Psyllid ID: psy8861

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550
MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKMEGVFKSEPNRSEFANDINDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSDNEEAIRQSARVLVDQLNVFAALENTPVKKELDSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIKLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIELLNQTKN
cccccccHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHccccccHHHHHHHHccccEEEccEEEccccEEcccccEEEEccccccHHHHHHHHHHcccccccccEEEEccccEEEEEcccccccccccHHHcccccEEEEEEEcccEEEEEEcccccccccHHHHHHHHHHHHcccccccEEEEEcEEEEEEcccccHHHHHHHHHHHcccEEEEEEcccEEEEEEEEccccEEEEccccccccEEEEcccEEEEEEccccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccHHHHHHccccccccccHHHHHHHHHHccccHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccccccHHHcccccHHHHHHHHHHHccccccccccEEEEEEEccccccccccEEEEEcccccc
ccccccHHHHHHHHccccccccccccccccccccccccccccccccccccHHEEEHHHHHHHHHHccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHcccEEEEcccEEEccccccccccEEEEcccHHHHHHHHHHHccccHccccccEEEccccccccEcccccHHHcccEHHHEEEEEEEEcccccccccEEEEccccccccccHHHHHHHHHHHHHccccccEEEEccHHHHHHccHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHcccEEEEEcHHHHHHHHHccccccEEEEccccHHHHHHHHHHHHHHHHHHHHHHccccHHHHHcHHHccccEEEccccccEEEEEcHHHHHHHHcHHHHHHHHHcHHHHHccccccHHHHHHHHHHHHHcccEEEEcccccHHcccccHHHHHHHHHHHHHHHHHcEEEEEHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHcccHHHHHHHHHcHHHHccccccccEEEEEEEEEcccccHHHHHHHHHHccc
maryigpkaklcRREGIDLFLKSARRSLDskckldlrpgqhgrisgsrtsdygyqfrEKQKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNiasykikpgdiisVREKAKKQTRIANslelsehstpfswITVDAKKMegvfksepnrsefandindllkpriidvktlgsnHAKVimepfergygytlGNALRRVLLSSMIGCAPTEVIISGALheysslegvqEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELlsdielvnpnhiiahlsDNEEAIRQSARVLVDQLNVFAalentpvkkeldsslekvdpillrpvddlelTVRSANCLKAENIHCIGDLIQRSEnellrtpnlgrkSLNEIKEILASRGKyymrhrhgfrklnrtssHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPiltlskkntlsnKRLAFSYLRDRKITIKLFSELgpryikinGGYVRILKmgfrvgdnaPMAFIELLNQTKN
maryigpkaklcrreGIDLFLKSARRSldskckldlrpgqhgrisgsrtsdygyqfrekqKVKRMYGILEKQFRRYFIegarlkgktgEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFlvnkkivniasykikpgdiisvrEKAKKQTRIanslelsehstpfsWITVDAKKMEGVfksepnrsefandindllkprIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSDNEEAIRQSARVLVDQLNVFAAlentpvkkeldsslekvdpillrpvddlELTVRSANCLKAENIHCIGDLIQRSENELlrtpnlgrkslnEIKEILAsrgkyymrhrhgfrklnrtsshrlIMLRNMTISLLRYEIIKTtlpkakelrrvvepiltlskkntlsnkrlafsylrdrKITIKLfselgpryikiNGGYVRILKMGFRVGDNAPMAFIELLNQTKN
MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKMEGVFKSEPNRSEFANDINDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSDNEEAIRQSARVLVDQLNVFAALENTPVKKELDSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIKLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIELLNQTKN
********AKLCRREGIDLFLK*****************************YGYQFREKQKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVR*******************TPFSWITVDAKKMEGV*********FANDINDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSDNEEAIRQSARVLVDQLNVFAALENTPVKKELDSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIKLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIELL*****
MARYIGPKAKLCRREGIDLFLKSARRS*************************GYQFREKQKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKMEGVFKSEPNRSEFANDINDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSDNEEAIRQSARVLVDQLNVFAALENTPVKKELDSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMR***************LIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIKLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIELLNQ***
MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKMEGVFKSEPNRSEFANDINDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSDNEEAIRQSARVLVDQLNVFAALENTPVKKELDSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIKLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIELLNQTKN
***YIGPKAKLCRREGIDLFLK**************************TSDYGYQFREKQKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKMEGVFKSEPNRSEFANDINDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSDNEEAIRQSARVLVDQLNVFAALENTPVKKELDSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIKLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIELLNQT**
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MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKMEGVFKSEPNRSEFANDINDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSDNEEAIRQSARVLVDQLNVFAALENTPVKKELDSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIKLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIELLNQTKN
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query550 2.2.26 [Sep-21-2011]
A6T3H9207 30S ribosomal protein S4 yes N/A 0.363 0.966 0.735 1e-85
A4G9R4207 30S ribosomal protein S4 yes N/A 0.363 0.966 0.73 9e-84
B2UEJ4207 30S ribosomal protein S4 yes N/A 0.363 0.966 0.685 2e-78
Q8XV37207 30S ribosomal protein S4 yes N/A 0.363 0.966 0.68 4e-78
Q63Q36207 30S ribosomal protein S4 yes N/A 0.363 0.966 0.68 6e-78
A3NEF4207 30S ribosomal protein S4 yes N/A 0.363 0.966 0.68 6e-78
Q3JMT8207 30S ribosomal protein S4 yes N/A 0.363 0.966 0.68 6e-78
A1V878207 30S ribosomal protein S4 yes N/A 0.363 0.966 0.68 6e-78
Q62GN0207 30S ribosomal protein S4 yes N/A 0.363 0.966 0.68 6e-78
A2S7K1207 30S ribosomal protein S4 yes N/A 0.363 0.966 0.68 6e-78
>sp|A6T3H9|RS4_JANMA 30S ribosomal protein S4 OS=Janthinobacterium sp. (strain Marseille) GN=rpsD PE=3 SV=1 Back     alignment and function desciption
 Score =  317 bits (813), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 147/200 (73%), Positives = 170/200 (85%)

Query: 1   MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQ 60
           MARYIGPKAKL RREG DLFLKSARRSLDSKCKLD +PGQHGR SG+RTSDYG Q REKQ
Sbjct: 1   MARYIGPKAKLSRREGTDLFLKSARRSLDSKCKLDSKPGQHGRTSGARTSDYGNQLREKQ 60

Query: 61  KVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLIS 120
           KVKRMYGILE+QFRRYF E  R KG TGE +LKLLE+R DNVVYRMGF STR+E RQL+S
Sbjct: 61  KVKRMYGILERQFRRYFAEADRRKGNTGETLLKLLEARLDNVVYRMGFGSTRAEGRQLVS 120

Query: 121 HRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKME 180
           H+AF VN  +VNIASY++KPGD+I+VREK+KKQ RI  +L L+E S   SW++VDAKKME
Sbjct: 121 HKAFTVNGIVVNIASYQVKPGDVIAVREKSKKQVRIVEALSLAEQSGMPSWVSVDAKKME 180

Query: 181 GVFKSEPNRSEFANDINDLL 200
           G +K+ P+RSE AND+N+ L
Sbjct: 181 GTYKAAPDRSEIANDVNESL 200
With S5 and S12 plays an important role in translational accuracy.
Janthinobacterium sp. (strain Marseille) (taxid: 375286)
>sp|A4G9R4|RS4_HERAR 30S ribosomal protein S4 OS=Herminiimonas arsenicoxydans GN=rpsD PE=3 SV=1 Back     alignment and function description
>sp|B2UEJ4|RS4_RALPJ 30S ribosomal protein S4 OS=Ralstonia pickettii (strain 12J) GN=rpsD PE=3 SV=1 Back     alignment and function description
>sp|Q8XV37|RS4_RALSO 30S ribosomal protein S4 OS=Ralstonia solanacearum (strain GMI1000) GN=rpsD PE=3 SV=1 Back     alignment and function description
>sp|Q63Q36|RS4_BURPS 30S ribosomal protein S4 OS=Burkholderia pseudomallei (strain K96243) GN=rpsD PE=3 SV=1 Back     alignment and function description
>sp|A3NEF4|RS4_BURP6 30S ribosomal protein S4 OS=Burkholderia pseudomallei (strain 668) GN=rpsD PE=3 SV=1 Back     alignment and function description
>sp|Q3JMT8|RS4_BURP1 30S ribosomal protein S4 OS=Burkholderia pseudomallei (strain 1710b) GN=rpsD PE=3 SV=1 Back     alignment and function description
>sp|A1V878|RS4_BURMS 30S ribosomal protein S4 OS=Burkholderia mallei (strain SAVP1) GN=rpsD PE=3 SV=1 Back     alignment and function description
>sp|Q62GN0|RS4_BURMA 30S ribosomal protein S4 OS=Burkholderia mallei (strain ATCC 23344) GN=rpsD PE=3 SV=1 Back     alignment and function description
>sp|A2S7K1|RS4_BURM9 30S ribosomal protein S4 OS=Burkholderia mallei (strain NCTC 10229) GN=rpsD PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query550
152980403207 30S ribosomal protein S4 [Janthinobacter 0.363 0.966 0.735 8e-84
398833116207 ribosomal protein S4, bacterial/organell 0.363 0.966 0.73 4e-83
340785621207 30S ribosomal protein S4 [Collimonas fun 0.363 0.966 0.73 1e-82
300309481207 30S ribosomal protein S4 [Herbaspirillum 0.363 0.966 0.725 4e-82
399017013207 ribosomal protein S4, bacterial/organell 0.363 0.966 0.715 4e-82
134096297207 30S ribosomal protein S4 [Herminiimonas 0.363 0.966 0.73 6e-82
409408726207 30S ribosomal protein S4 [Herbaspirillum 0.363 0.966 0.72 8e-82
415943236207 30S ribosomal protein S4 [Herbaspirillum 0.363 0.966 0.715 1e-81
237747389207 small subunit ribosomal protein S4 [Oxal 0.363 0.966 0.72 1e-80
445494447207 30S ribosomal protein S4 [Janthinobacter 0.363 0.966 0.715 2e-80
>gi|152980403|ref|YP_001355076.1| 30S ribosomal protein S4 [Janthinobacterium sp. Marseille] gi|179308084|sp|A6T3H9.1|RS4_JANMA RecName: Full=30S ribosomal protein S4 gi|151280480|gb|ABR88890.1| small subunit ribosomal protein S4 [Janthinobacterium sp. Marseille] Back     alignment and taxonomy information
 Score =  317 bits (813), Expect = 8e-84,   Method: Compositional matrix adjust.
 Identities = 147/200 (73%), Positives = 170/200 (85%)

