Citrus Sinensis ID: 006806

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-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630

MGNRRFAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEERKASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELKEGLTAEEMAKKEPDESEQMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASSLTIDGPGSAAKSVGIVPLATAKFDSLEKNLLSPRESEKLANDVLKKSSEAYMPVLEAQRSFGKSKTEENSDASNAKKADVQS

ccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccEEEccEEEEEcccEEEcccccccccEEEEEEEEEEcccccEEEEEEEEEccccccccccccccccccccEEEEccccccccccccccEEEEEcccccccccccccccEEEEEEEcccccEEcccccccccccccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccHHHHHHHHcccccccHHccccHHHHHHHHHHHHHHcccccHHHHHccccccccccccccccEEEEEcccccccccEEEEcccccEEcccccccccccccccccccccccccccccHHHHHHHcccccccccHHHHHHHHHHcccccHHHHHccccccccccccccccccHHHcccc

ccccEEEEEEcccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccEccccccccEEEEEEEEcccEEEEccEEEEEccccccccEEEEEEEEEEcccccEEEEEEEEEcHHHHHHHcccccccccccEEEEccccccccHHHEcccEEEEEEcccEEcccccccccEEEEEEEcccccEEEEccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccEEEEccccccEcccccccccccccccccccccccccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHcccccccHHEcccHHHHHccccHHHccccccccccHccccccccHHcccccccHHHHEEccccccEEEEEEcccccccccHHHHEEEEEcccccccccccccccHHcHHHHHHHHccccccccccHHHHHHccccccccHHHHHcccccccccccccccHcccccccc

mgnrrfaqvstsdededvpppssrtrkseeNKEQQSLRQSKRKRIklqeeedyeepeeERKASKRerrdkgkvreaekprndgvedeeeeeeeeeqpqedakpvgelvrfsgkgrgrrshyeafefdgnkyeledpvlltpedtnqkpYVAIIKEITqskdgsmmvtgqwfyrpeeadrkgggnwlsrdtRELFYSfhrdevpaesvmHKCVVHfvpihkqlpnrkqhpgfiVQKVYDTVERKLWKltdkdyednKQHEIDLLVQKTQarlgdlpdiepeetAAREQEDQLKAKRSLRkknispldvsreedsttrsdqyvkaetpgsctsnaSEYYNILSKFKALTGETHRDKWLERLLQGLQYICNsadsihadqngkggckgvdhesedksvgtengsrekgqkngksfiwpdTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLngelepskilnmspnelkegltaeemakkepdeseqmqmtdarcsrcneckVGLRDiiqaghgdryqlECIAcghswyasrdeassltidgpgsaaksvgivplatakfdsleknllspresEKLANDVLKKSSEAYMPVLEAQrsfgkskteensdasnakkadvqs

mgnrrfaqvstsdededvpppssrtrkseenkeqqslrqskrkriklqeeedyeepeeerkaskrerrdkgkvreaekprndgvedeeeeeeeeeqpqedakpvgelvrfsgkgrgrrshyeafefdgnkyeLEDPVLLtpedtnqkpyVAIIKEitqskdgsmmVTGQWFYRpeeadrkgggnwlsRDTRELFYSFHRDEVPAESVMHKCVVHFVPIhkqlpnrkqhpgfiVQKVYDTVERKLWKLtdkdyednkqHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLkakrslrkknispldvsreedsttrsdqyvkaetpgsctsnaSEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDhesedksvgtengsrekgqkngksfiwPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNgelepskilnmspneLKEGLTAEEMakkepdeseqmqmtdarCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASSLTIDGPGSAAKSVGIVPLATAKFDSleknllspreseKLANDVLKKSSEAYMPVLEaqrsfgkskteensdasnakkadvqs

MGNRRFAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQeeedyeepeeerkaskrerrdkGKVREAEKPRNDGVedeeeeeeeeeqpqedAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELKEGLTAEEMAKKEPDESEQMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASSLTIDGPGSAAKSVGIVPLATAKFDSLEKNLLSPRESEKLANDVLKKSSEAYMPVLEAQRSFGKSKTEENSDASNAKKADVQS

************************************************************************************************************************YEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLV*********************************************************************SEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSI*************************************SFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNG*****************************************CSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASR*****************VGIVPLATA*************************************************************

**********************************************************************************************************************SHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQA*********************************************************************ILSKFKALTGETHRDKWLERLLQG*************************************G**EKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMS*******************************SRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDE*************************************************************************************

******************************************************************************************************PVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPE****************LRKKNIS************************SCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQN*****************************NGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELKEGLTAEE******************CSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASSLTIDGPGSAAKSVGIVPLATAKFDSLEKNLLSPRESEKLANDVLKKSSEAYMPVLEAQ************************

**********************************************************************************************************LVRFS***RGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDI**********E**LKAKRSLRKKNISPLDVSR***********VK*ETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNS****************************************KSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELKEGLTAE*M*************TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASSLTIDGP**************A*F*S**KNLL**************KSSEAYMPV****R***********************

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MGNRRFAQVSTSDEDEDVPPPSSRTRKSExxxxxxxxxxxxxxxxxxxxxxDYEEPEEERKASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELKEGLTAEEMAKKEPDESEQMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASSLTIDGPGSAAKSVGIVPLATAKFDSLEKNLLSPRESEKLANDVLKKSSEAYMPVLEAQRSFGKSKTEENSDASNAKKADVQS

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		630	2.2.26 [Sep-21-2011]
Q8BSQ9		1634	Protein polybromo-1 OS=Mu	yes	no	0.163	0.063	0.283	5e-08
Q86U86		1689	Protein polybromo-1 OS=Ho	no	no	0.163	0.060	0.283	6e-08
Q90941		1633	Protein polybromo-1 OS=Ga	yes	no	0.152	0.058	0.292	7e-08
Q3UHR0		2643	BAH and coiled-coil domai	no	no	0.171	0.040	0.277	0.0002
P53236		928	Chromatin structure-remod	yes	no	0.215	0.146	0.301	0.0002

>sp\|Q8BSQ9\|PB1_MOUSE Protein polybromo-1 OS=Mus musculus GN=Pbrm1 PE=1 SV=4	Back alignment and function desciption

 Score = 60.1 bits (144), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 30/106 (28%), Positives = 53/106 (50%), Gaps = 3/106 (2%)

Query: 111  SGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQW 170
            +G     R++ +   F  + Y + D V + P + N +P++  I+ + +   G   + G W
Sbjct: 938  TGLSGLHRTYSQDCSFKNSMYHVGDYVYVEPAEANLQPHIVCIERLWEDSAGEKWLYGCW 997

