Citrus Sinensis ID: 027853

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-------22

MMPNQGFGDFDRLRHRSPSPMASSNLMSNVAGTGLGGWNGLPQERLGGPPGMTMDWQSAPASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELAMLNSNFREDSPGPSGSVSPFNSSGMKRAKTGR

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccccccccEEEEEccccccHHHHHHHHHccEEEEEcccccccccccccccccccccccccccEEEEEEcccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccc

ccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccEEEEEEEEEEccccccccEEEEEcccccccHHHHHHHcccEEEEEEccccccHHHHHHHcccccccHcccccEEEEEEEccHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccc

mmpnqgfgdfdrlrhrspspmassnlmsnvagtglggwnglpqerlggppgmtmdwqsapaspssytvKRILRleipvdtypnfnfvgrllgprgnslkRVEATTgcrvyirgkgsikdpdkedklrgrpgyehlndplhilieadlpanIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELAMLNSnfredspgpsgsvspfnssgmkraktgr

mmpnqgfgdfdrlrhRSPSPMASSNLMSNVAGTGLGGWNGLPQERLGGPPGMTMDWQSAPASPSSYTVKRILRLEIPVDTYPNFNfvgrllgprgnslkrveattgcrvyirgkgsikdpdkedkLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEEllkpvdesqDYIKRQQLRELAMLNSnfredspgpsgsvspfnssgmkraktgr

*****************************************************************YTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK*****************YEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKPV************************************************

*******************************************************************VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKG********************NDPLHILIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELA********************************

*****G*G*FDRLRHRSPSPMASSNLMSNVAGTGLGGWNGLPQERLGGPPGMTMDWQSAPASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELAMLNSNF**************************

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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		218	2.2.26 [Sep-21-2011]
Q9ZVI3		286	KH domain-containing prot	yes	no	0.990	0.755	0.890	1e-108
Q8GYR4		283	KH domain-containing prot	no	no	1.0	0.770	0.866	1e-102
Q75GR5		281	KH domain-containing prot	no	no	0.995	0.772	0.761	2e-88
Q0WLR1		308	KH domain-containing prot	no	no	0.917	0.649	0.595	2e-63
Q9FKT4		315	KH domain-containing prot	no	no	0.903	0.625	0.605	8e-63
Q8GWR3		298	KH domain-containing prot	no	no	0.926	0.677	0.506	1e-52
Q6P104		319	Protein quaking-B OS=Dani	yes	no	0.665	0.454	0.445	1e-31
Q6IRN2		342	Protein quaking-B OS=Xeno	N/A	no	0.559	0.356	0.491	1e-31
Q91XU1		341	Protein quaking OS=Rattus	yes	no	0.559	0.357	0.491	1e-31
Q5W9D5		341	Protein quaking OS=Sus sc	yes	no	0.559	0.357	0.491	1e-31

>sp\|Q9ZVI3\|QKIL3_ARATH KH domain-containing protein At2g38610 OS=Arabidopsis thaliana GN=At2g38610 PE=1 SV=1	Back alignment and function desciption

 Score =  391 bits (1005), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 196/220 (89%), Positives = 205/220 (93%), Gaps = 4/220 (1%)

Query: 1   MMPNQGFGDFDRLRHRSPSPMASSNLMSNVAGTGLGGWNGLPQERLGGPPGMTMDWQSAP 60
           MM NQGFGDFDRLRHRSPSPMASSNLMSNV+ TGLGGWNGL QERL G PGMTMDWQ AP
Sbjct: 67  MMSNQGFGDFDRLRHRSPSPMASSNLMSNVSNTGLGGWNGLSQERLSGTPGMTMDWQGAP 126

Query: 61  ASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDP 120
            SPSSYTVKRILRLEIPVD YPNFNFVGRLLGPRGNSLKRVEATTGCRV+IRGKGSIKDP
Sbjct: 127 GSPSSYTVKRILRLEIPVDNYPNFNFVGRLLGPRGNSLKRVEATTGCRVFIRGKGSIKDP 186