Query: 1   MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQ 60
           MARYIGPKAKL RREG DLFLKSARRSLDSKCKLD +PGQHGR SG+RTSDYG Q REKQ
Sbjct: 1   MARYIGPKAKLSRREGTDLFLKSARRSLDSKCKLDSKPGQHGRTSGARTSDYGNQLREKQ 60

Query: 61  KVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLIS 120
           KVKRMYGILE+QFRRYF E  R KG TGE +LKLLE+R DNVVYRMGF STR+E RQL+S
Sbjct: 61  KVKRMYGILERQFRRYFAEADRRKGNTGETLLKLLEARLDNVVYRMGFGSTRAEGRQLVS 120

Query: 121 HRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKME 180
           H+AF VN  +VNIASY++KPGD+I+VREK+KKQ RI  +L L+E S   SW++VDAKKME
Sbjct: 121 HKAFTVNGIVVNIASYQVKPGDVIAVREKSKKQVRIVEALSLAEQSGMPSWVSVDAKKME 180

Query: 181 GVFKSEPNRSEFANDINDLL 200
           G +K+ P+RSE AND+N+ L
Sbjct: 181 GTYKAAPDRSEIANDVNESL 200

Source: Janthinobacterium sp. Marseille

Species: Janthinobacterium sp. Marseille

Genus: Janthinobacterium

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria
>gi|398833116|ref|ZP_10591256.1| ribosomal protein S4, bacterial/organelle type [Herbaspirillum sp. YR522] gi|398222102|gb|EJN08490.1| ribosomal protein S4, bacterial/organelle type [Herbaspirillum sp. YR522] Back     alignment and taxonomy information
>gi|340785621|ref|YP_004751086.1| 30S ribosomal protein S4 [Collimonas fungivorans Ter331] gi|340550888|gb|AEK60263.1| SSU ribosomal protein S4p (S9e) [Collimonas fungivorans Ter331] Back     alignment and taxonomy information
>gi|300309481|ref|YP_003773573.1| 30S ribosomal protein S4 [Herbaspirillum seropedicae SmR1] gi|300072266|gb|ADJ61665.1| 30S ribosomal subunit S4 protein [Herbaspirillum seropedicae SmR1] Back     alignment and taxonomy information
>gi|399017013|ref|ZP_10719214.1| ribosomal protein S4, bacterial/organelle type [Herbaspirillum sp. CF444] gi|398104343|gb|EJL94485.1| ribosomal protein S4, bacterial/organelle type [Herbaspirillum sp. CF444] Back     alignment and taxonomy information
>gi|134096297|ref|YP_001101372.1| 30S ribosomal protein S4 [Herminiimonas arsenicoxydans] gi|172044175|sp|A4G9R4.1|RS4_HERAR RecName: Full=30S ribosomal protein S4 gi|133740200|emb|CAL63251.1| 30S ribosomal subunit protein S4 [Herminiimonas arsenicoxydans] Back     alignment and taxonomy information
>gi|409408726|ref|ZP_11257161.1| 30S ribosomal protein S4 [Herbaspirillum sp. GW103] gi|386432048|gb|EIJ44876.1| 30S ribosomal protein S4 [Herbaspirillum sp. GW103] Back     alignment and taxonomy information
>gi|415943236|ref|ZP_11556036.1| 30S ribosomal protein S4 [Herbaspirillum frisingense GSF30] gi|407758752|gb|EKF68536.1| 30S ribosomal protein S4 [Herbaspirillum frisingense GSF30] Back     alignment and taxonomy information
>gi|237747389|ref|ZP_04577869.1| small subunit ribosomal protein S4 [Oxalobacter formigenes HOxBLS] gi|229378740|gb|EEO28831.1| small subunit ribosomal protein S4 [Oxalobacter formigenes HOxBLS] Back     alignment and taxonomy information
>gi|445494447|ref|ZP_21461491.1| 30S ribosomal protein S4 [Janthinobacterium sp. HH01] gi|444790608|gb|ELX12155.1| 30S ribosomal protein S4 [Janthinobacterium sp. HH01] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query550
UNIPROTKB|P0A7Z4329 rpoA [Escherichia coli K-12 (t 0.258 0.431 0.535 8.7e-69
UNIPROTKB|P0A7V8206 rpsD [Escherichia coli K-12 (t 0.361 0.966 0.615 2.9e-64
TIGR_CMR|CPS_0626329 CPS_0626 "DNA-directed RNA pol 0.258 0.431 0.510 1.3e-63
UNIPROTKB|Q9KP07206 rpsD "30S ribosomal protein S4 0.361 0.966 0.605 1e-61
TIGR_CMR|VC_2572206 VC_2572 "ribosomal protein S4" 0.361 0.966 0.605 1e-61
TIGR_CMR|SO_0255206 SO_0255 "ribosomal protein S4" 0.361 0.966 0.575 8.1e-60
TIGR_CMR|CBU_0263327 CBU_0263 "DNA-directed RNA pol 0.247 0.415 0.507 9.2e-60
TIGR_CMR|CPS_0625206 CPS_0625 "ribosomal protein S4 0.361 0.966 0.585 2.2e-59
TIGR_CMR|CBU_0262206 CBU_0262 "ribosomal protein S4 0.345 0.922 0.596 3.6e-57
TIGR_CMR|SPO_0511338 SPO_0511 "DNA-directed RNA pol 0.238 0.387 0.466 4.5e-49
UNIPROTKB|P0A7Z4 rpoA [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms
 Score = 401 (146.2 bits), Expect = 8.7e-69, Sum P(2) = 8.7e-69
 Identities = 76/142 (53%), Positives = 103/142 (72%)

Query:   196 INDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGA 255
             + + LKPR++D++ + S HAKV +EP ERG+G+TLGNALRR+LLSSM GCA TEV I G 
Sbjct:     5 VTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 64

Query:   256 LHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELV 315
             LHEYS+ EGVQEDI++I+LNLKG+ +++  +D  IL L K G   V A+DI    D+E+V
Sbjct:    65 LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIV 124

Query:   316 NPNHIIAHLSDNEEAIRQSARV 337
              P H+I HL+D   +I    +V
Sbjct:   125 KPQHVICHLTDENASISMRIKV 146
GO:0008270 "zinc ion binding" evidence=IDA
GO:0046983 "protein dimerization activity" evidence=IEA
GO:0003677 "DNA binding" evidence=IEA
GO:0016020 "membrane" evidence=IDA
GO:0016779 "nucleotidyltransferase activity" evidence=IEA
GO:0016740 "transferase activity" evidence=IEA
GO:0006351 "transcription, DNA-dependent" evidence=IEA
GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA
GO:0005737 "cytoplasm" evidence=IDA
UNIPROTKB|P0A7V8 rpsD [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms
TIGR_CMR|CPS_0626 CPS_0626 "DNA-directed RNA polymerase, alpha subunit" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
UNIPROTKB|Q9KP07 rpsD "30S ribosomal protein S4" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)] Back     alignment and assigned GO terms
TIGR_CMR|VC_2572 VC_2572 "ribosomal protein S4" [Vibrio cholerae O1 biovar El Tor (taxid:686)] Back     alignment and assigned GO terms
TIGR_CMR|SO_0255 SO_0255 "ribosomal protein S4" [Shewanella oneidensis MR-1 (taxid:211586)] Back     alignment and assigned GO terms
TIGR_CMR|CBU_0263 CBU_0263 "DNA-directed RNA polymerase, alpha subunit" [Coxiella burnetii RSA 493 (taxid:227377)] Back     alignment and assigned GO terms
TIGR_CMR|CPS_0625 CPS_0625 "ribosomal protein S4" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
TIGR_CMR|CBU_0262 CBU_0262 "ribosomal protein S4" [Coxiella burnetii RSA 493 (taxid:227377)] Back     alignment and assigned GO terms
TIGR_CMR|SPO_0511 SPO_0511 "DNA-directed RNA polymerase, alpha subunit" [Ruegeria pomeroyi DSS-3 (taxid:246200)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
P0A4C5RS4_BORPENo assigned EC number0.6650.36360.9661yesN/A
B2UEJ4RS4_RALPJNo assigned EC number0.6850.36360.9661yesN/A
P0A4C7RS4_BORPANo assigned EC number0.6650.36360.9661yesN/A
B1JU47RS4_BURCCNo assigned EC number0.670.36360.9661yesN/A
A3P088RS4_BURP0No assigned EC number0.680.36360.9661yesN/A
Q2S936RS4_HAHCHNo assigned EC number0.6550.36180.9660yesN/A
Q62GN0RS4_BURMANo assigned EC number0.680.36360.9661yesN/A
Q12G78RS4_POLSJNo assigned EC number0.650.36360.9661yesN/A
B2T726RS4_BURPPNo assigned EC number0.6750.36360.9661yesN/A
B4E5E5RS4_BURCJNo assigned EC number0.670.36360.9661yesN/A
Q7NQH6RS4_CHRVONo assigned EC number0.680.36180.9660yesN/A
Q39KE2RS4_BURS3No assigned EC number0.670.36360.9661yesN/A
A1W332RS4_ACISJNo assigned EC number0.650.36360.9661yesN/A
A9IHR7RS4_BORPDNo assigned EC number0.660.36360.9661yesN/A
A6T3H9RS4_JANMANo assigned EC number0.7350.36360.9661yesN/A
A3NEF4RS4_BURP6No assigned EC number0.680.36360.9661yesN/A
A1TJU1RS4_ACIACNo assigned EC number0.6550.36360.9661yesN/A
B3R7E4RS4_CUPTRNo assigned EC number0.6650.36360.9661yesN/A
Q0BJ21RS4_BURCMNo assigned EC number0.670.36360.9661yesN/A
C5CQ76RS4_VARPSNo assigned EC number0.660.36360.9661yesN/A
Q1BRX3RS4_BURCANo assigned EC number0.670.36360.9661yesN/A
Q46WG8RS4_CUPPJNo assigned EC number0.670.36360.9661yesN/A
A3MRX9RS4_BURM7No assigned EC number0.680.36360.9661yesN/A
A2SLD2RS4_METPPNo assigned EC number0.660.36360.9661yesN/A
A2S7K1RS4_BURM9No assigned EC number0.680.36360.9661yesN/A
B9MBW1RS4_ACIETNo assigned EC number0.6550.36360.9661yesN/A
A4SUY5RS4_POLSQNo assigned EC number0.660.36360.9661yesN/A
B2JI40RS4_BURP8No assigned EC number0.6850.36360.9661yesN/A
P0A4C6RS4_BORBRNo assigned EC number0.6650.36360.9661yesN/A
Q2L242RS4_BORA1No assigned EC number0.650.36360.9661yesN/A
A4JAR5RS4_BURVGNo assigned EC number0.670.36360.9661yesN/A
B1YRQ4RS4_BURA4No assigned EC number0.6650.36360.9661yesN/A
A1WK93RS4_VEREINo assigned EC number0.6450.36360.9661yesN/A
C5BF28RS4_EDWI9No assigned EC number0.630.36180.9660yesN/A
Q2SU52RS4_BURTANo assigned EC number0.6850.36360.9661yesN/A
Q0K644RS4_CUPNHNo assigned EC number0.660.36360.9661yesN/A
A4G9R4RS4_HERARNo assigned EC number0.730.36360.9661yesN/A
A1V878RS4_BURMSNo assigned EC number0.680.36360.9661yesN/A
Q63Q36RS4_BURPSNo assigned EC number0.680.36360.9661yesN/A
A0K3Q0RS4_BURCHNo assigned EC number0.670.36360.9661yesN/A
Q1LI62RS4_RALMENo assigned EC number0.680.36360.9661yesN/A
B1XSS6RS4_POLNSNo assigned EC number0.6450.36360.9661yesN/A
Q21QP8RS4_RHOFDNo assigned EC number0.6450.36360.9661yesN/A
Q13TJ5RS4_BURXLNo assigned EC number0.6750.36360.9661yesN/A
A1VJ39RS4_POLNANo assigned EC number0.6650.36360.9661yesN/A
Q3JMT8RS4_BURP1No assigned EC number0.680.36360.9661yesN/A
C1DAU2RS4_LARHHNo assigned EC number0.6450.36180.9660yesN/A
A9ADL8RS4_BURM1No assigned EC number0.6650.36360.9661yesN/A
A9BRX4RS4_DELASNo assigned EC number0.650.36360.9661yesN/A
Q8XV37RS4_RALSONo assigned EC number0.680.36360.9661yesN/A