Query: 171  FYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFV 216
            FYRP E        +L    +E+F S + ++VP   ++ KCVV FV
Sbjct: 998  FYRPNETFHLATRKFLE---KEVFKSDYYNKVPVSKILGKCVVMFV 1040

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology) (By similarity). Act as a negative regulator of cell proliferation.
Mus musculus (taxid: 10090)

>sp\|Q86U86\|PB1_HUMAN Protein polybromo-1 OS=Homo sapiens GN=PBRM1 PE=1 SV=1	Back alignment and function description

>sp\|Q90941\|PB1_CHICK Protein polybromo-1 OS=Gallus gallus GN=PBRM1 PE=1 SV=1	Back alignment and function description

>sp\|Q3UHR0\|BAHC1_MOUSE BAH and coiled-coil domain-containing protein 1 OS=Mus musculus GN=Bahcc1 PE=2 SV=2	Back alignment and function description

>sp\|P53236\|RSC1_YEAST Chromatin structure-remodeling complex subunit RSC1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RSC1 PE=1 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		630
224058512		611	predicted protein [Populus trichocarpa]	0.960	0.990	0.719	0.0
224071890		607	predicted protein [Populus trichocarpa]	0.947	0.983	0.704	0.0
225426420		595	PREDICTED: uncharacterized protein LOC10	0.930	0.984	0.650	0.0
449452318		610	PREDICTED: uncharacterized protein LOC10	0.965	0.996	0.672	0.0
297742521		1085	unnamed protein product [Vitis vinifera]	0.884	0.513	0.687	0.0
359474210		584	PREDICTED: uncharacterized protein LOC10	0.912	0.984	0.639	0.0
356528332		605	PREDICTED: uncharacterized protein LOC10	0.942	0.981	0.675	0.0
356528334		596	PREDICTED: uncharacterized protein LOC10	0.928	0.981	0.671	0.0
357481593		596	BAH and coiled-coil domain-containing pr	0.934	0.988	0.599	0.0
356513389		571	PREDICTED: uncharacterized protein LOC10	0.765	0.844	0.722	0.0

>gi\|224058512\|ref\|XP_002299533.1\| predicted protein [Populus trichocarpa] gi\|222846791\|gb\|EEE84338.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  849 bits (2194), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 446/620 (71%), Positives = 505/620 (81%), Gaps = 15/620 (2%)

Query: 1   MGNRRFAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEER 60
           MGNRRFAQVSTSDE+++ PP   + R S        + + KRK++KLQEEE+ EE  E  
Sbjct: 1   MGNRRFAQVSTSDEEDEAPP---KARSSSTTTRPGDISERKRKKMKLQEEEEEEE--EVV 55

Query: 61  KASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSH 120
              +   R + K+RE +       E EE+ EEEEE PQEDAKPVG+  R SGKGRGRR+H
Sbjct: 56  TTRRGRGRPRKKLREEKSEDEVEEELEEDPEEEEEVPQEDAKPVGDSTRVSGKGRGRRTH 115

Query: 121 YEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRK 180
           Y+AFEFDGN+YELEDPVLL PED  QKPYVAIIK+I+Q+KDGSMMVTGQWFYRPEEA+RK
Sbjct: 116 YDAFEFDGNRYELEDPVLLVPEDKEQKPYVAIIKDISQTKDGSMMVTGQWFYRPEEAERK 175

Query: 181 GGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTV 240
           GGG+W SRDTRELFYSFHRDEVPAESVMHKCVVHFVP+HKQLPNRKQ+PGFIV+KVYDTV
Sbjct: 176 GGGSWQSRDTRELFYSFHRDEVPAESVMHKCVVHFVPVHKQLPNRKQYPGFIVRKVYDTV 235

Query: 241 ERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAR---EQEDQLKAKRSL 297
           ERKLWKLTDKDYEDNKQHEIDLLVQKT +R+GDLPDIE E+  A    E ED  KAKR+L
Sbjct: 236 ERKLWKLTDKDYEDNKQHEIDLLVQKTLSRMGDLPDIEVEDAPAAAPPELEDPTKAKRTL 295

Query: 298 RKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLE 357
           R+K +SPLDV+REE++TTRSD + KAETPGSCT N SEYY IL KF ALTG+THRDKWLE
Sbjct: 296 RRKTVSPLDVTREEEATTRSDNF-KAETPGSCTGNGSEYYAILVKFDALTGDTHRDKWLE 354

Query: 358 RLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDT 417
           RLLQ +QY+C S++S   D   KGG  GVDH+ E KS G  NGS E    N KSF WP+ 
Sbjct: 355 RLLQCIQYMCISSNSTLDDDKIKGGSDGVDHKKEQKSQGAANGSEE----NSKSFPWPEA 410

Query: 418 AIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPN 477
           A+ AV+ALEKASHD LS DFQKYNQKLRQL+FNLK+ A LARRLLN ELEPSKILNMSPN
Sbjct: 411 AVPAVSALEKASHDALSSDFQKYNQKLRQLVFNLKNNAFLARRLLNRELEPSKILNMSPN 470

Query: 478 ELKEGLTAEEMAKKEPDESEQMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGH 537
           ELKEGLTAEE AKKEP+ESE+MQMTDARCSRC+E KVGLRDIIQAGHG RYQLECIACG+
Sbjct: 471 ELKEGLTAEETAKKEPEESERMQMTDARCSRCSEFKVGLRDIIQAGHGARYQLECIACGN 530

Query: 538 SWYASRDEASSLTIDGPGSAAKSVGIVPLATAKFDSLEKNLLSPRESEKLANDVLKKSSE 597
           SWYASRDE S L+ID P S+A+SVG  P ATAKFD +EK L+SPRES+K A + LKK+SE
Sbjct: 531 SWYASRDEVSMLSIDTP-SSARSVGTAPWATAKFDEVEKKLVSPRESDKAA-EFLKKTSE 588

Query: 598 AYMPVLEAQRSFGKSKTEEN 617
            YMPVLE QRSF K K EEN
Sbjct: 589 PYMPVLENQRSFNKVKIEEN 608

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224071890\|ref\|XP_002303589.1\| predicted protein [Populus trichocarpa] gi\|222841021\|gb\|EEE78568.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|225426420\|ref\|XP_002270094.1\| PREDICTED: uncharacterized protein LOC100251356 isoform 1 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449452318\|ref\|XP_004143906.1\| PREDICTED: uncharacterized protein LOC101218620 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|297742521\|emb\|CBI34670.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|359474210\|ref\|XP_003631417.1\| PREDICTED: uncharacterized protein LOC100251356 isoform 2 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356528332\|ref\|XP_003532758.1\| PREDICTED: uncharacterized protein LOC100787670 isoform 1 [Glycine max]	Back alignment and taxonomy information