Query: 121 DKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQ 180
           +KEDKLRGRPGYEHLN+ LHILIEADLPA+IV+IRLRQAQEIIEELLKPVDESQD+IKRQ
Sbjct: 187 EKEDKLRGRPGYEHLNEQLHILIEADLPASIVEIRLRQAQEIIEELLKPVDESQDFIKRQ 246

Query: 181 QLRELAMLNS-NFREDSPGPS--GSVSPFNSSGMKRAKTG 217
           QLRELA+LNS N RE+SPGPS  GSVSPFNSSG KR KTG
Sbjct: 247 QLRELALLNSNNLREESPGPSGGGSVSPFNSSG-KRPKTG 285

Arabidopsis thaliana (taxid: 3702)

>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\|Q0WLR1\|QKIL1_ARATH KH domain-containing protein At4g26480 OS=Arabidopsis thaliana GN=At4g26480 PE=2 SV=1	Back alignment and function description

>sp\|Q9FKT4\|QKIL2_ARATH KH domain-containing protein At5g56140 OS=Arabidopsis thaliana GN=At5g56140 PE=2 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\|Q6P104\|QKIB_DANRE Protein quaking-B OS=Danio rerio GN=qkib PE=2 SV=1	Back alignment and function description

>sp\|Q6IRN2\|QKIB_XENLA Protein quaking-B OS=Xenopus laevis GN=qki-b PE=1 SV=1	Back alignment and function description

>sp\|Q91XU1\|QKI_RAT Protein quaking OS=Rattus norvegicus GN=Qki PE=1 SV=2	Back alignment and function description

>sp\|Q5W9D5\|QKI_PIG Protein quaking OS=Sus scrofa GN=QKI PE=2 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		218
255582022		680	conserved hypothetical protein [Ricinus	0.990	0.317	0.953	1e-118
224069102		281	predicted protein [Populus trichocarpa]	1.0	0.775	0.949	1e-118
356568258		281	PREDICTED: KH domain-containing protein	1.0	0.775	0.944	1e-117
225439096		281	PREDICTED: KH domain-containing protein	1.0	0.775	0.940	1e-117
356532119		281	PREDICTED: KH domain-containing protein	1.0	0.775	0.940	1e-117
255647494		281	unknown [Glycine max]	1.0	0.775	0.935	1e-116
356560101		281	PREDICTED: KH domain-containing protein	1.0	0.775	0.917	1e-114
356506347		281	PREDICTED: KH domain-containing protein	1.0	0.775	0.917	1e-113
357506731		281	KH domain-containing protein [Medicago t	1.0	0.775	0.908	1e-113
255637373		281	unknown [Glycine max]	1.0	0.775	0.912	1e-113

>gi\|255582022\|ref\|XP_002531808.1\| conserved hypothetical protein [Ricinus communis] gi\|223528542\|gb\|EEF30565.1\| conserved hypothetical protein [Ricinus communis]	Back alignment and taxonomy information

 Score =  430 bits (1106), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 206/216 (95%), Positives = 212/216 (98%)

Query: 1   MMPNQGFGDFDRLRHRSPSPMASSNLMSNVAGTGLGGWNGLPQERLGGPPGMTMDWQSAP 60
           MM NQGFGDFDRLRHRSPSPMASSNLMSNV+GTGLG WNGLPQERL GPPGMTMDWQSAP
Sbjct: 64  MMSNQGFGDFDRLRHRSPSPMASSNLMSNVSGTGLGSWNGLPQERLSGPPGMTMDWQSAP 123

Query: 61  ASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDP 120
           ASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDP
Sbjct: 124 ASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDP 183

Query: 121 DKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQ 180
           DKE+KLRGRPGYEHLNDPLHILIEADLPANIV++RLRQAQEII ELLKPVDESQD+IKRQ
Sbjct: 184 DKEEKLRGRPGYEHLNDPLHILIEADLPANIVEMRLRQAQEIIGELLKPVDESQDFIKRQ 243

Query: 181 QLRELAMLNSNFREDSPGPSGSVSPFNSSGMKRAKT 216
           QLRELAMLNSNFREDSPGPSGSVSPFN+SGMKRAKT
Sbjct: 244 QLRELAMLNSNFREDSPGPSGSVSPFNTSGMKRAKT 279