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.70.691
4th Layer2.7.7.60.737

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query550
PRK05327203 PRK05327, rpsD, 30S ribosomal protein S4; Validate 1e-100
TIGR01017200 TIGR01017, rpsD_bact, ribosomal protein S4, bacter 3e-75
COG0522205 COG0522, RpsD, Ribosomal protein S4 and related pr 4e-69
PRK05591113 PRK05591, rplQ, 50S ribosomal protein L17; Validat 2e-58
PRK05182310 PRK05182, PRK05182, DNA-directed RNA polymerase su 2e-58
COG0203116 COG0203, RplQ, Ribosomal protein L17 [Translation, 4e-58
cd06928215 cd06928, RNAP_alpha_NTD, N-terminal domain of the 6e-49
CHL00113201 CHL00113, rps4, ribosomal protein S4; Reviewed 2e-46
pfam0119697 pfam01196, Ribosomal_L17, Ribosomal protein L17 3e-46
TIGR00059112 TIGR00059, L17, ribosomal protein L17 5e-44
COG0202317 COG0202, RpoA, DNA-directed RNA polymerase, alpha 1e-43
PRK05182310 PRK05182, PRK05182, DNA-directed RNA polymerase su 1e-42
TIGR02027297 TIGR02027, rpoA, DNA-directed RNA polymerase, alph 8e-42
CHL00013327 CHL00013, rpoA, RNA polymerase alpha subunit 3e-28
COG0202317 COG0202, RpoA, DNA-directed RNA polymerase, alpha 2e-26
smart00662224 smart00662, RPOLD, RNA polymerases D 7e-26
pfam0311867 pfam03118, RNA_pol_A_CTD, Bacterial RNA polymerase 6e-24
pfam01000117 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA 7e-21
pfam0016393 pfam00163, Ribosomal_S4, Ribosomal protein S4/S9 N 5e-20
cd0016570 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding d 2e-15
pfam0147948 pfam01479, S4, S4 domain 3e-15
smart0036360 smart00363, S4, S4 RNA-binding domain 2e-14
PTZ00076 253 PTZ00076, PTZ00076, 60S ribosomal protein L17; Pro 2e-13
pfam0119388 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 di 2e-07
PRK04051177 PRK04051, rps4p, 30S ribosomal protein S4P; Valida 8e-06
TIGR01018162 TIGR01018, rpsD_arch, ribosomal protein S4(archaea 6e-05
PRK149061460 PRK14906, PRK14906, DNA-directed RNA polymerase su 2e-04
PTZ00155181 PTZ00155, PTZ00155, 40S ribosomal protein S9; Prov 0.001
COG1189245 COG1189, COG1189, Predicted rRNA methylase [Transl 0.001
>gnl|CDD|235411 PRK05327, rpsD, 30S ribosomal protein S4; Validated Back     alignment and domain information 
 Score =  302 bits (775), Expect = e-100
 Identities = 117/201 (58%), Positives = 140/201 (69%), Gaps = 6/201 (2%)

Query: 1   MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHG-RISGSRTSDYGYQFREK 59
           MARY GPK KL RR G+DLF    +R L  K      PGQHG R    + SDYG Q REK
Sbjct: 1   MARYTGPKCKLSRRLGVDLFKS-GKRCLKRKYP----PGQHGQRRRKPKLSDYGLQLREK 55

Query: 60  QKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLI 119
           QK++R+YG+LEKQFRRYF E AR KG TGE +L+LLESR DNVVYR+GF+ TR +ARQL+
Sbjct: 56  QKLRRIYGVLEKQFRRYFKEAARRKGNTGENLLQLLESRLDNVVYRLGFAPTRRQARQLV 115

Query: 120 SHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKM 179
           SH   LVN K VNI SY++KPGD+I VREK+KK  RI  +LEL+E      W+ VDA+K+
Sbjct: 116 SHGHILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEALELAERRGVPDWLEVDAEKL 175

