Psyllid ID: psy5572

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--
Protein Sequence
MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDDN
Secondary Structure (PSIPRED)
ccccEEEEEEHHHHHHHHHcccccccEEEEEEccccEEEEEEccccEEEEEEEccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEHHHHHHHHHHHHHcccccccEEEEEcccccEEEEEEcccccEEEEEEccccccccc
Coil and Loop (DISEMBL)
MQEPVSLNFACRYLLNfakaaplsnqVCLSmsldvplvvefkiddighiryylapkiesddn
Flexible Loop (DISEMBL)
MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYylapkiesddn
Low Complexity Region (SEG)
MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDDN
Disordered region (IsUnstruct)
*****SLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAP*******
Disordered Region (DISOPRED)
***PVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYL**KI*****
Disordered Region (DISEMBL)
MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDDN
Disordered Region (DISPRO)
*QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKI*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDDN
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	62	2.2.26 [Sep-21-2011]
P17917	260	Proliferating cell nuclea	yes	N/A	1.0	0.238	0.709	8e-20
O16852	260	Proliferating cell nuclea	N/A	N/A	1.0	0.238	0.709	1e-19
O01377	260	Proliferating cell nuclea	N/A	N/A	1.0	0.238	0.709	4e-19
P61258	261	Proliferating cell nuclea	N/A	N/A	1.0	0.237	0.661	2e-17
P12004	261	Proliferating cell nuclea	yes	N/A	1.0	0.237	0.661	2e-17
P57761	261	Proliferating cell nuclea	yes	N/A	1.0	0.237	0.661	3e-17
P17070	263	Proliferating cell nuclea	yes	N/A	0.983	0.231	0.622	4e-17
P24314	268	Proliferating cell nuclea	N/A	N/A	0.983	0.227	0.639	5e-17
P04961	261	Proliferating cell nuclea	yes	N/A	1.0	0.237	0.661	5e-17
Q3ZBW4	261	Proliferating cell nuclea	yes	N/A	1.0	0.237	0.661	6e-17

>sp|P17917|PCNA_DROME Proliferating cell nuclear antigen OS=Drosophila melanogaster GN=mus209 PE=1 SV=2

 Score = 95.5 bits (236), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 49/62 (79%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQEPV+L FACRYL  F KA PLS QV LSM  DVPLVVE+ I D+GHIRYYLAPKIE +
Sbjct: 199 MQEPVTLTFACRYLNAFTKATPLSTQVQLSMCADVPLVVEYAIKDLGHIRYYLAPKIEDN 258

Query: 61  DN 62
           + 
Sbjct: 259 ET 260

This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand.
Drosophila melanogaster (taxid: 7227)

>sp|O16852|PCNA_SARCR Proliferating cell nuclear antigen OS=Sarcophaga crassipalpis GN=PCNA PE=3 SV=1

 Score = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 50/62 (80%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQEPV+L FACRYL  F KA PLS QV LSM  DVPLVVE+ I ++GHIRYYLAPKIE D
Sbjct: 199 MQEPVTLTFACRYLNAFTKATPLSAQVQLSMCADVPLVVEYAIKELGHIRYYLAPKIEDD 258

Query: 61  DN 62
           ++
Sbjct: 259 ES 260

This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand.

Sarcophaga crassipalpis (taxid: 59312)

>sp|O01377|PCNA_BOMMO Proliferating cell nuclear antigen OS=Bombyx mori GN=PCNA PE=2 SV=1

 Score = 93.2 bits (230), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 51/62 (82%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M+EPV+L FAC+YL  F KA  LS QV LSMS DVPLVVE++I DIGHIRYYLAPKIE +
Sbjct: 199 MEEPVTLTFACQYLNYFTKATSLSPQVQLSMSADVPLVVEYRIPDIGHIRYYLAPKIEEE 258

Query: 61  DN 62
           D+
Sbjct: 259 DS 260

This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand.

Bombyx mori (taxid: 7091)

>sp|P61258|PCNA_MACFA Proliferating cell nuclear antigen OS=Macaca fascicularis GN=PCNA PE=2 SV=1

 Score = 87.8 bits (216), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 41/62 (66%), Positives = 48/62 (77%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M EPV L FA RYL  F KA PLS+ V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct: 199 MNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258

Query: 61  DN 62
           + 
Sbjct: 259 EG 260

This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Induces a robust stimulatory effect on the 3'-5' exonuclease and 3'-phosphodiesterase, but not apurinic-apyrimidinic (AP) endonuclease, APEX2 activities. Has to be loaded onto DNA in order to be able to stimulate APEX2.

Macaca fascicularis (taxid: 9541)

>sp|P12004|PCNA_HUMAN Proliferating cell nuclear antigen OS=Homo sapiens GN=PCNA PE=1 SV=1

 Score = 87.8 bits (216), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 41/62 (66%), Positives = 48/62 (77%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M EPV L FA RYL  F KA PLS+ V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct: 199 MNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258

Query: 61  DN 62
           + 
Sbjct: 259 EG 260

This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Induces a robust stimulatory effect on the 3'-5' exonuclease and 3'-phosphodiesterase, but not apurinic-apyrimidinic (AP) endonuclease, APEX2 activities. Has to be loaded onto DNA in order to be able to stimulate APEX2.

Homo sapiens (taxid: 9606)

>sp|P57761|PCNA_CRIGR Proliferating cell nuclear antigen OS=Cricetulus griseus GN=PCNA PE=1 SV=1

 Score = 87.0 bits (214), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 41/62 (66%), Positives = 47/62 (75%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M EPV L FA RYL  F KA PLS  V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct: 199 MNEPVQLTFALRYLNFFTKATPLSPTVTLSMSTDVPLVVEYKISDMGHLKYYLAPKIEDE 258

Query: 61  DN 62
           + 
Sbjct: 259 EG 260

This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Induces a robust stimulatory effect on the 3'-5' exonuclease and 3'-phosphodiesterase, but not apurinic-apyrimidinic (AP) endonuclease, APEX2 activities. Has to be loaded onto DNA in order to be able to stimulate APEX2.

Cricetulus griseus (taxid: 10029)

>sp|P17070|PCNA_ORYSJ Proliferating cell nuclear antigen OS=Oryza sativa subsp. japonica GN=Os02g0805200 PE=2 SV=2

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 38/61 (62%), Positives = 52/61 (85%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQEPVSL FA RY+ +F KA+PLS QV +S+S ++P+VVE+KI ++G+IR+YLAPKIE D
Sbjct: 199 MQEPVSLTFALRYMNSFTKASPLSEQVTISLSSELPVVVEYKIAEMGYIRFYLAPKIEED 258

Query: 61  D 61
           +
Sbjct: 259 E 259

This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|P24314|PCNA_CATRO Proliferating cell nuclear antigen OS=Catharanthus roseus PE=2 SV=1

 Score = 86.3 bits (212), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 39/61 (63%), Positives = 50/61 (81%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M EPVSL FA RYL +F KA PLSN V +S+S ++P+VVE+KI ++G+IR+YLAPKIE D
Sbjct: 199 MNEPVSLTFALRYLNSFTKATPLSNNVTISLSSELPVVVEYKIAEMGYIRFYLAPKIEED 258

Query: 61  D 61
           D
Sbjct: 259 D 259

This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand.

Catharanthus roseus (taxid: 4058)

>sp|P04961|PCNA_RAT Proliferating cell nuclear antigen OS=Rattus norvegicus GN=Pcna PE=1 SV=1

 Score = 86.3 bits (212), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 41/62 (66%), Positives = 47/62 (75%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M EPV L FA RYL  F KA PLS  V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct: 199 MNEPVQLTFALRYLNFFTKATPLSPTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258

Query: 61  DN 62
           + 
Sbjct: 259 EG 260

This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Induces a robust stimulatory effect on the 3'-5' exonuclease and 3'-phosphodiesterase, but not apurinic-apyrimidinic (AP) endonuclease, APEX2 activities (By similarity). Has to be loaded onto DNA in order to be able to stimulate APEX2.

Rattus norvegicus (taxid: 10116)

>sp|Q3ZBW4|PCNA_BOVIN Proliferating cell nuclear antigen OS=Bos taurus GN=PCNA PE=2 SV=1

 Score = 86.3 bits (212), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 41/62 (66%), Positives = 47/62 (75%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M EPV L FA RYL  F KA PLS  V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct: 199 MNEPVQLTFALRYLNFFTKATPLSPTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258

Query: 61  DN 62
           + 
Sbjct: 259 EG 260

This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Induces a robust stimulatory effect on the 3'-5' exonuclease and 3'-phosphodiesterase, but not apurinic-apyrimidinic (AP) endonuclease, APEX2 activities. Has to be loaded onto DNA in order to be able to stimulate APEX2.

Bos taurus (taxid: 9913)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	62
170046021	260	proliferating cell nuclear antigen [Cule	1.0	0.238	0.790	1e-21
157167857	260	proliferating cell nuclear antigen [Aede	1.0	0.238	0.774	4e-21
67866971	260	proliferating cell nuclear antigen [Aede	1.0	0.238	0.774	4e-21
58392487	260	AGAP010220-PA [Anopheles gambiae str. PE	1.0	0.238	0.758	3e-20
312379886	260	hypothetical protein AND_08153 [Anophele	1.0	0.238	0.741	9e-20
289742701	260	DNA polymerase delta processivity factor	1.0	0.238	0.725	7e-19
349501993	261	proliferating cell nuclear antigen [Lito	1.0	0.237	0.725	3e-18
122831052	260	proliferating cell nuclear antigen [Fenn	1.0	0.238	0.725	3e-18
17136790	260	mutagen-sensitive 209, isoform A [Drosop	1.0	0.238	0.709	4e-18
195124095	260	GI18526 [Drosophila mojavensis] gi|19391	1.0	0.238	0.709	4e-18

>gi|170046021|ref|XP_001850584.1| proliferating cell nuclear antigen [Culex quinquefasciatus] gi|167868946|gb|EDS32329.1| proliferating cell nuclear antigen [Culex quinquefasciatus]

 Score =  107 bits (266), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 49/62 (79%), Positives = 54/62 (87%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQEPV+L FACRYL +F KA PLSNQV LSMS DVPLVVE+KI D+GHIRYYLAPKIE D
Sbjct: 199 MQEPVTLTFACRYLNSFTKATPLSNQVQLSMSADVPLVVEYKIQDLGHIRYYLAPKIEDD 258

