Citrus Sinensis ID: 029290

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------
MASSGGGRFMAYSLSPSAPHSPHLPSLRSASSAILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTNGLASRFQSEISGLMQSSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARK
cccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccEEEEEEEEccccccccccccccEEcccccHHHHHHHHHccEEEEEccccccccccc
cccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccccccccEEEEEEEEEcccccccccEEEEEEcccccHHHHHHHHcccEEEEEEcccccccccc
massgggrfmayslspsaphsphlpslrsasSAILDQEKYLSELLAERhklnpflpvlpnAYRLLNQEIMRVTTLLGNasvlgqsglehaspltsggifsnggadtngLASRFQSEISGLMQSSSAQNWlssqgsssgliVKRTirvdipvekypnfnfvgrllgprgnslkrVEASTECRVLirgrgsikdpark
MASSGGGRFMAYSLSPSAPHSPHLPSLRSASSAILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTNGLASRFQSEISGLMQSSSAQNWlssqgsssgliVKRTIRvdipvekypnfnfvgrllgprgnslkrveastecrvlirgrgsikdpark
MASSGGGRFMAYslspsaphsphlpslrsassaILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTNGLASRFQSEISGLMQSSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARK
**************************************KYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQ*****************************************************GLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR***********
******************************************ELLAERHKLNPFLPVLPNAYRLLNQEIMR**********************************************************************KRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLI************
********FMAYSLSP***********RSASSAILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTNGLASRFQSEIS*******************GLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRG********
**********************************LDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLG*****HASPLTSGGIFSNGGADTNGLASRFQSEISGLMQSSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRG********
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MASSGGGRFMAYSLSPSAPHSPHLPSLRSASSAILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTNGLASRFQSEISGLMQSSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARK
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 ?
Query196 2.2.26 [Sep-21-2011]
Q9FKT4315 KH domain-containing prot yes no 0.954 0.593 0.737 6e-73
Q0WLR1308 KH domain-containing prot no no 0.943 0.600 0.706 2e-68
Q9ZVI3286 KH domain-containing prot no no 0.882 0.604 0.470 9e-38
Q8GWR3298 KH domain-containing prot no no 0.892 0.587 0.464 5e-37
Q8GYR4283 KH domain-containing prot no no 0.938 0.650 0.468 1e-35
Q75GR5281 KH domain-containing prot no no 0.836 0.583 0.458 1e-32
Q32NN2 341 Protein quaking-A OS=Xeno N/A no 0.510 0.293 0.376 4e-14
Q0VFL3 345 KH domain-containing, RNA yes no 0.556 0.315 0.329 7e-14
O01367 405 Protein held out wings OS yes no 0.576 0.279 0.299 2e-13
Q5VWX1 349 KH domain-containing, RNA yes no 0.571 0.320 0.319 3e-13
>sp|Q9FKT4|QKIL2_ARATH KH domain-containing protein At5g56140 OS=Arabidopsis thaliana GN=At5g56140 PE=2 SV=1 Back     alignment and function desciption
 Score =  273 bits (698), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 143/194 (73%), Positives = 158/194 (81%), Gaps = 7/194 (3%)

Query: 8   RFMAYSLS----PSAPHSPHLPS-LRSASSAILDQEKYLSELLAERHKLNPFLPVLPNAY 62
           RFM YS S    PSAP SP+    LRS SS  ++QEKYLSELLAERHKL PFLPVLP+A+
Sbjct: 28  RFMTYSSSLSVPPSAPQSPNYSGGLRSQSSVFVEQEKYLSELLAERHKLTPFLPVLPHAF 87

Query: 63  RLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTNGLASRFQSEISGLMQ 122
           RLLNQEI+RVTTLL NA+VL QSGL+H SPL SGGIF N  AD NG AS+F SE S  + 
Sbjct: 88  RLLNQEILRVTTLLENATVLSQSGLDHPSPLASGGIFQNARADMNGWASQFPSERS--VP 145

