Citrus Sinensis ID: 013091

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------45

MSSAPWYLNSEKPSLKHQRKWKSDPNYTKSWYDRGAKVFHAEKYRKGACANCGAMTHDAKSCMERPRKMGAKWTNINIAPDEKIETFELDYDGKRDRWNGYDTSSYARVVERYEARDDARRKFNKEQQLKKLEEKNNNNDSGGGGDSDGEDEDDDLRIDEAKVDESKQMDFAKVEKRVRTTGGGSTGTVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFYGGDNQYRNSGQALEFKELNIHAWEAFDKGQDIHMQAAPSQAELLYKNYIVIKDKLKSRTKETIMEKYGNAAAEEELPRELLLGQSEREIEYDRAGRIIKGQETALPRSKYEEDVYINNHTCVWGSWWKDHQWGYKCCKQVIRNSYCTGAAGIEAAEAASDLMKANIARKEASEETQTPVEGKRLATWGTDLPDDLVLDEDLLAEALKKVSMSSNL

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHccHHHHHHHHHcccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccEEccccHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHcccccEEEEcccccccccccccccccccccccccccccEEEEccccccccEEccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHcccccccccccccccccHHHHHHHHHHHHccccc

cccccEEEccccccccccccccccHHHHHHHHHccccccHHHHHcccccHcccccccccccHcccccccccEEcccccccccEEEEccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHccHHcccccccccccEEEcccccccEEEccEEHHHHHHHHHcccccccccccccccccccccccccHHHHHHcccccEEccccHHHHHHHHHHHHHHHHccccEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHcccccHHHHHHccccEEEEccccEEEcccccccEccccHHccEcccccEEEEccccccccccHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHcHHHHcccccHHHHHHHHHcccccccccEccHHHHHHHHHcccccccc

mssapwylnsekpslkhqrkwksdpnytkswydrgakvfhaekyrkgacancgamthdakscmerprkmgakwtniniapdekietfeldydgkrdrwngydtssyARVVERYEARDDARRKFNKEQQLKKLEEknnnndsggggdsdgededddlrideakvdeskqmDFAKVEKRVrttgggstgtvrnlRIREDTAKYLLNLdvnsahydpktrsmredplpdadpndkfyggdnqyrnsgqalefkELNIHAWEafdkgqdihmQAAPSQAELLYKNYIVIKDKLKSRTKETIMEKYgnaaaeeelprelllgqserEIEYDRAGriikgqetalprskyeedvyinnhtcvwgswwkdhqwgykcckqvirnsyctgaaGIEAAEAASDLMKANIARkeaseetqtpvegkrlatwgtdlpddlvLDEDLLAEALKKVSMSSNL

mssapwylnsekpslkhqrkwksdpnytkSWYDRGAKVFHAEKYRKGACANCGAMTHDAKSCMERPRKMGAkwtniniapdekietfeldydgkrdrwngydtssyarvvERYEARDDARRKFNKeqqlkkleeknnnndsggggdsdgedeDDDLRIdeakvdeskqmdfakvekrvrttgggstgtvrnlrirEDTAKYLlnldvnsahydpktrsmredplpdaDPNDKFYGGDNQYRNSGQALEFKELNIHAWEAFDKGQDIHMQAAPSQAELLYKNYIVIKDKLKSRTKETIMEKygnaaaeeelprelllgqsereieydragriikgqetalprskyeedVYINNHTCVWGSWWKDHQWGYKCCKQVIRNSYCTGAAGIEAAEAASDLMKANIARkeaseetqtpvegkrlatwgtdlpDDLVLDEDLLAEAlkkvsmssnl

MSSAPWYLNSEKPSLKHQRKWKSDPNYTKSWYDRGAKVFHAEKYRKGACANCGAMTHDAKSCMERPRKMGAKWTNINIAPDEKIETFELDYDGKRDRWNGYDTSSYARVVERYEARDDARRKFnkeqqlkkleeknnnndsggggdsdgededddLRIDEAKVDESKQMDFAKVEKRVRttgggstgtVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFYGGDNQYRNSGQALEFKELNIHAWEAFDKGQDIHMQAAPSQAELLYKNYIVIKDKLKSRTKETIMEKYGNaaaeeelprelllGQSEREIEYDRAGRIIKGQETALPRSKYEEDVYINNHTCVWGSWWKDHQWGYKCCKQVIRNSYCTgaagieaaeaaSDLMKANIARKEASEETQTPVEGKRLATWGTdlpddlvldedllaealKKVSMSSNL

**************************YTKSWYDRGAKVFHAEKYRKGACANCGAMTHDAKSCME**RKMGAKWTNINIAPDEKIETFELDYDGKRDRWNGYDTSSYARVVER****************************************************************************VRNLRIREDTAKYLLNLDVN************************************QALEFKELNIHAWEAFDKGQDIHMQAAPSQAELLYKNYIVIKDKLK*********************************EYDRAGRIIKGQETALPRSKYEEDVYINNHTCVWGSWWKDHQWGYKCCKQVIRNSYCTGAAGIEAA****************************LATWGTDLPDDLVLDEDLL*************

MSSAPWYLNSEKPSL*****************************************H***SCMERPRKMGAKWTNINIAPDEKIETFELDYDGKRDRWNGYDTSSYARVVERY***********************************************************************************DTAKYLLNLDVNSAHYD************************NQYRNSGQALEFKELNIHAWEAFDKG*******************************************************************************KYEEDVYINNHTCVWGSWWKDHQWGYKCCKQVIRNSYCTGAAGIEA*************************************************************