Query: 61  DN 62
           +N
Sbjct: 259 EN 260

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157167857|ref|XP_001662644.1| proliferating cell nuclear antigen [Aedes aegypti] gi|67866973|gb|AAY82461.1| proliferating cell nuclear antigen [Aedes aegypti] gi|108871048|gb|EAT35273.1| AAEL012545-PA [Aedes aegypti]

 Score =  105 bits (261), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 48/62 (77%), Positives = 54/62 (87%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQEPV+L FACRYL +F KA PLS+QV LSMS DVPLVVE+KI D+GHIRYYLAPKIE D
Sbjct: 199 MQEPVTLTFACRYLNSFTKATPLSSQVQLSMSADVPLVVEYKIQDLGHIRYYLAPKIEDD 258

Query: 61  DN 62
           +N
Sbjct: 259 EN 260

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|67866971|gb|AAY82460.1| proliferating cell nuclear antigen [Aedes albopictus]

 Score =  105 bits (261), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 48/62 (77%), Positives = 54/62 (87%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQEPV+L FACRYL +F KA PLS+QV LSMS DVPLVVE+KI D+GHIRYYLAPKIE D
Sbjct: 199 MQEPVTLTFACRYLNSFTKATPLSSQVQLSMSADVPLVVEYKIQDLGHIRYYLAPKIEDD 258

Query: 61  DN 62
           +N
Sbjct: 259 EN 260

Source: Aedes albopictus

Species: Aedes albopictus

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|58392487|ref|XP_319407.2| AGAP010220-PA [Anopheles gambiae str. PEST] gi|55236432|gb|EAA13806.2| AGAP010220-PA [Anopheles gambiae str. PEST]

 Score =  102 bits (254), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 47/62 (75%), Positives = 53/62 (85%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQEPV+L FACRYL +F KA PL NQV LSMS DVPLVVE++I D+GHIRYYLAPKIE D
Sbjct: 199 MQEPVTLTFACRYLNSFTKATPLCNQVQLSMSADVPLVVEYRIPDLGHIRYYLAPKIEDD 258

Query: 61  DN 62
           +N
Sbjct: 259 EN 260

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312379886|gb|EFR26039.1| hypothetical protein AND_08153 [Anopheles darlingi]

 Score =  100 bits (250), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 46/62 (74%), Positives = 52/62 (83%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQEPV+L FACRYL +F KA PL  QV LSMS DVPLVVE++I D+GHIRYYLAPKIE D
Sbjct: 199 MQEPVTLTFACRYLNSFTKATPLCQQVQLSMSADVPLVVEYRIPDLGHIRYYLAPKIEDD 258

Query: 61  DN 62
           +N
Sbjct: 259 EN 260

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|289742701|gb|ADD20098.1| DNA polymerase delta processivity factor [Glossina morsitans morsitans]

 Score = 97.8 bits (242), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 45/62 (72%), Positives = 51/62 (82%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQE V+L FACRYL  F KA PL NQV LSMS DVPLVVE++I D+GHIRYYLAPKIE D
Sbjct: 199 MQEQVTLTFACRYLNAFTKATPLCNQVQLSMSADVPLVVEYRISDLGHIRYYLAPKIEED 258

Query: 61  DN 62
           ++
Sbjct: 259 ES 260

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|349501993|gb|AEP83535.1| proliferating cell nuclear antigen [Litopenaeus vannamei]

 Score = 95.5 bits (236), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/62 (72%), Positives = 51/62 (82%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQEPV+L FACRYL  F KA PLS QV LSMS DVPLVVE+ I +IGHIRY+LAPKIE +
Sbjct: 200 MQEPVTLTFACRYLNMFTKATPLSPQVSLSMSPDVPLVVEYAIGEIGHIRYFLAPKIEDE 259

Query: 61  DN 62
           D+
Sbjct: 260 DS 261

Source: Litopenaeus vannamei

Species: Litopenaeus vannamei

Genus: Litopenaeus

Family: Penaeidae

Order: Decapoda

Class: Malacostraca

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|122831052|gb|ABM66815.1| proliferating cell nuclear antigen [Fenneropenaeus chinensis]

 Score = 95.5 bits (236), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/62 (72%), Positives = 51/62 (82%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQEPV+L FACRYL  F KA PLS QV LSMS DVPLVVE+ I +IGHIRY+LAPKIE +
Sbjct: 199 MQEPVTLTFACRYLNMFTKATPLSPQVSLSMSPDVPLVVEYSIGEIGHIRYFLAPKIEDE 258

Query: 61  DN 62
           D+
Sbjct: 259 DS 260

Source: Fenneropenaeus chinensis

Species: Fenneropenaeus chinensis

Genus: Fenneropenaeus

Family: Penaeidae

Order: Decapoda

Class: Malacostraca

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|17136790|ref|NP_476905.1| mutagen-sensitive 209, isoform A [Drosophila melanogaster] gi|45552759|ref|NP_995904.1| mutagen-sensitive 209, isoform B [Drosophila melanogaster] gi|194753480|ref|XP_001959040.1| mus209 [Drosophila ananassae] gi|194881527|ref|XP_001974882.1| mus209 [Drosophila erecta] gi|195486939|ref|XP_002091715.1| mus209 [Drosophila yakuba] gi|129693|sp|P17917.2|PCNA_DROME RecName: Full=Proliferating cell nuclear antigen; Short=PCNA; AltName: Full=Cyclin; AltName: Full=Mutagen-sensitive 209 protein gi|158038|gb|AAA28746.1| proliferating cell nuclear antigen [Drosophila melanogaster] gi|7302405|gb|AAF57493.1| mutagen-sensitive 209, isoform A [Drosophila melanogaster] gi|21483468|gb|AAM52709.1| LD45889p [Drosophila melanogaster] gi|45445452|gb|AAS64796.1| mutagen-sensitive 209, isoform B [Drosophila melanogaster] gi|190620338|gb|EDV35862.1| mus209 [Drosophila ananassae] gi|190658069|gb|EDV55282.1| mus209 [Drosophila erecta] gi|194177816|gb|EDW91427.1| mus209 [Drosophila yakuba] gi|220954336|gb|ACL89711.1| mus209-PA [synthetic construct]

 Score = 95.5 bits (236), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 49/62 (79%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQEPV+L FACRYL  F KA PLS QV LSM  DVPLVVE+ I D+GHIRYYLAPKIE +
Sbjct: 199 MQEPVTLTFACRYLNAFTKATPLSTQVQLSMCADVPLVVEYAIKDLGHIRYYLAPKIEDN 258

Query: 61  DN 62
           + 
Sbjct: 259 ET 260

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195124095|ref|XP_002006529.1| GI18526 [Drosophila mojavensis] gi|193911597|gb|EDW10464.1| GI18526 [Drosophila mojavensis]

 Score = 95.5 bits (236), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 49/62 (79%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQEPV+L FACRYL  F KA PLS QV LSM  DVPLVVE+ I D+GHIRYYLAPKIE +
Sbjct: 199 MQEPVTLTFACRYLNAFTKATPLSTQVQLSMCADVPLVVEYAIKDLGHIRYYLAPKIEDN 258

Query: 61  DN 62
           + 
Sbjct: 259 ET 260

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	62
FB|FBgn0005655	260	mus209 "mutagen-sensitive 209"	0.983	0.234	0.721	1.4e-18
UNIPROTKB|P12004	261	PCNA "Proliferating cell nucle	0.983	0.233	0.672	5.3e-17
UNIPROTKB|P61258	261	PCNA "Proliferating cell nucle	0.983	0.233	0.672	5.3e-17
UNIPROTKB|P57761	261	PCNA "Proliferating cell nucle	0.983	0.233	0.672	6.7e-17
UNIPROTKB|Q3ZBW4	261	PCNA "Proliferating cell nucle	0.983	0.233	0.672	1.1e-16
UNIPROTKB|E2R0D6	261	PCNA "Uncharacterized protein"	0.983	0.233	0.672	1.1e-16
UNIPROTKB|I3L813	261	PCNA "Proliferating cell nucle	0.983	0.233	0.672	1.1e-16
RGD|3269	261	Pcna "proliferating cell nucle	0.983	0.233	0.672	1.1e-16
MGI|MGI:97503	261	Pcna "proliferating cell nucle	0.983	0.233	0.672	1.4e-16
UNIPROTKB|F1NLS0	263	PCNA "Proliferating cell nucle	0.935	0.220	0.706	2.9e-16

FB|FBgn0005655 mus209 "mutagen-sensitive 209" [Drosophila melanogaster (taxid:7227)]

 Score = 224 (83.9 bits), Expect = 1.4e-18, P = 1.4e-18
 Identities = 44/61 (72%), Positives = 49/61 (80%)

Query:     1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
             MQEPV+L FACRYL  F KA PLS QV LSM  DVPLVVE+ I D+GHIRYYLAPKIE +
Sbjct:   199 MQEPVTLTFACRYLNAFTKATPLSTQVQLSMCADVPLVVEYAIKDLGHIRYYLAPKIEDN 258

Query:    61 D 61
             +
Sbjct:   259 E 259

GO:0006298 "mismatch repair" evidence=TAS

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

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0043626 "PCNA complex" evidence=ISS;NAS

GO:0006272 "leading strand elongation" evidence=NAS

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0006260 "DNA replication" evidence=IMP;TAS

GO:0007307 "eggshell chorion gene amplification" evidence=TAS

GO:0006275 "regulation of DNA replication" evidence=IEA

GO:0030337 "DNA polymerase processivity factor activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0019730 "antimicrobial humoral response" evidence=IMP

GO:0005875 "microtubule associated complex" evidence=IDA

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|P12004 PCNA "Proliferating cell nuclear antigen" [Homo sapiens (taxid:9606)]

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 41/61 (67%), Positives = 48/61 (78%)

Query:     1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
             M EPV L FA RYL  F KA PLS+ V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct:   199 MNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258

Query:    61 D 61
             +
Sbjct:   259 E 259

GO:0006275 "regulation of DNA replication" evidence=IEA

GO:0030337 "DNA polymerase processivity factor activity" evidence=IEA

GO:0043626 "PCNA complex" evidence=IEA

GO:0007507 "heart development" evidence=IEA

GO:0033993 "response to lipid" evidence=IEA

GO:0046686 "response to cadmium ion" evidence=IEA

GO:0005663 "DNA replication factor C complex" evidence=TAS

GO:0048015 "phosphatidylinositol-mediated signaling" evidence=NAS

GO:0006281 "DNA repair" evidence=NAS;TAS

GO:0006260 "DNA replication" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0032077 "positive regulation of deoxyribonuclease activity" evidence=IDA