Query: 123 SSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRV 182
           SS   NWL+S GSSSGLI KRTIRVDIPV+ YPNFNFVGRLLGPRGNSLKRVEAST+CRV
Sbjct: 146 SSPGPNWLNSPGSSSGLIAKRTIRVDIPVDNYPNFNFVGRLLGPRGNSLKRVEASTDCRV 205

Query: 183 LIRGRGSIKDPARK 196
           LIRGRGSIKDP ++
Sbjct: 206 LIRGRGSIKDPIKE 219

Arabidopsis thaliana (taxid: 3702)
>sp|Q0WLR1|QKIL1_ARATH KH domain-containing protein At4g26480 OS=Arabidopsis thaliana GN=At4g26480 PE=2 SV=1 Back     alignment and function description
>sp|Q9ZVI3|QKIL3_ARATH KH domain-containing protein At2g38610 OS=Arabidopsis thaliana GN=At2g38610 PE=1 SV=1 Back     alignment and function description
>sp|Q8GWR3|QKIL5_ARATH KH domain-containing protein At1g09660 OS=Arabidopsis thaliana GN=At1g09660 PE=2 SV=1 Back     alignment and function description
>sp|Q8GYR4|QKIL4_ARATH KH domain-containing protein At3g08620 OS=Arabidopsis thaliana GN=At3g08620 PE=2 SV=1 Back     alignment and function description
>sp|Q75GR5|SPIN1_ORYSJ KH domain-containing protein SPIN1 OS=Oryza sativa subsp. japonica GN=SPIN1 PE=1 SV=1 Back     alignment and function description
>sp|Q32NN2|QKIA_XENLA Protein quaking-A OS=Xenopus laevis GN=qki-a PE=1 SV=2 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|O01367|HOW_DROME Protein held out wings OS=Drosophila melanogaster GN=how 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

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 ?
Query196
225462037287 PREDICTED: KH domain-containing protein 0.954 0.651 0.821 6e-85
449444002296 PREDICTED: KH domain-containing protein 1.0 0.662 0.82 5e-80
255584412 300 nucleic acid binding protein, putative [ 0.964 0.63 0.873 3e-78
224056887 302 predicted protein [Populus trichocarpa] 0.974 0.632 0.865 2e-77
356508160291 PREDICTED: KH domain-containing protein 0.989 0.666 0.765 8e-77
224122252 301 predicted protein [Populus trichocarpa] 0.964 0.627 0.854 1e-75
357456069293 KH domain-containing protein [Medicago t 0.994 0.665 0.720 1e-73
15241136 315 RNA-binding KH domain-containing protein 0.954 0.593 0.737 3e-71
356517802292 PREDICTED: KH domain-containing protein 0.989 0.664 0.761 7e-71
125540946286 hypothetical protein OsI_08744 [Oryza sa 0.938 0.643 0.730 7e-69
>gi|225462037|ref|XP_002274648.1| PREDICTED: KH domain-containing protein At5g56140 isoform 1 [Vitis vinifera] gi|296089986|emb|CBI39805.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  318 bits (816), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 157/191 (82%), Positives = 178/191 (93%), Gaps = 4/191 (2%)

Query: 7   GRFMAYSLSPS-APHSPHLPSLRSASSAILDQEKYLSELLAERHKLNPFLPVLPNAYRLL 65
           GR+MAYS SPS APHSPH+  LRSA+SA+++QEKYLSELLAERHKL+PF+PVLP++YRLL
Sbjct: 4   GRYMAYSPSPSTAPHSPHIAGLRSATSALVEQEKYLSELLAERHKLSPFMPVLPHSYRLL 63

Query: 66  NQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTNGLASRFQSEISGLMQSSS 125
           NQEI+RVTTLLGNAS+L QSGLEHASPL SGGIFSNGGA+ NG AS FQSE+SGL   S+
Sbjct: 64  NQEILRVTTLLGNASILDQSGLEHASPLASGGIFSNGGANVNGWASPFQSEMSGL---SA 120