MSSAPWYLNS**************PNYTKSWYDRGAKVFHAEKYRKGACANCGAMTHDAKSCMERPRKMGAKWTNINIAPDEKIETFELDYDGKRDRWNGYDTSSYARVVERYEARDDARRKFNKEQQLKKLEEKNN***************DDDLRIDEAKVDESKQMDFAKVEKRVRTTGGGSTGTVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFYGGDNQYRNSGQALEFKELNIHAWEAFDKGQDIHMQAAPSQAELLYKNYIVIKDKLKSRTKETIMEKYGNAAAEEELPRELLLGQSEREIEYDRAGRIIKGQETALPRSKYEEDVYINNHTCVWGSWWKDHQWGYKCCKQVIRNSYCTGAAGIEAAEAASDLMKANIAR***********EGKRLATWGTDLPDDLVLDEDLLAEALK********

*SSAPWYLNSEKPSLKHQRKWKSDPNYTKSWYDRGAKVFHAEKYRKGACANCGAMTHDAKSCMERPRKMGAKWTNINIAPDEKIETFELDYDGKRDRWNGYDTSSYARVVERYEARDDARRKFNKEQQLKK***************************************FAKVEKRVRTTGGGSTGTVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFYGGDNQYRNSGQALEFKELNIHAWEAFDKGQDIHMQAAPSQAELLYKNYIVIKDKLKSRTKETIMEKYGNAAAEEELPRELLLGQSEREIEYDRAGRIIKGQETALPRSKYEEDVYINNHTCVWGSWWKDHQWGYKCCKQVIRNSYCTGAAGIEAAEAASDLMKANIAR******************WGTDLPDDLVLDEDLLAEALKK*******

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MSSAPWYLNSEKPSLKHQRKWKSDPNYTKSWYDRGAKVFHAEKYRKGACANCGAMTHDAKSCMERPRKMGAKWTNINIAPDEKIETFELDYDGKRDRWNGYDTSSYARVVERYExxxxxxxxxxxxxxxxxxxxxNNNNDSGGGGDSDGEDEDDDLRIDEAKVDESKQMDFAKVEKRVRTTGGGSTGTVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFYGGDNQYRNSGQALEFKELNIHAWEAFDKGQDIHMQAAPSQAELLYKNYIVIKDKLKSRTKETIMEKYGNAAAEEELPRELLLGQSEREIEYDRAGRIIKGQETALPRSKYEEDVYINNHTCVWGSWWKDHQWGYKCCKQVIRNSYCTGAAGIExxxxxxxxxxxxxxxxxxxxxTQTPVEGKRLATWGTDLPDDLVLDEDLLAEALKKVSMSSNL

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		449	2.2.26 [Sep-21-2011]
Q9SHY8		535	Pre-mRNA-splicing factor	yes	no	0.991	0.831	0.820	0.0
Q6ZK48		536	Pre-mRNA-splicing factor	yes	no	0.982	0.822	0.807	0.0
A2YQU8		536	Pre-mRNA-splicing factor	N/A	no	0.982	0.822	0.807	0.0
O23174		536	Pre-mRNA-splicing factor	no	no	0.991	0.830	0.775	0.0
Q5ZIG2		564	Pre-mRNA-splicing factor	yes	no	0.886	0.705	0.476	1e-101
Q5U3F2		571	Pre-mRNA-splicing factor	yes	no	0.879	0.691	0.457	1e-101
Q54TA0		558	Pre-mRNA-splicing factor	yes	no	0.806	0.648	0.497	1e-100
Q3ZBE5		586	Pre-mRNA-splicing factor	yes	no	0.837	0.641	0.481	2e-97
Q8BHJ9		585	Pre-mRNA-splicing factor	yes	no	0.864	0.663	0.465	3e-97
Q80ZG5		586	Pre-mRNA-splicing factor	yes	no	0.837	0.641	0.479	5e-97

>sp\|Q9SHY8\|SLU7A_ARATH Pre-mRNA-splicing factor SLU7-A OS=Arabidopsis thaliana GN=At1g65660 PE=1 SV=2	Back alignment and function desciption

 Score =  760 bits (1963), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/446 (82%), Positives = 415/446 (93%), Gaps = 1/446 (0%)

Query: 1   MSSAPWYLNSEKPSLKHQRKWKSDPNYTKSWYDRGAKVFHAEKYRKGACANCGAMTHDAK 60
           MSSAPWYLNSEKPSLKHQRKWKSDPNYTKSWYDRGAK+F AEKYRKGAC NCGAMTH AK
Sbjct: 48  MSSAPWYLNSEKPSLKHQRKWKSDPNYTKSWYDRGAKIFQAEKYRKGACQNCGAMTHTAK 107

Query: 61  SCMERPRKMGAKWTNINIAPDEKIETFELDYDGKRDRWNGYDTSSYARVVERYEARDDAR 120
           +CM+RPRK+GAK+TN+NIAPDEKIE+FELDYDGKRDRWNGYD S+Y RV++ YEA++DAR
Sbjct: 108 ACMDRPRKIGAKYTNMNIAPDEKIESFELDYDGKRDRWNGYDPSTYHRVIDLYEAKEDAR 167

Query: 121 RKFNKEQQLKKLEEKNNNNDSGGGGDSDGEDEDDDLRIDEAKVDESKQMDFAKVEKRVRT 180
           +K+ KEQQLKKLEEKNNN + G   +SDGE+++DDLR+DEAKVDES+QMDFAKVEKRVRT
Sbjct: 168 KKYLKEQQLKKLEEKNNN-EKGDDANSDGEEDEDDLRVDEAKVDESRQMDFAKVEKRVRT 226

Query: 181 TGGGSTGTVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFYGGDNQY 240
           TGGGSTGTVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFY GDNQY
Sbjct: 227 TGGGSTGTVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFYLGDNQY 286