Query: 180 EGVFKSEPNRSEFANDINDLL 200
           EG FK  P R E    IN+ L
Sbjct: 176 EGTFKRLPEREEIPVPINEQL 196

Length = 203
>gnl|CDD|200066 TIGR01017, rpsD_bact, ribosomal protein S4, bacterial/organelle type Back     alignment and domain information
>gnl|CDD|223596 COG0522, RpsD, Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|235522 PRK05591, rplQ, 50S ribosomal protein L17; Validated Back     alignment and domain information
>gnl|CDD|235359 PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha; Provisional Back     alignment and domain information
>gnl|CDD|223281 COG0203, RplQ, Ribosomal protein L17 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|132904 cd06928, RNAP_alpha_NTD, N-terminal domain of the Alpha subunit of Bacterial RNA polymerase Back     alignment and domain information
>gnl|CDD|177038 CHL00113, rps4, ribosomal protein S4; Reviewed Back     alignment and domain information
>gnl|CDD|216356 pfam01196, Ribosomal_L17, Ribosomal protein L17 Back     alignment and domain information
>gnl|CDD|129169 TIGR00059, L17, ribosomal protein L17 Back     alignment and domain information
>gnl|CDD|223280 COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription] Back     alignment and domain information
>gnl|CDD|235359 PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha; Provisional Back     alignment and domain information
>gnl|CDD|233691 TIGR02027, rpoA, DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type Back     alignment and domain information
>gnl|CDD|214333 CHL00013, rpoA, RNA polymerase alpha subunit Back     alignment and domain information
>gnl|CDD|223280 COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription] Back     alignment and domain information
>gnl|CDD|214766 smart00662, RPOLD, RNA polymerases D Back     alignment and domain information
>gnl|CDD|202541 pfam03118, RNA_pol_A_CTD, Bacterial RNA polymerase, alpha chain C terminal domain Back     alignment and domain information
>gnl|CDD|110031 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain Back     alignment and domain information
>gnl|CDD|215762 pfam00163, Ribosomal_S4, Ribosomal protein S4/S9 N-terminal domain Back     alignment and domain information
>gnl|CDD|238095 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes Back     alignment and domain information
>gnl|CDD|201819 pfam01479, S4, S4 domain Back     alignment and domain information
>gnl|CDD|214638 smart00363, S4, S4 RNA-binding domain Back     alignment and domain information
>gnl|CDD|173371 PTZ00076, PTZ00076, 60S ribosomal protein L17; Provisional Back     alignment and domain information
>gnl|CDD|216354 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerisation domain Back     alignment and domain information
>gnl|CDD|179730 PRK04051, rps4p, 30S ribosomal protein S4P; Validated Back     alignment and domain information
>gnl|CDD|213577 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type) Back     alignment and domain information
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional Back     alignment and domain information
>gnl|CDD|185484 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provisional Back     alignment and domain information
>gnl|CDD|224110 COG1189, COG1189, Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 550
CHL00013327 rpoA RNA polymerase alpha subunit 100.0
TIGR02027297 rpoA DNA-directed RNA polymerase, alpha subunit, b 100.0
PRK05182310 DNA-directed RNA polymerase subunit alpha; Provisi 100.0
COG0202317 RpoA DNA-directed RNA polymerase, alpha subunit/40 100.0
CHL00113201 rps4 ribosomal protein S4; Reviewed 100.0
COG0203116 RplQ Ribosomal protein L17 [Translation, ribosomal 100.0
PRK05327203 rpsD 30S ribosomal protein S4; Validated 100.0
TIGR00059112 L17 ribosomal protein L17. Eubacterial and mitocho 100.0
TIGR01017200 rpsD_bact ribosomal protein S4, bacterial/organell 100.0
PRK05591113 rplQ 50S ribosomal protein L17; Validated 100.0
COG0522205 RpsD Ribosomal protein S4 and related proteins [Tr 100.0
PTZ00076 253 60S ribosomal protein L17; Provisional 100.0
PF0119697 Ribosomal_L17: Ribosomal protein L17; InterPro: IP 100.0
cd06928215 RNAP_alpha_NTD N-terminal domain of the Alpha subu 100.0
KOG3280|consensus171 100.0
cd07028212 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The 99.96
PRK14979195 DNA-directed RNA polymerase subunit D; Provisional 99.93
smart00662224 RPOLD RNA polymerases D. DNA-directed RNA polymera 99.93
cd07030259 RNAP_D D subunit of Archaeal RNA polymerase. The D 99.93
PRK00783263 DNA-directed RNA polymerase subunit D; Provisional 99.91
cd07031265 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme 99.88
PF0311866 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha cha 99.76
PF0016394 Ribosomal_S4: Ribosomal protein S4/S9 N-terminal d 99.75
KOG3301|consensus183 99.72
PTZ00155181 40S ribosomal protein S9; Provisional 99.72
PF01000112 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert dom 99.7
PRK0775895 hypothetical protein; Provisional 99.65
PLN00189194 40S ribosomal protein S9; Provisional 99.48
TIGR01018162 rpsD_arch ribosomal protein S4(archaeal type)/S9(e 99.48
PRK04051177 rps4p 30S ribosomal protein S4P; Validated 99.42
PRK149061460 DNA-directed RNA polymerase subunit beta'/alpha do 99.37
PF0147948 S4: S4 domain; InterPro: IPR002942 Ribosomes are t 99.35
cd07032291 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly 99.34
COG1188100 Ribosome-associated heat shock protein implicated 99.11
PRK10348133 ribosome-associated heat shock protein Hsp15; Prov 99.03
TIGR0298859 YaaA_near_RecF S4 domain protein YaaA. This small 98.84
PF0119366 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation 98.83
KOG1522|consensus285 98.67
cd0016570 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The 98.54
COG1189245 Predicted rRNA methylase [Translation, ribosomal s 98.54
smart0036360 S4 S4 RNA-binding domain. 98.52
PLN00051267 RNA-binding S4 domain-containing protein; Provisio 98.43
TIGR00478228 tly hemolysin TlyA family protein. Hemolysins are 98.41
COG2302257 Uncharacterized conserved protein, contains S4-lik 98.41
TIGR03069257 PS_II_S4 photosystem II S4 domain protein. Members 98.4
cd0046086 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA pol 98.03
KOG1521|consensus338 97.88
PRK1150770 ribosome-associated protein; Provisional 97.72
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase 97.5
PRK10475290 23S rRNA pseudouridine synthase F; Provisional 97.48
PRK10839232 16S rRNA pseudouridylate synthase A; Provisional 97.44
PF1327565 S4_2: S4 domain; PDB: 1P9K_A. 97.34
PRK11180325 rluD 23S rRNA pseudouridine synthase D; Provisiona 97.23
PRK10700289 23S rRNA pseudouridylate synthase B; Provisional 97.15
TIGR00005299 rluA_subfam pseudouridine synthase, RluA family. m 97.11
COG250173 S4-like RNA binding protein [Replication, recombin 96.79
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 96.78
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [ 96.72
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 96.6
cd0692783 RNAP_L L subunit of Archaeal RNA polymerase. The a 96.31
PRK0114685 DNA-directed RNA polymerase subunit L; Provisional 96.22
KOG4655|consensus181 96.19
COG176199 RPB11 DNA-directed RNA polymerase, subunit L [Tran 95.91
cd0702783 RNAP_RPB11_like RPB11 subunit of RNA polymerase. T 95.55
PF1365677 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisatio 94.79
cd0702985 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA pol 94.11
TIGR02238 313 recomb_DMC1 meiotic recombinase Dmc1. This model d 94.06
PRK04313237 30S ribosomal protein S4e; Validated 93.61
PRK13354410 tyrosyl-tRNA synthetase; Provisional 92.9
PRK05912408 tyrosyl-tRNA synthetase; Validated 92.24
PTZ00035 337 Rad51 protein; Provisional 92.22
PTZ00118262 40S ribosomal protein S4; Provisional 92.16
PLN00036261 40S ribosomal protein S4; Provisional 92.14
PTZ00223273 40S ribosomal protein S4; Provisional 92.03
PLN03187 344 meiotic recombination protein DMC1 homolog; Provis 91.13
TIGR02239 316 recomb_RAD51 DNA repair protein RAD51. This eukary 91.12
PRK04301 317 radA DNA repair and recombination protein RadA; Va 91.05
TIGR0195450 nusA_Cterm_rpt transcription termination factor Nu 91.0
cd0692693 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA poly 88.87
COG1471241 RPS4A Ribosomal protein S4E [Translation, ribosoma 87.63
PLN03186 342 DNA repair protein RAD51 homolog; Provisional 87.37
COG0162401 TyrS Tyrosyl-tRNA synthetase [Translation, ribosom 86.23
PF0063330 HHH: Helix-hairpin-helix motif; InterPro: IPR00044 80.89
>CHL00013 rpoA RNA polymerase alpha subunit Back     alignment and domain information 
Probab=100.00  E-value=3.9e-65  Score=527.74  Aligned_cols=230  Identities=32%  Similarity=0.441  Sum_probs=207.5

Q ss_pred             CeeEEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECCcccccccccCccccHHHHHhcccccee
Q psy8861         202 PRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVIL  281 (550)
Q Consensus       202 p~~i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~gv~hEfs~i~Gv~Edv~~IilNLK~i~~  281 (550)
                      +-..++.+.+.+||+|+++||++|||+||||||||+|||++||+||++|+|+|+.|||++||||+|||+||++|||+|+|
T Consensus         9 ~ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~gv~hEfs~i~GV~Edv~eIilNLK~I~~   88 (327)
T CHL00013          9 CVESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEGVPHEYSTIPGIRESVLEILLNLKEIVL   88 (327)
T ss_pred             ceeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECCccccccCCCCcccCHHHHHHhhhcCeE
Confidence            33456666789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCceEEEEEEEeceeeEEeccCccCCCeEEeCCCceEEEcCC-----------------------------------
Q psy8861         282 KLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSD-----------------------------------  326 (550)
Q Consensus       282 ~~~~~~~~~~~l~~~Gp~~V~A~DI~~~~~veivnpd~~IatL~~-----------------------------------  326 (550)
                      +.+..+++.++|+++||++|||+||.+|++|+|+|||||||||++                                   
T Consensus        89 k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~ieivnpd~~Iatl~~~~~l~~el~ie~G~GY~~~~~~~~~~g~i~iDa~F  168 (327)
T CHL00013         89 KSNLYGPQKASICVQGPKYVTAQDIILPPSVEIVDPTQHIATITEPIDLEIELKIEKGRGYRLKTPKNFQDGSFPIDAVF  168 (327)
T ss_pred             EccCCCcEEEEEEEeCCeEEEeeeeccCCCeEEeCCCeEEEEeCCCCEEEEEEEEECccCceeccccccCCCcEEeCCCC
Confidence            998777899999999999999999999999999999999999987                                   


Q ss_pred             ----------------------------------hHHHHHHHHHHHHHHhhhhhccCCCCC----c-cc-----------
Q psy8861         327 ----------------------------------NEEAIRQSARVLVDQLNVFAALENTPV----K-KE-----------  356 (550)
Q Consensus       327 ----------------------------------P~~Al~~Aa~iL~~~~~~f~~~~~~~~----~-~~-----------  356 (550)
                                                        |++||.+||++|++||.+|.+++....    . ..           
T Consensus       169 sPV~kVny~Ve~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  248 (327)
T CHL00013        169 MPVRNVNYSIHSYGNGNEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPFLHAEEENLKLENNENRVTLLFTFHDRL  248 (327)
T ss_pred             CCeeEEEEEEEEcccCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhcchhhhcccccccccccccccccccc
Confidence                                              999999999999999999998764311    0 00           


Q ss_pred             -cCccccccCCcccccccccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHh-cCccccc
Q psy8861         357 -LDSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS-RGKYYMR  431 (550)
Q Consensus       357 -~~~~~~~~~~~l~~~I~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~-~gl~lmr  431 (550)
                       ..++....++.++++||+|+||||||||||+|||+||+||+++|++||+++||||+||++||+++|++ +|++|..
T Consensus       249 ~~~~~~~~~~~~~~~~Ie~L~LSvRs~NcLk~a~I~ti~dL~~~s~~dLl~ikN~GkKSl~EI~~~L~~~~gl~l~~  325 (327)
T CHL00013        249 TDLKKNKKEIALKQIFIEQLELSVRAYNCLKRANIHTLLDLLNYSQEDLLKIKNFGQKSAKEVLEALQKRFGIDLPK  325 (327)
T ss_pred             cccccchhhhhhhceeHHhccCchhhhhhhhhcCccCHHHHHhcCHHHHhhhhccCHhHHHHHHHHHHHHhCCCCCC
Confidence             10111123467889999999999999999999999999999999999999999999999999999988 9999864

