Citrus Sinensis ID: 022104

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--

MSSSAMDAESPDLVCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAKVYLQRELFVRYEYSAQGRPRFGVSLGLFADCLNTFSAPGHSSLIEIRYPGPDMQLLVKSVDSPDACIYAEVRTRIPDMISWDYNFEPAGSTPLTFTVKSAALKEAIDDLEWPGSSIQIKLQPVPPSVSFKGEGHGDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFLRATTSNLPGCVIKHNRGSKLIIGRGGMLKVQHLVSVARTSNQHPHTDSAGYQQPSQIAYIEFFVKPEEDEDTIN

cccccccccccEEEEEEccHHHHHHHHcccccccccEEEEEEccccEEEEEEccEEEEEEEEEcccccEEEEEccccccEEEEEcHHHHHHHHHcccccccEEEEEEEcccccEEEEEEEcccccEEEEEEEEEccccccccccccccccccEEEEEEHHHHHHHHHHccccccEEEEEEEEcccEEEEEEccccEEEEEEEEEcccccEEEEEEcccEEEEEEEHHHHHHHHccccccccccEEEEEEEccccEEEEEEEEEEccccccccccccccccccccEEEEEEEEcccccccccc

cccccccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEccccEEEEEEcccEEEEEEEEcHHHHHEEEEccccccEEEEcHHHHHHHHHHHcccccccEEEEEEccccccEEEEEEEcccEEEEEEEEEEccccccccccccccccccEEEEEcHHHHHHHHHHccccccEEEEEEcccccEEEEEEEccccEEEEEEccccccEEEEEEccccccccEHHHHHHHHHHHHHccEEEEEcccEEEEccccEEEEEEEEEcccccccccccccccccccccEEEEEEEEcccccccccc

msssamdaespdlVCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAKVYLQRELFVRYEysaqgrprfgvSLGLFADclntfsapghsslieirypgpdmqllvksvdspdaciyaevrtripdmiswdynfepagstpltfTVKSAALKEAIddlewpgssiqiklqpvppsvsfkgeghgdlQIDFMYYVNTDLLIAFhcdrevsyrYKYKFLRAttsnlpgcvikhnrgskliigrggmlKVQHLVSVArtsnqhphtdsagyqqpsqIAYIEFFvkpeededtin

msssamdaespDLVCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAKVYLQRELFVRYEYSAQGRPRFGVSLGLFADCLNTFSAPGHSSLIEIRYPGPDMQLLVKSVDSPDACIYAEVRTRIPDMISWDYNFEPAGSTPLTFTVKSAALKEAIDDLEWPGSSIQIKLQPVPPSVSFKGEGHGDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFLRattsnlpgcviKHNRGSKLIIGRGGMLKVQHLVSVARTSNQHPHTDSAGYQQPSQIAYIEFFVKPEEDEDTIN

************LVCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAKVYLQRELFVRYEYSAQGRPRFGVSLGLFADCLNTFSAPGHSSLIEIRYPGPDMQLLVKSVDSPDACIYAEVRTRIPDMISWDYNFEPAGSTPLTFTVKSAALKEAIDDLEWPGSSIQIKLQPVPPSVSFKGEGHGDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFLRATTSNLPGCVIKHNRGSKLIIGRGGMLKVQHLVSVA******************QIAYIEFFV**********

*************VCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAKVYLQRELFVRYEYSAQGRPRFGVSLGLFADCLNTFSAPGHSSLIEIRYPGPDMQLLVKSVDSPDACIYAEVRTRIPDMISWDYNFEPAGSTPLTFTVKSAALKEAIDDLEWPGSSIQIKLQPVPPSVSFKGEGHGDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFLRATTSNLPGCVIKHNRGSKLIIGRGGMLKVQHLVSVARTS*********GYQQPSQIAYIEFFVKP*E******

**********PDLVCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAKVYLQRELFVRYEYSAQGRPRFGVSLGLFADCLNTFSAPGHSSLIEIRYPGPDMQLLVKSVDSPDACIYAEVRTRIPDMISWDYNFEPAGSTPLTFTVKSAALKEAIDDLEWPGSSIQIKLQPVPPSVSFKGEGHGDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFLRATTSNLPGCVIKHNRGSKLIIGRGGMLKVQHLVSVAR*************QQPSQIAYIEFFVKP********

********ESPDLVCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAKVYLQRELFVRYEYSAQGRPRFGVSLGLFADCLNTFSAPGHSSLIEIRYPGPDMQLLVKSVDSPDACIYAEVRTRIPDMISWDYNFEPAGSTPLTFTVKSAALKEAIDDLEWPGSSIQIKLQPVPPSVSFKGEGHGDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFLRATTSNLPGCVIKHNRGSKLIIGRGGMLKVQHLVSVART**************PSQIAYIEFFVKPEE******

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		302	2.2.26 [Sep-21-2011]
Q9QWZ1		280	Cell cycle checkpoint pro	yes	no	0.844	0.910	0.244	1e-17
Q5R7X9		282	Cell cycle checkpoint pro	yes	no	0.844	0.904	0.237	5e-16
O60671		282	Cell cycle checkpoint pro	yes	no	0.844	0.904	0.237	5e-16

>sp\|Q9QWZ1\|RAD1_MOUSE Cell cycle checkpoint protein RAD1 OS=Mus musculus GN=Rad1 PE=1 SV=1	Back alignment and function desciption

 Score = 90.5 bits (223), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/290 (24%), Positives = 137/290 (47%), Gaps = 35/290 (12%)

Query: 13  LVCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAKVYLQRELFVRYE 72
           LV  LDNV+ L   L A+ ++ H  A    +++GI + VE   C+QA  ++Q ++F  + 
Sbjct: 17  LVASLDNVRNLSTVLKAIHFREH--ATCFATKNGIKVTVENAKCVQANAFIQADVFQEFV 74

Query: 73  YSAQGRPRFGVSLGLFADCLNTFSA---PGHSSLIEIRYPGPDMQLLVKSVDSPDACIYA 129
              +    F ++L +  DCL+ F +   PG  + + + Y G    L++  ++        
Sbjct: 75  IQEES-VTFRINLTILLDCLSIFGSSPTPGTLTALRMCYQGYGHPLML-FLEEGGVVTVC 132

Query: 130 EVRTRIPDMISWDYNFEPAGSTPLTFTVKSAALKEAIDDLEWPGSSIQIKLQPVPPSVSF 189
           ++ T+ P+  + D++F  + +      ++S  L+EA  +L+  G  +QI + P  P    
Sbjct: 133 KITTQEPEE-TLDFDF-CSTNVMNKIILQSEGLREAFSELDMTGDVLQITVSPDKPYFRL 190

Query: 190 KGEGH-GDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFLRATTSNLP-GCVIKHNRGSK 247
              G+ G+  +D  Y  ++DL+ AFHCD+    RYK   L+ +T  L   C +     ++
Sbjct: 191 STFGNAGNSHLD--YPKDSDLVEAFHCDKTQVNRYKLSLLKPSTKALALSCKVSIRTDNR 248

Query: 248 LIIGRGGMLKVQHLVSVARTSNQHPHTDSAGYQQPSQIAYIEFFVKPEED 297
                 G L +Q+++                  +  QI ++E++  P+E+
Sbjct: 249 ------GFLSLQYMIR----------------NEDGQICFVEYYCCPDEE 276

Component of the 9-1-1 cell-cycle checkpoint response complex that plays a major role in DNA repair. The 9-1-1 complex is recruited to DNA lesion upon damage by the RAD17-replication factor C (RFC) clamp loader complex. Acts then as a sliding clamp platform on DNA for several proteins involved in long-patch base excision repair (LP-BER). The 9-1-1 complex stimulates DNA polymerase beta (POLB) activity by increasing its affinity for the 3'-OH end of the primer-template and stabilizes POLB to those sites where LP-BER proceeds; endonuclease FEN1 cleavage activity on substrates with double, nick, or gap flaps of distinct sequences and lengths; and DNA ligase I (LIG1) on long-patch base excision repair substrates. The 9-1-1 complex is necessary for the recruitment of RHINO to sites of double-stranded breaks (DSB) occurring during the S phase. Isoform 1 possesses 3'->5' double stranded DNA exonuclease activity.
Mus musculus (taxid: 10090)
EC: 3EC: .EC: 1EC: .EC: 1EC: 1EC: .EC: 2

>sp\|Q5R7X9\|RAD1_PONAB Cell cycle checkpoint protein RAD1 OS=Pongo abelii GN=RAD1 PE=2 SV=1	Back alignment and function description

>sp\|O60671\|RAD1_HUMAN Cell cycle checkpoint protein RAD1 OS=Homo sapiens GN=RAD1 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		302
224138984		303	predicted protein [Populus trichocarpa]	1.0	0.996	0.850	1e-155
225427149		300	PREDICTED: cell cycle checkpoint protein	0.983	0.99	0.848	1e-150
297742066		325	unnamed protein product [Vitis vinifera]	0.983	0.913	0.848	1e-150
255573477		302	rad1 DNA damage checkpoint protein, puta	0.996	0.996	0.837	1e-150
449462759		301	PREDICTED: cell cycle checkpoint protein	0.983	0.986	0.811	1e-147
147770974		294	hypothetical protein VITISV_014888 [Viti	0.960	0.986	0.827	1e-144
297804406		300	damaged DNA binding protein [Arabidopsis	0.980	0.986	0.765	1e-138
30684177		300	cell cycle checkpoint protein [Arabidops	0.980	0.986	0.758	1e-137
11875164		304	Rad1-like protein [Oryza sativa Japonica	0.983	0.976	0.774	1e-137
89257677		297	hypothetical protein 40.t00049 [Brassica	0.970	0.986	0.762	1e-136