Query: 241 RNSGQALEFKELNIHAWEAFDKGQDIHMQAAPSQAELLYKNYIVIKDKLKSRTKETIMEK 300
           RNSGQALEFK+LNIH+WEAFDKGQD+HMQAAPSQAELLYK++ V K+KLKS+TK+TIM+K
Sbjct: 287 RNSGQALEFKQLNIHSWEAFDKGQDMHMQAAPSQAELLYKSFQVAKEKLKSQTKDTIMDK 346

Query: 301 YGNAAAEEELPRELLLGQSEREIEYDRAGRIIKGQETALPRSKYEEDVYINNHTCVWGSW 360
           YGNAA E+E+P ELLLGQSER++EYDRAGRIIKGQE  LP+SKYEEDV+ NNHT VWGS+
Sbjct: 347 YGNAATEDEIPMELLLGQSERQVEYDRAGRIIKGQEVILPKSKYEEDVHANNHTSVWGSY 406

Query: 361 WKDHQWGYKCCKQVIRNSYCTGAAGIEAAEAASDLMKANIARKEASEETQTPVEGKRLAT 420
           WKDHQWGYKCC+Q+IRNSYCTG+AGIEAAEAA DLMKANIARKEA+EE+   VE KR+A+
Sbjct: 407 WKDHQWGYKCCQQIIRNSYCTGSAGIEAAEAALDLMKANIARKEATEESPKKVEEKRMAS 466

Query: 421 WGTDLPDDLVLDEDLLAEALKKVSMS 446
           WGTD+P+DL L+E+ LA ALKK  +S
Sbjct: 467 WGTDIPEDLELNEEALANALKKEDLS 492

Participates in the second catalytic step of pre-mRNA splicing, when the free hydroxyl group of exon I attacks the 3'-splice site to generate spliced mRNA and the excised lariat intron.
Arabidopsis thaliana (taxid: 3702)

>sp\|Q6ZK48\|SLU7_ORYSJ Pre-mRNA-splicing factor SLU7 OS=Oryza sativa subsp. japonica GN=Os08g0127700 PE=2 SV=1	Back alignment and function description

>sp\|A2YQU8\|SLU7_ORYSI Pre-mRNA-splicing factor SLU7 OS=Oryza sativa subsp. indica GN=OsI_27673 PE=3 SV=2	Back alignment and function description

>sp\|O23174\|SLU7B_ARATH Pre-mRNA-splicing factor SLU7-B OS=Arabidopsis thaliana GN=At4g37120 PE=2 SV=3	Back alignment and function description

>sp\|Q5ZIG2\|SLU7_CHICK Pre-mRNA-splicing factor SLU7 OS=Gallus gallus GN=SLU7 PE=2 SV=1	Back alignment and function description

>sp\|Q5U3F2\|SLU7_DANRE Pre-mRNA-splicing factor SLU7 OS=Danio rerio GN=slu7 PE=2 SV=1	Back alignment and function description

>sp\|Q54TA0\|SLU7_DICDI Pre-mRNA-splicing factor slu7 OS=Dictyostelium discoideum GN=slu7 PE=2 SV=1	Back alignment and function description

>sp\|Q3ZBE5\|SLU7_BOVIN Pre-mRNA-splicing factor SLU7 OS=Bos taurus GN=SLU7 PE=2 SV=2	Back alignment and function description

>sp\|Q8BHJ9\|SLU7_MOUSE Pre-mRNA-splicing factor SLU7 OS=Mus musculus GN=Slu7 PE=1 SV=1	Back alignment and function description

>sp\|Q80ZG5\|SLU7_RAT Pre-mRNA-splicing factor SLU7 OS=Rattus norvegicus GN=Slu7 PE=2 SV=2	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		449
224121426		536	predicted protein [Populus trichocarpa]	0.982	0.822	0.868	0.0
186493263		535	Pre-mRNA-splicing factor SLU7-A [Arabido	0.991	0.831	0.820	0.0
297841113		536	Pre-mRNA-splicing factor SLU7-A [Arabido	0.991	0.830	0.825	0.0
6686410		537	F1E22.4 [Arabidopsis thaliana]	0.991	0.828	0.818	0.0
224135337		536	predicted protein [Populus trichocarpa]	0.982	0.822	0.864	0.0
356567955		540	PREDICTED: pre-mRNA-splicing factor SLU7	0.984	0.818	0.858	0.0
356520911		540	PREDICTED: pre-mRNA-splicing factor SLU7	0.984	0.818	0.849	0.0
255567264		536	step II splicing factor slu7, putative [	0.977	0.819	0.836	0.0
449482878		536	PREDICTED: pre-mRNA-splicing factor SLU7	0.982	0.822	0.828	0.0
449442853		536	PREDICTED: pre-mRNA-splicing factor SLU7	0.982	0.822	0.828	0.0

>gi\|224121426\|ref\|XP_002318579.1\| predicted protein [Populus trichocarpa] gi\|222859252\|gb\|EEE96799.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  766 bits (1978), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 384/442 (86%), Positives = 414/442 (93%), Gaps = 1/442 (0%)

Query: 1   MSSAPWYLNSEKPSLKHQRKWKSDPNYTKSWYDRGAKVFHAEKYRKGACANCGAMTHDAK 60
           MSSAPWYLN+EKPSLKHQRKWKSDPNYTKSWYDRGAKVF AEKYRKGAC NCGAMTHDAK
Sbjct: 48  MSSAPWYLNAEKPSLKHQRKWKSDPNYTKSWYDRGAKVFQAEKYRKGACINCGAMTHDAK 107