>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type Back     alignment and domain information
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional Back     alignment and domain information
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription] Back     alignment and domain information
>CHL00113 rps4 ribosomal protein S4; Reviewed Back     alignment and domain information
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK05327 rpsD 30S ribosomal protein S4; Validated Back     alignment and domain information
>TIGR00059 L17 ribosomal protein L17 Back     alignment and domain information
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type Back     alignment and domain information
>PRK05591 rplQ 50S ribosomal protein L17; Validated Back     alignment and domain information
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PTZ00076 60S ribosomal protein L17; Provisional Back     alignment and domain information
>PF01196 Ribosomal_L17: Ribosomal protein L17; InterPro: IPR000456 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase Back     alignment and domain information
>KOG3280|consensus Back     alignment and domain information
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase Back     alignment and domain information
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional Back     alignment and domain information
>smart00662 RPOLD RNA polymerases D Back     alignment and domain information
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase Back     alignment and domain information
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional Back     alignment and domain information
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals Back     alignment and domain information
>PF00163 Ribosomal_S4: Ribosomal protein S4/S9 N-terminal domain; InterPro: IPR001912 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>KOG3301|consensus Back     alignment and domain information
>PTZ00155 40S ribosomal protein S9; Provisional Back     alignment and domain information
>PF01000 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert domain; InterPro: IPR011262 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PRK07758 hypothetical protein; Provisional Back     alignment and domain information
>PLN00189 40S ribosomal protein S9; Provisional Back     alignment and domain information
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type) Back     alignment and domain information
>PRK04051 rps4p 30S ribosomal protein S4P; Validated Back     alignment and domain information
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional Back     alignment and domain information
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional Back     alignment and domain information
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA Back     alignment and domain information
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2 Back     alignment and domain information
>KOG1522|consensus Back     alignment and domain information
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes Back     alignment and domain information
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>smart00363 S4 S4 RNA-binding domain Back     alignment and domain information
>PLN00051 RNA-binding S4 domain-containing protein; Provisional Back     alignment and domain information
>TIGR00478 tly hemolysin TlyA family protein Back     alignment and domain information
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown] Back     alignment and domain information
>TIGR03069 PS_II_S4 photosystem II S4 domain protein Back     alignment and domain information
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase Back     alignment and domain information
>KOG1521|consensus Back     alignment and domain information
>PRK11507 ribosome-associated protein; Provisional Back     alignment and domain information
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional Back     alignment and domain information
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>PF13275 S4_2: S4 domain; PDB: 1P9K_A Back     alignment and domain information
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family Back     alignment and domain information
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Back     alignment and domain information
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A Back     alignment and domain information
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase Back     alignment and domain information
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional Back     alignment and domain information
>KOG4655|consensus Back     alignment and domain information
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription] Back     alignment and domain information
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase Back     alignment and domain information
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K Back     alignment and domain information
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1 Back     alignment and domain information
>PRK04313 30S ribosomal protein S4e; Validated Back     alignment and domain information
>PRK13354 tyrosyl-tRNA synthetase; Provisional Back     alignment and domain information
>PRK05912 tyrosyl-tRNA synthetase; Validated Back     alignment and domain information
>PTZ00035 Rad51 protein; Provisional Back     alignment and domain information
>PTZ00118 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PLN00036 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PTZ00223 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional Back     alignment and domain information
>TIGR02239 recomb_RAD51 DNA repair protein RAD51 Back     alignment and domain information
>PRK04301 radA DNA repair and recombination protein RadA; Validated Back     alignment and domain information
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication Back     alignment and domain information
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PLN03186 DNA repair protein RAD51 homolog; Provisional Back     alignment and domain information
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query550
1vs5_D206 Crystal Structure Of The Bacterial Ribosome From Es 8e-72
1p6g_D205 Real Space Refined Coordinates Of The 30s Subunit F 5e-71
2gy9_D204 Structure Of The 30s Subunit Of A Pre-Translocation 2e-70
1fka_D209 Structure Of Functionally Activated Small Ribosomal 2e-46
1i94_D208 Crystal Structures Of The Small Ribosomal Subunit W 1e-45
1fjg_D209 Structure Of The Thermus Thermophilus 30s Ribosomal 1e-45
1p85_L127 Real Space Refined Coordinates Of The 50s Subunit F 3e-41
3fik_N120 Ternary Complex-Bound E.Coli 70s Ribosome. This Ent 1e-40
3iyd_A329 Three-Dimensional Em Structure Of An Intact Activat 2e-40
3iyd_A329 Three-Dimensional Em Structure Of An Intact Activat 1e-29
1bdf_A235 Structure Of Escherichia Coli Rna Polymerase Alpha 1e-39
2gya_L114 Structure Of The 50s Subunit Of A Pre-Translocation 5e-39
1qd7_C159 Partial Model For 30s Ribosomal Subunit Length = 15 7e-34
3bbn_D201 Homology Model For The Spinach Chloroplast 30s Subu 7e-26
1lb2_B84 Structure Of The E. Coli Alpha C-Terminal Domain Of 3e-24
1xs9_D84 A Model Of The Ternary Complex Formed Between Mara, 3e-24
1coo_A98 The Cooh-Terminal Domain Of Rna Polymerase Alpha Su 3e-24
2jzb_A99 Solution Structure Of The Complex Between E.Coli Nu 4e-24
1iw7_A315 Crystal Structure Of The Rna Polymerase Holoenzyme 7e-24
1gd8_A118 The Crystal Structure Of Bacteria-Specific L17 Ribo 7e-23
1l9u_A314 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 1e-22
1l9u_A314 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 1e-04
1hqm_A313 Crystal Structure Of Thermus Aquaticus Core Rna Pol 2e-22
1hqm_A313 Crystal Structure Of Thermus Aquaticus Core Rna Pol 2e-04
1i6v_A314 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 2e-22
1i6v_A314 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 9e-05
3fin_R117 T. Thermophilus 70s Ribosome In Complex With Mrna, 3e-22
3k4g_A86 Crystal Structure Of E. Coli Rna Polymerase Alpha S 1e-21
3bbo_P205 Homology Model For The Spinach Chloroplast 50s Subu 9e-20
1nkw_L116 Crystal Structure Of The Large Ribosomal Subunit Fr 3e-19
1pnu_L114 Crystal Structure Of A Streptomycin Dependent Ribos 6e-18
2ftc_J116 Structural Model For The Large Subunit Of The Mamma 2e-09
2cqm_A122 Solution Structure Of The Mitochondrial Ribosomal P 3e-08
3ihq_B75 Crystal Structure Of Reduced C10s Spx In Complex Wi 1e-06
1z3e_B73 Crystal Structure Of Spx In Complex With The C-Term 1e-06
3gfk_B79 Crystal Structure Of Bacillus Subtilis SpxRNA POLYM 2e-06
>pdb|1VS5|D Chain D, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With The Antibiotic Kasugamyin At 3.5a Resolution. This File Contains The 30s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 206 Back     alignment and structure 
Iteration: 1

 Score =  268 bits (684), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 123/200 (61%), Positives = 157/200 (78%), Gaps = 1/200 (0%)
Query: 1   MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQ 60
           MARY+GPK KL RREG DLFLKS  R++D+KCK++  PGQHG     R SDYG Q REKQ
Sbjct: 1   MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHG-ARKPRLSDYGVQLREKQ 59
Query: 61  KVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLIS 120
           KV+R+YG+LE+QFR Y+ E ARLKG TGE +L LLE R DNVVYRMGF +TR+EARQL+S
Sbjct: 60  KVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVS 119
Query: 121 HRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKME 180
           H+A +VN ++VNIASY++ P D++S+REKAKKQ+R+  +LEL+E     +W+ VDA KME
Sbjct: 120 HKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKME 179
Query: 181 GVFKSEPNRSEFANDINDLL 200
           G FK +P RS+ + DIN+ L
Sbjct: 180 GTFKRKPERSDLSADINEHL 199
>pdb|1P6G|D Chain D, Real Space Refined Coordinates Of The 30s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 205 Back     alignment and structure
>pdb|2GY9|D Chain D, Structure Of The 30s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056 Length = 204 Back     alignment and structure
>pdb|1FKA|D Chain D, Structure Of Functionally Activated Small Ribosomal Subunit At 3.3 A Resolution Length = 209 Back     alignment and structure
>pdb|1I94|D Chain D, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 208 Back     alignment and structure
>pdb|1FJG|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal Subunit In Complex With The Antibiotics Streptomycin, Spectinomycin, And Paromomycin Length = 209 Back     alignment and structure
>pdb|1P85|L Chain L, Real Space Refined Coordinates Of The 50s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 127 Back     alignment and structure
>pdb|3FIK|N Chain N, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 50s Subunit. Length = 120 Back     alignment and structure
>pdb|3IYD|A Chain A, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 329 Back     alignment and structure
>pdb|3IYD|A Chain A, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 329 Back     alignment and structure
>pdb|1BDF|A Chain A, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit N-Terminal Domain Length = 235 Back     alignment and structure
>pdb|2GYA|L Chain L, Structure Of The 50s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056 Length = 114 Back     alignment and structure
>pdb|1QD7|C Chain C, Partial Model For 30s Ribosomal Subunit Length = 159 Back     alignment and structure
>pdb|3BBN|D Chain D, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 201 Back     alignment and structure
>pdb|1LB2|B Chain B, Structure Of The E. Coli Alpha C-Terminal Domain Of Rna Polymerase In Complex With Cap And Dna Length = 84 Back     alignment and structure
>pdb|1XS9|D Chain D, A Model Of The Ternary Complex Formed Between Mara, The Alpha-Ctd Of Rna Polymerase And Dna Length = 84 Back     alignment and structure
>pdb|1COO|A Chain A, The Cooh-Terminal Domain Of Rna Polymerase Alpha Subunit Length = 98 Back     alignment and structure
>pdb|2JZB|A Chain A, Solution Structure Of The Complex Between E.Coli Nusa-Ar2 And Rnap-Actd Length = 99 Back     alignment and structure
>pdb|1IW7|A Chain A, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 315 Back     alignment and structure
>pdb|1GD8|A Chain A, The Crystal Structure Of Bacteria-Specific L17 Ribosomal Protein. Length = 118 Back     alignment and structure
>pdb|1L9U|A Chain A, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 314 Back     alignment and structure
>pdb|1L9U|A Chain A, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 314 Back     alignment and structure
>pdb|1HQM|A Chain A, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase- Includes Complete Structure With Side-Chains (Except For Disordered Regions)-Further Refined From Original Deposition-Contains Additional Sequence Information Length = 313 Back     alignment and structure
>pdb|1HQM|A Chain A, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase- Includes Complete Structure With Side-Chains (Except For Disordered Regions)-Further Refined From Original Deposition-Contains Additional Sequence Information Length = 313 Back     alignment and structure
>pdb|1I6V|A Chain A, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 314 Back     alignment and structure
>pdb|1I6V|A Chain A, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 314 Back     alignment and structure
>pdb|3FIN|R Chain R, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A 6.4 A Cryo-Em Map. This File Contains The 50s Subunit. Length = 117 Back     alignment and structure
>pdb|3K4G|A Chain A, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain Length = 86 Back     alignment and structure
>pdb|3BBO|P Chain P, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 205 Back     alignment and structure
>pdb|1NKW|L Chain L, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Length = 116 Back     alignment and structure
>pdb|1PNU|L Chain L, Crystal Structure Of A Streptomycin Dependent Ribosome From Escherichia Coli, 50s Subunit Of 70s Ribosome. This File, 1pnu, Contains Only Molecules Of The 50s Ribosomal Subunit. The 30s Subunit, Mrna, P-Site Trna, And A-Site Trna Are In The Pdb File 1pns. Length = 114 Back     alignment and structure
>pdb|2FTC|J Chain J, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome Length = 116 Back     alignment and structure
>pdb|2CQM|A Chain A, Solution Structure Of The Mitochondrial Ribosomal Protein L17 Isolog Length = 122 Back     alignment and structure
>pdb|3IHQ|B Chain B, Crystal Structure Of Reduced C10s Spx In Complex With The Alpha C-Terminal Domain Of Rna Polymeras Length = 75 Back     alignment and structure
>pdb|1Z3E|B Chain B, Crystal Structure Of Spx In Complex With The C-Terminal Domain Of The Rna Polymerase Alpha Subunit Length = 73 Back     alignment and structure
>pdb|3GFK|B Chain B, Crystal Structure Of Bacillus Subtilis SpxRNA POLYMERASE Alpha Subunit C-Terminal Domain Complex Length = 79 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query550
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 3e-96
3r8n_D205 30S ribosomal protein S4; protein biosynthesis, RN 3e-96
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spi 7e-88
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, uni 7e-76
1bdf_A235 RNA polymerase alpha subunit; nucleotidyltransfera 8e-66
3r8s_N120 50S ribosomal protein L17; protein biosynthesis, R 4e-65
2zjr_K116 50S ribosomal protein L17; ribosome, large ribosom 2e-63
3lu0_A329 DNA-directed RNA polymerase subunit alpha; E. coli 6e-63
3lu0_A329 DNA-directed RNA polymerase subunit alpha; E. coli 2e-44
3bbo_P205 Ribosomal protein L17; large ribosomal subunit, sp 1e-62
1gd8_A118 50S ribosomal protein L17; two domains, ribosomal 9e-62
2a6h_A315 DNA-directed RNA polymerase alpha chain; RNA polym 4e-59
2a6h_A315 DNA-directed RNA polymerase alpha chain; RNA polym 2e-43
2cqm_A122 Ribosomal protein L17 isolog; alpha and beta (A+B) 3e-51
1coo_A98 RNA polymerase alpha subunit; transcription regula 7e-31
3gfk_B79 DNA-directed RNA polymerase subunit alpha; protein 2e-29
1z3e_B73 DNA-directed RNA polymerase alpha chain; bacterial 2e-28
3k4g_A86 DNA-directed RNA polymerase subunit alpha; bacteri 1e-24
2xzm_D181 Ribosomal protein S4 containing protein; ribosome, 3e-18
3u5c_J197 40S ribosomal protein S9-A; translation, ribosome, 5e-15
3iz6_C195 40S ribosomal protein S9 (S4P); eukaryotic ribosom 1e-14
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protei 1e-11
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-11
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-05
1twf_C318 B44.5, DNA-directed RNA polymerase II 45 kDa polyp 8e-09
3h0g_C297 DNA-directed RNA polymerase II subunit RPB3; trans 5e-08
2pa8_D265 DNA-directed RNA polymerase subunit D; ferredoxin- 6e-06
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ... Length = 209 Back     alignment and structure
 Score =  290 bits (745), Expect = 3e-96
 Identities = 92/203 (45%), Positives = 131/203 (64%), Gaps = 4/203 (1%)