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224069102\|ref\|XP_002326275.1\| predicted protein [Populus trichocarpa] gi\|222833468\|gb\|EEE71945.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356568258\|ref\|XP_003552330.1\| PREDICTED: KH domain-containing protein At2g38610-like [Glycine max]	Back alignment and taxonomy information

>gi\|225439096\|ref\|XP_002268790.1\| PREDICTED: KH domain-containing protein At2g38610 [Vitis vinifera] gi\|296085835\|emb\|CBI31159.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356532119\|ref\|XP_003534621.1\| PREDICTED: KH domain-containing protein At2g38610-like [Glycine max]	Back alignment and taxonomy information

>gi\|255647494\|gb\|ACU24211.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|356560101\|ref\|XP_003548334.1\| PREDICTED: KH domain-containing protein At2g38610-like [Glycine max]	Back alignment and taxonomy information

>gi\|356506347\|ref\|XP_003521946.1\| PREDICTED: KH domain-containing protein At2g38610-like [Glycine max]	Back alignment and taxonomy information

>gi\|357506731\|ref\|XP_003623654.1\| KH domain-containing protein [Medicago truncatula] gi\|355498669\|gb\|AES79872.1\| KH domain-containing protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|255637373\|gb\|ACU19015.1\| unknown [Glycine max]	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		218
TAIR\|locus:2077818		283	AT3G08620 "AT3G08620" [Arabido	1.0	0.770	0.866	4.2e-102
TAIR\|locus:2064097		286	AT2G38610 "AT2G38610" [Arabido	0.990	0.755	0.890	3e-101
UNIPROTKB\|Q75GR5		281	SPIN1 "KH domain-containing pr	0.981	0.761	0.772	4.1e-88
TAIR\|locus:2161845		315	AT5G56140 "AT5G56140" [Arabido	0.899	0.622	0.606	4.3e-61
TAIR\|locus:2024326		298	AT1G09660 "AT1G09660" [Arabido	0.935	0.684	0.511	6.5e-51
ZFIN\|ZDB-GENE-081028-54		345	qkib "QKI, KH domain containin	0.665	0.420	0.452	4.2e-31
ZFIN\|ZDB-GENE-040426-1462		319	qki2 "QKI, KH domain containin	0.665	0.454	0.445	4.2e-31
WB\|WBGene00001595		463	gld-1 [Caenorhabditis elegans	0.587	0.276	0.449	6.1e-31
UNIPROTKB\|F1N7N1		315	QKI "Protein quaking" [Bos tau	0.559	0.387	0.491	6.9e-31
UNIPROTKB\|Q5W9D7		341	QKI "Protein quaking" [Bos tau	0.559	0.357	0.491	6.9e-31

TAIR\|locus:2077818 AT3G08620 "AT3G08620" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1012 (361.3 bits), Expect = 4.2e-102, P = 4.2e-102
 Identities = 189/218 (86%), Positives = 205/218 (94%)

Query:     1 MMPNQGFGDFDRLRHRSPSPMASSNLMSNVAGTGLGGWNGLPQERLGGPPGMTMDWQSAP 60
             MMPNQGF DFDRLRHRSPSPMAS NLMSNV+G GLGGWNGLP ER+GGP GM M+WQ AP
Sbjct:    66 MMPNQGFTDFDRLRHRSPSPMASPNLMSNVSGGGLGGWNGLPPERIGGPHGMAMEWQGAP 125

Query:    61 ASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDP 120
             ASPSSY VKRILRL++PVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDP
Sbjct:   126 ASPSSYPVKRILRLDLPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDP 185

Query:   121 DKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQ 180
             +KE+KL+G+PGYEHLN+ LHILIEADLP +IVDI+LRQAQEIIEEL+KPVDESQDYIKRQ
Sbjct:   186 EKEEKLKGKPGYEHLNEQLHILIEADLPIDIVDIKLRQAQEIIEELVKPVDESQDYIKRQ 245

