Citrus Sinensis ID: 027518

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220--

MASSGGGRFMAYSLSPSAPHSPHLPSLRSASSAILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTNGLASRFQSEISGLMQSSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARVIVMLLLSLFVFIVHILYVSGISNEIF

ccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccEEEEEEEEcccccccccccccccccccccHHHHHHHHHccEEEEEcccccccHHHHHHHccccccccccccEEEEccccccc

cccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccEEEEEEEEEcccccccccEEEEEEcccccHHHHHHHHcccEEEEEEcccccccHHHHHHHHcccHHHEcccEEEEccccccc

massgggrfmayslspsaphsphlpslrsasSAILDQEKYLSELLAERhklnpflpvlpnAYRLLNQEIMRVTTLLGNasvlgqsglehaspltsggifsnggadtngLASRFQSEISGLMQSSSAQNWlssqgsssgliVKRTirvdipvekypnfnfvgrllgprgnslkrVEASTECRVLirgrgsikdPARVIVMLLLSLFVFIVHILYVsgisneif

MASSGGGRFMAYSLSPSAPHSPHLPSLRSASSAILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTNGLASRFQSEISGLMQSSSAQNWlssqgsssgliVKRTIRvdipvekypnfnfvgrllgprgnslkrveastecrvlirgrgsikdpaRVIVMLLLSLFVFIVHILYVSGISNEIF

MASSGGGRFMAYslspsaphsphlpslrsassaILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTNGLASRFQSEISGLMQSSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARVIVMLLLSLFVFIVHILYVSGISNEIF

**************************************KYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQ*****************************************************GLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARVIVMLLLSLFVFIVHILYVSGI*****

****************************************LSELLAERHKLNPFLPVLPNAYRLLNQEIMRVT*******************************************************************VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR**********************IVHILYVSGISNEIF

********FMAYSLSP***********RSASSAILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTNGLASRFQSEIS*******************GLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARVIVMLLLSLFVFIVHILYVSGISNEIF

**********************************LDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLG****EHASPLTSGGIFSNGGADTNGLASRFQSEISGLMQSSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARVIVMLLLSLFVFIVHILYVSGIS***F

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiii

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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
Query		222	2.2.26 [Sep-21-2011]
Q9FKT4		315	KH domain-containing prot	yes	no	0.855	0.603	0.730	3e-73
Q0WLR1		308	KH domain-containing prot	no	no	0.846	0.610	0.700	1e-68
Q9ZVI3		286	KH domain-containing prot	no	no	0.774	0.601	0.473	1e-37
Q8GWR3		298	KH domain-containing prot	no	no	0.770	0.573	0.474	7e-37
Q8GYR4		283	KH domain-containing prot	no	no	0.824	0.646	0.471	2e-35
Q75GR5		281	KH domain-containing prot	no	no	0.738	0.583	0.474	3e-32
Q32NN2		341	Protein quaking-A OS=Xeno	N/A	no	0.432	0.281	0.391	6e-14
Q0VFL3		345	KH domain-containing, RNA	yes	no	0.490	0.315	0.329	1e-13
O01367		405	Protein held out wings OS	yes	no	0.504	0.276	0.301	4e-13
Q5VWX1		349	KH domain-containing, RNA	yes	no	0.5	0.318	0.320	6e-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 =  274 bits (701), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 144/197 (73%), Positives = 159/197 (80%), Gaps = 7/197 (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 LIRGRGSIKDPARVIVM 199
           LIRGRGSIKDP +  +M
Sbjct: 206 LIRGRGSIKDPIKEEMM 222

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
Query		222
225462037		287	PREDICTED: KH domain-containing protein	0.855	0.662	0.814	4e-85
449444002		296	PREDICTED: KH domain-containing protein	0.896	0.672	0.812	6e-80
255584412		300	nucleic acid binding protein, putative [	0.864	0.64	0.864	2e-78
224056887		302	predicted protein [Populus trichocarpa]	0.873	0.642	0.857	2e-77
356508160		291	PREDICTED: KH domain-containing protein	0.887	0.676	0.758	7e-77
224122252		301	predicted protein [Populus trichocarpa]	0.864	0.637	0.846	2e-75
357456069		293	KH domain-containing protein [Medicago t	0.891	0.675	0.715	1e-73
15241136		315	RNA-binding KH domain-containing protein	0.855	0.603	0.730	2e-71
356517802		292	PREDICTED: KH domain-containing protein	0.887	0.674	0.755	6e-71
125540946		286	hypothetical protein OsI_08744 [Oryza sa	0.842	0.653	0.724	5e-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 =  320 bits (819), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 158/194 (81%), Positives = 179/194 (92%), Gaps = 4/194 (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 GRGSIKDPARVIVM 199
           GRGSIKDPAR  +M
Sbjct: 181 GRGSIKDPAREEMM 194