>gi\|356528334\|ref\|XP_003532759.1\| PREDICTED: uncharacterized protein LOC100787670 isoform 2 [Glycine max]	Back alignment and taxonomy information

>gi\|357481593\|ref\|XP_003611082.1\| BAH and coiled-coil domain-containing protein [Medicago truncatula] gi\|355512417\|gb\|AES94040.1\| BAH and coiled-coil domain-containing protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356513389\|ref\|XP_003525396.1\| PREDICTED: uncharacterized protein LOC100796051 [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		630
TAIR\|locus:2123136		587	AT4G11560 [Arabidopsis thalian	0.712	0.764	0.640	6.4e-166
TAIR\|locus:2040209		380	AT2G25120 [Arabidopsis thalian	0.311	0.515	0.529	9.3e-67
TAIR\|locus:2097134		380	AT3G43990 [Arabidopsis thalian	0.336	0.557	0.465	2.6e-63
TAIR\|locus:2121601		360	AT4G23120 [Arabidopsis thalian	0.333	0.583	0.486	2.6e-57
TAIR\|locus:2097915		1613	SUO "'shuttle' in chinese" [Ar	0.230	0.089	0.369	1.9e-18
TAIR\|locus:2097925		1611	AT3G48060 [Arabidopsis thalian	0.230	0.090	0.369	3e-18
ZFIN\|ZDB-GENE-010501-3		1648	pbrm1l "polybromo 1, like" [Da	0.201	0.077	0.305	4.2e-08
TAIR\|locus:2120693		234	EBS "EARLY BOLTING IN SHORT DA	0.165	0.444	0.330	2.5e-07
UNIPROTKB\|E1BNH8		1664	E1BNH8 "Uncharacterized protei	0.301	0.114	0.227	5.9e-07
UNIPROTKB\|E7EVG2		1461	PBRM1 "Protein polybromo-1" [H	0.301	0.130	0.227	1.4e-06

TAIR\|locus:2123136 AT4G11560 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1545 (548.9 bits), Expect = 6.4e-166, Sum P(2) = 6.4e-166
 Identities = 298/465 (64%), Positives = 360/465 (77%)

Query:   101 AKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSK 160
             A PVG+ V  +GKG+G+R+H+  F +DGN Y+LE PVLL PED +QKPYVAIIK+ITQ+K
Sbjct:   101 ACPVGDSVNVTGKGKGKRTHFNQFAYDGNTYDLEVPVLLVPEDKSQKPYVAIIKDITQTK 160

Query:   161 DGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHK 220
             DGSMM+ GQWFYRPEEA+++GGGNW S DTRELFYSFHRDEVPAESVMH+CVV+FVP HK
Sbjct:   161 DGSMMILGQWFYRPEEAEKRGGGNWQSSDTRELFYSFHRDEVPAESVMHRCVVYFVPAHK 220

Query:   221 QLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPE 280
             QLP RK +PGFIV+KVYDTVE+KLWKLTDKDYED+KQ EID+LV+KT   LGDLPD+E E
Sbjct:   221 QLPKRKNNPGFIVRKVYDTVEKKLWKLTDKDYEDSKQREIDVLVKKTMNVLGDLPDLESE 280

Query:   281 ETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNIL 340
             +    +QE+ LKAKRS RK NISP+DV REED++      +KAETPGS    +SE+Y IL
Sbjct:   281 DMLV-DQENVLKAKRSFRKVNISPVDVRREEDAS------LKAETPGSGAGISSEHYAIL 333

Query:   341 SKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENG 400
              KF +LTG+ HRDK L +LL+ +Q+IC   ++  A    K G      E ++K    ENG
Sbjct:   334 EKFDSLTGDAHRDKCLGKLLEAVQHICYIPENKQAGDEAKVGSDASHLEQDEKDTKPENG 393

Query:   401 SREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARR 460
               EK       F+WPD A+  V ALE ASH +L+ DFQKYNQK+R L+FNLK+TALLARR
Sbjct:   394 KDEK-------FLWPDAAVPQVCALENASHASLASDFQKYNQKMRTLVFNLKNTALLARR 446

Query:   461 LLNGELEPSKILNMSPNELKEGLTAEEMAKKEPDESEQMQMTDARCSRCNECKVGLRDII 520
             LLNGELEP+ ILNMSP ELKEGLTA+E  KKEPD++++MQMT  RCSRC++  VGLRDII
Sbjct:   447 LLNGELEPATILNMSPTELKEGLTADETTKKEPDDADRMQMTSVRCSRCSQLTVGLRDII 506

Query:   521 QAGHGDRYQLECIACGHSWYASRDEASSLTI--DGPGSAAKSVGI 563
             QAGHGDRYQLEC+ CG+SWYASRDE S+LTI  D P    +   I
Sbjct:   507 QAGHGDRYQLECVDCGYSWYASRDEVSTLTIVTDKPAQGTEKEDI 551

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

TAIR\|locus:2040209 AT2G25120 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2097134 AT3G43990 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2121601 AT4G23120 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2097915 SUO "'shuttle' in chinese" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2097925 AT3G48060 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-010501-3 pbrm1l "polybromo 1, like" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

TAIR\|locus:2120693 EBS "EARLY BOLTING IN SHORT DAYS" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BNH8 E1BNH8 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E7EVG2 PBRM1 "Protein polybromo-1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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:
	GSVIVG00000421001	SubName- Full=Chromosome chr2 scaffold_105, whole genome shotgun sequence; (595 aa)
		(Vitis vinifera)
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		630
cd04713		146	cd04713, BAH_plant_3, BAH, or Bromo Adjacent Homol	2e-79
smart00439		121	smart00439, BAH, Bromo adjacent homology domain	3e-22
cd04370		123	cd04370, BAH, BAH, or Bromo Adjacent Homology doma	3e-20
pfam01426		120	pfam01426, BAH, BAH domain	6e-20
cd04714		121	cd04714, BAH_BAHCC1, BAH, or Bromo Adjacent Homolo	3e-15
cd04717		121	cd04717, BAH_polybromo, BAH, or Bromo Adjacent Hom	2e-09
pfam07500		115	pfam07500, TFIIS_M, Transcription factor S-II (TFI	2e-09
smart00510		102	smart00510, TFS2M, Domain in the central regions o	6e-09
cd04716		122	cd04716, BAH_plantDCM_I, BAH, or Bromo Adjacent Ho	5e-05
cd04721		130	cd04721, BAH_plant_1, BAH, or Bromo Adjacent Homol	9e-05
cd04710		135	cd04710, BAH_fungalPHD, BAH, or Bromo Adjacent Hom	2e-04
cd04712		130	cd04712, BAH_DCM_I, BAH, or Bromo Adjacent Homolog	2e-04
cd11486		635	cd11486, SLC5sbd_SGLT1, Na(+)/glucose cotransporte	6e-04
cd04715		159	cd04715, BAH_Orc1p_like, BAH, or Bromo Adjacent Ho	0.001
PRK00247		429	PRK00247, PRK00247, putative inner membrane protei	0.002