Query: 61  SCMERPRKMGAKWTNINIAPDEKIETFELDYDGKRDRWNGYDTSSYARVVERYEARDDAR 120
           SC+ERPRK+GAKWTN +IAPDEKIET ELDYDGKRDRWNGYD SSYA VVERYEARD AR
Sbjct: 108 SCVERPRKVGAKWTNTHIAPDEKIETIELDYDGKRDRWNGYDPSSYAHVVERYEARDAAR 167

Query: 121 RKFNKEQQLKKLEEKNNNNDSGGGGDSDGEDEDDDLRIDEAKVDESKQMDFAKVEKRVRT 180
           RK  KEQQLKKLEEKN N +   G  SD ++++DDLR+DEAKVDESKQMDFAKVEKRVRT
Sbjct: 168 RKHMKEQQLKKLEEKNGNQNVEDGV-SDVDNDEDDLRVDEAKVDESKQMDFAKVEKRVRT 226

Query: 181 TGGGSTGTVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFYGGDNQY 240
           TGGGSTGTVRNLRIREDTAKYLLNLDV+SAHYDPKTRSMREDPLPDADPN+KFYGGDN+Y
Sbjct: 227 TGGGSTGTVRNLRIREDTAKYLLNLDVDSAHYDPKTRSMREDPLPDADPNEKFYGGDNRY 286

Query: 241 RNSGQALEFKELNIHAWEAFDKGQDIHMQAAPSQAELLYKNYIVIKDKLKSRTKETIMEK 300
           RNSGQALEFK LNIHAWEAFDKGQDIHMQAAPSQAELLYKN+ VIKDKLK+RTK+TIMEK
Sbjct: 287 RNSGQALEFKHLNIHAWEAFDKGQDIHMQAAPSQAELLYKNHKVIKDKLKTRTKDTIMEK 346

Query: 301 YGNAAAEEELPRELLLGQSEREIEYDRAGRIIKGQETALPRSKYEEDVYINNHTCVWGSW 360
           YGNAA+EEE+PRELLLGQSER++EYDRAGRIIKGQET LPRSKYEEDV+INNHT VWGSW
Sbjct: 347 YGNAASEEEIPRELLLGQSERQVEYDRAGRIIKGQETVLPRSKYEEDVFINNHTTVWGSW 406

Query: 361 WKDHQWGYKCCKQVIRNSYCTGAAGIEAAEAASDLMKANIARKEASEETQTPVEGKRLAT 420
           WKDHQWGYKCCKQ+IRNSYCTGAAGI+AAEAA+DLMK NI RKEA+EE   PVE +RLAT
Sbjct: 407 WKDHQWGYKCCKQMIRNSYCTGAAGIKAAEAATDLMKTNIDRKEATEEAPAPVEERRLAT 466

Query: 421 WGTDLPDDLVLDEDLLAEALKK 442
           WGT++P+DLVLDE LLAEAL+K
Sbjct: 467 WGTEVPEDLVLDEKLLAEALRK 488

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|186493263\|ref\|NP_564859.2\| Pre-mRNA-splicing factor SLU7-A [Arabidopsis thaliana] gi\|150417956\|sp\|Q9SHY8.2\|SLU7A_ARATH RecName: Full=Pre-mRNA-splicing factor SLU7-A gi\|27754341\|gb\|AAO22622.1\| putative step II splicing factor [Arabidopsis thaliana] gi\|332196287\|gb\|AEE34408.1\| Pre-mRNA-splicing factor SLU7-A [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|297841113\|ref\|XP_002888438.1\| Pre-mRNA-splicing factor SLU7-A [Arabidopsis lyrata subsp. lyrata] gi\|297334279\|gb\|EFH64697.1\| Pre-mRNA-splicing factor SLU7-A [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|6686410\|gb\|AAF23844.1\|AC007234_16 F1E22.4 [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|224135337\|ref\|XP_002322045.1\| predicted protein [Populus trichocarpa] gi\|222869041\|gb\|EEF06172.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356567955\|ref\|XP_003552180.1\| PREDICTED: pre-mRNA-splicing factor SLU7-A-like [Glycine max]	Back alignment and taxonomy information

>gi\|356520911\|ref\|XP_003529103.1\| PREDICTED: pre-mRNA-splicing factor SLU7-A-like [Glycine max]	Back alignment and taxonomy information

>gi\|255567264\|ref\|XP_002524613.1\| step II splicing factor slu7, putative [Ricinus communis] gi\|223536166\|gb\|EEF37821.1\| step II splicing factor slu7, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|449482878\|ref\|XP_004156430.1\| PREDICTED: pre-mRNA-splicing factor SLU7-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449442853\|ref\|XP_004139195.1\| PREDICTED: pre-mRNA-splicing factor SLU7-like [Cucumis sativus]	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		449
TAIR\|locus:2018496		535	SMP1 "SWELLMAP 1" [Arabidopsis	0.939	0.788	0.718	1.7e-169
TAIR\|locus:2115115		536	SMP2 "SWELLMAP 2" [Arabidopsis	0.939	0.787	0.673	2e-159
TAIR\|locus:2077157		385	AT3G45950 [Arabidopsis thalian	0.679	0.792	0.601	1.5e-97
DICTYBASE\|DDB_G0281901		558	slu7 "putative RNA splicing fa	0.427	0.344	0.518	8.9e-92
UNIPROTKB\|F1NNB9		564	SLU7 "Pre-mRNA-splicing factor	0.554	0.441	0.430	6.2e-91
UNIPROTKB\|F1NRP0		582	SLU7 "Pre-mRNA-splicing factor	0.554	0.427	0.430	6.2e-91
UNIPROTKB\|Q5ZIG2		564	SLU7 "Pre-mRNA-splicing factor	0.554	0.441	0.430	2.7e-90
UNIPROTKB\|F1RR54		586	SLU7 "Uncharacterized protein"	0.552	0.423	0.442	3.9e-89
UNIPROTKB\|E2RRD5		633	SLU7 "Uncharacterized protein"	0.552	0.391	0.434	2.7e-88
UNIPROTKB\|Q3ZBE5		586	SLU7 "Pre-mRNA-splicing factor	0.481	0.368	0.481	3.5e-88