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
Query		222
TAIR\|locus:2161845		315	AT5G56140 "AT5G56140" [Arabido	0.887	0.625	0.656	5.4e-63
TAIR\|locus:2064097		286	AT2G38610 "AT2G38610" [Arabido	0.702	0.545	0.508	7.2e-36
TAIR\|locus:2077818		283	AT3G08620 "AT3G08620" [Arabido	0.698	0.547	0.506	2.8e-34
TAIR\|locus:2024326		298	AT1G09660 "AT1G09660" [Arabido	0.693	0.516	0.496	5.8e-34
UNIPROTKB\|Q75GR5		281	SPIN1 "KH domain-containing pr	0.693	0.548	0.490	4.1e-33
UNIPROTKB\|F1RZV6		277	KHDRBS2 "Uncharacterized prote	0.247	0.198	0.563	1e-17
UNIPROTKB\|E1BP48		348	KHDRBS2 "Uncharacterized prote	0.247	0.158	0.563	2.7e-17
UNIPROTKB\|E1BVW8		348	KHDRBS2 "Uncharacterized prote	0.247	0.158	0.563	3.4e-17
UNIPROTKB\|E2QWN2		349	KHDRBS2 "Uncharacterized prote	0.247	0.157	0.563	5.6e-17
UNIPROTKB\|Q5VWX1		349	KHDRBS2 "KH domain-containing,	0.247	0.157	0.563	5.6e-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 = 134/204 (65%), Positives = 149/204 (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 ASTECRVLIRGRGSIKDPARVIVM 199
             AST+CRVLIRGRGSIKDP +  +M
Sbjct:   199 ASTDCRVLIRGRGSIKDPIKEEMM 222

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)
Q9FKT4	QKIL2_ARATH	No assigned EC number	0.7309	0.8558	0.6031	yes	no

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
Query		222
cd02395		120	cd02395, SF1_like-KH, Splicing factor 1 (SF1) K ho	5e-25
COG5176		269	COG5176, MSL5, Splicing factor (branch point bindi	9e-13
smart00322		68	smart00322, KH, K homology RNA-binding domain	6e-05
cd00105		64	cd00105, KH-I, K homology RNA-binding domain, type	1e-04
smart01101		215	smart01101, CRISPR_assoc, This domain forms an ant	0.002

>gnl\|CDD\|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology RNA-binding domain (KH)	Back alignment and domain information

 Score = 94.6 bits (236), Expect = 5e-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