Query: 1   MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLR---PGQHGRISGSRTSDYGYQFR 57
           M RYIGP  +LCRREG+ L+LK   R    KC ++ R   PGQHG+    R SDY  + R
Sbjct: 1   MGRYIGPVCRLCRREGVKLYLKG-ERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLR 59

Query: 58  EKQKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQ 117
           EKQK++R+YGI E+QFR  F E ++ KG TG + L LLESR DNVVYR+GF+ +R +ARQ
Sbjct: 60  EKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQ 119

Query: 118 LISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAK 177
           L+ H    VN + V++ SY+++PGD I+V EK++    I  +LE  +      W+++D +
Sbjct: 120 LVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVE 179

Query: 178 KMEGVFKSEPNRSEFANDINDLL 200
            M+G F   P+R + A  +N+ L
Sbjct: 180 GMKGKFLRLPDREDLALPVNEQL 202
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 201 Back     alignment and structure
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C Length = 159 Back     alignment and structure
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1 Length = 235 Back     alignment and structure
>3r8s_N 50S ribosomal protein L17; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 3fik_N 2wwq_N 3oat_N* 3oas_N* 3ofd_N 3ofc_N 3ofr_N* 3ofz_N* 3og0_N 3ofq_N 3r8t_N 3i1n_N 1p85_L 1p86_L 1vs8_N 1vs6_N 2aw4_N 2awb_N 1vt2_N 2i2v_N ... Length = 120 Back     alignment and structure
>2zjr_K 50S ribosomal protein L17; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.188.1.1 PDB: 1nwx_L* 1nwy_L* 1sm1_L* 1xbp_L* 2zjp_K* 2zjq_K 1nkw_L 3cf5_K* 3dll_K* 3pio_K* 3pip_K* 1pnu_L 1pny_L 1vor_O 1vou_O 1vow_O 1voy_O 1vp0_O Length = 116 Back     alignment and structure
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A Length = 329 Back     alignment and structure
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A Length = 329 Back     alignment and structure
>3bbo_P Ribosomal protein L17; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.2 Length = 205 Back     alignment and structure
>1gd8_A 50S ribosomal protein L17; two domains, ribosomal protein S8-like domain, Trp repressor-like domain, helix-turn-helix motif; 2.30A {Thermus thermophilus} SCOP: d.188.1.1 PDB: 1vsa_L 1vsp_L 1yl3_0 2b66_R 2b9n_R 2b9p_R 2hgj_Q 2hgq_Q 2hgu_Q 2j01_R 2j03_R 2jl6_R 2jl8_R 2v47_R 2v49_R 2wdi_R 2wdj_R 2wdl_R 2wdn_R 2wh2_R ... Length = 118 Back     alignment and structure
>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3aoh_A* 3aoi_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* ... Length = 315 Back     alignment and structure
>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3aoh_A* 3aoi_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* ... Length = 315 Back     alignment and structure
>2cqm_A Ribosomal protein L17 isolog; alpha and beta (A+B), structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.188.1.1 PDB: 2ftc_J 3iy9_S Length = 122 Back     alignment and structure
>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli} SCOP: a.60.3.1 PDB: 2jzb_A Length = 98 Back     alignment and structure
>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} Length = 79 Back     alignment and structure
>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 PDB: 3ihq_B Length = 73 Back     alignment and structure
>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} PDB: 3n4m_B* 1lb2_B* 3n97_B* 1xs9_D Length = 86 Back     alignment and structure
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D Length = 181 Back     alignment and structure
>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D* Length = 197 Back     alignment and structure
>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Length = 195 Back     alignment and structure
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ... Length = 318 Back     alignment and structure
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 297 Back     alignment and structure
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D Length = 265 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query550
3lu0_A329 DNA-directed RNA polymerase subunit alpha; E. coli 100.0
2a6h_A315 DNA-directed RNA polymerase alpha chain; RNA polym 100.0
3r8n_D205 30S ribosomal protein S4; protein biosynthesis, RN 100.0
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spi 100.0
3r8s_N120 50S ribosomal protein L17; protein biosynthesis, R 100.0
1gd8_A118 50S ribosomal protein L17; two domains, ribosomal 100.0
2zjr_K116 50S ribosomal protein L17; ribosome, large ribosom 100.0
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 100.0
3bbo_P205 Ribosomal protein L17; large ribosomal subunit, sp 100.0
2cqm_A122 Ribosomal protein L17 isolog; alpha and beta (A+B) 100.0
1bdf_A235 RNA polymerase alpha subunit; nucleotidyltransfera 100.0
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, uni 100.0
2pa8_D265 DNA-directed RNA polymerase subunit D; ferredoxin- 99.96
1twf_C318 B44.5, DNA-directed RNA polymerase II 45 kDa polyp 99.95
3h0g_C297 DNA-directed RNA polymerase II subunit RPB3; trans 99.92
3k4g_A86 DNA-directed RNA polymerase subunit alpha; bacteri 99.88
3gfk_B79 DNA-directed RNA polymerase subunit alpha; protein 99.87
1coo_A98 RNA polymerase alpha subunit; transcription regula 99.87
1z3e_B73 DNA-directed RNA polymerase alpha chain; bacterial 99.86
2xzm_D181 Ribosomal protein S4 containing protein; ribosome, 99.75
3j20_D180 30S ribosomal protein S4P; archaea, archaeal, KINK 99.7
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protei 99.57
3u5c_J197 40S ribosomal protein S9-A; translation, ribosome, 99.55
3iz6_C195 40S ribosomal protein S9 (S4P); eukaryotic ribosom 99.5
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-bindin 98.72
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergen 98.71
3hp7_A291 Hemolysin, putative; structural genomics, APC64019 98.56
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RN 98.53
3j20_E243 30S ribosomal protein S4E; archaea, archaeal, KINK 98.2
3kbg_A213 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2 97.95
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 97.94
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; 97.91
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 97.9
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; 97.52
2pa8_L92 DNA-directed RNA polymerase subunit L; ferredoxin- 96.88
1twf_K120 B13.6, DNA-directed RNA polymerase II 13.6 kDa pol 95.94
1xpp_A115 TA1416, DNA-directed RNA polymerase subunit L; str 95.88
1b22_A114 DNA repair protein RAD51; DNA binding, riken struc 95.71
3h0g_K123 DNA-directed RNA polymerase II subunit RPB11; tran 94.92
1wcn_A70 Transcription elongation protein NUSA; RNA-binding 94.77
1u9l_A70 Transcription elongation protein NUSA; escherichia 94.22
1jil_A420 Tyrrs, tyrosyl-tRNA synthetase; truncation, based 93.76
2jan_A432 Tyrosyl-tRNA synthetase; protein biosynthesis, ami 93.33
1h3f_A432 Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy 93.16
2kz3_A83 Putative uncharacterized protein RAD51L3; RAD51D, 91.35
2ts1_A419 Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30 90.94
3lda_A 400 DNA repair protein RAD51; DNA binding protein, ATP 90.72
2i1q_A 322 DNA repair and recombination protein RADA; ATPase, 90.64
3u5c_E261 RP5, S7, YS6, 40S ribosomal protein S4-A; translat 90.26
2ktl_A164 Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA s 89.8
3iz6_D265 40S ribosomal protein S4 (S4E); eukaryotic ribosom 89.46
2xzm_W260 40S ribosomal protein S4; ribosome, translation; 3 89.37
2z43_A 324 DNA repair and recombination protein RADA; archaea 87.21
1pzn_A 349 RAD51, DNA repair and recombination protein RAD51, 86.28
1v5w_A 343 DMC1, meiotic recombination protein DMC1/LIM15 hom 86.08
4glx_A586 DNA ligase; inhibitor, ligase-ligase inhibitor-DNA 80.52
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A Back     alignment and structure
Probab=100.00  E-value=3.5e-69  Score=556.38  Aligned_cols=243  Identities=56%  Similarity=0.880  Sum_probs=151.7