GO:0019985 "translesion synthesis" evidence=IDA

GO:0070557 "PCNA-p21 complex" evidence=IDA

GO:0030971 "receptor tyrosine kinase binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0008283 "cell proliferation" evidence=TAS

GO:0032405 "MutLalpha complex binding" evidence=IDA

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0000083 "regulation of transcription involved in G1/S phase of mitotic cell cycle" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0000722 "telomere maintenance via recombination" evidence=TAS

GO:0000723 "telomere maintenance" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006271 "DNA strand elongation involved in DNA replication" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006284 "base-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0006297 "nucleotide-excision repair, DNA gap filling" evidence=TAS

GO:0032201 "telomere maintenance via semi-conservative replication" evidence=TAS

GO:0042802 "identical protein binding" evidence=IPI

GO:0032139 "dinucleotide insertion or deletion binding" evidence=IDA

GO:0000701 "purine-specific mismatch base pair DNA N-glycosylase activity" evidence=IDA

GO:0006298 "mismatch repair" evidence=IDA

GO:0043596 "nuclear replication fork" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0015630 "microtubule cytoskeleton" evidence=IDA

UNIPROTKB|P61258 PCNA "Proliferating cell nuclear antigen" [Macaca fascicularis (taxid:9541)]

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 41/61 (67%), Positives = 48/61 (78%)

Query:     1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
             M EPV L FA RYL  F KA PLS+ V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct:   199 MNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258

Query:    61 D 61
             +
Sbjct:   259 E 259

GO:0019985 "translesion synthesis" evidence=ISS

GO:0032077 "positive regulation of deoxyribonuclease activity" evidence=ISS

GO:0070557 "PCNA-p21 complex" evidence=ISS

UNIPROTKB|P57761 PCNA "Proliferating cell nuclear antigen" [Cricetulus griseus (taxid:10029)]

 Score = 208 (78.3 bits), Expect = 6.7e-17, P = 6.7e-17
 Identities = 41/61 (67%), Positives = 47/61 (77%)

Query:     1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
             M EPV L FA RYL  F KA PLS  V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct:   199 MNEPVQLTFALRYLNFFTKATPLSPTVTLSMSTDVPLVVEYKISDMGHLKYYLAPKIEDE 258

Query:    61 D 61
             +
Sbjct:   259 E 259

GO:0019985 "translesion synthesis" evidence=ISS

GO:0032077 "positive regulation of deoxyribonuclease activity" evidence=ISS

GO:0042802 "identical protein binding" evidence=IPI

GO:0070557 "PCNA-p21 complex" evidence=ISS

UNIPROTKB|Q3ZBW4 PCNA "Proliferating cell nuclear antigen" [Bos taurus (taxid:9913)]

 Score = 206 (77.6 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 41/61 (67%), Positives = 47/61 (77%)

Query:     1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
             M EPV L FA RYL  F KA PLS  V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct:   199 MNEPVQLTFALRYLNFFTKATPLSPTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258

Query:    61 D 61
             +
Sbjct:   259 E 259

GO:0032077 "positive regulation of deoxyribonuclease activity" evidence=ISS

GO:0019985 "translesion synthesis" evidence=ISS

GO:0070557 "PCNA-p21 complex" evidence=ISS

GO:0043596 "nuclear replication fork" evidence=IEA

GO:0042802 "identical protein binding" evidence=IEA

GO:0032405 "MutLalpha complex binding" evidence=IEA

GO:0032139 "dinucleotide insertion or deletion binding" evidence=IEA

GO:0030971 "receptor tyrosine kinase binding" evidence=IEA

GO:0015630 "microtubule cytoskeleton" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0000701 "purine-specific mismatch base pair DNA N-glycosylase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0043626 "PCNA complex" evidence=IEA

GO:0030337 "DNA polymerase processivity factor activity" evidence=IEA

GO:0006275 "regulation of DNA replication" evidence=IEA

UNIPROTKB|E2R0D6 PCNA "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 206 (77.6 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 41/61 (67%), Positives = 47/61 (77%)

Query:     1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
             M EPV L FA RYL  F KA PLS  V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct:   199 MNEPVQLTFALRYLNFFTKATPLSPTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258

Query:    61 D 61
             +
Sbjct:   259 E 259

GO:0070557 "PCNA-p21 complex" evidence=IEA

GO:0043596 "nuclear replication fork" evidence=IEA

GO:0042802 "identical protein binding" evidence=IEA

GO:0032405 "MutLalpha complex binding" evidence=IEA

GO:0032139 "dinucleotide insertion or deletion binding" evidence=IEA

GO:0032077 "positive regulation of deoxyribonuclease activity" evidence=IEA

GO:0030971 "receptor tyrosine kinase binding" evidence=IEA

GO:0019985 "translesion synthesis" evidence=IEA

GO:0015630 "microtubule cytoskeleton" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0000701 "purine-specific mismatch base pair DNA N-glycosylase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0043626 "PCNA complex" evidence=IEA

GO:0030337 "DNA polymerase processivity factor activity" evidence=IEA

GO:0006275 "regulation of DNA replication" evidence=IEA

UNIPROTKB|I3L813 PCNA "Proliferating cell nuclear antigen" [Sus scrofa (taxid:9823)]

 Score = 206 (77.6 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 41/61 (67%), Positives = 47/61 (77%)

Query:     1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
             M EPV L FA RYL  F KA PLS  V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct:   199 MNEPVQLTFALRYLNFFTKATPLSPTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258

Query:    61 D 61
             +
Sbjct:   259 E 259

GO:0070557 "PCNA-p21 complex" evidence=IEA

GO:0043596 "nuclear replication fork" evidence=IEA

GO:0042802 "identical protein binding" evidence=IEA

GO:0032405 "MutLalpha complex binding" evidence=IEA

GO:0032139 "dinucleotide insertion or deletion binding" evidence=IEA

GO:0032077 "positive regulation of deoxyribonuclease activity" evidence=IEA

GO:0030971 "receptor tyrosine kinase binding" evidence=IEA

GO:0019985 "translesion synthesis" evidence=IEA

GO:0015630 "microtubule cytoskeleton" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0000701 "purine-specific mismatch base pair DNA N-glycosylase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0043626 "PCNA complex" evidence=IEA

GO:0030337 "DNA polymerase processivity factor activity" evidence=IEA

GO:0006275 "regulation of DNA replication" evidence=IEA

RGD|3269 Pcna "proliferating cell nuclear antigen" [Rattus norvegicus (taxid:10116)]

 Score = 206 (77.6 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 41/61 (67%), Positives = 47/61 (77%)

Query:     1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
             M EPV L FA RYL  F KA PLS  V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct:   199 MNEPVQLTFALRYLNFFTKATPLSPTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258

Query:    61 D 61
             +
Sbjct:   259 E 259

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0000307 "cyclin-dependent protein kinase holoenzyme complex" evidence=ISO

GO:0000701 "purine-specific mismatch base pair DNA N-glycosylase activity" evidence=IEA;ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005622 "intracellular" evidence=ISO

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005652 "nuclear lamina" evidence=ISO

GO:0005657 "replication fork" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0006260 "DNA replication" evidence=IEA

GO:0006275 "regulation of DNA replication" evidence=IEA

GO:0006287 "base-excision repair, gap-filling" evidence=ISO

GO:0006298 "mismatch repair" evidence=IEA;ISO

GO:0007507 "heart development" evidence=IEP

GO:0008134 "transcription factor binding" evidence=ISO

GO:0015630 "microtubule cytoskeleton" evidence=IEA;ISO

GO:0019985 "translesion synthesis" evidence=ISO;ISS

GO:0030337 "DNA polymerase processivity factor activity" evidence=IEA

GO:0030971 "receptor tyrosine kinase binding" evidence=IEA;ISO

GO:0032077 "positive regulation of deoxyribonuclease activity" evidence=ISO;ISS

GO:0032139 "dinucleotide insertion or deletion binding" evidence=IEA;ISO

GO:0032405 "MutLalpha complex binding" evidence=IEA;ISO

GO:0033993 "response to lipid" evidence=IDA

GO:0042802 "identical protein binding" evidence=IEA;ISO

GO:0043596 "nuclear replication fork" evidence=IEA;ISO

GO:0043626 "PCNA complex" evidence=IEA

GO:0046686 "response to cadmium ion" evidence=IEP

GO:0070557 "PCNA-p21 complex" evidence=ISO;ISS

GO:0005730 "nucleolus" evidence=ISO

MGI|MGI:97503 Pcna "proliferating cell nuclear antigen" [Mus musculus (taxid:10090)]

 Score = 205 (77.2 bits), Expect = 1.4e-16, P = 1.4e-16
 Identities = 41/61 (67%), Positives = 47/61 (77%)

Query:     1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
             M EPV L FA RYL  F KA PLS  V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct:   199 MNEPVHLTFALRYLNFFTKATPLSPTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258

Query:    61 D 61
             +
Sbjct:   259 E 259

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0000307 "cyclin-dependent protein kinase holoenzyme complex" evidence=IPI

GO:0000701 "purine-specific mismatch base pair DNA N-glycosylase activity" evidence=ISO

GO:0003677 "DNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005622 "intracellular" evidence=IDA

GO:0005634 "nucleus" evidence=ISO;ISS;IDA

GO:0005652 "nuclear lamina" evidence=IDA

GO:0005657 "replication fork" evidence=IDA

GO:0006260 "DNA replication" evidence=IEA

GO:0006275 "regulation of DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006287 "base-excision repair, gap-filling" evidence=IDA

GO:0006298 "mismatch repair" evidence=ISO

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IPI

GO:0019985 "translesion synthesis" evidence=ISO

GO:0030337 "DNA polymerase processivity factor activity" evidence=IEA

GO:0030971 "receptor tyrosine kinase binding" evidence=ISO

GO:0032077 "positive regulation of deoxyribonuclease activity" evidence=ISO

GO:0032139 "dinucleotide insertion or deletion binding" evidence=ISO

GO:0032405 "MutLalpha complex binding" evidence=ISO

GO:0033993 "response to lipid" evidence=ISO

GO:0042802 "identical protein binding" evidence=ISO

GO:0043596 "nuclear replication fork" evidence=ISO

GO:0043626 "PCNA complex" evidence=IEA

GO:0070557 "PCNA-p21 complex" evidence=ISO

UNIPROTKB|F1NLS0 PCNA "Proliferating cell nuclear antigen" [Gallus gallus (taxid:9031)]