>gi\|224138984\|ref\|XP_002326739.1\| predicted protein [Populus trichocarpa] gi\|222834061\|gb\|EEE72538.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  553 bits (1425), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 257/302 (85%), Positives = 279/302 (92%)

Query: 1   MSSSAMDAESPDLVCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAK 60
           MSSSA++A++ DLVCQLDNVQG+VDALS VRWKRHQDAV+ELSEHGI+LIVEETGCLQAK
Sbjct: 1   MSSSAIEADTSDLVCQLDNVQGIVDALSTVRWKRHQDAVVELSEHGIVLIVEETGCLQAK 60

Query: 61  VYLQRELFVRYEYSAQGRPRFGVSLGLFADCLNTFSAPGHSSLIEIRYPGPDMQLLVKSV 120
           VYLQ+ELF+RYEY+AQGRPRFG+SLGLF DCLNTFS PGHSS IEIRYPGPDMQLL+KS 
Sbjct: 61  VYLQKELFIRYEYTAQGRPRFGLSLGLFVDCLNTFSVPGHSSTIEIRYPGPDMQLLIKSA 120

Query: 121 DSPDACIYAEVRTRIPDMISWDYNFEPAGSTPLTFTVKSAALKEAIDDLEWPGSSIQIKL 180
           DS D CIYAE+RTRIP+ ISWDYNFEPAGSTPL+FTVKSAALKEAIDDLEWPGS IQI L
Sbjct: 121 DSLDDCIYAEIRTRIPETISWDYNFEPAGSTPLSFTVKSAALKEAIDDLEWPGSCIQIIL 180

Query: 181 QPVPPSVSFKGEGHGDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFLRATTSNLPGCVI 240
           +PVPPSV+F+GEGHGDLQIDFMYY NTDLLIAFHCD +VSYRYKYKFLRATTSN+P  V 
Sbjct: 181 KPVPPSVTFRGEGHGDLQIDFMYYANTDLLIAFHCDHQVSYRYKYKFLRATTSNMPSSVT 240

Query: 241 KHNRGSKLIIGRGGMLKVQHLVSVARTSNQHPHTDSAGYQQPSQIAYIEFFVKPEEDEDT 300
           K NRGSKL IGRGGMLKVQHLVSVAR S  H H DSAGYQQPS+IAYIEFFVKPEEDEDT
Sbjct: 241 KDNRGSKLTIGRGGMLKVQHLVSVARPSTSHQHIDSAGYQQPSRIAYIEFFVKPEEDEDT 300

Query: 301 IN 302
           +N
Sbjct: 301 VN 302

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225427149\|ref\|XP_002277302.1\| PREDICTED: cell cycle checkpoint protein RAD1-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297742066\|emb\|CBI33853.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255573477\|ref\|XP_002527664.1\| rad1 DNA damage checkpoint protein, putative [Ricinus communis] gi\|223532969\|gb\|EEF34735.1\| rad1 DNA damage checkpoint protein, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|449462759\|ref\|XP_004149108.1\| PREDICTED: cell cycle checkpoint protein RAD1-like [Cucumis sativus] gi\|449526215\|ref\|XP_004170109.1\| PREDICTED: cell cycle checkpoint protein RAD1-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|147770974\|emb\|CAN64545.1\| hypothetical protein VITISV_014888 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297804406\|ref\|XP_002870087.1\| damaged DNA binding protein [Arabidopsis lyrata subsp. lyrata] gi\|297315923\|gb\|EFH46346.1\| damaged DNA binding protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi|30684177|ref|NP_193511.2| cell cycle checkpoint protein [Arabidopsis thaliana] gi|22136654|gb|AAM91646.1| unknown protein [Arabidopsis thaliana] gi|38603844|gb|AAR24667.1| At4g17760 [Arabidopsis thaliana] gi|46016025|emb|CAE55213.1| Rad1-like protein [Arabidopsis thaliana] gi|51970172|dbj|BAD43778.1| unknown protein [Arabidopsis thaliana] gi|332658546|gb|AEE83946.1| cell cycle checkpoint protein [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|11875164\|dbj\|BAB19377.1\| Rad1-like protein [Oryza sativa Japonica Group] gi\|28190670\|gb\|AAO33148.1\| unknown [Oryza sativa Japonica Group] gi\|215704325\|dbj\|BAG93759.1\| unnamed protein product [Oryza sativa Japonica Group]	Back alignment and taxonomy information

>gi\|89257677\|gb\|ABD65164.1\| hypothetical protein 40.t00049 [Brassica oleracea]	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		302
TAIR\|locus:2129420		300	AT4G17760 [Arabidopsis thalian	0.980	0.986	0.758	2.9e-126
UNIPROTKB\|E1C4I3		279	RAD1 "Uncharacterized protein"	0.781	0.845	0.273	6e-22
MGI\|MGI:1316678		280	Rad1 "RAD1 homolog (S. pombe)"	0.745	0.803	0.282	1.6e-21
RGD\|1306496		280	Rad1 "RAD1 homolog (S. pombe)"	0.745	0.803	0.282	4.1e-21
UNIPROTKB\|Q8AY27		281	rad1 "PCNA-like DNA checkpoint	0.741	0.797	0.276	8.4e-21
ZFIN\|ZDB-GENE-040426-1873		279	rad1 "RAD1 homolog (S. pombe)"	0.817	0.885	0.259	1.1e-20
UNIPROTKB\|O60671		282	RAD1 "Cell cycle checkpoint pr	0.741	0.794	0.264	4.5e-20
UNIPROTKB\|F1SND5		281	RAD1 "Uncharacterized protein"	0.758	0.814	0.265	7.3e-20
UNIPROTKB\|E1BB72		279	RAD1 "Uncharacterized protein"	0.741	0.802	0.260	2.4e-19
UNIPROTKB\|E2QYH8		281	RAD1 "Uncharacterized protein"	0.741	0.797	0.256	9.7e-16

TAIR\|locus:2129420 AT4G17760 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1240 (441.6 bits), Expect = 2.9e-126, P = 2.9e-126
 Identities = 226/298 (75%), Positives = 264/298 (88%)

Query:     2 SSSAMDAESPDLVCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAKV 61
             SS A++ ++PDL+CQLDNVQG+VDAL+ VRWKRHQDA++ELSEHGI+LIVEE+GCLQAKV
Sbjct:     5 SSPAIEPDTPDLICQLDNVQGMVDALTCVRWKRHQDALVELSEHGIVLIVEESGCLQAKV 64

Query:    62 YLQRELFVRYEYSAQGRPRFGVSLGLFADCLNTFSAPGHSSLIEIRYPGPDMQLLVKSVD 121
             YLQRELF +YEY AQGRPRFG+SLGL  DCLNTFS+PGHS+ IEI+YPGPDM+LL+KSVD
Sbjct:    65 YLQRELFTKYEYGAQGRPRFGISLGLLVDCLNTFSSPGHSNTIEIKYPGPDMELLLKSVD 124

Query:   122 SPDACIYAEVRTRIPDMISWDYNFEPAGSTPLTFTVKSAALKEAIDDLEWPGSSIQIKLQ 181
             + ++CIY+E+RTRIP+ ++WDYNFE AG  PLTFTVKSAALKEAIDDLEWPGSS+QI LQ
Sbjct:   125 TLNSCIYSEIRTRIPETVTWDYNFEQAGIAPLTFTVKSAALKEAIDDLEWPGSSVQISLQ 184

Query:   182 PVPPSVSFKGEGHGDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFLRATTSNLPGCVIK 241
               PP V F+GEGHGDLQIDFMYY NTDLL+AFHCD EVSY YKYKFL+ATT+N+PG V++
Sbjct:   185 KEPPCVIFRGEGHGDLQIDFMYYANTDLLLAFHCDTEVSYGYKYKFLKATTANIPGNVVR 244

Query:   242 HNRGSKLIIGRGGMLKVQHLVSVARTSNQHPHTDSAGYQQPSQIAYIEFFVKPEEDED 299
              NRGSKL IGRGGMLKVQHLVSV++     P  +SAGYQ PS+IAYIEFFVKPEE  D
Sbjct:   245 ENRGSKLTIGRGGMLKVQHLVSVSKALA--PQVESAGYQPPSRIAYIEFFVKPEEPAD 300

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0008853 "exodeoxyribonuclease III activity" evidence=IEA

GO:0006261 "DNA-dependent DNA replication" evidence=RCA

UNIPROTKB\|E1C4I3 RAD1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

MGI\|MGI:1316678 Rad1 "RAD1 homolog (S. pombe)" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1306496 Rad1 "RAD1 homolog (S. pombe)" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q8AY27 rad1 "PCNA-like DNA checkpoint protein Rad1" [Xenopus laevis (taxid:8355)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040426-1873 rad1 "RAD1 homolog (S. pombe)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|O60671 RAD1 "Cell cycle checkpoint protein RAD1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SND5 RAD1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BB72 RAD1 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2QYH8 RAD1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.11.2	LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_fgenesh4_pg.C_290233	hypothetical protein (303 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		302
cd00577		248	cd00577, PCNA, Proliferating Cell Nuclear Antigen	1e-38
pfam02144		251	pfam02144, Rad1, Repair protein Rad1/Rec1/Rad17	2e-19

>gnl\|CDD\|238322 cd00577, PCNA, Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea	Back alignment and domain information