>gnl\|CDD\|240064 cd04713, BAH_plant_3, BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function	Back alignment and domain information

 Score =  247 bits (633), Expect = 2e-79
 Identities = 94/147 (63%), Positives = 117/147 (79%), Gaps = 1/147 (0%)

Query: 111 SGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQW 170
           +GKG+ ++ HY +FE DGNKY LED VLL PED +QKPY+AIIK+I + ++GS+ +  QW
Sbjct: 1   TGKGKKKKCHYTSFEKDGNKYRLEDCVLLVPED-DQKPYIAIIKDIYKQEEGSLKLEVQW 59

Query: 171 FYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPG 230
            YRPEE ++K GGNW + D RELFYSFHRDEVPAESV+H C V FVP  KQ+P RK H G
Sbjct: 60  LYRPEEIEKKKGGNWKAEDPRELFYSFHRDEVPAESVLHPCKVAFVPKGKQIPLRKGHSG 119

Query: 231 FIVQKVYDTVERKLWKLTDKDYEDNKQ 257
           FIV++VYD V +KLWKLTD+DYED +Q
Sbjct: 120 FIVRRVYDNVNKKLWKLTDQDYEDERQ 146

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. Length = 146

>gnl\|CDD\|214664 smart00439, BAH, Bromo adjacent homology domain	Back alignment and domain information

>gnl\|CDD\|239835 cd04370, BAH, BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif)	Back alignment and domain information

>gnl\|CDD\|216495 pfam01426, BAH, BAH domain	Back alignment and domain information

>gnl\|CDD\|240065 cd04714, BAH_BAHCC1, BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240068 cd04717, BAH_polybromo, BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2	Back alignment and domain information

>gnl\|CDD\|219433 pfam07500, TFIIS_M, Transcription factor S-II (TFIIS), central domain	Back alignment and domain information

>gnl\|CDD\|128786 smart00510, TFS2M, Domain in the central regions of transcription elongation factor S-II (and elsewhere)	Back alignment and domain information

>gnl\|CDD\|240067 cd04716, BAH_plantDCM_I, BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants	Back alignment and domain information

>gnl\|CDD\|240072 cd04721, BAH_plant_1, BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function	Back alignment and domain information

>gnl\|CDD\|240061 cd04710, BAH_fungalPHD, BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains	Back alignment and domain information

>gnl\|CDD\|240063 cd04712, BAH_DCM_I, BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1	Back alignment and domain information

>gnl\|CDD\|212055 cd11486, SLC5sbd_SGLT1, Na(+)/glucose cotransporter SGLT1;solute binding domain	Back alignment and domain information

>gnl\|CDD\|240066 cd04715, BAH_Orc1p_like, BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins	Back alignment and domain information

>gnl\|CDD\|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		630
KOG1886		464	consensus BAH domain proteins [Transcription]	100.0
TIGR01385		299	TFSII transcription elongation factor S-II. This m	100.0
KOG1105		296	consensus Transcription elongation factor TFIIS/Co	100.0
cd04713		146	BAH_plant_3 BAH, or Bromo Adjacent Homology domain	100.0
cd04716		122	BAH_plantDCM_I BAH, or Bromo Adjacent Homology dom	99.93
cd04717		121	BAH_polybromo BAH, or Bromo Adjacent Homology doma	99.93
cd04715		159	BAH_Orc1p_like BAH, or Bromo Adjacent Homology dom	99.93
cd04714		121	BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain,	99.93
cd04370		123	BAH BAH, or Bromo Adjacent Homology domain (also c	99.92
smart00439		120	BAH Bromo adjacent homology domain.	99.92
PF01426		119	BAH: BAH domain; InterPro: IPR001025 The BAH (brom	99.91
cd04710		135	BAH_fungalPHD BAH, or Bromo Adjacent Homology doma	99.91
cd04721		130	BAH_plant_1 BAH, or Bromo Adjacent Homology domain	99.9
cd04709		164	BAH_MTA BAH, or Bromo Adjacent Homology domain, as	99.89
smart00510		102	TFS2M Domain in the central regions of transcripti	99.89
cd04712		130	BAH_DCM_I BAH, or Bromo Adjacent Homology domain,	99.87
cd04708		202	BAH_plantDCM_II BAH, or Bromo Adjacent Homology do	99.87
PF07500		115	TFIIS_M: Transcription factor S-II (TFIIS), centra	99.86
cd04760		124	BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain	99.86
cd04720		179	BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology do	99.79
cd04718		148	BAH_plant_2 BAH, or Bromo Adjacent Homology domain	99.78
cd04719		128	BAH_Orc1p_animal BAH, or Bromo Adjacent Homology d	99.78
cd04711		137	BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domai	99.7
KOG1827		629	consensus Chromatin remodeling complex RSC, subuni	99.51
smart00440		40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	99.21
PF01096		39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	99.15
KOG2906		105	consensus RNA polymerase III subunit C11 [Transcri	99.07
COG1594		113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	99.04
KOG1634		778	consensus Predicted transcription factor DATF1, co	99.04
PHA02998		195	RNA polymerase subunit; Provisional	98.99
TIGR01384		104	TFS_arch transcription factor S, archaeal. There h	98.92
KOG3554		693	consensus Histone deacetylase complex, MTA1 compon	98.57
KOG2907		116	consensus RNA polymerase I transcription factor TF	98.44
KOG2691		113	consensus RNA polymerase II subunit 9 [Transcripti	98.03
PF09855		64	DUF2082: Nucleic-acid-binding protein containing Z	93.18
COG5076		371	Transcription factor involved in chromatin remodel	92.92
COG3478		68	Predicted nucleic-acid-binding protein containing	87.19
PRK09678		72	DNA-binding transcriptional regulator; Provisional	85.4
COG2051		67	RPS27A Ribosomal protein S27E [Translation, riboso	85.02
PF08274		30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	83.89
PF13717		36	zinc_ribbon_4: zinc-ribbon domain	83.7
TIGR00686		109	phnA alkylphosphonate utilization operon protein P	82.75
TIGR00244		147	transcriptional regulator NrdR. Members of this al	80.62
PF04606		47	Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I	80.35

>KOG1886 consensus BAH domain proteins [Transcription]	Back alignment and domain information

Probab=100.00  E-value=4.2e-45  Score=392.46  Aligned_cols=434  Identities=35%  Similarity=0.542  Sum_probs=364.4

Q ss_pred             hhhhhccCCCCCccccccceeecCCCCCcceeeeeEEEcCeEEee-CCeEEEcCCCCCCCCeEEEEeEEeeCCC-CceEE
Q 006806           89 EEEEEEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYEL-EDPVLLTPEDTNQKPYVAIIKEITQSKD-GSMMV  166 (630)
Q Consensus        89 ~~~~~~~~~~~~a~~iG~pvk~~gKG~~~r~~Y~sf~~dG~~YkV-GD~VyV~~e~~~~~pyIArI~~I~e~~d-G~~~V  166 (630)
                      ...+.++.+.++|.|+|...++.|+|...++||.+|.+.|..|.. ||+|++.+++++.+||||+|..||.+.. +.+.+
T Consensus         8 ~~~~~~~~~~~~a~~~g~a~~~qGv~~~k~~h~~t~~~~~g~~~~~~d~vllvped~~~pPyvaii~~i~a~~~g~~~k~   87 (464)
T KOG1886|consen    8 PKLKSELRPRDEASSMGDANKEQGVGGVKSLHFETFIYRGGRYINYGDSVLLVPEDPGKPPYVAIIEDIYAQERGGNVKV   87 (464)
T ss_pred             ccccccCCccchhhhhhhhhhhccccccccccccceeeccCcccccCcceeecCCCCCCCCeeEEEeeeeccccCCCcce
Confidence            334568999999999999999999999999999999999988888 9999999999999999999999998766 58999


Q ss_pred             EEEEEecccccCCCCCCCCCCCCCCeeEeeCCcccccccccceecEEEEcCccccCCCCCCCCceEEeeeeecCCcEEee
Q 006806          167 TGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWK  246 (630)
Q Consensus       167 rVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~plesIigKC~V~~i~ey~qlP~~~~~~~F~Cr~vYD~~~kkl~~  246 (630)
                      +|+|||||+|+.....+.|....++|||+|+|+|.+++++|.++|.|+|++.|.++|.+..+++|+|+++||..+.++|.
T Consensus        88 ev~W~YrPee~~~~~~~~~~a~~~relF~SfH~De~~A~ti~~rC~V~fvp~~kqlp~~~~~~~f~~r~vYd~~~~~~~~  167 (464)
T KOG1886|consen   88 EVQWFYRPEESEGGGSGKWGAKQPRELFLSFHEDEAFAETILHRCKVHFVPAYKQLPNRVGHESFICRRVYDAVTSKLRK  167 (464)
T ss_pred             ecccccCCCccCCCCCCCcccCCCccccccccccchhhhhhcccceeeeccccccccccCCCCCcccccccccccccccC
Confidence            99999999999988888888889999999999999999999999999999999999988889999999999999999999


Q ss_pred             cCCccccccccchhhHHHHHhhhhcCCCCCCCccccccchhhhhhhcccccccCCCCCCcccccccccCCcccccccCCC
Q 006806          247 LTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETP  326 (630)
Q Consensus       247 l~dkDy~~~~q~Evd~ll~kt~~~lG~lpd~~~~e~~~~~~~~~~~~k~~~r~~~~~~~~~~~~~~~~~~~~~~~k~etp  326 (630)
                      +++.+|....+.++|.++.++..++++++++....+.     ..+++++..++++++  .++|.                
T Consensus       168 ~~~~~~~~~~k~e~d~~~~kt~~~~~~~~~p~~~~t~-----~~~~~~~~~~~s~~~--~~~r~----------------  224 (464)
T KOG1886|consen  168 LRDGDFGDGQKLEIDMLVPKTGPRRGTLPDPKKVQTL-----NAAASKRSQQKSEIS--SLSRA----------------  224 (464)
T ss_pred             ccccchhcccccCCccchhhhcccCCCCCCccccccc-----cccccceeccccccc--ccccc----------------
Confidence            9999999999999999999999999999999999833     477888999998887  22222                


Q ss_pred             CccCCCCcchhhhhccccCCcChhhHHHHHHHHHHHh-hhhcCCCcccccccCCCCCCCCCCCCcccccccccCCccccc
Q 006806          327 GSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGL-QYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKG  405 (630)
Q Consensus       327 ~~~~~~~~~~~~~l~~~~~lTgd~~RDK~le~L~~al-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (630)
                           ..+.++.++..|..+||++.|||++..|++.+ +..|.......                               
T Consensus       225 -----ss~~~~~~~e~~~~~t~~~~~~k~~g~~~~~v~~~~~~~s~~~~-------------------------------  268 (464)
T KOG1886|consen  225 -----SSSVDGEILESFDLLTGRSDRDKVLGKLLEVVWQNSCSTSEAKP-------------------------------  268 (464)
T ss_pred             -----ccccccccccCCCCCCCcccccccccccchhhccccccccccCC-------------------------------
Confidence                 34577888999999999999999999999999 66665432211                               


Q ss_pred             cCCCCCCCChhhHHHHHHHHHHHHHHHcCcChHHHHHHHHHHHHhcccCHHHHHHhhcCC-CCccccccCChhhhcChHh
Q 006806          406 QKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGE-LEPSKILNMSPNELKEGLT  484 (630)
Q Consensus       406 ~~~~~~~~w~~~v~~~A~~IE~alf~~~~~~~~kYk~KiRSL~fNLKkNp~Lr~rVl~Ge-IsP~~La~Ms~eEMASdel  484 (630)
                      ....++ .||+.++..+.+||.+.|+.++.+..+|..+...|+++||.--.|+.+.++|. +.|+-++.|.+-++-..-.
T Consensus       269 ~~~~~~-~~p~~~v~~~~~le~~s~~s~a~d~~~~~~~~~~l~~~~k~~~~l~~~~ln~~~~~~e~~~~l~~p~~p~~~~  347 (464)
T KOG1886|consen  269 AGDQGS-LWPNPSVSPCGALEQPSHASLAKDLESYLGLRETLVLLLKGQALLKPEPLNPGETKPEPKQELHPPSFPDGQS  347 (464)
T ss_pred             Cccccc-CCCCcccchhhhhhhhhhhhHhhhhhhhhhhhhHHHhhhcchhhhccccCCCcccCchhhhhccCCCCCCCcc
Confidence            111222 78999999999999999999998889999999999999998889999999995 9999999988877766532


Q ss_pred             HHHHHhcCCchhhhcccCccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccccccccceeecCCCCCCCccccc
Q 006806          485 AEEMAKKEPDESEQMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASSLTIDGPGSAAKSVGIV  564 (630)
Q Consensus       485 keer~k~~~e~i~~~~m~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~srd~~s~l~~~~~~~~~~~~~~~  564 (630)
                      ...-.+....-.....|+...|..|-.--|+-.++|+..+.+-....|..|+.+|...|+++..+++-.+.+++   ++.
T Consensus       348 ~~~~~~~~~d~~~~l~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~~~~~~~~~~~~~~---~q~  424 (464)
T KOG1886|consen  348 SPSSMKLNDDDYDGLCVGLELTAGSLYLYCGQEGLICAGHLPCPMLPEVKLSPVAAVHREGLLLAPSSVPKGTP---FQH  424 (464)
T ss_pred             CccccccCchhHHHHHHhhhhhccchhhhcccccceeccccCCCCCCCcCcccccccchhhhcccceeccCCCC---ccC
Confidence            11111122222233344556788877777777777766667768889999999999999999999988777633   443


Q ss_pred             CccchhhhhhhhhhcCCccccchhhhh
Q 006806          565 PLATAKFDSLEKNLLSPRESEKLANDV  591 (630)
Q Consensus       565 ~~~~~~~~~~~~~~~~~~~~~~~~~~~  591 (630)
                      |      ..-||+|.|||++.++.+.+
T Consensus       425 ~------~~~~k~~~~~ret~~~~ea~  445 (464)
T KOG1886|consen  425 P------PWPEKRLCSPRETGVNGEAI  445 (464)
T ss_pred             C------CChhhcccCccccCCchhcc
Confidence            2      35799999999998665554

>TIGR01385 TFSII transcription elongation factor S-II	Back alignment and domain information

>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]	Back alignment and domain information

>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function	Back alignment and domain information

>cd04716 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants	Back alignment and domain information

>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2	Back alignment and domain information

>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins	Back alignment and domain information

>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins	Back alignment and domain information

>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif)	Back alignment and domain information

>smart00439 BAH Bromo adjacent homology domain	Back alignment and domain information

>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation	Back alignment and domain information

>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains	Back alignment and domain information

>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function	Back alignment and domain information

>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins	Back alignment and domain information

>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere)	Back alignment and domain information

>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1	Back alignment and domain information

>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants	Back alignment and domain information

>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites	Back alignment and domain information

>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins	Back alignment and domain information

>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p	Back alignment and domain information

>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function	Back alignment and domain information

>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p	Back alignment and domain information

>cd04711 BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins	Back alignment and domain information

>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]	Back alignment and domain information

>smart00440 ZnF_C2C2 C2C2 Zinc finger	Back alignment and domain information

>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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

>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]	Back alignment and domain information

>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]	Back alignment and domain information

>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]	Back alignment and domain information

>PHA02998 RNA polymerase subunit; Provisional	Back alignment and domain information

>TIGR01384 TFS_arch transcription factor S, archaeal	Back alignment and domain information

>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]	Back alignment and domain information

>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12	Back alignment and domain information

>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]	Back alignment and domain information

>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins	Back alignment and domain information

>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]	Back alignment and domain information

>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]	Back alignment and domain information

>PRK09678 DNA-binding transcriptional regulator; Provisional	Back alignment and domain information

>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues	Back alignment and domain information

>PF13717 zinc_ribbon_4: zinc-ribbon domain	Back alignment and domain information

>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA	Back alignment and domain information

>TIGR00244 transcriptional regulator NrdR	Back alignment and domain information

>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr	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		630
1w4s_A		174	Crystal Structure Of The Proximal Bah Domain Of Pol		2e-08

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		630
1w4s_A		174	Polybromo, polybromo 1 protein; BAH, bromo-associa	1e-39
3av4_A		1330	DNA (cytosine-5)-methyltransferase 1; CXXC-type zi	5e-19
3av4_A		1330	DNA (cytosine-5)-methyltransferase 1; CXXC-type zi	2e-06
3swr_A		1002	DNA (cytosine-5)-methyltransferase 1; epigenetics,	2e-18
3swr_A		1002	DNA (cytosine-5)-methyltransferase 1; epigenetics,	3e-08
3po3_S		178	Transcription elongation factor S-II; RNA polymera	4e-12
4dov_A		163	ORC1, origin recognition complex subunit 1; DNA re	5e-12
3ndq_A		108	Transcription elongation factor A protein 1; helix	7e-08
2dme_A		120	PHD finger protein 3; PHF3, TFS2M, glioblastoma mu	4e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-05
3lvg_D		190	LCB, clathrin light chain B; SELF assembly, coated	2e-06
1pqv_S		309	STP-alpha, transcription elongation factor S-II, D	1e-05
3k1f_M		197	Transcription initiation factor IIB; RNA polymeras	8e-05

>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus musculus} PDB: 3av5_A* 3av6_A* Length = 1330	Back alignment and structure

>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus musculus} PDB: 3av5_A* 3av6_A* Length = 1330	Back alignment and structure

>3swr_A DNA (cytosine-5)-methyltransferase 1; epigenetics, DNA methyltransferase fold, maintenance methyla transferase; HET: DNA SFG MES; 2.49A {Homo sapiens} PDB: 3pta_A* 3pt6_A* 3pt9_A* 4da4_A* Length = 1002	Back alignment and structure

>3swr_A DNA (cytosine-5)-methyltransferase 1; epigenetics, DNA methyltransferase fold, maintenance methyla transferase; HET: DNA SFG MES; 2.49A {Homo sapiens} PDB: 3pta_A* 3pt6_A* 3pt9_A* 4da4_A* Length = 1002	Back alignment and structure

>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A Length = 178	Back alignment and structure

>4dov_A ORC1, origin recognition complex subunit 1; DNA replication, replication; 1.70A {Mus musculus} PDB: 4dow_A* Length = 163	Back alignment and structure

>3ndq_A Transcription elongation factor A protein 1; helix bundle; 1.93A {Homo sapiens} Length = 108	Back alignment and structure

>2dme_A PHD finger protein 3; PHF3, TFS2M, glioblastoma multiforme, brain tumor, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 120	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

>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

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190	Back alignment and structure

>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A Length = 309	Back alignment and structure

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		630
3po3_S		178	Transcription elongation factor S-II; RNA polymera	100.0
1pqv_S		309	STP-alpha, transcription elongation factor S-II, D	100.0
1w4s_A		174	Polybromo, polybromo 1 protein; BAH, bromo-associa	99.96
2lw4_A		113	Transcription elongation factor A protein 2; struc	99.93
3swr_A		1002	DNA (cytosine-5)-methyltransferase 1; epigenetics,	99.92
3ndq_A		108	Transcription elongation factor A protein 1; helix	99.91
3av4_A		1330	DNA (cytosine-5)-methyltransferase 1; CXXC-type zi	99.9
2dme_A		120	PHD finger protein 3; PHF3, TFS2M, glioblastoma mu	99.88
4dov_A		163	ORC1, origin recognition complex subunit 1; DNA re	99.82
3swr_A		1002	DNA (cytosine-5)-methyltransferase 1; epigenetics,	99.76
4ft4_B		784	DNA (cytosine-5)-methyltransferase 1; chromodomain	99.75
3av4_A		1330	DNA (cytosine-5)-methyltransferase 1; CXXC-type zi	99.72
1tfi_A		50	Transcriptional elongation factor SII; transcripti	99.29
2fl7_A		232	Regulatory protein SIR3; ORC, silencing, chromatin	99.18
1m4z_A		238	Origin recognition complex subunit 1; DNA replicat	99.17
1qyp_A		57	RNA polymerase II; transcription, RPB9, Zn ribbon,	99.06
3h0g_I		113	DNA-directed RNA polymerases I, II, and III subuni	98.89
1twf_I		122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	98.86
3qt1_I		133	DNA-directed RNA polymerases I, II, and III subun;	98.72
1k81_A		36	EIF-2-beta, probable translation initiation factor	81.64

>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A	Back alignment and structure

Probab=100.00  E-value=7.5e-40  Score=317.38  Aligned_cols=160  Identities=18%  Similarity=0.283  Sum_probs=135.1

Q ss_pred             hhhhccccCCcChhhHHHHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCcccccccccCCccccccCCCCCCCChh
Q 006806          337 YNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPD  416 (630)
Q Consensus       337 ~~~l~~~~~lTgd~~RDK~le~L~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~  416 (630)
                      -++.|+++ +|||++||||+++|++||+...+..                                            +.
T Consensus         4 ~~d~v~~~-~~~d~vRdk~~~lL~~aL~~~~~~~--------------------------------------------~~   38 (178)
T 3po3_S            4 KNDGVDTA-IYHHKLRDQVLKALYDVLAKESEHP--------------------------------------------PQ   38 (178)
T ss_dssp             ------------CHHHHHHHHHHHHHTTSSSSCS--------------------------------------------TT
T ss_pred             cCCCcCcC-cCCChHHHHHHHHHHHHHhcCCCCc--------------------------------------------hh
Confidence            35678888 7999999999999999998865321                                            34


Q ss_pred             hHHHHHHHHHHHHHHHcCc-ChH-HHHHHHHHHHHhcc--cCHHHHHHhhcCCCCccccccCChhhhcChHhHHHHHhcC
Q 006806          417 TAIAAVTALEKASHDTLSL-DFQ-KYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKEGLTAEEMAKKE  492 (630)
Q Consensus       417 ~v~~~A~~IE~alf~~~~~-~~~-kYk~KiRSL~fNLK--kNp~Lr~rVl~GeIsP~~La~Ms~eEMASdelkeer~k~~  492 (630)
                      .+..+|.+||.+||..|++ ++. +|++++|||+||||  +||.|+++|++|+|+|..||.|+++||||+++++++++.+
T Consensus        39 ~~~~~A~~IE~~if~~~~~~~~~k~Yk~k~Rsl~~NLKd~~N~~Lr~~vl~g~isp~~lv~Ms~eElas~elk~~~e~~~  118 (178)
T 3po3_S           39 SILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIA  118 (178)
T ss_dssp             HHHHHHHHHHHHHHHHTSCSSSSTHHHHHHHHHHHHHHSSSCSHHHHHHHHCCCTTHHHHCCTTTTSSCSHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhcCCCchhhhhhhhhHHHHHcCCCCCHHHHHHHhcCCCCHHHHHhcCchhhCCHHHHHHHHHHH
Confidence            7789999999999999986 454 89999999999998  9999999999999999999999999999999999998777


Q ss_pred             Cchhhhccc--------CccccCCCCCCceEEEEeeeccCCCc---eEEEcCcCCcccccc
Q 006806          493 PDESEQMQM--------TDARCSRCNECKVGLRDIIQAGHGDR---YQLECIACGHSWYAS  542 (630)
Q Consensus       493 ~e~i~~~~m--------~~~~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~Cg~rWk~s  542 (630)
                      .+.|.++++        +.+.|++||++++.|+|+| +|||||   +||.|.+|||+|+||
T Consensus       119 ~e~l~~~~~~~~~~~~t~~~~Cp~C~~~~a~~~q~Q-~rsaDE~mt~f~~C~~C~~~w~f~  178 (178)
T 3po3_S          119 KQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQ-TRSAAAPLTTFCTCEACGNRWKFS  178 (178)
T ss_dssp             HHHHHHTBCCCCCCCCBSSSCCSSSCCSCEECCCCC-CSCTTSCCCCCEEETTTCCEECCC
T ss_pred             HHHHHHhhhccccCCCcCCcCCCCCCCCceEEEEee-cccCCCCCcEEEEcCCCCCeeccC
Confidence            778877765        2479999999999999999 999999   899999999999986

PyMOL of 3po3

>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A	Back alignment and structure

>2lw4_A Transcription elongation factor A protein 2; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}	Back alignment and structure

>3swr_A DNA (cytosine-5)-methyltransferase 1; epigenetics, DNA methyltransferase fold, maintenance methyla transferase; HET: DNA SFG MES; 2.49A {Homo sapiens} PDB: 3pta_A* 3pt6_A* 3pt9_A* 4da4_A*	Back alignment and structure

>3ndq_A Transcription elongation factor A protein 1; helix bundle; 1.93A {Homo sapiens}	Back alignment and structure

>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus musculus} PDB: 3av5_A* 3av6_A*	Back alignment and structure