 Score = 202 (76.2 bits), Expect = 2.9e-16, P = 2.9e-16
 Identities = 41/58 (70%), Positives = 45/58 (77%)

Query:     1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58
             M EPV L FA RYL  F KA PLS  V LSMS DVPLVVE+KI D+GH++YYLAPKIE
Sbjct:   200 MNEPVQLTFALRYLNFFTKATPLSPTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIE 257

GO:0006275 "regulation of DNA replication" evidence=IEA

GO:0030337 "DNA polymerase processivity factor activity" evidence=IEA

GO:0043626 "PCNA complex" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0000701 "purine-specific mismatch base pair DNA N-glycosylase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0015630 "microtubule cytoskeleton" evidence=IEA

GO:0019985 "translesion synthesis" evidence=IEA

GO:0030971 "receptor tyrosine kinase binding" evidence=IEA

GO:0032077 "positive regulation of deoxyribonuclease activity" evidence=IEA

GO:0032139 "dinucleotide insertion or deletion binding" evidence=IEA

GO:0032405 "MutLalpha complex binding" evidence=IEA

GO:0042802 "identical protein binding" evidence=IEA

GO:0043596 "nuclear replication fork" evidence=IEA

GO:0070557 "PCNA-p21 complex" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9M7Q7	PCNA1_ARATH	No assigned EC number	0.5645	1.0	0.2357	yes	N/A
P17917	PCNA_DROME	No assigned EC number	0.7096	1.0	0.2384	yes	N/A
Q9PTP1	PCNA_DANRE	No assigned EC number	0.6333	0.9677	0.2307	yes	N/A
Q9DEA3	PCNA_CHICK	No assigned EC number	0.7068	0.9354	0.2213	yes	N/A
Q9ZW35	PCNA2_ARATH	No assigned EC number	0.5645	1.0	0.2348	yes	N/A
P17918	PCNA_MOUSE	No assigned EC number	0.6721	0.9838	0.2337	yes	N/A
Q3ZBW4	PCNA_BOVIN	No assigned EC number	0.6612	1.0	0.2375	yes	N/A
Q54K47	PCNA_DICDI	No assigned EC number	0.6140	0.9193	0.2209	yes	N/A
P17070	PCNA_ORYSJ	No assigned EC number	0.6229	0.9838	0.2319	yes	N/A
P57761	PCNA_CRIGR	No assigned EC number	0.6612	1.0	0.2375	yes	N/A
P12004	PCNA_HUMAN	No assigned EC number	0.6612	1.0	0.2375	yes	N/A
P04961	PCNA_RAT	No assigned EC number	0.6612	1.0	0.2375	yes	N/A
Q03392	PCNA_SCHPO	No assigned EC number	0.5081	0.9677	0.2307	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	62
PLN00057	263	PLN00057, PLN00057, proliferating cell nuclear ant	2e-29
TIGR00590	259	TIGR00590, pcna, proliferating cell nuclear antige	4e-28
pfam02747	128	pfam02747, PCNA_C, Proliferating cell nuclear anti	5e-27
cd00577	248	cd00577, PCNA, Proliferating Cell Nuclear Antigen	5e-20
PTZ00483	264	PTZ00483, PTZ00483, proliferating cell nuclear ant	5e-11
PTZ00113	275	PTZ00113, PTZ00113, proliferating cell nuclear ant	1e-09
PRK01115	247	PRK01115, PRK01115, DNA polymerase sliding clamp;	1e-08
PHA03383	262	PHA03383, PHA03383, PCNA-like protein; Provisional	3e-06

>gnl|CDD|177688 PLN00057, PLN00057, proliferating cell nuclear antigen; Provisional

 Score =  103 bits (259), Expect = 2e-29
 Identities = 40/62 (64%), Positives = 52/62 (83%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           MQEPVSL FA RYL +F KA PLS+ V LS+S ++P+VVE+KI ++G+IRYYLAPKIE D
Sbjct: 199 MQEPVSLTFALRYLNSFTKATPLSDTVTLSLSKELPVVVEYKIAEMGYIRYYLAPKIEED 258

Query: 61  DN 62
           ++
Sbjct: 259 ED 260

Length = 263

>gnl|CDD|188067 TIGR00590, pcna, proliferating cell nuclear antigen (pcna)

 Score =  100 bits (250), Expect = 4e-28
 Identities = 37/61 (60%), Positives = 50/61 (81%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M++PV+L FA +YL  F KA PLS++V LSMS DVPLVVE+KI D+G +R++LAPKIE +
Sbjct: 199 MKQPVTLTFAIKYLNLFTKATPLSDRVTLSMSNDVPLVVEYKIKDMGFLRFFLAPKIEDE 258

Query: 61  D 61
           +
Sbjct: 259 E 259

All proteins in this family for which functions are known form sliding DNA clamps that are used in DNA replication processes. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 259

>gnl|CDD|202372 pfam02747, PCNA_C, Proliferating cell nuclear antigen, C-terminal domain

 Score = 94.1 bits (234), Expect = 5e-27
 Identities = 36/56 (64%), Positives = 44/56 (78%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 56
           M EPV+L FA RYL +F KA PLS  V +SMS ++PLVVE+KI D+G +RYYLAPK
Sbjct: 73  MNEPVTLTFALRYLNSFTKATPLSPTVTISMSSELPLVVEYKIADMGLLRYYLAPK 128

N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA. Length = 128

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

 Score = 78.8 bits (195), Expect = 5e-20
 Identities = 33/58 (56%), Positives = 42/58 (72%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58
             EPVS  ++ +YL +F KAAPLS++V LS   D PL +EFKI D GH+ +YLAPKIE
Sbjct: 191 CSEPVSSTYSLKYLKDFTKAAPLSDKVTLSFGSDGPLSLEFKIADGGHLTFYLAPKIE 248

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|185661 PTZ00483, PTZ00483, proliferating cell nuclear antigen; Provisional

 Score = 54.9 bits (132), Expect = 5e-11
 Identities = 25/63 (39%), Positives = 38/63 (60%), Gaps = 7/63 (11%)

Query: 3   EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFK-------IDDIGHIRYYLAP 55
           E +S  FA RYL+ F+KA  L+++V +++S  +PL V+F        + D   I +YLAP
Sbjct: 201 ESLSQEFATRYLVLFSKATSLADEVSINLSAGIPLSVKFNFKDPLTDLQDSSFINFYLAP 260

Query: 56  KIE 58
            IE
Sbjct: 261 NIE 263

Length = 264

>gnl|CDD|240275 PTZ00113, PTZ00113, proliferating cell nuclear antigen; Provisional

 Score = 51.4 bits (123), Expect = 1e-09
 Identities = 22/69 (31%), Positives = 43/69 (62%), Gaps = 10/69 (14%)

Query: 2   QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDD----------IGHIRY 51
           ++P+  ++A +YL  FAK+  LS+ V L +S + P+ V+++I D          +G +++
Sbjct: 202 RKPIKQSYATKYLNMFAKSGCLSDVVTLGLSDNRPIEVKYEIKDTSPDARHTHKLGEVKF 261

Query: 52  YLAPKIESD 60
           +LAPK++ D
Sbjct: 262 FLAPKMDDD 270

Length = 275

>gnl|CDD|234903 PRK01115, PRK01115, DNA polymerase sliding clamp; Validated

 Score = 48.3 bits (116), Expect = 1e-08
 Identities = 19/46 (41%), Positives = 28/46 (60%)

Query: 13  YLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58
           YL +  KA   S++V +    D+PL +EF+I   G + Y LAP+IE
Sbjct: 202 YLKDMVKATSASDEVTIEFGSDMPLKLEFEIAGGGKVTYLLAPRIE 247

Length = 247

>gnl|CDD|177619 PHA03383, PHA03383, PCNA-like protein; Provisional

 Score = 41.4 bits (97), Expect = 3e-06
 Identities = 14/50 (28%), Positives = 34/50 (68%)

Query: 9   FACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58
           F+ +YL +F KA+ +S+ V + +    PL++++ +  +G++++ +APK+ 
Sbjct: 213 FSLKYLTSFTKASGMSSSVEIYLKESNPLILKYNVGSLGNLKFVIAPKVS 262

Length = 262

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	62
PTZ00113	275	proliferating cell nuclear antigen; Provisional	99.9
PF02747	128	PCNA_C: Proliferating cell nuclear antigen, C-term	99.9
PLN00057	263	proliferating cell nuclear antigen; Provisional	99.89
PTZ00483	264	proliferating cell nuclear antigen; Provisional	99.89
TIGR00590	259	pcna proliferating cell nuclear antigen (pcna). Al	99.89
PHA03383	262	PCNA-like protein; Provisional	99.87
KOG1636|consensus	260		99.87
PRK01115	247	DNA polymerase sliding clamp; Validated	99.5
cd00577	248	PCNA Proliferating Cell Nuclear Antigen (PCNA) dom	99.3
COG0592	364	DnaN DNA polymerase sliding clamp subunit (PCNA ho	98.12
cd00140	365	beta_clamp Beta clamp domain. The beta subunit (pr	97.77
PRK05643	367	DNA polymerase III subunit beta; Validated	97.46
PF02768	121	DNA_pol3_beta_3: DNA polymerase III beta subunit,	96.24
PRK14947	384	DNA polymerase III subunit beta; Provisional	95.11
PRK14940	367	DNA polymerase III subunit beta; Provisional	93.99
KOG3194|consensus	279		93.82
PRK14945	362	DNA polymerase III subunit beta; Provisional	93.46
smart00480	345	POL3Bc DNA polymerase III beta subunit.	92.97
PF04005	292	Hus1: Hus1-like protein; InterPro: IPR007150 Hus1,	92.76
cd00577	248	PCNA Proliferating Cell Nuclear Antigen (PCNA) dom	92.05
PRK14941	374	DNA polymerase III subunit beta; Provisional	91.78
PRK14942	373	DNA polymerase III subunit beta; Provisional	90.66
PRK14943	374	DNA polymerase III subunit beta; Provisional	90.6
PRK06673	376	DNA polymerase III subunit beta; Validated	90.55
TIGR00663	367	dnan DNA polymerase III, beta subunit. University)	90.02
PRK14944	375	DNA polymerase III subunit beta; Provisional	89.59
PRK07761	376	DNA polymerase III subunit beta; Validated	88.58
PRK14946	366	DNA polymerase III subunit beta; Provisional	88.43
PF04139	252	Rad9: Rad9; InterPro: IPR007268 Rad9 is required f	86.33
PF00705	127	PCNA_N: Proliferating cell nuclear antigen, N-term	85.62
PF02144	275	Rad1: Repair protein Rad1/Rec1/Rad17; InterPro: IP	84.71
COG0592	364	DnaN DNA polymerase sliding clamp subunit (PCNA ho	83.58