 Score =  136 bits (344), Expect = 1e-38
 Identities = 57/252 (22%), Positives = 94/252 (37%), Gaps = 24/252 (9%)

Query: 14  VCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGC-LQAKVYLQRELFVRYE 72
           +     ++ +VDALS    K   +A  +++E GI L   ++       ++L +ELF   E
Sbjct: 3   LSNAKLLKKIVDALS----KLVDEANFDITEDGISLQAMDSSHVALVSLFLPKELFE--E 56

Query: 73  YSAQGRPRFGVSLGLFADCLNTFSAPGHSSLIEIRYPGPDMQLLVKSVDSPDACIYAEVR 132
           Y        GV+L      L           + +R    D   ++   +S    + +E  
Sbjct: 57  YRCDEEISLGVNLKSLLKILKCAGN---EDCVTLRADDEDPLKIL--FESSKGDVTSEFS 111

Query: 133 TRIPDMISWDYNFEPAGSTPLTFTVKSAALKEAIDDLEWPGSSIQIKLQPVPPSVSFKGE 192
            ++ D+ S      P      T T+ S  LK+ + DLE    S+ I         S +GE
Sbjct: 112 LKLMDIDSEQLPI-PELEYDATVTLPSDELKDIVRDLESISDSVTISASKDGFKFSAEGE 170

Query: 193 GHGDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFLRATTSNLPGCVIKHNRGSKLIIGR 252
             G            DLL+   C   VS  Y  K+L+  T   P          K+ +  
Sbjct: 171 LGGASVTLLPKDS--DLLVTIECSEPVSSTYSLKYLKDFTKAAPLS-------DKVTLSF 221

Query: 253 G--GMLKVQHLV 262
           G  G L ++  +
Sbjct: 222 GSDGPLSLEFKI 233

These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY]. . Length = 248

>gnl\|CDD\|216900 pfam02144, Rad1, Repair protein Rad1/Rec1/Rad17	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		302
PF02144		275	Rad1: Repair protein Rad1/Rec1/Rad17; InterPro: IP	100.0
KOG1636		260	consensus DNA polymerase delta processivity factor	100.0
TIGR00590		259	pcna proliferating cell nuclear antigen (pcna). Al	100.0
PLN00057		263	proliferating cell nuclear antigen; Provisional	100.0
PTZ00113		275	proliferating cell nuclear antigen; Provisional	100.0
PTZ00483		264	proliferating cell nuclear antigen; Provisional	100.0
PHA03383		262	PCNA-like protein; Provisional	100.0
KOG3194		279	consensus Checkpoint 9-1-1 complex, RAD1 component	100.0
PRK01115		247	DNA polymerase sliding clamp; Validated	99.98
cd00577		248	PCNA Proliferating Cell Nuclear Antigen (PCNA) dom	99.97
PF02747		128	PCNA_C: Proliferating cell nuclear antigen, C-term	99.87
PF00705		127	PCNA_N: Proliferating cell nuclear antigen, N-term	99.85
COG0592		364	DnaN DNA polymerase sliding clamp subunit (PCNA ho	99.45
PF04139		252	Rad9: Rad9; InterPro: IPR007268 Rad9 is required f	99.16
PF04005		292	Hus1: Hus1-like protein; InterPro: IPR007150 Hus1,	98.97
cd00140		365	beta_clamp Beta clamp domain. The beta subunit (pr	98.86
PRK05643		367	DNA polymerase III subunit beta; Validated	98.54
smart00480		345	POL3Bc DNA polymerase III beta subunit.	98.31
PRK14945		362	DNA polymerase III subunit beta; Provisional	98.19
PRK14940		367	DNA polymerase III subunit beta; Provisional	98.09
KOG3999		284	consensus Checkpoint 9-1-1 complex, HUS1 component	97.97
TIGR00663		367	dnan DNA polymerase III, beta subunit. University)	97.86
PRK14942		373	DNA polymerase III subunit beta; Provisional	97.84
PRK06673		376	DNA polymerase III subunit beta; Validated	97.82
PRK14944		375	DNA polymerase III subunit beta; Provisional	97.81
PRK07761		376	DNA polymerase III subunit beta; Validated	97.79
KOG2810		394	consensus Checkpoint 9-1-1 complex, RAD9 component	97.64
PRK14947		384	DNA polymerase III subunit beta; Provisional	97.54
PRK14941		374	DNA polymerase III subunit beta; Provisional	97.52
PRK14943		374	DNA polymerase III subunit beta; Provisional	97.44
PF02768		121	DNA_pol3_beta_3: DNA polymerase III beta subunit,	97.33
PF00705		127	PCNA_N: Proliferating cell nuclear antigen, N-term	97.12
PRK01115		247	DNA polymerase sliding clamp; Validated	97.03
cd00140		365	beta_clamp Beta clamp domain. The beta subunit (pr	96.97
PRK14946		366	DNA polymerase III subunit beta; Provisional	96.62
COG0592		364	DnaN DNA polymerase sliding clamp subunit (PCNA ho	95.75
cd00577		248	PCNA Proliferating Cell Nuclear Antigen (PCNA) dom	95.68
PF02747		128	PCNA_C: Proliferating cell nuclear antigen, C-term	95.49
TIGR00590		259	pcna proliferating cell nuclear antigen (pcna). Al	95.4
PLN00057		263	proliferating cell nuclear antigen; Provisional	95.36
PF04139		252	Rad9: Rad9; InterPro: IPR007268 Rad9 is required f	95.29
PTZ00113		275	proliferating cell nuclear antigen; Provisional	95.28
PHA03383		262	PCNA-like protein; Provisional	95.12
PTZ00483		264	proliferating cell nuclear antigen; Provisional	95.11
smart00480		345	POL3Bc DNA polymerase III beta subunit.	94.68
PRK14945		362	DNA polymerase III subunit beta; Provisional	94.3
PRK05643		367	DNA polymerase III subunit beta; Validated	93.71
PRK07761		376	DNA polymerase III subunit beta; Validated	92.51
PF02768		121	DNA_pol3_beta_3: DNA polymerase III beta subunit,	92.17
TIGR00663		367	dnan DNA polymerase III, beta subunit. University)	90.3
PRK14943		374	DNA polymerase III subunit beta; Provisional	90.07
PRK14947		384	DNA polymerase III subunit beta; Provisional	87.73
PRK14940		367	DNA polymerase III subunit beta; Provisional	85.62
PRK14942		373	DNA polymerase III subunit beta; Provisional	83.05
PRK14946		366	DNA polymerase III subunit beta; Provisional	81.3
PRK06673		376	DNA polymerase III subunit beta; Validated	80.68

>PF02144 Rad1: Repair protein Rad1/Rec1/Rad17; InterPro: IPR003021 REC1 of Ustilago maydis plays a key role in regulating the genetic system of the fungus	Back alignment and domain information

Probab=100.00  E-value=1.2e-51  Score=379.70  Aligned_cols=237  Identities=27%  Similarity=0.567  Sum_probs=195.6

Q ss_pred             eEEEEECChHHHHHHhcccccceeeeEEEEEeCCccEEEEEcCcEEEEEEEecccCceeEEeC-----------CCCcce
Q 022104           12 DLVCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAKVYLQRELFVRYEYS-----------AQGRPR   80 (302)
Q Consensus        12 ~f~a~~~~a~~l~~iL~aI~~~d~~~a~~~is~~Gi~l~vd~s~~~~~~~~l~~~~F~~Y~~~-----------~~~~~~   80 (302)
                      +|+|++.+++.|.++|+||.|++.  |++.|+++||+|+||++|++|+++||++++|++|+++           ++..++
T Consensus         1 ~f~A~~~~~~~l~~lL~~I~~~~~--a~v~is~~Gi~~~vE~~~~~qa~a~l~k~LF~~Y~~~~~~~~~~~~~~~~~~~~   78 (275)
T PF02144_consen    1 IFSASTSNVRHLYQLLKCIAFKNK--ATVEISEDGIKFTVEDSKSIQASAFLDKSLFSEYTFNPPPDADDDDEEEEDEVS   78 (275)
T ss_dssp             -EEEEES-THHHHHHHHTT-SSSE--EEEEEETTEEEEEEEETTTEEEEEEEEGGGSSEEEE------------SSS-EE
T ss_pred             CeEEEECCHHHHHHHHHhcccCCe--EEEEEcCCEEEEEEECCcEEEEEEEEChhhceEEEEeccccccccccCCCCceE
Confidence            599999999999999999999887  9999999999999999999999999999999999991           123699


Q ss_pred             EEEEchhHHHHHHhCCCCCCc-------------------eEEEEEEcCC--CeEEEEEECCCCCeEEEEEEEecCCCCc
Q 022104           81 FGVSLGLFADCLNTFSAPGHS-------------------SLIEIRYPGP--DMQLLVKSVDSPDACIYAEVRTRIPDMI  139 (302)
Q Consensus        81 fgInL~~L~~~L~~f~~~~~~-------------------~~l~l~y~g~--~l~l~le~~~~~~~~~~~~i~t~e~d~~  139 (302)
                      |+|||+.|++||++||.++..                   ++|+|+|+|+  ||.|+||++|+.++|   +|+|++++.+
T Consensus        79 F~I~L~~LlecL~ifg~~~~~~~~~~~~~~~~~~~~~~~~~~~~lsY~g~G~pL~l~led~gv~t~c---~i~T~~~~~~  155 (275)
T PF02144_consen   79 FGINLSALLECLNIFGSSDSSSSSSSSGGDPSRNNASGEPTSCRLSYPGEGSPLVLILEDSGVTTTC---EIRTYEPDDP  155 (275)
T ss_dssp             EEEEHHHHHHHHTTT-SS--TT-----------------EEEEEEEESSSCCEEEEEEEETTEEEEE---EEEEE-----
T ss_pred             EEEEhHHHHHHHHHhCCCCCccccccccccccccccccCCceEEEEEcCCCCeEEEEEEeCCEEEEE---EEEEecCCcc
Confidence            999999999999999875532                   3899999876  999999998877777   9999999865


Q ss_pred             cCccccCCCCCccEEEEEehHHHHHHHHHhcCC-CCeEEEEEec-CCCcEEEEEee-ceEEEEEEeccCCCCcEEEEEeC
Q 022104          140 SWDYNFEPAGSTPLTFTVKSAALKEAIDDLEWP-GSSIQIKLQP-VPPSVSFKGEG-HGDLQIDFMYYVNTDLLIAFHCD  216 (302)
Q Consensus       140 ~ld~~f~~~~~~~~~v~m~s~~l~~a~~dL~~~-sd~v~i~~~p-~~~~~~~s~~G-~G~~~i~~~~~~~s~~l~~f~~~  216 (302)
                       ++++|+++ ++.++++|+|+||++|++||++. ++.++|.++| ++|+|+|+++| +|+++|+||  ++++++++|+|.
T Consensus       156 -~d~~f~~~-~~~~kiimks~~L~~al~eL~~~~~~~l~i~~s~~~~p~f~l~s~G~~G~s~v~fp--~~~~~le~f~~~  231 (275)
T PF02144_consen  156 -LDFPFDRS-DVVNKIIMKSDWLRDALSELDWSNSEELTIYISPPDKPHFRLSSKGPLGSSKVDFP--NDSDVLETFECY  231 (275)
T ss_dssp             -------TT-TEEEEEEEEHHHHHHHHHTT-TS-CSEEEEEE-S-SSSSEEEEEEETTEEEEEEE---TTSTSEEEEEE-
T ss_pred             -cCcccccc-cceeEEEEEhHHHHHHHHHHhhccCCeEEEEEEeCCCCEEEEEEEcCCCeEEEEEC--CCCCceeEEEEe
Confidence             89999876 88999999999999999999999 8999999998 78999999999 999999999  889999999999


Q ss_pred             ---cceEEEEehhhHHHhhccCCCCcccCCcceEEEEcCCceEEEEEEE
Q 022104          217 ---REVSYRYKYKFLRATTSNLPGCVIKHNRGSKLIIGRGGMLKVQHLV  262 (302)
Q Consensus       217 ---e~v~~~Y~l~yL~~~~KAl~lS~~~~~~~~~V~i~~~g~L~~q~~i  262 (302)
                         +++.++|++++|++++|||++|     .+.+++++.+|+|++||||
T Consensus       232 ~~~~~~~~~Y~f~~i~~~~kAl~~s-----sKv~ir~d~~GlLs~Q~mi  275 (275)
T PF02144_consen  232 DGEEPVISRYKFSLIKKAMKALKIS-----SKVSIRIDENGLLSLQFMI  275 (275)
T ss_dssp             ---S-EEEEEEHHHHCCHHHHHTTS-----SEEEEEEESSS-EEEEEEE
T ss_pred             ccCceEEEEEeHHHHHHHHHHhhhc-----cEEEEEeCCCcEEEEEEeC
Confidence               6788889999999999999988     4444555999999999997

REC1 mutants are very sensitive to UV light. Mutation leads to a complex phenotype with alterations in DNA repair, recombination, mutagenesis, meiosis and cell division []. The predicted product of the REC1 gene is a polypeptide of 522 amino acid residues with molecular mass 57kDa. The protein shows 3'--5' exonuclease activity, but only in cells over-expressing REC1 []. While it is distinguishable from the major bacterial nucleases, the protein has certain enzymatic features in common with epsilon, the proof-reading exonuclease subunit of Escherichia coli DNA polymerase III holoenzyme []. The rad1 gene of Schizosaccharomyces pombe comprises three exons and encodes a 37kDa protein that exhibits partial similarity to the REC1 gene of U. maydis []. The two genes share putative functional similarities in their respective organisms.; GO: 0003684 damaged DNA binding, 0008853 exodeoxyribonuclease III activity, 0006281 DNA repair, 0005634 nucleus; PDB: 3G65_B 3GGR_C 3A1J_C.

>KOG1636 consensus DNA polymerase delta processivity factor (proliferating cell nuclear antigen) [Replication, recombination and repair]	Back alignment and domain information

>TIGR00590 pcna proliferating cell nuclear antigen (pcna)	Back alignment and domain information

>PLN00057 proliferating cell nuclear antigen; Provisional	Back alignment and domain information

>PTZ00113 proliferating cell nuclear antigen; Provisional	Back alignment and domain information

>PTZ00483 proliferating cell nuclear antigen; Provisional	Back alignment and domain information

>PHA03383 PCNA-like protein; Provisional	Back alignment and domain information

>KOG3194 consensus Checkpoint 9-1-1 complex, RAD1 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]	Back alignment and domain information

>PRK01115 DNA polymerase sliding clamp; Validated	Back alignment and domain information

>cd00577 PCNA Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea	Back alignment and domain information

>PF02747 PCNA_C: Proliferating cell nuclear antigen, C-terminal domain; InterPro: IPR022649 Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [] that plays a key role in the control of eukaryotic DNA replication []	Back alignment and domain information

>PF00705 PCNA_N: Proliferating cell nuclear antigen, N-terminal domain; InterPro: IPR022648 Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [] that plays a key role in the control of eukaryotic DNA replication []	Back alignment and domain information

>COG0592 DnaN DNA polymerase sliding clamp subunit (PCNA homolog) [DNA replication, recombination, and repair]	Back alignment and domain information

>PF04139 Rad9: Rad9; InterPro: IPR007268 Rad9 is required for transient cell-cycle arrests and transcriptional induction of DNA repair in response to DNA damage	Back alignment and domain information

>PF04005 Hus1: Hus1-like protein; InterPro: IPR007150 Hus1, Rad1, and Rad9 are three evolutionarily conserved proteins required for checkpoint control in fission yeast	Back alignment and domain information

>cd00140 beta_clamp Beta clamp domain	Back alignment and domain information

>PRK05643 DNA polymerase III subunit beta; Validated	Back alignment and domain information

>smart00480 POL3Bc DNA polymerase III beta subunit	Back alignment and domain information

>PRK14945 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>PRK14940 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>KOG3999 consensus Checkpoint 9-1-1 complex, HUS1 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]	Back alignment and domain information

>TIGR00663 dnan DNA polymerase III, beta subunit	Back alignment and domain information

>PRK14942 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>PRK06673 DNA polymerase III subunit beta; Validated	Back alignment and domain information

>PRK14944 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>PRK07761 DNA polymerase III subunit beta; Validated	Back alignment and domain information

>KOG2810 consensus Checkpoint 9-1-1 complex, RAD9 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]	Back alignment and domain information

>PRK14947 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>PRK14941 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>PRK14943 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>PF02768 DNA_pol3_beta_3: DNA polymerase III beta subunit, C-terminal domain; InterPro: IPR022635 This entry describes the C-terminal domain of the beta chain of DNA polymerase III	Back alignment and domain information

>PF00705 PCNA_N: Proliferating cell nuclear antigen, N-terminal domain; InterPro: IPR022648 Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [] that plays a key role in the control of eukaryotic DNA replication []	Back alignment and domain information

>PRK01115 DNA polymerase sliding clamp; Validated	Back alignment and domain information

>cd00140 beta_clamp Beta clamp domain	Back alignment and domain information

>PRK14946 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>COG0592 DnaN DNA polymerase sliding clamp subunit (PCNA homolog) [DNA replication, recombination, and repair]	Back alignment and domain information

>cd00577 PCNA Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea	Back alignment and domain information

>PF02747 PCNA_C: Proliferating cell nuclear antigen, C-terminal domain; InterPro: IPR022649 Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [] that plays a key role in the control of eukaryotic DNA replication []	Back alignment and domain information

>TIGR00590 pcna proliferating cell nuclear antigen (pcna)	Back alignment and domain information

>PLN00057 proliferating cell nuclear antigen; Provisional	Back alignment and domain information

>PF04139 Rad9: Rad9; InterPro: IPR007268 Rad9 is required for transient cell-cycle arrests and transcriptional induction of DNA repair in response to DNA damage	Back alignment and domain information

>PTZ00113 proliferating cell nuclear antigen; Provisional	Back alignment and domain information

>PHA03383 PCNA-like protein; Provisional	Back alignment and domain information

>PTZ00483 proliferating cell nuclear antigen; Provisional	Back alignment and domain information

>smart00480 POL3Bc DNA polymerase III beta subunit	Back alignment and domain information

>PRK14945 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>PRK05643 DNA polymerase III subunit beta; Validated	Back alignment and domain information

>PRK07761 DNA polymerase III subunit beta; Validated	Back alignment and domain information

>PF02768 DNA_pol3_beta_3: DNA polymerase III beta subunit, C-terminal domain; InterPro: IPR022635 This entry describes the C-terminal domain of the beta chain of DNA polymerase III	Back alignment and domain information

>TIGR00663 dnan DNA polymerase III, beta subunit	Back alignment and domain information

>PRK14943 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>PRK14947 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>PRK14940 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>PRK14942 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>PRK14946 DNA polymerase III subunit beta; Provisional	Back alignment and domain information

>PRK06673 DNA polymerase III subunit beta; Validated	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		302
3g65_B		282	Crystal Structure Of The Human Rad9-Rad1-Hus1 Dna D		3e-17
3a1j_C		263	Crystal Structure Of The Human Rad9-Hus1-Rad1 Compl		6e-15

>pdb|3G65|B Chain B, Crystal Structure Of The Human Rad9-Rad1-Hus1 Dna Damage Checkpoint Complex Length = 282

Back alignment and structure

Iteration: 1

Score = 85.5 bits (210), Expect = 3e-17, Method: Compositional matrix adjust. Identities = 69/290 (23%), Positives = 135/290 (46%), Gaps = 35/290 (12%) Query: 13 LVCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAKVYLQRELFVRYE 72 LV LDNV+ L L A+ ++ H A +++GI + VE C+QA ++Q +F ++ Sbjct: 17 LVASLDNVRNLSTILKAIHFREH--ATCFATKNGIKVTVENAKCVQANAFIQAGIFQEFK 74 Query: 73 YSAQGRPRFGVSLGLFADCLNTFSA---PGHSSLIEIRYPGPDMQLLVKSVDSPDACIYA 129 + F ++L + DCL+ F + PG + + + Y G L++ ++ Sbjct: 75 VQEES-VTFRINLTVLLDCLSIFGSSPMPGTLTALRMCYQGYGYPLML-FLEEGGVVTVC 132 Query: 130 EVRTRIPDMISWDYNFEPAGSTPLTFTVKSAALKEAIDDLEWPGSSIQIKLQPVPPSVSF 189 ++ T+ P+ + D++F + + ++S L+EA +L+ +QI + P P Sbjct: 133 KINTQEPEE-TLDFDF-CSTNVINKIILQSEGLREAFSELDMTSEVLQITMSPDKPYFRL 190 Query: 190 KGEGH-GDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFLRATTSNLP-GCVIKHNRGSK 247 G+ G +D Y ++DL+ AFHC++ RYK L+ +T L C + ++ Sbjct: 191 STFGNAGSSHLD--YPKDSDLMEAFHCNQTQVNRYKISLLKPSTKALVLSCKVSIRTDNR 248 Query: 248 LIIGRGGMLKVQHLVSVARTSNQHPHTDSAGYQQPSQIAYIEFFVKPEED 297 G L +Q+++ + QI ++E++ P+E+ Sbjct: 249 ------GFLSLQYMIR----------------NEDGQICFVEYYCCPDEE 276

PyMOL of 3g65

>pdb|3A1J|C Chain C, Crystal Structure Of The Human Rad9-Hus1-Rad1 Complex Length = 263

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		302
3a1j_C		263	Cell cycle checkpoint protein RAD1; DNA damage, DN	1e-60
3aiz_A		248	DNA polymerase sliding clamp B; protein-protein co	1e-05

>3a1j_C Cell cycle checkpoint protein RAD1; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3g65_B 3ggr_C Length = 263	Back alignment and structure

 Score =  192 bits (490), Expect = 1e-60
 Identities = 67/294 (22%), Positives = 131/294 (44%), Gaps = 37/294 (12%)

Query: 9   ESPDLVCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAKVYLQRELF 68
           +   LV  LDNV+ L   L A+ ++  + A    +++GI + VE   C+QA  ++Q  +F
Sbjct: 1   DQYSLVASLDNVRNLSTILKAIHFR--EHATCFATKNGIKVTVENAKCVQANAFIQAGIF 58

Query: 69  VRYEYSAQGRPRFGVSLGLFADCLNTFSA---PGHSSLIEIRYPGPDMQLLVKSVDSPDA 125
             ++   +    F ++L +  DCL+ F +   PG  + + + Y G    L++  ++    
Sbjct: 59  QEFKVQEES-VTFRINLTVLLDCLSIFGSSPMPGTLTALRMCYQGYGYPLMLF-LEEGGV 116

Query: 126 CIYAEVRTRIPDMISWDYNFEPAGSTPLTFTVKSAALKEAIDDLEWPGSSIQIKLQPVPP 185
               ++ T+ P+    D++F    +      ++S  L+EA  +L+     +QI + P  P
Sbjct: 117 VTVCKINTQEPEET-LDFDFCST-NVINKIILQSEGLREAFSELDMTSEVLQITMSPDKP 174

Query: 186 SVSFKGEGH-GDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFLRATTSNLPGCVIKHNR 244
                  G+ G   +D+    ++DL+ AFHC++    RYK   L+ +T  L         
Sbjct: 175 YFRLSTFGNAGSSHLDY--PKDSDLMEAFHCNQTQVNRYKISLLKPSTKALVLS------ 226

Query: 245 GSK--LIIGRGGMLKVQHLVSVARTSNQHPHTDSAGYQQPSQIAYIEFFVKPEE 296
             K  +     G L +Q+++                  +  QI ++E++  P+E
Sbjct: 227 -CKVSIRTDNRGFLSLQYMIR----------------NEDGQICFVEYYCCPDE 263

PyMOL of 3a1j

>3aiz_A DNA polymerase sliding clamp B; protein-protein complex, replication; HET: DNA; 2.80A {Sulfolobus tokodaii} PDB: 3aix_B* Length = 248	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		302
3a1j_C		263	Cell cycle checkpoint protein RAD1; DNA damage, DN	100.0
3fds_C		249	DNA polymerase sliding clamp B; protein-protein co	100.0
3k4x_A		798	PCNA, proliferating cell nuclear antigen; DNA repl	100.0
3p91_A		265	Proliferating cell nuclear antigen; DNA binding pr	100.0
3lx2_A		259	DNA polymerase sliding clamp 2; PCNA, DNA processi	100.0
3k4x_A		798	PCNA, proliferating cell nuclear antigen; DNA repl	100.0
3fds_D		245	DNA polymerase sliding clamp C; protein-protein co	100.0
3ifv_A		247	PCNA; processivity factor, sliding clamp, halophil	100.0
1plq_A		258	Proliferating cell nuclear antigen (PCNA); DNA-bin	100.0
1u7b_A		261	PCNA, cyclin, proliferating cell nuclear antigen;	100.0
2zvv_A		276	PCNA 1, proliferating cellular nuclear antigen 1;	100.0
1iz5_A		249	Proliferating cell nuclear antigen; DNA, replicati	100.0
3aiz_A		248	DNA polymerase sliding clamp B; protein-protein co	100.0
2ijx_A		244	DNA polymerase sliding clamp A; PCNA3 subunit, pro	100.0
1ud9_A		245	DNA polymerase sliding clamp A; DNA-binding, DNA r	100.0
3aiz_C		246	DNA polymerase sliding clamp C; protein-protein co	99.97
1rwz_A		245	DNA polymerase sliding clamp; torus, processivity	99.97
3a1j_A		266	Cell cycle checkpoint control protein RAD9A; DNA d	99.96
3a1j_B		281	HHUS1, checkpoint protein HUS1; DNA damage, DNA re	99.96
3g65_A		296	Cell cycle checkpoint control protein RAD9A; PCNA,	99.8
3pge_A		200	SUMO-modified proliferating cell nuclear antigen;	99.66
3l0w_B		169	Monoubiquitinated proliferating cell nuclear antig	99.58
1vpk_A		378	DNA polymerase III, beta subunit; TM0262, structur	98.81
2avt_A		378	DNA polymerase III beta subunit; beta clamp, slidi	98.68
3d1g_A		366	DNA polymerase III subunit beta; chemical probe, D	98.64
3t0p_A		371	DNA polymerase III, beta subunit; DNA clamp, struc	98.35
3p16_A		408	DNA polymerase III subunit beta; DNA polymerase II	97.99
3a1j_A		266	Cell cycle checkpoint control protein RAD9A; DNA d	96.62
3fds_C		249	DNA polymerase sliding clamp B; protein-protein co	96.62
1iz5_A		249	Proliferating cell nuclear antigen; DNA, replicati	96.41
1vpk_A		378	DNA polymerase III, beta subunit; TM0262, structur	96.37
3g65_A		296	Cell cycle checkpoint control protein RAD9A; PCNA,	96.29
1u7b_A		261	PCNA, cyclin, proliferating cell nuclear antigen;	95.98
3a1j_C		263	Cell cycle checkpoint protein RAD1; DNA damage, DN	95.82
3fds_D		245	DNA polymerase sliding clamp C; protein-protein co	95.81
2zvv_A		276	PCNA 1, proliferating cellular nuclear antigen 1;	95.67
3lx2_A		259	DNA polymerase sliding clamp 2; PCNA, DNA processi	95.66
1plq_A		258	Proliferating cell nuclear antigen (PCNA); DNA-bin	95.57
3p91_A		265	Proliferating cell nuclear antigen; DNA binding pr	95.41
2ijx_A		244	DNA polymerase sliding clamp A; PCNA3 subunit, pro	95.04
1rwz_A		245	DNA polymerase sliding clamp; torus, processivity	94.49
3aiz_C		246	DNA polymerase sliding clamp C; protein-protein co	94.43
3ifv_A		247	PCNA; processivity factor, sliding clamp, halophil	94.27
1ud9_A		245	DNA polymerase sliding clamp A; DNA-binding, DNA r	94.23
3aiz_A		248	DNA polymerase sliding clamp B; protein-protein co	94.02
3p16_A		408	DNA polymerase III subunit beta; DNA polymerase II	90.64
3a1j_B		281	HHUS1, checkpoint protein HUS1; DNA damage, DNA re	88.58
3t0p_A		371	DNA polymerase III, beta subunit; DNA clamp, struc	82.68
3d1g_A		366	DNA polymerase III subunit beta; chemical probe, D	81.45

>3a1j_C Cell cycle checkpoint protein RAD1; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3g65_B 3ggr_C	Back alignment and structure

Probab=100.00  E-value=4.4e-56  Score=405.68  Aligned_cols=255  Identities=27%  Similarity=0.533  Sum_probs=229.4

Q ss_pred             CCCeEEEEECChHHHHHHhcccccceeeeEEEEEeCCccEEEEEcCcEEEEEEEecccCceeEEeCCCCcceEEEEchhH
Q 022104            9 ESPDLVCQLDNVQGLVDALSAVRWKRHQDAVIELSEHGIILIVEETGCLQAKVYLQRELFVRYEYSAQGRPRFGVSLGLF   88 (302)
Q Consensus         9 ~~~~f~a~~~~a~~l~~iL~aI~~~d~~~a~~~is~~Gi~l~vd~s~~~~~~~~l~~~~F~~Y~~~~~~~~~fgInL~~L   88 (302)
                      +++||+|++.+++.|+++|+||.|+++  |+|+|+++||+++++|+|++||+++|++++|++|+|+++ .++|||||+.|
T Consensus         1 ~~~~f~a~~~~a~~l~~il~ai~l~~e--a~~~~s~~Gi~l~a~Ds~v~~v~l~l~~~~F~~Y~~~~~-~~~~gi~l~~l   77 (263)
T 3a1j_C            1 DQYSLVASLDNVRNLSTILKAIHFREH--ATCFATKNGIKVTVENAKCVQANAFIQAGIFQEFKVQEE-SVTFRINLTVL   77 (263)
T ss_dssp             CCCSEEEEESCTHHHHHHHHTTCSSSE--EEEEEETTEEEEEEEETTTEEEEEEEEGGGSSEEEESSS-CEEEEEEHHHH
T ss_pred             CCeEEEEEeCCHHHHHHHHhheecCcE--EEEEEcCCeEEEEEEeCCEEEEEEEECHHHCceEEEcCC-CcEEEEEhHHH
Confidence            468999999999999999999998888  999999999999965699999999999999999999942 38999999999


Q ss_pred             HHHHHhCCCCC---CceEEEEEEcC--CCeEEEEEECCCCCeEEEEEEEecCCCCccCccccCCCCCccEEEEEehHHHH
Q 022104           89 ADCLNTFSAPG---HSSLIEIRYPG--PDMQLLVKSVDSPDACIYAEVRTRIPDMISWDYNFEPAGSTPLTFTVKSAALK  163 (302)
Q Consensus        89 ~~~L~~f~~~~---~~~~l~l~y~g--~~l~l~le~~~~~~~~~~~~i~t~e~d~~~ld~~f~~~~~~~~~v~m~s~~l~  163 (302)
                      .|||++|++.+   ...+|+|+|++  +++.|.||+++..+.|   +|+|++++.. ++++|+.. +..++|+|+|++|+
T Consensus        78 ~k~L~~~~~~~~~~d~~~l~i~~~~~~~~l~l~~e~~~~~~~~---~l~~~~~~~~-~d~~f~~~-~~~~~v~m~s~~l~  152 (263)
T 3a1j_C           78 LDCLSIFGSSPMPGTLTALRMCYQGYGYPLMLFLEEGGVVTVC---KINTQEPEET-LDFDFCST-NVINKIILQSEGLR  152 (263)
T ss_dssp             HHHHTTTCSCCCTTCCCEEEEEECSTTCCEEEEEEETTEEEEE---EECCBCCCCC-CCCCCCTT-TEEEEEEEEGGGGH
T ss_pred             HHHHHHhcCCcCCCCceEEEEEECCCCCcEEEEEEeCCeEEEE---EEEEEcCCcc-cCcccCcc-cceEEEEEehHHHH
Confidence            99999998751   24689999977  4899999987755555   9999999874 68888876 88899999999999


Q ss_pred             HHHHHhcCCCCeEEEEEecCCCcEEEEEee-ceEEEEEEeccCCCCcEEEEEeCcceEEEEehhhHHHhhccCCCCcccC
Q 022104          164 EAIDDLEWPGSSIQIKLQPVPPSVSFKGEG-HGDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFLRATTSNLPGCVIKH  242 (302)
Q Consensus       164 ~a~~dL~~~sd~v~i~~~p~~~~~~~s~~G-~G~~~i~~~~~~~s~~l~~f~~~e~v~~~Y~l~yL~~~~KAl~lS~~~~  242 (302)
                      +||+||+++|++|+|.++|++|+|+|+++| .|+++++||  ++++.+++|+|.+|++++|+++||++++||+++|    
T Consensus       153 ~~~~dl~~~~d~v~i~~~~~~p~~~~~~~Gd~g~~~i~~~--~~~~~~~~~~~~~~~~~~y~l~yL~~~~ka~~~s----  226 (263)
T 3a1j_C          153 EAFSELDMTSEVLQITMSPDKPYFRLSTFGNAGSSHLDYP--KDSDLMEAFHCNQTQVNRYKISLLKPSTKALVLS----  226 (263)
T ss_dssp             HHHHTSCTTSSEEEEEECSSSSSEEEEEEETTEEEEEEEC--TTCSSEEEEEECSCEEEEEEHHHHTTHHHHHHHC----
T ss_pred             HHHHHHhccCCeEEEEEEcCCCEEEEEEEcCCccEEEEEc--CCCCeEEEEEeCChhhcEEeHHHHHHHHhhhhhc----
Confidence            999999999999999999877899999999 999999999  7788999999999999999999999999999988    


Q ss_pred             CcceEEEE--cCCceEEEEEEEeecccCCCCCCCCCCCcCCCCceeEEEEEEecCC
Q 022104          243 NRGSKLII--GRGGMLKVQHLVSVARTSNQHPHTDSAGYQQPSQIAYIEFFVKPEE  296 (302)
Q Consensus       243 ~~~~~V~i--~~~g~L~~q~~i~~~~~~~~~~~~~~~~~~~~~~~~~v~f~~aP~~  296 (302)
                         ++|+|  +.+|||++||+|..                ++|+.+||+|||||++
T Consensus       227 ---~~v~i~~~~~~pL~l~~~i~~----------------~~g~~~~v~f~laP~~  263 (263)
T 3a1j_C          227 ---CKVSIRTDNRGFLSLQYMIRN----------------EDGQICFVEYYCCPDE  263 (263)
T ss_dssp             ---SEEEEEEETTCCEEEEEEEEC----------------TTSCEEEEEEEECCCC
T ss_pred             ---CEEEEEECCCeeEEEEEEEec----------------CCCCEEEEEEEEEECC
Confidence               55555  99999999999985                1366899999999985

PyMOL of 3a1j

>3fds_C DNA polymerase sliding clamp B; protein-protein complex, DNA damage, DNA repair, DNA replica DNA-binding, DNA-directed DNA polymerase; HET: DNA 1PE PGE; 2.05A {Sulfolobus solfataricus} PDB: 2io4_A* 2nti_D* 2hii_A 2hik_A 2ix2_A* 2izo_C*	Back alignment and structure

>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae}	Back alignment and structure

>3p91_A Proliferating cell nuclear antigen; DNA binding protein, DNA replication, processivity, sliding; 2.40A {Entamoeba histolytica}	Back alignment and structure

>3lx2_A DNA polymerase sliding clamp 2; PCNA, DNA processivity factor, trimer, toroidal, DNA replica DNA-binding, DNA binding protein; HET: DNA; 2.40A {Thermococcus kodakarensis}	Back alignment and structure

>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae}	Back alignment and structure

>3fds_D DNA polymerase sliding clamp C; protein-protein complex, DNA damage, DNA repair, DNA replica DNA-binding, DNA-directed DNA polymerase; HET: DNA 1PE PGE; 2.05A {Sulfolobus solfataricus} PDB: 2nti_E* 2io4_B* 2ix2_B* 2hik_B 2hii_B* 2izo_B*	Back alignment and structure

>3ifv_A PCNA; processivity factor, sliding clamp, halophilic, replication; 2.00A {Haloferax volcanii} PDB: 3hi8_A	Back alignment and structure

>1plq_A Proliferating cell nuclear antigen (PCNA); DNA-binding, nuclear protein, DNA replication, processivity; 2.30A {Saccharomyces cerevisiae} SCOP: d.131.1.2 d.131.1.2 PDB: 1plr_A 2od8_A* 1sxj_F* 3f1w_A 3v60_B 3v61_B 3v62_B* 3gpn_A 3gpm_A 3l0w_A 3l0x_A 3l10_A 3pge_B 3l0x_B	Back alignment and structure

>1u7b_A PCNA, cyclin, proliferating cell nuclear antigen; sliding clamp, DNA processing, FEN1, PIP- BOX, replication; 1.88A {Homo sapiens} SCOP: d.131.1.2 d.131.1.2 PDB: 1u76_A 1axc_A 1ul1_A 1vyj_A 1vym_A 1w60_A 2zvk_A* 2zvl_A* 2zvm_A* 3p87_A 3vkx_A*	Back alignment and structure

>2zvv_A PCNA 1, proliferating cellular nuclear antigen 1; protein-peptide complex, DNA replication, DNA-binding, nucleus, DNA binding protein; 2.00A {Arabidopsis thaliana} PDB: 2zvw_A	Back alignment and structure

>1iz5_A Proliferating cell nuclear antigen; DNA, replication, processivity, sliding clamp, DNA binding protein; 1.80A {Pyrococcus furiosus} SCOP: d.131.1.2 d.131.1.2 PDB: 3a2f_B* 1iz4_A 1ge8_A 1isq_A 3lx1_A*	Back alignment and structure

>3aiz_A DNA polymerase sliding clamp B; protein-protein complex, replication; HET: DNA; 2.80A {Sulfolobus tokodaii} PDB: 3aix_B*	Back alignment and structure

>2ijx_A DNA polymerase sliding clamp A; PCNA3 subunit, protein-protein interaction, PCNA123 heterotr binding protein; HET: DNA; 1.90A {Sulfolobus solfataricus} PDB: 2nti_F* 2hii_C 2hik_C 2ix2_C*	Back alignment and structure

>1ud9_A DNA polymerase sliding clamp A; DNA-binding, DNA replication, DNA binding protein; HET: DNA; 1.68A {Sulfolobus tokodaii} SCOP: d.131.1.2 d.131.1.2	Back alignment and structure

>3aiz_C DNA polymerase sliding clamp C; protein-protein complex, replication; HET: DNA; 2.80A {Sulfolobus tokodaii} PDB: 3aix_A*	Back alignment and structure

>1rwz_A DNA polymerase sliding clamp; torus, processivity factor, replication; HET: DNA; 1.80A {Archaeoglobus fulgidus} SCOP: d.131.1.2 d.131.1.2 PDB: 1rxm_A* 1rxz_A* 3p83_A*	Back alignment and structure

>3a1j_A Cell cycle checkpoint control protein RAD9A; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3ggr_A	Back alignment and structure

>3a1j_B HHUS1, checkpoint protein HUS1; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3g65_C 3ggr_B	Back alignment and structure

>3g65_A Cell cycle checkpoint control protein RAD9A; PCNA, DNA binding clamp, DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein; 2.90A {Homo sapiens}	Back alignment and structure

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}	Back alignment and structure

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B	Back alignment and structure

>1vpk_A DNA polymerase III, beta subunit; TM0262, structural genomic center for structural genomics, JCSG, protein structure INI PSI, transferase; HET: DNA; 2.00A {Thermotoga maritima} SCOP: d.131.1.1 d.131.1.1 d.131.1.1	Back alignment and structure

>2avt_A DNA polymerase III beta subunit; beta clamp, sliding clamp, replication, transferase; HET: DNA; 2.00A {Streptococcus pyogenes} PDB: 2awa_A*	Back alignment and structure

>3d1g_A DNA polymerase III subunit beta; chemical probe, DNA sliding clamp, DNA replication, rational drug design, antibiotic target, transferase; HET: DNA 322; 1.64A {Escherichia coli} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 PDB: 1mmi_A* 1unn_A* 2pol_A* 3bep_A* 3d1e_A* 3d1f_A* 1ok7_A* 3q4j_A* 3q4k_A* 3qsb_A* 3q4l_A* 2xur_A* 1jql_A* 1jqj_A* 3f1v_A* 3pwe_A*	Back alignment and structure

>3t0p_A DNA polymerase III, beta subunit; DNA clamp, structural genomics, joint center for structural JCSG, protein structure initiative; HET: DNA MSE; 2.26A {Eubacterium rectale}	Back alignment and structure

>3p16_A DNA polymerase III subunit beta; DNA polymerase III sliding clamp, transferase; HET: DNA; 2.89A {Mycobacterium tuberculosis} PDB: 3rb9_A*	Back alignment and structure

>3a1j_A Cell cycle checkpoint control protein RAD9A; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3ggr_A	Back alignment and structure

>3fds_C DNA polymerase sliding clamp B; protein-protein complex, DNA damage, DNA repair, DNA replica DNA-binding, DNA-directed DNA polymerase; HET: DNA 1PE PGE; 2.05A {Sulfolobus solfataricus} PDB: 2io4_A* 2nti_D* 2hii_A 2hik_A 2ix2_A* 2izo_C*	Back alignment and structure

>1iz5_A Proliferating cell nuclear antigen; DNA, replication, processivity, sliding clamp, DNA binding protein; 1.80A {Pyrococcus furiosus} SCOP: d.131.1.2 d.131.1.2 PDB: 3a2f_B* 1iz4_A 1ge8_A 1isq_A 3lx1_A*	Back alignment and structure

>1vpk_A DNA polymerase III, beta subunit; TM0262, structural genomic center for structural genomics, JCSG, protein structure INI PSI, transferase; HET: DNA; 2.00A {Thermotoga maritima} SCOP: d.131.1.1 d.131.1.1 d.131.1.1	Back alignment and structure

>3g65_A Cell cycle checkpoint control protein RAD9A; PCNA, DNA binding clamp, DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein; 2.90A {Homo sapiens}	Back alignment and structure

>1u7b_A PCNA, cyclin, proliferating cell nuclear antigen; sliding clamp, DNA processing, FEN1, PIP- BOX, replication; 1.88A {Homo sapiens} SCOP: d.131.1.2 d.131.1.2 PDB: 1u76_A 1axc_A 1ul1_A 1vyj_A 1vym_A 1w60_A 2zvk_A* 2zvl_A* 2zvm_A* 3p87_A 3vkx_A*	Back alignment and structure

>3a1j_C Cell cycle checkpoint protein RAD1; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3g65_B 3ggr_C	Back alignment and structure

>3fds_D DNA polymerase sliding clamp C; protein-protein complex, DNA damage, DNA repair, DNA replica DNA-binding, DNA-directed DNA polymerase; HET: DNA 1PE PGE; 2.05A {Sulfolobus solfataricus} PDB: 2nti_E* 2io4_B* 2ix2_B* 2hik_B 2hii_B* 2izo_B*	Back alignment and structure

>2zvv_A PCNA 1, proliferating cellular nuclear antigen 1; protein-peptide complex, DNA replication, DNA-binding, nucleus, DNA binding protein; 2.00A {Arabidopsis thaliana} PDB: 2zvw_A	Back alignment and structure

>3lx2_A DNA polymerase sliding clamp 2; PCNA, DNA processivity factor, trimer, toroidal, DNA replica DNA-binding, DNA binding protein; HET: DNA; 2.40A {Thermococcus kodakarensis}	Back alignment and structure

>1plq_A Proliferating cell nuclear antigen (PCNA); DNA-binding, nuclear protein, DNA replication, processivity; 2.30A {Saccharomyces cerevisiae} SCOP: d.131.1.2 d.131.1.2 PDB: 1plr_A 2od8_A* 1sxj_F* 3f1w_A 3v60_B 3v61_B 3v62_B* 3gpn_A 3gpm_A 3l0w_A 3l0x_A 3l10_A 3pge_B 3l0x_B	Back alignment and structure

>3p91_A Proliferating cell nuclear antigen; DNA binding protein, DNA replication, processivity, sliding; 2.40A {Entamoeba histolytica}	Back alignment and structure

>2ijx_A DNA polymerase sliding clamp A; PCNA3 subunit, protein-protein interaction, PCNA123 heterotr binding protein; HET: DNA; 1.90A {Sulfolobus solfataricus} PDB: 2nti_F* 2hii_C 2hik_C 2ix2_C*	Back alignment and structure

>1rwz_A DNA polymerase sliding clamp; torus, processivity factor, replication; HET: DNA; 1.80A {Archaeoglobus fulgidus} SCOP: d.131.1.2 d.131.1.2 PDB: 1rxm_A* 1rxz_A* 3p83_A*	Back alignment and structure

>3aiz_C DNA polymerase sliding clamp C; protein-protein complex, replication; HET: DNA; 2.80A {Sulfolobus tokodaii} PDB: 3aix_A*	Back alignment and structure

>3ifv_A PCNA; processivity factor, sliding clamp, halophilic, replication; 2.00A {Haloferax volcanii} PDB: 3hi8_A	Back alignment and structure

>1ud9_A DNA polymerase sliding clamp A; DNA-binding, DNA replication, DNA binding protein; HET: DNA; 1.68A {Sulfolobus tokodaii} SCOP: d.131.1.2 d.131.1.2	Back alignment and structure

>3aiz_A DNA polymerase sliding clamp B; protein-protein complex, replication; HET: DNA; 2.80A {Sulfolobus tokodaii} PDB: 3aix_B*	Back alignment and structure

>3p16_A DNA polymerase III subunit beta; DNA polymerase III sliding clamp, transferase; HET: DNA; 2.89A {Mycobacterium tuberculosis} PDB: 3rb9_A*	Back alignment and structure

>3a1j_B HHUS1, checkpoint protein HUS1; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3g65_C 3ggr_B	Back alignment and structure

>3t0p_A DNA polymerase III, beta subunit; DNA clamp, structural genomics, joint center for structural JCSG, protein structure initiative; HET: DNA MSE; 2.26A {Eubacterium rectale}	Back alignment and structure

>3d1g_A DNA polymerase III subunit beta; chemical probe, DNA sliding clamp, DNA replication, rational drug design, antibiotic target, transferase; HET: DNA 322; 1.64A {Escherichia coli} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 PDB: 1mmi_A* 1unn_A* 2pol_A* 3bep_A* 3d1e_A* 3d1f_A* 1ok7_A* 3q4j_A* 3q4k_A* 3qsb_A* 3q4l_A* 2xur_A* 1jql_A* 1jqj_A* 3f1v_A* 3pwe_A*	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		302
d1ud9a2		119	d.131.1.2 (A:127-245) Proliferating cell nuclear a	4e-06

>d1ud9a2 d.131.1.2 (A:127-245) Proliferating cell nuclear antigen (PCNA) {Archaeon Sulfolobus tokodaii [TaxId: 111955]} Length = 119	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: DNA clamp
superfamily: DNA clamp
family: DNA polymerase processivity factor
domain: Proliferating cell nuclear antigen (PCNA)
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

 Score = 42.9 bits (101), Expect = 4e-06
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 4/87 (4%)

Query: 152 PLTFTVKSAALKEAIDDLEWPGSSIQIKLQPVPPSVSFKGEGHGDLQIDFMYYVNTDLLI 211
            +  T+ ++ LK AI ++     ++ I        V  KGEG   ++++F    +T  L 
Sbjct: 3   DIKATINASGLKNAIGEIAEVADTLLISG--NEEKVVVKGEGENKVEVEFSK--DTGSLA 58

Query: 212 AFHCDREVSYRYKYKFLRATTSNLPGC 238
               ++E S  Y  ++L    S     
Sbjct: 59  DIEFNKESSSAYDVEYLNDIISLTKLS 85

PyMOL of d1ud9a2

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		302
d1iz5a2		121	Proliferating cell nuclear antigen (PCNA) {Archaeo	99.88
d1plqa2		132	Proliferating cell nuclear antigen (PCNA) {Baker's	99.87
d1ud9a2		119	Proliferating cell nuclear antigen (PCNA) {Archaeo	99.85
d1rwza2		122	Proliferating cell nuclear antigen (PCNA) {Archaeo	99.85
d1u7ba1		126	Proliferating cell nuclear antigen (PCNA) {Human (	99.83
d1plqa1		126	Proliferating cell nuclear antigen (PCNA) {Baker's	99.83
d1u7ba2		129	Proliferating cell nuclear antigen (PCNA) {Human (	99.8
d1iz5a1		119	Proliferating cell nuclear antigen (PCNA) {Archaeo	99.8
d1rwza1		122	Proliferating cell nuclear antigen (PCNA) {Archaeo	99.75
d1ud9a1		119	Proliferating cell nuclear antigen (PCNA) {Archaeo	99.75
d1rwza1		122	Proliferating cell nuclear antigen (PCNA) {Archaeo	97.69
d1u7ba1		126	Proliferating cell nuclear antigen (PCNA) {Human (	97.39
d1iz5a1		119	Proliferating cell nuclear antigen (PCNA) {Archaeo	97.3
d1iz5a2		121	Proliferating cell nuclear antigen (PCNA) {Archaeo	97.2
d1plqa1		126	Proliferating cell nuclear antigen (PCNA) {Baker's	97.15
d1ok7a3		122	DNA polymerase III, beta subunit {Escherichia coli	97.03
d1ud9a2		119	Proliferating cell nuclear antigen (PCNA) {Archaeo	96.88
d1ud9a1		119	Proliferating cell nuclear antigen (PCNA) {Archaeo	96.67
d1vpka3		123	DNA polymerase III, beta subunit {Thermotoga marit	96.5
d1rwza2		122	Proliferating cell nuclear antigen (PCNA) {Archaeo	95.04
d1u7ba2		129	Proliferating cell nuclear antigen (PCNA) {Human (	94.86
d1vpka3		123	DNA polymerase III, beta subunit {Thermotoga marit	93.81
d1plqa2		132	Proliferating cell nuclear antigen (PCNA) {Baker's	93.63
d1ok7a3		122	DNA polymerase III, beta subunit {Escherichia coli	91.91

>d1iz5a2 d.131.1.2 (A:126-246) Proliferating cell nuclear antigen (PCNA) {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: DNA clamp
superfamily: DNA clamp
family: DNA polymerase processivity factor
domain: Proliferating cell nuclear antigen (PCNA)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.88  E-value=5.2e-22  Score=158.18  Aligned_cols=115  Identities=17%  Similarity=0.282  Sum_probs=105.0

Q ss_pred             CccEEEEEehHHHHHHHHHhcCCCCeEEEEEecCCCcEEEEEee-ceEEEEEEeccCCCCcEEEEEeCcceEEEEehhhH
Q 022104          150 STPLTFTVKSAALKEAIDDLEWPGSSIQIKLQPVPPSVSFKGEG-HGDLQIDFMYYVNTDLLIAFHCDREVSYRYKYKFL  228 (302)
Q Consensus       150 ~~~~~v~m~s~~l~~a~~dL~~~sd~v~i~~~p~~~~~~~s~~G-~G~~~i~~~~~~~s~~l~~f~~~e~v~~~Y~l~yL  228 (302)
                      ++.++|.|+|+.|+++++|++.+||.|+|.++  ++.|.|++.| .|+++++++  .+++.+.+++|+++++++|+++||
T Consensus         4 ~~~~~i~~~s~~f~~ii~~l~~~~d~i~i~~~--~~~i~f~~~gd~g~~~v~~~--~~~~~~~~~~~~~~~~~~ysl~yL   79 (121)
T d1iz5a2           4 PFTAKVVVLGEVLKAAVKAASLVSDSIKFIAR--ENEFIMKAEGETQEVEIKLT--LEDEGLLDIEVQEETKSAYGVSYL   79 (121)
T ss_dssp             CCCEEEEEEHHHHHHHHHHHTTTCSEEEEEEE--TTEEEEEEECSSCEEEEEEE--TTTTSSSEEEESSCEEEEEEHHHH
T ss_pred             CceEEEEEEHHHHHHHHHHHHhcCCeEEEEEc--CCEEEEEEEccCcEEEEEEc--CCCCccEEEEcCCceEEEEEHHHH
Confidence            34589999999999999999999999999998  6799999999 999999998  666777889999999999999999


Q ss_pred             HHhhccCCCCcccCCcceEEEE--cCCceEEEEEEEeecccCCCCCCCCCCCcCCCCceeEEEEEEecC
Q 022104          229 RATTSNLPGCVIKHNRGSKLII--GRGGMLKVQHLVSVARTSNQHPHTDSAGYQQPSQIAYIEFFVKPE  295 (302)
Q Consensus       229 ~~~~KAl~lS~~~~~~~~~V~i--~~~g~L~~q~~i~~~~~~~~~~~~~~~~~~~~~~~~~v~f~~aP~  295 (302)
                      ..++|+.++|       +.|.|  +++.||+++|.+..                    .|+|+||||||
T Consensus        80 ~~~~K~~~ls-------~~V~i~~~~~~Pl~l~y~~~~--------------------~g~i~f~LAPr  121 (121)
T d1iz5a2          80 SDMVKGLGKA-------DEVTIKFGNEMPMQMEYYIRD--------------------EGRLTFLLAPR  121 (121)
T ss_dssp             HHHHTTSCTT-------CEEEEEECTTCCEEEEEEETT--------------------TEEEEEEECCC
T ss_pred             HHHhhhccCC-------CEEEEEEcCCCCEEEEEEeCC--------------------CcEEEEEEccC
Confidence            9999999988       66766  99999999999953                    38999999997

PyMOL of d1iz5a2

>d1plqa2 d.131.1.2 (A:127-258) Proliferating cell nuclear antigen (PCNA) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1ud9a2 d.131.1.2 (A:127-245) Proliferating cell nuclear antigen (PCNA) {Archaeon Sulfolobus tokodaii [TaxId: 111955]}	Back information, alignment and structure

>d1rwza2 d.131.1.2 (A:123-244) Proliferating cell nuclear antigen (PCNA) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1u7ba1 d.131.1.2 (A:1-126) Proliferating cell nuclear antigen (PCNA) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1plqa1 d.131.1.2 (A:1-126) Proliferating cell nuclear antigen (PCNA) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1u7ba2 d.131.1.2 (A:127-255) Proliferating cell nuclear antigen (PCNA) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1iz5a1 d.131.1.2 (A:2-120) Proliferating cell nuclear antigen (PCNA) {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1rwza1 d.131.1.2 (A:1-122) Proliferating cell nuclear antigen (PCNA) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1ud9a1 d.131.1.2 (A:1-119) Proliferating cell nuclear antigen (PCNA) {Archaeon Sulfolobus tokodaii [TaxId: 111955]}	Back information, alignment and structure

>d1rwza1 d.131.1.2 (A:1-122) Proliferating cell nuclear antigen (PCNA) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1u7ba1 d.131.1.2 (A:1-126) Proliferating cell nuclear antigen (PCNA) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1iz5a1 d.131.1.2 (A:2-120) Proliferating cell nuclear antigen (PCNA) {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1iz5a2 d.131.1.2 (A:126-246) Proliferating cell nuclear antigen (PCNA) {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1plqa1 d.131.1.2 (A:1-126) Proliferating cell nuclear antigen (PCNA) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1ud9a2 d.131.1.2 (A:127-245) Proliferating cell nuclear antigen (PCNA) {Archaeon Sulfolobus tokodaii [TaxId: 111955]}	Back information, alignment and structure

>d1ud9a1 d.131.1.2 (A:1-119) Proliferating cell nuclear antigen (PCNA) {Archaeon Sulfolobus tokodaii [TaxId: 111955]}	Back information, alignment and structure

>d1vpka3 d.131.1.1 (A:244-366) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1rwza2 d.131.1.2 (A:123-244) Proliferating cell nuclear antigen (PCNA) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1u7ba2 d.131.1.2 (A:127-255) Proliferating cell nuclear antigen (PCNA) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1vpka3 d.131.1.1 (A:244-366) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1plqa2 d.131.1.2 (A:127-258) Proliferating cell nuclear antigen (PCNA) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure