Citrus Sinensis ID: 038865

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-----
MEFAVSGNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDVYTVSGAQVQCSVLLKAVCAVLRTPTASIDNLTVQLPNSDAPKVQWTLKCYNGMKKAYWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIATEPTSLPSDAASEIGGKAVELRSYIDPTKDNDSTLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKELKAFLSFCEGCEVDIHLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATMLVSQLQLANSSEHQQAAASIPGQNGNRTESQAQKERRRMNVSEHPSDHTRVWSELSGSYTTVF
cEEEEccccHHHHHHHHHHHHHcccEEEEEEccccEEEEEEcccccEEEEEEEccccccEEEEcccEEEEEEEcHHHHHHHccccccEEEEEEEEccccccEEEEEEEEcccEEEEEEEEEccccccccccccccccccEEEEccHHHHHHHHHHcccccEEEEEEcccccccccccccccccEEEEccccccccccccccEEEEEEcccHHHHHccccccccEEEEEcHHHHHHHHHHHccccEEEEEEccccccEEEccccccccccccEEEEEEEEEEcccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccc
ccEEEcHHHHHHHHHHHHHHHHccccEEEEcccccEEEEEEcccccEEEEEEEcHHHHHHccccccccEEEEEHHHHHHHHHcHHHHccEEEEEEccccccEEEEEEEEcccEEEEEEEEEccccccEEEEEcccccccEEEEcHHHHHHHHHHccccccEEEEEEccccEEEEEccccccccEEEEEEcccccccccccEEEEEEEcccHHHHHEEEccccEEEEEEHHHHHHHHHHHHHccccEEEEEccccccEEEEEEccccccccccEEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
MEFAVSGNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDVYTVSGAQVQCSVLLKAVCAVLrtptasidnltvqlpnsdapkvqWTLKCYNGMKKAYWITcnvepdiqhlsldrrrfpsnfvvrprdLNRLLSNFQSSLQEITViateptslpsdaaseiggkAVELRsyidptkdndstlhtqlwidpteefvqythsgdpvdvtFGVKELKAFLSFCEGCEVDIHLffdkagepilmapkfglddgsgsnfDATLVLATMLVSQLQLANSSEHQQaaasipgqngnrtesQAQKERRrmnvsehpsdhtrvwselsgsyttvf
mefavsgnALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDVYTVSGAQVQCSVLLKAVCAVLRTPtasidnltvqlpnsdapkvQWTLKCYNGMKKAYWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIateptslpsdaaSEIGGKAVELRSYIDPTKDNDSTLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKELKAFLSFCEGCEVDIHLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATMLVSQLQLANSSEHQQaaasipgqngnrTESQAQKERRrmnvsehpsdhtrvwselsgsyttvf
MEFAVSGNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDVYTVSGAQVQCSVLLKAVCAVLRTPTASIDNLTVQLPNSDAPKVQWTLKCYNGMKKAYWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIATEPTSLPSDAASEIGGKAVELRSYIDPTKDNDSTLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKELKAFLSFCEGCEVDIHLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATMLVSQLQLANSSEHQQAAASIPGQNGNRTESQAQKERRRMNVSEHPSDHTRVWSELSGSYTTVF
******GNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDVYTVSGAQVQCSVLLKAVCAVLRTPTASIDNLTVQLPNSDAPKVQWTLKCYNGMKKAYWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIA********************LRSYI*******STLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKELKAFLSFCEGCEVDIHLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATMLVSQL**********************************************************
MEFA**GNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDVYTVSGAQVQCSVLLKAVCAVLRTPTASIDNLTVQLPNSDAPKVQWTLKCYNGMKKAYWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIATEPTSLPSDAASEIGGKAVELRSYI***********TQLWIDPTEEFVQYTHSGDPVDVTFGVKELKAFLSFCEGCEVDIHLFFDKAGEPILMAPKFGLDDGSGSNFDATLVL******************************************************************
MEFAVSGNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDVYTVSGAQVQCSVLLKAVCAVLRTPTASIDNLTVQLPNSDAPKVQWTLKCYNGMKKAYWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIATEPTSLPSDAASEIGGKAVELRSYIDPTKDNDSTLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKELKAFLSFCEGCEVDIHLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATMLVSQLQL*****************************************TRVWSEL********
MEFAVSGNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDVYTVSGAQVQCSVLLKAVCAVLRTPTASIDNLTVQLPNSDAPKVQWTLKCYNGMKKAYWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIATEPTSLPSDAASEIGGKAVELRSYIDPTKDNDSTLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKELKAFLSFCEGCEVDIHLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATML**************************************************************
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MEFAVSGNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDVYTVSGAQVQCSVLLKAVCAVLRTPTASIDNLTVQLPNSDAPKVQWTLKCYNGMKKAYWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIATEPTSLPSDAASEIGGKAVELRSYIDPTKDNDSTLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKELKAFLSFCEGCEVDIHLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATMLVSQLQLANSSEHQQAAASIPGQNGNRTESQAQKERRRMNVSEHPSDHTRVWSELSGSYTTVF
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 ?
Query345 2.2.26 [Sep-21-2011]
Q9Z0F6389 Cell cycle checkpoint con yes no 0.747 0.663 0.295 4e-20
Q99638391 Cell cycle checkpoint con yes no 0.744 0.657 0.275 2e-18
Q6WBX8426 Cell cycle checkpoint con no no 0.834 0.676 0.250 1e-16
Q5E9X8442 Cell cycle checkpoint con yes no 0.8 0.624 0.253 1e-16
Q4R5X9379 Cell cycle checkpoint con N/A no 0.710 0.646 0.273 4e-16
Q499V3398 Cell cycle checkpoint con no no 0.849 0.736 0.246 2e-12
P48013432 DNA repair protein rad9 O N/A no 0.771 0.615 0.226 2e-12
P26306426 DNA repair protein rad9 O yes no 0.823 0.666 0.230 1e-11
Q6WBX7403 Cell cycle checkpoint con no no 0.742 0.635 0.234 4e-11
>sp|Q9Z0F6|RAD9A_MOUSE Cell cycle checkpoint control protein RAD9A OS=Mus musculus GN=Rad9a PE=1 SV=1 Back     alignment and function desciption
 Score = 99.4 bits (246), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 86/291 (29%), Positives = 138/291 (47%), Gaps = 33/291 (11%)

Query: 1   MEFAVSGNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDV 60
           M+  ++G  +K   + +  LSRIG+EL ++     L+  T+NSSRSAY    F P FF  
Sbjct: 1   MKCLITGGNVKVLGKAVHSLSRIGDELYLEPLKDGLSLRTVNSSRSAYACFLFAPLFFQQ 60

Query: 61  YTVSGAQ---VQCSVLLKAVCAVLRTPT---ASIDNLTVQLPNSDAPKVQWTLKCYNGMK 114
           Y  +      ++C +L+KA  +V R+      S++   + L  S +  V   L C  G+K
Sbjct: 61  YQAASPGQDLLRCKILMKAFLSVFRSLAIVEKSVEKCCISLSGSHSHLV-VQLHCKYGVK 119

Query: 115 KAYWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIATEPTSLPS 174
           K + ++      +Q +  D    P       R L   + +F  +L E+T+          
Sbjct: 120 KTHNLSFQDCESLQAV-FDPASCPHLLRTPARVLAEAVLSFPLALTEVTL---------- 168

Query: 175 DAASEIG-GKAVELRSYIDPTKDNDS-TLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKEL 232
                IG G+ V LRSY +   D+ S  + T+  I   +E  Q  H+ + + VTF +KE 
Sbjct: 169 ----GIGRGRRVILRSYQEEEADSTSKAMVTETSIG--DEDFQQLHAPEGIAVTFCLKEF 222

Query: 233 KAFLSFCEGCEVDIHLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATML 283
           +  LSF E   + + + FD  G P++    F ++D   S  DA  VLAT+L
Sbjct: 223 RGLLSFAESANLPLTIHFDVPGRPVI----FTIED---SLLDAHFVLATLL 266
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. RAD9A possesses 3'->5' double stranded DNA exonuclease activity.
Mus musculus (taxid: 10090)
EC: 3EC: .EC: 1EC: .EC: 1EC: 1EC: .EC: 2
>sp|Q99638|RAD9A_HUMAN Cell cycle checkpoint control protein RAD9A OS=Homo sapiens GN=RAD9A PE=1 SV=1 Back     alignment and function description
>sp|Q6WBX8|RAD9B_HUMAN Cell cycle checkpoint control protein RAD9B OS=Homo sapiens GN=RAD9B PE=1 SV=2 Back     alignment and function description
>sp|Q5E9X8|RAD9B_BOVIN Cell cycle checkpoint control protein RAD9B OS=Bos taurus GN=RAD9B PE=2 SV=1 Back     alignment and function description
>sp|Q4R5X9|RAD9A_MACFA Cell cycle checkpoint control protein RAD9A OS=Macaca fascicularis GN=RAD9A PE=2 SV=1 Back     alignment and function description
>sp|Q499V3|RAD9B_RAT Cell cycle checkpoint control protein RAD9B OS=Rattus norvegicus GN=Rad9b PE=2 SV=1 Back     alignment and function description
>sp|P48013|RAD9_SCHOT DNA repair protein rad9 OS=Schizosaccharomyces octosporus GN=rad9 PE=2 SV=1 Back     alignment and function description
>sp|P26306|RAD9_SCHPO DNA repair protein rad9 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rad9 PE=1 SV=1 Back     alignment and function description
>sp|Q6WBX7|RAD9B_MOUSE Cell cycle checkpoint control protein RAD9B OS=Mus musculus GN=Rad9b PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query345
255542724 481 DNA repair protein rad9, putative [Ricin 0.982 0.704 0.805 1e-161
225450767 447 PREDICTED: cell cycle checkpoint control 0.985 0.760 0.805 1e-161
449454079 453 PREDICTED: cell cycle checkpoint control 0.985 0.750 0.779 1e-154
449490884 453 PREDICTED: LOW QUALITY PROTEIN: cell cyc 0.985 0.750 0.776 1e-154
224125190437 predicted protein [Populus trichocarpa] 0.979 0.773 0.764 1e-154
297829070438 cell cycle checkpoint control protein fa 0.988 0.778 0.736 1e-149
20152532439 putative auxin response factor 75 [Arabi 0.988 0.776 0.736 1e-148
30679518439 cell cycle checkpoint control-like prote 0.988 0.776 0.736 1e-148
124360013 476 Rad9 [Medicago truncatula] 0.985 0.714 0.699 1e-147
356572988 449 PREDICTED: cell cycle checkpoint control 0.985 0.757 0.733 1e-146
>gi|255542724|ref|XP_002512425.1| DNA repair protein rad9, putative [Ricinus communis] gi|223548386|gb|EEF49877.1| DNA repair protein rad9, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  573 bits (1478), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 274/340 (80%), Positives = 299/340 (87%), Gaps = 1/340 (0%)

Query: 1   MEFAVSGNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDV 60
           MEF++SGNALKTF+R + CL+R+GNEL IQAS  QL FHTLNSSRSAYQSIT    FFDV
Sbjct: 1   MEFSLSGNALKTFSRSITCLARVGNELAIQASPSQLVFHTLNSSRSAYQSITLKSGFFDV 60

Query: 61  YTVSGAQVQCSVLLKAVCAVLRTPTASIDNLTVQLPNSDAPKVQWTLKCYNGMKKAYWIT 120
           YTVSG QVQCSVLLKA+C+VLRTP  SIDNLTV+LP+ DA KVQWTL+CY+GM+KAYWI 
Sbjct: 61  YTVSGTQVQCSVLLKAICSVLRTPIPSIDNLTVRLPDPDASKVQWTLECYSGMRKAYWIN 120

Query: 121 CNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIATEPTSLPSDAASEI 180
           CNVEP+IQ+LSLDRRRFPS+ VVRPRDLNRLL+NFQSSLQEITVIATEP SLPSD ASEI
Sbjct: 121 CNVEPEIQNLSLDRRRFPSSLVVRPRDLNRLLANFQSSLQEITVIATEPASLPSDGASEI 180

Query: 181 GGKAVELRSYIDPTKDNDSTLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKELKAFLSFCE 240
           GGKAVELRSYIDPTKDNDS+LHTQLWIDP EEFVQYTH+GDPVDVTFGVKELKAFL+FCE
Sbjct: 181 GGKAVELRSYIDPTKDNDSSLHTQLWIDPAEEFVQYTHTGDPVDVTFGVKELKAFLAFCE 240

Query: 241 GCEVDIHLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATMLVSQLQLANSSEHQQAAA 300
           GCEVDIHL+FDK GEPILMAPKFGLDDGS SNFDATLVLATML+SQL   N +E  Q A 
Sbjct: 241 GCEVDIHLYFDKTGEPILMAPKFGLDDGSSSNFDATLVLATMLISQLHEGNPTEPPQVAT 300

Query: 301 SIPGQNGNRTESQAQKERRRMNVSEHPSDHTRVWSELSGS 340
           +I GQ    T SQ Q  R R NVSEHPSDHTR+WSELSGS
Sbjct: 301 AIHGQPVPVTGSQPQC-RSRANVSEHPSDHTRIWSELSGS 339

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225450767|ref|XP_002279397.1| PREDICTED: cell cycle checkpoint control protein RAD9A [Vitis vinifera] gi|296089705|emb|CBI39524.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|449454079|ref|XP_004144783.1| PREDICTED: cell cycle checkpoint control protein RAD9A-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449490884|ref|XP_004158738.1| PREDICTED: LOW QUALITY PROTEIN: cell cycle checkpoint control protein RAD9A-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|224125190|ref|XP_002319522.1| predicted protein [Populus trichocarpa] gi|222857898|gb|EEE95445.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|297829070|ref|XP_002882417.1| cell cycle checkpoint control protein family [Arabidopsis lyrata subsp. lyrata] gi|297328257|gb|EFH58676.1| cell cycle checkpoint control protein family [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|20152532|emb|CAD29645.1| putative auxin response factor 75 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|30679518|ref|NP_187199.2| cell cycle checkpoint control-like protein [Arabidopsis thaliana] gi|115646872|gb|ABJ17148.1| At3g05480 [Arabidopsis thaliana] gi|332640724|gb|AEE74245.1| cell cycle checkpoint control-like protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|124360013|gb|ABN08029.1| Rad9 [Medicago truncatula] Back     alignment and taxonomy information
>gi|356572988|ref|XP_003554647.1| PREDICTED: cell cycle checkpoint control protein RAD9A-like [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 ?
Query345
ZFIN|ZDB-GENE-040426-935381 rad9a "RAD9 homolog A" [Danio 0.698 0.632 0.281 7.4e-22
UNIPROTKB|I3LL42272 RAD9B "Uncharacterized protein 0.701 0.889 0.265 2.1e-20
UNIPROTKB|E2R6J4390 RAD9A "Uncharacterized protein 0.724 0.641 0.297 8.2e-20
DICTYBASE|DDB_G0274525 480 rad9 "component of 9-1-1 compl 0.460 0.331 0.284 9.4e-20
UNIPROTKB|F6XPS6414 RAD9A "Uncharacterized protein 0.724 0.603 0.297 1.2e-19
MGI|MGI:1328356389 Rad9a "RAD9 homolog A" [Mus mu 0.721 0.640 0.294 2.6e-19
UNIPROTKB|F1RNM9386 RAD9B "Uncharacterized protein 0.744 0.665 0.261 9.2e-18
RGD|2319938392 Rad9a "RAD9 homolog A (S. pomb 0.814 0.716 0.282 9.9e-18
UNIPROTKB|J9NRI3376 RAD9B "Uncharacterized protein 0.733 0.672 0.267 1.1e-17
UNIPROTKB|I3L841427 RAD9B "Uncharacterized protein 0.744 0.601 0.261 1.5e-17
ZFIN|ZDB-GENE-040426-935 rad9a "RAD9 homolog A" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
 Score = 255 (94.8 bits), Expect = 7.4e-22, P = 7.4e-22
 Identities = 74/263 (28%), Positives = 135/263 (51%)

Query:     1 MEFAVSGNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDV 60
             M+   +G  +K  A+ +  LSRIG EL ++     LA  ++NSSRSA+ S    P FF  
Sbjct:     1 MDCVATGANVKVLAKAIHSLSRIGEELYLEPVDDGLALRSVNSSRSAFASFQLSPLFFQR 60

Query:    61 YTVSGAQ-VQCSVLLKAVCAVLRTPTA---SIDNLTVQLPNSDAPKVQWTLKCYNGMKKA 116
             Y     Q  +C + +K+V AV ++ ++   S++   +QL NS+  ++  TL C +G+ K 
Sbjct:    61 YQAPTDQSFRCKMPIKSVQAVFKSLSSLERSVEKCRIQL-NSEKSRLTITLHCKHGLLKT 119

Query:   117 YWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIATEPTSLPSDA 176
             + ++      +Q +  D+    +    +PR +   + +F  SL+E+ +      S+ SD 
Sbjct:   120 HNLSFQDCESLQAV-FDKESCTNVLQAQPRLMVDTVLHFPPSLEEVNL------SVSSDR 172

Query:   177 ASEIGGKAVELRSYIDPTKDNDSTLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKELKAFL 236
                     V LR++++   D+   + T+L +  +EEF  +  S     +TF +KEL+  L
Sbjct:   173 --------VWLRNHVEDDADSSRAMMTELCLS-SEEFDHFAISSQ-TSITFCLKELRGLL 222

Query:   237 SFCEGCEVDIHLFFDKAGEPILM 259
              F E   + I ++FD+ G P+++
Sbjct:   223 GFAESSCLPISMYFDEPGSPVIL 245
GO:0030896 "checkpoint clamp complex" evidence=IEA
GO:0000075 "cell cycle checkpoint" evidence=IEA
GO:0000077 "DNA damage checkpoint" evidence=IEA
GO:0006281 "DNA repair" evidence=IEA
UNIPROTKB|I3LL42 RAD9B "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|E2R6J4 RAD9A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0274525 rad9 "component of 9-1-1 complex" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
UNIPROTKB|F6XPS6 RAD9A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:1328356 Rad9a "RAD9 homolog A" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|F1RNM9 RAD9B "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
RGD|2319938 Rad9a "RAD9 homolog A (S. pombe)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|J9NRI3 RAD9B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|I3L841 RAD9B "Uncharacterized protein" [Sus scrofa (taxid:9823)] 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

Fail to connect to STRING server

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 ?
Query345
pfam04139252 pfam04139, Rad9, Rad9 1e-76
cd00577248 cd00577, PCNA, Proliferating Cell Nuclear Antigen 3e-16
>gnl|CDD|217922 pfam04139, Rad9, Rad9 Back     alignment and domain information 
 Score =  235 bits (602), Expect = 1e-76
 Identities = 96/276 (34%), Positives = 145/276 (52%), Gaps = 30/276 (10%)

Query: 13  FARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDVY---TVSGAQVQ 69
             R + CLSRIG+EL ++ S   LA  T+NSSRSAY    F P FF  Y   T    Q++
Sbjct: 1   LGRAVQCLSRIGDELYLEPSEDGLALRTVNSSRSAYACFLFSPLFFQSYQGTTDGSPQIR 60

Query: 70  CSVLLKAVCAVLR---TPTASIDNLTVQLPNSDAPKVQWTLKCYNGMKKAYWITCNVEPD 126
           C +L+K+V +V R   T   S++   + L +    ++ + L C +G+ K + I+      
Sbjct: 61  CKILMKSVLSVFRSLSTLEKSVEKCQISL-DDLKSRLIFQLLCKHGVTKTHNISYEDSEP 119

Query: 127 IQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIATEPTSLPSDAASEIGGKAVE 186
           +     D+   P+   + PR L+ LL +F SSL+EIT+ A+                 V 
Sbjct: 120 L-QAVFDKNTCPNILRIPPRLLSDLLVHFPSSLEEITINASP--------------GRVL 164

Query: 187 LRSYIDPTKDNDSTLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKELKAFLSFCEGCEVDI 246
           L+SY +   DN   LHT+L IDP EEF QY    D VD+TF +KE +A L+F E   + +
Sbjct: 165 LKSYTEEGVDNKKPLHTELSIDP-EEFDQYQLGED-VDITFCLKEFRAILAFAESLSLPL 222

Query: 247 HLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATM 282
            ++F + G+P L++    L D S    +A  +LAT+
Sbjct: 223 AIYFSEPGKPALLS----LSDSSL--IEANFILATL 252

Rad9 is required for transient cell-cycle arrests and transcriptional induction of DNA repair in response to DNA damage. It contains a Bcl-2 homology domain 3 (BH3). Length = 252
>gnl|CDD|238322 cd00577, PCNA, Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 345
PF04139252 Rad9: Rad9; InterPro: IPR007268 Rad9 is required f 100.0
KOG2810394 consensus Checkpoint 9-1-1 complex, RAD9 component 100.0
KOG1636260 consensus DNA polymerase delta processivity factor 100.0
PTZ00113275 proliferating cell nuclear antigen; Provisional 100.0
PHA03383262 PCNA-like protein; Provisional 100.0
TIGR00590259 pcna proliferating cell nuclear antigen (pcna). Al 100.0
PLN00057263 proliferating cell nuclear antigen; Provisional 100.0
PTZ00483264 proliferating cell nuclear antigen; Provisional 100.0
cd00577248 PCNA Proliferating Cell Nuclear Antigen (PCNA) dom 99.95
PRK01115247 DNA polymerase sliding clamp; Validated 99.91
PF00705127 PCNA_N: Proliferating cell nuclear antigen, N-term 99.77
PF02144275 Rad1: Repair protein Rad1/Rec1/Rad17; InterPro: IP 99.4
PF02747128 PCNA_C: Proliferating cell nuclear antigen, C-term 99.28
COG0592364 DnaN DNA polymerase sliding clamp subunit (PCNA ho 99.12
PF04005292 Hus1: Hus1-like protein; InterPro: IPR007150 Hus1, 99.1
cd00140365 beta_clamp Beta clamp domain. The beta subunit (pr 98.92
PRK05643367 DNA polymerase III subunit beta; Validated 98.5
KOG3999284 consensus Checkpoint 9-1-1 complex, HUS1 component 98.45
KOG2810 394 consensus Checkpoint 9-1-1 complex, RAD9 component 98.37
smart00480345 POL3Bc DNA polymerase III beta subunit. 98.28
PRK14945362 DNA polymerase III subunit beta; Provisional 98.2
PRK14941374 DNA polymerase III subunit beta; Provisional 97.98
PRK14940367 DNA polymerase III subunit beta; Provisional 97.93
PRK14944375 DNA polymerase III subunit beta; Provisional 97.91
PRK14943374 DNA polymerase III subunit beta; Provisional 97.91
PRK07761376 DNA polymerase III subunit beta; Validated 97.83
PRK06673376 DNA polymerase III subunit beta; Validated 97.82
TIGR00663367 dnan DNA polymerase III, beta subunit. University) 97.78
PRK14942373 DNA polymerase III subunit beta; Provisional 97.7
cd00140365 beta_clamp Beta clamp domain. The beta subunit (pr 97.58
PRK14947384 DNA polymerase III subunit beta; Provisional 97.48
PRK14946366 DNA polymerase III subunit beta; Provisional 97.38
PF02768121 DNA_pol3_beta_3: DNA polymerase III beta subunit, 96.98
PRK01115247 DNA polymerase sliding clamp; Validated 96.95
KOG3194279 consensus Checkpoint 9-1-1 complex, RAD1 component 96.88
PF02747128 PCNA_C: Proliferating cell nuclear antigen, C-term 96.81
PLN00057263 proliferating cell nuclear antigen; Provisional 96.7
TIGR00590259 pcna proliferating cell nuclear antigen (pcna). Al 96.66
PF00705127 PCNA_N: Proliferating cell nuclear antigen, N-term 96.29
PRK14943374 DNA polymerase III subunit beta; Provisional 95.69
PRK05643367 DNA polymerase III subunit beta; Validated 95.32
PHA03383262 PCNA-like protein; Provisional 95.11
PRK14945362 DNA polymerase III subunit beta; Provisional 95.03
cd00577248 PCNA Proliferating Cell Nuclear Antigen (PCNA) dom 95.01
TIGR00663367 dnan DNA polymerase III, beta subunit. University) 94.76
PRK14941374 DNA polymerase III subunit beta; Provisional 94.53
smart00480345 POL3Bc DNA polymerase III beta subunit. 94.37
PRK14940367 DNA polymerase III subunit beta; Provisional 94.27
PTZ00113275 proliferating cell nuclear antigen; Provisional 93.63
PTZ00483264 proliferating cell nuclear antigen; Provisional 93.51
PF00712120 DNA_pol3_beta: DNA polymerase III beta subunit, N- 93.23
PRK14947384 DNA polymerase III subunit beta; Provisional 93.15
PRK06673376 DNA polymerase III subunit beta; Validated 92.1
PRK14946366 DNA polymerase III subunit beta; Provisional 91.83
PRK07761376 DNA polymerase III subunit beta; Validated 91.32
PF02144275 Rad1: Repair protein Rad1/Rec1/Rad17; InterPro: IP 89.96
PRK14942373 DNA polymerase III subunit beta; Provisional 89.91
PF04139252 Rad9: Rad9; InterPro: IPR007268 Rad9 is required f 87.67
PRK14944375 DNA polymerase III subunit beta; Provisional 84.36
PF02767116 DNA_pol3_beta_2: DNA polymerase III beta subunit, 83.14
>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 
Probab=100.00  E-value=8.4e-60  Score=441.36  Aligned_cols=246  Identities=35%  Similarity=0.642  Sum_probs=196.4

Q ss_pred             HHHHHHHHhhcCceEEEEEcCCeEEEEEEcCCccEEEEEEeCccCCceeee---cCCEEEEEEEchhhHHHhcCC---CC
Q 038865           13 FARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDVYTV---SGAQVQCSVLLKAVCAVLRTP---TA   86 (345)
Q Consensus        13 f~rai~~Lskigdel~ie~~~~gL~L~avNsSrSA~~~~~f~~~FF~~Y~~---~~~~~~~~i~~Ksll~vfk~~---~~   86 (345)
                      |+|+|+||+||||||+|+++++||.|+|||+|||||++|.|+++||++|..   +.+.+.|+|++|++++|||+.   .+
T Consensus         1 f~ral~~Lskigeel~ie~~~~~L~l~avNss~Sa~~~~~F~~~FF~~y~~~~~~~~~~~~~i~~K~~l~vfr~~~~~~~   80 (252)
T PF04139_consen    1 FARALQCLSKIGEELYIEITEDGLSLRAVNSSRSAYAQFRFSKSFFDKYQADSDSQDSFSCKISMKSLLSVFRSLSTLEK   80 (252)
T ss_dssp             HHHHHHHHHTT-SEEEEEEETTEEEEEEE-TTSSEEEEEEETGGGSSEEE--SSSS----EEEEHHHHHHHHSSCTCCHH
T ss_pred             CHHHHHHHHhhCCeEEEEEcCCeEEEEEECccccEEEEEEEChHHhhhhcccCCCCCcEEEEEEchhhhhhhcccccccc
Confidence            799999999999999999999999999999999999999999999999922   235689999999999999963   36


Q ss_pred             ccceEEEEecCCCCCeEEEEEEeCCCeEEEEEeeecccCcccccccCCCCCceEEEEcchhHHHHHhhhcCCcceEEEEE
Q 038865           87 SIDNLTVQLPNSDAPKVQWTLKCYNGMKKAYWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIA  166 (345)
Q Consensus        87 ~vd~~~i~l~d~d~~~L~~~l~c~~gI~Kt~~L~~~~~~~~~~~~~~~~~~~~~l~i~~~~L~~~l~~F~~~~eeItl~~  166 (345)
                      +||+|.|++ +.++++|+|+|+|++||+|||+|+|+++ +..++.+|++.++|+|+++|++|+++++||+++.|||||.+
T Consensus        81 ~Ve~c~i~i-~~~~~~L~~~l~c~~gI~Kt~~l~~~~~-~~~~a~~d~~~~~n~l~~~~~~l~~~l~~f~~~~eeitl~~  158 (252)
T PF04139_consen   81 NVESCEISI-DNDESRLIFQLFCKNGIIKTYNLPYEEC-ESLQAVFDKESCPNYLVISPRLLKDLLDHFPSSTEEITLEV  158 (252)
T ss_dssp             CEEEEEEEE--TTSSEEEEEEEEGGGEEEEEEEE-CE----------GGGSSEEEEEEHHHHHHHHTTS-TT--EEEEEE
T ss_pred             ceeEEEEEE-cCCCcEEEEEEEeccceEEEEEEEEEec-cccccccchhcCCceEEEChHHHHHHHhhcCCChhhEEEEe
Confidence            899999999 6789999999999999999999999874 66789999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCcccccCCeEEEEEeccCCCCCCCCceeEEEEecCCccceeecccCCceEEEEEhHHHHHHHhhhccCCCeE
Q 038865          167 TEPTSLPSDAASEIGGKAVELRSYIDPTKDNDSTLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKELKAFLSFCEGCEVDI  246 (345)
Q Consensus       167 t~~~~~~s~~~~~~g~~~v~lks~~e~~~~~~~~l~Tev~I~~~eEF~~y~~~~~~~~itF~LKefkail~fae~~~~~i  246 (345)
                      ++              ++|.+++|+++..+.+++|+|+|+|+++ ||++|. +.++++|||+||||||+++|||+++++|
T Consensus       159 ~~--------------~~v~~~s~~~~~~~~~~~l~t~v~i~~~-ef~~~~-~~~~~~itF~lKefka~l~~ae~~~~~i  222 (252)
T PF04139_consen  159 TD--------------DKVSFKSYTEEIQDSKQPLSTEVTISTE-EFDEYN-VQEDTDITFSLKEFKAILSFAESLSLPI  222 (252)
T ss_dssp             EC--------------TCEEEEEE-----SSS---EEEEEE-GG-GSSEEE---TT-EEEEEHHHHHHHHHHHHHTTEEE
T ss_pred             cC--------------CEEEEEeecccccccccceEEEEEEehH-hcceEE-cCCCCEEEEEeHHHHHHHHHHHhcCCcE
Confidence            86              3799999999998888999999999997 999998 6777999999999999999999999999


Q ss_pred             EEEeeCCCCcEEEeeeccCCCCCCCceEEEEEEEec
Q 038865          247 HLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATM  282 (345)
Q Consensus       247 ~i~f~~~G~Pl~~~~~f~l~d~~~~~~~a~fvLAT~  282 (345)
                      ++||+.||+||+|+.+    +  +++|+++|||||+
T Consensus       223 ~~~f~~pG~Pi~~~~~----~--~~~~~~~~vlaTl  252 (252)
T PF04139_consen  223 SIYFDNPGRPILFELE----Q--NDHFEAEFVLATL  252 (252)
T ss_dssp             EEEESSTTS-EEEEEE--------SSEEEEEEE--B
T ss_pred             EEEECCCCCcEEEEEC----C--CCcEEEEEEEEcC
Confidence            9999999999999843    2  2589999999997

; GO: 0006281 DNA repair; PDB: 3GGR_A 3G65_A 3A1J_A.
>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
>KOG1636 consensus DNA polymerase delta processivity factor (proliferating cell nuclear antigen) [Replication, recombination and repair] 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
>TIGR00590 pcna proliferating cell nuclear antigen (pcna) Back     alignment and domain information
>PLN00057 proliferating cell nuclear antigen; Provisional Back     alignment and domain information
>PTZ00483 proliferating cell nuclear antigen; Provisional Back     alignment and domain information
>cd00577 PCNA Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea Back     alignment and domain information
>PRK01115 DNA polymerase sliding clamp; Validated 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
>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
>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
>COG0592 DnaN DNA polymerase sliding clamp subunit (PCNA homolog) [DNA replication, recombination, and repair] 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
>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
>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
>smart00480 POL3Bc DNA polymerase III beta subunit Back     alignment and domain information
>PRK14945 DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>PRK14941 DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>PRK14940 DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>PRK14944 DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>PRK14943 DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>PRK07761 DNA polymerase III subunit beta; Validated Back     alignment and domain information
>PRK06673 DNA polymerase III subunit beta; Validated 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
>cd00140 beta_clamp Beta clamp domain Back     alignment and domain information
>PRK14947 DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>PRK14946 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
>PRK01115 DNA polymerase sliding clamp; Validated 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
>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
>PLN00057 proliferating cell nuclear antigen; Provisional Back     alignment and domain information
>TIGR00590 pcna proliferating cell nuclear antigen (pcna) 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
>PRK14943 DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>PRK05643 DNA polymerase III subunit beta; Validated Back     alignment and domain information
>PHA03383 PCNA-like protein; Provisional Back     alignment and domain information
>PRK14945 DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>cd00577 PCNA Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea Back     alignment and domain information
>TIGR00663 dnan DNA polymerase III, beta subunit Back     alignment and domain information
>PRK14941 DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>smart00480 POL3Bc DNA polymerase III beta subunit Back     alignment and domain information
>PRK14940 DNA polymerase III subunit beta; 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
>PF00712 DNA_pol3_beta: DNA polymerase III beta subunit, N-terminal domain; InterPro: IPR022634 This entry describes the N-terminal domain of the beta chain of DNA polymerase III Back     alignment and domain information
>PRK14947 DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>PRK06673 DNA polymerase III subunit beta; Validated Back     alignment and domain information
>PRK14946 DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>PRK07761 DNA polymerase III subunit beta; Validated Back     alignment and domain information
>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
>PRK14942 DNA polymerase III subunit beta; 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
>PRK14944 DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>PF02767 DNA_pol3_beta_2: DNA polymerase III beta subunit, central domain; InterPro: IPR022637 This entry describes the central domain of the beta chain of DNA polymerase III 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 ?
Query345
3g65_A296 Crystal Structure Of The Human Rad9-Rad1-Hus1 Dna D 3e-19
3ggr_A270 Crystal Structure Of The Human Rad9-Hus1-Rad1 Compl 4e-19
3a1j_A266 Crystal Structure Of The Human Rad9-Hus1-Rad1 Compl 3e-18
>pdb|3G65|A Chain A, Crystal Structure Of The Human Rad9-Rad1-Hus1 Dna Damage Checkpoint Complex Length = 296 Back     alignment and structure 
Iteration: 1

 Score = 92.8 bits (229), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 80/290 (27%), Positives = 134/290 (46%), Gaps = 33/290 (11%)
Query: 1   MEFAVSGNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDV 60
           M+  V+G  +K   + +  LSRIG+EL ++     L+  T+NSSRSAY    F P FF  
Sbjct: 1   MKCLVTGGNVKVLGKAVHSLSRIGDELYLEPLEDGLSLRTVNSSRSAYACFLFAPLFFQQ 60
Query: 61  Y---TVSGAQVQCSVLLKAVCAVLRTPT---ASIDNLTVQLPNSDAPKVQWTLKCYNGMK 114
           Y   T     ++C +L+K+  +V R+      +++   + L N  + ++   L C  G++
Sbjct: 61  YQAATPGQDLLRCKILMKSFLSVFRSLAMLEKTVEKCCISL-NGRSSRLVVQLHCKFGVR 119
Query: 115 KAYWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIATEPTSLPS 174
           K + ++      +Q +  D    P       R L   +  F  +L E+T+          
Sbjct: 120 KTHNLSFQDCESLQAV-FDPASCPHMLRAPARVLGEAVLPFSPALAEVTL---------- 168
Query: 175 DAASEIG-GKAVELRSYIDPTKDNDS-TLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKEL 232
                IG G+ V LRSY +   D+ +  + T++ +   EE  Q   + + V +TF +KE 
Sbjct: 169 ----GIGRGRRVILRSYHEEEADSTAKAMVTEMCLG--EEDFQQLQAQEGVAITFCLKEF 222
Query: 233 KAFLSFCEGCEVDIHLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATM 282
           +  LSF E   +++ + FD  G P +   K  L DG         VLAT+
Sbjct: 223 RGLLSFAESANLNLSIHFDAPGRPAIFTIKDSLLDGH-------FVLATL 265
>pdb|3GGR|A Chain A, Crystal Structure Of The Human Rad9-Hus1-Rad1 Complex Length = 270 Back     alignment and structure
>pdb|3A1J|A Chain A, Crystal Structure Of The Human Rad9-Hus1-Rad1 Complex Length = 266 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 ?
Query345
3a1j_A266 Cell cycle checkpoint control protein RAD9A; DNA d 1e-70
3g65_A296 Cell cycle checkpoint control protein RAD9A; PCNA, 9e-70
3fds_C249 DNA polymerase sliding clamp B; protein-protein co 3e-13
1iz5_A249 Proliferating cell nuclear antigen; DNA, replicati 3e-09
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 7e-05
>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 Length = 266 Back     alignment and structure
 Score =  220 bits (561), Expect = 1e-70
 Identities = 74/289 (25%), Positives = 130/289 (44%), Gaps = 31/289 (10%)

Query: 1   MEFAVSGNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDV 60
           M+  V+G  +K   + +  LSRIG+EL ++     L+  T+NSSRSAY    F P FF  
Sbjct: 1   MKCLVTGGNVKVLGKAVHSLSRIGDELYLEPLEDGLSLRTVNSSRSAYACFLFAPLFFQQ 60

Query: 61  YTVSGAQ---VQCSVLLKAVCAVLRTPTA---SIDNLTVQLPNSDAPKVQWTLKCYNGMK 114
           Y  +      ++C +L+K+  +V R+      +++   +   N  + ++   L C  G++
Sbjct: 61  YQAATPGQDLLRCKILMKSFLSVFRSLAMLEKTVEKCCIS-LNGRSSRLVVQLHCKFGVR 119

Query: 115 KAYWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSNFQSSLQEITVIATEPTSLPS 174
           K + ++   + +      D    P       R L   +  F  +L E+T+          
Sbjct: 120 KTHNLSFQ-DCESLQAVFDPASCPHMLRAPARVLGEAVLPFSPALAEVTLGIGR------ 172

Query: 175 DAASEIGGKAVELRSYIDPTKDNDS-TLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKELK 233
                  G+ V LRSY +   D+ +  + T++ +   E+F Q   + + V +TF +KE +
Sbjct: 173 -------GRRVILRSYHEEEADSTAKAMVTEMCLGE-EDFQQL-QAQEGVAITFCLKEFR 223

Query: 234 AFLSFCEGCEVDIHLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATM 282
             LSF E   +++ + FD  G P +   K        S  D   VLAT+
Sbjct: 224 GLLSFAESANLNLSIHFDAPGRPAIFTIK-------DSLLDGHFVLATL 265
>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} Length = 296 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* Length = 249 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* Length = 249 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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query345
3g65_A296 Cell cycle checkpoint control protein RAD9A; PCNA, 100.0
3a1j_A266 Cell cycle checkpoint control protein RAD9A; DNA d 100.0
3fds_C249 DNA polymerase sliding clamp B; protein-protein co 100.0
3lx2_A259 DNA polymerase sliding clamp 2; PCNA, DNA processi 99.97
3p91_A265 Proliferating cell nuclear antigen; DNA binding pr 99.97
3fds_D245 DNA polymerase sliding clamp C; protein-protein co 99.97
1plq_A258 Proliferating cell nuclear antigen (PCNA); DNA-bin 99.96
3a1j_C263 Cell cycle checkpoint protein RAD1; DNA damage, DN 99.96
1u7b_A261 PCNA, cyclin, proliferating cell nuclear antigen; 99.96
3k4x_A 798 PCNA, proliferating cell nuclear antigen; DNA repl 99.96
3ifv_A247 PCNA; processivity factor, sliding clamp, halophil 99.96
2zvv_A276 PCNA 1, proliferating cellular nuclear antigen 1; 99.94
3k4x_A798 PCNA, proliferating cell nuclear antigen; DNA repl 99.94
1iz5_A249 Proliferating cell nuclear antigen; DNA, replicati 99.94
2ijx_A244 DNA polymerase sliding clamp A; PCNA3 subunit, pro 99.94
3aiz_A248 DNA polymerase sliding clamp B; protein-protein co 99.93
1ud9_A245 DNA polymerase sliding clamp A; DNA-binding, DNA r 99.93
3aiz_C246 DNA polymerase sliding clamp C; protein-protein co 99.92
1rwz_A245 DNA polymerase sliding clamp; torus, processivity 99.91
3a1j_B281 HHUS1, checkpoint protein HUS1; DNA damage, DNA re 99.9
1vpk_A378 DNA polymerase III, beta subunit; TM0262, structur 98.83
3d1g_A366 DNA polymerase III subunit beta; chemical probe, D 98.72
2avt_A378 DNA polymerase III beta subunit; beta clamp, slidi 98.65
3pge_A200 SUMO-modified proliferating cell nuclear antigen; 98.43
3t0p_A371 DNA polymerase III, beta subunit; DNA clamp, struc 98.32
3l0w_B169 Monoubiquitinated proliferating cell nuclear antig 98.28
3p16_A408 DNA polymerase III subunit beta; DNA polymerase II 97.88
1vpk_A378 DNA polymerase III, beta subunit; TM0262, structur 97.42
3a1j_C263 Cell cycle checkpoint protein RAD1; DNA damage, DN 96.97
3fds_C249 DNA polymerase sliding clamp B; protein-protein co 96.97
3p91_A265 Proliferating cell nuclear antigen; DNA binding pr 96.86
3p16_A408 DNA polymerase III subunit beta; DNA polymerase II 96.35
3t0p_A371 DNA polymerase III, beta subunit; DNA clamp, struc 96.28
3d1g_A366 DNA polymerase III subunit beta; chemical probe, D 96.16
3lx2_A259 DNA polymerase sliding clamp 2; PCNA, DNA processi 95.79
1u7b_A261 PCNA, cyclin, proliferating cell nuclear antigen; 95.63
2avt_A378 DNA polymerase III beta subunit; beta clamp, slidi 95.54
1plq_A258 Proliferating cell nuclear antigen (PCNA); DNA-bin 95.46
1iz5_A249 Proliferating cell nuclear antigen; DNA, replicati 95.38
3fds_D245 DNA polymerase sliding clamp C; protein-protein co 94.94
2zvv_A276 PCNA 1, proliferating cellular nuclear antigen 1; 94.64
3aiz_A248 DNA polymerase sliding clamp B; protein-protein co 94.43
3a1j_A266 Cell cycle checkpoint control protein RAD9A; DNA d 94.14
3ifv_A247 PCNA; processivity factor, sliding clamp, halophil 93.86
1rwz_A245 DNA polymerase sliding clamp; torus, processivity 93.85
3aiz_C246 DNA polymerase sliding clamp C; protein-protein co 93.59
2ijx_A244 DNA polymerase sliding clamp A; PCNA3 subunit, pro 92.92
1ud9_A245 DNA polymerase sliding clamp A; DNA-binding, DNA r 92.7
3a1j_B281 HHUS1, checkpoint protein HUS1; DNA damage, DNA re 92.58
1dml_A319 DNA polymerase processivity factor; herpes simplex 90.33
3g65_A296 Cell cycle checkpoint control protein RAD9A; PCNA, 90.08
>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
Probab=100.00  E-value=2.9e-66  Score=494.02  Aligned_cols=264  Identities=28%  Similarity=0.491  Sum_probs=235.2

Q ss_pred             CeeEEecccHHHHHHHHHHHhhcCceEEEEEcCCeEEEEEEcCCccEEEEEEeCccCCceeeecC---CEEEEEEEchhh
Q 038865            1 MEFAVSGNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDVYTVSG---AQVQCSVLLKAV   77 (345)
Q Consensus         1 M~~~l~~~~~k~f~rai~~Lskigdel~ie~~~~gL~L~avNsSrSA~~~~~f~~~FF~~Y~~~~---~~~~~~i~~Ksl   77 (345)
                      |+|+|++.++|+|+|+|+||+|||||++|+++++||.|||||+|||||++|.|++.||++|+++.   +.++|+|++|+|
T Consensus         1 M~~~i~g~~~K~f~kai~~LskigdEl~~e~~~dgL~LravNsSrSA~~~~~f~~~FF~~Y~~~~~~~~~~~c~i~~K~l   80 (296)
T 3g65_A            1 MKCLVTGGNVKVLGKAVHSLSRIGDELYLEPLEDGLSLRTVNSSRSAYACFLFAPLFFQQYQAATPGQDLLRCKILMKSF   80 (296)
T ss_dssp             CEEEEETHHHHHHHHHHHHHHTTCSEEEEEEETTEEEEEEECTTSCEEEEEEETTSSCCCCCC-------CCEEEEHHHH
T ss_pred             CEEEEecccHHHHHHHHHHHHhhCceEEEEEcCCeEEEEEECCcceEEEEEEeChHHhhheecCCCCCccEEEEEEhHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999974   468999999999


Q ss_pred             HHHhcCCC---CccceEEEEecCCCCCeEEEEEEeCCCeEEEEEeeecccCcccccccCCCCCceEEEEcchhHHHHHhh
Q 038865           78 CAVLRTPT---ASIDNLTVQLPNSDAPKVQWTLKCYNGMKKAYWITCNVEPDIQHLSLDRRRFPSNFVVRPRDLNRLLSN  154 (345)
Q Consensus        78 l~vfk~~~---~~vd~~~i~l~d~d~~~L~~~l~c~~gI~Kt~~L~~~~~~~~~~~~~~~~~~~~~l~i~~~~L~~~l~~  154 (345)
                      ++|||++.   +++|+|.|++ +.+++||+|+|+|++||+|||+|+|++ .+.+++.+|++.|+|.|+++|++|+++|+|
T Consensus        81 l~vfr~~~~~d~~ve~c~i~l-~~~~~rl~i~l~ck~gi~Kt~~l~~~~-~~~l~a~~~~~~~~n~~~i~~~~l~e~l~~  158 (296)
T 3g65_A           81 LSVFRSLAMLEKTVEKCCISL-NGRSSRLVVQLHCKFGVRKTHNLSFQD-CESLQAVFDPASCPHMLRAPARVLGEAVLP  158 (296)
T ss_dssp             HTTTSSTTC----CCEEEEEE-CCC---EEEEEECGGGCEEEEEECCCC-CCCCCCCCCGGGCSCEEEEEHHHHHHHSTT
T ss_pred             HHHhccccccccceeEEEEEE-eCCCCEEEEEEEeCCCeEEEEEEEeEe-ccccccccCchhCcEEEEEchHHHHHHHHh
Confidence            99999863   6899999999 568999999999999999999999987 577888999999999999999999999999


Q ss_pred             hcCCcceEEEEEcCCCCCCCCcccccCCeEEEEEeccCCCCCCC-CceeEEEEecCCccceeecccCCceEEEEEhHHHH
Q 038865          155 FQSSLQEITVIATEPTSLPSDAASEIGGKAVELRSYIDPTKDND-STLHTQLWIDPTEEFVQYTHSGDPVDVTFGVKELK  233 (345)
Q Consensus       155 F~~~~eeItl~~t~~~~~~s~~~~~~g~~~v~lks~~e~~~~~~-~~l~Tev~I~~~eEF~~y~~~~~~~~itF~LKefk  233 (345)
                      |+++.|||||.++++             +++.+++|+|+..|.. ++|+|+++|+++ ||++|. +++++++||||||||
T Consensus       159 f~~~~eevtl~~~~~-------------~~v~~~s~~e~~~d~~~~~~~Tel~i~~~-ef~~~~-v~~~~~itf~lKefr  223 (296)
T 3g65_A          159 FSPALAEVTLGIGRG-------------RRVILRSYHEEEADSTAKAMVTEMCLGEE-DFQQLQ-AQEGVAITFCLKEFR  223 (296)
T ss_dssp             SCTTCCEEEEEEETT-------------TEEEEEECCC-----CCCCCEEEEEECGG-GCSEEE-CCTTCEEEEEHHHHH
T ss_pred             CcCCcceEEEEECCC-------------CeEEEEEeccccccccCceEEEEEEEChh-HheeEe-cCCCcEEEEEHHHHH
Confidence            999999999999842             4899999999887754 899999999996 999997 799999999999999


Q ss_pred             HHHhhhccCCCeEEEEeeCCCCcEEEeeeccCCCCCCCceEEEEEEEeccccccc
Q 038865          234 AFLSFCEGCEVDIHLFFDKAGEPILMAPKFGLDDGSGSNFDATLVLATMLVSQLQ  288 (345)
Q Consensus       234 ail~fae~~~~~i~i~f~~~G~Pl~~~~~f~l~d~~~~~~~a~fvLAT~~~~~~~  288 (345)
                      +|++|||+++.+|+++|+.||+||+|+  |.  +   .+++++|||||+.+++.+
T Consensus       224 ail~~ae~~~~~i~i~f~~pG~Pl~~~--~~--~---~~~~~~fvLaT~~~~~~~  271 (296)
T 3g65_A          224 GLLSFAESANLNLSIHFDAPGRPAIFT--IK--D---SLLDGHFVLATLSDTDSG  271 (296)
T ss_dssp             HHHHHHHHTTCEEEEECCSTTSCEEEE--EE--C---SSCEEEEEECCCCSSSCS
T ss_pred             HHHHHHHhcCCeEEEEECCCCCcEEEE--Ee--C---CcEEEEEEEEECCCCCCc
Confidence            999999999999999999999999988  43  3   378999999999997544
>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
>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
>3p91_A Proliferating cell nuclear antigen; DNA binding protein, DNA replication, processivity, sliding; 2.40A {Entamoeba histolytica} 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
>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
>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
>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
>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae} Back     alignment and structure
>3ifv_A PCNA; processivity factor, sliding clamp, halophilic, replication; 2.00A {Haloferax volcanii} PDB: 3hi8_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
>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae} 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
>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
>3aiz_A DNA polymerase sliding clamp B; protein-protein complex, replication; HET: DNA; 2.80A {Sulfolobus tokodaii} PDB: 3aix_B* 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_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
>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
>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
>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
>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae} 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
>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
>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
>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
>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_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
>3p91_A Proliferating cell nuclear antigen; DNA binding protein, DNA replication, processivity, sliding; 2.40A {Entamoeba histolytica} 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
>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
>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
>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
>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
>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
>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
>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
>3aiz_A DNA polymerase sliding clamp B; protein-protein complex, replication; HET: DNA; 2.80A {Sulfolobus tokodaii} PDB: 3aix_B* 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
>3ifv_A PCNA; processivity factor, sliding clamp, halophilic, replication; 2.00A {Haloferax volcanii} PDB: 3hi8_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
>3aiz_C DNA polymerase sliding clamp C; protein-protein complex, replication; HET: DNA; 2.80A {Sulfolobus tokodaii} PDB: 3aix_A* 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
>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
>1dml_A DNA polymerase processivity factor; herpes simplex virus, DNA synthesis, sliding clamps, PCNA, processivity, DNA binding protein/transferase complex; HET: DNA; 2.70A {Human herpesvirus 1} SCOP: d.131.1.2 d.131.1.2 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

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query345
d1plqa1126 Proliferating cell nuclear antigen (PCNA) {Baker's 99.75
d1u7ba1126 Proliferating cell nuclear antigen (PCNA) {Human ( 99.74
d1iz5a1119 Proliferating cell nuclear antigen (PCNA) {Archaeo 99.74
d1ud9a1119 Proliferating cell nuclear antigen (PCNA) {Archaeo 99.71
d1rwza1122 Proliferating cell nuclear antigen (PCNA) {Archaeo 99.64
d1plqa2132 Proliferating cell nuclear antigen (PCNA) {Baker's 99.28
d1iz5a2121 Proliferating cell nuclear antigen (PCNA) {Archaeo 99.27
d1rwza2122 Proliferating cell nuclear antigen (PCNA) {Archaeo 99.26
d1ud9a2119 Proliferating cell nuclear antigen (PCNA) {Archaeo 99.19
d1u7ba2129 Proliferating cell nuclear antigen (PCNA) {Human ( 99.18
d1iz5a2121 Proliferating cell nuclear antigen (PCNA) {Archaeo 97.39
d1ok7a3122 DNA polymerase III, beta subunit {Escherichia coli 97.24
d1vpka3123 DNA polymerase III, beta subunit {Thermotoga marit 97.17
d1ud9a2119 Proliferating cell nuclear antigen (PCNA) {Archaeo 96.78
d1rwza1122 Proliferating cell nuclear antigen (PCNA) {Archaeo 96.77
d1u7ba1126 Proliferating cell nuclear antigen (PCNA) {Human ( 96.64
d1rwza2122 Proliferating cell nuclear antigen (PCNA) {Archaeo 96.51
d1plqa2132 Proliferating cell nuclear antigen (PCNA) {Baker's 96.25
d1ud9a1119 Proliferating cell nuclear antigen (PCNA) {Archaeo 96.1
d1plqa1126 Proliferating cell nuclear antigen (PCNA) {Baker's 96.1
d1u7ba2129 Proliferating cell nuclear antigen (PCNA) {Human ( 96.04
d1iz5a1119 Proliferating cell nuclear antigen (PCNA) {Archaeo 95.81
d1ok7a1122 DNA polymerase III, beta subunit {Escherichia coli 93.1
d1vpka1120 DNA polymerase III, beta subunit {Thermotoga marit 91.73
d1dmla1141 UL42 {Human herpesvirus type 1 [TaxId: 10298]} 86.34
>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
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: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.75  E-value=2.4e-17  Score=135.87  Aligned_cols=122  Identities=14%  Similarity=0.139  Sum_probs=108.9

Q ss_pred             eEEecccHHHHHHHHHHHhhcCceEEEEEcCCeEEEEEEcCCccEEEEEEeCccCCceeeecCCEEEEEEEchhhHHHhc
Q 038865            3 FAVSGNALKTFARCLACLSRIGNELVIQASSHQLAFHTLNSSRSAYQSITFMPNFFDVYTVSGAQVQCSVLLKAVCAVLR   82 (345)
Q Consensus         3 ~~l~~~~~k~f~rai~~Lskigdel~ie~~~~gL~L~avNsSrSA~~~~~f~~~FF~~Y~~~~~~~~~~i~~Ksll~vfk   82 (345)
                      |.+...+.+.|++++.+|+++.++++|+++++||.+++||+||++++.+.++++.|++|+|++ +..++|++..+.+|+|
T Consensus         2 fe~~~~~a~~fk~i~~~lk~l~~~~~~~~~~~Gi~iq~mD~shv~lv~l~L~~~~F~~Y~~~~-~~~iGi~~~~l~kIlk   80 (126)
T d1plqa1           2 LEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDH-PVTLGMDLTSLSKILR   80 (126)
T ss_dssp             EEEEESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEECTTSSEEEEEEEEGGGSSEECCSS-CEEEEEEHHHHHHHTT
T ss_pred             eEEEEcchHHHHHHHHHHHHHhceEEEEECCCeEEEEEeCCCcEEEEEEEECHHHCceeeecc-CEEEEEEHHHHHHHHh
Confidence            456678899999999999999999999999999999999999999999999999999999987 5999999999999999


Q ss_pred             CCCCccceEEEEecCCCCCeEEEEEEeC-CCeEEEEEeeecccCccc
Q 038865           83 TPTASIDNLTVQLPNSDAPKVQWTLKCY-NGMKKAYWITCNVEPDIQ  128 (345)
Q Consensus        83 ~~~~~vd~~~i~l~d~d~~~L~~~l~c~-~gI~Kt~~L~~~~~~~~~  128 (345)
                      + .++-|.+++... .+.++|.+.+... .+.+++|.|++.+ .+.+
T Consensus        81 ~-~~~~d~l~l~~~-~~~~~l~i~~~~~~~~~~~~f~l~Lid-id~e  124 (126)
T d1plqa1          81 C-GNNTDTLTLIAD-NTPDSIILLFEDTKKDRIAEYSLKLMD-IDAD  124 (126)
T ss_dssp             C-STTTSEEEEEEC-SSCSEEEEEEECSSSSCEEEEEEECBC-CCCC
T ss_pred             h-cCCCCEEEEEEe-CCCCEEEEEEEcCCCCEEEEEEEeeec-cCcc
Confidence            9 678999999984 4677899988653 4688999999985 5544
>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
>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
>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
>d1iz5a2 d.131.1.2 (A:126-246) Proliferating cell nuclear antigen (PCNA) {Archaeon Pyrococcus furiosus [TaxId: 2261]} 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
>d1ud9a2 d.131.1.2 (A:127-245) Proliferating cell nuclear antigen (PCNA) {Archaeon Sulfolobus tokodaii [TaxId: 111955]} 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
>d1iz5a2 d.131.1.2 (A:126-246) Proliferating cell nuclear antigen (PCNA) {Archaeon Pyrococcus furiosus [TaxId: 2261]} 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
>d1ud9a2 d.131.1.2 (A:127-245) 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
>d1rwza2 d.131.1.2 (A:123-244) Proliferating cell nuclear antigen (PCNA) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} 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
>d1ud9a1 d.131.1.2 (A:1-119) Proliferating cell nuclear antigen (PCNA) {Archaeon Sulfolobus tokodaii [TaxId: 111955]} 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
>d1vpka1 d.131.1.1 (A:1-120) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1dmla1 d.131.1.2 (A:29-169) UL42 {Human herpesvirus type 1 [TaxId: 10298]} Back     information, alignment and structure