>PTZ00113 proliferating cell nuclear antigen; Provisional

Probab=99.90  E-value=1.2e-23  Score=144.23  Aligned_cols=62  Identities=35%  Similarity=0.744  Sum_probs=57.8

Q ss_pred             CCCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCC----------CeEEEEEEeecCCCCCC
Q psy5572           1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDD----------IGHIRYYLAPKIESDDN   62 (62)
Q Consensus         1 ~~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~----------~g~l~~~lAPrie~e~~   62 (62)
                      ++++++++||++||++|+||+++|++|+|+|++|+||+++|++++          +|+|+||||||+++|++
T Consensus       201 v~~~~~~~ysl~YL~~f~Ka~~ls~~V~l~l~~d~Pl~ley~i~~~~~~~~~~~~~G~l~fyLAPkie~~~~  272 (275)
T PTZ00113        201 VRKPIKQSYATKYLNMFAKSGCLSDVVTLGLSDNRPIEVKYEIKDTSPDARHTHKLGEVKFFLAPKMDDDMD  272 (275)
T ss_pred             ecCceeeEEhHHHHHHhhccccCCCeEEEEEcCCCCEEEEEEeccccccccccCCccEEEEEEcCccCcccc
Confidence            368999999999999999999999999999999999999999962          59999999999998874

>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 []

Probab=99.90  E-value=2.6e-23  Score=128.31  Aligned_cols=55  Identities=51%  Similarity=0.910  Sum_probs=52.5

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeec
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK   56 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPr   56 (62)
                      +++++++|+++||++|+||+++|++|+|+|++|+||+++|+++++|+++||||||
T Consensus        74 ~~~~~~~fsl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~f~~~~~g~l~f~LAPK  128 (128)
T PF02747_consen   74 KEPVSSSFSLDYLNDFSKAAPLSDEVTLELGEDMPLKLEFELADGGSLKFYLAPK  128 (128)
T ss_dssp             SSEEEEEEEHHHHHHHGGGGGTTSEEEEEEETTSEEEEEEEETTTEEEEEEE-BB
T ss_pred             ccceeeEEeHHHHHhhhccccCCceEEEEEcCCCCEEEEEEeCCCeEEEEEEcCC
Confidence            5788999999999999999999999999999999999999999999999999997

It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNA replication []. The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes []. In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta. Homologues of PCNA have also been identified in the archaea (Euryarchaeota and Crenarchaeota) and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses. ; GO: 0003677 DNA binding, 0030337 DNA polymerase processivity factor activity, 0006275 regulation of DNA replication, 0043626 PCNA complex; PDB: 1IZ5_A 1IZ4_A 1GE8_A 1ISQ_A 3A2F_B 1RWZ_A 3P83_A 1RXM_A 1RXZ_A 1SXJ_F ....

>PLN00057 proliferating cell nuclear antigen; Provisional

Probab=99.89  E-value=2.4e-23  Score=141.18  Aligned_cols=61  Identities=64%  Similarity=1.053  Sum_probs=58.3

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDDN   62 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~~   62 (62)
                      ++++++.|+++||+.|+||+++|++|+|+|++++||+|+|+++++|+|+||||||+++|++
T Consensus       200 ~e~~~~~y~l~YL~~~~Ka~~ls~~V~i~~~~~~Pl~l~y~l~~~g~l~f~LAPri~~~~~  260 (263)
T PLN00057        200 QEPVSLTFALRYLNSFTKATPLSDTVTLSLSKELPVVVEYKIAEMGYIRYYLAPKIEEDED  260 (263)
T ss_pred             cCceEEEEhHHHHHHhhccccCCCeEEEEEcCCCCEEEEEEeCCCeEEEEEEcCCCCCccc
Confidence            5789999999999999999999999999999999999999999899999999999998763

>PTZ00483 proliferating cell nuclear antigen; Provisional

Probab=99.89  E-value=3.1e-23  Score=141.51  Aligned_cols=59  Identities=42%  Similarity=0.765  Sum_probs=55.8

Q ss_pred             CCCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeC-------CCeEEEEEEeecCCC
Q psy5572           1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKID-------DIGHIRYYLAPKIES   59 (62)
Q Consensus         1 ~~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~-------~~g~l~~~lAPrie~   59 (62)
                      +++|++++|+++||++|+||+++|++|+|+|++++||+++|+++       ++|+|+||||||+|+
T Consensus       199 ~~~~v~~~fsl~YL~~f~Ka~~lsd~V~i~l~~~~Pl~ley~i~~~~~~~~~~G~l~fyLAPrie~  264 (264)
T PTZ00483        199 STESLSQEFATRYLVLFSKATSLADEVSINLSAGIPLSVKFNFKDPLTDLQDSSFINFYLAPNIEE  264 (264)
T ss_pred             ecCcchheehHHHHHHhhccccCCCeEEEEEcCCCCEEEEEEecccccCCCCceEEEEEEccccCC
Confidence            46899999999999999999999999999999999999999995       589999999999985

>TIGR00590 pcna proliferating cell nuclear antigen (pcna)

Probab=99.89  E-value=5.8e-23  Score=138.94  Aligned_cols=60  Identities=62%  Similarity=1.042  Sum_probs=57.9

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD   61 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~   61 (62)
                      ++|++++|+++||+.|+||+++|++|+|+|++++||+++|++.++|+|+||||||+++|+
T Consensus       200 ~~~~~~~y~l~YL~~~~Ka~~ls~~V~l~~~~~~Pl~l~y~i~~~g~l~f~lAPrie~~~  259 (259)
T TIGR00590       200 KEPVTLTFAIKYLNLFTKATPLSDRVTLSMSNDVPLVVEYKIKDMGFLRFFLAPKIEDEE  259 (259)
T ss_pred             cCceeeeeeHHHHHHhhhhccCCCeEEEEEcCCCCEEEEEEeCCCeEEEEEEcCccCCCC
Confidence            578999999999999999999999999999999999999999989999999999999885

All proteins in this family for which functions are known form sliding DNA clamps that are used in DNA replication processes. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PHA03383 PCNA-like protein; Provisional

Probab=99.87  E-value=3.4e-22  Score=136.14  Aligned_cols=57  Identities=25%  Similarity=0.595  Sum_probs=54.4

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE   58 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie   58 (62)
                      ++|++++|+++||++|+||+++|++|+|+|++|+||+++|+++++|+++||||||+.
T Consensus       206 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~i~l~~d~Pl~ley~i~~~G~l~fyLAPri~  262 (262)
T PHA03383        206 SPDYTGKFSLKYLTSFTKASGMSSSVEIYLKESNPLILKYNVGSLGNLKFVIAPKVS  262 (262)
T ss_pred             CCceEEEEeHHHHHHhhccccCCCeEEEEEcCCCCEEEEEEeCCCcEEEEEEccccC
Confidence            367899999999999999999999999999999999999999999999999999984

>KOG1636|consensus

Probab=99.87  E-value=1.7e-22  Score=136.98  Aligned_cols=61  Identities=62%  Similarity=1.111  Sum_probs=59.0

Q ss_pred             CCCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCC
Q psy5572           1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD   61 (62)
Q Consensus         1 ~~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~   61 (62)
                      |++|++.+|+++|||.|+||++||++|+|+++++.|+.++|.+.+.|+++||||||++++|
T Consensus       199 ~~~pVtltfa~kYln~ftKatpLs~rV~lsls~~~P~~vey~i~~~g~lr~YLAPKieD~e  259 (260)
T KOG1636|consen  199 MNEPVTLTFALKYLNQFTKATPLSDRVTLSLSSEVPVVVEYKIEDMGHLRYYLAPKIEDEE  259 (260)
T ss_pred             ecCcchhhhHHHHHHHhhccccccceEEEEecCCCcEEEEEecccCceEEEEEccccCCCC
Confidence            5799999999999999999999999999999999999999999999999999999999776

>PRK01115 DNA polymerase sliding clamp; Validated

Probab=99.50  E-value=1.2e-13  Score=91.31  Aligned_cols=57  Identities=37%  Similarity=0.693  Sum_probs=54.2

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE   58 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie   58 (62)
                      +++++..|+.+||.++.|+.+.+++|+|+|+++.|++++|.+.++|++.||||||++
T Consensus       191 ~e~~~i~fn~~YL~d~lk~~~~~~~V~l~~~~~~P~~l~~~~~~~~~~~~~i~P~~~  247 (247)
T PRK01115        191 EEPAKSSYSLDYLKDMVKATSASDEVTIEFGSDMPLKLEFEIAGGGKVTYLLAPRIE  247 (247)
T ss_pred             cCceeEEEhHHHHHHhhccccCCCeEEEEECCCCCEEEEEEeCCCeEEEEEEecccC
Confidence            367899999999999999999999999999999999999999999999999999986

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

Probab=99.30  E-value=1.4e-11  Score=80.02  Aligned_cols=57  Identities=58%  Similarity=0.942  Sum_probs=54.3

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE   58 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie   58 (62)
                      .++++..|+.+||.++.|+..++++|+|++..+.|+.++|.+.+.|.+.|||||+++
T Consensus       192 ~~~~~~~fn~~yL~~~l~~~~~s~~v~i~~~~~~p~~i~~~~~~~~~~~f~lap~~~  248 (248)
T cd00577         192 SEPVSSTYSLKYLKDFTKAAPLSDKVTLSFGSDGPLSLEFKIADGGHLTFYLAPKIE  248 (248)
T ss_pred             CCceEEEEhHHHHHHHhhhcccCCeEEEEEcCCCCEEEEEEcCCCcEEEEEEccccC
Confidence            478899999999999999999999999999999999999999889999999999975

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].

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

Probab=98.12  E-value=2.4e-07  Score=65.37  Aligned_cols=57  Identities=28%  Similarity=0.284  Sum_probs=51.7

Q ss_pred             CceeeEEehHHHHhhhcccCCCc-eEEEEeeCCCcEEEEEEeCCC-----eEEEEEEeecCCC
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSN-QVCLSMSLDVPLVVEFKIDDI-----GHIRYYLAPKIES   59 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~-~V~l~l~~~~Pl~l~~~l~~~-----g~l~~~lAPrie~   59 (62)
                      ++++..|++.|++.+.+...+++ +|+|+++++.|.++++++..+     |++.|++||++|.
T Consensus       263 ~al~r~~~l~~~~~~~~~~~~~~~~v~i~~~~~~~g~~~eei~~~~~g~~~~I~fn~~ylld~  325 (364)
T COG0592         263 EALKRVYSLSYLKDRGKKLSLADGEVKLSLGNDEPGKAEEEIDVGYTGEELKIGFNLAYLLDV  325 (364)
T ss_pred             HHHHHHHHHHhcccCceEEEeeCCeEEEEecCCCccceEEEEEeccCCceEEEEECHHHHHHH
Confidence            45567899999999999999999 999999999999999999864     8999999999974

>cd00140 beta_clamp Beta clamp domain

Probab=97.77  E-value=9.2e-05  Score=50.59  Aligned_cols=51  Identities=27%  Similarity=0.419  Sum_probs=44.8

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEeec
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAPK   56 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAPr   56 (62)
                      ++.+..|+.+||.++.|+.+ +++|+|.++.+ .|+.+++.-  ++...|+|+|.
T Consensus       313 ~~~~i~~~~~yL~d~lk~~~-~~~v~i~~~~~~~p~~i~~~~--~~~~~~limP~  364 (365)
T cd00140         313 EELEIGFNPKYLLDALKAID-SEEVRLSFTDSNSPVLITPED--DDNFLYLIMPV  364 (365)
T ss_pred             CcEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEEcCC--CCcEEEEEEeC
Confidence            46788999999999999987 68999999998 899998864  57899999993

The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric ring formed by PCNA (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.

>PRK05643 DNA polymerase III subunit beta; Validated

Probab=97.46  E-value=0.00059  Score=47.28  Aligned_cols=50  Identities=30%  Similarity=0.495  Sum_probs=44.1

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      ++.+..|..+||.++.|+.. +++|+|.|++. .|+.++.  .+++...|+|+|
T Consensus       314 ~~~~i~~n~~yL~d~l~~~~-~~~v~i~~~~~~~p~~i~~--~~~~~~~~limP  364 (367)
T PRK05643        314 EELEIGFNVKYLLDVLKALD-SEEVRLSFNDANSPFLIRP--PDDDSFLYVIMP  364 (367)
T ss_pred             CcEEEEEcHHHHHHHHhcCC-CCEEEEEECCCCCCEEEEc--CCCCceEEEEEe
Confidence            46788999999999999988 88999999996 7999988  456779999999

>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

Probab=96.24  E-value=0.036  Score=33.04  Aligned_cols=50  Identities=28%  Similarity=0.546  Sum_probs=37.8

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      ++.+-.|..+||.+..|+.. +++|+|+|.... |+.++=  .++....|+|-|
T Consensus        69 ~~~~i~fN~~yL~d~L~~~~-~~~V~l~~~~~~~p~~i~~--~~d~~~~~liMP  119 (121)
T PF02768_consen   69 EPLEIAFNPKYLLDALKAID-GEEVTLEFSDPSSPILITP--EEDPDFKYLIMP  119 (121)
T ss_dssp             S-EEEEEEHHHHHHHHHCC--SSEEEEEESSTTS-EEEEE--TTSSCEEEEE--
T ss_pred             CceEEEECHHHHHHHHhhcC-CCEEEEEEcCCCCCEEEEe--CCCCceEEEEEe
Confidence            57788999999999999987 789999999888 987654  345667888877

This is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication from an RNA primer, nucleotide triphosphate (dNTP) residues being added to the 5'-end of the growing DNA chain.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 3P16_A 3RB9_B 2AVT_B 2XUR_B 3Q4K_A 3BEP_A 3D1G_A 1UNN_B 3Q4J_D 2POL_A ....

>PRK14947 DNA polymerase III subunit beta; Provisional

Probab=95.11  E-value=0.12  Score=36.84  Aligned_cols=55  Identities=16%  Similarity=0.222  Sum_probs=42.8

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee-cCCCC
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP-KIESD   60 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP-rie~e   60 (62)
                      ++.+-.|..+||.++.++.. +++|.|+|.+. .|+.++ ..+ +....|.|-| |+.++
T Consensus       320 e~~~I~fN~~YL~d~L~~i~-~~~i~l~~~~~~~p~~i~-~~~-~~~~~~lIMPvr~~~~  376 (384)
T PRK14947        320 DIKKIAFPTKNLIEILGHFQ-SDKITLTLTGAEGPCGIT-GED-DPDYLVIVMPMKIVEE  376 (384)
T ss_pred             CcEEEEECHHHHHHHHhcCC-CCeEEEEECCCCCCEEEE-cCC-CCceEEEEeceEECCC
Confidence            46788999999999999986 68999999886 599886 332 3345688988 66544

>PRK14940 DNA polymerase III subunit beta; Provisional

Probab=93.99  E-value=0.35  Score=34.09  Aligned_cols=50  Identities=14%  Similarity=0.094  Sum_probs=40.1

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      ++.+-.|..+||.+..|+.. +++|+|+|.+.. |+.++=.  ++....|.|-|
T Consensus       313 e~~~I~fN~~yl~d~L~~i~-~~~v~l~~~~~~~p~~i~~~--~~~~~~~liMP  363 (367)
T PRK14940        313 EEEVIALNYLYLEEPLKVFT-SKEVQVEFTEAAKAITLRPV--PETDCFHIIMP  363 (367)
T ss_pred             CcEEEEECHHHHHHHHhCCC-CCEEEEEECCCCCCEEEEeC--CCCcEEEEEEe
Confidence            56788999999999999986 689999998865 9987542  33456688887

>KOG3194|consensus

Probab=93.82  E-value=0.22  Score=34.93  Aligned_cols=54  Identities=24%  Similarity=0.320  Sum_probs=47.5

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCC-Ce---EEEEEEeec
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDD-IG---HIRYYLAPK   56 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~-~g---~l~~~lAPr   56 (62)
                      +++..+|-+.-+..++||..++..|.|++.+.=-|-+.|-+.+ .|   .+.|+.-|-
T Consensus       214 ~ev~~sy~fSli~~~tkAl~lasKv~lR~DerGvLS~qimi~~~dg~itfiefc~vp~  271 (279)
T KOG3194|consen  214 DEVIGSYDFSLIDKITKALKLASKVLLRMDERGVLSVQIMIQTDDGIITFIEFCMVPI  271 (279)
T ss_pred             hhhhceEeehhhHHHHHHHhhhheEEEEEcCCcEEEEEEEEecCCceEEEEEEEEeec
Confidence            4567789999999999999999999999999999999999863 45   678999993

>PRK14945 DNA polymerase III subunit beta; Provisional

Probab=93.46  E-value=0.42  Score=33.38  Aligned_cols=49  Identities=22%  Similarity=0.255  Sum_probs=38.2

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      ++.+-.|+.+||.++.|+..  ++|+|+|... .|+.++=  .++....|.|-|
T Consensus       310 ~~~~i~fN~~yl~d~L~~~~--~~v~l~~~~~~~p~~i~~--~~~~~~~~limP  359 (362)
T PRK14945        310 PAMALAYNARYLLDALAPIE--GDARLGFSGPTSPSVLRS--VDDPGYLAVVVP  359 (362)
T ss_pred             CCEEEEECHHHHHHHHHhCC--CcEEEEECCCCCCEEEEe--CCCCcEEEEEEe
Confidence            47899999999999999887  4699999875 4988743  223446777777

>smart00480 POL3Bc DNA polymerase III beta subunit

Probab=92.97  E-value=0.29  Score=33.79  Aligned_cols=37  Identities=27%  Similarity=0.490  Sum_probs=32.9

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEE
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVE   40 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~   40 (62)
                      ++.+-.|..+||.++.|+.. ++.|+|.|.+.. |+.++
T Consensus       296 ~~~~i~fN~~yL~d~l~~~~-~~~v~l~~~~~~~p~~i~  333 (345)
T smart00480      296 EDLEIAFNPKYLLDALKALK-SEEIELKFTDSSSPFLIS  333 (345)
T ss_pred             CcEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEE
Confidence            56788999999999999986 689999999977 99885

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

Probab=92.76  E-value=1  Score=30.98  Aligned_cols=51  Identities=24%  Similarity=0.359  Sum_probs=42.4

Q ss_pred             ceeeEEehHHHHhhhcccCCC-ceEEEEeeCCCcEEEEEEeCCCeEEEEEEe
Q psy5572           4 PVSLNFACRYLLNFAKAAPLS-NQVCLSMSLDVPLVVEFKIDDIGHIRYYLA   54 (62)
Q Consensus         4 ~~~~~ysl~YL~~~~Ka~~ls-~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lA   54 (62)
                      .++....++-+..+.+...++ +.|.+.+..+.-+.+-.-+++.|.|.|||-
T Consensus       238 ~~sV~Vd~K~~~~~l~~~~~~p~~vi~~I~~~~~~vl~~~~~~~~~l~yyip  289 (292)
T PF04005_consen  238 FASVRVDIKDLAKFLKSHQLSPSRVICCICHNKALVLHVYLDEDVSLTYYIP  289 (292)
T ss_dssp             -EEEEEEHHHHHHHHHH--S--SEEEEEEETTTEEEEEEEE-TTEEEEEEEE
T ss_pred             EEEEEEEHHHHHHhhCccccCCCEEEEEEccCCeEEEEEEEcCCEEEEEEEe
Confidence            467788899999999988887 999999999999999999988999999984

These proteins are known to form a stable complex in vivo []. Hus1-Rad1-Rad9 complex may form a PCNA-like ring structure, and could function as a sliding clamp during checkpoint control.; PDB: 3A1J_B 3G65_C 3GGR_B.

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

Probab=92.05  E-value=2.1  Score=27.45  Aligned_cols=46  Identities=26%  Similarity=0.259  Sum_probs=37.9

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeE
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGH   48 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~   48 (62)
                      ++.+...+++.|..+.|...-.+.|+|+++.+.|+.+.+.....|.
T Consensus        61 ~~~~~~i~~k~l~~~lk~~~~~~~v~i~~~~~~~l~i~~~~~~~~~  106 (248)
T cd00577          61 EEISLGVNLKSLLKILKCAGNEDCVTLRADDEDPLKILFESSKGDV  106 (248)
T ss_pred             CceEEEEEHHHHHHHHhhCCCCCEEEEEecCCCeEEEEEEcCCCce
Confidence            3457788899999999998888999999998888988888654333

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].

>PRK14941 DNA polymerase III subunit beta; Provisional

Probab=91.78  E-value=0.85  Score=32.21  Aligned_cols=52  Identities=10%  Similarity=0.278  Sum_probs=40.6

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEE-eCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFK-IDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~-l~~~g~l~~~lAP   55 (62)
                      ++.+-.|..+||.++.|+.. +++|.|+|.+.. |+.++=. -.++....|.|-|
T Consensus       316 ~~~~I~fN~~yl~d~L~~~~-~~~v~l~~~~~~~p~~i~~~~~~~~~~~~~limP  369 (374)
T PRK14941        316 EDITIGFNSKFIEAALAHLD-EEEIIIELSSPTTAVIFKPKKEEENDDLIILVMP  369 (374)
T ss_pred             CcEEEEEcHHHHHHHHhcCC-CCEEEEEECCCCCCEEEecCCCCCCCceEEEEee
Confidence            56788999999999999986 689999998865 9888621 1134457888888

>PRK14942 DNA polymerase III subunit beta; Provisional

Probab=90.66  E-value=1.5  Score=31.16  Aligned_cols=50  Identities=18%  Similarity=0.377  Sum_probs=39.5

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      ++.+-.|..+||.+..++.. +++|.|+|.+.. |+.++ . .++....|.|-|
T Consensus       320 ~~~~I~fN~~ylld~L~~i~-~~~v~l~~~~~~~P~~i~-~-~~~~~~~~liMP  370 (373)
T PRK14942        320 EEITIAFKGEYLMDIFRSID-DNEVKIEFSDSSSPVIFK-D-PSDPEFISVIMP  370 (373)
T ss_pred             CcEEEEECHHHHHHHHhcCC-CCeEEEEECCCCCCEEEE-e-CCCCceEEEEee
Confidence            56788999999999999986 789999998855 98774 2 234556788877

>PRK14943 DNA polymerase III subunit beta; Provisional

Probab=90.60  E-value=1.4  Score=30.85  Aligned_cols=48  Identities=15%  Similarity=0.207  Sum_probs=38.4

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      ++.+-.|..+||.+..|+.. +++|+|+|... .|+.+.=   +. ...|.|-|
T Consensus       322 ~~~~i~fN~~yl~d~l~~~~-~~~v~l~~~~~~~p~~i~~---~~-~~~~limP  370 (374)
T PRK14943        322 PELQVAFNPDFFMAPLKALT-KDEVFFELKDEMSPGVFKT---LD-EFLCVIMP  370 (374)
T ss_pred             CcEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEec---CC-CeEEEEEe
Confidence            56788999999999999986 68999999884 5998872   22 34677777

>PRK06673 DNA polymerase III subunit beta; Validated

Probab=90.55  E-value=1.5  Score=31.07  Aligned_cols=49  Identities=22%  Similarity=0.399  Sum_probs=39.1

Q ss_pred             ceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee
Q psy5572           4 PVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         4 ~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      +.+-.|..+||.++.|+.. +++|+|+|.+. .|+.++=  .++....|.+-|
T Consensus       323 ~~~I~fN~~YLld~L~~i~-~e~v~l~~~~~~~p~li~~--~~~~~~~~limP  372 (376)
T PRK06673        323 QLNISFDGRFMLDALRAIK-EETVTLSFSGSMRPILIEA--GTQSAAIHLISP  372 (376)
T ss_pred             cEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEEc--CCCCceEEEEEe
Confidence            6788999999999999986 78999999876 5987753  233446788887

>TIGR00663 dnan DNA polymerase III, beta subunit

Probab=90.02  E-value=1.9  Score=29.93  Aligned_cols=50  Identities=28%  Similarity=0.511  Sum_probs=38.4

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      ++.+-.|..+||.++.|+.. +++|+|.+.+.. |+.+.=  .++....|.|-|
T Consensus       314 ~~~~i~fN~~yL~d~l~~~~-~~~v~l~~~~~~~p~~i~~--~~~~~~~~limP  364 (367)
T TIGR00663       314 EDLVIAFNIKYLLDALKALK-SKEIQIQFNDPSKPLLIEP--ENDEKITYLIMP  364 (367)
T ss_pred             CcEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEec--CCCCcEEEEEEe
Confidence            46677899999999999975 589999998755 987632  233446788888

University).

>PRK14944 DNA polymerase III subunit beta; Provisional

Probab=89.59  E-value=2.1  Score=30.47  Aligned_cols=50  Identities=14%  Similarity=0.356  Sum_probs=38.5

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      ++.+-.|..+||.++.|+.. +++|+|.|.+.. |+.++= . ++....|.|-|
T Consensus       322 e~~~I~fN~~YL~d~L~~i~-~~~v~i~~~~~~~p~~i~~-~-~~~~~~~lImP  372 (375)
T PRK14944        322 NSFEIAFNAKYLEDILKVLS-VKEIVFYFDSPLKPFIVTT-L-EKDSSIHLILP  372 (375)
T ss_pred             CcEEEEEcHHHHHHHHhcCC-CCEEEEEECCCCCCEEEEc-C-CCCceEEEEEe
Confidence            57888999999999999986 689999998765 987742 2 22345677776

>PRK07761 DNA polymerase III subunit beta; Validated

Probab=88.58  E-value=2.4  Score=29.79  Aligned_cols=52  Identities=25%  Similarity=0.402  Sum_probs=40.2

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCC----CeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDD----IGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~----~g~l~~~lAP   55 (62)
                      ++.+-.|..+||.+..|+.. +++|+|.|.+.. |+.++=.-.+    +....|.|-|
T Consensus       315 e~~~i~fN~~yl~d~L~~~~-~~~v~l~~~~~~~p~~i~~~~~~~~~~~~~~~~limP  371 (376)
T PRK07761        315 EDLTIAFNPQYLLDGLSALH-TPRVRFGFTTPSKPALLTGQPEDDGEPSTDYRYLLMP  371 (376)
T ss_pred             CcEEEEECHHHHHHHHhcCC-CCeEEEEECCCCCCEEEecCcccccCCCCceEEEEEe
Confidence            56788999999999999987 689999999864 9977522111    1357888888

>PRK14946 DNA polymerase III subunit beta; Provisional

Probab=88.43  E-value=2.2  Score=30.36  Aligned_cols=48  Identities=10%  Similarity=0.142  Sum_probs=36.3

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEe
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLA   54 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lA   54 (62)
                      ++.+-.|..+||.++.|+..  ++|.|.|.+.. |+.++  =.++....|.+|
T Consensus       314 e~~~IafN~~YL~D~L~~i~--~~v~l~~~~~~~p~~i~--~~~~~~~~~li~  362 (366)
T PRK14946        314 ELAQVNVNYKYLKDAISVFD--KVINIFINEKKTKMLIV--SPEKKEICQLVG  362 (366)
T ss_pred             CcEEEEEcHHHHHHHHHhCC--CeEEEEECCCCCCEEEE--CCCCCCeEEEEE
Confidence            57788999999999999998  56999998764 98763  123344566665

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

Probab=86.33  E-value=4.1  Score=27.07  Aligned_cols=54  Identities=20%  Similarity=0.316  Sum_probs=38.2

Q ss_pred             CCceeeEEehHHHHhhhc-ccCCCceEEEEe-eCCCcEEEEEEeCCCeEEEEEEee
Q psy5572           2 QEPVSLNFACRYLLNFAK-AAPLSNQVCLSM-SLDVPLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~K-a~~ls~~V~l~l-~~~~Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      .+++.-.|+++=++.|.. |-.++..|.+.| ..+.|+.+++.=.++=...|.||-
T Consensus       196 ~~~~~itF~lKefka~l~~ae~~~~~i~~~f~~pG~Pi~~~~~~~~~~~~~~vlaT  251 (252)
T PF04139_consen  196 QEDTDITFSLKEFKAILSFAESLSLPISIYFDNPGRPILFELEQNDHFEAEFVLAT  251 (252)
T ss_dssp             -TT-EEEEEHHHHHHHHHHHHHTTEEEEEEESSTTS-EEEEEE--SSEEEEEEE--
T ss_pred             CCCCEEEEEeHHHHHHHHHHHhcCCcEEEEECCCCCcEEEEECCCCcEEEEEEEEc
Confidence            345778999999998886 445678999999 678899999994355578888873

; GO: 0006281 DNA repair; PDB: 3GGR_A 3G65_A 3A1J_A.

>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 []

Probab=85.62  E-value=6.2  Score=24.15  Aligned_cols=49  Identities=18%  Similarity=0.246  Sum_probs=39.0

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEE
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIR   50 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~   50 (62)
                      +++.+-..+++.|..+.|.+.-.+.++|+..++. =+.+.|+-...+.++
T Consensus        63 d~~~~igvnl~~l~kiLk~~~~~D~l~l~~~~~~~~l~i~~~~~~~~~~~  112 (127)
T PF00705_consen   63 DKELSIGVNLSDLKKILKRAKKDDSLELESDEEPDKLNIVFENEKKGRVR  112 (127)
T ss_dssp             SSSEEEEEEHHHHHHHHTTSSTTSEEEEEEESSSSEEEEEEEETTSSEEE
T ss_pred             CCCEEEEEEHHHHHHHHhhccCCCEEEEEEeCCCCEEEEEEEcCCCCeEE
Confidence            4577888999999999999999999999987664 244677777667654

It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNA replication []. The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes []. In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta. Homologues of PCNA have also been identified in the archaea (Euryarchaeota and Crenarchaeota) and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses. ; GO: 0003677 DNA binding, 0030337 DNA polymerase processivity factor activity, 0006275 regulation of DNA replication, 0043626 PCNA complex; PDB: 1U76_E 2ZVK_B 1VYJ_A 1UL1_B 3P87_D 2ZVM_C 2ZVL_A 1AXC_C 3VKX_A 3TBL_B ....

>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

Probab=84.71  E-value=2.8  Score=28.66  Aligned_cols=39  Identities=23%  Similarity=0.350  Sum_probs=32.2

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEE
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEF   41 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~   41 (62)
                      +++.+.|....|....||.++|..|.|++..+==|.+.|
T Consensus       235 ~~~~~~Y~f~~i~~~~kAl~~ssKv~ir~d~~GlLs~Q~  273 (275)
T PF02144_consen  235 EPVISRYKFSLIKKAMKALKISSKVSIRIDENGLLSLQF  273 (275)
T ss_dssp             S-EEEEEEHHHHCCHHHHHTTSSEEEEEEESSS-EEEEE
T ss_pred             ceEEEEEeHHHHHHHHHHhhhccEEEEEeCCCcEEEEEE
Confidence            566777999999999999999999999998776666555

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.