Query:   181 QLRELAMLNSNFREDSPGPSGSVSPFNSSGMKRAKTGR 218
             QLRELA+LNSN RE+SPGPSGSVSPFNS+ MKR KTGR
Sbjct:   246 QLRELALLNSNLRENSPGPSGSVSPFNSNAMKRPKTGR 283

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0010048 "vernalization response" evidence=RCA

TAIR\|locus:2064097 AT2G38610 "AT2G38610" [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

TAIR\|locus:2161845 AT5G56140 "AT5G56140" [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

ZFIN\|ZDB-GENE-081028-54 qkib "QKI, KH domain containing, RNA binding b" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040426-1462 qki2 "QKI, KH domain containing, RNA binding 2" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

WB\|WBGene00001595 gld-1 [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

UNIPROTKB\|F1N7N1 QKI "Protein quaking" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5W9D7 QKI "Protein quaking" [Bos taurus (taxid:9913)]	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)
Q9ZVI3	QKIL3_ARATH	No assigned EC number	0.8909	0.9908	0.7552	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:
	estExt_fgenesh4_pm.C_280159	hypothetical protein (281 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		218
cd02395		120	cd02395, SF1_like-KH, Splicing factor 1 (SF1) K ho	2e-51
COG5176		269	COG5176, MSL5, Splicing factor (branch point bindi	3e-23
smart00322		68	smart00322, KH, K homology RNA-binding domain	2e-05
cd00105		64	cd00105, KH-I, K homology RNA-binding domain, type	4e-05
pfam00013		59	pfam00013, KH_1, KH domain	0.004

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

 Score =  162 bits (411), Expect = 2e-51
 Identities = 67/122 (54%), Positives = 90/122 (73%), Gaps = 5/122 (4%)

Query: 73  RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGY 132
           ++ IPV  YP +NFVG +LGPRGN+LK++E  TG ++ IRGKGS+KD  KE++LRG P Y
Sbjct: 3   KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRG-PKY 61

Query: 133 EHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKP-VDESQDYIKRQQLRELAMLNSN 191
            HLN+PLH+LI A+ P    +  L +A E IEELLKP ++   D +KR+QLRELA+LN  
Sbjct: 62  AHLNEPLHVLITAETPP---EEALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGT 118

Query: 192 FR 193
           +R
Sbjct: 119 YR 120

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 120

>gnl\|CDD\|227503 COG5176, MSL5, Splicing factor (branch point binding protein) [RNA processing and modification]	Back alignment and domain information

>gnl\|CDD\|197652 smart00322, KH, K homology RNA-binding domain	Back alignment and domain information

>gnl\|CDD\|238053 cd00105, KH-I, K homology RNA-binding domain, type I	Back alignment and domain information

>gnl\|CDD\|215657 pfam00013, KH_1, KH domain	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		218
KOG1588		259	consensus RNA-binding protein Sam68 and related KH	100.0
cd02395		120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	100.0
KOG0119		554	consensus Splicing factor 1/branch point binding p	100.0
COG5176		269	MSL5 Splicing factor (branch point binding protein	99.97
KOG1960		531	consensus Predicted RNA-binding protein, contains	98.59
cd00105		64	KH-I K homology RNA-binding domain, type I. KH bin	98.5
cd02393		61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.47
PF00013		60	KH_1: KH domain syndrome, contains KH motifs.; Int	98.37
smart00322		69	KH K homology RNA-binding domain.	98.33
PF13014		43	KH_3: KH domain	98.25
cd02396		65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	98.15
cd02394		62	vigilin_like_KH K homology RNA-binding domain_vigi	98.1
TIGR03665		172	arCOG04150 arCOG04150 universal archaeal KH domain	97.98
PRK13763		180	putative RNA-processing protein; Provisional	97.89
PRK13763		180	putative RNA-processing protein; Provisional	97.51
COG1094		194	Predicted RNA-binding protein (contains KH domains	97.5
TIGR03665		172	arCOG04150 arCOG04150 universal archaeal KH domain	97.45
TIGR02696		719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.39
KOG2874		356	consensus rRNA processing protein [Translation, ri	96.97
TIGR03591		684	polynuc_phos polyribonucleotide nucleotidyltransfe	96.87
KOG1676		600	consensus K-homology type RNA binding proteins [RN	96.71
KOG1676		600	consensus K-homology type RNA binding proteins [RN	96.61
KOG2193		584	consensus IGF-II mRNA-binding protein IMP, contain	96.39
PRK04163		235	exosome complex RNA-binding protein Rrp4; Provisio	96.28
PLN00207		891	polyribonucleotide nucleotidyltransferase; Provisi	96.15
KOG1960		531	consensus Predicted RNA-binding protein, contains	95.83
KOG2191		402	consensus RNA-binding protein NOVA1/PASILLA and re	95.64
KOG2193		584	consensus IGF-II mRNA-binding protein IMP, contain	95.57
PRK11824		693	polynucleotide phosphorylase/polyadenylase; Provis	95.49
KOG2814		345	consensus Transcription coactivator complex, P50 c	94.93
KOG2191		402	consensus RNA-binding protein NOVA1/PASILLA and re	94.67
PRK00106		535	hypothetical protein; Provisional	94.5
PRK12704		520	phosphodiesterase; Provisional	94.23
TIGR03319		514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	94.19
KOG2190		485	consensus PolyC-binding proteins alphaCP-1 and rel	93.4
COG1185		692	Pnp Polyribonucleotide nucleotidyltransferase (pol	92.41
cd02134		61	NusA_KH NusA_K homology RNA-binding domain (KH). N	91.64
KOG0336		629	consensus ATP-dependent RNA helicase [RNA processi	87.27
KOG1067		760	consensus Predicted RNA-binding polyribonucleotide	85.86
PF13184		69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	82.18
PRK12705		508	hypothetical protein; Provisional	81.2

>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=1.4e-53  Score=376.95  Aligned_cols=155  Identities=55%  Similarity=0.896  Sum_probs=147.5

Q ss_pred             CCCCccceeeEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCce
Q 027853           61 ASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLH  140 (218)
Q Consensus        61 ~~~~~~~vk~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLH  140 (218)
                      -.++.+++|.+.||+|||++||+||||||||||||+|+||||++|||||+||||||+||..||+++|++|+|+|+++|||
T Consensus        83 ~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLH  162 (259)
T KOG1588|consen   83 DVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLH  162 (259)
T ss_pred             cCccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcE
Confidence            47889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecCchhhHHHHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHHHhcCc-cCCCCCCCCC---CCCCCCccccccccc
Q 027853          141 ILIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELAMLNSN-FREDSPGPSG---SVSPFNSSGMKRAKT  216 (218)
Q Consensus       141 VlI~a~~~~~~~~~rl~~A~e~Ie~LL~pv~e~~d~~K~~QL~ELA~lNGt-~r~~~~~~~~---~~~p~~~~~~~~~~~  216 (218)
                      |+|++++++++|+.||++|++.|++||+|.+++.|  |++||+|||++||| +++.+..++|   +.+||++.++||+||
T Consensus       163 VlIe~~~p~~ea~~rl~~AleeI~klL~P~~e~~d--k~~QL~ELa~lngt~~~~~~~~~~g~~~~~~~~~~~~~~r~~~  240 (259)
T KOG1588|consen  163 VLIETEAPPAEAYARLAYALEEIKKLLVPDHEDED--KREQLRELAILNGTYLRSESRKPSGGNGRGVPGNSAGGKRGKT  240 (259)
T ss_pred             EEEEEeCCHHHHHHHHHHHHHHHHHhcCCCCCCch--HHHHHHHHhhcCCccccccccccCCCCCcCCCCCCCCcccccC
Confidence            99999999999999999999999999999998888  99999999999999 6666666666   799999999999998


Q ss_pred             C
Q 027853          217 G  217 (218)
Q Consensus       217 ~  217 (218)
                      +
T Consensus       241 ~  241 (259)
T KOG1588|consen  241 G  241 (259)
T ss_pred             C
Confidence            6

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

>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

>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]	Back alignment and domain information

>cd00105 KH-I K homology RNA-binding domain, type I	Back alignment and domain information

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)	Back alignment and domain information

>PF00013 KH_1: KH domain syndrome, contains KH motifs	Back alignment and domain information

>smart00322 KH K homology RNA-binding domain	Back alignment and domain information

>PF13014 KH_3: KH domain	Back alignment and domain information

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like	Back alignment and domain information

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like	Back alignment and domain information

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

>PRK13763 putative RNA-processing protein; Provisional	Back alignment and domain information

>PRK13763 putative RNA-processing protein; Provisional	Back alignment and domain information

>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

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase	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

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase	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

>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

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional	Back alignment and domain information

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional	Back alignment and domain information

>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [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

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional	Back alignment and domain information

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

>PRK00106 hypothetical protein; Provisional	Back alignment and domain information

>PRK12704 phosphodiesterase; Provisional	Back alignment and domain information

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF	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

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

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

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]	Back alignment and domain information

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

>PRK12705 hypothetical protein; 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		218
2bl5_A		140	Solution Structure Of The Kh-Qua2 Region Of The Xen		7e-32
1k1g_A		131	Structural Basis For Recognition Of The Intron Bran		9e-18

>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 = 133 bits (335), Expect = 7e-32, Method: Compositional matrix adjust. Identities = 58/122 (47%), Positives = 92/122 (75%) Query: 73 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGY 132 +L +PV YP+FNFVGR+LGPRG + K++EA TGC++ +RGKGS++D KE++ RG+P + Sbjct: 5 KLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNW 64 Query: 133 EHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELAMLNSNF 192 EHLN+ LH+LI + N +++L++A E +++LL P E +D +K+ +L ELA+LN + Sbjct: 65 EHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLMELAILNGTY 124 Query: 193 RE 194 R+ Sbjct: 125 RD 126

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		218
2bl5_A		140	MGC83862 protein, quaking protein; STAR proteins,	3e-58
1k1g_A		131	SF1-BO isoform; splicing, branch point sequence, p	5e-49
2yqr_A		119	KIAA0907 protein; structure genomics, KH domain, s	4e-29
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-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

>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

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		218
2bl5_A		140	MGC83862 protein, quaking protein; STAR proteins,	100.0
1k1g_A		131	SF1-BO isoform; splicing, branch point sequence, p	100.0
2yqr_A		119	KIAA0907 protein; structure genomics, KH domain, s	99.96
2opv_A		85	KHSRP protein; KH domain, RNA binding protein, KSR	98.91
1dtj_A		76	RNA-binding neurooncological ventral antigen 2; KH	98.84
1x4m_A		94	FAR upstream element binding protein 1; KH domain,	98.73
1x4n_A		92	FAR upstream element binding protein 1; KH domain,	98.67
2hh2_A		107	KH-type splicing regulatory protein; KH-RNA bindin	98.65
1zzk_A		82	Heterogeneous nuclear ribonucleoprotein K; KH domi	98.61
1ec6_A		87	RNA-binding protein NOVA-2; KH domain, alpha-beta	98.58
2p2r_A		76	Poly(RC)-binding protein 2; protein-DNA complex, R	98.57
1we8_A		104	Tudor and KH domain containing protein; structural	98.55
1wvn_A		82	Poly(RC)-binding protein 1; KH domain, RNA binding	98.54
2dgr_A		83	Ring finger and KH domain-containing protein 1; st	98.51
2cte_A		94	Vigilin; K homology type I domain, RNA-binding, ce	98.51
2hh3_A		106	KH-type splicing regulatory protein; KH-RNA bindin	98.5
1vig_A		71	Vigilin; RNA-binding protein, ribonucleoprotein; N	98.48
1j5k_A		89	Heterogeneous nuclear ribonucleoprotein K; single-	98.48
2axy_A		73	Poly(RC)-binding protein 2; protein-DNA complex, D	98.42
2ctk_A		104	Vigilin; K homology type I domain, RNA-binding, ce	98.38
2ctl_A		97	Vigilin; K homology type I domain, RNA-binding, ce	98.32
2ctm_A		95	Vigilin; K homology type I domain, RNA-binding, ce	98.29
3krm_A		163	Insulin-like growth factor 2 mRNA-binding protein	98.24
1j4w_A		174	FUSE binding protein; single-stranded DNA binding	98.14
2jvz_A		164	KH type-splicing, FAR upstream element-binding pro	98.08
2jvz_A		164	KH type-splicing, FAR upstream element-binding pro	98.0
2jzx_A		160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	97.95
2ctj_A		95	Vigilin; K homology type I domain, RNA-binding, ce	97.92
1tua_A		191	Hypothetical protein APE0754; structural genomics,	97.87
1j4w_A		174	FUSE binding protein; single-stranded DNA binding	97.85
2jzx_A		160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	97.82
2anr_A		178	Neuro-oncological ventral antigen 1; protein-RNA c	97.8
2anr_A		178	Neuro-oncological ventral antigen 1; protein-RNA c	97.78
2e3u_A		219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	97.73
3krm_A		163	Insulin-like growth factor 2 mRNA-binding protein	97.7
2cpq_A		91	FragIle X mental retardation syndrome related prot	97.66
3u1k_A		630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.27
2qnd_A		144	FMR1 protein; KH domain, eukaryotic KH domains, ta	96.52
2e3u_A		219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	96.25
2ctf_A		102	Vigilin; K homology type I domain, RNA-binding, ce	95.78
4aid_A		726	Polyribonucleotide nucleotidyltransferase; transfe	95.74
3n89_A		376	Defective in GERM LINE development protein 3, ISO;	95.56
2qnd_A		144	FMR1 protein; KH domain, eukaryotic KH domains, ta	94.29
3v69_A		140	Protein filia; RNA-binding, embryogenesis, KH doma	92.24
3cdi_A		723	Polynucleotide phosphorylase; mRNA turnover, RNAse	91.63
3n89_A		376	Defective in GERM LINE development protein 3, ISO;	88.09
4fxw_B		124	Splicing factor 1; UHM, protein binding, phosphory	87.41
1e3p_A		757	Guanosine pentaphosphate synthetase; polyribonucle	85.99
1tua_A		191	Hypothetical protein APE0754; structural genomics,	85.06

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

Probab=100.00  E-value=6.3e-50  Score=326.23  Aligned_cols=129  Identities=45%  Similarity=0.851  Sum_probs=124.8

Q ss_pred             eEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCch
Q 027853           70 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPA  149 (218)
Q Consensus        70 ~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~  149 (218)
                      .++|||||+++||+|||||+||||||+|+|+||++|||||.|||+||+|+.++|+.++|+|+|+|++|||||+|+|++++
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            57899999999999999999999999999999999999999999999999999988999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHHHhcCccCCCCCC
Q 027853          150 NIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELAMLNSNFREDSPG  198 (218)
Q Consensus       150 ~~~~~rl~~A~e~Ie~LL~pv~e~~d~~K~~QL~ELA~lNGt~r~~~~~  198 (218)
                      ++|+++|++|+++|++||.|+++++|++|++||+|||+||||||++...
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p~~e~~de~K~~QL~eLA~lNGt~r~~~~~  130 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLMELAILNGTYRDANLK  130 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCSSSSSHHHHHHHTGGGSSSTTTSGGGGS
T ss_pred             hhHHHHHHHHHHHHHHHCCCCCcchhHHHHHHHHHHHHhcCCcCCCccc
Confidence            9999999999999999999999999999999999999999999998653

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

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

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A	Back alignment and structure

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1	Back alignment and structure

>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

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; 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

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

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1	Back alignment and structure

>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

>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

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

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

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

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

>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

>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

>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

>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

>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

>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

>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

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*	Back alignment and structure

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*	Back alignment and structure

>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

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}	Back alignment and structure

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

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

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A	Back alignment and structure

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

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>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

>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

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_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

>4fxw_B Splicing factor 1; UHM, protein binding, phosphorylat; HET: SEP; 2.29A {Homo sapiens} PDB: 4fxx_A	Back alignment and structure