TAIR\|locus:2018496 SMP1 "SWELLMAP 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1648 (585.2 bits), Expect = 1.7e-169, P = 1.7e-169
 Identities = 304/423 (71%), Positives = 340/423 (80%)

Query:     1 MSSAPWYLNSEKPSLKHQRKWKSDPNYTKSWYDRGAKVFHAEKYRKGACANCGAMTHDAK 60
             MSSAPWYLNSEKPSLKHQRKWKSDPNYTKSWYDRGAK+F AEKYRKGAC NCGAMTH AK
Sbjct:    48 MSSAPWYLNSEKPSLKHQRKWKSDPNYTKSWYDRGAKIFQAEKYRKGACQNCGAMTHTAK 107

Query:    61 SCMERPRKMGAKWTNINIAPDEKIETFELDYDGKRDRWNGYDTSSYARVVERYEARDDAR 120
             +CM+RPRK+GAK+TN+NIAPDEKIE+FELDYDGKRDRWNGYD S+Y RV++ YEA++DAR
Sbjct:   108 ACMDRPRKIGAKYTNMNIAPDEKIESFELDYDGKRDRWNGYDPSTYHRVIDLYEAKEDAR 167

Query:   121 RKFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLRIDEAKVDESKQMDFAKVEKRVRX 180
             +K+                                LR+DEAKVDES+QMDFAKVEKRVR 
Sbjct:   168 KKYLKEQQLKKLEEKNNNEKGDDANSDGEEDEDD-LRVDEAKVDESRQMDFAKVEKRVRT 226

Query:   181 XXXXXXXXVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFYGGDNQY 240
                     VRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFY GDNQY
Sbjct:   227 TGGGSTGTVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFYLGDNQY 286

Query:   241 RNSGQALEFKELNIHAWEAFDKGQDIHMQAAPSQAELLYKNYIVIKDKLKSRTKETIMEK 300
             RNSGQALEFK+LNIH+WEAFDKGQD+HMQAAPSQAELLYK++ V K+KLKS+TK+TIM+K
Sbjct:   287 RNSGQALEFKQLNIHSWEAFDKGQDMHMQAAPSQAELLYKSFQVAKEKLKSQTKDTIMDK 346

Query:   301 YGNXXXXXXXXXXXXXGQSEREIEYDRAGRIIKGQETALPRSKYEEDVYINNHTCVWGSW 360
             YGN             GQSER++EYDRAGRIIKGQE  LP+SKYEEDV+ NNHT VWGS+
Sbjct:   347 YGNAATEDEIPMELLLGQSERQVEYDRAGRIIKGQEVILPKSKYEEDVHANNHTSVWGSY 406

Query:   361 WKDHQWGYKCCKQVIRNSYCTXXXXXXXXXXXSDLMKANIARKEASEETQTPVEGKRLAT 420
             WKDHQWGYKCC+Q+IRNSYCT            DLMKANIARKEA+EE+   VE KR+A+
Sbjct:   407 WKDHQWGYKCCQQIIRNSYCTGSAGIEAAEAALDLMKANIARKEATEESPKKVEEKRMAS 466

Query:   421 WGT 423
             WGT
Sbjct:   467 WGT 469

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003727 "single-stranded RNA binding" evidence=TAS

GO:0008284 "positive regulation of cell proliferation" evidence=RCA;IMP

GO:0008380 "RNA splicing" evidence=TAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

GO:0009410 "response to xenobiotic stimulus" evidence=RCA

GO:0030422 "production of siRNA involved in RNA interference" evidence=RCA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

GO:0048522 "positive regulation of cellular process" evidence=RCA

GO:0051276 "chromosome organization" evidence=RCA

TAIR\|locus:2115115 SMP2 "SWELLMAP 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2077157 AT3G45950 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0281901 slu7 "putative RNA splicing factor" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NNB9 SLU7 "Pre-mRNA-splicing factor SLU7" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NRP0 SLU7 "Pre-mRNA-splicing factor SLU7" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5ZIG2 SLU7 "Pre-mRNA-splicing factor SLU7" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RR54 SLU7 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|E2RRD5 SLU7 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q3ZBE5 SLU7 "Pre-mRNA-splicing factor SLU7" [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)
Q6ZK48	SLU7_ORYSJ	No assigned EC number	0.8076	0.9821	0.8227	yes	no
Q9SHY8	SLU7A_ARATH	No assigned EC number	0.8206	0.9910	0.8317	yes	no
A2YQU8	SLU7_ORYSI	No assigned EC number	0.8076	0.9821	0.8227	N/A	no
Q4WWR2	SLU7_ASPFU	No assigned EC number	0.4109	0.8619	0.8130	yes	no
O23174	SLU7B_ARATH	No assigned EC number	0.7757	0.9910	0.8302	no	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:
	fgenesh4_pg.C_LG_XII000590	hypothetical protein (536 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		449
pfam11708		236	pfam11708, Slu7, Pre-mRNA splicing Prp18-interacti	6e-94

>gnl\|CDD\|221177 pfam11708, Slu7, Pre-mRNA splicing Prp18-interacting factor	Back alignment and domain information

 Score =  283 bits (725), Expect = 6e-94
 Identities = 131/272 (48%), Positives = 170/272 (62%), Gaps = 36/272 (13%)