>2dme_A PHD finger protein 3; PHF3, TFS2M, glioblastoma multiforme, brain tumor, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>4dov_A ORC1, origin recognition complex subunit 1; DNA replication, replication; 1.70A {Mus musculus} PDB: 4dow_A*	Back alignment and structure

>3swr_A DNA (cytosine-5)-methyltransferase 1; epigenetics, DNA methyltransferase fold, maintenance methyla transferase; HET: DNA SFG MES; 2.49A {Homo sapiens} PDB: 3pta_A* 3pt6_A* 3pt9_A* 4da4_A*	Back alignment and structure

>4ft4_B DNA (cytosine-5)-methyltransferase 1; chromodomain, BAH domain, DNA methyltransferase domain, H3K9 binding, methylation, transferase; HET: DNA MLY SAH; 2.70A {Zea mays} PDB: 4ft2_A* 4fsx_A*	Back alignment and structure

>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus musculus} PDB: 3av5_A* 3av6_A*	Back alignment and structure

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1	Back alignment and structure

>2fl7_A Regulatory protein SIR3; ORC, silencing, chromatin, transcription; 1.85A {Saccharomyces cerevisiae} PDB: 2fvu_A 3tu4_K*	Back alignment and structure

>1m4z_A Origin recognition complex subunit 1; DNA replication, transcriptional silencing, chromatin, BAH D gene regulation; 2.20A {Saccharomyces cerevisiae} SCOP: b.34.12.1 PDB: 1zhi_A 1zbx_A	Back alignment and structure

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1	Back alignment and structure

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}	Back alignment and structure

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...	Back alignment and structure

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}	Back alignment and structure

>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1	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		630
d1m4za_		217	b.34.12.1 (A:) Origin-recognition complex protein	8e-18
d1enwa_		114	a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Bak	1e-06

>d1m4za_ b.34.12.1 (A:) Origin-recognition complex protein 120kDa subunit, Orc1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 217	Back information, alignment and structure


class: All beta proteins
fold: SH3-like barrel
superfamily: BAH domain
family: BAH domain
domain: Origin-recognition complex protein 120kDa subunit, Orc1p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 80.4 bits (198), Expect = 8e-18
 Identities = 24/198 (12%), Positives = 49/198 (24%), Gaps = 32/198 (16%)

Query: 99  EDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQ 158
           E    +    +   +   +  HY     DG K    D V++  E       V +I+E+  
Sbjct: 21  EQGNIIDGGQKRLRRRGAKTEHYLKRSSDGIKLGRGDSVVMHNEAAG-TYSVYMIQELRL 79

Query: 159 S-----------------------KDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFY 195
           +                                    RP            + +  EL+ 
Sbjct: 80  NTLNNVVELWALTYLRWFEVNPLAHYRQFNPDANILNRPLN--YYNKLFSETANKNELYL 137

Query: 196 SFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPG-FIVQKVYDTVERKL-----WKLTD 249
           +    E+   + +    V      + L         F V+ + +    K        +  
Sbjct: 138 TAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDINIEDVKA 197

Query: 250 KDYEDNKQHEIDLLVQKT 267
              +   +   + L   T
Sbjct: 198 YIKKVEPREAQEYLKDLT 215

PyMOL of d1m4za_

>d1enwa_ a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 114	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		630
d1enwa_		114	Elongation factor TFIIS domain 2 {Baker's yeast (S	99.77
d1m4za_		217	Origin-recognition complex protein 120kDa subunit,	99.65
d1tfia_		50	Transcriptional factor SII, C-terminal domain {Hum	99.4
d1qypa_		57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	99.28
d1twfi2		72	RBP9 subunit of RNA polymerase II {Baker's yeast (	99.12
d2akla2		38	Hypothetical protein PA0128, N-terminal domain {Ps	89.71

>d1enwa_ a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: Elongation factor TFIIS domain 2
family: Elongation factor TFIIS domain 2
domain: Elongation factor TFIIS domain 2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.77  E-value=4.2e-20  Score=165.16  Aligned_cols=96  Identities=17%  Similarity=0.270  Sum_probs=84.1

Q ss_pred             ccccCCcChhhHHHHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCcccccccccCCccccccCCCCCCCChhhHHH
Q 006806          341 SKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIA  420 (630)
Q Consensus       341 ~~~~~lTgd~~RDK~le~L~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~v~~  420 (630)
                      |+.+ +|+|.+||+|+++|+++|.......                                            +..+..
T Consensus        13 v~~~-~~~d~~R~~~~~~L~~aL~~~~~~~--------------------------------------------~~~~~~   47 (114)
T d1enwa_          13 VDTA-IYHHKLRDQVLKALYDVLAKESEHP--------------------------------------------PQSILH   47 (114)
T ss_dssp             CCCC-SSTTTTHHHHHHHHHHHHHHHCSSS--------------------------------------------CSCHHH
T ss_pred             CCCc-cCCcHHHHHHHHHHHHHHhCcCccc--------------------------------------------hhHHHH
Confidence            4444 7999999999999999998654321                                            346778


Q ss_pred             HHHHHHHHHHHHcCc--ChHHHHHHHHHHHHhcc--cCHHHHHHhhcCCCCccccccCChhhhcC
Q 006806          421 AVTALEKASHDTLSL--DFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKE  481 (630)
Q Consensus       421 ~A~~IE~alf~~~~~--~~~kYk~KiRSL~fNLK--kNp~Lr~rVl~GeIsP~~La~Ms~eEMAS  481 (630)
                      +|.+||.+||..|++  +..+|++|+|||+||||  +||.|+++|++|+|+|.+|+.|+++|||+
T Consensus        48 la~~IE~~lf~~~~~~~~~~~Y~~k~rsi~~NLkd~~N~~L~~~v~~g~i~p~~l~~M~~~ElaP  112 (114)
T d1enwa_          48 TAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAP  112 (114)
T ss_dssp             HHHHHTTTTTSSCTTTTTHHHHHHHHHHHHHHHTTSCCCCTTTHHHHCSSCCSSHHHHTTTTTCS
T ss_pred             HHHHHHHHHHHHhcccCCcHHHHHHHHHHHHHcCccchHHHHHHHHcCCCCHHHHhCCCHHHcCC
Confidence            999999999999864  45689999999999998  89999999999999999999999999997

PyMOL of d1enwa_

>d1m4za_ b.34.12.1 (A:) Origin-recognition complex protein 120kDa subunit, Orc1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]}	Back information, alignment and structure

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}	Back information, alignment and structure