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A	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		218
d2bl5a1		134	d.51.1.1 (A:1-134) Quaking protein A (Xqua) {Afric	6e-59
d1k1ga_		122	d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo s	2e-47
d1dtja_		74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	3e-05
d2ctka1		91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-04
d1e3ha4		54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	3e-04
d2je6i3		69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	4e-04
d2z0sa2		87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	8e-04
d2ctea1		81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	0.001
d1viga_		71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	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 =  179 bits (457), Expect = 6e-59
 Identities = 59/129 (45%), Positives = 95/129 (73%), Gaps = 1/129 (0%)

Query: 73  RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGY 132
           +L +PV  YP+FNFVGR+LGPRG + K++EA TGC++ +RGKGS++D  KE++ RG+P +
Sbjct: 5   KLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNW 64

Query: 133 EHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELAMLNSNF 192
           EHLN+ LH+LI  +   N  +++L++A E +++LL P  E +D +K+ +L ELA+LN  +
Sbjct: 65  EHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLMELAILNGTY 124

Query: 193 REDS-PGPS 200
           R+ +   P+
Sbjct: 125 RDANLKSPA 133

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

>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

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91	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]} Length = 54	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

>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

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81	Back information, alignment and structure

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71	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		218
d2bl5a1		134	Quaking protein A (Xqua) {African clawed frog (Xen	100.0
d1k1ga_		122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	100.0
d1dtja_		74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	98.75
d1j4wa2		71	Far upstream binding element, FBP {Human (Homo sap	98.67
d1x4ma1		81	Far upstream binding element, FBP {Mouse (Mus musc	98.66
d1we8a_		104	Tudor and KH domain containing protein, Tdrkh {Mou	98.61
d1tuaa2		104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.52
d1zzka1		75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	98.52
d1j4wa1		74	Far upstream binding element, FBP {Human (Homo sap	98.51
d2cpqa1		78	Fragile X mental retardation syndrome related prot	98.5
d1x4na1		79	Far upstream binding element, FBP {Mouse (Mus musc	98.49
d1tuaa1		84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.42
d1wvna1		70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	98.41
d2ctka1		91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.37
d2ctma1		81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.34
d2ctea1		81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.29
d2z0sa2		87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.29
d2axya1		71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	98.26
d1viga_		71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.23
d2ba0a3		84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.19
d2je6i3		69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.16
d2ctla1		84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.09
d2ctja1		82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.81
d1e3ha4		54	Polynucleotide phosphorylase/guanosine pentaphosph	97.73
d2ctfa1		90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.63
d2ja9a2		85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	90.24

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}	Back information, alignment and structure

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

Probab=100.00  E-value=2.2e-51  Score=330.73  Aligned_cols=129  Identities=45%  Similarity=0.857  Sum_probs=124.9

Q ss_pred             eeEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCc
Q 027853           69 KRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLP  148 (218)
Q Consensus        69 k~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~  148 (218)
                      |.++|||||+++||+|||||+||||||+|+|+||++|||||+||||||+|+.++++.++++++|+|++|||||+|+|+++
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            56899999999999999999999999999999999999999999999999999998889999999999999999999999


Q ss_pred             hhhHHHHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHHHhcCccCCCCC
Q 027853          149 ANIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELAMLNSNFREDSP  197 (218)
Q Consensus       149 ~~~~~~rl~~A~e~Ie~LL~pv~e~~d~~K~~QL~ELA~lNGt~r~~~~  197 (218)
                      +.+++++|++|+++|++||.|+++++|++|++||+|||+||||||++..
T Consensus        81 ~~~a~~kl~~A~~~I~~lL~p~~e~~de~k~~QL~eLa~lNGt~r~~~~  129 (134)
T d2bl5a1          81 QNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLMELAILNGTYRDANL  129 (134)
T ss_dssp             CHHHHHHHHHHHHHHHHHSSCCSSSSSHHHHHHHTGGGSSSTTTSGGGG
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCccchHHHHHHHHHHHHHhcCccccccC
Confidence            9999999999999999999999999999999999999999999999974

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

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {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

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}	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

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {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

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}	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

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {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

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

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}	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

>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

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}	Back information, alignment and structure