Psyllid ID: psy1580

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 (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-------
MKHQEPHGRKMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILKEDGGAASCSESSESSVNNPLLYAENTSPVENLTPPEYTLVDPAFNRIQPATEAINIPTKTMTTAALVNRKRPLLTAGSSRPTMSPTKRTVLSILTRARVSQSKPTGVLATSKHHYITNG
cccccccccccccccccccccEEEEEEEcccccccccEEEEEEcccccHHHHHHHHHccEEEEEcccccccccHHHHHHccccccccccccccEEEEEEcccHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccccccccccc
cccccccccEEEEEEccccEEEEEEEEEEccccccccEEEEEccccccHHHHHHHHcccEEEEEcccccccHHHHHHHHHccccccHHcccccEEEEEEEccHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccHHHccccccEEEEcccEEEEcc
mkhqephgrkmvditrdkpikvTIRVivpvrdhpkfnfvgkllgpkgnslkRLQEDTMTRMAILGrgsirdrhkeeelrisgdpKFLHLLEELHVEitafappaEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILkedggaascsessessvnnpllyaentspvenltppeytlvdpafnriqpateainiptktMTTAALvnrkrplltagssrptmsptkrTVLSILTRarvsqskptgvlatskHHYITNG
mkhqephgrkmvditrdkpikvtirvivpvrdhpkfnfvgkllgpkgnslKRLQEDTMTRmailgrgsirdrhkeeelrisgdPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILKEDGGAASCSESSESSVNNPLLYAENTSPVENLTPPEYTLVDPAFNRIQPateainiptktmttaalvnrkrplltagssrptmsptkrTVLSILtrarvsqskptgvlatskhhyitng
MKHQEPHGRKMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILKEDGGAAscsessessVNNPLLYAENTSPVENLTPPEYTLVDPAFNRIQPATEAINIPTKTMTTAALVNRKRPLLTAGSSRPTMSPTKRTVLSILTRARVSQSKPTGVLATSKHHYITNG
*************ITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGP*****************IL***************ISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQIL************************************EYTLVDPAFNRIQPATEAINIPTKTMTTAALV****************************************************
************DITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAI*************************LLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQD*NDEIRQEQMWEMQ**************************************************************************************************************************
*********KMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILK****************NNPLLYAENTSPVENLTPPEYTLVDPAFNRIQPATEAINIPTKTMTTAALVNRKRPLLTAGSSRPTMSPTKRTVLSILTRAR**********ATSKHHYITNG
*****PHGRKMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILKED*******************************************RIQPATEAINIPTK********N**RPLLTAGSSRPTMSPTKRTVLSILTRARVSQSKPTGVLATSKHHYITNG
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MKHQEPHGRKMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILKEDGGAASCSESSESSVNNPLLYAENTSPVENLTPPEYTLVDPAFNRIQPATEAINIPTKTMTTAALVNRKRPLLTAGSSRPTMSPTKRTVLSILTRARVSQSKPTGVLATSKHHYITNG
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 ?
Query267 2.2.26 [Sep-21-2011]
Q9R226346 KH domain-containing, RNA yes N/A 0.756 0.583 0.428 9e-44
Q920F3349 KH domain-containing, RNA yes N/A 0.513 0.392 0.569 1e-43
Q5VWX1349 KH domain-containing, RNA yes N/A 0.513 0.392 0.569 1e-43
Q9WU01349 KH domain-containing, RNA no N/A 0.513 0.392 0.569 2e-43
Q9JLP1346 KH domain-containing, RNA no N/A 0.726 0.560 0.431 4e-43
O75525346 KH domain-containing, RNA no N/A 0.550 0.424 0.528 4e-43
Q08BJ2346 KH domain-containing, RNA yes N/A 0.494 0.381 0.575 5e-43
Q0VFL3345 KH domain-containing, RNA no N/A 0.516 0.4 0.558 2e-41
Q91V33443 KH domain-containing, RNA no N/A 0.483 0.291 0.514 7e-36
Q60749443 KH domain-containing, RNA no N/A 0.483 0.291 0.514 8e-36
>sp|Q9R226|KHDR3_MOUSE KH domain-containing, RNA-binding, signal transduction-associated protein 3 OS=Mus musculus GN=Khdrbs3 PE=1 SV=1 Back     alignment and function desciption
 Score =  177 bits (448), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 99/231 (42%), Positives = 146/231 (63%), Gaps = 29/231 (12%)

Query: 2   KHQEPHGR---KMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTM 58
           K Q+  G+   K +D+  +K +K+  +V++PV+  PKFNFVGKLLGP+GNSLKRLQE+T+
Sbjct: 33  KFQKGEGKEEEKYIDVVINKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETL 92

Query: 59  TRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVR 118
           T+M+ILG+GS+RD+ KEEELR SG+ K+ HL ++LHV I  FAPPAEA+AR+ +AL E++
Sbjct: 93  TKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVLIEVFAPPAEAYARMGHALEEIK 152

Query: 119 RFLVPFTRSLFQDYNDEIRQEQMWEMQILKEDGGAASCSESSESSVNNPLLYAENTSPVE 178
           +FL+P       DYNDEIRQ Q+ E+  L  +GG+ +         + P++  ++T    
Sbjct: 153 KFLIP-------DYNDEIRQAQLQELTYL--NGGSENA--------DVPVVRGKSTLRTR 195