>gnl\|CDD\|215025 smart01101, CRISPR_assoc, This domain forms an anti-parallel beta strand structure with flanking alpha helical regions	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		222
KOG1588		259	consensus RNA-binding protein Sam68 and related KH	100.0
KOG0119		554	consensus Splicing factor 1/branch point binding p	100.0
COG5176		269	MSL5 Splicing factor (branch point binding protein	99.96
cd02395		120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	99.93
PF13014		43	KH_3: KH domain	98.09
cd02393		61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.04
cd00105		64	KH-I K homology RNA-binding domain, type I. KH bin	98.01
smart00322		69	KH K homology RNA-binding domain.	97.78
PF00013		60	KH_1: KH domain syndrome, contains KH motifs.; Int	97.71
cd02396		65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	97.65
cd02394		62	vigilin_like_KH K homology RNA-binding domain_vigi	97.64
KOG2193		584	consensus IGF-II mRNA-binding protein IMP, contain	97.03
PRK13763		180	putative RNA-processing protein; Provisional	96.58
TIGR03665		172	arCOG04150 arCOG04150 universal archaeal KH domain	96.38
COG1094		194	Predicted RNA-binding protein (contains KH domains	96.07
TIGR03665		172	arCOG04150 arCOG04150 universal archaeal KH domain	95.76
PRK13763		180	putative RNA-processing protein; Provisional	95.57
TIGR03591		684	polynuc_phos polyribonucleotide nucleotidyltransfe	94.73
KOG2874		356	consensus rRNA processing protein [Translation, ri	94.6
KOG2191		402	consensus RNA-binding protein NOVA1/PASILLA and re	93.82
KOG1960		531	consensus Predicted RNA-binding protein, contains	93.79
TIGR02696		719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	93.67
KOG1676		600	consensus K-homology type RNA binding proteins [RN	93.13
KOG1676		600	consensus K-homology type RNA binding proteins [RN	92.47
KOG2814		345	consensus Transcription coactivator complex, P50 c	88.43
KOG2190		485	consensus PolyC-binding proteins alphaCP-1 and rel	87.77
PLN00207		891	polyribonucleotide nucleotidyltransferase; Provisi	87.67
KOG2193		584	consensus IGF-II mRNA-binding protein IMP, contain	87.43
cd02134		61	NusA_KH NusA_K homology RNA-binding domain (KH). N	87.26
PRK04163		235	exosome complex RNA-binding protein Rrp4; Provisio	86.91
KOG2191		402	consensus RNA-binding protein NOVA1/PASILLA and re	85.8
KOG2190		485	consensus PolyC-binding proteins alphaCP-1 and rel	84.71
PRK11824		693	polynucleotide phosphorylase/polyadenylase; Provis	84.11

>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=1.1e-45  Score=328.20  Aligned_cols=147  Identities=45%  Similarity=0.669  Sum_probs=124.2

Q ss_pred             cCCcccchhHHHHHHHHHHHHhhcCCCCCChhhHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCcCCCCCCcc
Q 027518           28 RSASSAILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTN  107 (222)
Q Consensus        28 r~~~~~~~~~~~YL~ELl~Ek~kL~pf~~v~ph~~rLL~qEI~RV~~~l~~~~~~~~d~~~~~SP~~s~g~~~N~~~d~~  107 (222)
                      +.++......++||.||++|+++|++|+. |+||.|||++||.||...+++.+        ..+|               
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            33444456789999999999999999987 88999999999999999877542        0000               


Q ss_pred             chhhhhHHHhhhhhhccccCCCCCCCCCCCCCceeeEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecc
Q 027518          108 GLASRFQSEISGLMQSSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR  187 (222)
Q Consensus       108 ~~~~~l~~Er~~li~~~~~~~~~~pp~~~~~p~vK~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGk  187 (222)
                              ++.          .  -.+.++.+++|+++||+|||++||+||||||||||||||+||||++|||||+||||
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                    000          0  00234456799999999999999999999999999999999999999999999999


Q ss_pred             cCCCCchHHHHhhccCCccce---eeEEEEecCc
Q 027518          188 GSIKDPARVIVMLLLSLFVFI---VHILYVSGIS  218 (222)
Q Consensus       188 GS~kd~~kEe~lr~~~~~e~~---lHvli~~~~~  218 (222)
                      |||||..|||+||++|+|||+   |||||++...
T Consensus       137 gSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p  170 (259)
T KOG1588|consen  137 GSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAP  170 (259)
T ss_pred             CcccchHHHHHhhcCcchHHhCCCcEEEEEEeCC
Confidence            999999999999999999997   9999998654

>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

>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

>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

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein	Back alignment and domain information

>PRK13763 putative RNA-processing protein; Provisional	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

>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

>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

>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

>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

>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH)	Back alignment and domain information

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional	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

>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

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional	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
Query		222
2bl5_A		140	Solution Structure Of The Kh-Qua2 Region Of The Xen		1e-12
1k1g_A		131	Structural Basis For Recognition Of The Intron Bran		6e-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 = 25/47 (53%), Positives = 41/47 (87%)
Query: 149 IPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAR 195
           +PV++YP+FNFVGR+LGPRG + K++EA T C++++RG+GS++D  +
Sbjct: 8   VPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKK 54

PyMOL of 2bl5

>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
Query		222
1k1g_A		131	SF1-BO isoform; splicing, branch point sequence, p	1e-22
2bl5_A		140	MGC83862 protein, quaking protein; STAR proteins,	2e-21
2yqr_A		119	KIAA0907 protein; structure genomics, KH domain, s	4e-14
3k6t_A		60	Female germline-specific tumor suppressor GLD-1; Q	3e-04
2cte_A		94	Vigilin; K homology type I domain, RNA-binding, ce	9e-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 = 88.0 bits (218), Expect = 1e-22
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 138 GLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAR 195
            +  + + +V IP ++YP  NFVG L+GPRGN+LK +E     +++IRG+GS+K+   
Sbjct: 2   AMATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKV 59

PyMOL of 1k1g

>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

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		222
2bl5_A		140	MGC83862 protein, quaking protein; STAR proteins,	99.96
1k1g_A		131	SF1-BO isoform; splicing, branch point sequence, p	99.89
2yqr_A		119	KIAA0907 protein; structure genomics, KH domain, s	99.82
2xa6_A		41	KH domain-containing\,RNA-binding\,signal transduc	99.15
3k6t_A		60	Female germline-specific tumor suppressor GLD-1; Q	99.13
4dnn_A		56	Protein quaking, MQKI, QKI; helix-turn-helix, hydr	99.05
4fxw_B		124	Splicing factor 1; UHM, protein binding, phosphory	98.46
1dtj_A		76	RNA-binding neurooncological ventral antigen 2; KH	98.12
2opv_A		85	KHSRP protein; KH domain, RNA binding protein, KSR	98.07
1we8_A		104	Tudor and KH domain containing protein; structural	97.95
2dgr_A		83	Ring finger and KH domain-containing protein 1; st	97.9
1zzk_A		82	Heterogeneous nuclear ribonucleoprotein K; KH domi	97.86
1ec6_A		87	RNA-binding protein NOVA-2; KH domain, alpha-beta	97.84
1wvn_A		82	Poly(RC)-binding protein 1; KH domain, RNA binding	97.8
1x4m_A		94	FAR upstream element binding protein 1; KH domain,	97.8
1x4n_A		92	FAR upstream element binding protein 1; KH domain,	97.76
2p2r_A		76	Poly(RC)-binding protein 2; protein-DNA complex, R	97.75
1j5k_A		89	Heterogeneous nuclear ribonucleoprotein K; single-	97.7
1vig_A		71	Vigilin; RNA-binding protein, ribonucleoprotein; N	97.67
2hh2_A		107	KH-type splicing regulatory protein; KH-RNA bindin	97.67
2axy_A		73	Poly(RC)-binding protein 2; protein-DNA complex, D	97.64
2hh3_A		106	KH-type splicing regulatory protein; KH-RNA bindin	97.64
2cte_A		94	Vigilin; K homology type I domain, RNA-binding, ce	97.62
2ctk_A		104	Vigilin; K homology type I domain, RNA-binding, ce	97.6
2ctl_A		97	Vigilin; K homology type I domain, RNA-binding, ce	97.6
2ctm_A		95	Vigilin; K homology type I domain, RNA-binding, ce	97.28
2jvz_A		164	KH type-splicing, FAR upstream element-binding pro	97.23
2jzx_A		160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	97.05
3krm_A		163	Insulin-like growth factor 2 mRNA-binding protein	96.99
3krm_A		163	Insulin-like growth factor 2 mRNA-binding protein	96.96
2anr_A		178	Neuro-oncological ventral antigen 1; protein-RNA c	96.89
1j4w_A		174	FUSE binding protein; single-stranded DNA binding	96.89
1j4w_A		174	FUSE binding protein; single-stranded DNA binding	96.88
2anr_A		178	Neuro-oncological ventral antigen 1; protein-RNA c	96.76
2jzx_A		160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	96.66
2jvz_A		164	KH type-splicing, FAR upstream element-binding pro	96.62
2e3u_A		219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	96.5
2ctj_A		95	Vigilin; K homology type I domain, RNA-binding, ce	96.49
1tua_A		191	Hypothetical protein APE0754; structural genomics,	96.45
2cpq_A		91	FragIle X mental retardation syndrome related prot	95.71
3u1k_A		630	Polyribonucleotide nucleotidyltransferase 1, MITO;	95.02
2e3u_A		219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	94.09
2qnd_A		144	FMR1 protein; KH domain, eukaryotic KH domains, ta	92.78
3v69_A		140	Protein filia; RNA-binding, embryogenesis, KH doma	92.24
2ctf_A		102	Vigilin; K homology type I domain, RNA-binding, ce	91.8
4aid_A		726	Polyribonucleotide nucleotidyltransferase; transfe	91.21
2qnd_A		144	FMR1 protein; KH domain, eukaryotic KH domains, ta	91.09
3n89_A		376	Defective in GERM LINE development protein 3, ISO;	89.76
1tua_A		191	Hypothetical protein APE0754; structural genomics,	88.72

>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=99.96  E-value=2.3e-30  Score=211.73  Aligned_cols=77  Identities=35%  Similarity=0.665  Sum_probs=73.2

Q ss_pred             eEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccCCCCchHHHHhhccCCccc---eeeEEEEecCcc
Q 027518          143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARVIVMLLLSLFVF---IVHILYVSGISN  219 (222)
Q Consensus       143 ~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~kd~~kEe~lr~~~~~e~---~lHvli~~~~~~  219 (222)
                      +++|||||+++||+|||||+||||+|+|+|+||++|||||.||||||+||.++|++++++|+|+|   +|||+|+|.+..
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            57899999999999999999999999999999999999999999999999999999999999986   499999997763

PyMOL of 2bl5

>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

>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

>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

>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

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

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

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

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		222
d2bl5a1		134	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	9e-22
d2ctka1		91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	6e-04
d2je6i3		69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.002
d2ctea1		81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	0.002
d2z0sa2		87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	0.002
d1dtja_		74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	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 = 86.8 bits (215), 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

PyMOL of d2bl5a1

>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

>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

>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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		222
d2bl5a1		134	Quaking protein A (Xqua) {African clawed frog (Xen	99.97
d1k1ga_		122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	99.95
d1dtja_		74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	98.07
d1zzka1		75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	97.98
d1x4ma1		81	Far upstream binding element, FBP {Mouse (Mus musc	97.91
d1we8a_		104	Tudor and KH domain containing protein, Tdrkh {Mou	97.9
d1wvna1		70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	97.88
d1x4na1		79	Far upstream binding element, FBP {Mouse (Mus musc	97.87
d1j4wa2		71	Far upstream binding element, FBP {Human (Homo sap	97.81
d1j4wa1		74	Far upstream binding element, FBP {Human (Homo sap	97.79
d1e3ha4		54	Polynucleotide phosphorylase/guanosine pentaphosph	97.76
d1tuaa1		84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	97.72
d2je6i3		69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	97.67
d2ctka1		91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.64
d2axya1		71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	97.59
d2ctma1		81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.59
d2ba0a3		84	Exosome complex RNA-binding protein 1, ECR1 {Archa	97.58
d2ctea1		81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.53
d2cpqa1		78	Fragile X mental retardation syndrome related prot	97.53
d2z0sa2		87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	97.52
d1tuaa2		104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	97.38
d1viga_		71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.36
d2ctla1		84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.35
d2ctja1		82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	96.79
d2ctfa1		90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	96.61

>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=99.97  E-value=2.6e-32  Score=220.02  Aligned_cols=78  Identities=35%  Similarity=0.663  Sum_probs=74.3

Q ss_pred             eeEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccCCCCchHHHHhhccCCccc---eeeEEEEecCc
Q 027518          142 KRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARVIVMLLLSLFVF---IVHILYVSGIS  218 (222)
Q Consensus       142 K~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~kd~~kEe~lr~~~~~e~---~lHvli~~~~~  218 (222)
                      |+++|||||+++||+|||||+||||||+|+|+||++|||||.||||||+||.++|+++++.++|+|   +|||+|+|+++
T Consensus         1 kl~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~   80 (134)
T d2bl5a1           1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDA   80 (134)
T ss_dssp             CEEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSC
T ss_pred             CcceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCc
Confidence            578999999999999999999999999999999999999999999999999999999999999987   49999999875


Q ss_pred             c
Q 027518          219 N  219 (222)
Q Consensus       219 ~  219 (222)
                      .
T Consensus        81 ~   81 (134)
T d2bl5a1          81 Q   81 (134)
T ss_dssp             C
T ss_pred             H
Confidence            4

PyMOL of d2bl5a1

>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

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, 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

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {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

>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

>d2ctma1 d.51.1.1 (A:8-88) 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

>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

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}	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

>d2ctla1 d.51.1.1 (A:8-91) 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