Query: 126 AQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185
           AQNWL SQGSSSGLIVKRTIRVDIPVEK+P++NFVGRLLGPRGNSLKR+EA+TECRVLIR
Sbjct: 121 AQNWLGSQGSSSGLIVKRTIRVDIPVEKFPSYNFVGRLLGPRGNSLKRMEATTECRVLIR 180

Query: 186 GRGSIKDPARK 196
           GRGSIKDPAR+
Sbjct: 181 GRGSIKDPARE 191

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449444002|ref|XP_004139764.1| PREDICTED: KH domain-containing protein At5g56140-like [Cucumis sativus] gi|449508337|ref|XP_004163285.1| PREDICTED: KH domain-containing protein At5g56140-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|255584412|ref|XP_002532938.1| nucleic acid binding protein, putative [Ricinus communis] gi|223527289|gb|EEF29442.1| nucleic acid binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224056887|ref|XP_002299073.1| predicted protein [Populus trichocarpa] gi|222846331|gb|EEE83878.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356508160|ref|XP_003522828.1| PREDICTED: KH domain-containing protein At5g56140-like [Glycine max] Back     alignment and taxonomy information
>gi|224122252|ref|XP_002330577.1| predicted protein [Populus trichocarpa] gi|222872135|gb|EEF09266.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|357456069|ref|XP_003598315.1| KH domain-containing protein [Medicago truncatula] gi|355487363|gb|AES68566.1| KH domain-containing protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|15241136|ref|NP_200425.1| RNA-binding KH domain-containing protein [Arabidopsis thaliana] gi|75262628|sp|Q9FKT4.1|QKIL2_ARATH RecName: Full=KH domain-containing protein At5g56140; AltName: Full=Quaking-like protein 2 gi|9758634|dbj|BAB09296.1| RNA-binding protein-like [Arabidopsis thaliana] gi|24030184|gb|AAN41273.1| putative RNA-binding protein [Arabidopsis thaliana] gi|332009342|gb|AED96725.1| RNA-binding KH domain-containing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|356517802|ref|XP_003527575.1| PREDICTED: KH domain-containing protein At5g56140-like [Glycine max] Back     alignment and taxonomy information
>gi|125540946|gb|EAY87341.1| hypothetical protein OsI_08744 [Oryza sativa Indica Group] gi|215769394|dbj|BAH01623.1| unnamed protein product [Oryza sativa Japonica Group] 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 ?
Query196
TAIR|locus:2161845315 AT5G56140 "AT5G56140" [Arabido 0.989 0.615 0.661 5.4e-63
TAIR|locus:2064097286 AT2G38610 "AT2G38610" [Arabido 0.801 0.548 0.505 5.7e-36
TAIR|locus:2077818283 AT3G08620 "AT3G08620" [Arabido 0.795 0.551 0.503 2.2e-34
TAIR|locus:2024326298 AT1G09660 "AT1G09660" [Arabido 0.790 0.520 0.493 4.6e-34
UNIPROTKB|Q75GR5281 SPIN1 "KH domain-containing pr 0.790 0.551 0.487 3.2e-33
UNIPROTKB|F1RZV6 277 KHDRBS2 "Uncharacterized prote 0.285 0.202 0.553 7.6e-18
UNIPROTKB|E1BP48 348 KHDRBS2 "Uncharacterized prote 0.285 0.160 0.553 2.1e-17
UNIPROTKB|E1BVW8 348 KHDRBS2 "Uncharacterized prote 0.285 0.160 0.553 2.7e-17
UNIPROTKB|E2QWN2 349 KHDRBS2 "Uncharacterized prote 0.285 0.160 0.553 4.4e-17
UNIPROTKB|Q5VWX1 349 KHDRBS2 "KH domain-containing, 0.285 0.160 0.553 4.4e-17
TAIR|locus:2161845 AT5G56140 "AT5G56140" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 643 (231.4 bits), Expect = 5.4e-63, P = 5.4e-63
 Identities = 133/201 (66%), Positives = 148/201 (73%)

Query:     1 MASSGGGRFMAYXXXXXXXXXX-----XXXXXXXXXXXILDQEKYLSELLAERHKLNPFL 55
             +   GGGRFM Y                           ++QEKYLSELLAERHKL PFL
Sbjct:    21 IGGGGGGRFMTYSSSLSVPPSAPQSPNYSGGLRSQSSVFVEQEKYLSELLAERHKLTPFL 80

Query:    56 PVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTNGLASRFQS 115
             PVLP+A+RLLNQEI+RVTTLL NA+VL QSGL+H SPL SGGIF N  AD NG AS+F S
Sbjct:    81 PVLPHAFRLLNQEILRVTTLLENATVLSQSGLDHPSPLASGGIFQNARADMNGWASQFPS 140

Query:   116 EISGLMQSSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVE 175
             E S  + SS   NWL+S GSSSGLI KRTIRVDIPV+ YPNFNFVGRLLGPRGNSLKRVE
Sbjct:   141 ERS--VPSSPGPNWLNSPGSSSGLIAKRTIRVDIPVDNYPNFNFVGRLLGPRGNSLKRVE 198

Query:   176 ASTECRVLIRGRGSIKDPARK 196
             AST+CRVLIRGRGSIKDP ++
Sbjct:   199 ASTDCRVLIRGRGSIKDPIKE 219
GO:0003676 "nucleic acid binding" evidence=ISS
GO:0003723 "RNA binding" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
GO:0008150 "biological_process" evidence=ND
TAIR|locus:2064097 AT2G38610 "AT2G38610" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2077818 AT3G08620 "AT3G08620" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2024326 AT1G09660 "AT1G09660" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q75GR5 SPIN1 "KH domain-containing protein SPIN1" [Oryza sativa Japonica Group (taxid:39947)] 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
UNIPROTKB|E1BVW8 KHDRBS2 "Uncharacterized protein" [Gallus gallus (taxid:9031)] 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

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) ?
Q9FKT4QKIL2_ARATHNo assigned EC number0.73710.95400.5936yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
grail3.0051017601
hypothetical protein (302 aa)
(Populus trichocarpa)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query196
cd02395120 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K ho 4e-25
COG5176269 COG5176, MSL5, Splicing factor (branch point bindi 2e-12
smart0032268 smart00322, KH, K homology RNA-binding domain 2e-05
cd0010564 cd00105, KH-I, K homology RNA-binding domain, type 1e-04
>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology RNA-binding domain (KH) Back     alignment and domain information 
 Score = 93.8 bits (234), Expect = 4e-25
 Identities = 28/51 (54%), Positives = 40/51 (78%)

Query: 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPA 194
           T +V IPV++YP +NFVG +LGPRGN+LK++E  T  ++ IRG+GS+KD  
Sbjct: 1   TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGK 51