Query: 88  ELDYDGKRDRWNGYDTSSYARVVERYEARDDARRKFNKEQQLKKLEEKNNNNDSGGGGDS 147
           ELDYD KRDRWNGYD S Y  VVE YE  ++ R+K                         
Sbjct: 1   ELDYDAKRDRWNGYDPSEYKEVVEEYEKLEELRKK------------------------- 35

Query: 148 DGEDEDDDLRIDEAKVDESKQMDFAKVEKRVRTTGGGSTGTVRNLRIREDTAKYLLNLDV 207
             + + +D   D    DE +++   + +  +  +   +  TVRNLRIREDTAKYLLNLD 
Sbjct: 36  -LKAKKEDDSDDTDYEDEDEELYLDESD--MGDSDSKTRTTVRNLRIREDTAKYLLNLDS 92

Query: 208 NSAHYDPKTRSMREDPLPDADPNDKFYGGDNQYRNSGQALEFKELNIHAWEAFDKGQDIH 267
           NSA+YDPK+RSMR+DPL  ADP D  + GDN  R SG+ALEF+EL   AWEA +KG D+H
Sbjct: 93  NSAYYDPKSRSMRDDPL--ADPEDVLFAGDNFVRLSGEALEFEELQKFAWEAAEKGGDVH 150

Query: 268 MQAAPSQAELLYKNYIVIKDKLKSRTKETIMEKYGNAAAEEELPRELLLGQSEREIEYDR 327
           +QA P++ ELL K     K++LK + K++++EKYG     ++ P+ELLLGQSE  +EYDR
Sbjct: 151 LQANPTKLELLRKKEKEKKEQLKIQKKQSLLEKYGGEEHLDKPPKELLLGQSEDYVEYDR 210

Query: 328 AGRIIKGQETALPRSKYEEDVYINNHTCVWGS 359
           AG+  K       +SKYEEDV+INNHT VWGS
Sbjct: 211 AGKKKK------AKSKYEEDVFINNHTSVWGS 236

The spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and U5) and proteins, catalyzes the excision of introns from pre-mRNAs in two successive trans-esterification reactions. Step 2 depends upon integral spliceosome constituents such as U5 snRNA and Prp8 and non-spliceosomal proteins Prp16, Slu7, Prp18, and Prp22. ATP hydrolysis by the DEAH-box enzyme Prp16 promotes a conformational change in the spliceosome that leads to protection of the 3'ss from targeted RNase H cleavage. This change, which probably reflects binding of the 3'ss PyAG in the catalytic centre of the spliceosome, requires the ordered recruitment of Slu7, Prp18, and Prp22 to the spliceosome. There is a close functional relationship between Prp8, Prp18, and Slu7, and Prp18 interacts with Slu7, so that together they recruit Prp22 to the spliceosome. Most members of the family carry a zinc-finger of the CCHC-type upstream of this domain. Length = 236

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		449
KOG2560		529	consensus RNA splicing factor - Slu7p [RNA process	100.0
PF11708		239	Slu7: Pre-mRNA splicing Prp18-interacting factor;	100.0
PF00098		18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	92.58

>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]	Back alignment and domain information

Probab=100.00  E-value=4.4e-146  Score=1114.82  Aligned_cols=422  Identities=59%  Similarity=0.997  Sum_probs=379.9

Q ss_pred             CCCCCcccCCCCCccccccccCCCCC---CccchhccCccc-ccccccccccccccccCCCCcccccCccccccccccCC
Q 013091            1 MSSAPWYLNSEKPSLKHQRKWKSDPN---YTKSWYDRGAKV-FHAEKYRKGACANCGAMTHDAKSCMERPRKMGAKWTNI   76 (449)
Q Consensus         1 Is~aPWY~~~~~p~LkHQR~~~~~~~---~~~~wy~RGik~-~~atKyRKGACeNCGAmtHk~KDClERPRK~gAk~t~~   76 (449)
                      |+++|||+.+.+|+|+|||+|+.++.   ..++||.||.+. +++||||||||+|||||||+.|||||||||+||+|||.
T Consensus        63 is~aPwY~~s~~ptLkHQr~~~~epk~m~~~~ewy~rG~kk~~~atkyRKGACeNCGAmtHk~KDCmERPRK~gAk~t~~  142 (529)
T KOG2560|consen   63 ISKAPWYVHSEGPTLKHQRPWKEEPKIMGIKDEWYDRGKKKGSVATKYRKGACENCGAMTHKVKDCMERPRKVGAKYTDL  142 (529)
T ss_pred             ccCCCceecccCccccccCCCccCCccccccchhhhcccccchHHHHHhhhhhhhhhhhhcchHHHhhcchhhcccCCCc
Confidence            89999999999999999999987554   689999999965 99999999999999999999999999999999999999


Q ss_pred             cCCCCcceec-cccccccccCccCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCCCCcch
Q 013091           77 NIAPDEKIET-FELDYDGKRDRWNGYDTSSYARVVERYEARDDARRKFNKEQQLKKLEEKNNNNDSGGGGDSDGEDEDDD  155 (449)
Q Consensus        77 ~I~~De~iq~-~~ldyDaKRDRWnGYd~~ey~~vve~~e~~e~~rk~~~~e~~~~~~~~~~~~~~~~~~~~~d~dd~d~e  155 (449)
                      ||++||+||+ +.+|||+||||||||||++|.+||++|++++++|.+-..+++++        .    .+.. .|.+++.
T Consensus       143 Nia~De~iq~~~~~dyD~KRDRWnGYdps~y~~vIe~yEk~eeak~K~l~~~q~~--------~----d~~~-~d~eE~~  209 (529)
T KOG2560|consen  143 NIAPDEKIQSVLELDYDGKRDRWNGYDPSEYKEVIERYEKLEEAKIKGLKEQQKN--------G----DEAL-WDTEEGI  209 (529)
T ss_pred             ccCcccccccccccccccccccccCCChHHHHHHHHHHHHHHHHHHHHHHHhhcc--------C----cccc-ccccccc
Confidence            9999999999 89999999999999999999999999999999996543333311        1    1110 1111222