Query: 179 NLTPPEYTLVDPAFNRIQPATEAINIPTKT------MTTAALVNRKRPLLT 223
            +T P  T        +     A+ +P  T      ++T   V+R R LLT
Sbjct: 196 GVTTPAITR---GRGGVTARPVAVGVPRGTPTPRGVLSTRGPVSRGRGLLT 243
RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. May play a role as a negative regulator of cell growth. Inhibits cell proliferation. Involved in splice site selection of vascular endothelial growth factor. Induces an increased concentration-dependent incorporation of exon in CD44 pre-mRNA by direct binding to purine-rich exonic enhancer. RNA-binding abilities are down-regulated by tyrosine kinase PTK6. Binds preferentially to the 5'-[AU]UAAA-3' motif in vitro.
Mus musculus (taxid: 10090)
>sp|Q920F3|KHDR2_RAT KH domain-containing, RNA-binding, signal transduction-associated protein 2 OS=Rattus norvegicus GN=Khdrbs2 PE=1 SV=1 Back     alignment and function description
>sp|Q5VWX1|KHDR2_HUMAN KH domain-containing, RNA-binding, signal transduction-associated protein 2 OS=Homo sapiens GN=KHDRBS2 PE=1 SV=1 Back     alignment and function description
>sp|Q9WU01|KHDR2_MOUSE KH domain-containing, RNA-binding, signal transduction-associated protein 2 OS=Mus musculus GN=Khdrbs2 PE=1 SV=1 Back     alignment and function description
>sp|Q9JLP1|KHDR3_RAT KH domain-containing, RNA-binding, signal transduction-associated protein 3 OS=Rattus norvegicus GN=Khdrbs3 PE=1 SV=1 Back     alignment and function description
>sp|O75525|KHDR3_HUMAN KH domain-containing, RNA-binding, signal transduction-associated protein 3 OS=Homo sapiens GN=KHDRBS3 PE=1 SV=1 Back     alignment and function description
>sp|Q08BJ2|KHDR2_DANRE KH domain-containing, RNA-binding, signal transduction-associated protein 2 OS=Danio rerio GN=khdrbs2 PE=2 SV=1 Back     alignment and function description
>sp|Q0VFL3|KHDR2_XENTR KH domain-containing, RNA-binding, signal transduction-associated protein 2 OS=Xenopus tropicalis GN=khdrbs2 PE=2 SV=1 Back     alignment and function description
>sp|Q91V33|KHDR1_RAT KH domain-containing, RNA-binding, signal transduction-associated protein 1 OS=Rattus norvegicus GN=Khdrbs1 PE=1 SV=1 Back     alignment and function description
>sp|Q60749|KHDR1_MOUSE KH domain-containing, RNA-binding, signal transduction-associated protein 1 OS=Mus musculus GN=Khdrbs1 PE=1 SV=2 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 ?
Query267
193688144318 PREDICTED: KH domain-containing, RNA-bin 0.902 0.757 0.579 2e-71
189239469310 PREDICTED: similar to AGAP003355-PA [Tri 0.838 0.722 0.576 1e-64
345489725359 PREDICTED: hypothetical protein LOC10011 0.760 0.565 0.580 2e-60
195441840 435 GK17902 [Drosophila willistoni] gi|19416 0.569 0.349 0.691 3e-59
347969752 466 AGAP003355-PA [Anopheles gambiae str. PE 0.561 0.321 0.668 7e-59
195027135 429 GH21368 [Drosophila grimshawi] gi|193902 0.486 0.303 0.766 2e-58
195384515 424 GJ19910 [Drosophila virilis] gi|19414576 0.486 0.306 0.766 4e-58
282158097367 quaking related [Tribolium castaneum] 0.771 0.561 0.478 3e-52
270010990340 quaking related [Tribolium castaneum] 0.771 0.605 0.478 4e-52
209418000 492 IP21806p [Drosophila melanogaster] 0.610 0.331 0.656 5e-52
>gi|193688144|ref|XP_001946009.1| PREDICTED: KH domain-containing, RNA-binding, signal transduction-associated protein 2-like [Acyrthosiphon pisum] Back     alignment and taxonomy information
 Score =  274 bits (701), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 153/264 (57%), Positives = 184/264 (69%), Gaps = 23/264 (8%)

Query: 9   RKMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGS 68
           R+MVDITRDKPIKV+IRV VPVRDHPKFNFVGKLLGPKGNSLKRLQEDT+T+MAILGRGS
Sbjct: 41  RRMVDITRDKPIKVSIRVAVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTITKMAILGRGS 100

Query: 69  IRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSL 128
           +RDR+KEE+LR SGDPKF HL ++LHVEITAFAPPAEAHARIAYAL EVRRFLVP     
Sbjct: 101 MRDRNKEEKLRNSGDPKFSHLKDDLHVEITAFAPPAEAHARIAYALTEVRRFLVP----- 155

Query: 129 FQDYNDEIRQEQMWEMQILKEDGGAAS-----CSESSESSVNNPLLYAENTSPVENLTPP 183
             DYNDEIRQEQMWEMQIL++  G A+      S SS  SV++     +N S V   +  
Sbjct: 156 --DYNDEIRQEQMWEMQILQKGSGDATDSETGESGSSSHSVDD---NRQNYSAVH--SAG 208

Query: 184 EYTLVDPAFNRIQPATEAIN------IPTKTMTTAALVNRKRPLLTAGSSRPTMSPTKRT 237
           E + V    + +      IN       P  +        RKRPLL+   ++ +M+P+KRT
Sbjct: 209 ECSPVHTKHSNVNTNQTIINGSEKHVAPNNSNGLTETPGRKRPLLSGECAKVSMTPSKRT 268