Q ss_pred             ccccccCCCeeEEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECCcccccccccCccccHHHHH
Q psy8861         194 NDINDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDII  273 (550)
Q Consensus       194 l~inEll~p~~i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~gv~hEfs~i~Gv~Edv~~Ii  273 (550)
                      ..|.++.+|+.+++.+.+++||+|+++|||+|||+|+||||||+|||++||+||++|+|+|+.|||++||||+|||+||+
T Consensus         3 ~~~~~~~~p~~~~v~~~~~~~~kF~l~PlerG~g~TlgNaLRRvLLssvpg~AIt~V~I~gv~Hefs~Ipgv~Edv~eii   82 (329)
T 3lu0_A            3 GSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEIL   82 (329)
T ss_dssp             CSTTTSSSCCCCCEEECTTSEEEEEECCCCTTCHHHHHHHHHHHTTTSSCEEEEEEEEESSCSSTTCCCTTBSSCHHHHH
T ss_pred             hhhhhccCCceEEEEEcCCCEEEEEEEecCCCChhHHHHHHHHHHHhcCCceEEEEEEEeCccccccccccccCCHHHHH
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccceeeeccCceEEEEEEEeceeeEEeccCccCCCeEEeCCCceEEEcC-C--------------------------
Q psy8861         274 LNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLS-D--------------------------  326 (550)
Q Consensus       274 lNLK~i~~~~~~~~~~~~~l~~~Gp~~V~A~DI~~~~~veivnpd~~IatL~-~--------------------------  326 (550)
                      +|||+++|+.++.|++.++|+++||++|||+||++|++|+|+|||+|||||+ +                          
T Consensus        83 lNlK~i~~k~~~~~~~~~~L~~~Gp~~VtA~DI~~~~~veivnpd~~IatL~~~~~~L~me~~i~~G~GY~~a~~~~~~~  162 (329)
T 3lu0_A           83 LNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSE  162 (329)
T ss_dssp             HHHHSCCCEESSCSCEEEEECCCSSSCEETTSSCCCSSEECSCTTCEEECBCSSCCCCCEEEEEEEESSEECTTTSCCCS
T ss_pred             hhhccceEecCCCceEEEEEEEeCCeEEEeeeeccCCCCEEeCCCcEEEEEccCCcEEEEEEEEECcccceechhccccc
Confidence            9999999999989999999999999999999999999999999999999999 5                          


Q ss_pred             --------------------------------------------------hHHHHHHHHHHHHHHhhhhhccCCCCCccc
Q psy8861         327 --------------------------------------------------NEEAIRQSARVLVDQLNVFAALENTPVKKE  356 (550)
Q Consensus       327 --------------------------------------------------P~~Al~~Aa~iL~~~~~~f~~~~~~~~~~~  356 (550)
                                                                        |+||+.+||+||++||++|.+++.......
T Consensus       163 ~~~~~ig~i~iDa~fsPV~~Vny~Ve~~rvgq~td~dkL~leI~TdGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~  242 (329)
T 3lu0_A          163 EDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEV  242 (329)
T ss_dssp             TTSSSCCCEECCEECCCEEEEEEEEEEECCSSCSCEEEEEEEEEECSSSCHHHHHHHHHHHHHHHTTTSSSCC-------
T ss_pred             cccCcCceEeeCCCCCceeeEEEEEeccccCCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhcccccccccc
Confidence                                                              999999999999999999998764333221


Q ss_pred             cCccccccCCcccccccccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhcCcccccccccc
Q psy8861         357 LDSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMRHRHGF  436 (550)
Q Consensus       357 ~~~~~~~~~~~l~~~I~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~gl~lmrhrk~~  436 (550)
                      .++. +..++++.++||+|+||||||||||+|||+||+||+++|++||+++||||+||++||+++|+++||+|++.--.|
T Consensus       243 ~~~~-~~~~~~l~~~I~eLeLsvRs~NCLKra~I~tv~dL~~~se~dLlki~n~G~kSl~EI~~~L~~~gl~l~~~~~~~  321 (329)
T 3lu0_A          243 KEEK-PEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENW  321 (329)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccc-chhhhhhhhhHHhhcCCHHHHHHHHHcCCcCHHHHhhCCHHHHhhCcCCChhhHHHHHHHHHHcCCCcCCccccC
Confidence            1111 345677889999999999999999999999999999999999999999999999999999999999999876655


Q ss_pred             c
Q psy8861         437 R  437 (550)
Q Consensus       437 r  437 (550)
                      .
T Consensus       322 ~  322 (329)
T 3lu0_A          322 P  322 (329)
T ss_dssp             -
T ss_pred             C
Confidence            3
>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3aoh_A* 3aoi_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* ... Back     alignment and structure
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>3r8s_N 50S ribosomal protein L17; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 3fik_N 3j19_N 2wwq_N 3oat_N* 3oas_N* 3ofd_N 3ofc_N 3ofr_N* 3ofz_N* 3og0_N 3ofq_N 3r8t_N 3i1n_N 1p85_L 1p86_L 1vs8_N 1vs6_N 2aw4_N 2awb_N 1vt2_N ... Back     alignment and structure
>1gd8_A 50S ribosomal protein L17; two domains, ribosomal protein S8-like domain, Trp repressor-like domain, helix-turn-helix motif; 2.30A {Thermus thermophilus} SCOP: d.188.1.1 PDB: 1vsa_L 1vsp_L 1yl3_0 2b66_R 2b9n_R 2b9p_R 2hgj_Q 2hgq_Q 2hgu_Q 2j01_R 2j03_R 2jl6_R 2jl8_R 2v47_R 2v49_R 2wdi_R 2wdj_R 2wdl_R 2wdn_R 2wh2_R ... Back     alignment and structure
>2zjr_K 50S ribosomal protein L17; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.188.1.1 PDB: 1nwx_L* 1nwy_L* 1sm1_L* 1xbp_L* 2zjp_K* 2zjq_K 1nkw_L 3cf5_K* 3dll_K* 3pio_K* 3pip_K* 1pnu_L 1pny_L 1vor_O 1vou_O 1vow_O 1voy_O 1vp0_O Back     alignment and structure
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ... Back     alignment and structure
>3bbo_P Ribosomal protein L17; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.2 Back     alignment and structure
>2cqm_A Ribosomal protein L17 isolog; alpha and beta (A+B), structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.188.1.1 PDB: 2ftc_J 3iy9_S Back     alignment and structure
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1 Back     alignment and structure
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C Back     alignment and structure
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D Back     alignment and structure
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ... Back     alignment and structure
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} SCOP: a.60.3.1 PDB: 3n4m_B* 1lb2_B* 3n97_B* 1xs9_D Back     alignment and structure
>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} SCOP: a.60.3.1 Back     alignment and structure
>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli} SCOP: a.60.3.1 PDB: 2jzb_A Back     alignment and structure
>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 PDB: 3ihq_B Back     alignment and structure
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D Back     alignment and structure
>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D* Back     alignment and structure
>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Back     alignment and structure
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6 Back     alignment and structure
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A Back     alignment and structure
>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein STR initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.53A {Streptococcus thermophilus} Back     alignment and structure
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Back     alignment and structure
>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} Back     alignment and structure
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Back     alignment and structure
>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} Back     alignment and structure
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A* Back     alignment and structure
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Back     alignment and structure
>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L 2y0s_L Back     alignment and structure
>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ... Back     alignment and structure
>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} SCOP: d.74.3.2 Back     alignment and structure
>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1 Back     alignment and structure
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B Back     alignment and structure
>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A Back     alignment and structure
>1jil_A Tyrrs, tyrosyl-tRNA synthetase; truncation, based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A* Back     alignment and structure
>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} Back     alignment and structure
>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYE; 2.00A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A* Back     alignment and structure
>2kz3_A Putative uncharacterized protein RAD51L3; RAD51D, homologous recombination, unknown function; NMR {Homo sapiens} Back     alignment and structure
>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A Back     alignment and structure
>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A* Back     alignment and structure
>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A* Back     alignment and structure
>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E Back     alignment and structure
>2ktl_A Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA synthetase, ligase; NMR {Aspergillus nidulans fgsc A4} Back     alignment and structure
>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Back     alignment and structure
>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W Back     alignment and structure
>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A* Back     alignment and structure
>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11 Back     alignment and structure
>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A Back     alignment and structure
>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 550
d2gy9d1204 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherich 9e-67
d2uubd1208 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus t 1e-59
d1c06a_159 d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stear 6e-48
d2qamn1120 d.188.1.1 (N:1-120) Prokaryotic ribosomal protein 1e-46
d2zjrk1113 d.188.1.1 (K:3-115) Prokaryotic ribosomal protein 2e-41
d1gd8a_105 d.188.1.1 (A:) Prokaryotic ribosomal protein L17 { 7e-34
d2cqma1109 d.188.1.1 (A:28-136) Prokaryotic ribosomal protein 5e-31
d1lb2b_72 a.60.3.1 (B:) C-terminal domain of RNA polymerase 3e-26
d1z3eb167 a.60.3.1 (B:245-311) C-terminal domain of RNA poly 3e-25
d1doqa_69 a.60.3.1 (A:) C-terminal domain of RNA polymerase 1e-23
d1bdfa2126 d.181.1.1 (A:53-178) RNA polymerase alpha subunit 3e-22
d1bdfa1105 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha { 3e-20
d1smya2123 d.181.1.1 (A:50-172) RNA polymerase alpha subunit 3e-19
d1smya1106 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha { 7e-18
d1dm9a_104 d.66.1.3 (A:) Heat shock protein 15 kD {Escherichi 2e-11
d1vioa258 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-te 3e-11
d1kska359 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-te 1e-08
d1p9ka_79 d.66.1.6 (A:) Hypothetical protein YbcJ {Escherich 1e-06
>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]} Length = 204 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Escherichia coli [TaxId: 562]

 Score =  213 bits (543), Expect = 9e-67
 Identities = 121/198 (61%), Positives = 155/198 (78%), Gaps = 1/198 (0%)

Query: 3   RYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQKV 62
           RY+GPK KL RREG DLFLKS  R++D+KCK++  PGQHG     R SDYG Q REKQKV
Sbjct: 1   RYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKP-RLSDYGVQLREKQKV 59

Query: 63  KRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHR 122
           +R+YG+LE+QFR Y+ E ARLKG TGE +L LLE R DNVVYRMGF +TR+EARQL+SH+
Sbjct: 60  RRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHK 119

Query: 123 AFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKMEGV 182
           A +VN ++VNIASY++ P D++S+REKAKKQ+R+  +LEL+E     +W+ VDA KMEG 
Sbjct: 120 AIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGT 179

Query: 183 FKSEPNRSEFANDINDLL 200
           FK +P RS+ + DIN+ L
Sbjct: 180 FKRKPERSDLSADINEHL 197
>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]} Length = 208 Back     information, alignment and structure
>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]} Length = 159 Back     information, alignment and structure
>d2qamn1 d.188.1.1 (N:1-120) Prokaryotic ribosomal protein L17 {Escherichia coli [TaxId: 562]} Length = 120 Back     information, alignment and structure
>d2zjrk1 d.188.1.1 (K:3-115) Prokaryotic ribosomal protein L17 {Deinococcus radiodurans [TaxId: 1299]} Length = 113 Back     information, alignment and structure
>d1gd8a_ d.188.1.1 (A:) Prokaryotic ribosomal protein L17 {Thermus thermophilus [TaxId: 274]} Length = 105 Back     information, alignment and structure
>d2cqma1 d.188.1.1 (A:28-136) Prokaryotic ribosomal protein L17 {Human (Homo sapiens) [TaxId: 9606]} Length = 109 Back     information, alignment and structure
>d1lb2b_ a.60.3.1 (B:) C-terminal domain of RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} Length = 72 Back     information, alignment and structure
>d1z3eb1 a.60.3.1 (B:245-311) C-terminal domain of RNA polymerase alpha subunit {Bacillus subtilis [TaxId: 1423]} Length = 67 Back     information, alignment and structure
>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Length = 69 Back     information, alignment and structure
>d1bdfa2 d.181.1.1 (A:53-178) RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} Length = 126 Back     information, alignment and structure
>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Escherichia coli [TaxId: 562]} Length = 105 Back     information, alignment and structure
>d1smya2 d.181.1.1 (A:50-172) RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Length = 123 Back     information, alignment and structure
>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus thermophilus [TaxId: 274]} Length = 106 Back     information, alignment and structure
>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]} Length = 104 Back     information, alignment and structure
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Length = 58 Back     information, alignment and structure
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]} Length = 59 Back     information, alignment and structure
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} Length = 79 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query550
d2gy9d1204 Ribosomal protein S4 {Escherichia coli [TaxId: 562 100.0
d2uubd1208 Ribosomal protein S4 {Thermus thermophilus [TaxId: 100.0
d1c06a_159 Ribosomal protein S4 {Bacillus stearothermophilus 100.0
d2qamn1120 Prokaryotic ribosomal protein L17 {Escherichia col 100.0
d2zjrk1113 Prokaryotic ribosomal protein L17 {Deinococcus rad 100.0
d1gd8a_105 Prokaryotic ribosomal protein L17 {Thermus thermop 100.0
d2cqma1109 Prokaryotic ribosomal protein L17 {Human (Homo sap 100.0
d1bdfa2126 RNA polymerase alpha subunit {Escherichia coli [Ta 99.94
d1smya2123 RNA polymerase alpha subunit {Thermus thermophilus 99.94
d1lb2b_72 C-terminal domain of RNA polymerase alpha subunit 99.88
d1z3eb167 C-terminal domain of RNA polymerase alpha subunit 99.86
d1doqa_69 C-terminal domain of RNA polymerase alpha subunit 99.84
d1bdfa1105 RNA polymerase alpha {Escherichia coli [TaxId: 562 99.73
d1smya1106 RNA polymerase alpha {Thermus thermophilus [TaxId: 99.54
d1dm9a_104 Heat shock protein 15 kD {Escherichia coli [TaxId: 99.47
d1kska359 Pseudouridine synthase RsuA N-terminal domain {Esc 99.24
d1vioa258 Pseudouridine synthase RsuA N-terminal domain {Hae 99.23
d1p9ka_79 Hypothetical protein YbcJ {Escherichia coli [TaxId 99.03
d1twfc1135 RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta 97.8
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker 97.78
d1h3fa281 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 97.67
d1b22a_70 DNA repair protein Rad51, N-terminal domain {Human 97.43
d1jh3a_99 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 97.06
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 95.95
d1xppa_99 DNA-directed RNA polymerase subunit L, RpoL {Therm 95.67
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 95.28
d1twfk_114 RPB11 {Baker's yeast (Saccharomyces cerevisiae) [T 91.76
d1twfc2131 RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta 87.98
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 86.89
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 86.05
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filif 84.91
d1jx4a2240 DinB homolog (DBH) {Archaeon Sulfolobus solfataric 82.8
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 81.74
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 81.13
>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=3.5e-61  Score=464.44  Aligned_cols=198  Identities=61%  Similarity=1.028  Sum_probs=188.0

Q ss_pred             CCCCCchhhhhhcCCCCccccccccccccccCCCCCCCCCCCCcccccchhhhhHhhhhhHhhhCCcHHHHHHHHHHhhc
Q psy8861           3 RYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQKVKRMYGILEKQFRRYFIEGAR   82 (550)
Q Consensus         3 r~~gp~~Ki~Rrlg~~l~~~~~~~~~~~k~~~~~~pg~~~~~~~~k~s~y~~~L~~Kqkl~~~YG~~ekq~~~~~~~a~~   82 (550)
                      ||+||++|+|||+|+++|++++.++++.++..+++|||||.+++ |.|+||.||+||||+|++||++|+||++||++|.+
T Consensus         1 Ry~GPk~Ki~RRlG~~l~~~~~~~~~~~~~~~~~~PG~hg~~~~-k~S~yg~qL~EKQklr~~YGi~EkQ~~~~~~~a~~   79 (204)
T d2gy9d1           1 RYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKP-RLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAAR   79 (204)
T ss_dssp             CCCSCCHHHHHHHSSCCCSSTTSSSCSGGGTCCSCSSSSSSSCC-CCCHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCchhhhcccCCCCcccCCCCccccccccccCCCCCCCCCCC-cccHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHH
Confidence            89999999999999999988666777777777899999998654 89999999999999999999999999999999999


Q ss_pred             cCCCchHHHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCchhhHHHHhhhhc
Q psy8861          83 LKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLEL  162 (550)
Q Consensus        83 ~~g~~~~~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~~~~~~i~~~~~~  162 (550)
                      .+|+|+++|+++||+|||++|||+|||+|+.+|||||+||||+|||++||+|||.|++||+|+|++++++...++++++.
T Consensus        80 ~~g~tg~~l~~~LE~RLDnvv~R~gfa~t~~~ARQ~v~Hghi~VNgk~VnIPSy~vk~GDvIsvkeksk~~~~i~~~~e~  159 (204)
T d2gy9d1          80 LKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALEL  159 (204)
T ss_dssp             SSSCHHHHHHHHHTTBHHHHHHHHTSSSSHHHHHHHHHTTCEEESSSBCCCTTCBCCTTCBEEECTTGGGCHHHHHHHHH
T ss_pred             cCCcHHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHhcceecCCEEEEeccEeecCCCEEEeccchhHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCCCCCCCcEEEecCccEEEEecccCcccccccccccCC
Q psy8861         163 SEHSTPFSWITVDAKKMEGVFKSEPNRSEFANDINDLLK  201 (550)
Q Consensus       163 ~~~~~~p~~l~vd~~~~~g~~~~~P~~~~Ipl~inEll~  201 (550)
                      .....+|+||++|.++++|+|++.|+++|||.++||+++
T Consensus       160 ~~~~~~P~wLevd~~~l~g~v~~~P~reei~~~ineqLV  198 (204)
T d2gy9d1         160 AEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLI  198 (204)
T ss_dssp             HTTCCCCTTEEEETTTTEEEECSCCCTTTCCCSCCHHHH
T ss_pred             cccCCCCCeEEEecccCEEEEEeccCHHHCCCCCCccEE
Confidence            766788999999999999999999999999999999764
>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d2qamn1 d.188.1.1 (N:1-120) Prokaryotic ribosomal protein L17 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2zjrk1 d.188.1.1 (K:3-115) Prokaryotic ribosomal protein L17 {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d1gd8a_ d.188.1.1 (A:) Prokaryotic ribosomal protein L17 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2cqma1 d.188.1.1 (A:28-136) Prokaryotic ribosomal protein L17 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1bdfa2 d.181.1.1 (A:53-178) RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1smya2 d.181.1.1 (A:50-172) RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1lb2b_ a.60.3.1 (B:) C-terminal domain of RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1z3eb1 a.60.3.1 (B:245-311) C-terminal domain of RNA polymerase alpha subunit {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1twfc1 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1xppa_ d.74.3.2 (A:) DNA-directed RNA polymerase subunit L, RpoL {Thermoplasma acidophilum [TaxId: 2303]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d1twfk_ d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1twfc2 d.181.1.1 (C:42-172) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} Back     information, alignment and structure
>d1jx4a2 e.8.1.7 (A:1-240) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]} Back     information, alignment and structure
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure