+.+|+ ++-|+||||.|.|||.++..||+.|.|.+        +...|.|+|. +-.-+.|...+..++.
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~~~~~rre~a~~~l~~l~~  275 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPIRREIARLALEKLVQ  275 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--------CCCeEEEecCChhhHHHHHHHHHHHHh
Confidence            3455667887 66799999999999999999999999976        3467889994 5444455555555444

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

Probab=97.30  E-value=0.00064  Score=56.99  Aligned_cols=53  Identities=21%  Similarity=0.337  Sum_probs=47.1

Q ss_pred             ccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        45 ~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      ..|+|||++|.|-+.|++-|+|.|.|..          ..|.|-|.++++..|++.|..++..
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG~~~~v~iAr~AVemli~G  164 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIGGFEQVEIAREAVEMLING  164 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEecChhhhHHHHHHHHHHHcC
Confidence            4699999999999999999999999953          5699999999999999999866543

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=97.19  E-value=0.028  Score=48.27  Aligned_cols=131  Identities=13%  Similarity=0.105  Sum_probs=93.6

Q ss_pred             EEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCC
Q 022837           38 RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADD  117 (291)
Q Consensus        38 rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~  117 (291)
                      .+.++....-++...+|..++.|-...|++|.+..        .+..|.|+|+...+..+...|.+.+..-         
T Consensus        29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--------~~~~i~I~g~k~~~~~i~~~i~~~l~~i---------   91 (210)
T PF14611_consen   29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--------SENRIRITGTKSTAEYIEASINEILSNI---------   91 (210)
T ss_pred             EEEecchheeeeecCCchHHHHHHHhcCceEEEec--------CCcEEEEEccHHHHHHHHHHHHHHHhhc---------
Confidence            34445778889999999999999888899999965        3468999999998888888887555332         


Q ss_pred             CCCceEEEEEecCCccceee----ccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEE-----cCHHHHHHHHHHH
Q 022837          118 VGTKTKLRLIVPNSSCGSII----GKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT-----GTLDEQMRALELI  188 (291)
Q Consensus       118 ~~~~~~~~i~VP~~~vg~II----Gk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~-----G~~~~v~~A~~~I  188 (291)
                          .+..+.++.-.--..-    -.....++.|++.|++.|...++        +..+.|+     -....++.|+.++
T Consensus        92 ----~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~--------~~~~~i~~~~~~~~~~~~~~a~RlL  159 (210)
T PF14611_consen   92 ----RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD--------GNKLKISWLASPENEKRADRAKRLL  159 (210)
T ss_pred             ----EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC--------CCeEEEEEEeeccccchHHHHHHHH
Confidence                3444444432211111    12356799999999999998763        2334444     4678899999999


Q ss_pred             HHHHhcCcc
Q 022837          189 LLKLSEDTL  197 (291)
Q Consensus       189 ~~~l~e~~~  197 (291)
                      ...+..++.
T Consensus       160 ~~a~~~~~~  168 (210)
T PF14611_consen  160 LWALDYNPH  168 (210)
T ss_pred             HHhccCCcc
Confidence            998864444

>TIGR01953 NusA transcription termination factor NusA

Probab=97.12  E-value=0.0011  Score=61.14  Aligned_cols=95  Identities=20%  Similarity=0.311  Sum_probs=66.0

Q ss_pred             cccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCce
Q 022837           44 PLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKT  122 (291)
Q Consensus        44 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~  122 (291)
                      +-+|+.||++|.+|+.|.++. |-+|.|-..++      +        +      ..+|...|.-..-..-...+ ....
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~------d--------~------~~fi~nal~Pa~v~~v~i~~-~~~~  301 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSD------D--------P------AEFIANALSPAKVISVEVLD-EDKH  301 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcCC------C--------H------HHHHHHhcCCceEEEEEEEc-CCCc
Confidence            358999999999999999998 88888865332      1        1      11222111110000000001 1225


Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEec
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~  159 (291)
                      ...+.||.+..+..|||+|.|++-...-||.+|.|..
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            7899999999999999999999999999999999976

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

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.11  E-value=0.0011  Score=61.37  Aligned_cols=95  Identities=17%  Similarity=0.182  Sum_probs=66.6

Q ss_pred             cccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCce
Q 022837           44 PLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKT  122 (291)
Q Consensus        44 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~  122 (291)
                      +-+|..||++|.+|+.|.++. |-+|.|-..++      +              -..+|...|.-..-.. .... ....
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~------D--------------~~~fI~Nal~Pa~V~~-V~i~-~~~~  308 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSN------V--------------PEIFIARALAPAIISS-VKIE-EEEK  308 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCC------C--------------HHHHHHHhCCCceeeE-EEEc-CCCc
Confidence            458999999999999999998 88888865332      1              1122222221110000 0000 2235


Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL  160 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  160 (291)
                      ...+.||.+..+..|||+|.|++-...-||.+|.|..-
T Consensus       309 ~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~  346 (374)
T PRK12328        309 KAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI  346 (374)
T ss_pred             EEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence            78889999999999999999999999999999999873

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=97.10  E-value=0.00099  Score=61.85  Aligned_cols=96  Identities=23%  Similarity=0.329  Sum_probs=67.2

Q ss_pred             cccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCce
Q 022837           44 PLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKT  122 (291)
Q Consensus        44 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~  122 (291)
                      +-+|+.||++|.+|+.|.++. |-+|.|-..++      +              ...+|...|.-..-..-...+ ....
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~------d--------------~~~fi~nal~Pa~v~~v~i~~-~~~~  303 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSE------D--------------PAEFVANALSPAKVVSVEVDD-EEEK  303 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCC------C--------------HHHHHHHhCCCceEEEEEEEc-CCCc
Confidence            358999999999999999998 88888865432      1              112222222111000000001 2235


Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL  160 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  160 (291)
                      ...+.||.+..+..|||+|.|++-...-||.+|.|...
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            78899999999999999999999999999999999873

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

Probab=97.06  E-value=0.00077  Score=60.58  Aligned_cols=72  Identities=24%  Similarity=0.293  Sum_probs=59.5

Q ss_pred             ceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCc
Q 022837          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDT  196 (291)
Q Consensus       121 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~  196 (291)
                      .....+.|+..+.|.|||++|.+.++|+++|+++|.++....    ..+.++.+.+..++|.+|.+.|..+|.+..
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~----n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r  127 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT----NKEEIKIIGISRNCVIQALERIAKLIDSDR  127 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC----CcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence            356778899999999999999999999999999999987321    234455555679999999999999988754

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

Probab=97.05  E-value=0.0011  Score=45.39  Aligned_cols=36  Identities=28%  Similarity=0.452  Sum_probs=33.8

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEE
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKI  157 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i  157 (291)
                      ....+.|+.+..|..|||+|.+|+.++..+|-+|.+
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            688999999999999999999999999999988876

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.

>PRK00468 hypothetical protein; Provisional

Probab=97.03  E-value=0.00077  Score=48.16  Aligned_cols=35  Identities=23%  Similarity=0.321  Sum_probs=30.8

Q ss_pred             CCCcEEEEEEecccccceeeccCChhHHHHHHHhC
Q 022837           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSG   65 (291)
Q Consensus        31 ~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tg   65 (291)
                      .++.+.+++.|..+.+|+||||+|.+|+.||.--.
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~   60 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK   60 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence            44568999999999999999999999999998644

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.90  E-value=0.0021  Score=56.43  Aligned_cols=65  Identities=17%  Similarity=0.231  Sum_probs=55.2

Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcCc
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSEDT  196 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I~~~l~e~~  196 (291)
                      -+.+.||..+++++||++|.+|+.|.+.++++|.+-.         +..|.|.++ .+.+.+|..+|..+-++..
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~---------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~  211 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ---------NGRIWIKGPDEEDEEIAIEAIKKIEREAH  211 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC---------CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence            3568899999999999999999999999999999864         367889888 5588889999988766643

>PRK02821 hypothetical protein; Provisional

Probab=96.86  E-value=0.0013  Score=47.17  Aligned_cols=36  Identities=25%  Similarity=0.377  Sum_probs=31.2

Q ss_pred             CCCcEEEEEEecccccceeeccCChhHHHHHHHhCC
Q 022837           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGA   66 (291)
Q Consensus        31 ~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga   66 (291)
                      .++.+.+++.|..+.+|+||||+|.+|+.||.--.+
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            345588999999999999999999999999987654

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.86  E-value=0.0015  Score=61.51  Aligned_cols=95  Identities=23%  Similarity=0.275  Sum_probs=65.8

Q ss_pred             cccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCce
Q 022837           44 PLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKT  122 (291)
Q Consensus        44 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~  122 (291)
                      +-+|..||++|.+|+.|.++. |-+|.|-.-++      +        +      ..+|...|.-..-..-...+ ....
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~------D--------p------~~fI~NaLsPA~V~~V~i~~-~~~k  335 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSP------D--------P------ATYIANALSPARVDEVRLVD-PEGR  335 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCC------C--------H------HHHHHHhcCCceeeEEEEEc-CCCc
Confidence            458999999999999999999 88888865332      1        1      12222222111000000001 1224


Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEec
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~  159 (291)
                      ...+.||.+..+..|||+|.|++-...-||.+|.|..
T Consensus       336 ~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        336 HAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             EEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            6789999999999999999999999999999999975

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

Probab=96.83  E-value=0.0023  Score=53.90  Aligned_cols=41  Identities=29%  Similarity=0.440  Sum_probs=35.8

Q ss_pred             CCceEEEEEec------CCccceeeccCChhHHHHHHhccceEEEec
Q 022837          119 GTKTKLRLIVP------NSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (291)
Q Consensus       119 ~~~~~~~i~VP------~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~  159 (291)
                      ....+-++.||      .++||.|||..|.|.|++++.|+|+|.|-.
T Consensus       145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG  191 (269)
T COG5176         145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG  191 (269)
T ss_pred             cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence            34467778887      679999999999999999999999999976

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.72  E-value=0.0022  Score=65.56  Aligned_cols=66  Identities=15%  Similarity=0.315  Sum_probs=54.9

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCc-EEEcCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHHh
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGAR-IQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVIDKLL  106 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~-I~v~~~~~~~p~~~er~v~I~G-~~~~v~~A~~~I~~~i~  106 (291)
                      .-+....|.||.++++.|||.||.+||.|.++||++ |++.+         +-.|.|.+ ..+.+.+|+++|.+.+.
T Consensus       682 ~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---------dg~V~I~a~d~~~i~~A~~~I~~l~~  749 (891)
T PLN00207        682 YAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---------DGTVKITAKDLSSLEKSKAIISSLTM  749 (891)
T ss_pred             cCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---------CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            345678899999999999999999999999999999 99964         24466666 57889999999876554

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

Probab=96.72  E-value=0.002  Score=45.94  Aligned_cols=34  Identities=35%  Similarity=0.432  Sum_probs=30.6

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhC
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSG   65 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tg   65 (291)
                      ++.+.+++.+..+..|.||||+|.+|+.||.--.
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~   60 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLS   60 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHHHH
Confidence            6678999999999999999999999999997543

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=96.61  E-value=0.0021  Score=61.71  Aligned_cols=94  Identities=21%  Similarity=0.298  Sum_probs=65.9

Q ss_pred             ccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCceE
Q 022837           45 LAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTK  123 (291)
Q Consensus        45 ~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~  123 (291)
                      -+|+.||++|.+|+.|.++. |-+|.|-.-++      +        +      ..+|...|.-..-.. -..+ .....
T Consensus       246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~------d--------~------~~fi~nal~pa~v~~-v~~~-~~~~~  303 (470)
T PRK09202        246 PVGACVGMRGSRIQAISNELGGEKIDIILWSD------D--------P------AQFIINALSPAEVSS-VVVD-EDEHS  303 (470)
T ss_pred             hhHccCCCCCchHHHHHHHhCCCeEEEEEcCC------C--------H------HHHHHHhCCCCEEEE-EEEe-CCCCE
Confidence            48999999999999999998 78888865332      1        1      122222221110000 0000 11248


Q ss_pred             EEEEecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837          124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL  160 (291)
Q Consensus       124 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  160 (291)
                      ..+.||.+..+..|||+|.|++...+.||.+|.|...
T Consensus       304 ~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        304 ADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             EEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            8899999999999999999999999999999999763

>PRK12705 hypothetical protein; Provisional

Probab=96.60  E-value=0.0053  Score=59.43  Aligned_cols=65  Identities=18%  Similarity=0.188  Sum_probs=44.4

Q ss_pred             ceEEEEEecC-CccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHh
Q 022837          121 KTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLS  193 (291)
Q Consensus       121 ~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I~~~l~  193 (291)
                      .....+.+|+ ++-|+||||.|.|||.++..||+.|.|.+        ..+.|+|++. +..-+.|...+..++.
T Consensus       197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--------tp~~V~ls~fdp~rreia~~~l~~Li~  263 (508)
T PRK12705        197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD--------TPEAVVISSFNPIRREIARLTLEKLLA  263 (508)
T ss_pred             heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC--------CccchhhcccCccchHHHHHHHHHHHh
Confidence            3455566776 56699999999999999999999999976        2344666664 3333334444444433

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

Probab=96.55  E-value=0.0037  Score=61.54  Aligned_cols=62  Identities=18%  Similarity=0.284  Sum_probs=51.8

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCH-HHHHHHHHHHHHHH
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTI-DEILRAVDLVIDKL  105 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~-~~v~~A~~~I~~~i  105 (291)
                      -...+.|+.+.++.+||++|.+|++|.++||++|++.++         -.|.|.++. +.+.+|++.|....
T Consensus       552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd---------Gtv~i~~s~~~~~~~ak~~I~~i~  614 (692)
T COG1185         552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD---------GTVKIAASDGESAKKAKERIEAIT  614 (692)
T ss_pred             ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC---------CcEEEEecchHHHHHHHHHHHHHH
Confidence            456788899999999999999999999999999999743         347777765 67888888887555

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

Probab=96.54  E-value=0.0069  Score=58.22  Aligned_cols=93  Identities=16%  Similarity=0.168  Sum_probs=71.6

Q ss_pred             HHHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEE
Q 022837           94 ILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVT  173 (291)
Q Consensus        94 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~  173 (291)
                      ...|+..|++.+.+.+............+...+.|+.+....+||.+|...|+|..+||+.-++          ++.+++
T Consensus       569 a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v----------De~t~~  638 (760)
T KOG1067|consen  569 AREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV----------DEGTFS  638 (760)
T ss_pred             hhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee----------cCceEE
Confidence            3456677888787776544333344566788899999999999999999999999999954444          346788


Q ss_pred             EEcC-HHHHHHHHHHHHHHHhcCc
Q 022837          174 LTGT-LDEQMRALELILLKLSEDT  196 (291)
Q Consensus       174 I~G~-~~~v~~A~~~I~~~l~e~~  196 (291)
                      |.-. +.+.++|++.|..++..+.
T Consensus       639 i~A~~~~am~~Ak~~I~~i~~~~~  662 (760)
T KOG1067|consen  639 IFAPTQAAMEEAKEFIDGIIKDDQ  662 (760)
T ss_pred             EEecCHHHHHHHHHHHHHHhcCcc
Confidence            7775 7888999999999887743

>PRK01064 hypothetical protein; Provisional

Probab=96.50  E-value=0.0036  Score=45.06  Aligned_cols=34  Identities=26%  Similarity=0.398  Sum_probs=30.5

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhC
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSG   65 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tg   65 (291)
                      ++.+.+++.|..+..|.+|||+|.+|+.||.-..
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~   60 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV   60 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence            4668999999999999999999999999998643

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.43  E-value=0.0086  Score=52.51  Aligned_cols=62  Identities=26%  Similarity=0.324  Sum_probs=50.4

Q ss_pred             EEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecC-HHHHHHHHHHHHHHHhhh
Q 022837           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~-~~~v~~A~~~I~~~i~~~  108 (291)
                      +.+.||..+++.+||++|.+|+.|.++|+++|.+-.+         -.|.|.+. .+++..|+.+|. .+.++
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N---------G~VwI~~~~~~~~~~a~~~I~-~~e~~  209 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN---------GRIWIKGPDEEDEEIAIEAIK-KIERE  209 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC---------cEEEEeeCCHHHHHHHHHHHH-HHHhh
Confidence            5588999999999999999999999999999999542         34777775 558888888886 45444

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=96.41  E-value=0.0038  Score=50.24  Aligned_cols=103  Identities=15%  Similarity=0.150  Sum_probs=69.1

Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCCC
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTM  202 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~  202 (291)
                      ..-++|....+|..||++|++|+.|++..|-+|.+-.-+              .++      .++|...|.-..-.  ..
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys--------------~D~------~~fI~N~l~PA~V~--~V   91 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYS--------------ENL------EEFVANKLAPAEVK--NV   91 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcC--------------CCH------HHHHHHcCCCceEE--EE
Confidence            777889999999999999999999999999888886521              111      12222222110000  00


Q ss_pred             CCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehccccc
Q 022837          203 TVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSI  282 (291)
Q Consensus       203 ~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~t  282 (291)
                      .  ..                                      .........+.||.+..|..|||  +|.||+-.++=+
T Consensus        92 ~--i~--------------------------------------~~~~~~~a~V~V~~~d~~~AIGk--~G~Ni~la~~l~  129 (141)
T TIGR01952        92 T--VS--------------------------------------EFNGKKVAYVEVHPRDKGIAIGK--GGKNIERAKELA  129 (141)
T ss_pred             E--EE--------------------------------------cCCCCEEEEEEEChhhhhhhhCC--CchhHHHHHHHh
Confidence            0  00                                      00011347789999999999999  999999998888


Q ss_pred             cceEEee
Q 022837          283 YEEIRLN  289 (291)
Q Consensus       283 ga~i~~~  289 (291)
                      |-.+-|.
T Consensus       130 ~~~~dI~  136 (141)
T TIGR01952       130 KRHHDID  136 (141)
T ss_pred             cCccCCe
Confidence            8776553

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.

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

Probab=96.33  E-value=0.011  Score=49.93  Aligned_cols=40  Identities=25%  Similarity=0.390  Sum_probs=33.9

Q ss_pred             cEEEEEEecc------cccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837           34 PTYIRFLVSN------PLAGAVIGKGGSTINDFQSQSGARIQLSRS   73 (291)
Q Consensus        34 ~~~~rilvp~------~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~   73 (291)
                      .+.-++.||.      +.||+|||..|.|+|+|+..|+|+|-|...
T Consensus       147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            3566677764      479999999999999999999999999653

>PRK02821 hypothetical protein; Provisional

Probab=96.33  E-value=0.0071  Score=43.38  Aligned_cols=35  Identities=23%  Similarity=0.320  Sum_probs=29.7

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQA  153 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa  153 (291)
                      .....+.+.+..+.+|+||||+|.+|+.|+.--.+
T Consensus        28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            34478899999999999999999999999876443

>PRK00468 hypothetical protein; Provisional

Probab=96.32  E-value=0.0049  Score=44.05  Aligned_cols=33  Identities=27%  Similarity=0.343  Sum_probs=29.0

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDS  151 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t  151 (291)
                      ......++.+..+.+|+||||+|.+|+.|+.--
T Consensus        27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            445788999999999999999999999998754

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

Probab=95.92  E-value=0.0099  Score=42.41  Aligned_cols=33  Identities=27%  Similarity=0.391  Sum_probs=29.2

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDS  151 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t  151 (291)
                      ......+|.+.....|+||||+|.+|+.|+.--
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            456789999999999999999999999998653

>PRK12704 phosphodiesterase; Provisional

Probab=95.63  E-value=0.032  Score=54.57  Aligned_cols=49  Identities=22%  Similarity=0.480  Sum_probs=39.2

Q ss_pred             CcEEEEEEecc-cccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec
Q 022837           33 KPTYIRFLVSN-PLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG   89 (291)
Q Consensus        33 ~~~~~rilvp~-~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G   89 (291)
                      ..++--+.+|+ +.-|+||||.|.||+.++.-||+.|-|.+        +..+|.|+|
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~  257 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSG  257 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--------CCCeEEEec
Confidence            34445566777 58999999999999999999999999964        234577888

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.55  E-value=0.015  Score=58.95  Aligned_cols=63  Identities=21%  Similarity=0.313  Sum_probs=50.2

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHH
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVIDKL  105 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G-~~~~v~~A~~~I~~~i  105 (291)
                      +....+.|+.+.++.+||.+|.+||+|.++||++|.+.++         -.|.|.+ ..+.+.+|+++|....
T Consensus       553 p~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~---------G~v~i~~~~~~~~~~a~~~I~~~~  616 (693)
T PRK11824        553 PRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD---------GTVKIAATDGEAAEAAKERIEGIT  616 (693)
T ss_pred             chheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC---------ceEEEEcccHHHHHHHHHHHHHhc
Confidence            3445666799999999999999999999999999998542         3366666 5678889988887544

>PRK01064 hypothetical protein; Provisional

Probab=95.50  E-value=0.019  Score=41.32  Aligned_cols=33  Identities=33%  Similarity=0.391  Sum_probs=29.0

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDS  151 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t  151 (291)
                      ...+.+++.+..+..|++|||+|.+|+.|+.-.
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            455788999999999999999999999998753

>PRK00106 hypothetical protein; Provisional

Probab=95.48  E-value=0.046  Score=53.36  Aligned_cols=49  Identities=20%  Similarity=0.511  Sum_probs=39.5

Q ss_pred             CcEEEEEEecc-cccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec
Q 022837           33 KPTYIRFLVSN-PLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG   89 (291)
Q Consensus        33 ~~~~~rilvp~-~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G   89 (291)
                      ..++--+.+|+ +.-|+||||.|.||+.++.-||+.+-|.+.        ...|+|+|
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt--------p~~v~lS~  272 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT--------PEVVVLSG  272 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC--------CCeEEEeC
Confidence            44556677787 589999999999999999999999999642        23466777

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=95.48  E-value=0.043  Score=53.61  Aligned_cols=49  Identities=20%  Similarity=0.473  Sum_probs=39.2

Q ss_pred             CcEEEEEEecc-cccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec
Q 022837           33 KPTYIRFLVSN-PLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG   89 (291)
Q Consensus        33 ~~~~~rilvp~-~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G   89 (291)
                      ..++--+.+|+ +.-|+||||.|.||+.++.-||+.|-|.+.        ...|+|++
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt--------p~~v~ls~  251 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT--------PEAVILSG  251 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC--------CCeEEecC
Confidence            44555677787 589999999999999999999999999642        23466777

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=95.01  E-value=0.011  Score=41.93  Aligned_cols=37  Identities=32%  Similarity=0.352  Sum_probs=30.6

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcE
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARI   68 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I   68 (291)
                      .+...+.+-+..+..|.||||+|.+++.||.-.+.-+
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~   62 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA   62 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence            3456688888999999999999999999998766443

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

Probab=94.48  E-value=0.036  Score=57.51  Aligned_cols=71  Identities=17%  Similarity=0.176  Sum_probs=60.7

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      ...++.+|.....+|||++|.+|+.++.-|||.|.+.+-..  .+..||.+.+.|.++.+.-|...|.-.+.+
T Consensus      1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~--~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQP--DNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCC--ccchhhhcccCCCChhhhhhhccccceeec
Confidence            45678899999999999999999999999999999987211  234789999999999999999888876654

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=94.42  E-value=0.45  Score=40.76  Aligned_cols=66  Identities=18%  Similarity=0.170  Sum_probs=57.1

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED  195 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~  195 (291)
                      ..+.+.++....-.|...+|..++.|....||+|.+..        .+..|.|+|+...+..+...|.+.+..-
T Consensus        26 g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--------~~~~i~I~g~k~~~~~i~~~i~~~l~~i   91 (210)
T PF14611_consen   26 GDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--------SENRIRITGTKSTAEYIEASINEILSNI   91 (210)
T ss_pred             ceeEEEecchheeeeecCCchHHHHHHHhcCceEEEec--------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence            35556667888899999999999999888899999987        4579999999999999999999988764

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

Probab=94.37  E-value=0.079  Score=36.19  Aligned_cols=35  Identities=29%  Similarity=0.337  Sum_probs=29.1

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcE
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARI   68 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I   68 (291)
                      ...+.+.+.....|.+|||+|.+++.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            45666777776789999999999999999998554

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.