Query: 238 VLSILTRARVSQSKPTGVLATSKH 261
           V++IL RAR +Q     ++  S H
Sbjct: 269 VMAILARARTAQVHVKDMVTFSPH 292

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|189239469|ref|XP_975258.2| PREDICTED: similar to AGAP003355-PA [Tribolium castaneum] gi|270010553|gb|EFA07001.1| hypothetical protein TcasGA2_TC009970 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|345489725|ref|XP_001602161.2| PREDICTED: hypothetical protein LOC100118106 [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|195441840|ref|XP_002068671.1| GK17902 [Drosophila willistoni] gi|194164756|gb|EDW79657.1| GK17902 [Drosophila willistoni] Back     alignment and taxonomy information
>gi|347969752|ref|XP_001230997.3| AGAP003355-PA [Anopheles gambiae str. PEST] gi|333469255|gb|EAU76797.3| AGAP003355-PA [Anopheles gambiae str. PEST] Back     alignment and taxonomy information
>gi|195027135|ref|XP_001986439.1| GH21368 [Drosophila grimshawi] gi|193902439|gb|EDW01306.1| GH21368 [Drosophila grimshawi] Back     alignment and taxonomy information
>gi|195384515|ref|XP_002050963.1| GJ19910 [Drosophila virilis] gi|194145760|gb|EDW62156.1| GJ19910 [Drosophila virilis] Back     alignment and taxonomy information
>gi|282158097|ref|NP_001164092.1| quaking related [Tribolium castaneum] Back     alignment and taxonomy information
>gi|270010990|gb|EFA07438.1| quaking related [Tribolium castaneum] Back     alignment and taxonomy information
>gi|209418000|gb|ACI46538.1| IP21806p [Drosophila melanogaster] 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 ?
Query267
FB|FBgn0034731 470 CG10384 [Drosophila melanogast 0.486 0.276 0.766 2.6e-61
FB|FBgn0022987428 qkr54B "quaking related 54B" [ 0.483 0.301 0.625 8.6e-45
UNIPROTKB|E2QWN2349 KHDRBS2 "Uncharacterized prote 0.531 0.406 0.562 2e-40
UNIPROTKB|Q5VWX1349 KHDRBS2 "KH domain-containing, 0.531 0.406 0.562 2e-40
UNIPROTKB|F1RZV6277 KHDRBS2 "Uncharacterized prote 0.531 0.512 0.562 2e-40
UNIPROTKB|E1BP48348 KHDRBS2 "Uncharacterized prote 0.528 0.405 0.566 4.2e-40
MGI|MGI:2159649349 Khdrbs2 "KH domain containing, 0.531 0.406 0.556 5.3e-40
RGD|621738349 Khdrbs2 "KH domain containing, 0.531 0.406 0.556 5.3e-40
UNIPROTKB|E1BVW8348 KHDRBS2 "Uncharacterized prote 0.513 0.393 0.569 8.7e-40
UNIPROTKB|F1NKE9327 KHDRBS3 "Uncharacterized prote 0.535 0.437 0.541 1.1e-39
FB|FBgn0034731 CG10384 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 543 (196.2 bits), Expect = 2.6e-61, Sum P(2) = 2.6e-61
 Identities = 105/137 (76%), Positives = 119/137 (86%)

Query:    11 MVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIR 70
             M+DITRDKP+KV ++V VPVRDHPKFNFVGKLLGPKGNS+KRLQEDTM +MA+LGRGS+R
Sbjct:     1 MLDITRDKPVKVAVKVAVPVRDHPKFNFVGKLLGPKGNSMKRLQEDTMCKMAVLGRGSMR 60

Query:    71 DRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQ 130
             DR KEEELR SGD ++ HL E+LHVEI+ FA PAEAHARIAYALAEVRRFLVP       
Sbjct:    61 DRRKEEELRGSGDSRYAHLFEDLHVEISTFAAPAEAHARIAYALAEVRRFLVP------- 113

Query:   131 DYNDEIRQEQMWEMQIL 147
             DY+D+IRQEQMWEMQ L
Sbjct:   114 DYHDDIRQEQMWEMQAL 130
GO:0003723 "RNA binding" evidence=IEA
FB|FBgn0022987 qkr54B "quaking related 54B" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|E2QWN2 KHDRBS2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q5VWX1 KHDRBS2 "KH domain-containing, RNA-binding, signal transduction-associated protein 2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1RZV6 KHDRBS2 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|E1BP48 KHDRBS2 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
MGI|MGI:2159649 Khdrbs2 "KH domain containing, RNA binding, signal transduction associated 2" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|621738 Khdrbs2 "KH domain containing, RNA binding, signal transduction associated 2" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|E1BVW8 KHDRBS2 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1NKE9 KHDRBS3 "Uncharacterized protein" [Gallus gallus (taxid:9031)] 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) ?
Q08BJ2KHDR2_DANRENo assigned EC number0.57550.49430.3815yesN/A
Q5VWX1KHDR2_HUMANNo assigned EC number0.56940.51310.3925yesN/A
Q920F3KHDR2_RATNo assigned EC number0.56940.51310.3925yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

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 ?
Query267
cd02395120 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K ho 1e-42
COG5176269 COG5176, MSL5, Splicing factor (branch point bindi 4e-10
smart0032268 smart00322, KH, K homology RNA-binding domain 8e-06
cd0010564 cd00105, KH-I, K homology RNA-binding domain, type 1e-05
pfam0001359 pfam00013, KH_1, KH domain 0.002
pfam1301442 pfam13014, KH_3, KH domain 0.003
>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology RNA-binding domain (KH) Back     alignment and domain information 
 Score =  141 bits (357), Expect = 1e-42
 Identities = 53/125 (42%), Positives = 82/125 (65%), Gaps = 10/125 (8%)