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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 196
KOG1588 259 consensus RNA-binding protein Sam68 and related KH 100.0
KOG0119 554 consensus Splicing factor 1/branch point binding p 99.97
COG5176269 MSL5 Splicing factor (branch point binding protein 99.94
cd02395120 SF1_like-KH Splicing factor 1 (SF1) K homology RNA 99.86
PF1301443 KH_3: KH domain 98.16
cd0239361 PNPase_KH Polynucleotide phosphorylase (PNPase) K 98.1
cd0010564 KH-I K homology RNA-binding domain, type I. KH bin 98.08
smart0032269 KH K homology RNA-binding domain. 97.85
PF0001360 KH_1: KH domain syndrome, contains KH motifs.; Int 97.8
cd0239665 PCBP_like_KH K homology RNA-binding domain, PCBP_l 97.76
cd0239462 vigilin_like_KH K homology RNA-binding domain_vigi 97.72
PRK13763180 putative RNA-processing protein; Provisional 96.75
KOG2193 584 consensus IGF-II mRNA-binding protein IMP, contain 96.62
TIGR03665172 arCOG04150 arCOG04150 universal archaeal KH domain 96.56
COG1094194 Predicted RNA-binding protein (contains KH domains 96.23
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransfe 95.02
KOG2874 356 consensus rRNA processing protein [Translation, ri 94.94
KOG1960 531 consensus Predicted RNA-binding protein, contains 94.44
TIGR02696719 pppGpp_PNP guanosine pentaphosphate synthetase I/p 94.0
KOG1676 600 consensus K-homology type RNA binding proteins [RN 93.45
KOG1676 600 consensus K-homology type RNA binding proteins [RN 92.86
KOG2191 402 consensus RNA-binding protein NOVA1/PASILLA and re 92.78
KOG2193 584 consensus IGF-II mRNA-binding protein IMP, contain 89.33
KOG2814 345 consensus Transcription coactivator complex, P50 c 89.32
KOG2190 485 consensus PolyC-binding proteins alphaCP-1 and rel 89.02
PLN00207 891 polyribonucleotide nucleotidyltransferase; Provisi 88.82
PRK04163235 exosome complex RNA-binding protein Rrp4; Provisio 88.62
cd0213461 NusA_KH NusA_K homology RNA-binding domain (KH). N 88.43
KOG2191 402 consensus RNA-binding protein NOVA1/PASILLA and re 88.0
PRK11824693 polynucleotide phosphorylase/polyadenylase; Provis 85.94
KOG2190485 consensus PolyC-binding proteins alphaCP-1 and rel 84.86
KOG0336 629 consensus ATP-dependent RNA helicase [RNA processi 83.77
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification] Back     alignment and domain information 
Probab=100.00  E-value=2.2e-38  Score=276.61  Aligned_cols=125  Identities=51%  Similarity=0.789  Sum_probs=104.2

Q ss_pred             cCCcccchhHHHHHHHHHHHHhhcCCCCCChhhHHHHHHHHHHHHHHhhcCCccCCCCCCCCCCCCCCCCCcCCCCCCcc
Q 029290           28 RSASSAILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTN  107 (196)
Q Consensus        28 r~~~~~~~~~~~YL~ELl~Ek~kL~pf~~vlph~~rLLnqEI~RV~~~l~~~~~~~~d~~~~~SP~~s~g~~~N~~~~~~  107 (196)
                      +.++......++||.||++|+++|++|+. |+||.|||++||.||...+++.+        ...|               
T Consensus        21 ~~~~~~~~~~~~yl~el~~e~~~l~~~~~-~~~~~rLL~~Ei~rv~~~~~~~~--------~~~~---------------   76 (259)
T KOG1588|consen   21 RYQPQLNEKASKYLSELLAERKSLSPFFP-FPHAERLLDEEIERVQTSGRQHG--------SKEP---------------   76 (259)
T ss_pred             ccccchhhHHHHHHHHHHhhHHhcCcccc-hHHHHHHHHHHHHHHHhhhhhcc--------CCCc---------------
Confidence            44455566788999999999999999987 88999999999999998876542        0000               


Q ss_pred             chhhhhhHHhhhhhhccccCCCCCCCCCCCCCceeeEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecc
Q 029290          108 GLASRFQSEISGLMQSSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR  187 (196)
Q Consensus       108 ~~~~~~~~Er~~li~~~~~~~~~~pp~~~~~p~vk~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGk  187 (196)
                              ++.          +  -.+.++.+++|+++||+|||++||+||||||||||||||+||||++|||||+||||
T Consensus        77 --------~~~----------~--~~~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr  136 (259)
T KOG1588|consen   77 --------EEL----------P--YADVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR  136 (259)
T ss_pred             --------hhc----------c--cccCccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence                    100          0  00234567899999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCC
Q 029290          188 GSIKDPARK  196 (196)
Q Consensus       188 GS~kd~~KE  196 (196)
                      |||||+.||
T Consensus       137 gSmrD~~KE  145 (259)
T KOG1588|consen  137 GSMRDKAKE  145 (259)
T ss_pred             CcccchHHH
Confidence            999999997

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification] Back     alignment and domain information
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH) Back     alignment and domain information
>PF13014 KH_3: KH domain Back     alignment and domain information
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH) Back     alignment and domain information
>cd00105 KH-I K homology RNA-binding domain, type I 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
>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
>PRK13763 putative RNA-processing protein; Provisional Back     alignment and domain information
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only] 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
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification] Back     alignment and domain information
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase Back     alignment and domain information
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification] Back     alignment and domain information
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification] Back     alignment and domain information
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only] Back     alignment and domain information
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only] Back     alignment and domain information
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription] Back     alignment and domain information
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only] Back     alignment and domain information
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional Back     alignment and domain information
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional Back     alignment and domain information
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH) Back     alignment and domain information
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only] Back     alignment and domain information
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only] Back     alignment and domain information
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification] 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 ?
Query196
2bl5_A140 Solution Structure Of The Kh-Qua2 Region Of The Xen 1e-12
1k1g_A131 Structural Basis For Recognition Of The Intron Bran 3e-10
>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 = 69.3 bits (168), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 25/48 (52%), Positives = 42/48 (87%)
Query: 149 IPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARK 196
           +PV++YP+FNFVGR+LGPRG + K++EA T C++++RG+GS++D  ++
Sbjct: 8   VPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKE 55
>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 ?
Query196
1k1g_A131 SF1-BO isoform; splicing, branch point sequence, p 2e-22
2bl5_A140 MGC83862 protein, quaking protein; STAR proteins, 3e-21
2yqr_A119 KIAA0907 protein; structure genomics, KH domain, s 6e-14
3k6t_A60 Female germline-specific tumor suppressor GLD-1; Q 3e-04
>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
 Score = 86.8 bits (215), Expect = 2e-22
 Identities = 24/59 (40%), Positives = 39/59 (66%)

Query: 138 GLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARK 196
            +  + + +V IP ++YP  NFVG L+GPRGN+LK +E     +++IRG+GS+K+    
Sbjct: 2   AMATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVG 60
>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
>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
>3k6t_A Female germline-specific tumor suppressor GLD-1; QUA1 homodimerization domain, helix-turn-helix motif, hydrophobic homodimer interface; 2.04A {Caenorhabditis elegans} PDB: 3kbl_A Length = 60 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query196
2bl5_A140 MGC83862 protein, quaking protein; STAR proteins, 99.89
1k1g_A131 SF1-BO isoform; splicing, branch point sequence, p 99.84
2yqr_A119 KIAA0907 protein; structure genomics, KH domain, s 99.75
2xa6_A41 KH domain-containing\,RNA-binding\,signal transduc 99.2
3k6t_A60 Female germline-specific tumor suppressor GLD-1; Q 99.17
4dnn_A56 Protein quaking, MQKI, QKI; helix-turn-helix, hydr 99.09
4fxw_B124 Splicing factor 1; UHM, protein binding, phosphory 98.65
1dtj_A76 RNA-binding neurooncological ventral antigen 2; KH 98.21
2opv_A85 KHSRP protein; KH domain, RNA binding protein, KSR 98.12
1we8_A104 Tudor and KH domain containing protein; structural 98.0
2dgr_A83 Ring finger and KH domain-containing protein 1; st 97.97
1zzk_A82 Heterogeneous nuclear ribonucleoprotein K; KH domi 97.93
1ec6_A87 RNA-binding protein NOVA-2; KH domain, alpha-beta 97.9
1wvn_A82 Poly(RC)-binding protein 1; KH domain, RNA binding 97.88
1x4m_A94 FAR upstream element binding protein 1; KH domain, 97.86
2p2r_A76 Poly(RC)-binding protein 2; protein-DNA complex, R 97.83
1x4n_A92 FAR upstream element binding protein 1; KH domain, 97.83
1j5k_A89 Heterogeneous nuclear ribonucleoprotein K; single- 97.77
2axy_A73 Poly(RC)-binding protein 2; protein-DNA complex, D 97.74
2hh2_A107 KH-type splicing regulatory protein; KH-RNA bindin 97.74
2hh3_A106 KH-type splicing regulatory protein; KH-RNA bindin 97.72
1vig_A71 Vigilin; RNA-binding protein, ribonucleoprotein; N 97.72
2cte_A94 Vigilin; K homology type I domain, RNA-binding, ce 97.68
2ctl_A97 Vigilin; K homology type I domain, RNA-binding, ce 97.66
2ctk_A104 Vigilin; K homology type I domain, RNA-binding, ce 97.65
2ctm_A95 Vigilin; K homology type I domain, RNA-binding, ce 97.38
3krm_A163 Insulin-like growth factor 2 mRNA-binding protein 97.11
1j4w_A174 FUSE binding protein; single-stranded DNA binding 97.0
2jvz_A164 KH type-splicing, FAR upstream element-binding pro 96.97
2anr_A178 Neuro-oncological ventral antigen 1; protein-RNA c 96.88
2jzx_A160 Poly(RC)-binding protein 2; PCBP2, KH domains, RNA 96.8
2e3u_A219 PH-DIM2P, hypothetical protein PH1566; PRE-ribosom 96.65
1tua_A191 Hypothetical protein APE0754; structural genomics, 96.62
2ctj_A95 Vigilin; K homology type I domain, RNA-binding, ce 96.6
2cpq_A91 FragIle X mental retardation syndrome related prot 95.84
3u1k_A630 Polyribonucleotide nucleotidyltransferase 1, MITO; 94.85
2e3u_A 219 PH-DIM2P, hypothetical protein PH1566; PRE-ribosom 94.36
2qnd_A144 FMR1 protein; KH domain, eukaryotic KH domains, ta 93.36
3v69_A140 Protein filia; RNA-binding, embryogenesis, KH doma 92.71
2qnd_A144 FMR1 protein; KH domain, eukaryotic KH domains, ta 92.03
2ctf_A102 Vigilin; K homology type I domain, RNA-binding, ce 92.02
4aid_A 726 Polyribonucleotide nucleotidyltransferase; transfe 91.96
3n89_A 376 Defective in GERM LINE development protein 3, ISO; 90.16
>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=99.89  E-value=1.5e-24  Score=174.09  Aligned_cols=53  Identities=47%  Similarity=1.037  Sum_probs=50.6

Q ss_pred             eEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecccCCCCCCC
Q 029290          143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAR  195 (196)
Q Consensus       143 ~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS~kd~~K  195 (196)
                      +++|||||+++||+|||||+||||+|+|+|+||++|||||.|||+||+||..|
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~   54 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKK   54 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHH
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccc
Confidence            58899999999999999999999999999999999999999999999998654
>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
>2xa6_A KH domain-containing\,RNA-binding\,signal transduction-associated protein 1; transcription, STAR proteins, CD44, cell cycle; NMR {Homo sapiens} Back     alignment and structure
>3k6t_A Female germline-specific tumor suppressor GLD-1; QUA1 homodimerization domain, helix-turn-helix motif, hydrophobic homodimer interface; 2.04A {Caenorhabditis elegans} PDB: 3kbl_A Back     alignment and structure
>4dnn_A Protein quaking, MQKI, QKI; helix-turn-helix, hydrophobic homodimer interface, perpendic stacking of protomers, developmental protein, RNA-binding; HET: MSE; 2.10A {Mus musculus} Back     alignment and structure
>4fxw_B Splicing factor 1; UHM, protein binding, phosphorylat; HET: SEP; 2.29A {Homo sapiens} PDB: 4fxx_A 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
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {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
>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
>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
>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
>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
>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
>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
>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
>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
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} 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
>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
>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus} 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
>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
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A 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