Q ss_pred             hhhhhhhhhhhhccchhhhhhhhcccCCCCCCcccccccccchHHHhccCCCCCCcccCCCcccccCCCCCCCCCCCCCC
Q 013091          156 LRIDEAKVDESKQMDFAKVEKRVRTTGGGSTGTVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFYG  235 (449)
Q Consensus       156 ~~~de~ky~d~~d~~~~k~d~~~r~~~~~~~~tvrnLRIREDtAKYL~NLd~nSa~YDPKSRsMRe~p~~~~d~~~~~f~  235 (449)
                      ++.+++.|+|.++|...     +|.+++++++|||||||||||||||+|||+|||||||||||||++|+|+.+|...+|.
T Consensus       210 ~~~dee~y~D~a~~~k~-----v~~~d~~s~iTvrnLRiRED~AkYL~nld~Nsa~YDPKSRsMReep~~~~~~~e~~~~  284 (529)
T KOG2560|consen  210 EDLDEELYADFADMLKT-----VRDTDDGSRITVRNLRIREDTAKYLRNLDVNSAYYDPKSRSMREEPLPGKDPNEDEYS  284 (529)
T ss_pred             chhhHHhhhhhhccccc-----ccccCCCceeeeecceechhHHHHHHhcCCcccccCccccccccCCCCCCChhhhhhc
Confidence            23478899998887654     4556777788999999999999999999999999999999999999999999999999


Q ss_pred             CCCceecccchHHHHHHHHHHHHHhhCCCCcccccCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHhcCccccccchhhhh
Q 013091          236 GDNQYRNSGQALEFKELNIHAWEAFDKGQDIHMQAAPSQAELLYKNYIVIKDKLKSRTKETIMEKYGNAAAEEELPRELL  315 (449)
Q Consensus       236 GdNFvR~SGea~e~~~lQ~FAWea~~kG~DvHl~AnPT~~Ell~Ke~~~kke~~k~~~k~~il~KYGg~e~~~~~p~el~  315 (449)
                      |+||||+||++.+|.+||+|||+|+.+|++|||||+||++|||++.|+.+++.|+.+++++||+||||.+|++.+|++||
T Consensus       285 gdnfvr~SGe~~~~~qlq~FAweA~~kG~~~H~~A~Ptk~Ell~k~~k~kke~lK~q~kq~il~kYG~~~~~d~~p~ell  364 (529)
T KOG2560|consen  285 GDNFVRNSGEALEFNQLQMFAWEAFDKGVDVHMQADPTKLELLYKENKVKKETLKKQTKQEILDKYGGGEHKDLPPKELL  364 (529)
T ss_pred             ccceeeccchhhhHHHHHHHHHHHhcccceeeeecCcHHHHHHHHHhHHHHHHHHHHHHHHHHhhcCCccccccChHhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccchhhhhcccccccccCccccccCccchhhhccCCCcccccccccCCccccccccccccccccCchhhHHHHHHHHHH
Q 013091          316 LGQSEREIEYDRAGRIIKGQETALPRSKYEEDVYINNHTCVWGSWWKDHQWGYKCCKQVIRNSYCTGAAGIEAAEAASDL  395 (449)
Q Consensus       316 l~qtE~yvEY~~~G~vikg~~~~~~kSkY~EDv~~~nHtsVwGS~~~~~~WGy~CC~s~~k~SyCtge~g~~a~~~~~~~  395 (449)
                      |+|||.|+||++.|.||||+++++++|+|+||||+|||||||||||..|+|||+|||||++||||||.+||+|+  +.++
T Consensus       365 l~qte~~iey~rkg~v~KG~e~~~~~S~yeedV~~~nht~vwgs~w~~~rwgykcc~~f~~~syctg~~g~e~~--~~~~  442 (529)
T KOG2560|consen  365 LAQTEEYIEYSRKGKVIKGQEKIVPKSKYEEDVYINNHTSVWGSFWKEGRWGYKCCHQFIKNSYCTGSAGIEAV--AEEL  442 (529)
T ss_pred             ccccHHHHHHhhccceecccccccccccchhheeccccchhhhhhhhccchhHHHHHHHHhhhcccCccchhHH--hHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999993  3345


Q ss_pred             HHHhhhhhhhhhccCCccccccccccCCCCCCcccCCHHHHHHHHHHhh
Q 013091          396 MKANIARKEASEETQTPVEGKRLATWGTDLPDDLVLDEDLLAEALKKVS  444 (449)
Q Consensus       396 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~l~~a~~~~~  444 (449)
                      |.+  ..+++..+.|+..++..+.+||...+.+++++...|..+++++.
T Consensus       443 ~~~--~~~~~~~~~~~~~e~k~~~~~~~~~~~~~~~~~~~~~ss~~~~e  489 (529)
T KOG2560|consen  443 SKA--SRKEASKEPPKKVEEKEMERWGERKPEDLDSNEESLPSSLSKEE  489 (529)
T ss_pred             hhh--hhhhccCCChhhhHHhhhhcccccchhhhccccccccccccchh
Confidence            544  56677777777888889999999999999999999888877643

>PF11708 Slu7: Pre-mRNA splicing Prp18-interacting factor; InterPro: IPR021715 The spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and U5) and proteins, catalyses the excision of introns from pre-mRNAs in two successive trans-esterification reactions	Back alignment and domain information

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		449
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-05

>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

 Score = 48.7 bits (115), Expect = 3e-06
 Identities = 53/355 (14%), Positives = 100/355 (28%), Gaps = 113/355 (31%)

Query: 71  AKWTNINIAPDEKIETFELDYDGKRDR-WNGYDTSSYARV-VERYEARDDARRKFNKEQQ 128
           +        P          Y  +RDR +N  D   +A+  V R +     R+       
Sbjct: 96  SPIKTEQRQPSMMTRM----YIEQRDRLYN--DNQVFAKYNVSRLQPYLKLRQA------ 143

Query: 129 LKKLEEKNNNNDS----GGGGDSDGEDEDDDLRIDEAKVDES--KQMDFAKVEKRVRTTG 182
           L +L  +   N       G G +        + +D          +MDF           
Sbjct: 144 LLEL--RPAKNVLIDGVLGSGKTW-------VALDVCL-SYKVQCKMDF----------- 182

Query: 183 GGSTG----TVRNLRIREDTAKYLLNLDVN-SAHYDPKTRSMREDPLP--DADPNDKFYG 235
                     ++N    E   + L  L      ++  ++       L         +   
Sbjct: 183 ----KIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLL 238

Query: 236 GDNQYRNSGQALEFKEL-------NIHAWEAFDKG-------QDIHMQAAPSQAELLYKN 281
               Y N         L       N  AW AF+         +   +    S A      
Sbjct: 239 KSKPYENC--------LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAAT---TT 287

Query: 282 YIVIKDKLKSRTK---ETIMEKYGNAAAEEELPREL---------LLGQSERE------- 322
           +I +     + T    ++++ KY +    ++LPRE+         ++ +S R+       
Sbjct: 288 HISLDHHSMTLTPDEVKSLLLKYLDCRP-QDLPREVLTTNPRRLSIIAESIRDGLATWDN 346

Query: 323 ---IEYDRAGRIIKG----QETALPRSKYE------EDVYINNHT-CVWGSWWKD 363
              +  D+   II+      E A  R  ++         +I      +   W+  
Sbjct: 347 WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLI--WFDV 399

PyMOL of 1vt4

>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		449
1nc8_A		29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	95.5
1u6p_A		56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	92.94
1dsq_A		26	Nucleic acid binding protein P14; CCHC type zinc f	92.2
1a6b_B		40	Momulv, zinc finger protein NCP10; nucleocapsid pr	88.39
1cl4_A		60	Protein (GAG polyprotein); nucleocapsid protein, R	88.22
2ec7_A		49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	87.52
1a1t_A		55	Nucleocapsid protein; stem-loop RNA, viral protein	87.26
3nyb_B		83	Protein AIR2; polya RNA polymerase, zinc knuckle p	86.91
2cqf_A		63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	86.7
2cqf_A		63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	85.61
2a51_A		39	Nucleocapsid protein; sivlhoest, structure, NCP8,	85.21
3ts2_A		148	Protein LIN-28 homolog A; microrna biogenesis, pro	81.8
2li8_A		74	Protein LIN-28 homolog A; zinc finger, micro RNA,	81.34
2ihx_A		61	Nucleocapsid (NC) protein; protein-RNA complex, vi	81.33
3nyb_B		83	Protein AIR2; polya RNA polymerase, zinc knuckle p	81.28

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A	Back alignment and structure

Probab=95.50  E-value=0.0068  Score=40.24  Aligned_cols=24  Identities=42%  Similarity=0.857  Sum_probs=20.2

Q ss_pred             cccccccccCCCCcccccCcccccc
Q 013091           46 KGACANCGAMTHDAKSCMERPRKMG   70 (449)
Q Consensus        46 KGACeNCGAmtHk~KDClERPRK~g   70 (449)
                      ...|-|||..+|-.++|-. |||+|
T Consensus         6 ~~~C~nCgk~GH~ar~C~~-prkkg   29 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRA-PRRQG   29 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCS-SSSCC
T ss_pred             CCEEEECCccccCHhHCcc-cccCC
Confidence            4679999999999999975 67765

PyMOL of 1nc8

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A	Back alignment and structure

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1	Back alignment and structure

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A	Back alignment and structure

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1	Back alignment and structure

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A	Back alignment and structure

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}	Back alignment and structure

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}	Back alignment and structure

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*	Back alignment and structure

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}	Back alignment and structure

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}	Back alignment and structure

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		449
d1nc8a_		29	HIV nucleocapsid {Human immunodeficiency virus typ	96.41
d1dsqa_		26	Nucleic acid binding protein p14 {Mouse mammary tu	90.2
d2exfa1		42	HIV nucleocapsid {Human immunodeficiency virus typ	89.36
d2exfa1		42	HIV nucleocapsid {Human immunodeficiency virus typ	85.45

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}	Back information, alignment and structure

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=96.41  E-value=0.00054  Score=44.29  Aligned_cols=23  Identities=43%  Similarity=0.910  Sum_probs=20.1

Q ss_pred             ccccccccCCCCcccccCcccccc
Q 013091           47 GACANCGAMTHDAKSCMERPRKMG   70 (449)
Q Consensus        47 GACeNCGAmtHk~KDClERPRK~g   70 (449)
                      --|-|||.++|..+.|- -|||+|
T Consensus         7 ikCfNCGkeGH~ar~Cr-APRkkg   29 (29)
T d1nc8a_           7 IRCWNCGKEGHSARQCR-APRRQG   29 (29)
T ss_dssp             CBCTTTSCBSSCGGGCC-SSSSCC
T ss_pred             eEeecCCccchhhhhcc-CcccCC
Confidence            45999999999999995 688876

PyMOL of d1nc8a_

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}	Back information, alignment and structure

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}	Back information, alignment and structure