Query: 23  TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISG 82
           T +V +PV+ +PK+NFVG +LGP+GN+LK+L+++T  +++I G+GS++D  KEEELR   
Sbjct: 1   TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPK 60

Query: 83  DPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMW 142
                HL E LHV ITA  PP EA A+   A+ E+ +  +          NDE+++EQ+ 
Sbjct: 61  YA---HLNEPLHVLITAETPPEEALAKAVEAIEELLKPAIE-------GGNDELKREQLR 110

Query: 143 EMQIL 147
           E+ +L
Sbjct: 111 ELALL 115

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 120
>gnl|CDD|227503 COG5176, MSL5, Splicing factor (branch point binding protein) [RNA processing and modification] Back     alignment and domain information
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain Back     alignment and domain information
>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I Back     alignment and domain information
>gnl|CDD|215657 pfam00013, KH_1, KH domain Back     alignment and domain information
>gnl|CDD|221895 pfam13014, KH_3, KH domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 267
KOG1588|consensus259 100.0
KOG0119|consensus 554 100.0
cd02395120 SF1_like-KH Splicing factor 1 (SF1) K homology RNA 100.0
COG5176269 MSL5 Splicing factor (branch point binding protein 99.96
cd0010564 KH-I K homology RNA-binding domain, type I. KH bin 98.45
cd0239361 PNPase_KH Polynucleotide phosphorylase (PNPase) K 98.4
smart0032269 KH K homology RNA-binding domain. 98.35
PF0001360 KH_1: KH domain syndrome, contains KH motifs.; Int 98.19
PF1301443 KH_3: KH domain 98.15
cd0239665 PCBP_like_KH K homology RNA-binding domain, PCBP_l 98.11
cd0239462 vigilin_like_KH K homology RNA-binding domain_vigi 98.06
KOG1960|consensus531 97.79
COG5082190 AIR1 Arginine methyltransferase-interacting protei 97.47
TIGR03665172 arCOG04150 arCOG04150 universal archaeal KH domain 97.36
PRK13763180 putative RNA-processing protein; Provisional 97.34
PRK13763180 putative RNA-processing protein; Provisional 97.01
TIGR03665172 arCOG04150 arCOG04150 universal archaeal KH domain 97.0
COG1094194 Predicted RNA-binding protein (contains KH domains 96.85
TIGR02696719 pppGpp_PNP guanosine pentaphosphate synthetase I/p 96.73
KOG1676|consensus 600 96.63
PTZ00368148 universal minicircle sequence binding protein (UMS 96.38
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransfe 96.34
KOG1676|consensus 600 96.06
KOG2193|consensus584 95.78
PTZ00368148 universal minicircle sequence binding protein (UMS 95.59
PF0009818 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi 95.52
PRK04163235 exosome complex RNA-binding protein Rrp4; Provisio 95.26
PLN00207891 polyribonucleotide nucleotidyltransferase; Provisi 95.01
KOG4400|consensus261 94.96
KOG2190|consensus 485 94.52
PRK11824693 polynucleotide phosphorylase/polyadenylase; Provis 94.3
KOG2874|consensus356 93.64
KOG2814|consensus345 93.3
COG5082190 AIR1 Arginine methyltransferase-interacting protei 92.75
PF1369632 zf-CCHC_2: Zinc knuckle 92.63
KOG2191|consensus 402 92.54
KOG2193|consensus 584 92.16
KOG1960|consensus 531 90.58
KOG4400|consensus261 89.91
TIGR03319514 YmdA_YtgF conserved hypothetical protein YmdA/YtgF 89.59
KOG2191|consensus402 89.12
PF0009818 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi 88.76
COG1185692 Pnp Polyribonucleotide nucleotidyltransferase (pol 88.73
PRK00106535 hypothetical protein; Provisional 88.72
cd0213461 NusA_KH NusA_K homology RNA-binding domain (KH). N 88.38
PF1391742 zf-CCHC_3: Zinc knuckle 88.28
PF1528840 zf-CCHC_6: Zinc knuckle 87.47
PRK12704520 phosphodiesterase; Provisional 86.91
KOG0336|consensus 629 86.9
PF1391742 zf-CCHC_3: Zinc knuckle 83.81
KOG2190|consensus485 83.2
PF12353128 eIF3g: Eukaryotic translation initiation factor 3 82.95
KOG2113|consensus 394 81.75
PF1318469 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW 81.69
>KOG1588|consensus Back     alignment and domain information 
Probab=100.00  E-value=1.9e-50  Score=368.15  Aligned_cols=140  Identities=54%  Similarity=0.857  Sum_probs=132.8

Q ss_pred             CCCCCCccccCCCCCcceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCC
Q psy1580           5 EPHGRKMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDP   84 (267)
Q Consensus         5 ~~~~~~~~d~~~~kp~k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp   84 (267)
                      +++.+.|.|+++.+++|+++||+|||++||+||||||||||||||+||||++|||||+||||||+||..+|++||  +||
T Consensus        75 ~~~~~~~~~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR--~~p  152 (259)
T KOG1588|consen   75 EPEELPYADVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELR--GDP  152 (259)
T ss_pred             CchhcccccCccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhh--cCc
Confidence            678888889999999999999999999999999999999999999999999999999999999999999999999  499