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

Probab=94.12  E-value=0.17  Score=40.59  Aligned_cols=95  Identities=17%  Similarity=0.261  Sum_probs=65.1

Q ss_pred             eeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCceEEEEEe
Q 022837           49 VIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIV  128 (291)
Q Consensus        49 IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~V  128 (291)
                      .+=.+|..|++|-++..-+|.|..+...           .-   .=..|.+.|.+.+-++..-   .+-.-+..+-++.|
T Consensus        20 ~~~~~~dli~~lAk~lrKRIvvR~dps~-----------l~---~~e~A~~~I~~ivP~ea~i---~di~Fd~~tGEV~I   82 (145)
T cd02410          20 LFAEDGDLVKDLAKDLRKRIVIRPDPSV-----------LK---PPEEAIKIILEIVPEEAGI---TDIYFDDDTGEVII   82 (145)
T ss_pred             HHhcccHHHHHHHHHHhceEEEcCChhh-----------cC---CHHHHHHHHHHhCCCccCc---eeeEecCCCcEEEE
Confidence            4446788999999999988888654211           11   1145878887655333110   00011224667788


Q ss_pred             cCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837          129 PNSSCGSIIGKAGATIKSFMDDSQAVIKISRL  160 (291)
Q Consensus       129 P~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  160 (291)
                      -...-|.+||++|.++++|..+||-.-.+...
T Consensus        83 eaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          83 EAEKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             EEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence            88888999999999999999999988888763

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

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

Probab=93.81  E-value=0.051  Score=38.17  Aligned_cols=37  Identities=30%  Similarity=0.444  Sum_probs=30.2

Q ss_pred             EEEEecccc-----cceeeccCChhHHHHHHHh-CCcEEEcCC
Q 022837           37 IRFLVSNPL-----AGAVIGKGGSTINDFQSQS-GARIQLSRS   73 (291)
Q Consensus        37 ~rilvp~~~-----vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~   73 (291)
                      .++.|-+..     +|..||++|.+|+.|.++. |-+|+|-..
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            567777777     9999999999999999999 899988654

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

Probab=93.69  E-value=0.077  Score=50.36  Aligned_cols=67  Identities=19%  Similarity=0.232  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCC
Q 022837           94 ILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLD  161 (291)
Q Consensus        94 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~  161 (291)
                      ...|.+.|...+.+.++.. ....-.......+.||..+++.+|||+|.+|++|+++.|.+|.|...+
T Consensus       459 ~~~a~~~i~~~i~r~~p~~-~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e  525 (604)
T COG1855         459 LKLAEEEIEREIKRYLPGD-VEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE  525 (604)
T ss_pred             hHHHHHHHHHHHHHhCCCC-ceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence            4456666665555554421 111112234677889999999999999999999999999999998743

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=93.54  E-value=0.037  Score=39.17  Aligned_cols=35  Identities=20%  Similarity=0.324  Sum_probs=29.8

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQA  153 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa  153 (291)
                      .......+.+..+..|.||||.|.+++.||.-.+.
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            34568888899999999999999999999976554

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

Probab=93.43  E-value=0.034  Score=46.71  Aligned_cols=56  Identities=30%  Similarity=0.381  Sum_probs=49.0

Q ss_pred             ccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           43 NPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        43 ~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      +..+|+|+||+|.+--.|++.|.++|.+..          ..|.|-|..+|+.-|...|...|.-.
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad----------~kIHiLG~~~niriAR~avcsLIlGs  232 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD----------SKIHILGAFQNIRIARDAVCSLILGS  232 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEecC----------ceEEEeecchhhHHHHHhhHhhhccC
Confidence            457899999999999999999999999953          55999999999999999998776543

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

Probab=93.10  E-value=0.19  Score=34.19  Aligned_cols=34  Identities=24%  Similarity=0.456  Sum_probs=27.6

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceE
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVI  155 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I  155 (291)
                      ....+.+.....|.+||++|.+++.++..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            5556666666789999999999999999987544

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=93.08  E-value=0.063  Score=45.12  Aligned_cols=150  Identities=11%  Similarity=0.047  Sum_probs=88.4

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccc--
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAE--  112 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~--  112 (291)
                      -+-++.||....--+=-.==....-|-+..+..|.+.-...   ..+-|.+.-+-.+.+++++.+.|...+.-..-.+  
T Consensus        74 e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK~r---~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DAi  150 (252)
T KOG3273|consen   74 ETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLKAR---SVELRTCKDTEDPSALQKGADFVRAFILGFDIDDAI  150 (252)
T ss_pred             ceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecccc---eeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhHH
Confidence            34567777765433211111112345566666666632211   1122333334456788888777765443220000  


Q ss_pred             -----cc-cC---CCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHH
Q 022837          113 -----DQ-AD---DVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR  183 (291)
Q Consensus       113 -----~~-~~---~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~  183 (291)
                           ++ ..   +-.+..+++=.=-...+|+|+||+|.+--.|++.|.++|.+..          ..|-|-|..+++.-
T Consensus       151 ALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVlad----------~kIHiLG~~~niri  220 (252)
T KOG3273|consen  151 ALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLAD----------SKIHILGAFQNIRI  220 (252)
T ss_pred             HHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEecC----------ceEEEeecchhhHH
Confidence                 00 00   0011112222222456899999999999999999999999864          57999999999999


Q ss_pred             HHHHHHHHHhcCcc
Q 022837          184 ALELILLKLSEDTL  197 (291)
Q Consensus       184 A~~~I~~~l~e~~~  197 (291)
                      |+..|+.++-.+|.
T Consensus       221 AR~avcsLIlGspp  234 (252)
T KOG3273|consen  221 ARDAVCSLILGSPP  234 (252)
T ss_pred             HHHhhHhhhccCCc
Confidence            99999999987654

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

Probab=93.08  E-value=0.21  Score=43.49  Aligned_cols=55  Identities=22%  Similarity=0.317  Sum_probs=43.7

Q ss_pred             EEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHH-HHHHHHHHHH
Q 022837           39 FLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTID-EILRAVDLVI  102 (291)
Q Consensus        39 ilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~-~v~~A~~~I~  102 (291)
                      +.|+...|.++||++|+.++.|.++|+|+|-|-.+.         .|.|.+..+ ...-|...|.
T Consensus       150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG---------~IWV~~~~~~~e~~~~~aI~  205 (239)
T COG1097         150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG---------RIWVDGENESLEELAIEAIR  205 (239)
T ss_pred             EEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCC---------EEEecCCCcchHHHHHHHHH
Confidence            688999999999999999999999999999996533         377777665 3444545554

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

Probab=92.93  E-value=0.2  Score=44.31  Aligned_cols=51  Identities=16%  Similarity=0.221  Sum_probs=45.9

Q ss_pred             ceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          134 GSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       134 g~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      -+|||.+|.|+|.|+--|.|.|-|..          .+|.+.|....+..+...+.+.+..
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            38999999999999999999999975          4799999999999999988887765

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

Probab=92.88  E-value=0.087  Score=54.82  Aligned_cols=69  Identities=20%  Similarity=0.131  Sum_probs=58.3

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHH
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI  102 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~  102 (291)
                      -.....++.+|.....+|||++|.+|..++..||+.|.|.+-..  .+..||.+.+.|.++.+.-|...|.
T Consensus      1337 ~~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~--~Nqaers~~~kg~p~~~r~a~~~I~ 1405 (2131)
T KOG4369|consen 1337 VPANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQP--DNQAERSKAPKGRPPSQRVATSPIG 1405 (2131)
T ss_pred             CcccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCC--ccchhhhcccCCCChhhhhhhcccc
Confidence            34457789999999999999999999999999999999976221  1346899999999999998887775

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=92.80  E-value=0.13  Score=36.86  Aligned_cols=35  Identities=23%  Similarity=0.321  Sum_probs=28.7

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEE
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQL   70 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v   70 (291)
                      .+.+-+..+..|.+|||+|.++..||--.+.-++-
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~   59 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR   59 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence            35666777889999999999999999987765554

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.

>PRK13764 ATPase; Provisional

Probab=92.60  E-value=0.14  Score=50.80  Aligned_cols=66  Identities=23%  Similarity=0.238  Sum_probs=47.4

Q ss_pred             HHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCC
Q 022837           95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLD  161 (291)
Q Consensus        95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~  161 (291)
                      ..|.+.|.+.+.+..... ...+........+.||...++.+|||+|.+|++|.++.|.+|.|.+.+
T Consensus       455 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~  520 (602)
T PRK13764        455 RLAEKEIEREIKRYLPGP-VEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD  520 (602)
T ss_pred             HHHHHHHHHHHHHhcCCc-eEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence            445556655555443111 111112345788899999999999999999999999999999998744

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

Probab=92.41  E-value=0.21  Score=47.87  Aligned_cols=97  Identities=20%  Similarity=0.261  Sum_probs=70.2

Q ss_pred             ceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCceEEEE
Q 022837           47 GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRL  126 (291)
Q Consensus        47 G~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i  126 (291)
                      ..++-+.|..||+|-++..-+|.+..+...+              ..-+.|.+.|++.+-++..-.   +..-+..+-++
T Consensus        41 P~~~~~~~dlik~lAk~lrKRI~iR~dPsvl--------------~~~e~A~~~I~eivP~ea~i~---~i~Fd~~tGEV  103 (637)
T COG1782          41 PELFAKDGDLIKDLAKDLRKRIIIRPDPSVL--------------KPPEEARKIILEIVPEEAGIT---DIYFDDDTGEV  103 (637)
T ss_pred             HHHhccchhHHHHHHHHHhhceEeccCchhc--------------CCHHHHHHHHHHhCccccCce---eEEecCCCceE
Confidence            4567789999999999999999997643211              123568888886664441111   11122346778


Q ss_pred             EecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837          127 IVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL  160 (291)
Q Consensus       127 ~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  160 (291)
                      +|-...=|.+|||+|++.++|..+||-.-.|.+.
T Consensus       104 iIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~  137 (637)
T COG1782         104 IIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT  137 (637)
T ss_pred             EEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence            8889999999999999999999999987777763

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

Probab=92.02  E-value=0.12  Score=36.27  Aligned_cols=37  Identities=24%  Similarity=0.476  Sum_probs=30.0

Q ss_pred             EEEEEecCCc-----cceeeccCChhHHHHHHhc-cceEEEec
Q 022837          123 KLRLIVPNSS-----CGSIIGKAGATIKSFMDDS-QAVIKISR  159 (291)
Q Consensus       123 ~~~i~VP~~~-----vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~  159 (291)
                      ..++.|-...     +|..||++|.+||.|+++. |-+|++-.
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            4566666666     8999999999999999999 99999876

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=92.01  E-value=0.086  Score=37.69  Aligned_cols=35  Identities=26%  Similarity=0.449  Sum_probs=30.1

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEE
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQ   69 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~   69 (291)
                      -.+.+.+...+.|.|||++|++|++|++..+-.+.
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            34678889999999999999999999998876664

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

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=91.95  E-value=0.21  Score=35.75  Aligned_cols=34  Identities=21%  Similarity=0.390  Sum_probs=27.6

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceE
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVI  155 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I  155 (291)
                      ....+.+..+..|.||||.|++++.||--...-+
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~   57 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVL   57 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence            3566778889999999999999999997765433

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.

>PRK12705 hypothetical protein; Provisional

Probab=91.78  E-value=0.28  Score=47.75  Aligned_cols=40  Identities=18%  Similarity=0.439  Sum_probs=33.1

Q ss_pred             cEEEEEEecc-cccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837           34 PTYIRFLVSN-PLAGAVIGKGGSTINDFQSQSGARIQLSRS   73 (291)
Q Consensus        34 ~~~~rilvp~-~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~   73 (291)
                      .++--+.+|+ +.-|+||||.|.||+.++..||+.|-|.+.
T Consensus       197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt  237 (508)
T PRK12705        197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT  237 (508)
T ss_pred             heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence            3444556666 589999999999999999999999999753

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=90.61  E-value=0.26  Score=41.70  Aligned_cols=37  Identities=22%  Similarity=0.294  Sum_probs=35.2

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcC
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSR   72 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~   72 (291)
                      .+.+.||.++.+.+|||+|.+++.+.+-||-++.|..
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            7889999999999999999999999999999999965

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

Probab=90.58  E-value=0.2  Score=47.67  Aligned_cols=39  Identities=26%  Similarity=0.406  Sum_probs=35.5

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCC
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSH   74 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~   74 (291)
                      ...+.||..+++.+|||+|.+|++|++..|.+|.|....
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            366889999999999999999999999999999997654

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=90.57  E-value=0.11  Score=37.07  Aligned_cols=35  Identities=23%  Similarity=0.495  Sum_probs=29.9

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEE
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIK  156 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~  156 (291)
                      ....+.+...+-|.|||++|++|++|....+-.+.
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            46788899999999999999999999887765553

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

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

Probab=90.56  E-value=0.83  Score=39.80  Aligned_cols=59  Identities=19%  Similarity=0.261  Sum_probs=45.5

Q ss_pred             EEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHH-HHHHHHHHHHH
Q 022837          124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE-QMRALELILLK  191 (291)
Q Consensus       124 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~-v~~A~~~I~~~  191 (291)
                      .-+.|+...+.++||++|+.++-|.+.++|+|-+-.+         ..|=|.|..+. ...|...|..+
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N---------G~IWV~~~~~~~e~~~~~aI~~i  207 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN---------GRIWVDGENESLEELAIEAIRKI  207 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC---------CEEEecCCCcchHHHHHHHHHHH
Confidence            5578999999999999999999999999999999752         45777777653 44444444443

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

Probab=90.28  E-value=0.51  Score=41.81  Aligned_cols=51  Identities=18%  Similarity=0.274  Sum_probs=44.1

Q ss_pred             ceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           47 GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        47 G~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      -++||.+|.|+|.|+--|.|.|-|..          ..|.+.|....+..+.+.+.+.+..
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            46999999999999999999999953          4588999999999998888877754

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=90.02  E-value=0.46  Score=44.30  Aligned_cols=40  Identities=20%  Similarity=0.172  Sum_probs=36.8

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCC
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSH   74 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~   74 (291)
                      -.+.+.||.++.++.|||+|.|++-..+-||.+|.|..-.
T Consensus       308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~  347 (374)
T PRK12328        308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG  347 (374)
T ss_pred             cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence            4788999999999999999999999999999999997643

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

Probab=89.82  E-value=0.55  Score=45.66  Aligned_cols=99  Identities=19%  Similarity=0.268  Sum_probs=68.6

Q ss_pred             CCCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHHhh
Q 022837           29 DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        29 ~~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G-~~~~v~~A~~~I~~~i~~  107 (291)
                      +....++...+.|+.+....+||.+|-..|+|+.+||+.-.+.          +-.+.|.. ++...++|++.|...+..
T Consensus       591 ~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD----------e~t~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  591 DKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD----------EGTFSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             ccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec----------CceEEEEecCHHHHHHHHHHHHHHhcC
Confidence            3445678889999999999999999999999999999666663          23455554 577889999998765544


Q ss_pred             hhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEec
Q 022837          108 ELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (291)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~  159 (291)
                      +-.++                  -..|.|-   -.+|++|+ ++|+-+.+.+
T Consensus       661 ~~~~~------------------l~~g~vy---~~tIt~~r-d~G~~V~l~p  690 (760)
T KOG1067|consen  661 DQVQD------------------LEFGGVY---TATITEIR-DTGVMVELYP  690 (760)
T ss_pred             ccccc------------------eEeeeEE---EEEEeeec-ccceEEEecC
Confidence            31111                  1112111   23466766 4889888887

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=89.81  E-value=0.51  Score=38.98  Aligned_cols=36  Identities=22%  Similarity=0.440  Sum_probs=31.5

Q ss_pred             EEEEecccccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS   73 (291)
Q Consensus        37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~   73 (291)
                      +-|+|.... |..|||+|.+++++++..|-+|.+-..
T Consensus        63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~   98 (166)
T PRK06418         63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK   98 (166)
T ss_pred             EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence            456777777 999999999999999999999999754

>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein

Probab=89.71  E-value=0.58  Score=46.98  Aligned_cols=97  Identities=15%  Similarity=0.201  Sum_probs=67.9

Q ss_pred             ceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCceEEEE
Q 022837           47 GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRL  126 (291)
Q Consensus        47 G~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i  126 (291)
                      ...+=.+|..||+|-++..-+|.|..+..           +.-.   -+.|.+.|.+.+-++..   -.+-.-+..+-++
T Consensus        35 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~~-----------~~~~---~~~~~~~i~~~~~~~~~---~~~~~f~~~~~~v   97 (630)
T TIGR03675        35 PELFAKDDDLVKELAKKLRKRIVIRPDPS-----------VLLP---PEEAIEKIKEIVPEEAG---ITDIYFDDVTGEV   97 (630)
T ss_pred             HHHhccchHHHHHHHHHhhceEEEecChh-----------hcCC---HHHHHHHHHHhCCCcCC---ceeEEecCCCceE
Confidence            34566788999999999999999965432           1111   24577777755533311   0011112346778


Q ss_pred             EecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837          127 IVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL  160 (291)
Q Consensus       127 ~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  160 (291)
                      .|-...-|.||||+|.++++|..+||-.-.|.+.
T Consensus        98 ~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~  131 (630)
T TIGR03675        98 IIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT  131 (630)
T ss_pred             EEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence            8888999999999999999999999998888763

This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.

>TIGR01953 NusA transcription termination factor NusA

Probab=89.41  E-value=0.45  Score=44.03  Aligned_cols=38  Identities=21%  Similarity=0.317  Sum_probs=35.8

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcC
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSR   72 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~   72 (291)
                      -.+.+.||.++.+..|||+|.|++-..+-||.+|.|..
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            47899999999999999999999999999999999965

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.

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

Probab=89.08  E-value=0.51  Score=34.19  Aligned_cols=36  Identities=17%  Similarity=0.341  Sum_probs=30.8

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEc
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLS   71 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~   71 (291)
                      .+++.|....-|.|||++|.+|++|+++..-...+.
T Consensus        31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~   66 (81)
T cd02413          31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP   66 (81)
T ss_pred             eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence            378888889999999999999999999887666663

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.

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=89.07  E-value=0.48  Score=45.45  Aligned_cols=126  Identities=14%  Similarity=0.072  Sum_probs=82.1

Q ss_pred             eeeccCChhHHHHHHHhCCcEE--EcCCCCCCCCCCceE-EEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCceEE
Q 022837           48 AVIGKGGSTINDFQSQSGARIQ--LSRSHEFFPGTTDRI-IMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKL  124 (291)
Q Consensus        48 ~IIGk~G~~Ik~I~~~tga~I~--v~~~~~~~p~~~er~-v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~  124 (291)
                      .+=||+--.+.+|++...|.+.  +...+      ..++ -.+.|..-.-.++...+.    .+++           ...
T Consensus       393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~~------gs~~~~~~~g~~~~F~k~~~~~~----~EFp-----------ae~  451 (657)
T COG5166         393 FLRGKKNGKATRIMKGVSCSELSSIVSST------GSIVETNGIGEKMSFSKKLSIPP----TEFP-----------AEI  451 (657)
T ss_pred             HhccccCcchhhhhhhcccceeeEEEecC------CcEEEEeccCcchhhHHHhcCCc----ccCc-----------hhe
Confidence            5667777779999999999844  44322      2233 334566555565554443    2222           256


Q ss_pred             EEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHH---HHHHHHHHHHHHHhc
Q 022837          125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD---EQMRALELILLKLSE  194 (291)
Q Consensus       125 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~---~v~~A~~~I~~~l~e  194 (291)
                      .+.||...+..|||-||..|++++...++.|++...-....+.--.-|.|.-+..   ++.-++.-+.+++.+
T Consensus       452 ~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~  524 (657)
T COG5166         452 AFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ  524 (657)
T ss_pred             EEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhh
Confidence            7889999999999999999999999999999997632221111122377776643   344456666666664

>PRK13764 ATPase; Provisional

Probab=89.00  E-value=0.34  Score=48.18  Aligned_cols=41  Identities=27%  Similarity=0.357  Sum_probs=36.5

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCC
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHE   75 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~   75 (291)
                      -...+.||...++.+|||+|.+|++|+++.|.+|.|....+
T Consensus       481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~  521 (602)
T PRK13764        481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE  521 (602)
T ss_pred             CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence            34668899999999999999999999999999999977543

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

Probab=87.52  E-value=0.75  Score=33.32  Aligned_cols=36  Identities=17%  Similarity=0.369  Sum_probs=29.5

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEE
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKI  157 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i  157 (291)
                      ...++.|....-|.|||++|+.|++|++.-.-...+
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~   65 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF   65 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence            458888999999999999999999998876544433

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=86.46  E-value=0.82  Score=42.69  Aligned_cols=40  Identities=20%  Similarity=0.244  Sum_probs=36.6

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS   73 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~   73 (291)
                      .-.+.+.||.++.++.|||+|.|++-..+-||.+|.|...
T Consensus       302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            3568899999999999999999999999999999999753

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=86.18  E-value=1.1  Score=37.01  Aligned_cols=37  Identities=19%  Similarity=0.283  Sum_probs=32.4

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEec
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~  159 (291)
                      ..+-++|-... |.-|||+|.+++++++..|-+|.+-.
T Consensus        61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE   97 (166)
T PRK06418         61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE   97 (166)
T ss_pred             CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence            35667777777 99999999999999999999999876

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=86.09  E-value=0.66  Score=44.84  Aligned_cols=39  Identities=18%  Similarity=0.268  Sum_probs=36.2

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS   73 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~   73 (291)
                      -.+.+.||..+.+..|||+|.|++...+-||.+|.|...
T Consensus       302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            378899999999999999999999999999999999753

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

Probab=85.19  E-value=0.88  Score=34.85  Aligned_cols=31  Identities=19%  Similarity=0.402  Sum_probs=26.2

Q ss_pred             EEEEecccccceeeccCChhHHHHHHHhCCc
Q 022837           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGAR   67 (291)
Q Consensus        37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~   67 (291)
                      +++.|-...-|.|||++|++|++|++.....
T Consensus        63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~   93 (109)
T cd02412          63 VEVTIHTARPGIIIGKKGAGIEKLRKELQKL   93 (109)
T ss_pred             EEEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence            6777788889999999999999999876543

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.

>TIGR00436 era GTP-binding protein Era

Probab=84.69  E-value=2.5  Score=37.57  Aligned_cols=30  Identities=30%  Similarity=0.279  Sum_probs=23.6

Q ss_pred             ceEEEEEecCC-ccceeeccCChhHHHHHHh
Q 022837          121 KTKLRLIVPNS-SCGSIIGKAGATIKSFMDD  150 (291)
Q Consensus       121 ~~~~~i~VP~~-~vg~IIGk~G~~Ik~I~~~  150 (291)
                      .+...+.|..+ +-+.|||++|+.||+|...
T Consensus       220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~  250 (270)
T TIGR00436       220 KIHALISVERESQKKIIIGKNGSMIKAIGIA  250 (270)
T ss_pred             EEEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence            36677788855 5599999999999988654

Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=84.19  E-value=0.99  Score=42.95  Aligned_cols=38  Identities=21%  Similarity=0.267  Sum_probs=35.4

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcC
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSR   72 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~   72 (291)
                      -.+.+.||.++.++.|||+|.|++-..+-||.+|.|..
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            45789999999999999999999999999999999964

>PRK15494 era GTPase Era; Provisional

Probab=84.18  E-value=2.6  Score=38.97  Aligned_cols=29  Identities=24%  Similarity=0.328  Sum_probs=22.7

Q ss_pred             eEEEEEecCC-ccceeeccCChhHHHHHHh
Q 022837          122 TKLRLIVPNS-SCGSIIGKAGATIKSFMDD  150 (291)
Q Consensus       122 ~~~~i~VP~~-~vg~IIGk~G~~Ik~I~~~  150 (291)
                      +...|.|..+ +-+.|||++|+.||+|...
T Consensus       273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~  302 (339)
T PRK15494        273 INQVIVVSRESYKTIILGKNGSKIKEIGAK  302 (339)
T ss_pred             EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence            5577778855 5599999999999987543

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

Probab=84.14  E-value=1.2  Score=32.34  Aligned_cols=29  Identities=24%  Similarity=0.460  Sum_probs=23.7

Q ss_pred             EEEEecccccceeeccCChhHHHHHHHhC
Q 022837           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSG   65 (291)
Q Consensus        37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tg   65 (291)
                      +++.|....-|.+||++|.+|++|++.-.
T Consensus        40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l~   68 (85)
T cd02411          40 TQITIYAERPGMVIGRGGKNIRELTEILE   68 (85)
T ss_pred             EEEEEEECCCCceECCCchhHHHHHHHHH
Confidence            55666668889999999999999888753

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=82.12  E-value=1.9  Score=34.68  Aligned_cols=36  Identities=31%  Similarity=0.580  Sum_probs=31.4

Q ss_pred             EEEecccccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837           38 RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS   73 (291)
Q Consensus        38 rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~   73 (291)
                      ++.|-.+.-|.+|||+|.++++|..+||-+-.+.+.
T Consensus        79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence            466677888999999999999999999988888653

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.

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

Probab=81.65  E-value=1.8  Score=31.55  Aligned_cols=29  Identities=17%  Similarity=0.367  Sum_probs=24.3

Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhc
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDS  151 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t  151 (291)
                      ..++.|....-|.+||++|++|++|++.-
T Consensus        39 ~i~V~I~t~~pg~iIGk~G~~I~~l~~~l   67 (85)
T cd02411          39 GTQITIYAERPGMVIGRGGKNIRELTEIL   67 (85)
T ss_pred             cEEEEEEECCCCceECCCchhHHHHHHHH
Confidence            36777777889999999999999987764

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.

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

Probab=81.59  E-value=1.4  Score=33.67  Aligned_cols=30  Identities=30%  Similarity=0.511  Sum_probs=25.9

Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhcc
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQ  152 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tG  152 (291)
                      .+++.|....-|.|||++|++|++|++...
T Consensus        62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~   91 (109)
T cd02412          62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ   91 (109)
T ss_pred             CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence            477888888899999999999999987644

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.

>COG1159 Era GTPase [General function prediction only]

Probab=80.88  E-value=4.5  Score=36.54  Aligned_cols=30  Identities=37%  Similarity=0.444  Sum_probs=22.8

Q ss_pred             ceEEEEEecCC-ccceeeccCChhHHHHHHh
Q 022837          121 KTKLRLIVPNS-SCGSIIGKAGATIKSFMDD  150 (291)
Q Consensus       121 ~~~~~i~VP~~-~vg~IIGk~G~~Ik~I~~~  150 (291)
                      .+...|.|+.+ +-+-||||+|++||+|-..
T Consensus       228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~  258 (298)
T COG1159         228 KIHATIYVERESQKGIIIGKNGAMIKKIGTA  258 (298)
T ss_pred             EEEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence            45666778854 5599999999999887543

>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]

Probab=80.39  E-value=3.4  Score=37.68  Aligned_cols=34  Identities=21%  Similarity=0.318  Sum_probs=26.8

Q ss_pred             CCceEEEEEecCCc-cceeeccCChhHHHHHHhcc
Q 022837          119 GTKTKLRLIVPNSS-CGSIIGKAGATIKSFMDDSQ  152 (291)
Q Consensus       119 ~~~~~~~i~VP~~~-vg~IIGk~G~~Ik~I~~~tG  152 (291)
                      ...+..++.+|... ...||||||..|++|-++-+
T Consensus       325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~  359 (379)
T KOG1423|consen  325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN  359 (379)
T ss_pred             EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence            34578899999665 46889999999999976643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	291
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		4e-26
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		4e-25
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		4e-14
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		8e-05
1dtj_A	76	Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Bind		2e-08
1ec6_A	87	Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Bind		2e-08
1dt4_A	73	Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Bind		2e-08
1j4w_A	174	Complex Of The Kh3 And Kh4 Domains Of Fbp With A Si		2e-08
3vke_A	76	Contribution Of The First K-Homology Domain Of Poly		4e-06
3vke_A	76	Contribution Of The First K-Homology Domain Of Poly		4e-05
1ztg_A	74	Human Alpha Polyc Binding Protein Kh1 Length = 74		6e-06
1ztg_A	74	Human Alpha Polyc Binding Protein Kh1 Length = 74		6e-05
2axy_A	73	Crystal Structure Of Kh1 Domain Of Human Poly(C)-Bi		3e-05
2axy_A	73	Crystal Structure Of Kh1 Domain Of Human Poly(C)-Bi		9e-04
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		3e-05
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		5e-05
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		3e-05
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		4e-05
1we8_A	104	Solution Structure Of Kh Domain In Protein Bab28342		6e-05
2jvz_A	164	Solution Nmr Structure Of The Second And Third Kh D		3e-04
1khm_A	89	C-Terminal Kh Domain Of Hnrnp K (Kh3) Length = 89		3e-04
1khm_A	89	C-Terminal Kh Domain Of Hnrnp K (Kh3) Length = 89		4e-04
3krm_A	163	Imp1 Kh34 Length = 163		7e-04
2p2r_A	76	Crystal Structure Of The Third Kh Domain Of Human P		8e-04

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

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

Iteration: 1
 Score =  111 bits (278), 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|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains Length = 160

Iteration: 1
 Score = 75.5 bits (184), Expect = 4e-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 = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 5/78 (6%)
Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
           +RL++     GSIIGK G ++K   ++S A     R++ S     +R++TL G  +   +
Sbjct: 7   IRLLMHGKEVGSIIGKKGESVKKMREESGA-----RINISEGNCPERIITLAGPTNAIFK 61
Query: 184 ALELILLKLSEDTLYSQT 201
           A  +I+ KL ED   S T
Sbjct: 62  AFAMIIDKLEEDISSSMT 79

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 24/54 (44%), Positives = 37/54 (68%)
Query: 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT 90
          +   V   L GA++GKGG T+ ++Q  +GARIQ+S+  EF PGT +R + I+G+
Sbjct: 5  VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58

>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 = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 24/54 (44%), Positives = 37/54 (68%)
Query: 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT 90
          +   V   L GA++GKGG T+ ++Q  +GARIQ+S+  EF PGT +R + I+G+
Sbjct: 5  VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 24/54 (44%), Positives = 36/54 (66%)
Query: 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT 90
          +   V   L GA++GKGG T+ ++Q  +G RIQ+S+  EF PGT +R + I+GT
Sbjct: 5  VEIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGT 58

>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 = 56.6 bits (135), Expect = 2e-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|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 = 48.5 bits (114), Expect = 4e-06,   Method: Composition-based stats.
 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 = 45.4 bits (106), Expect = 4e-05,   Method: Composition-based stats.
 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 = 48.1 bits (113), Expect = 6e-06,   Method: Composition-based stats.
 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 = 44.7 bits (104), Expect = 6e-05,   Method: Composition-based stats.
 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   IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN-----CPERIITLTGPTNAIFK 59
Query: 184 ALELILLKLSED 195
           A  +I+ KL ED
Sbjct: 60  AFAMIIDKLEED 71

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   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|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 = 40.8 bits (94), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
           +RL+      GSIIGK G ++K   ++S A I IS  +       +R++TL G  +   +
Sbjct: 7   IRLLXHGKEVGSIIGKKGESVKKXREESGARINISEGN-----CPERIITLAGPTNAIFK 61
Query: 184 ALELILLKLSED 195
           A   I+ KL ED
Sbjct: 62  AFAXIIDKLEED 73

>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 = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 34/53 (64%), Gaps = 3/53 (5%)
Query: 45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRA 97
          LAG++IGKGG  I   + +SGA I++    E   G+ DRII I+GT D+I  A
Sbjct: 24 LAGSIIGKGGQRIKQIRHESGASIKID---EPLEGSEDRIITITGTQDQIQNA 73

>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 = 5e-05,   Method: Compositional matrix adjust.
 Identities = 30/89 (33%), Positives = 42/89 (47%), Gaps = 16/89 (17%)
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 LELILLKLSEDTLYSQTMTVPYTYAGVFF 213
             L+   + +             Y+G FF
Sbjct: 74  QYLLQNSVKQ-------------YSGKFF 89

>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 = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 34/53 (64%), Gaps = 3/53 (5%)
Query: 45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRA 97
          LAG++IGKGG  I   + +SGA I++    E   G+ DRII I+GT D+I  A
Sbjct: 17 LAGSIIGKGGQRIKQIRHESGASIKID---EPLEGSEDRIITITGTQDQIQNA 66

>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 = 4e-05,   Method: Compositional matrix adjust.
 Identities = 30/89 (33%), Positives = 42/89 (47%), Gaps = 16/89 (17%)
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 LELILLKLSEDTLYSQTMTVPYTYAGVFF 213
             L+   + +             Y+G FF
Sbjct: 67  QYLLQNSVKQ-------------YSGKFF 82

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-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|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|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3) Length = 89

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 33/53 (62%), Gaps = 3/53 (5%)
Query: 45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRA 97
          LA ++IGKGG  I   + +SGA I++    E   G+ DRII I+GT D+I  A
Sbjct: 24 LARSIIGKGGQRIKQIRHESGASIKID---EPLEGSEDRIITITGTQDQIQNA 73

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/89 (32%), Positives = 41/89 (46%), Gaps = 16/89 (17%)
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 LELILLKLSEDTLYSQTMTVPYTYAGVFF 213
             L+   + +             Y+G FF
Sbjct: 74  QYLLQNSVKQ-------------YSGKFF 89

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-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|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 = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQ 181
           T   L +PN   G IIG+ GA I      S A IKI+   +   G  DR VT+TG+    
Sbjct: 5   TSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIA---NPVEGSTDRQVTITGSAASI 61
Query: 182 MRALELILLKLSEDT 196
             A  LI ++LS +T
Sbjct: 62  SLAQYLINVRLSSET 76

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	291
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-49
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-19
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-44
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	4e-18
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-16
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	1e-43
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	6e-19
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-15
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-42
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	6e-17
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	4e-16
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-42
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-18
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-18
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-22
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-19
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	5e-22
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	2e-19
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	7e-21
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-18
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-19
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-18
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	8e-19
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	2e-14
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	9e-19
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	7e-18
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-18
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	5e-17
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-18
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-16
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	4e-18
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-16
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	6e-18
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-15
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	6e-18
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	3e-16
1we8_A	104	Tudor and KH domain containing protein; structural	8e-17
1we8_A	104	Tudor and KH domain containing protein; structural	1e-16
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-16
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	6e-15
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	3e-13
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	8e-05
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	1e-11
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	6e-04
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	5e-11
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	3e-07
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-10
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-09
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	2e-10
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	5e-09
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	8e-09
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	1e-06
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	1e-08
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	1e-07
1tua_A	191	Hypothetical protein APE0754; structural genomics,	1e-06
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-06
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-06
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	8e-06

>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 =  161 bits (409), Expect = 1e-49
 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 = 82.2 bits (203), Expect = 3e-19
 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

>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 =  148 bits (375), Expect = 1e-44
 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 = 78.7 bits (194), Expect = 4e-18
 Identities = 27/97 (27%), Positives = 44/97 (45%), Gaps = 10/97 (10%)

Query: 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQ 181
             +++ +P  + G+IIGK G  IK     + A IKI+  +        R+V +TG  + Q
Sbjct: 3   EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETP--DSKVRMVIITGPPEAQ 60

Query: 182 MRALELILLKLSEDTLYSQ--------TMTVPYTYAG 210
            +A   I  KL E+  +           + VP + AG
Sbjct: 61  FKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAG 97

>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 = 74.4 bits (183), Expect = 2e-16
 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 =  145 bits (367), Expect = 1e-43
 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 = 80.6 bits (199), Expect = 6e-19
 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 = 70.2 bits (172), Expect = 5e-15
 Identities = 30/100 (30%), Positives = 47/100 (47%), Gaps = 18/100 (18%)

Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
           +RL++     GSIIGK G ++K   ++S A I IS  +       +R++TL G  +   +
Sbjct: 7   IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP-----ERIITLAGPTNAIFK 61

Query: 184 ALELILLKLSEDTLYSQT-------------MTVPYTYAG 210
           A  +I+ KL ED   S T             + VP +  G
Sbjct: 62  AFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCG 101

>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 =  143 bits (361), Expect = 1e-42
 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 = 75.6 bits (186), Expect = 6e-17
 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 = 73.3 bits (180), Expect = 4e-16
 Identities = 20/103 (19%), Positives = 38/103 (36%), Gaps = 15/103 (14%)

Query: 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQ 181
           T   +++P    G +IGK G TIK   + +   + + + D S     D+ + + G   + 
Sbjct: 2   TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQ-DGSQNTNVDKPLRIIGDPYKV 60

Query: 182 MRALELILLKL--------------SEDTLYSQTMTVPYTYAG 210
            +A E+++  L                       + VP    G
Sbjct: 61  QQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVG 103

>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 =  142 bits (360), Expect = 2e-42
 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 = 79.9 bits (197), Expect = 2e-18
 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

>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 = 79.1 bits (195), Expect = 4e-18
 Identities = 24/121 (19%), Positives = 40/121 (33%), Gaps = 5/121 (4%)

Query: 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTL 178
           G+   + + +P  + G +IG+ G  IK   +D+   I+    D +     +R+  +TG  
Sbjct: 1   GSHM-IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTT---PERIAQITGPP 56

Query: 179 DEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVP-AVPHNTAA 237
           D    A E+I   L      +     P         G   M            VP     
Sbjct: 57  DRAQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTG 116

Query: 238 H 238
            
Sbjct: 117 L 117

>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 = 88.1 bits (219), Expect = 1e-22
 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 = 79.6 bits (197), Expect = 2e-19
 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 = 87.0 bits (216), Expect = 5e-22
 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 = 79.7 bits (197), Expect = 2e-19
 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

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

 Score = 83.5 bits (207), Expect = 7e-21
 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 = 77.7 bits (192), Expect = 1e-18
 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

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

 Score = 81.1 bits (200), Expect = 1e-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 = 78.4 bits (193), Expect = 1e-18
 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

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

 Score = 79.1 bits (195), Expect = 8e-19
 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 = 67.5 bits (165), Expect = 2e-14
 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

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

 Score = 78.2 bits (193), Expect = 9e-19
 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 = 75.9 bits (187), Expect = 7e-18
 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

>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 = 77.7 bits (192), Expect = 1e-18
 Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 4/84 (4%)

Query: 25  SLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRI 84
           S         T  +  +   LAG++IGKGG  I   + +SGA I++        G+ DRI
Sbjct: 5   SYGDLGGPIIT-TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL---EGSEDRI 60

Query: 85  IMISGTIDEILRAVDLVIDKLLTE 108
           I I+GT D+I  A  L+ + +   
Sbjct: 61  ITITGTQDQIQNAQYLLQNSVKQY 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 = 73.5 bits (181), Expect = 5e-17
 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

>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 = 77.3 bits (191), Expect = 2e-18
 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 = 71.5 bits (176), Expect = 2e-16
 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

>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 = 76.5 bits (189), Expect = 4e-18
 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 = 71.9 bits (177), Expect = 2e-16
 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

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

 Score = 75.4 bits (186), Expect = 6e-18
 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 = 69.2 bits (170), Expect = 1e-15
 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

>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 = 75.9 bits (187), Expect = 6e-18
 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 = 71.7 bits (176), Expect = 3e-16
 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

>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 = 73.3 bits (180), Expect = 8e-17
 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 = 73.3 bits (180), Expect = 1e-16
 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

>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 = 72.5 bits (178), Expect = 1e-16
 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 = 68.2 bits (167), Expect = 6e-15
 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

>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 = 65.0 bits (158), Expect = 3e-13
 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 = 41.2 bits (96), Expect = 8e-05
 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

>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 = 62.0 bits (150), Expect = 1e-11
 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 = 39.3 bits (91), Expect = 6e-04
 Identities = 12/60 (20%), Positives = 21/60 (35%), Gaps = 10/60 (16%)

Query: 47  GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL 106
           G +IG+ G T    +  SGA + +            + + I G   +I  A   +     
Sbjct: 141 GRIIGRKGRTRQIIEEMSGASVSV----------YGKTVAIIGNPIQIEIAKTAIEKLAR 190

>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 = 57.5 bits (139), Expect = 5e-11
 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 = 47.1 bits (112), Expect = 3e-07
 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

>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 = 55.9 bits (135), Expect = 2e-10
 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 = 52.8 bits (127), Expect = 2e-09
 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

>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 = 55.6 bits (134), Expect = 2e-10
 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 = 51.7 bits (124), Expect = 5e-09
 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

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

 Score = 50.4 bits (121), Expect = 8e-09
 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 = 44.7 bits (106), Expect = 1e-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 = 50.7 bits (121), Expect = 1e-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 = 47.6 bits (113), Expect = 1e-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

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Length = 191

 Score = 47.3 bits (112), Expect = 1e-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

>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 = 44.4 bits (105), Expect = 2e-06
 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

>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 = 44.4 bits (105), Expect = 2e-06
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 5/80 (6%)

Query: 116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT 175
            ++       + + +     IIG  G  I+  MD+ +  I+  +        +   VT+T
Sbjct: 11  GELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP----DPNCVTVT 66

Query: 176 GTLDEQMRALELILLKLSED 195
           G  +    A++ I L L E+
Sbjct: 67  GLPENVEEAIDHI-LNLEEE 85

>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 = 42.8 bits (101), Expect = 8e-06
 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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	291
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.98
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.97
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.97
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.96
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.96
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.88
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.88
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.87
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.87
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.86
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.85
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.84
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.8
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.72
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.69
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.68
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.66
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.66
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.64
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.64
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.64
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.64
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.64
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.64
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.62
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.62
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.6
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.6
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.6
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.6
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.59
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.59
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.58
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.57
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.57
1we8_A	104	Tudor and KH domain containing protein; structural	99.57
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.56
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.56
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.56
1we8_A	104	Tudor and KH domain containing protein; structural	99.54
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.54
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.53
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.5
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.49
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.49
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.49
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.47
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.47
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.47
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.45
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.44
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.44
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.43
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.4
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.4
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.33
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.32
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.23
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.22
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.13
2cpq_A	91	FragIle X mental retardation syndrome related prot	99.04
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.89
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.89
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.83
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.81
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.79
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.49
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.46
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.45
2cxc_A	144	NUSA; transcription termination, RNA binding prote	98.17
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	98.06
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	98.0
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.89
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.82
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.08
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.98
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	96.96
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.85
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	96.73
2cxc_A	144	NUSA; transcription termination, RNA binding prote	96.02
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	95.97
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	93.7
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	90.51
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	89.88
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	87.07
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	86.43
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	85.52

>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=99.98  E-value=4.5e-32  Score=226.94  Aligned_cols=165  Identities=35%  Similarity=0.628  Sum_probs=140.0

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcc
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHA  111 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~  111 (291)
                      +..++++|+||.+++|.||||+|++||+|+++|||+|+|++..+..|++.+|+|+|+|++++|.+|+.+|.+.+.+....
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~~~   82 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQN   82 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCCCC
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhccCCc
Confidence            46799999999999999999999999999999999999998777788899999999999999999999999877654221


Q ss_pred             ccc-----------cCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHH
Q 022837          112 EDQ-----------ADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE  180 (291)
Q Consensus       112 ~~~-----------~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~  180 (291)
                      ...           ........+.+|+||.+++|+||||+|++||+|+++|||+|+|.+.. ..++..++.|+|+|++++
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~-~~~~~~~~~v~I~G~~~~  161 (178)
T 2anr_A           83 VAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKP-DGINLQNRVVTVSGEPEQ  161 (178)
T ss_dssp             -----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC-----CCEEEEEEESSHHH
T ss_pred             cccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCC-CCCCCCceEEEEEcCHHH
Confidence            100           00112347899999999999999999999999999999999998743 234567899999999999


Q ss_pred             HHHHHHHHHHHHhcCcc
Q 022837          181 QMRALELILLKLSEDTL  197 (291)
Q Consensus       181 v~~A~~~I~~~l~e~~~  197 (291)
                      |++|+.+|.++|+++|.
T Consensus       162 v~~A~~~I~~~i~e~p~  178 (178)
T 2anr_A          162 NRKAVELIIQKIQEDPQ  178 (178)
T ss_dssp             HHHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHHHHHHHhCCC
Confidence            99999999999999763

>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=99.97  E-value=6.4e-30  Score=210.85  Aligned_cols=157  Identities=22%  Similarity=0.329  Sum_probs=133.6

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcccc
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAED  113 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~  113 (291)
                      +-+++|+||.+.+|.||||+|++||+|+++|||+|+|++..  .+++.+|+|+|+|+++++.+|+.+|++.+.+....  
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            35799999999999999999999999999999999998753  47889999999999999999999999888765211  


Q ss_pred             ccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 022837          114 QADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLS  193 (291)
Q Consensus       114 ~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~  193 (291)
                       ........+.+|.||.+++|+||||+|++|++|+++|||+|+|.++.. .....++.|+|+|++++|++|+.+|.++++
T Consensus        78 -~~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~-~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~  155 (163)
T 3krm_A           78 -GPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQT-PDENDQVIVKIIGHFYASQMAQRKIRDILA  155 (163)
T ss_dssp             -CSSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCC-CCTTSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             -ccccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCC-CCCCCceEEEEEeCHHHHHHHHHHHHHHHH
Confidence             112234568899999999999999999999999999999999976432 223345589999999999999999999998


Q ss_pred             cCc
Q 022837          194 EDT  196 (291)
Q Consensus       194 e~~  196 (291)
                      +..
T Consensus       156 ~~~  158 (163)
T 3krm_A          156 QVK  158 (163)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            743

>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=99.97  E-value=2.7e-30  Score=212.45  Aligned_cols=157  Identities=29%  Similarity=0.525  Sum_probs=136.3

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcc
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHA  111 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~  111 (291)
                      +.++.++|+||.+++|.||||+|++||+|+++|||+|+|++.     ++.+|.|+|+|+.+++.+|+.+|.+.+.+....
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            357899999999999999999999999999999999999874     357899999999999999999999888776432


Q ss_pred             cccc--CCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 022837          112 EDQA--DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL  189 (291)
Q Consensus       112 ~~~~--~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~  189 (291)
                      ....  .......+.++.||.+++|+||||+|++|++|+++|||+|+|.++  ..++..++.|+|+|++++|++|+.+|.
T Consensus        77 ~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~--~~~~~~~~~v~I~G~~~~v~~A~~~I~  154 (160)
T 2jzx_A           77 SMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD--MLPNSTERAITIAGIPQSIIECVKQIC  154 (160)
T ss_dssp             CCCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCC--CSTTCCEEEEEEEECHHHHHHHHHHHH
T ss_pred             cCCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCC--CCCCCCceEEEEEcCHHHHHHHHHHHH
Confidence            2111  112345899999999999999999999999999999999999863  345678999999999999999999999


Q ss_pred             HHHhcC
Q 022837          190 LKLSED  195 (291)
Q Consensus       190 ~~l~e~  195 (291)
                      +++.|+
T Consensus       155 ~~i~e~  160 (160)
T 2jzx_A          155 VVMLET  160 (160)
T ss_dssp             HHHHHC
T ss_pred             HHHhcC
Confidence            998873

>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=99.96  E-value=2.1e-29  Score=209.97  Aligned_cols=156  Identities=31%  Similarity=0.404  Sum_probs=129.5

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcccc
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAED  113 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~  113 (291)
                      ..+++|+||.+++|.||||+|++||+|+++|||+|+|.+..   +++.+|+|+|+|++++|.+|+.+|.+.+.+......
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            46799999999999999999999999999999999998643   457899999999999999999999987765421100


Q ss_pred             ---------------cc--CCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEc
Q 022837          114 ---------------QA--DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG  176 (291)
Q Consensus       114 ---------------~~--~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G  176 (291)
                                     ..  .......+.+|.||.+++|+||||+|++||+|+++|||+|+|.+..+...+..++.|+|+|
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                           00  0011246889999999999999999999999999999999998754444456789999999


Q ss_pred             CHHHHHHHHHHHHHHH
Q 022837          177 TLDEQMRALELILLKL  192 (291)
Q Consensus       177 ~~~~v~~A~~~I~~~l  192 (291)
                      ++++|++|+.+|.++|
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            9999999999999875

>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=99.96  E-value=3.8e-29  Score=206.30  Aligned_cols=156  Identities=24%  Similarity=0.340  Sum_probs=131.1

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccc-c
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAE-D  113 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~-~  113 (291)
                      ++++|+||.+++|+||||+|++||+|+++|||+|++.++. ..++..+|.|+|+|++++|.+|+.+|.+.+.+..... .
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            6889999999999999999999999999999999998643 2356789999999999999999999998776542110 0


Q ss_pred             cc--CCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 022837          114 QA--DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLK  191 (291)
Q Consensus       114 ~~--~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~  191 (291)
                      ..  .......+.+|.||.+++|+||||+|++||+|+++|||+|+|.+.+   +...++.|+|+|++++|++|+.+|.++
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            00  0011135688999999999999999999999999999999998743   244689999999999999999999999


Q ss_pred             Hhc
Q 022837          192 LSE  194 (291)
Q Consensus       192 l~e  194 (291)
                      +++
T Consensus       158 i~~  160 (164)
T 2jvz_A          158 LQS  160 (164)
T ss_dssp             HHH
T ss_pred             Hhh
Confidence            876

>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=99.88  E-value=1.5e-23  Score=175.17  Aligned_cols=138  Identities=22%  Similarity=0.312  Sum_probs=108.1

Q ss_pred             CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccC
Q 022837          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS  199 (291)
Q Consensus       120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~  199 (291)
                      ..++++|+||.+++|.||||+|++||+|+++|||+|+|.+..+..++..+|.|+|+|++++|.+|+.+|.+++.+.+...
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            45899999999999999999999999999999999999875545567789999999999999999999999998865422


Q ss_pred             CCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehcc
Q 022837          200 QTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFS  279 (291)
Q Consensus       200 ~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~  279 (291)
                      ... .+..               . .+     +.+         ........+.+|.||.+++|+||||  ||.+||+|+
T Consensus        84 ~~~-~~~~---------------~-~~-----~~~---------~~~~~~~~~~~i~Vp~~~vg~iIGk--gG~~Ik~i~  130 (178)
T 2anr_A           84 AKT-EPVS---------------I-LQ-----PQT---------TVNPDRANQVKIIVPNSTAGLIIGK--GGATVKAIM  130 (178)
T ss_dssp             -----------------------------------------------CGGGGEEEEEEEHHHHHHHHCG--GGHHHHHHH
T ss_pred             ccC-Cccc---------------c-cC-----Ccc---------CCCCCCceEEEEEEchhheeeeECC--CcHHHHHHH
Confidence            100 0000               0 00     000         0011223568999999999999999  999999999


Q ss_pred             ccccceEEeec
Q 022837          280 LSIYEEIRLNE  290 (291)
Q Consensus       280 ~~tga~i~~~~  290 (291)
                      ++|||+|+|.+
T Consensus       131 ~~tga~I~i~~  141 (178)
T 2anr_A          131 EQSGAWVQLSQ  141 (178)
T ss_dssp             HHSSCEEEECC
T ss_pred             HHHCCEEEEeC
Confidence            99999999975

>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=99.88  E-value=4.7e-23  Score=169.63  Aligned_cols=120  Identities=22%  Similarity=0.295  Sum_probs=103.2

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCC
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQT  201 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~  201 (291)
                      .+++|+||.+++|.||||+|++||+|+++|||+|+|.+..  .++..+|.|+|+|+++++.+|+.+|.+++.+...+.+ 
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~--~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~~~~-   79 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPE--TPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFGP-   79 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCS--STTCSEEEEEEEECHHHHHHHHHHHHHHHHHTTSSCS-
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCC--CCCCCceEEEEEcCHHHHHHHHHHHHHHHhccccccc-
Confidence            5899999999999999999999999999999999998742  3567899999999999999999999999987532110 


Q ss_pred             CCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehcccc
Q 022837          202 MTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLS  281 (291)
Q Consensus       202 ~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~  281 (291)
                                         .                         .....+.+|.||.+++|+||||  ||.+|++|+++
T Consensus        80 -------------------~-------------------------~~~~~~~~i~vp~~~~g~iIGk--gG~~I~~i~~~  113 (163)
T 3krm_A           80 -------------------K-------------------------EEVKLETHIRVPASAAGRVIGK--GGKTVNELQNL  113 (163)
T ss_dssp             -------------------S-------------------------CCCCEEEEEEEETTTHHHHHCG--GGHHHHHHHHH
T ss_pred             -------------------c-------------------------cCCceEEEEEcChhheeeEEcC--CChHHHHHHHH
Confidence                               0                         0001347899999999999999  99999999999


Q ss_pred             ccceEEeec
Q 022837          282 IYEEIRLNE  290 (291)
Q Consensus       282 tga~i~~~~  290 (291)
                      |||+|+|++
T Consensus       114 tga~I~i~~  122 (163)
T 3krm_A          114 TAAEVVVPR  122 (163)
T ss_dssp             HCCEEECCT
T ss_pred             hCCeEEECC
Confidence            999999975

>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=99.87  E-value=2.6e-22  Score=161.65  Aligned_cols=137  Identities=22%  Similarity=0.284  Sum_probs=109.5

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcccc
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAED  113 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~  113 (291)
                      .++.+|+||.+.+|++||++|++|++|++++|  |++....+    ..++.+...++++.|.+|+.++.     .     
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~~----~~~~~i~~~~~p~~v~~~~~~l~-----~-----   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLDE----DTCTFHIYGEDQDAVKKARSFLE-----F-----   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEET----TTTEEEEEESSHHHHHHHHHHHC-----E-----
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccCC----CchheeeccCCHHHHHHHHHhhh-----c-----
Confidence            46889999999999999999999999999999  44432221    24566666678999988866431     1     


Q ss_pred             ccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccc-eEEEecCCCCCCCCCc--eEEEEEcCHHHHHHHHHHHHH
Q 022837          114 QADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQA-VIKISRLDHSYYGLND--RLVTLTGTLDEQMRALELILL  190 (291)
Q Consensus       114 ~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa-~I~i~~~~~~~~~~~e--r~V~I~G~~~~v~~A~~~I~~  190 (291)
                              ...++.||.+++|++|||+|++||.|++.||| +|+|.+.++......+  +.|+|+|++++|++|+.+|.+
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 8999985443211223  458999999999999999999


Q ss_pred             HHhc
Q 022837          191 KLSE  194 (291)
Q Consensus       191 ~l~e  194 (291)
                      +|.+
T Consensus       139 ~l~~  142 (144)
T 2qnd_A          139 HLNY  142 (144)
T ss_dssp             HHHT
T ss_pred             HHHh
Confidence            9875

>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=99.87  E-value=2e-22  Score=165.97  Aligned_cols=127  Identities=19%  Similarity=0.271  Sum_probs=103.2

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCC
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQT  201 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~  201 (291)
                      ++.+|+||.+++|+||||+|++||+|+++|||+|++.++. ..++..+|.|+|+|++++|.+|+.+|.+++.+.....  
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            5789999999999999999999999999999999998643 2345678999999999999999999999998753210  


Q ss_pred             CCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehcccc
Q 022837          202 MTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLS  281 (291)
Q Consensus       202 ~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~  281 (291)
                            |.          |.          ..|     ++.      ...+.+|.||.+++|+||||  ||.+|++|+++
T Consensus        79 ------~~----------~~----------~~~-----~~~------~~~~~~i~vp~~~~g~iIGk--~G~~I~~i~~~  119 (164)
T 2jvz_A           79 ------FG----------DR----------NEY-----GSR------IGGGIDVPVPRHSVGVVIGR--SGEMIKKIQND  119 (164)
T ss_dssp             ------CS----------SC----------SSC-----TTS------CSSSBCCEEETTTHHHHHCS--SSHHHHHHHHH
T ss_pred             ------CC----------Cc----------ccc-----CCC------CCceEEEEEChhhccccCCC--CcHhHHHHHHH
Confidence                  00          00          011     110      01348899999999999999  99999999999


Q ss_pred             ccceEEeec
Q 022837          282 IYEEIRLNE  290 (291)
Q Consensus       282 tga~i~~~~  290 (291)
                      |||+|+|++
T Consensus       120 tg~~I~i~~  128 (164)
T 2jvz_A          120 AGVRIQFKQ  128 (164)
T ss_dssp             TCCEEEECC
T ss_pred             HCCeEEEeC
Confidence            999999975

>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=99.86  E-value=1.5e-22  Score=168.43  Aligned_cols=138  Identities=21%  Similarity=0.215  Sum_probs=101.4

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCC
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQT  201 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~  201 (291)
                      .+.+|+||.+++|+||||+|++||+|+++|||+|+|.+.+   ++..+|.|+|+|++++|.+|+.+|.+++.+.....  
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            5789999999999999999999999999999999998633   34578999999999999999999999998743110  


Q ss_pred             CCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCeEEEeecCCCcceeEEeecCccceehccc
Q 022837          202 MTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGR-KFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSL  280 (291)
Q Consensus       202 ~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~-~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~  280 (291)
                            +++.      + |..         ..++ +.. .+...+ .......+|.||.+++|+||||  ||.+||+|++
T Consensus        78 ------~~~~------~-p~~---------~~~~-~~~-~~~~~~~~~~~~~~~i~vp~~~~g~iIGk--gG~~Ik~I~~  131 (174)
T 1j4w_A           78 ------PGGP------G-PGG---------RGRG-RGQ-GNWNMGPPGGLQEFNFIVPTGKTGLIIGK--GGETIKSISQ  131 (174)
T ss_dssp             --------------------------------------------------CEEEEEEETTTHHHHHCG--GGHHHHHHHH
T ss_pred             ------CCCC------C-CCC---------CCCC-CCC-CccccCCCCCcEEEEEEEChHHcCeeECC--CchHHHHHHH
Confidence                  0000      0 000         0000 000 000001 1123468999999999999999  9999999999


Q ss_pred             cccceEEeec
Q 022837          281 SIYEEIRLNE  290 (291)
Q Consensus       281 ~tga~i~~~~  290 (291)
                      +|||+|+|++
T Consensus       132 ~tga~I~i~~  141 (174)
T 1j4w_A          132 QSGARIELQR  141 (174)
T ss_dssp             HHCCEEEEEC
T ss_pred             HHCCEEEECC
Confidence            9999999975

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

Probab=99.85  E-value=1.4e-21  Score=178.46  Aligned_cols=197  Identities=10%  Similarity=0.029  Sum_probs=139.6

Q ss_pred             CCCCCCcEEEEEEecccccceeeccCC--hhHHHHHHHhCCcEEEcCCC--CCCCCCCceEEEEecCHHHHHHHHHHHHH
Q 022837           28 SDPTEKPTYIRFLVSNPLAGAVIGKGG--STINDFQSQSGARIQLSRSH--EFFPGTTDRIIMISGTIDEILRAVDLVID  103 (291)
Q Consensus        28 ~~~~~~~~~~rilvp~~~vG~IIGk~G--~~Ik~I~~~tga~I~v~~~~--~~~p~~~er~v~I~G~~~~v~~A~~~I~~  103 (291)
                      -+.....+++++.||..+++.||||+|  ++|++|+++|||+|+|++.+  ...+......|+|+|.+++|++|+.+|.+
T Consensus        23 le~~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~  102 (376)
T 3n89_A           23 IEINPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRR  102 (376)
T ss_dssp             CCCCTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEecCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHh
Confidence            355677899999999999999999999  99999999999999998754  21122345789999999999999999985


Q ss_pred             HHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHH
Q 022837          104 KLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR  183 (291)
Q Consensus       104 ~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~  183 (291)
                      .+               ..+..+.+|...++.  ..-+..|.+ ++..+++|.|+..... .+.....|+|+|...++..
T Consensus       103 l~---------------Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~-~~~~sd~V~IrG~~~nv~~  163 (376)
T 3n89_A          103 NC---------------HFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEK-NGIVTTYLRITAREKNQHE  163 (376)
T ss_dssp             SC---------------EEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC------CEEEEEEEEEGGGHHH
T ss_pred             cC---------------CceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCcccc-cCCCCCEEEEEcChhhHHH
Confidence            21               235666666554332  122334554 5678999999764221 1113567999999876666


Q ss_pred             HHHHHHHHHhcCcccCCCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcc
Q 022837          184 ALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVG  263 (291)
Q Consensus       184 A~~~I~~~l~e~~~~~~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG  263 (291)
                      |++.+..+++.-....  .                                           ......+.+|.|+.+++.
T Consensus       164 akeA~~~Ll~~l~~~e--~-------------------------------------------~~~~~~s~~v~V~~~~H~  198 (376)
T 3n89_A          164 LIEAAKRLNEILFRES--P-------------------------------------------APENNFTLHFTLSTYYVD  198 (376)
T ss_dssp             HHHHHHHHHHHHCC----C-------------------------------------------CCSSCEEEEEEEEGGGHH
T ss_pred             HHHHHHHHHHHHHhhh--c-------------------------------------------ccccceEEEEEeCHHHHH
Confidence            5555444443311010  0                                           000114589999999999


Q ss_pred             eeEEeecCccc--eehccccccceEEeec
Q 022837          264 MLLIILIAQPI--ICHFSLSIYEEIRLNE  290 (291)
Q Consensus       264 ~iIG~~~gg~~--ik~~~~~tga~i~~~~  290 (291)
                      .||||  ||.+  |++|+++||++|+|++
T Consensus       199 ~IIGk--~G~n~~IkkIr~eTGv~I~FP~  225 (376)
T 3n89_A          199 QVLGS--SSTAQLMPVIERETTTIISYPC  225 (376)
T ss_dssp             HHTCC--TTSCCHHHHHHHHHTCEEECC-
T ss_pred             HhhcC--CCcchHHHHHHHhhCCEEECCC
Confidence            99999  9855  5999999999999985

>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=99.84  E-value=2.9e-22  Score=164.39  Aligned_cols=124  Identities=26%  Similarity=0.336  Sum_probs=102.5

Q ss_pred             CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccC
Q 022837          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS  199 (291)
Q Consensus       120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~  199 (291)
                      ..++++|+||.+++|.||||+|++||+|+++|||+|+|++.     +..+|.|+|+|+.++|.+|+.+|.+++.++....
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            45789999999999999999999999999999999999873     3468999999999999999999999998742210


Q ss_pred             CCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehcc
Q 022837          200 QTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFS  279 (291)
Q Consensus       200 ~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~  279 (291)
                              ++           ..           +          .......+.+|.||.+++|+||||  ||.+|++|+
T Consensus        78 --------~~-----------~~-----------~----------~~~~~~~~~~i~vp~~~~g~iIGk--gG~~Ik~i~  115 (160)
T 2jzx_A           78 --------MT-----------NS-----------T----------AASRPPVTLRLVVPASQCGSLIGK--GGCKIKEIR  115 (160)
T ss_dssp             --------CC-----------SS-----------S----------CCCCCSEEEEEEEEHHHHHHHHCG--GGHHHHHHH
T ss_pred             --------CC-----------CC-----------c----------cCCCCCEEEEEEEChhheeeEECC--CCHHHHHHH
Confidence                    00           00           0          000012468999999999999999  999999999


Q ss_pred             ccccceEEeec
Q 022837          280 LSIYEEIRLNE  290 (291)
Q Consensus       280 ~~tga~i~~~~  290 (291)
                      ++|||+|+|++
T Consensus       116 ~~tga~I~i~~  126 (160)
T 2jzx_A          116 ESTGAQVQVAG  126 (160)
T ss_dssp             HHHSSEECCCC
T ss_pred             HHhCCeEEECC
Confidence            99999999974

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.80  E-value=1.1e-19  Score=155.38  Aligned_cols=146  Identities=16%  Similarity=0.097  Sum_probs=111.6

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecC-----HHHHHHHHHHHHHHHhhh
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-----IDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~-----~~~v~~A~~~I~~~i~~~  108 (291)
                      +-..++.||.+.+|.|||++|.+|+.|+++|||+|++..        .++.|.|.++     ++++.+|+++|.+.+...
T Consensus        33 P~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~--------~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg~  104 (219)
T 2e3u_A           33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS--------ETGEVWITSTKETEDPLAVWKARDIVLAIGRGF  104 (219)
T ss_dssp             CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT--------TTCEEEEEECTTCCSHHHHHHHHHHHHHHHTTC
T ss_pred             CEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc--------CCCEEEEecCCCCCCHHHHHHHHHHHHHHhccC
Confidence            346799999999999999999999999999999999963        2466888875     699999999998765211


Q ss_pred             hccccccCCCCCceEEEEEecC-----------CccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC
Q 022837          109 LHAEDQADDVGTKTKLRLIVPN-----------SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT  177 (291)
Q Consensus       109 ~~~~~~~~~~~~~~~~~i~VP~-----------~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~  177 (291)
                      ..........++.....+.++.           ..+|+||||+|++|+.|++.|||+|.|..          +.|+|.|+
T Consensus       105 ~~e~g~~ll~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~~----------~~v~i~G~  174 (219)
T 2e3u_A          105 SPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG----------KTVAIIGN  174 (219)
T ss_dssp             CHHHHGGGGSTTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEET----------TEEEEEEC
T ss_pred             CccccceeccCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEECC----------eEEEEEeC
Confidence            0000000000111122233332           26899999999999999999999999963          57999999


Q ss_pred             HHHHHHHHHHHHHHHhcCcc
Q 022837          178 LDEQMRALELILLKLSEDTL  197 (291)
Q Consensus       178 ~~~v~~A~~~I~~~l~e~~~  197 (291)
                      +++++.|+.+|.+++.+.++
T Consensus       175 ~~~i~~A~~~i~~li~g~~~  194 (219)
T 2e3u_A          175 PIQIEIAKTAIEKLARGSPH  194 (219)
T ss_dssp             HHHHHHHHHHHHHHHTTCCH
T ss_pred             HHHHHHHHHHHHHHHcCCCc
Confidence            99999999999999987653

>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=99.72  E-value=1.3e-17  Score=139.28  Aligned_cols=143  Identities=17%  Similarity=0.239  Sum_probs=112.2

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEe-----cCHHHHHHHHHHHHHHHhhhhc
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMIS-----GTIDEILRAVDLVIDKLLTELH  110 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~-----G~~~~v~~A~~~I~~~i~~~~~  110 (291)
                      .++++||.+.+|.|||++|++++.|++++|++|++..        .++.|+|.     |++..+.+|.++|...... +.
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~--------~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rg-f~   75 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT--------ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLG-FP   75 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET--------TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHT-CC
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc--------CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcC-CC
Confidence            3699999999999999999999999999999999964        35777887     9999999999999754432 22


Q ss_pred             cccccC-CCCCceEEEEEec----------CCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHH
Q 022837          111 AEDQAD-DVGTKTKLRLIVP----------NSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD  179 (291)
Q Consensus       111 ~~~~~~-~~~~~~~~~i~VP----------~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~  179 (291)
                      .++... ..++.....+.++          ....|+||||+|.+|+.|++.|||+|.|..          +.|.|.|+++
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            111110 0111222233344          235899999999999999999999999964          4899999999


Q ss_pred             HHHHHHHHHHHHHhcCcc
Q 022837          180 EQMRALELILLKLSEDTL  197 (291)
Q Consensus       180 ~v~~A~~~I~~~l~e~~~  197 (291)
                      +++.|+..|.+++...++
T Consensus       146 ~i~~Ar~~i~~li~g~~h  163 (191)
T 1tua_A          146 RAMAAKQAIEMLAEGRMH  163 (191)
T ss_dssp             HHHHHHHHHHHHHTTCCH
T ss_pred             HHHHHHHHHHHHHcCCCc
Confidence            999999999999976543

>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=99.69  E-value=5e-17  Score=116.52  Aligned_cols=73  Identities=29%  Similarity=0.408  Sum_probs=67.1

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      .+.+|.||.+++|+||||+|++||+|+++|||+|+|.+.++..++..++.|+|+|+++++.+|+.+|.+++.+
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            5889999999999999999999999999999999999865556677899999999999999999999999875

>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=8.8e-17  Score=115.21  Aligned_cols=74  Identities=35%  Similarity=0.627  Sum_probs=67.9

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      .++++|+||.+.+|.||||+|++|++|+++|||+|+|.++.+..|++.+|.|+|+|+++++.+|+.+|.+.+.+
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            46789999999999999999999999999999999999876677888999999999999999999999977654

>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=99.66  E-value=1.3e-16  Score=113.42  Aligned_cols=71  Identities=34%  Similarity=0.628  Sum_probs=65.5

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      +..+.++|+||.+.+|.||||+|++||+|+++|||+|+|++.     ++.+|+|+|+|+++++.+|+.+|.++|.+
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            356899999999999999999999999999999999999874     36799999999999999999999988765

>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=99.66  E-value=7.9e-17  Score=114.50  Aligned_cols=71  Identities=35%  Similarity=0.579  Sum_probs=65.1

Q ss_pred             CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED  195 (291)
Q Consensus       120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~  195 (291)
                      ..++++|+||.+++|.||||+|++||+|+++|||+|+|.+.     +..+|.|+|+|+++++.+|+.+|.++|+|+
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~-----~~~er~v~I~G~~~~v~~A~~~I~~~l~ed   73 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKLEED   73 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-----CCSEEEEEEEECHHHHHHHHHHHHHHHHC-
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-----CCCcEEEEEEeCHHHHHHHHHHHHHHHhcC
Confidence            35789999999999999999999999999999999999874     347899999999999999999999999874

>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=5.2e-16  Score=112.80  Aligned_cols=72  Identities=35%  Similarity=0.491  Sum_probs=66.1

Q ss_pred             CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      ..++.+|.||.+++|+||||+|++||+|+++|||+|+|.+.   .++..+|.|+|+|++++|++|+.+|.+++.+
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~---~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   76 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   76 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT---TSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC---CCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            45899999999999999999999999999999999999863   3456789999999999999999999999987

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

Probab=99.64  E-value=2.1e-16  Score=113.28  Aligned_cols=73  Identities=38%  Similarity=0.467  Sum_probs=66.8

Q ss_pred             CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED  195 (291)
Q Consensus       120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~  195 (291)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|+|.+.   .++..+|.|+|+|++++|++|+.+|.+++.++
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            34789999999999999999999999999999999999872   45668999999999999999999999999864

>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=99.64  E-value=3e-16  Score=114.11  Aligned_cols=73  Identities=37%  Similarity=0.451  Sum_probs=65.8

Q ss_pred             CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED  195 (291)
Q Consensus       120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~  195 (291)
                      ..++.+|.||.+++|+||||+|++||+|+++|||+|+|.+.   .++..+|.|+|+|++++|++|+.+|.+++.++
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            45789999999999999999999999999999999999873   34567999999999999999999999999886

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

Probab=99.64  E-value=3.8e-16  Score=119.18  Aligned_cols=74  Identities=24%  Similarity=0.395  Sum_probs=66.6

Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCc
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDT  196 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~  196 (291)
                      +.+|.||.+++|+||||+|++||+|+++|||+|+|.+..+...+..++.|+|+|++++|++|+.+|.+++.+..
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~   81 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhccc
Confidence            78999999999999999999999999999999999875433334578999999999999999999999998854

>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=99.64  E-value=3.2e-16  Score=115.21  Aligned_cols=75  Identities=36%  Similarity=0.632  Sum_probs=69.2

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      .++++|+||.+.+|.||||+|++|++|+++|||+|+|.++.++.|++.+|.|+|+|+++++..|+.+|.+.+.+.
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            357899999999999999999999999999999999998767778889999999999999999999999887654

>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=99.64  E-value=1.8e-16  Score=116.53  Aligned_cols=76  Identities=28%  Similarity=0.385  Sum_probs=69.3

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcc
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTL  197 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~  197 (291)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|.+.++..++..++.|+|+|+++++.+|+.+|.+++.+...
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~   78 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQG   78 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccc
Confidence            5789999999999999999999999999999999999865555677899999999999999999999999987543

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

Probab=99.62  E-value=5.9e-16  Score=110.89  Aligned_cols=73  Identities=33%  Similarity=0.540  Sum_probs=66.8

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      ..++++|+||.+++|.||||+|++|++|+++|||+|+|.+.   .+++.+|.|+|+|+++++.+|+.+|.+.+.++
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   46788999999999999999999999877654

>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=99.62  E-value=1.9e-15  Score=109.78  Aligned_cols=73  Identities=34%  Similarity=0.555  Sum_probs=66.3

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      ..++++|+||.+++|.||||+|++|++|+++|||+|+|++.   .+++.+|.|+|+|+++++.+|+.+|.+.+.+.
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~---~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT---TSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC---CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            46899999999999999999999999999999999999863   35678999999999999999999999877654

>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=99.60  E-value=1.8e-15  Score=109.97  Aligned_cols=73  Identities=30%  Similarity=0.519  Sum_probs=65.5

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      ..++++|+||.+++|.||||+|++|++|+++|||+|+|.+.   .+++.+|.|+|+|+++++.+|+.+|.+.+.++
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            56889999999999999999999999999999999999864   35678999999999999999999999877654

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

Probab=99.60  E-value=3.7e-15  Score=109.00  Aligned_cols=75  Identities=23%  Similarity=0.321  Sum_probs=66.3

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      ......+|.||.+++|+||||+|++||+|+++|||+|+|.++. ..+...+|.|+|+|+++++++|+.+|.+++.|
T Consensus        11 ~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~-~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           11 QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG-SQNTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             CSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSS-CSSTTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCC-CCCCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            3457889999999999999999999999999999999998743 22456789999999999999999999999865

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

Probab=99.60  E-value=8e-16  Score=113.55  Aligned_cols=73  Identities=36%  Similarity=0.515  Sum_probs=66.9

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      ...++.+|.||.+++|+||||+|++||+|+++|||+|+|.+.   .++..+|.|+|+|++++|++|+.+|.+++.+
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~---~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e   83 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   83 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC---CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC---CCCCCccEEEEEcCHHHHHHHHHHHHHHHHh
Confidence            456899999999999999999999999999999999999863   3456789999999999999999999999987

>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=99.60  E-value=1.8e-15  Score=112.39  Aligned_cols=75  Identities=27%  Similarity=0.333  Sum_probs=67.7

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDT  196 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~  196 (291)
                      ...++.+|.||.+++|+||||+|++||+|+++|||+|+|.+..   ++..+|.|+|+|++++|++|+.+|.+++.+..
T Consensus        12 ~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~---~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~   86 (92)
T 1x4n_A           12 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCMLTGTPESVQSAKRLLDQIVEKGR   86 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC---TTCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            3457899999999999999999999999999999999998743   34578999999999999999999999998854

>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=99.59  E-value=1.8e-15  Score=111.61  Aligned_cols=76  Identities=33%  Similarity=0.515  Sum_probs=67.8

Q ss_pred             CCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        30 ~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      .....++++|+||.+.+|.||||+|++||+|+++|||+|+|++.   .+++.+|.|+|+|+++++.+|+.+|.+.+.+.
T Consensus         9 ~~~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~---~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A            9 LGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             -CCCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC---CSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC---CCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            34567999999999999999999999999999999999999763   35678999999999999999999999877654

>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=99.59  E-value=5.6e-15  Score=109.66  Aligned_cols=73  Identities=26%  Similarity=0.445  Sum_probs=66.4

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      ..++++|+||.+++|+||||+|++|++|+++|||+|+|.+..   ++..+|.|+|+|++++|.+|+.+|.+.+.+.
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~---~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~   85 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC---TTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            468999999999999999999999999999999999998754   4668999999999999999999999877654

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

Probab=99.58  E-value=1.1e-14  Score=106.39  Aligned_cols=76  Identities=28%  Similarity=0.423  Sum_probs=66.4

Q ss_pred             CCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHh
Q 022837           30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL  106 (291)
Q Consensus        30 ~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~  106 (291)
                      ........+|.||.+.+|+||||+|++||+|+++|||+|+|.++.. .+...+|.|+|+|+++++.+|+.+|.+.+.
T Consensus         9 ~g~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~-~~~~~er~v~I~G~~~~v~~A~~~I~~i~~   84 (85)
T 2opv_A            9 GGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRIIGDPYKVQQACEMVMDILR   84 (85)
T ss_dssp             CSCSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSC-SSTTSCEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             CCCCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCC-CCCCCceEEEEEeCHHHHHHHHHHHHHHhc
Confidence            3445688999999999999999999999999999999999987532 345679999999999999999999987653

>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=99.57  E-value=2.7e-15  Score=111.85  Aligned_cols=78  Identities=21%  Similarity=0.301  Sum_probs=68.6

Q ss_pred             CCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCc
Q 022837          118 VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDT  196 (291)
Q Consensus       118 ~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~  196 (291)
                      ....++.+|.||.+++|+||||+|++||+|+++|||+|+|.++... ....+|.|+|+|++++|++|+.+|.+++.+..
T Consensus        11 ~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~-~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   88 (94)
T 1x4m_A           11 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQ-NTGADKPLRITGDPYKVQQAKEMVLELIRDQG   88 (94)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCC-SSCSCEEEEEEECTTTHHHHHHHHHHHHCCCS
T ss_pred             CCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCC-CCCCceEEEEEeCHHHHHHHHHHHHHHHhccC
Confidence            3456899999999999999999999999999999999999874322 23478999999999999999999999998754

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

Probab=99.57  E-value=4.2e-15  Score=113.38  Aligned_cols=73  Identities=25%  Similarity=0.408  Sum_probs=65.0

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      +++|+||.+++|+||||+|++||+|+++|||+|+|.++.+...+..+|.|+|+|++++|.+|+.+|.+++.+.
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            6899999999999999999999999999999999987644334457899999999999999999999877654

>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=99.57  E-value=3.3e-15  Score=113.43  Aligned_cols=82  Identities=37%  Similarity=0.434  Sum_probs=70.9

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCccc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLY  198 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~  198 (291)
                      ....+.+|.||.+++|+||||+|++||+|+++|||+|+|.+..+.. ...++.|+|+|+.++|++|+.+|.+++.+++.+
T Consensus        12 ~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~-~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~~~   90 (104)
T 1we8_A           12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT-LLLSRLIKISGTQKEVAAAKHLILEKVSEDEEL   90 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS-SSSEEEEEEEEEHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCC-CCCcceEEEEcCHHHHHHHHHHHHHHHhhChHH
Confidence            4567899999999999999999999999999999999998744321 236899999999999999999999999987765


Q ss_pred             CCC
Q 022837          199 SQT  201 (291)
Q Consensus       199 ~~~  201 (291)
                      ...
T Consensus        91 ~~~   93 (104)
T 1we8_A           91 RKR   93 (104)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.3e-15  Score=110.60  Aligned_cols=70  Identities=27%  Similarity=0.396  Sum_probs=63.6

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      ....+.+|.||.+++|+||||+|++||+|+++|||+|+|++.+      +++.|+|+|++++|++|+++|.+++..
T Consensus         7 ~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~------~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            7 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD------KEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS------SCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC------CCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            3457899999999999999999999999999999999998633      368999999999999999999998765

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

Probab=99.56  E-value=6e-15  Score=112.11  Aligned_cols=71  Identities=24%  Similarity=0.322  Sum_probs=64.3

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED  195 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~  195 (291)
                      .+++|.||.+++++||||+|++||+|+++|||+|+|.+++   ....+|.|+|+|++++|++|+.+|.+++.+.
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            5789999999999999999999999999999999998643   2456899999999999999999999999874

>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=8.6e-15  Score=109.09  Aligned_cols=76  Identities=22%  Similarity=0.389  Sum_probs=66.9

Q ss_pred             CCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        31 ~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      ....++++|+||.+++|+||||+|++||+|+++|||+|+|.++.... ...+|.|+|+|+++++.+|+.+|.+++.+
T Consensus        11 ~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~-~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   86 (94)
T 1x4m_A           11 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN-TGADKPLRITGDPYKVQQAKEMVLELIRD   86 (94)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS-SCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCC-CCCceEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            45779999999999999999999999999999999999998754322 34789999999999999999999977654

>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=2.3e-14  Score=108.81  Aligned_cols=77  Identities=31%  Similarity=0.490  Sum_probs=66.7

Q ss_pred             CCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        31 ~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      ...+++++|+||.+.+|.||||+|++||+|+++|||+|+|.+..+.. ...++.|+|+|+.+++.+|+.+|.+++.++
T Consensus        11 ~~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~-~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT-LLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS-SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCC-CCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            34568899999999999999999999999999999999998754311 235899999999999999999999887655

>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=99.54  E-value=4.8e-15  Score=107.61  Aligned_cols=70  Identities=20%  Similarity=0.305  Sum_probs=62.9

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      ...++++|.||.+++|+||||+|++||+|+++|||+|+|++.+      ++++++|+|+++++++|+.+|.+.+..
T Consensus         7 ~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~------~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            7 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD------KEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS------SCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC------CCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            3568999999999999999999999999999999999998633      368999999999999999999986543

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

Probab=99.53  E-value=1.6e-14  Score=109.75  Aligned_cols=71  Identities=28%  Similarity=0.391  Sum_probs=63.4

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      -+++|+||.+++|+||||+|++||+|+++|+|+|+|.++.   +...+|.|+|+|+++++.+|+++|.+++.+.
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            3689999999999999999999999999999999998654   3567899999999999999999999777654

>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=99.50  E-value=3e-14  Score=106.61  Aligned_cols=76  Identities=17%  Similarity=0.243  Sum_probs=66.4

Q ss_pred             CCCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHh
Q 022837           29 DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL  106 (291)
Q Consensus        29 ~~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~  106 (291)
                      |.....++++|.||.+++|.||||+|.+|++|+++|||+|+|+++.+  ++..+|.|+|+|+.+++.+|+.+|.+.+.
T Consensus        11 d~~~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~--~~~~~~~V~I~G~~e~v~~A~~~I~~iv~   86 (97)
T 2ctl_A           11 DRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQITITGYEKNTEAARDAILRIVG   86 (97)
T ss_dssp             HHHHTTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT--CSSCSSEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             hhhccceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC--CCCCccEEEEEeCHHHHHHHHHHHHHHHH
Confidence            34456789999999999999999999999999999999999987653  44468999999999999999999986553

>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=2.7e-14  Score=106.38  Aligned_cols=72  Identities=24%  Similarity=0.336  Sum_probs=64.9

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED  195 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~  195 (291)
                      ...++.+|.||.+++|.|||++|++||+|+++|||+|+|++.+     ..++.|+|+|+++++++|+.+|.+++.+.
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-----~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-----DPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-----SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-----CCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            4568999999999999999999999999999999999998632     24579999999999999999999999874

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

Probab=99.49  E-value=2.7e-14  Score=100.74  Aligned_cols=67  Identities=18%  Similarity=0.246  Sum_probs=60.6

Q ss_pred             ceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 022837          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL  192 (291)
Q Consensus       121 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l  192 (291)
                      ..+..|.||.+++|.|||++|++|++|+++|||+|+|+++.     ..++.|+|+|+.+++++|+.+|.+++
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            46889999999999999999999999999999999998732     25689999999999999999998864

>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=4.7e-14  Score=105.59  Aligned_cols=72  Identities=25%  Similarity=0.258  Sum_probs=64.8

Q ss_pred             ceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       121 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      ..+..|.||.++++.|||++|++|++|+++|||+|+|++...  ++..++.|+|+|+.+++++|+.+|..++.+
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~--~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT--CSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC--CCCCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            469999999999999999999999999999999999987432  334678999999999999999999999876

>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=99.47  E-value=8.9e-15  Score=117.51  Aligned_cols=102  Identities=16%  Similarity=0.094  Sum_probs=81.0

Q ss_pred             ceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCC
Q 022837          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQ  200 (291)
Q Consensus       121 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~  200 (291)
                      .++.+++||.+.+|.+||++|++|++|++++|++|....+      ..+..+...++++.|.+|+.++    .-      
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            4688999999999999999999999999999944333321      1344555556799999887643    10      


Q ss_pred             CCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehccc
Q 022837          201 TMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSL  280 (291)
Q Consensus       201 ~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~  280 (291)
                                                                        ...++.||++.+|.+|||  ||.+|+.+++
T Consensus        67 --------------------------------------------------~e~~v~Vp~~~~g~~IGK--~G~nIr~i~~   94 (144)
T 2qnd_A           67 --------------------------------------------------AEDVIQVPRNLVGKVIGK--NGKLIQEIVD   94 (144)
T ss_dssp             --------------------------------------------------EEEEEEEEGGGHHHHHCG--GGHHHHHHHH
T ss_pred             --------------------------------------------------ceEEEEECHHHcCeeECC--CCHHHHHHHH
Confidence                                                              016789999999999999  9999999999


Q ss_pred             cccc-eEEeec
Q 022837          281 SIYE-EIRLNE  290 (291)
Q Consensus       281 ~tga-~i~~~~  290 (291)
                      .||+ +|+|..
T Consensus        95 ~tG~~~I~i~~  105 (144)
T 2qnd_A           95 KSGVVRVRIEA  105 (144)
T ss_dssp             HHTCSEEEEEE
T ss_pred             HHCCEEEEEcC
Confidence            9997 999874

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.47  E-value=6.4e-15  Score=125.93  Aligned_cols=118  Identities=14%  Similarity=0.058  Sum_probs=88.7

Q ss_pred             CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-----HHHHHHHHHHHHHHHhc
Q 022837          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-----LDEQMRALELILLKLSE  194 (291)
Q Consensus       120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-----~~~v~~A~~~I~~~l~e  194 (291)
                      .+...++.||.+.+|.|||++|++|+.|+++|||+|++..        .++.|+|+|+     ++++++|+.+|..+.+.
T Consensus        32 aP~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~--------~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg  103 (219)
T 2e3u_A           32 FKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS--------ETGEVWITSTKETEDPLAVWKARDIVLAIGRG  103 (219)
T ss_dssp             -CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT--------TTCEEEEEECTTCCSHHHHHHHHHHHHHHHTT
T ss_pred             CCEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc--------CCCEEEEecCCCCCCHHHHHHHHHHHHHHhcc
Confidence            3457799999999999999999999999999999999975        3567999886     69999999999998854


Q ss_pred             Cccc-CCCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEee-----c------CCCc
Q 022837          195 DTLY-SQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPW-----P------LNPV  262 (291)
Q Consensus       195 ~~~~-~~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i-----P------~~~v  262 (291)
                      .+.. ...+..    ...                                       .-..+.+     +      ...+
T Consensus       104 ~~~e~g~~ll~----dd~---------------------------------------~~e~i~i~~~~v~~~~~~~~r~~  140 (219)
T 2e3u_A          104 FSPERAFRLLN----EGE---------------------------------------YLEIINLTDIIIGNEKNALPRVR  140 (219)
T ss_dssp             CCHHHHGGGGS----TTC---------------------------------------EEEEEEGGGCC------CHHHHH
T ss_pred             CCccccceecc----CCc---------------------------------------cceeEEcccccccCCchhhhhhh
Confidence            2111 000000    000                                       0011111     2      2369


Q ss_pred             ceeEEeecCccceehccccccceEEeec
Q 022837          263 GMLLIILIAQPIICHFSLSIYEEIRLNE  290 (291)
Q Consensus       263 G~iIG~~~gg~~ik~~~~~tga~i~~~~  290 (291)
                      |.||||  ||.+||.|++.|||+|+|.+
T Consensus       141 GriIGk--~G~tik~ie~~Tg~~I~v~~  166 (219)
T 2e3u_A          141 GRIIGR--KGRTRQIIEEMSGASVSVYG  166 (219)
T ss_dssp             HHHHCG--GGHHHHHHHHHHCCEEEEET
T ss_pred             heeECC--CchHHHHHHHHhCceEEECC
Confidence            999999  99999999999999999976

>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=99.47  E-value=7.6e-14  Score=104.00  Aligned_cols=73  Identities=22%  Similarity=0.282  Sum_probs=65.3

Q ss_pred             CCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          118 VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       118 ~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      ....++..|.||.++++.|||++|++||+|+++|||+|+|+++.    ...++.|+|+|++++|++|+++|..++.+
T Consensus        13 l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g----~~~~~~V~I~G~~e~v~~A~~~I~~i~~e   85 (95)
T 2ctm_A           13 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG----APDPNCVTVTGLPENVEEAIDHILNLEEE   85 (95)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT----CSCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC----CCCCcEEEEEcCHHHHHHHHHHHHHHHHH
Confidence            35568999999999999999999999999999999999997632    12468999999999999999999999876

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

Probab=99.45  E-value=1.2e-13  Score=97.37  Aligned_cols=67  Identities=18%  Similarity=0.373  Sum_probs=60.7

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHH
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDK  104 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~  104 (291)
                      ...+..|.||.+++|.|||++|.+|++|+++|||+|+|++++     ..+|.|+|+|+.+++.+|+++|.+.
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-----~~~~~V~I~G~~~~v~~A~~~I~~i   69 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-----EKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-----SSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-----CcccEEEEEcCHHHHHHHHHHHHHH
Confidence            457889999999999999999999999999999999998754     3678999999999999999999753

>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=99.44  E-value=3.7e-15  Score=112.51  Aligned_cols=88  Identities=22%  Similarity=0.237  Sum_probs=73.9

Q ss_pred             EecCHHHHHHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHh-ccceEEEecCCCCCC
Q 022837           87 ISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDD-SQAVIKISRLDHSYY  165 (291)
Q Consensus        87 I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~-tGa~I~i~~~~~~~~  165 (291)
                      |+|++++|.+|+.+|.+.+             ...++.+|.||..+++.|||++|++||+|+++ ++++|+|++      
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            5677777777777765332             12278999999999999999999999999997 589999986      


Q ss_pred             CCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837          166 GLNDRLVTLTGTLDEQMRALELILLKLSED  195 (291)
Q Consensus       166 ~~~er~V~I~G~~~~v~~A~~~I~~~l~e~  195 (291)
                        .++.|+|+|+++.|.+|+.+|..++.+.
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              3569999999999999999999999773

>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=99.44  E-value=1.6e-13  Score=102.08  Aligned_cols=72  Identities=22%  Similarity=0.320  Sum_probs=63.8

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      +..++.+|.||.+.+|.|||++|.+||+|+++|||+|+|++..     ..++.|+|+|+++++.+|+.+|.+.+.+.
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-----~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-----DPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-----SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-----CCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            4568999999999999999999999999999999999998643     24578999999999999999999766554

>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=99.43  E-value=2.2e-13  Score=101.44  Aligned_cols=73  Identities=14%  Similarity=0.238  Sum_probs=64.0

Q ss_pred             CCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        31 ~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      .+..++..|.||.+++|.|||++|.+|++|+++|||+|+|+++.+    ..+|.|+|+|.+++|.+|+++|.+.+.+
T Consensus        13 l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~----~~~~~V~I~G~~e~v~~A~~~I~~i~~e   85 (95)
T 2ctm_A           13 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLPENVEEAIDHILNLEEE   85 (95)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC----SCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC----CCCcEEEEEcCHHHHHHHHHHHHHHHHH
Confidence            356789999999999999999999999999999999999987542    3468999999999999999999865543

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

Probab=99.40  E-value=4.4e-13  Score=122.43  Aligned_cols=155  Identities=8%  Similarity=0.079  Sum_probs=103.6

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcccc
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAED  113 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~  113 (291)
                      ++.+.+.+|...++.  ...+..|.+ ++.++++|.|+...+. .+.....|+|+|...++.+|++.+...+......  
T Consensus       105 Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~-~~~~sd~V~IrG~~~nv~~akeA~~~Ll~~l~~~--  178 (376)
T 3n89_A          105 HFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEK-NGIVTTYLRITAREKNQHELIEAAKRLNEILFRE--  178 (376)
T ss_dssp             EEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC------CEEEEEEEEEGGGHHHHHHHHHHHHHHHCC---
T ss_pred             CceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCcccc-cCCCCCEEEEEcChhhHHHHHHHHHHHHHHHHhh--
Confidence            345677777654443  122334544 5678999999654321 1112567999999987777666655433332111  


Q ss_pred             ccCCCCCceEEEEEecCCccceeeccCC--hhHHHHHHhccceEEEecCCCCC-CCCCceEEEEEcCHHHHHHHHHHHHH
Q 022837          114 QADDVGTKTKLRLIVPNSSCGSIIGKAG--ATIKSFMDDSQAVIKISRLDHSY-YGLNDRLVTLTGTLDEQMRALELILL  190 (291)
Q Consensus       114 ~~~~~~~~~~~~i~VP~~~vg~IIGk~G--~~Ik~I~~~tGa~I~i~~~~~~~-~~~~er~V~I~G~~~~v~~A~~~I~~  190 (291)
                       .......+++.+.|+..++..||||+|  ..|++|+++|||+|+|++.++.. .......|+|+|+.++|.+|+.+|.+
T Consensus       179 -e~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~  257 (376)
T 3n89_A          179 -SPAPENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMD  257 (376)
T ss_dssp             --CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHHHHHHHHHHHH
T ss_pred             -hcccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHh
Confidence             112234589999999999999999999  56799999999999998643211 11245689999999999999999999


Q ss_pred             HHhcC
Q 022837          191 KLSED  195 (291)
Q Consensus       191 ~l~e~  195 (291)
                      +|--.
T Consensus       258 lLPv~  262 (376)
T 3n89_A          258 LLPIS  262 (376)
T ss_dssp             TSEEE
T ss_pred             hCCEE
Confidence            88543

>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=2.4e-13  Score=102.94  Aligned_cols=71  Identities=23%  Similarity=0.357  Sum_probs=63.6

Q ss_pred             CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED  195 (291)
Q Consensus       120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~  195 (291)
                      .+.+..|.||.+++|.|||++|++||+|+++|||+|+|+++.     ...+.|+|+|+.+++++|+.+|.+++.+.
T Consensus        15 ap~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g-----~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   85 (104)
T 2ctk_A           15 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-----LQSDIIAITGLAANLDRAKAGLLERVKEL   85 (104)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-----TTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-----CCcceEEEEcCHHHHHHHHHHHHHHHhhH
Confidence            357899999999999999999999999999999999998732     23569999999999999999999998764

>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=99.33  E-value=1.7e-12  Score=98.32  Aligned_cols=69  Identities=25%  Similarity=0.320  Sum_probs=61.5

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      ++...|.||.+++|.|||++|.+|++|+++|||+|+|+++++     ..+.|+|+|+.+++.+|+.+|.+.+.+
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~-----~~~~V~I~G~~e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL-----QSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT-----TCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCC-----CcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            488999999999999999999999999999999999987542     456899999999999999999866543

>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=99.32  E-value=1.6e-12  Score=96.61  Aligned_cols=72  Identities=21%  Similarity=0.336  Sum_probs=64.9

Q ss_pred             CCCceEEEEEecCCccceeeccCChhHHHHHHhc-cceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          118 VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDS-QAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       118 ~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      ..+.++..|.||.++++.|||++|++||+|+++| ||+|+|+++     +...+.|+|+|+.++|++|+.+|.+++.+
T Consensus        13 ~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~-----g~~~~~V~I~G~~~~v~~A~~~I~~iv~e   85 (95)
T 2ctj_A           13 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-----GSGSDTVVIRGPSSDVEKAKKQLLHLAEE   85 (95)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-----TTTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             HhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC-----CCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            3556899999999999999999999999999999 999999863     23567999999999999999999999976

>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=99.23  E-value=1.6e-11  Score=91.20  Aligned_cols=73  Identities=14%  Similarity=0.257  Sum_probs=64.3

Q ss_pred             CCCCcEEEEEEecccccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        30 ~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      ..++.++..|.||.++++.|||++|.+|++|+++| ||+|+|++++     ...+.|+|.|..+++.+|+++|.+.+.+
T Consensus        12 e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g-----~~~~~V~I~G~~~~v~~A~~~I~~iv~e   85 (95)
T 2ctj_A           12 DLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-----SGSDTVVIRGPSSDVEKAKKQLLHLAEE   85 (95)
T ss_dssp             CCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-----TTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             HHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC-----CCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            45677889999999999999999999999999999 9999998743     4567899999999999999999865543

>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=99.22  E-value=1.5e-12  Score=108.70  Aligned_cols=115  Identities=14%  Similarity=0.081  Sum_probs=90.0

Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEE-----cCHHHHHHHHHHHHHHHhcCcc
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT-----GTLDEQMRALELILLKLSEDTL  197 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~-----G~~~~v~~A~~~I~~~l~e~~~  197 (291)
                      ..++.||.+.+|.|||++|++++.|++.+|++|++..        .++.|+|+     |++.++.+|..+|..+.+.-+.
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            4789999999999999999999999999999999975        46788998     9999999999999998876432


Q ss_pred             cCCC-CCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEee----------cCCCcceeE
Q 022837          198 YSQT-MTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPW----------PLNPVGMLL  266 (291)
Q Consensus       198 ~~~~-~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i----------P~~~vG~iI  266 (291)
                      .+.. +..    ..+                                       .--.+.+          +...+|.||
T Consensus        77 e~A~~Ll~----Dd~---------------------------------------~~e~i~i~~~~~~~~~~~~r~~GrII  113 (191)
T 1tua_A           77 EKAFRLLE----EDQ---------------------------------------ILVVVDLKQVVGDSQNHLKRIKGRII  113 (191)
T ss_dssp             HHHGGGGS----TTE---------------------------------------EEEEEETHHHHTTCHHHHHHHHHHHH
T ss_pred             HHhhhccc----Ccc---------------------------------------eeEEEEcccccccCchhHHHHhhhee
Confidence            1110 000    000                                       0011222          234689999


Q ss_pred             EeecCccceehccccccceEEeec
Q 022837          267 IILIAQPIICHFSLSIYEEIRLNE  290 (291)
Q Consensus       267 G~~~gg~~ik~~~~~tga~i~~~~  290 (291)
                      ||  +|.+|+.|.+-|||+|.|.+
T Consensus       114 Gk--~G~tik~iE~~Tg~~I~v~~  135 (191)
T 1tua_A          114 GE--GGRARRTIEEMTDTYINVGE  135 (191)
T ss_dssp             CG--GGHHHHHHHHHHTCEEEECS
T ss_pred             CC--CccHHHHHHHHHCceEEEcC
Confidence            99  99999999999999999976

>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=99.13  E-value=1.1e-10  Score=87.97  Aligned_cols=65  Identities=17%  Similarity=0.235  Sum_probs=58.3

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHh
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL  106 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~  106 (291)
                      .++.+|.||..+++.|||++|++|++|++++ +++|+|++        .++.|+|+|.++.|.+|+.+|.+.+.
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~--------~~~~ItI~G~~~~V~~a~~~I~~~v~   91 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE--------GEDKITLEGPTEDVSVAQEQIEGMVK   91 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS--------SSCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC--------CCCEEEEECCHHHHHHHHHHHHHHHH
Confidence            3789999999999999999999999999985 89999975        25789999999999999999975553

>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=99.04  E-value=1.4e-10  Score=84.76  Aligned_cols=65  Identities=15%  Similarity=0.238  Sum_probs=58.0

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccce-EEEecCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHH
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV-IKISRLDHSYYGLNDRLVTLTG-TLDEQMRALELILLK  191 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~-I~i~~~~~~~~~~~er~V~I~G-~~~~v~~A~~~I~~~  191 (291)
                      ...+...|.||.+++|.|||++|++||+|+++|||+ |.|..        ++..|+|.| +.+++++|+.+|..+
T Consensus        12 ~~~~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           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE--------DTGTFRIYGESADAVKKARGFLEFV   78 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET--------TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc--------CCCEEEEEECCHHHHHHHHHHHHhh
Confidence            345789999999999999999999999999999998 99974        358999999 799999999998763

>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=98.89  E-value=5.1e-09  Score=82.16  Aligned_cols=75  Identities=21%  Similarity=0.268  Sum_probs=61.9

Q ss_pred             CceEEEEEecCC------ccceeeccCChhHHHHHHhccceEEEecCCCCC-------------CCCCceEEEEEcC-HH
Q 022837          120 TKTKLRLIVPNS------SCGSIIGKAGATIKSFMDDSQAVIKISRLDHSY-------------YGLNDRLVTLTGT-LD  179 (291)
Q Consensus       120 ~~~~~~i~VP~~------~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~-------------~~~~er~V~I~G~-~~  179 (291)
                      ..++.+|.||.+      ++|.|||++|.+||+|+++|||+|.|.......             ....+-.|.|+++ .+
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            357899999988      889999999999999999999999997632100             1123668999995 88


Q ss_pred             HHHHHHHHHHHHHhc
Q 022837          180 EQMRALELILLKLSE  194 (291)
Q Consensus       180 ~v~~A~~~I~~~l~e  194 (291)
                      .+.+|+++|.++|.+
T Consensus        85 ~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999976

>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=98.89  E-value=1.2e-09  Score=79.77  Aligned_cols=63  Identities=25%  Similarity=0.376  Sum_probs=56.0

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCc-EEEcCCCCCCCCCCceEEEEec-CHHHHHHHHHHHH
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGAR-IQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVI  102 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~-I~v~~~~~~~p~~~er~v~I~G-~~~~v~~A~~~I~  102 (291)
                      ...+...|.||.+++|.|||++|.+|++|+++||++ |.+.+        ++..|+|.| +.+.+.+|+.+|.
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e--------ddG~V~I~g~~~ea~~~A~~~I~   76 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE--------DTGTFRIYGESADAVKKARGFLE   76 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET--------TTTEEEEEESSHHHHHHHHHHHS
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc--------CCCEEEEEECCHHHHHHHHHHHH
Confidence            345889999999999999999999999999999998 99963        247799999 7899999988885

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.83  E-value=2.2e-08  Score=77.08  Aligned_cols=78  Identities=22%  Similarity=0.181  Sum_probs=57.5

Q ss_pred             CCCCcEEEEEEeccc-------ccceeeccCChhHHHHHHHhCCcEEEcCCCCCC--C-----CCCceEEEEe-cCHHHH
Q 022837           30 PTEKPTYIRFLVSNP-------LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFF--P-----GTTDRIIMIS-GTIDEI   94 (291)
Q Consensus        30 ~~~~~~~~rilvp~~-------~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~--p-----~~~er~v~I~-G~~~~v   94 (291)
                      ..-..+..||.||.+       .+|.|||++|.+||+|+++|||+|.|.......  +     ..++-.|.|. .+.+.+
T Consensus         7 ~~~~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i   86 (119)
T 2yqr_A            7 GGMHYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGL   86 (119)
T ss_dssp             SCCSCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHH
T ss_pred             CCeeEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHH
Confidence            344568889999876       689999999999999999999999997431100  0     0122345555 568999


Q ss_pred             HHHHHHHHHHHhh
Q 022837           95 LRAVDLVIDKLLT  107 (291)
Q Consensus        95 ~~A~~~I~~~i~~  107 (291)
                      .+|+++|.+.+..
T Consensus        87 ~~A~~~Ie~Ll~~   99 (119)
T 2yqr_A           87 AAAKKLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhc
Confidence            9999999876643

>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=1.1e-08  Score=78.71  Aligned_cols=74  Identities=9%  Similarity=0.018  Sum_probs=58.3

Q ss_pred             ceEEEEEecCC-------ccceeeccCChhHHHHHHhccceEEEecCCCC-------CCCCCceEEEEEcC-HHHHHHHH
Q 022837          121 KTKLRLIVPNS-------SCGSIIGKAGATIKSFMDDSQAVIKISRLDHS-------YYGLNDRLVTLTGT-LDEQMRAL  185 (291)
Q Consensus       121 ~~~~~i~VP~~-------~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~-------~~~~~er~V~I~G~-~~~v~~A~  185 (291)
                      ..+.+|.||-+       ++|.|||++|.+||+|+++|||+|.|..+...       ....++-.|.|++. .+++++|+
T Consensus        11 ~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~   90 (119)
T 2yqr_A           11 YVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAK   90 (119)
T ss_dssp             CEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHH
T ss_pred             EEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHH
Confidence            46788888865       78999999999999999999999999743110       01123457888865 99999999


Q ss_pred             HHHHHHHhc
Q 022837          186 ELILLKLSE  194 (291)
Q Consensus       186 ~~I~~~l~e  194 (291)
                      .+|.++|.+
T Consensus        91 ~~Ie~Ll~~   99 (119)
T 2yqr_A           91 KLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhhc
Confidence            999999876

>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=98.79  E-value=1.1e-08  Score=80.15  Aligned_cols=75  Identities=15%  Similarity=0.306  Sum_probs=59.5

Q ss_pred             CcEEEEEEeccc------ccceeeccCChhHHHHHHHhCCcEEEcCCCCCC-------------CCCCceEEEEec-CHH
Q 022837           33 KPTYIRFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFF-------------PGTTDRIIMISG-TID   92 (291)
Q Consensus        33 ~~~~~rilvp~~------~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~-------------p~~~er~v~I~G-~~~   92 (291)
                      ..++.+|.||.+      .+|.|||++|.+||+|+++|||+|.|.......             ....+-.|.|++ +.+
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            468899999988      889999999999999999999999997632100             011245677877 588


Q ss_pred             HHHHHHHHHHHHHhh
Q 022837           93 EILRAVDLVIDKLLT  107 (291)
Q Consensus        93 ~v~~A~~~I~~~i~~  107 (291)
                      .+.+|+++|.+.+..
T Consensus        85 ~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999877754

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

Probab=98.49  E-value=1.4e-07  Score=92.11  Aligned_cols=89  Identities=11%  Similarity=0.113  Sum_probs=66.8

Q ss_pred             HHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEE
Q 022837           95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL  174 (291)
Q Consensus        95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I  174 (291)
                      .+++..|++.+.+.+...........+....+.||.++++.|||+||++||+|+++|||+|.|..         +..|.|
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            33445555555555443322223344578889999999999999999999999999999999973         468999


Q ss_pred             EcC-HHHHHHHHHHHHHHH
Q 022837          175 TGT-LDEQMRALELILLKL  192 (291)
Q Consensus       175 ~G~-~~~v~~A~~~I~~~l  192 (291)
                      .|+ .+.+++|+++|..++
T Consensus       611 ~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          611 FAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EESSHHHHHHHHHHTTC--
T ss_pred             EeCCHHHHHHHHHHHHHHh
Confidence            997 688999999987664

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.46  E-value=2.4e-07  Score=73.13  Aligned_cols=74  Identities=23%  Similarity=0.169  Sum_probs=56.3

Q ss_pred             eEEEEEecCC------ccceeeccCChhHHHHHHhccceEEEecCCCCC---------------CCCCceEEEEEcC-H-
Q 022837          122 TKLRLIVPNS------SCGSIIGKAGATIKSFMDDSQAVIKISRLDHSY---------------YGLNDRLVTLTGT-L-  178 (291)
Q Consensus       122 ~~~~i~VP~~------~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~---------------~~~~er~V~I~G~-~-  178 (291)
                      .+.++.||.+      ++|+|||++|.++|+|+++|||+|.|..+....               ...++-.|.|++. + 
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            4667888854      489999999999999999999999998632110               0112337889985 3 


Q ss_pred             ----HHHHHHHHHHHHHHhcC
Q 022837          179 ----DEQMRALELILLKLSED  195 (291)
Q Consensus       179 ----~~v~~A~~~I~~~l~e~  195 (291)
                          ..+.+|+++|.++|...
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p~  102 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVPA  102 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCC
T ss_pred             hhHHHHHHHHHHHHHHHCCCC
Confidence                37999999999999753

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.45  E-value=2.1e-07  Score=73.36  Aligned_cols=72  Identities=19%  Similarity=0.267  Sum_probs=54.0

Q ss_pred             EEEEEEecccc------cceeeccCChhHHHHHHHhCCcEEEcCCCCCCC---------------CCCceEEEEecC-H-
Q 022837           35 TYIRFLVSNPL------AGAVIGKGGSTINDFQSQSGARIQLSRSHEFFP---------------GTTDRIIMISGT-I-   91 (291)
Q Consensus        35 ~~~rilvp~~~------vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p---------------~~~er~v~I~G~-~-   91 (291)
                      +.-||.||.+.      +|+|||++|.++|+|+++|||+|.|........               ...+--|.|++. + 
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            56789999766      999999999999999999999999986442110               012236778774 3 


Q ss_pred             ----HHHHHHHHHHHHHHh
Q 022837           92 ----DEILRAVDLVIDKLL  106 (291)
Q Consensus        92 ----~~v~~A~~~I~~~i~  106 (291)
                          ..+.+|+++|.+.|.
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                268899999987664

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=98.17  E-value=6.9e-07  Score=70.87  Aligned_cols=105  Identities=21%  Similarity=0.275  Sum_probs=75.8

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccc
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQ  114 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~  114 (291)
                      -.+.|+|+...+|+.||++|++|+.|+++.|-+|.+-..++      +              -..+|...|.-..-..-.
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------D--------------LERIVKNLFPGVKIESIN   95 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCS------S--------------HHHHHHHHSTTSCEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCC------C--------------HHHHHHHhcCCceEEEEE
Confidence            35789999999999999999999999999999999976432      1              122333222111000000


Q ss_pred             cCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEec
Q 022837          115 ADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (291)
Q Consensus       115 ~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~  159 (291)
                      ...........+.||.+..+..|||+|.+++-..+-||.+|.|..
T Consensus        96 i~~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~~  140 (144)
T 2cxc_A           96 VRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVEK  140 (144)
T ss_dssp             EEEETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEEE
T ss_pred             EeecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCceE
Confidence            000023467889999999999999999999999999999888753

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

Probab=98.06  E-value=2.1e-06  Score=84.73  Aligned_cols=90  Identities=14%  Similarity=0.209  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEE
Q 022837           96 RAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT  175 (291)
Q Consensus        96 ~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~  175 (291)
                      +++..|++.+.+.+...........+....+.||.++++.|||+||.+||+|.++|||+|.|..         +..|.|.
T Consensus       544 ~g~~~I~~~m~~al~~~r~~~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d---------dG~v~I~  614 (726)
T 4aid_A          544 EGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND---------DGVVKVS  614 (726)
T ss_dssp             HHHHHHHHHHHTTCSSCCSSCCSSCCC----------------------------------------------------C
T ss_pred             HHHHHHHHHHHHHHHhhhhhhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC---------CceEEEE
Confidence            3444555555555433222222334557788999999999999999999999999999999863         3567887


Q ss_pred             cC-HHHHHHHHHHHHHHHhc
Q 022837          176 GT-LDEQMRALELILLKLSE  194 (291)
Q Consensus       176 G~-~~~v~~A~~~I~~~l~e  194 (291)
                      +. .+++++|+.+|..++.+
T Consensus       615 ~~~~~~~~~A~~~i~~i~~~  634 (726)
T 4aid_A          615 ASDGAKIKAAIDWIKSITDE  634 (726)
T ss_dssp             CSCHHHHHHHHHC-------
T ss_pred             eCCHHHHHHHHHHHHHHhhh
Confidence            77 88899999999988764

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=98.00  E-value=1.6e-05  Score=61.57  Aligned_cols=66  Identities=20%  Similarity=0.121  Sum_probs=57.6

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHH
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL  105 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i  105 (291)
                      ++.|.|....++.|+|++|+.|+.|+..|++.|+|..-+    .+.+-.|+|.|++..-.+|+.+|....
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~----s~g~tEVtIfG~~~~Q~rak~MI~sLA  122 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWG----PERRAEIWIFGPPPFRRDVDRMLTDLA  122 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC----TTSCEEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC----CCCcEEEEEECCHHHHHHHHHHHHHHH
Confidence            467788999999999999999999999999999998643    235677999999999999999997544

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.89  E-value=2.5e-05  Score=60.44  Aligned_cols=68  Identities=13%  Similarity=0.057  Sum_probs=60.0

Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      ...+.+.+..++.|+|++|+.|+.|+..|++.|++..-+.    +..-.|+|.|++..-.+|+.+|..+..-
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s----~g~tEVtIfG~~~~Q~rak~MI~sLA~~  124 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP----ERRAEIWIFGPPPFRRDVDRMLTDLAHY  124 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT----TSCEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC----CCcEEEEEECCHHHHHHHHHHHHHHHHH
Confidence            5778899999999999999999999999999999987422    2567899999999999999999987653

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

Probab=97.82  E-value=1.3e-05  Score=78.31  Aligned_cols=62  Identities=16%  Similarity=0.301  Sum_probs=52.8

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecC-HHHHHHHHHHHHH
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLVID  103 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~-~~~v~~A~~~I~~  103 (291)
                      -+....|.||.+.+|.|||++|.+||.|+++|||+|.|.+         +-.|.|.+. .+.+.+|+++|.+
T Consensus       565 ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d---------~G~V~I~~~~~~~~~~A~~~I~~  627 (630)
T 3u1k_A          565 GPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD---------EETFSVFAPTPSAMHEARDFITE  627 (630)
T ss_dssp             CCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS---------SSEEEEEESSHHHHHHHHHHTTC
T ss_pred             CCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC---------CcEEEEEeCCHHHHHHHHHHHHH
Confidence            3567889999999999999999999999999999999964         245788776 6788999888854

>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=97.08  E-value=0.00034  Score=60.13  Aligned_cols=97  Identities=22%  Similarity=0.237  Sum_probs=68.1

Q ss_pred             cccceeeccCChhHHHH-HHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCce
Q 022837           44 PLAGAVIGKGGSTINDF-QSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKT  122 (291)
Q Consensus        44 ~~vG~IIGk~G~~Ik~I-~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~  122 (291)
                      +-+|+.||++|.+|+.| ++..|-+|.|-..++      +              ...+|...|.-..-.. .........
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~------d--------------p~~fi~nalsPA~V~~-V~i~~~~~~  184 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDD------D--------------PARFVANALSPAKVVS-VSVIDQTAR  184 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS------S--------------HHHHHHHHTTTSCCSE-EEEEETTTT
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecC------C--------------HHHHHHhccCCcceEE-EEEEcCCCc
Confidence            45899999999999999 677789999976432      2              1223332222110000 000011225


Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCC
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLD  161 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~  161 (291)
                      ...+.||.+..+.-|||+|.|++--..-||.+|.|....
T Consensus       185 ~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  223 (251)
T 2asb_A          185 AARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  223 (251)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             EEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHH
Confidence            788999999999999999999999999999999998744

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

Probab=96.98  E-value=0.00024  Score=70.17  Aligned_cols=63  Identities=21%  Similarity=0.393  Sum_probs=11.0

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecC-HHHHHHHHHHHHHHH
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLVIDKL  105 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~-~~~v~~A~~~I~~~i  105 (291)
                      +....|.||.++++.|||++|.+||+|+++||++|.+.++         -.|.|.+. .+.+.+|+++|...+
T Consensus       569 p~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~dd---------G~v~I~~~~~~~~~~A~~~i~~i~  632 (726)
T 4aid_A          569 PKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDD---------GVVKVSASDGAKIKAAIDWIKSIT  632 (726)
T ss_dssp             CC----------------------------------------------------CCSCHHHHHHHHHC-----
T ss_pred             CeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEECC---------ceEEEEeCCHHHHHHHHHHHHHHh
Confidence            3457889999999999999999999999999999999642         33566654 778888888887443

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

Probab=96.96  E-value=0.00029  Score=69.81  Aligned_cols=89  Identities=17%  Similarity=0.200  Sum_probs=7.0

Q ss_pred             HHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEc
Q 022837           97 AVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG  176 (291)
Q Consensus        97 A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G  176 (291)
                      +...|++.+.+.+...........+....+.||.++++.+||++|.+|+.|.++||+.|.+..         +..|.|.+
T Consensus       535 ~~~~I~~~m~~al~~~~~~~~~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~---------dg~v~I~~  605 (723)
T 3cdi_A          535 ARLHILGVMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED---------DGTVKIAA  605 (723)
T ss_dssp             HHHHHHHHHHHHCC------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHhhhcchhccccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC---------CccEEEec
Confidence            444455555555433212222234567788899999999999999999999999999998763         35677766


Q ss_pred             C-HHHHHHHHHHHHHHHhc
Q 022837          177 T-LDEQMRALELILLKLSE  194 (291)
Q Consensus       177 ~-~~~v~~A~~~I~~~l~e  194 (291)
                      . .+.+++|.++|..++.+
T Consensus       606 ~~~~~~~~a~~~i~~i~~~  624 (723)
T 3cdi_A          606 TDGEKAKHAIRRIEEITAE  624 (723)
T ss_dssp             -------------------
T ss_pred             CCHHHHHHHHHHHHHHhhh
Confidence            5 66778888888776543

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=96.85  E-value=0.0006  Score=61.83  Aligned_cols=104  Identities=22%  Similarity=0.262  Sum_probs=73.1

Q ss_pred             EEEEecc-----cccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhc
Q 022837           37 IRFLVSN-----PLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH  110 (291)
Q Consensus        37 ~rilvp~-----~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~  110 (291)
                      .++-|-+     +-+|..||++|.+|+.|.++. |-+|.|-..++      +              ...+|...|.-..-
T Consensus       237 aKIAV~s~d~~iDpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~------d--------------p~~fi~nalsPA~V  296 (366)
T 1k0r_A          237 SKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYDD------D--------------PARFVANALSPAKV  296 (366)
T ss_dssp             EEEEEEESSTTCCHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS------S--------------HHHHHHHHTTTSCC
T ss_pred             EEEEEEeCCCCCCCcccccCCcchHHHHHHHHhCCCeEEEEEcCC------C--------------HHHHHHHhcCCcce
Confidence            4555544     568999999999999999999 89999876432      1              12233322221100


Q ss_pred             cccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCC
Q 022837          111 AEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLD  161 (291)
Q Consensus       111 ~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~  161 (291)
                      ..-...+ .......+.||....+..|||+|.|++-...-||.+|.|....
T Consensus       297 ~~V~~~~-~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  346 (366)
T 1k0r_A          297 VSVSVID-QTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  346 (366)
T ss_dssp             SEEEEEE-TTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESS
T ss_pred             eEEEEEc-CCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHH
Confidence            0000011 1245789999999999999999999999999999999998743

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

Probab=96.73  E-value=0.00016  Score=71.93  Aligned_cols=87  Identities=16%  Similarity=0.181  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEE
Q 022837           96 RAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT  175 (291)
Q Consensus        96 ~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~  175 (291)
                      +++..|++.+.+.+... .......+....+.||.++++.+||++|.+||+|.+++|+.|.|..         +..|.|+
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            34445565665554433 2222233455678899999999999999999999999999998863         3567776


Q ss_pred             cC-HHHHHHHHHHHHHHH
Q 022837          176 GT-LDEQMRALELILLKL  192 (291)
Q Consensus       176 G~-~~~v~~A~~~I~~~l  192 (291)
                      .. ....++|+.+|..+.
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 667777877776654

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=96.02  E-value=0.0008  Score=53.19  Aligned_cols=104  Identities=13%  Similarity=0.172  Sum_probs=73.9

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCC
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQT  201 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~  201 (291)
                      ....++|+...+|..||++|++|+.|+++.|-+|.+-.-++      +              -..+|...|.-..-.  .
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~------d--------------~~~fI~naLsPA~V~--~   93 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSS------D--------------LERIVKNLFPGVKIE--S   93 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCS------S--------------HHHHHHHHSTTSCEE--E
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCC------C--------------HHHHHHHhcCCceEE--E
Confidence            58899999999999999999999999999999999986321      1              123333333211100  0


Q ss_pred             CCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehcccc
Q 022837          202 MTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLS  281 (291)
Q Consensus       202 ~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~  281 (291)
                      ..  ..                                      .........+.||++..+..|||  +|.|++-.++=
T Consensus        94 V~--i~--------------------------------------~~~~~~~~~V~V~~~q~slAIGk--~G~NvrLa~~L  131 (144)
T 2cxc_A           94 IN--VR--------------------------------------ERNGVKQVVIKVSEDDKGAAIGK--GGKNVKRARLV  131 (144)
T ss_dssp             EE--EE--------------------------------------EETTEEEEEEEECTTTHHHHHCG--GGHHHHHHHHH
T ss_pred             EE--Ee--------------------------------------ecCCcEEEEEEEChHHhhhccCC--CCHHHHHHHHH
Confidence            00  00                                      00011347889999999999999  99999999998


Q ss_pred             ccceEEee
Q 022837          282 IYEEIRLN  289 (291)
Q Consensus       282 tga~i~~~  289 (291)
                      ||..|.|.
T Consensus       132 tg~~idI~  139 (144)
T 2cxc_A          132 LSKLFGVE  139 (144)
T ss_dssp             HHHHHCEE
T ss_pred             hCCeeCce
Confidence            88877654

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=95.97  E-value=0.0047  Score=55.73  Aligned_cols=96  Identities=23%  Similarity=0.304  Sum_probs=67.2

Q ss_pred             cccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCce
Q 022837           44 PLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKT  122 (291)
Q Consensus        44 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~  122 (291)
                      +-+|+.||.+|.+|+.+.++. |-+|.+-..++      +              -..+|...|.-..-.. -........
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s~------d--------------~~~fi~nal~Pa~v~~-v~~~d~~~~  303 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWSD------D--------------PKQLIANALAPATVIE-VEILDKENK  303 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECCS------S--------------HHHHHHHHTCSSCCSE-EEEEETTTT
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecCC------C--------------HHHHHHHhcCccEEEE-EEEEcCCCC
Confidence            358999999999999999998 78888865332      1              1123332221110000 000012235


Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL  160 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  160 (291)
                      ...+.||.++.+.-|||+|.|++--..-||.+|.|...
T Consensus       304 ~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          304 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            78999999999999999999999999999999999763

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

Probab=93.70  E-value=0.012  Score=58.35  Aligned_cols=60  Identities=25%  Similarity=0.402  Sum_probs=0.0

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecC-HHHHHHHHHHHH
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLVI  102 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~-~~~v~~A~~~I~  102 (291)
                      +....+.||.+.++.|||++|.+|+.|.++||+.|.+..         +..+.|.+. .+.+.+|.++|.
T Consensus       559 p~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~---------dg~v~I~~~~~~~~~~a~~~i~  619 (723)
T 3cdi_A          559 PRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED---------DGTVKIAATDGEKAKHAIRRIE  619 (723)
T ss_dssp             ----------------------------------------------------------------------
T ss_pred             ceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC---------CccEEEecCCHHHHHHHHHHHH
Confidence            455778899999999999999999999999999999853         344666554 455666766654

>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=90.51  E-value=0.045  Score=54.45  Aligned_cols=36  Identities=14%  Similarity=0.301  Sum_probs=12.8

Q ss_pred             EEEeecCCCcceeEEeecCccceehccccccceEEeec
Q 022837          253 VLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNE  290 (291)
Q Consensus       253 ~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tga~i~~~~  290 (291)
                      .++.||.+++|.+||.  ||.+||+|.+++|+.|.|.+
T Consensus       600 ~~~~I~~~ki~~vIG~--gGk~Ik~I~~~~G~~IdI~~  635 (757)
T 1e3p_A          600 ITVKIPVDKIGEVIGP--KRQMINQIQEDTGAEITIED  635 (757)
T ss_dssp             CCC--------------------CTTCCCCCSCC----
T ss_pred             EEEEEChHHeehcccc--cceeeehhhHhhCCEEEecC
Confidence            5678999999999999  99999999999999998864

>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=89.88  E-value=0.23  Score=42.56  Aligned_cols=41  Identities=22%  Similarity=0.233  Sum_probs=37.4

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCC
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHE   75 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~   75 (291)
                      -.+.+.||.++.++.|||+|.|++.-.+-||.+|.|....+
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            46889999999999999999999999999999999976543

>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=87.07  E-value=0.37  Score=43.36  Aligned_cols=41  Identities=24%  Similarity=0.304  Sum_probs=36.9

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS   73 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~   73 (291)
                      +.-.+.+.||.++.++.|||+|.|++.-.+-||.+|.|...
T Consensus       301 ~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          301 ENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             TTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             CCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            34578899999999999999999999999999999999653

>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=86.43  E-value=0.39  Score=43.45  Aligned_cols=41  Identities=22%  Similarity=0.240  Sum_probs=37.6

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCC
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSH   74 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~   74 (291)
                      .-.+.+.||.++.++.|||+|.|++-..+-||.+|.|....
T Consensus       306 ~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  346 (366)
T 1k0r_A          306 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  346 (366)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESS
T ss_pred             CcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHH
Confidence            45789999999999999999999999999999999997654

>2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori}

Probab=85.52  E-value=0.37  Score=38.12  Aligned_cols=67  Identities=10%  Similarity=0.089  Sum_probs=46.5

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhh
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTEL  109 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~  109 (291)
                      ++.+.+..+..|.+|||.|.|++.||--+...++-..       ...-.+-+.+-.+.-.+.+..+...+.+..
T Consensus        34 ~i~i~i~ged~glLIGK~G~TL~ALQyL~~~~vn~~~-------~~~V~LDve~YRerReetL~~lA~~~A~kV  100 (152)
T 2pt7_G           34 VLLIDIDGEDSALLIGEKGYRYKALSYLLFNWIHPTY-------GYSIRLEISTFLQNQEKVMDTQLQSVIMTV  100 (152)
T ss_dssp             EEEEEEEEGGGTTTTCGGGHHHHHHHHHHHHHHHHHH-------SCEEEEEETTHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEecCCcceEECCCCcchHHHHHHHHHHhhhcC-------CceEEEEhHHhHHHHHHHHHHHHHHHHHHH
Confidence            4566677889999999999999999998743333211       112335566767777777777777776653

---

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	291
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	7e-19
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	7e-17
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-18
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	5e-15
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-17
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-15
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	1e-13
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	7e-14
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	7e-15
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	3e-12
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	2e-14
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	1e-13
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	7e-14
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	4e-12
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-13
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	2e-12
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	6e-13
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	4e-12
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	6e-13
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	9e-10
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-12
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-12
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	7e-12
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	5e-08
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-09
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	4e-08
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-08
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-06
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	4e-08
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	4e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	2e-05
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	0.001
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	2e-05
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	3e-04
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	4e-05
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	4e-05
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	5e-05
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	2e-04
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	5e-04
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	0.004
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	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 = 7e-19
 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 = 71.4 bits (175), Expect = 7e-17
 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 = 76.5 bits (188), Expect = 1e-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 = 66.5 bits (162), Expect = 5e-15
 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

>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 = 72.5 bits (178), Expect = 3e-17
 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 = 67.5 bits (165), Expect = 2e-15
 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 = 68.3 bits (167), Expect = 1e-15
 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 = 62.5 bits (152), Expect = 1e-13
 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 = 67.2 bits (164), Expect = 2e-15
 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 = 63.3 bits (154), Expect = 7e-14
 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

>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 = 66.0 bits (161), Expect = 7e-15
 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 = 58.7 bits (142), Expect = 3e-12
 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 = 65.8 bits (160), Expect = 2e-14
 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 = 63.8 bits (155), Expect = 1e-13
 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

>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 = 63.7 bits (155), Expect = 7e-14
 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 = 58.7 bits (142), Expect = 4e-12
 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

>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 = 62.7 bits (152), Expect = 1e-13
 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 = 59.6 bits (144), Expect = 2e-12
 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

>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 = 60.9 bits (148), Expect = 6e-13
 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 = 58.6 bits (142), Expect = 4e-12
 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

>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 = 61.4 bits (149), Expect = 6e-13
 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 = 52.5 bits (126), Expect = 9e-10
 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 = 59.1 bits (143), Expect = 2e-12
 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

>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 = 59.1 bits (143), Expect = 2e-12
 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

>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 = 57.8 bits (140), Expect = 7e-12
 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 = 47.0 bits (112), Expect = 5e-08
 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

>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 = 50.6 bits (121), Expect = 3e-09
 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 = 47.5 bits (113), Expect = 4e-08
 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 = 49.0 bits (117), Expect = 1e-08
 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 = 43.2 bits (102), Expect = 1e-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 = 47.5 bits (113), Expect = 4e-08
 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 = 47.5 bits (113), Expect = 4e-08
 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

>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 = 39.2 bits (92), Expect = 2e-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 = 34.2 bits (79), Expect = 0.001
 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

>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 = 39.3 bits (92), Expect = 2e-05
 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 = 36.3 bits (84), Expect = 3e-04
 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 = 39.4 bits (92), Expect = 4e-05
 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

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 39.0 bits (91), Expect = 4e-05
 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

>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 = 38.9 bits (91), Expect = 5e-05
 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

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.8 bits (88), Expect = 2e-04
 Identities = 9/50 (18%), Positives = 18/50 (36%)

Query: 47 GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
          G +IG+GG      +  +   I +        G  +R +     I+ +  
Sbjct: 25 GRIIGEGGRARRTIEEMTDTYINVGEYEVAIIGDYERAMAAKQAIEMLAE 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 = 36.0 bits (83), Expect = 5e-04
 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 = 33.7 bits (77), Expect = 0.004
 Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 6/70 (8%)

Query: 102 IDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV-IKISRL 160
           + + LTE++A+  A+     +   +  P+     IIGK G  +         V I+ +  
Sbjct: 6   LGQALTEVYAK--ANSFTVSS---VAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG 60

Query: 161 DHSYYGLNDR 170
           +         
Sbjct: 61  EDKITLEGPT 70

>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 = 33.7 bits (77), Expect = 0.004
 Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 10/79 (12%)

Query: 32  EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQ-SGARIQLSRSHEFFPGTTDRIIMISGT 90
              T       + L   +IGK G  +     Q     I+       F    D+I +  G 
Sbjct: 18  NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIE-------FTEGEDKITL-EGP 69

Query: 91  IDEILRAVDLVIDKLLTEL 109
            +++  A +  I+ ++ +L
Sbjct: 70  TEDVSVAQEQ-IEGMVKDL 87

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	291
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.72
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.72
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.7
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.7
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.68
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.68
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.68
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.68
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.66
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.66
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.66
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.65
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.65
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.63
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.63
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.62
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.61
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.61
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.55
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.55
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.54
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.54
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.5
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.5
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.5
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.47
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.46
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.45
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.45
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.4
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.37
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.35
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.27
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.26
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.24
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.08
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.05
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.99
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.97
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.92
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.88
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.79
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.77
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.62
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.59
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.48
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.39
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.14
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.01
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	96.38
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	96.17
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.8
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	95.68
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	91.09
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	90.6
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	90.39
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	89.48
d1wf3a2	118	GTPase Era C-terminal domain {Thermus thermophilus	86.79
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	86.58
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	85.84
d2uubc1	105	Ribosomal protein S3 N-terminal domain {Thermus th	82.38
d1wf3a2	118	GTPase Era C-terminal domain {Thermus thermophilus	82.23

>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=99.72  E-value=6.6e-18  Score=118.76  Aligned_cols=71  Identities=30%  Similarity=0.425  Sum_probs=66.2

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL  192 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l  192 (291)
                      ..++|.||.+++|+||||+|++||+|+++|||+|+|.+.++..++..+|.|+|+|++++|++|+.+|.++|
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            46899999999999999999999999999999999998766667778999999999999999999999886

>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=99.72  E-value=5.8e-18  Score=118.05  Aligned_cols=70  Identities=37%  Similarity=0.447  Sum_probs=64.1

Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL  192 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l  192 (291)
                      +.+|.||++++|+||||+|++||+|+++|||+|+|+++.+...+..+|.|+|+|++++|++|+.+|.++|
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            5689999999999999999999999999999999988655556678999999999999999999999875

>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=2e-17  Score=116.23  Aligned_cols=71  Identities=37%  Similarity=0.672  Sum_probs=66.3

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHH
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL  105 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i  105 (291)
                      ..++|+||.+++|+||||+|++|++|+++|||+|+|++..+..+++.+|.|+|+|++++|.+|+.+|.++|
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            45899999999999999999999999999999999998877778889999999999999999999998765

>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=99.70  E-value=1.7e-17  Score=115.61  Aligned_cols=70  Identities=36%  Similarity=0.522  Sum_probs=64.3

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHH
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL  105 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i  105 (291)
                      .++|+||..++|+||||+|++|++|+++|||+|+|+++.+..+++.+|.|+|+|++++|.+|+++|.++|
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            4789999999999999999999999999999999988766666778999999999999999999998764

>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=99.68  E-value=1.4e-17  Score=116.04  Aligned_cols=69  Identities=35%  Similarity=0.573  Sum_probs=64.0

Q ss_pred             ceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       121 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      .++++|+||.+++|+||||+|++|++|+++|||+|++++.     +..+|.|+|+|++++|.+|+.+|.++|+|
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~-----~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-----CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC-----CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            4789999999999999999999999999999999999863     34689999999999999999999999975

>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=99.68  E-value=2.4e-17  Score=114.83  Aligned_cols=69  Identities=35%  Similarity=0.642  Sum_probs=63.9

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHh
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL  106 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~  106 (291)
                      ..+++||+||.+++|+||||+|++|++|+++|||+|++++.     +.++|+|+|+|++++|.+|+.+|.++|.
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~-----~~~er~v~I~G~~~~v~~A~~~I~~~l~   70 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKLE   70 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-----CCSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC-----CCCcceEEEEECHHHHHHHHHHHHHHhc
Confidence            46899999999999999999999999999999999999864     3578999999999999999999998775

>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=99.68  E-value=5.2e-17  Score=114.42  Aligned_cols=71  Identities=35%  Similarity=0.479  Sum_probs=65.3

Q ss_pred             ceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       121 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      .++.++.||.+++|+||||+|++|++|+++|||+|+|.+.+   ++..+|.|+|+|++++|.+|+.+|.++|++
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~---~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL---EGSEDRIITITGTQDQIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT---SCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCC---CCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            46899999999999999999999999999999999997633   456789999999999999999999999986

>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=99.68  E-value=3e-17  Score=114.00  Aligned_cols=68  Identities=38%  Similarity=0.436  Sum_probs=62.7

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL  192 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l  192 (291)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|.+..   ++..+|.|+|+|++++|++|+.+|.++|
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 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV---EGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCC---TTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCC---CCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            5889999999999999999999999999999999997633   4567899999999999999999999886

>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=99.66  E-value=7.5e-17  Score=111.95  Aligned_cols=69  Identities=30%  Similarity=0.524  Sum_probs=63.2

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHH
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL  105 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i  105 (291)
                      +++.+|+||.+++|+||||+|.+|++|+++|||+|+|++..   +++.+|+|+|+|++++|.+|+.+|.++|
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            36889999999999999999999999999999999997654   4678999999999999999999998765

>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=99.66  E-value=3.8e-17  Score=116.79  Aligned_cols=77  Identities=21%  Similarity=0.301  Sum_probs=68.8

Q ss_pred             CCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837          118 VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED  195 (291)
Q Consensus       118 ~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~  195 (291)
                      ....++.+|+||..++|+||||+|++||+|+++|||+|+|.+.++ .+...+|.|+|+|++++|.+|+.+|.++|+|.
T Consensus         4 ~~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~-~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   80 (81)
T d1x4ma1           4 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGP-QNTGADKPLRITGDPYKVQQAKEMVLELIRDQ   80 (81)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCC-CSSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCC-CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            345689999999999999999999999999999999999987443 34457899999999999999999999999873

>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=4.9e-17  Score=114.21  Aligned_cols=71  Identities=25%  Similarity=0.379  Sum_probs=64.9

Q ss_pred             ceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       121 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      ...++|.||.+++|+||||+|++|++|+++|||+|+|.+.+   ++..+|.|+|+|++++|++|+.+|.++|++
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            35789999999999999999999999999999999998753   345789999999999999999999999975

>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=99.65  E-value=2.3e-16  Score=110.99  Aligned_cols=71  Identities=35%  Similarity=0.568  Sum_probs=65.1

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      .++.+|.||.+++|+||||+|++|++|+++|||+|+|.+..   +++.+|+|+|+|++++|.+|+.+|.+++.+
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~---~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL---EGSEDRIITITGTQDQIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT---SCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCC---CCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            47899999999999999999999999999999999997643   467899999999999999999999987765

>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=99.65  E-value=1.4e-16  Score=111.91  Aligned_cols=71  Identities=30%  Similarity=0.472  Sum_probs=64.7

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      ...++|+||.+++|+||||+|++|++|+++|||+|+|++..   ++..+|.|+|+|++++|.+|..+|.+.+.+
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            46799999999999999999999999999999999998754   356789999999999999999999977754

>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=99.63  E-value=2e-16  Score=112.96  Aligned_cols=75  Identities=23%  Similarity=0.394  Sum_probs=67.2

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      ...++.+|+||..++|+||||+|++|++|+++|||+|.|++.. ..+...+|.|+|+|++++|.+|+.+|.+.|.+
T Consensus         5 ~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~-~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           5 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG-PQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSC-CCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCC-CCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            4679999999999999999999999999999999999998753 33456789999999999999999999987754

>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=99.63  E-value=2.3e-16  Score=112.13  Aligned_cols=74  Identities=27%  Similarity=0.339  Sum_probs=67.3

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED  195 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~  195 (291)
                      ...++.+|.||..++|+|||++|.+|++|+++|||+|+|++.+   ++..++.|+|+|++++|++|+.+|.++|.++
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC---TTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCC---CCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            3458999999999999999999999999999999999998743   4567899999999999999999999999874

>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=1.5e-16  Score=119.11  Aligned_cols=80  Identities=38%  Similarity=0.439  Sum_probs=70.0

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCccc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLY  198 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~  198 (291)
                      ...++.+|.||..++|+||||+|.+||+|+++|||+|+|.+..+. ....+|+|+|+|++++|.+|+.+|.++|.++..+
T Consensus        12 ~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~-~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~~   90 (104)
T d1we8a_          12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG-TLLLSRLIKISGTQKEVAAAKHLILEKVSEDEEL   90 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC-SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC-CCCCccEEEEEeCHHHHHHHHHHHHHHHhCcHHH
Confidence            456889999999999999999999999999999999999875433 2346899999999999999999999999886544


Q ss_pred             C
Q 022837          199 S  199 (291)
Q Consensus       199 ~  199 (291)
                      .
T Consensus        91 ~   91 (104)
T d1we8a_          91 R   91 (104)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.61  E-value=8e-16  Score=109.29  Aligned_cols=74  Identities=26%  Similarity=0.441  Sum_probs=67.2

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      ...++.+|+||..++|.|||++|.+|++|+++|||+|.|++..   +++.+|.|+|+|++++|.+|+.+|.+.|.+.
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC---TTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCC---CCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            3568999999999999999999999999999999999998754   4678999999999999999999999887653

>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=99.61  E-value=1.3e-15  Score=113.80  Aligned_cols=79  Identities=30%  Similarity=0.471  Sum_probs=68.7

Q ss_pred             CCCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           29 DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        29 ~~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      .+...+++.+|+||..++|+||||+|.+|++|+++|||+|+|++..+. ....+|+|+|+|++++|.+|+.+|.++|.++
T Consensus         9 ~~~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~-~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_           9 LTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG-TLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CSSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC-SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC-CCCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            345567999999999999999999999999999999999999876542 2346899999999999999999999888654

>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=99.55  E-value=4.1e-15  Score=106.78  Aligned_cols=72  Identities=25%  Similarity=0.258  Sum_probs=65.0

Q ss_pred             ceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       121 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      .++.++.||..++++|||++|++|++|+++|||+|+|++...  .+..++.|+|+|+.++|.+|+.+|.+++.+
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~--~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT--CSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC--CCCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            368899999999999999999999999999999999986433  455688999999999999999999999876

>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=99.55  E-value=6e-15  Score=105.89  Aligned_cols=74  Identities=16%  Similarity=0.229  Sum_probs=65.5

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      ...++++|.||..++++|||++|++|++|+++|||+|+|++...  ++..++.|+|+|+.++|.+|+.+|.+.+.+
T Consensus         7 ~~~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~--~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1           7 LRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             HTTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT--CSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hccEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC--CCCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            35688999999999999999999999999999999999986443  456789999999999999999999976644

>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=99.54  E-value=4.2e-15  Score=105.97  Aligned_cols=72  Identities=22%  Similarity=0.272  Sum_probs=64.3

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      ...++.++.||..++++|||++|++|++|+++|||+|+|++.++    ..++.|+|+|++++|++|+.+|.++++|
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~----~~~~~v~I~G~~~~V~~A~~~I~~i~~e   78 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLPENVEEAIDHILNLEEE   78 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC----SCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC----CCCCEEEEeCCHHHHHHHHHHHHHHHHH
Confidence            45578999999999999999999999999999999999987432    2357899999999999999999999886

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=4.1e-15  Score=105.99  Aligned_cols=72  Identities=22%  Similarity=0.315  Sum_probs=65.4

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED  195 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~  195 (291)
                      ....+.++.||..++|+|||++|.+|++|+++|||+|+|++.     +..++.|+|+|+.++|++|+.+|.+++.+.
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-----~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-----DDPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-----TSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC-----CCCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            455799999999999999999999999999999999999863     336789999999999999999999999873

>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=99.52  E-value=1.1e-14  Score=103.79  Aligned_cols=75  Identities=13%  Similarity=0.218  Sum_probs=65.0

Q ss_pred             CCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        30 ~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      +.+..++..|.||..+++.|||++|.+|++|+++|||+|+|++.++    ...+.|+|+|++++|.+|+++|.+.+.+.
T Consensus         5 e~~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~----~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           5 ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             CTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC----SCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             HhhcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC----CCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            3456678899999999999999999999999999999999987543    23578999999999999999999766543

>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=99.50  E-value=9.2e-15  Score=101.46  Aligned_cols=67  Identities=18%  Similarity=0.245  Sum_probs=60.7

Q ss_pred             ceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 022837          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL  192 (291)
Q Consensus       121 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l  192 (291)
                      ..+.+|.||..++++|||++|++|++|+++|||+|+|++.     +..++.|+|+|++++|++|+.+|.++.
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            3678999999999999999999999999999999999763     346789999999999999999999864

>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=99.50  E-value=8.2e-15  Score=104.69  Aligned_cols=72  Identities=21%  Similarity=0.332  Sum_probs=64.1

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHh-ccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDD-SQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED  195 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~-tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~  195 (291)
                      .+.++.+|.||..++|+||||+|++|++|+++ ++|+|++++.     +..++.|+|+|++++|++|+.+|.+++++.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~-----~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-----GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-----TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC-----CCCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            44578999999999999999999999999987 5899998763     346789999999999999999999999874

>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=99.50  E-value=1.7e-14  Score=102.69  Aligned_cols=72  Identities=22%  Similarity=0.320  Sum_probs=64.6

Q ss_pred             CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      +..++.+|.||..++|+|||++|.+|++|+++|||+|+|++.+     +.++.|+|+|++++|.+|+.+|++.+.+.
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-----~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-----DPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-----SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC-----CCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            3558899999999999999999999999999999999998743     56789999999999999999999766553

>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=99.47  E-value=7.9e-16  Score=111.86  Aligned_cols=68  Identities=21%  Similarity=0.249  Sum_probs=61.8

Q ss_pred             CCceEEEEEecCCccceeeccCChhHHHHHHhc-cceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDS-QAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      ...++..+.||..++++|||++|++|++|++++ |++|.++.        .+..|+|+|++++|++|+.+|.+++.+
T Consensus        18 ~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~--------~~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          18 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE--------GEDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS--------SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC--------CCceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            446899999999999999999999999999995 89999975        346899999999999999999999876

>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=99.46  E-value=5.7e-14  Score=97.38  Aligned_cols=67  Identities=18%  Similarity=0.373  Sum_probs=60.7

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHH
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDK  104 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~  104 (291)
                      +-..++|.||..++++|||++|++|++|+++|||+|+|++..     ..++.|+|+|++++|.+|+++|++.
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~-----~~~~~v~I~G~~~~v~~A~~~I~~i   69 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-----EKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-----SSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCC-----CCCCEEEEECCHHHHHHHHHHHHHH
Confidence            456789999999999999999999999999999999998643     5678999999999999999999853

>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=99.45  E-value=5.4e-14  Score=100.33  Aligned_cols=73  Identities=14%  Similarity=0.266  Sum_probs=63.6

Q ss_pred             CCCcEEEEEEecccccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        31 ~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~  108 (291)
                      ....++.+|.||..++|+||||+|++|++|++++ +++|++++.+     ..++.|+|+|++++|.+|+.+|++.+.+.
T Consensus         6 ~~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~-----~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           6 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-----SGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-----TTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hcCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCC-----CCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            3456789999999999999999999999999884 9999998643     46799999999999999999999766543

>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=99.45  E-value=3e-14  Score=103.69  Aligned_cols=70  Identities=23%  Similarity=0.364  Sum_probs=64.0

Q ss_pred             CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE  194 (291)
Q Consensus       120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e  194 (291)
                      ..++..+.||..+++.|||++|.+|++|+++|||+|.|++.     +..++.|+|+|+.++|++|+.+|.+++.+
T Consensus         8 ~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-----~~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           8 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-----ELQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT-----TTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC-----CCCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            35899999999999999999999999999999999999873     33567999999999999999999999876

>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=99.40  E-value=2e-13  Score=99.27  Aligned_cols=69  Identities=25%  Similarity=0.327  Sum_probs=62.8

Q ss_pred             cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      +++..|.||..++|.|||++|.+|++|+++|||+|.|++.+     ..++.|+|+|+.++|.+|+.+|.+.+.+
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            68999999999999999999999999999999999998643     4678999999999999999999976654

>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=99.37  E-value=3e-13  Score=96.43  Aligned_cols=64  Identities=22%  Similarity=0.259  Sum_probs=58.3

Q ss_pred             EEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCc
Q 022837          124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDT  196 (291)
Q Consensus       124 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~  196 (291)
                      ..+.||.+++|+|||++|++|++|+++|||+|+|.+         ++.|+|+|+++++++|+.+|..++++..
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            457899999999999999999999999999999964         3589999999999999999999988753

>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=99.35  E-value=2.7e-13  Score=95.34  Aligned_cols=65  Identities=14%  Similarity=0.134  Sum_probs=57.7

Q ss_pred             CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHH
Q 022837          120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG-TLDEQMRALELILLK  191 (291)
Q Consensus       120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G-~~~~v~~A~~~I~~~  191 (291)
                      ..++.++.||.+++|+|||++|++||+|+++|||+|.+..+       +++.|+|.| ++++|++|+.+|..+
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~-------~~g~v~I~g~~~eav~~A~~~Ie~~   71 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-------DTGTFRIYGESADAVKKARGFLEFV   71 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-------TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC-------CCceEEEEECCHHHHHHHHHHHHHh
Confidence            45788999999999999999999999999999999998753       357899999 699999999999543

>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=99.27  E-value=2.4e-12  Score=91.67  Aligned_cols=60  Identities=20%  Similarity=0.238  Sum_probs=53.8

Q ss_pred             EEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHh
Q 022837           38 RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL  106 (291)
Q Consensus        38 rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~  106 (291)
                      -+.||.+.+|+||||+|++|++|+++|||+|+|.+         +..|+|.|+++++.+|+.+|.+.+.
T Consensus         4 vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~---------~g~v~I~G~~e~v~~A~~~I~~i~~   63 (84)
T d2ba0a3           4 IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ---------NGLIWVNGDRRKVSIAEEAIYLIEQ   63 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT---------TSEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC---------CCEEEEEeCHHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999964         3569999999999999999975443

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=7.5e-12  Score=90.42  Aligned_cols=69  Identities=16%  Similarity=0.237  Sum_probs=60.6

Q ss_pred             CCCcEEEEEEecccccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837           31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT  107 (291)
Q Consensus        31 ~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~  107 (291)
                      .+..++..|.||..++++|||++|++|++|++++ +++|.++++        +..|+|+|++++|++|+++|.+.+.+
T Consensus        17 ~~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~--------~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          17 ANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG--------EDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS--------SCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cCCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC--------CceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            3456899999999999999999999999999995 899999752        46799999999999999999865543

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=2.1e-12  Score=90.67  Aligned_cols=63  Identities=22%  Similarity=0.279  Sum_probs=56.1

Q ss_pred             CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec-CHHHHHHHHHHHH
Q 022837           33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVI  102 (291)
Q Consensus        33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G-~~~~v~~A~~~I~  102 (291)
                      ..++.+|.||.+++|+|||++|++|++|+++|||+|.+.+.       .++.|.|.| +++++.+|+++|.
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~-------~~g~v~I~g~~~eav~~A~~~Ie   69 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-------DTGTFRIYGESADAVKKARGFLE   69 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-------TTTEEEEEESSHHHHHHHHHHHS
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC-------CCceEEEEECCHHHHHHHHHHHH
Confidence            45788999999999999999999999999999999998653       346799999 6999999999984

>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=99.08  E-value=1.9e-12  Score=88.72  Aligned_cols=62  Identities=15%  Similarity=0.072  Sum_probs=48.4

Q ss_pred             EEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcC
Q 022837          125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSED  195 (291)
Q Consensus       125 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I~~~l~e~  195 (291)
                      .+.||.+++|+||||+|++||+|+++|||+|.|.+         +..|+|+|. .+.+++|..+|..+.++.
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~---------~g~v~I~g~~~~~v~~A~~~I~~i~~ea   66 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN---------NGRIWATCPSRFSEEILIEAIRKIENES   66 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT---------TSEEEC-----CTTCCTHHHHTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC---------CCEEEEEeCCHHHHHHHHHHHHHHHHhh
Confidence            47799999999999999999999999999999963         357999996 678999999998877664

>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=99.05  E-value=9.5e-11  Score=83.00  Aligned_cols=63  Identities=19%  Similarity=0.239  Sum_probs=53.4

Q ss_pred             EEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEE-----cCHHHHHHHHHHHHHHHhc
Q 022837          124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT-----GTLDEQMRALELILLKLSE  194 (291)
Q Consensus       124 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~-----G~~~~v~~A~~~I~~~l~e  194 (291)
                      +.+.||.+.+|.|||++|++||+|+++|||+|+|..+        +..|.+.     |.+.++++|..+|.++.+.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d--------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~rG   72 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE--------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLG   72 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT--------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHT
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC--------CCeEEEecCCccccHHHHHHHHHHHHHHhCC
Confidence            4688999999999999999999999999999999763        2345544     5689999999999988664

>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=98.99  E-value=4e-10  Score=79.96  Aligned_cols=62  Identities=16%  Similarity=0.209  Sum_probs=55.6

Q ss_pred             EEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcC
Q 022837          125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSED  195 (291)
Q Consensus       125 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I~~~l~e~  195 (291)
                      .+.||.+++|.|||++|++||.|+++|||+|.|..         +..|.|.|. .+.+..|+.+|..+.++.
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d---------~G~V~I~g~~~~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR---------NGRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET---------TTEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC---------CcEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            47799999999999999999999999999999974         347999995 889999999999987764

>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=98.97  E-value=8.2e-11  Score=83.34  Aligned_cols=65  Identities=18%  Similarity=0.173  Sum_probs=49.9

Q ss_pred             EEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHH
Q 022837           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDK  104 (291)
Q Consensus        37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~  104 (291)
                      +.+.||.+.+|.||||+|++||+|+++|||+|+|.+++.   ....+.....+.+.++.+|.++|.+.
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 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENS---MVIVEPEAEGIPPVNLMKAAEVVKAI   69 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTT---EEEEEESSTTSCHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCC---eEEEecCCccccHHHHHHHHHHHHHH
Confidence            458999999999999999999999999999999965321   00111122356788999999998754

>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=98.92  E-value=1.6e-11  Score=83.97  Aligned_cols=57  Identities=18%  Similarity=0.108  Sum_probs=43.7

Q ss_pred             EEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecC-HHHHHHHHHHHHH
Q 022837           38 RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLVID  103 (291)
Q Consensus        38 rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~-~~~v~~A~~~I~~  103 (291)
                      -+.||.+.+|+||||+|++||+|+++|||+|+|.+         +..|+|.|. .+++..|..+|.+
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~---------~g~v~I~g~~~~~v~~A~~~I~~   61 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN---------NGRIWATCPSRFSEEILIEAIRK   61 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT---------TSEEEC-----CTTCCTHHHHTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC---------CCEEEEEeCCHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999954         235899995 6789999999863

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.88  E-value=1.7e-09  Score=76.63  Aligned_cols=61  Identities=20%  Similarity=0.155  Sum_probs=51.7

Q ss_pred             EEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecC-HHHHHHHHHHHHHHHhhh
Q 022837           38 RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLVIDKLLTE  108 (291)
Q Consensus        38 rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~-~~~v~~A~~~I~~~i~~~  108 (291)
                      -+.||.+.+|.|||++|++|+.|+++|||+|.|.++         -.|.|.|. .+.+..|+.+|. .|.++
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 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN---------GRIHLECPNEDLEAIAVMAIK-IIDEE   65 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETT---------TEEEEECSCHHHHHHHHHHHH-HHHHC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCC---------cEEEEEeCCHHHHHHHHHHHH-HHHHh
Confidence            467999999999999999999999999999999643         24899995 788899999987 44443

>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=98.79  E-value=1.6e-10  Score=74.54  Aligned_cols=46  Identities=22%  Similarity=0.390  Sum_probs=14.2

Q ss_pred             EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC
Q 022837          123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT  177 (291)
Q Consensus       123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~  177 (291)
                      ...|.||.+++|.|||++|.+||+|+++|||+|.+..         +..|+|.|.
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            4578899999999999999999999999999999963         456777664

>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=98.77  E-value=2.8e-09  Score=78.03  Aligned_cols=54  Identities=20%  Similarity=0.318  Sum_probs=48.5

Q ss_pred             ccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837          132 SCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED  195 (291)
Q Consensus       132 ~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~  195 (291)
                      ..|+|||++|++|+.|++.|||.|.|..          ..|.|.|++++++.|+.+|..++.+.
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d----------~~v~iig~~e~i~~A~~~Ie~li~~~   76 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGE----------YEVAIIGDYERAMAAKQAIEMLAEGR   76 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS----------SEEEEEEEHHHHHHHHHHHHHHHTTC
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeC----------CeEEEEECchhHHHHHHHHHHHHcCC
Confidence            3689999999999999999999999953          35888899999999999999999764

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.62  E-value=1.4e-09  Score=69.97  Aligned_cols=36  Identities=14%  Similarity=0.301  Sum_probs=10.6

Q ss_pred             EEEeecCCCcceeEEeecCccceehccccccceEEeec
Q 022837          253 VLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNE  290 (291)
Q Consensus       253 ~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tga~i~~~~  290 (291)
                      .+|.||.+++|.|||+  ||.+||+|+++|||+|.+.|
T Consensus         5 ~~i~Ip~~kig~vIG~--GG~~Ik~I~~~tga~I~i~d   40 (54)
T d1e3ha4           5 ITVKIPVDKIGEVIGP--KRQMINQIQEDTGAEITIED   40 (54)
T ss_dssp             C-----------------------CHHHHSCCCC----
T ss_pred             EEEEeCHHHeeEEECC--ccHHHHHHHHHHCCEEEEeC
Confidence            6789999999999999  99999999999999999976

>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=98.59  E-value=1.9e-08  Score=73.56  Aligned_cols=52  Identities=17%  Similarity=0.300  Sum_probs=45.1

Q ss_pred             ccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHh
Q 022837           45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL  106 (291)
Q Consensus        45 ~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~  106 (291)
                      ..|+|||++|.+|+.|++.|||+|.|..          ..+.|.|+++++..|+++|.+.+.
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d----------~~v~iig~~e~i~~A~~~Ie~li~   74 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGE----------YEVAIIGDYERAMAAKQAIEMLAE   74 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS----------SEEEEEEEHHHHHHHHHHHHHHHT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeC----------CeEEEEECchhHHHHHHHHHHHHc
Confidence            4799999999999999999999999952          236777999999999999986664

>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=98.48  E-value=3.4e-07  Score=68.87  Aligned_cols=75  Identities=17%  Similarity=0.384  Sum_probs=56.2

Q ss_pred             cEEEEEEecccc------cceeeccCChhHHHHHHHhCCcEEEcCCCC------------CCCCC-CceEEEEec-CHHH
Q 022837           34 PTYIRFLVSNPL------AGAVIGKGGSTINDFQSQSGARIQLSRSHE------------FFPGT-TDRIIMISG-TIDE   93 (291)
Q Consensus        34 ~~~~rilvp~~~------vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~------------~~p~~-~er~v~I~G-~~~~   93 (291)
                      .++-+|+||.+.      +|+|||.+|.++|+|+++|||+|.|.-...            ..+.. ..--|.|++ +.+.
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            467899999875      999999999999999999999999964221            00111 223466666 5779


Q ss_pred             HHHHHHHHHHHHhhh
Q 022837           94 ILRAVDLVIDKLLTE  108 (291)
Q Consensus        94 v~~A~~~I~~~i~~~  108 (291)
                      +..|+.+|.+.|...
T Consensus        82 ~~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          82 VKKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999998777554

>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=98.39  E-value=9.4e-07  Score=66.36  Aligned_cols=74  Identities=22%  Similarity=0.305  Sum_probs=57.8

Q ss_pred             ceEEEEEecCC------ccceeeccCChhHHHHHHhccceEEEecCCC------------CCCC-CCceEEEEEcC-HHH
Q 022837          121 KTKLRLIVPNS------SCGSIIGKAGATIKSFMDDSQAVIKISRLDH------------SYYG-LNDRLVTLTGT-LDE  180 (291)
Q Consensus       121 ~~~~~i~VP~~------~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~------------~~~~-~~er~V~I~G~-~~~  180 (291)
                      ..+.++.||-+      ++|+|||.+|.++|+|+++|||+|.|-....            .... ..+=-|.|+++ .+.
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            35788999976      4899999999999999999999999975211            0011 12335888887 778


Q ss_pred             HHHHHHHHHHHHhc
Q 022837          181 QMRALELILLKLSE  194 (291)
Q Consensus       181 v~~A~~~I~~~l~e  194 (291)
                      +.+|+.+|..+|..
T Consensus        82 ~~~A~~~i~~ll~~   95 (122)
T d1k1ga_          82 VKKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999965

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=98.14  E-value=2.1e-06  Score=65.25  Aligned_cols=74  Identities=23%  Similarity=0.161  Sum_probs=56.4

Q ss_pred             eEEEEEecC------CccceeeccCChhHHHHHHhccceEEEecCCCC--------C-------CCCCceEEEEEcCH--
Q 022837          122 TKLRLIVPN------SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHS--------Y-------YGLNDRLVTLTGTL--  178 (291)
Q Consensus       122 ~~~~i~VP~------~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~--------~-------~~~~er~V~I~G~~--  178 (291)
                      .+.++.||.      +++|+|||++|.++|+|+++|||+|.|-.....        .       ...++=-|.|+++.  
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            466788883      578999999999999999999999999873211        0       01234468888862  


Q ss_pred             ----HHHHHHHHHHHHHHhcC
Q 022837          179 ----DEQMRALELILLKLSED  195 (291)
Q Consensus       179 ----~~v~~A~~~I~~~l~e~  195 (291)
                          ..+.+|+.+|..+|...
T Consensus        82 ~~a~~kl~~A~~~I~~lL~p~  102 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLVPA  102 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHHHHHHHHHHcCCC
Confidence                45889999999998653

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=98.01  E-value=3.2e-06  Score=64.13  Aligned_cols=72  Identities=19%  Similarity=0.275  Sum_probs=52.4

Q ss_pred             EEEEEEeccc------ccceeeccCChhHHHHHHHhCCcEEEcCCCCC--------CC-------CCCceEEEEecCH--
Q 022837           35 TYIRFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSRSHEF--------FP-------GTTDRIIMISGTI--   91 (291)
Q Consensus        35 ~~~rilvp~~------~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~--------~p-------~~~er~v~I~G~~--   91 (291)
                      +.-||+||.+      .+|+|||.+|.++|+|+++|||+|.|.-....        ..       ...+--|.|++..  
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            5678888854      68999999999999999999999999764321        00       1133456777642  


Q ss_pred             ----HHHHHHHHHHHHHHh
Q 022837           92 ----DEILRAVDLVIDKLL  106 (291)
Q Consensus        92 ----~~v~~A~~~I~~~i~  106 (291)
                          ..+.+|+.+|...|.
T Consensus        82 ~~a~~kl~~A~~~I~~lL~  100 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLV  100 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHHcC
Confidence                357888888876664

>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=96.38  E-value=0.001  Score=43.77  Aligned_cols=40  Identities=23%  Similarity=0.243  Sum_probs=36.5

Q ss_pred             EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCC
Q 022837           35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSH   74 (291)
Q Consensus        35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~   74 (291)
                      -.+.+.||.++.+..|||+|.|++-..+-||.+|+|....
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~es   65 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA   65 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeCC
Confidence            4678899999999999999999999999999999997643

>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=96.17  E-value=0.0017  Score=42.82  Aligned_cols=38  Identities=26%  Similarity=0.324  Sum_probs=35.2

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS   73 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~   73 (291)
                      .+.+.||.++.+..|||+|.|++-..+-||.+|.|...
T Consensus        28 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~   65 (68)
T d1hh2p3          28 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI   65 (68)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEc
Confidence            57889999999999999999999999999999999653

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.80  E-value=0.0029  Score=41.46  Aligned_cols=40  Identities=23%  Similarity=0.213  Sum_probs=36.7

Q ss_pred             ceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837          121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL  160 (291)
Q Consensus       121 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  160 (291)
                      .....+.||.+.....|||+|.|+|-..+-||.+|.|..+
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            3478899999999999999999999999999999999864

>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=95.68  E-value=0.0042  Score=40.77  Aligned_cols=38  Identities=24%  Similarity=0.291  Sum_probs=35.6

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhccceEEEec
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR  159 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~  159 (291)
                      ....+.||.+..+..|||+|.++|-..+-||.+|.|..
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            46889999999999999999999999999999999976

>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=91.09  E-value=0.07  Score=38.37  Aligned_cols=30  Identities=23%  Similarity=0.300  Sum_probs=24.2

Q ss_pred             ceEEEEEecCCcc-ceeeccCChhHHHHHHh
Q 022837          121 KTKLRLIVPNSSC-GSIIGKAGATIKSFMDD  150 (291)
Q Consensus       121 ~~~~~i~VP~~~v-g~IIGk~G~~Ik~I~~~  150 (291)
                      .+...+.|+.+.. +.|||++|++||+|...
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            4677888886544 89999999999988654

>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=90.60  E-value=0.15  Score=34.63  Aligned_cols=56  Identities=7%  Similarity=0.085  Sum_probs=44.6

Q ss_pred             EEEecccccceeeccCCh-hHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec-CHHHHHHHHHHHH
Q 022837           38 RFLVSNPLAGAVIGKGGS-TINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVI  102 (291)
Q Consensus        38 rilvp~~~vG~IIGk~G~-~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G-~~~~v~~A~~~I~  102 (291)
                      -+-||..++.++||+++. .++.|.+.+++.|.|-.++         .|.|.| +.++...+.+.|.
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~NG---------rIWi~~~~~~~~i~i~~aI~   61 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNG---------KIWVKCEELSNTLACYRTIM   61 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETTT---------EEEEECSSHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecCc---------EEEEECCCHHHHHHHHHHHH
Confidence            456888999999999998 7899999999999996532         378888 4666666666664

>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=90.39  E-value=0.19  Score=34.07  Aligned_cols=61  Identities=8%  Similarity=0.047  Sum_probs=48.1

Q ss_pred             EEEecCCccceeeccCCh-hHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 022837          125 RLIVPNSSCGSIIGKAGA-TIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSE  194 (291)
Q Consensus       125 ~i~VP~~~vg~IIGk~G~-~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I~~~l~e  194 (291)
                      -+.||..++.+|||+++. .++.|.+.+++.|.|-.         ...|=|.|. .+....+...|...-++
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~---------NGrIWi~~~~~~~~i~i~~aI~~~e~~   66 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL---------NGKIWVKCEELSNTLACYRTIMECCQK   66 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET---------TTEEEEECSSHHHHHHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec---------CcEEEEECCCHHHHHHHHHHHHHHHHh
Confidence            456889999999999998 79999999999999975         357889995 66666666666554444

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.48  E-value=0.058  Score=37.29  Aligned_cols=35  Identities=14%  Similarity=0.303  Sum_probs=28.4

Q ss_pred             EEEEEecccccceeeccCChhHHHHHHHhCCcEEE
Q 022837           36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQL   70 (291)
Q Consensus        36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v   70 (291)
                      .+++.|....-|.||||+|.+|++|++...-++.+
T Consensus        36 ~i~I~I~tarPGivIGrkG~~I~~L~~~l~k~~~~   70 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGF   70 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHHHHHHHCC
T ss_pred             eEEEEEEeCCCceeeccCchhHHHHHHHHHHHHCC
Confidence            36788888999999999999999998876544433

>d1wf3a2 d.52.3.1 (A:181-298) GTPase Era C-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: GTPase Era C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=86.79  E-value=0.16  Score=36.64  Aligned_cols=29  Identities=31%  Similarity=0.337  Sum_probs=22.8

Q ss_pred             ceEEEEEecCCc-cceeeccCChhHHHHHH
Q 022837          121 KTKLRLIVPNSS-CGSIIGKAGATIKSFMD  149 (291)
Q Consensus       121 ~~~~~i~VP~~~-vg~IIGk~G~~Ik~I~~  149 (291)
                      .+...|.|+... -+.|||++|++||+|..
T Consensus        49 ~I~~~I~V~~~sqK~IiIGk~G~~ik~Ig~   78 (118)
T d1wf3a2          49 YIKAILYVERPSQKAIVIGEGGRKIKEIGQ   78 (118)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHH
T ss_pred             EEEEEEEeCccchhhhhhccCchhHHHHHH
Confidence            457778888654 48999999999997753

>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=86.58  E-value=0.094  Score=36.17  Aligned_cols=31  Identities=19%  Similarity=0.412  Sum_probs=26.8

Q ss_pred             eEEEEEecCCccceeeccCChhHHHHHHhcc
Q 022837          122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQ  152 (291)
Q Consensus       122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tG  152 (291)
                      ..+++.|....-|.|||++|+.|++|++.-.
T Consensus        35 ~~i~I~I~tarPGivIGrkG~~I~~L~~~l~   65 (92)
T d1wh9a_          35 TRTEIIILATRTQNVLGEKGRRIRELTAVVQ   65 (92)
T ss_dssp             SCEEEEEEESCHHHHHCGGGHHHHHHHHHHH
T ss_pred             CeEEEEEEeCCCceeeccCchhHHHHHHHHH
Confidence            4678899999999999999999999986643

>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=85.84  E-value=0.14  Score=36.64  Aligned_cols=31  Identities=23%  Similarity=0.244  Sum_probs=25.6

Q ss_pred             cEEEEEEeccc-ccceeeccCChhHHHHHHHh
Q 022837           34 PTYIRFLVSNP-LAGAVIGKGGSTINDFQSQS   64 (291)
Q Consensus        34 ~~~~rilvp~~-~vG~IIGk~G~~Ik~I~~~t   64 (291)
                      .+...+.|+.+ +.+.|||++|++||+|..+.
T Consensus        48 ~I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~a   79 (113)
T d1egaa2          48 DINGLILVEREGQKKMVIGNKGAKIKTIGIEA   79 (113)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             EEEEEEEECCcchhhhhhcccchHHHHHHHHH
Confidence            36777888876 78999999999999887654

>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=82.38  E-value=0.16  Score=35.90  Aligned_cols=29  Identities=28%  Similarity=0.491  Sum_probs=25.1

Q ss_pred             EEEEecccccceeeccCChhHHHHHHHhC
Q 022837           37 IRFLVSNPLAGAVIGKGGSTINDFQSQSG   65 (291)
Q Consensus        37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tg   65 (291)
                      +++.|....-|.|||++|+.|++|+++..
T Consensus        63 i~I~I~tarPG~iIGkkG~~i~~L~~~l~   91 (105)
T d2uubc1          63 VAVTVHVAKPGVVIGRGGERIRVLREELA   91 (105)
T ss_dssp             EECCEEESCHHHHHCSTTSHHHHHHHHHH
T ss_pred             EEEEEEECCCceEEcCCchhHHHHHHHHH
Confidence            77778888999999999999999888753

>d1wf3a2 d.52.3.1 (A:181-298) GTPase Era C-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: GTPase Era C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=82.23  E-value=0.25  Score=35.56  Aligned_cols=29  Identities=28%  Similarity=0.473  Sum_probs=23.5

Q ss_pred             EEEEEEeccc-ccceeeccCChhHHHHHHH
Q 022837           35 TYIRFLVSNP-LAGAVIGKGGSTINDFQSQ   63 (291)
Q Consensus        35 ~~~rilvp~~-~vG~IIGk~G~~Ik~I~~~   63 (291)
                      +...+.|+.+ +.+.|||++|++||+|..+
T Consensus        50 I~~~I~V~~~sqK~IiIGk~G~~ik~Ig~~   79 (118)
T d1wf3a2          50 IKAILYVERPSQKAIVIGEGGRKIKEIGQA   79 (118)
T ss_dssp             EEEEEEESSHHHHHHHHCGGGHHHHHHHHH
T ss_pred             EEEEEEeCccchhhhhhccCchhHHHHHHH
Confidence            5666888876 7899999999999976554