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 196
d2bl5a1134 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {Afric 2e-22
d1k1ga_122 d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo s 1e-21
d2ctka191 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T 4e-04
d2je6i369 d.51.1.1 (I:153-221) Exosome complex RNA-binding p 8e-04
d2ctea181 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T 0.002
d1dtja_74 d.51.1.1 (A:) Neuro-oncological ventral antigen 2, 0.002
d2z0sa287 d.51.1.1 (A:148-234) Exosome complex RNA-binding p 0.004
>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 = 86.0 bits (213), Expect = 2e-22
 Identities = 25/50 (50%), Positives = 43/50 (86%)

Query: 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAR 195
           ++ +PV++YP+FNFVGR+LGPRG + K++EA T C++++RG+GS++D  +
Sbjct: 5   KLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKK 54
>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 122 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
>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69 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
>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
>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87 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 ?
Query196
d1k1ga_122 RNA splicing factor 1 {Human (Homo sapiens) [TaxId 99.92
d2bl5a1134 Quaking protein A (Xqua) {African clawed frog (Xen 99.92
d1dtja_74 Neuro-oncological ventral antigen 2, nova-2, KH3 { 98.25
d1zzka175 HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} 98.04
d1we8a_104 Tudor and KH domain containing protein, Tdrkh {Mou 97.98
d1x4ma181 Far upstream binding element, FBP {Mouse (Mus musc 97.96
d1wvna170 Poly(RC)-binding protein 1 {Human (Homo sapiens) [ 97.95
d1x4na179 Far upstream binding element, FBP {Mouse (Mus musc 97.95
d1j4wa271 Far upstream binding element, FBP {Human (Homo sap 97.95
d1j4wa174 Far upstream binding element, FBP {Human (Homo sap 97.88
d1e3ha454 Polynucleotide phosphorylase/guanosine pentaphosph 97.83
d1tuaa184 Hypothetical protein APE0754 {Aeropyrum pernix [Ta 97.77
d2je6i369 Exosome complex RNA-binding protein 1, ECR1 {Sulfo 97.75
d2ctma181 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 97.68
d2axya171 Poly(RC)-binding protein 2 {Human (Homo sapiens) [ 97.68
d2ctka191 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 97.68
d2ba0a384 Exosome complex RNA-binding protein 1, ECR1 {Archa 97.64
d2cpqa178 Fragile X mental retardation syndrome related prot 97.63
d2ctea181 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 97.6
d2z0sa287 Exosome complex RNA-binding protein 1, ECR1 {Aerop 97.59
d2ctla184 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 97.51
d1tuaa2104 Hypothetical protein APE0754 {Aeropyrum pernix [Ta 97.49
d1viga_71 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 97.41
d2ctja182 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 96.89
d2ctfa190 Vigilin {Human (Homo sapiens) [TaxId: 9606]} 96.72
>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]} 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: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=9.1e-27  Score=181.06  Aligned_cols=55  Identities=44%  Similarity=0.867  Sum_probs=52.7

Q ss_pred             eeEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecccCCCCCCCC
Q 029290          142 KRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARK  196 (196)
Q Consensus       142 k~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS~kd~~KE  196 (196)
                      |+++|||||+++||+|||||+||||+|+|+|+||++|||||+||||||+||..+|
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~   56 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVG   56 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSS
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCccccccc
Confidence            7899999999999999999999999999999999999999999999999997654
>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]} 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
>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {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
>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1x4na1 d.51.1.1 (A:8-86) 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
>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {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
>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {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
>d2ctma1 d.51.1.1 (A:8-88) 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
>d2ctka1 d.51.1.1 (A:8-98) 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
>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
>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} 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
>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} 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
>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} 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