Q ss_pred             ccCCCCCccEEEEEecCChhHHHHHHHHHHHHHHHhhcCCCcCCCCcchhHHHHHHHHHHHHhhCCCCC
Q psy1580          85 KFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILKEDGGA  153 (267)
Q Consensus        85 ~~~hl~EpLHVlIsa~~~~~~a~~rl~~Av~~I~~lL~P~~~s~~~d~~DelK~~QL~ELA~lNGt~r~  153 (267)
                      +|+||++||||+|++++++++|+.||++|+++|++||+|..       +|+.|++||+|||++||||..
T Consensus       153 ~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~~-------e~~dk~~QL~ELa~lngt~~~  214 (259)
T KOG1588|consen  153 GYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPDH-------EDEDKREQLRELAILNGTYLR  214 (259)
T ss_pred             chHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCC-------CCchHHHHHHHHhhcCCcccc
Confidence            99999999999999999999999999999999999999954       455599999999999999543

>KOG0119|consensus Back     alignment and domain information
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH) Back     alignment and domain information
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification] Back     alignment and domain information
>cd00105 KH-I K homology RNA-binding domain, type I Back     alignment and domain information
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH) Back     alignment and domain information
>smart00322 KH K homology RNA-binding domain Back     alignment and domain information
>PF00013 KH_1: KH domain syndrome, contains KH motifs Back     alignment and domain information
>PF13014 KH_3: KH domain Back     alignment and domain information
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like Back     alignment and domain information
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like Back     alignment and domain information
>KOG1960|consensus Back     alignment and domain information
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] Back     alignment and domain information
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein Back     alignment and domain information
>PRK13763 putative RNA-processing protein; Provisional Back     alignment and domain information
>PRK13763 putative RNA-processing protein; Provisional Back     alignment and domain information
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein Back     alignment and domain information
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only] Back     alignment and domain information
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase Back     alignment and domain information
>KOG1676|consensus Back     alignment and domain information
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>KOG1676|consensus Back     alignment and domain information
>KOG2193|consensus Back     alignment and domain information
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional Back     alignment and domain information
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional Back     alignment and domain information
>KOG4400|consensus Back     alignment and domain information
>KOG2190|consensus Back     alignment and domain information
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>KOG2874|consensus Back     alignment and domain information
>KOG2814|consensus Back     alignment and domain information
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] Back     alignment and domain information
>PF13696 zf-CCHC_2: Zinc knuckle Back     alignment and domain information
>KOG2191|consensus Back     alignment and domain information
>KOG2193|consensus Back     alignment and domain information
>KOG1960|consensus Back     alignment and domain information
>KOG4400|consensus Back     alignment and domain information
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF Back     alignment and domain information
>KOG2191|consensus Back     alignment and domain information
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK00106 hypothetical protein; Provisional Back     alignment and domain information
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH) Back     alignment and domain information
>PF13917 zf-CCHC_3: Zinc knuckle Back     alignment and domain information
>PF15288 zf-CCHC_6: Zinc knuckle Back     alignment and domain information
>PRK12704 phosphodiesterase; Provisional Back     alignment and domain information
>KOG0336|consensus Back     alignment and domain information
>PF13917 zf-CCHC_3: Zinc knuckle Back     alignment and domain information
>KOG2190|consensus Back     alignment and domain information
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes Back     alignment and domain information
>KOG2113|consensus Back     alignment and domain information
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A 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 ?
Query267
2bl5_A140 Solution Structure Of The Kh-Qua2 Region Of The Xen 8e-19
1k1g_A131 Structural Basis For Recognition Of The Intron Bran 2e-07
>pdb|2BL5|A Chain A, Solution Structure Of The Kh-Qua2 Region Of The Xenopus Star-Gsg Quaking Protein Length = 140 Back     alignment and structure 
Iteration: 1

 Score = 90.5 bits (223), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 46/123 (37%), Positives = 78/123 (63%), Gaps = 7/123 (5%)
Query: 25  RVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDP 84
           ++ VPV+++P FNFVG++LGP+G + K+L+ +T  ++ + G+GS+RD+ KEE+ R  G P
Sbjct: 5   KLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKP 62
Query: 85  KFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEM 144
            + HL E+LHV IT       A  ++  A+ EV++ LVP          D +++ ++ E+
Sbjct: 63  NWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEG-----EDSLKKMKLMEL 117
Query: 145 QIL 147
            IL
Sbjct: 118 AIL 120
>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site Rna By Splicing Factor 1 Length = 131 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 ?
Query267
2bl5_A140 MGC83862 protein, quaking protein; STAR proteins, 2e-39
1k1g_A131 SF1-BO isoform; splicing, branch point sequence, p 3e-35
2yqr_A119 KIAA0907 protein; structure genomics, KH domain, s 1e-11
2cte_A94 Vigilin; K homology type I domain, RNA-binding, ce 3e-06
1x4m_A94 FAR upstream element binding protein 1; KH domain, 7e-06
2dgr_A83 Ring finger and KH domain-containing protein 1; st 7e-06
2jvz_A164 KH type-splicing, FAR upstream element-binding pro 2e-05
2jvz_A164 KH type-splicing, FAR upstream element-binding pro 2e-05
1dtj_A76 RNA-binding neurooncological ventral antigen 2; KH 3e-05
2opv_A85 KHSRP protein; KH domain, RNA binding protein, KSR 6e-05
1ec6_A87 RNA-binding protein NOVA-2; KH domain, alpha-beta 9e-05
2axy_A73 Poly(RC)-binding protein 2; protein-DNA complex, D 1e-04
1vig_A71 Vigilin; RNA-binding protein, ribonucleoprotein; N 3e-04
1j4w_A174 FUSE binding protein; single-stranded DNA binding 4e-04
2ctk_A104 Vigilin; K homology type I domain, RNA-binding, ce 5e-04
2anr_A178 Neuro-oncological ventral antigen 1; protein-RNA c 7e-04
>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1 Length = 140 Back     alignment and structure
 Score =  133 bits (335), Expect = 2e-39
 Identities = 46/127 (36%), Positives = 81/127 (63%), Gaps = 7/127 (5%)

Query: 21  KVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRI 80
           ++  ++ VPV+++P FNFVG++LGP+G + K+L+ +T  ++ + G+GS+RD+ KEE+ R 
Sbjct: 1   QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR- 59

Query: 81  SGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQ 140
            G P + HL E+LHV IT       A  ++  A+ EV++ LVP       +  D +++ +
Sbjct: 60  -GKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVP-----AAEGEDSLKKMK 113

Query: 141 MWEMQIL 147
           + E+ IL
Sbjct: 114 LMELAIL 120
>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 131 Back     alignment and structure
>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 119 Back     alignment and structure
>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94 Back     alignment and structure
>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94 Back     alignment and structure
>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83 Back     alignment and structure
>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164 Back     alignment and structure
>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164 Back     alignment and structure
>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76 Back     alignment and structure
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85 Back     alignment and structure
>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87 Back     alignment and structure
>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73 Back     alignment and structure
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71 Back     alignment and structure
>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174 Back     alignment and structure
>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104 Back     alignment and structure
>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query267
2bl5_A140 MGC83862 protein, quaking protein; STAR proteins, 100.0
1k1g_A131 SF1-BO isoform; splicing, branch point sequence, p 100.0
2yqr_A119 KIAA0907 protein; structure genomics, KH domain, s 99.95
2opv_A85 KHSRP protein; KH domain, RNA binding protein, KSR 98.79
1dtj_A76 RNA-binding neurooncological ventral antigen 2; KH 98.74
1x4m_A94 FAR upstream element binding protein 1; KH domain, 98.66
1ec6_A87 RNA-binding protein NOVA-2; KH domain, alpha-beta 98.5
2p2r_A76 Poly(RC)-binding protein 2; protein-DNA complex, R 98.49
1we8_A104 Tudor and KH domain containing protein; structural 98.48
2dgr_A83 Ring finger and KH domain-containing protein 1; st 98.46
2axy_A73 Poly(RC)-binding protein 2; protein-DNA complex, D 98.43
1zzk_A82 Heterogeneous nuclear ribonucleoprotein K; KH domi 98.43
2hh2_A107 KH-type splicing regulatory protein; KH-RNA bindin 98.41
1wvn_A82 Poly(RC)-binding protein 1; KH domain, RNA binding 98.41
1x4n_A92 FAR upstream element binding protein 1; KH domain, 98.4
2cte_A94 Vigilin; K homology type I domain, RNA-binding, ce 98.38
2hh3_A106 KH-type splicing regulatory protein; KH-RNA bindin 98.37
1vig_A71 Vigilin; RNA-binding protein, ribonucleoprotein; N 98.26
1j5k_A89 Heterogeneous nuclear ribonucleoprotein K; single- 98.25
2ctm_A95 Vigilin; K homology type I domain, RNA-binding, ce 98.24
2ctl_A97 Vigilin; K homology type I domain, RNA-binding, ce 98.12
2ctk_A104 Vigilin; K homology type I domain, RNA-binding, ce 98.11
3krm_A163 Insulin-like growth factor 2 mRNA-binding protein 98.1
2jvz_A164 KH type-splicing, FAR upstream element-binding pro 97.96
2jzx_A160 Poly(RC)-binding protein 2; PCBP2, KH domains, RNA 97.9
1j4w_A174 FUSE binding protein; single-stranded DNA binding 97.85
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 97.81
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 97.79
1j4w_A174 FUSE binding protein; single-stranded DNA binding 97.76
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 97.75
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 97.74
2jzx_A160 Poly(RC)-binding protein 2; PCBP2, KH domains, RNA 97.7
2jvz_A164 KH type-splicing, FAR upstream element-binding pro 97.69
2anr_A178 Neuro-oncological ventral antigen 1; protein-RNA c 97.69
2anr_A178 Neuro-oncological ventral antigen 1; protein-RNA c 97.69
2ctj_A95 Vigilin; K homology type I domain, RNA-binding, ce 97.66
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 97.66
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 97.57
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 97.56
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 97.56
3krm_A163 Insulin-like growth factor 2 mRNA-binding protein 97.46
2cpq_A91 FragIle X mental retardation syndrome related prot 97.45
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 97.42
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 97.33
1tua_A191 Hypothetical protein APE0754; structural genomics, 97.21
2e3u_A219 PH-DIM2P, hypothetical protein PH1566; PRE-ribosom 97.07
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 96.86
3u1k_A630 Polyribonucleotide nucleotidyltransferase 1, MITO; 96.56
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 96.52
2qnd_A144 FMR1 protein; KH domain, eukaryotic KH domains, ta 96.08
2e3u_A219 PH-DIM2P, hypothetical protein PH1566; PRE-ribosom 95.89
2ctf_A102 Vigilin; K homology type I domain, RNA-binding, ce 95.07
1a6b_B40 Momulv, zinc finger protein NCP10; nucleocapsid pr 95.05
3n89_A 376 Defective in GERM LINE development protein 3, ISO; 94.96
1u6p_A56 GAG polyprotein; MLV, A-minor K-turn, stem loop, b 94.65
4aid_A726 Polyribonucleotide nucleotidyltransferase; transfe 94.41
1dsq_A26 Nucleic acid binding protein P14; CCHC type zinc f 94.39
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 94.36
2qnd_A144 FMR1 protein; KH domain, eukaryotic KH domains, ta 93.68
1nc8_A29 Nucleocapsid protein; HIV-2, RNA recognition, zinc 91.74
1tua_A191 Hypothetical protein APE0754; structural genomics, 90.12
3v69_A140 Protein filia; RNA-binding, embryogenesis, KH doma 89.55
2ysa_A55 Retinoblastoma-binding protein 6; zinc finger, CCH 88.58
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 87.44
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 85.74
2hqh_E26 Restin; beta/BETA structure, zinc finger motif, st 85.18
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 84.24
3n89_A376 Defective in GERM LINE development protein 3, ISO; 82.48
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 80.68
>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1 Back     alignment and structure
Probab=100.00  E-value=5.1e-48  Score=324.63  Aligned_cols=127  Identities=37%  Similarity=0.672  Sum_probs=120.9

Q ss_pred             ceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEec
Q psy1580          21 KVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAF  100 (267)
Q Consensus        21 k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~  100 (267)
                      .+++|||||+++||+|||||+||||||+|+|+||++|||||.|||+||+|++++++.++  |+|+|+|++|||||+|+++
T Consensus         1 ~~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~--g~~~~~~~~epLHV~Isa~   78 (140)
T 2bl5_A            1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKPNWEHLNEDLHVLITVE   78 (140)
T ss_dssp             CEEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTST--TSHHHHTTTSCCEEEEEEC
T ss_pred             CceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCccccccccccc--CCCCccccCCCcEEEEEec
Confidence            37899999999999999999999999999999999999999999999999999887654  8899999999999999999


Q ss_pred             CChhHHHHHHHHHHHHHHHhhcCCCcCCCCcchhHHHHHHHHHHHHhhCCCCCC
Q psy1580         101 APPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILKEDGGAA  154 (267)
Q Consensus       101 ~~~~~a~~rl~~Av~~I~~lL~P~~~s~~~d~~DelK~~QL~ELA~lNGt~r~~  154 (267)
                      +++++|+++|++|+++|++||+|++     +++|++|++||+|||+||||||+.
T Consensus        79 ~~~~~~~~~l~~A~~~I~~lL~p~~-----e~~de~K~~QL~eLA~lNGt~r~~  127 (140)
T 2bl5_A           79 DAQNRAELKLKRAVEEVKKLLVPAA-----EGEDSLKKMKLMELAILNGTYRDA  127 (140)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHSSCCS-----SSSSHHHHHHHTGGGSSSTTTSGG
T ss_pred             CchhhHHHHHHHHHHHHHHHCCCCC-----cchhHHHHHHHHHHHHhcCCcCCC
Confidence            9999999999999999999999976     889999999999999999999974
>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1 Back     alignment and structure
>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Back     alignment and structure
>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Back     alignment and structure
>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Back     alignment and structure
>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Back     alignment and structure
>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Back     alignment and structure
>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Back     alignment and structure
>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Back     alignment and structure
>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Back     alignment and structure
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Back     alignment and structure
>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Back     alignment and structure
>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Back     alignment and structure
>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Back     alignment and structure
>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Back     alignment and structure
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Back     alignment and structure
>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Back     alignment and structure
>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Back     alignment and structure
>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Back     alignment and structure
>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Back     alignment and structure
>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Back     alignment and structure
>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Back     alignment and structure
>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Back     alignment and structure
>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Back     alignment and structure
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Back     alignment and structure
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Back     alignment and structure
>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Back     alignment and structure
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Back     alignment and structure
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1 Back     alignment and structure
>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Back     alignment and structure
>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Back     alignment and structure
>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Back     alignment and structure
>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Back     alignment and structure
>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Back     alignment and structure
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Back     alignment and structure
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A* Back     alignment and structure
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Back     alignment and structure
>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Back     alignment and structure
>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Back     alignment and structure
>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A Back     alignment and structure
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Back     alignment and structure
>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Back     alignment and structure
>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Back     alignment and structure
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Back     alignment and structure
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Back     alignment and structure
>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Back     alignment and structure
>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Back     alignment and structure
>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1 Back     alignment and structure
>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Back     alignment and structure
>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A Back     alignment and structure
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Back     alignment and structure
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Back     alignment and structure
>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Back     alignment and structure
>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A Back     alignment and structure
>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Back     alignment and structure
>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus} Back     alignment and structure
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Back     alignment and structure
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Back     alignment and structure
>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens} Back     alignment and structure
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1 Back     alignment and structure
>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Back     alignment and structure
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} 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 267
d2bl5a1134 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {Afric 9e-45
d1k1ga_122 d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo s 4e-37
d1dtja_74 d.51.1.1 (A:) Neuro-oncological ventral antigen 2, 8e-07
d1x4ma181 d.51.1.1 (A:8-88) Far upstream binding element, FB 1e-05
d2ctea181 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T 5e-05
d1zzka175 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie 2e-04
d1x4na179 d.51.1.1 (A:8-86) Far upstream binding element, FB 2e-04
d1wvna170 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma 3e-04
d2ctka191 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T 4e-04
d1viga_71 d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId 5e-04
d1j4wa174 d.51.1.1 (A:1-74) Far upstream binding element, FB 0.002
>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 134 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

 Score =  145 bits (368), Expect = 9e-45
 Identities = 46/127 (36%), Positives = 81/127 (63%), Gaps = 7/127 (5%)

Query: 21  KVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRI 80
           ++  ++ VPV+++P FNFVG++LGP+G + K+L+ +T  ++ + G+GS+RD+ KEE+ R 
Sbjct: 1   QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR- 59

Query: 81  SGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQ 140
            G P + HL E+LHV IT       A  ++  A+ EV++ LVP       +  D +++ +
Sbjct: 60  -GKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVP-----AAEGEDSLKKMK 113

Query: 141 MWEMQIL 147
           + E+ IL
Sbjct: 114 LMELAIL 120
>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 122 Back     information, alignment and structure
>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74 Back     information, alignment and structure
>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81 Back     information, alignment and structure
>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81 Back     information, alignment and structure
>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75 Back     information, alignment and structure
>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79 Back     information, alignment and structure
>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70 Back     information, alignment and structure
>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91 Back     information, alignment and structure
>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71 Back     information, alignment and structure
>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74 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 ?
Query267
d2bl5a1134 Quaking protein A (Xqua) {African clawed frog (Xen 100.0
d1k1ga_122 RNA splicing factor 1 {Human (Homo sapiens) [TaxId 100.0
d1dtja_74 Neuro-oncological ventral antigen 2, nova-2, KH3 { 98.67
d1x4ma181 Far upstream binding element, FBP {Mouse (Mus musc 98.65
d1j4wa271 Far upstream binding element, FBP {Human (Homo sap 98.49
d1we8a_104 Tudor and KH domain containing protein, Tdrkh {Mou 98.48
d1x4na179 Far upstream binding element, FBP {Mouse (Mus musc 98.46
d1zzka175 HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} 98.44
d1wvna170 Poly(RC)-binding protein 1 {Human (Homo sapiens) [ 98.37
d1j4wa174 Far upstream binding element, FBP {Human (Homo sap 98.36
d2ctea181 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 98.34
d2cpqa178 Fragile X mental retardation syndrome related prot 98.32
d2ctma181 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 98.29
d2ctka191 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 98.27
d2axya171 Poly(RC)-binding protein 2 {Human (Homo sapiens) [ 98.21
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 98.19
d1tuaa2104 Hypothetical protein APE0754 {Aeropyrum pernix [Ta 98.16
d2ctla184 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 98.13
d1viga_71 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 98.12
d2ba0a384 Exosome complex RNA-binding protein 1, ECR1 {Archa 98.06
d1tuaa184 Hypothetical protein APE0754 {Aeropyrum pernix [Ta 97.99
d2z0sa287 Exosome complex RNA-binding protein 1, ECR1 {Aerop 97.94
d2je6i369 Exosome complex RNA-binding protein 1, ECR1 {Sulfo 97.91
d2ctja182 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 97.76
d2ctfa190 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 97.75
d1e3ha454 Polynucleotide phosphorylase/guanosine pentaphosph 97.64
d1dsqa_26 Nucleic acid binding protein p14 {Mouse mammary tu 93.07
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 90.92
d1nc8a_29 HIV nucleocapsid {Human immunodeficiency virus typ 90.59
>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=100.00  E-value=2.3e-50  Score=334.84  Aligned_cols=128  Identities=37%  Similarity=0.669  Sum_probs=121.5

Q ss_pred             ceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEec
Q psy1580          21 KVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAF  100 (267)
Q Consensus        21 k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~  100 (267)
                      |+++|||||+++||+|||||+||||||+|+|+||+||||||+||||||+|+++++.+++  +++.|+|++|||||+|+++
T Consensus         1 kl~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~--~~~~~~~~~epLHv~I~a~   78 (134)
T d2bl5a1           1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKPNWEHLNEDLHVLITVE   78 (134)
T ss_dssp             CEEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTST--TSHHHHTTTSCCEEEEEEC
T ss_pred             CcceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCcccccccc--CCCCCcCCCCCCEEEEEec
Confidence            68999999999999999999999999999999999999999999999999998877655  6788999999999999999


Q ss_pred             CChhHHHHHHHHHHHHHHHhhcCCCcCCCCcchhHHHHHHHHHHHHhhCCCCCCC
Q psy1580         101 APPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILKEDGGAAS  155 (267)
Q Consensus       101 ~~~~~a~~rl~~Av~~I~~lL~P~~~s~~~d~~DelK~~QL~ELA~lNGt~r~~~  155 (267)
                      +++.+|+.+|++|+++|++||+|++     +++|++|++||+|||+||||||++.
T Consensus        79 ~~~~~a~~kl~~A~~~I~~lL~p~~-----e~~de~k~~QL~eLa~lNGt~r~~~  128 (134)
T d2bl5a1          79 DAQNRAELKLKRAVEEVKKLLVPAA-----EGEDSLKKMKLMELAILNGTYRDAN  128 (134)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHSSCCS-----SSSSHHHHHHHTGGGSSSTTTSGGG
T ss_pred             CcHHHHHHHHHHHHHHHHHHcCCCc-----cchHHHHHHHHHHHHHhcCcccccc
Confidence            9999999999999999999999976     8899999999999999999999753
>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Back     information, alignment and structure
>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Back     information, alignment and structure
>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]} Back     information, alignment and structure
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Back     information, alignment and structure
>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]} Back     information, alignment and structure