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

Probab=83.58  E-value=6.1  Score=28.01  Aligned_cols=50  Identities=24%  Similarity=0.501  Sum_probs=40.6

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      ++.+-.|.+.|+-+..|+.+ ++.|.+.|.+.. |+.++-  .++....|.|.|
T Consensus       311 ~~~~I~fn~~ylld~l~~~~-~~~v~~~~~~~~~p~~i~~--~~~~~~~~~imP  361 (364)
T COG0592         311 EELKIGFNLAYLLDVLKALD-SEEVQFGFNDSSSPFLIRP--EENDDFKYLIMP  361 (364)
T ss_pred             ceEEEEECHHHHHHHHhcCC-CCeEEEEEcCCCCcEEEEe--CCCCCceEEEEE
Confidence            46788999999999999988 899999998766 677665  344558888888

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	62
1axc_A	261	Human Pcna Length = 261		1e-18
1axc_C	261	Human Pcna Length = 261		1e-18
2zvv_A	276	Crystal Structure Of Proliferating Cellular Nuclear		3e-16
2zvw_A	275	Crystal Structure Of Proliferating Cell Nuclear Ant		3e-15
3p91_A	265	Crystal Structure Of Proliferating Cellular Nuclear		1e-06
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		2e-06
3l0x_B	94	Structure Of Split Yeast Pcna Length = 94		2e-06
3k4x_A	798	Eukaryotic Sliding Clamp Pcna Bound To Dna Length =		2e-06
3gpm_A	258	Structure Of The Trimeric Form Of The E113g Pcna Mu		3e-06
3v60_B	258	Structure Of S. Cerevisiae Pcna Conjugated To Sumo		3e-06
2od8_A	258	Structure Of A Peptide Derived From Cdc9 Bound To P		3e-06
3f1w_A	258	Crystal Structure Of A Mutant Proliferating Cell Nu		3e-06
3pge_A	200	Structure Of Sumoylated Pcna Length = 200		4e-06
1sxj_F	283	Crystal Structure Of The Eukaryotic Clamp Loader (R		3e-05

>pdb|1AXC|A Chain A, Human Pcna Length = 261

Iteration: 1
 Score = 87.8 bits (216), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 41/62 (66%), Positives = 48/62 (77%)
Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M EPV L FA RYL  F KA PLS+ V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct: 199 MNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258
Query: 61  DN 62
           + 
Sbjct: 259 EG 260

>pdb|1AXC|C Chain C, Human Pcna Length = 261

Iteration: 1
 Score = 87.8 bits (216), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 41/62 (66%), Positives = 48/62 (77%)
Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M EPV L FA RYL  F KA PLS+ V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct: 199 MNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258
Query: 61  DN 62
           + 
Sbjct: 259 EG 260

>pdb|2ZVV|A Chain A, Crystal Structure Of Proliferating Cellular Nuclear Antigen 1 And Short Peptide From Human P21 Length = 276

Iteration: 1
 Score = 79.7 bits (195), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 35/58 (60%), Positives = 50/58 (86%)
Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58
           M+EPVSL+FA RY+ +F KA PLS+ V +S+S ++P+VVE+K+ ++G+IRYYLAPKIE
Sbjct: 219 MKEPVSLSFALRYMNSFTKATPLSDTVTISLSSELPVVVEYKVAEMGYIRYYLAPKIE 276

>pdb|2ZVW|A Chain A, Crystal Structure Of Proliferating Cell Nuclear Antigen 2 And Short Peptide From Human P21 Length = 275

Iteration: 1
 Score = 77.0 bits (188), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 34/57 (59%), Positives = 47/57 (82%)
Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKI 57
           M EPVSL+FA RY+ +F KA PLS  V +S+S ++P+VVE+K+ ++G+IRYYLAPKI
Sbjct: 219 MNEPVSLSFALRYMNSFTKATPLSETVTISLSSELPVVVEYKVAEMGYIRYYLAPKI 275

>pdb|3P91|A Chain A, Crystal Structure Of Proliferating Cellular Nuclear Antigen From Entamoeba Histolytica Length = 265

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 24/57 (42%), Positives = 40/57 (70%), Gaps = 1/57 (1%)
Query: 5   VSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD 61
           V+ +FA + +  FAK+APL++ V LS+S   PL++EFK  +   +++YLAPK + +D
Sbjct: 206 VTASFALKQISEFAKSAPLADNVKLSLSGQAPLIMEFK-GEACVLKFYLAPKFDEED 261

>pdb|3L0W|B Chain B, Structure Of Split Monoubiquitinated Pcna With Ubiquitin In Position Two Length = 169

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 56
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK
Sbjct: 113 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPK 167

>pdb|3L0X|B Chain B, Structure Of Split Yeast Pcna Length = 94

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 1  MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
          M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK   +
Sbjct: 35 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPKFNDE 93
Query: 61 D 61
          +
Sbjct: 94 E 94

>pdb|3K4X|A Chain A, Eukaryotic Sliding Clamp Pcna Bound To Dna Length = 798

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 56
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK
Sbjct: 205 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPK 259

>pdb|3GPM|A Chain A, Structure Of The Trimeric Form Of The E113g Pcna Mutant Protein Length = 258

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 56
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK
Sbjct: 199 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPK 253

>pdb|3V60|B Chain B, Structure Of S. Cerevisiae Pcna Conjugated To Sumo On Lysine 164 Length = 258

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 56
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK
Sbjct: 199 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPK 253

>pdb|2OD8|A Chain A, Structure Of A Peptide Derived From Cdc9 Bound To Pcna Length = 258

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 56
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK
Sbjct: 199 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPK 253

>pdb|3F1W|A Chain A, Crystal Structure Of A Mutant Proliferating Cell Nuclear Antigen That Blocks Translesion Synthesis Length = 258

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 56
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK
Sbjct: 199 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPK 253

>pdb|3PGE|A Chain A, Structure Of Sumoylated Pcna Length = 200

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 20/61 (32%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK   +
Sbjct: 141 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPKFNDE 199
Query: 61  D 61
           +
Sbjct: 200 E 200

>pdb|1SXJ|F Chain F, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 283

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 19/59 (32%), Positives = 37/59 (62%), Gaps = 1/59 (1%)
Query: 3   EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD 61
           +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK   ++
Sbjct: 226 QPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPKFNDEE 283

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	62
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	1e-23
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	6e-23
1u7b_A	261	PCNA, cyclin, proliferating cell nuclear antigen;	1e-19
3lx2_A	259	DNA polymerase sliding clamp 2; PCNA, DNA processi	1e-19
1plq_A	258	Proliferating cell nuclear antigen (PCNA); DNA-bin	4e-18
2zvv_A	276	PCNA 1, proliferating cellular nuclear antigen 1;	8e-18
3aiz_C	246	DNA polymerase sliding clamp C; protein-protein co	2e-17
3aiz_A	248	DNA polymerase sliding clamp B; protein-protein co	2e-17
3k4x_A	798	PCNA, proliferating cell nuclear antigen; DNA repl	2e-17
3k4x_A	798	PCNA, proliferating cell nuclear antigen; DNA repl	4e-14
3k4x_A	798	PCNA, proliferating cell nuclear antigen; DNA repl	4e-14
3p91_A	265	Proliferating cell nuclear antigen; DNA binding pr	4e-17
1iz5_A	249	Proliferating cell nuclear antigen; DNA, replicati	6e-17
2ijx_A	244	DNA polymerase sliding clamp A; PCNA3 subunit, pro	7e-17
3ifv_A	247	PCNA; processivity factor, sliding clamp, halophil	9e-17
1ud9_A	245	DNA polymerase sliding clamp A; DNA-binding, DNA r	1e-16
3fds_C	249	DNA polymerase sliding clamp B; protein-protein co	2e-16
1rwz_A	245	DNA polymerase sliding clamp; torus, processivity	4e-16
3fds_D	245	DNA polymerase sliding clamp C; protein-protein co	1e-15
3a1j_C	263	Cell cycle checkpoint protein RAD1; DNA damage, DN	1e-07

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B Length = 169

 Score = 85.8 bits (212), Expect = 1e-23
 Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 1/58 (1%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK  
Sbjct: 113 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPKFN 169

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae} Length = 200

 Score = 85.0 bits (209), Expect = 6e-23
 Identities = 20/61 (32%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK   +
Sbjct: 141 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPKFNDE 199

Query: 61  D 61
           +
Sbjct: 200 E 200

>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* Length = 261

 Score = 77.7 bits (190), Expect = 1e-19
 Identities = 41/61 (67%), Positives = 48/61 (78%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M EPV L FA RYL  F KA PLS+ V LSMS DVPLVVE+KI D+GH++YYLAPKIE +
Sbjct: 199 MNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDE 258

Query: 61  D 61
           +
Sbjct: 259 E 259

>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} Length = 259

 Score = 77.7 bits (190), Expect = 1e-19
 Identities = 11/61 (18%), Positives = 30/61 (49%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
                   +   YL +  ++   +++V +    D+PL++++ + D G + + +AP++E  
Sbjct: 192 KMTKAKSAYGVAYLEDILRSLADADEVIIRFGFDIPLLLKYMVRDAGEVSFLIAPRVEEG 251

Query: 61  D 61
            
Sbjct: 252 R 252

>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 Length = 258

 Score = 73.4 bits (179), Expect = 4e-18
 Identities = 20/61 (32%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK   +
Sbjct: 199 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPKFNDE 257

Query: 61  D 61
           +
Sbjct: 258 E 258

>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 Length = 276

 Score = 73.1 bits (178), Expect = 8e-18
 Identities = 35/58 (60%), Positives = 50/58 (86%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58
           M+EPVSL+FA RY+ +F KA PLS+ V +S+S ++P+VVE+K+ ++G+IRYYLAPKIE
Sbjct: 219 MKEPVSLSFALRYMNSFTKATPLSDTVTISLSSELPVVVEYKVAEMGYIRYYLAPKIE 276

>3aiz_C DNA polymerase sliding clamp C; protein-protein complex, replication; HET: DNA; 2.80A {Sulfolobus tokodaii} PDB: 3aix_A* Length = 246

 Score = 71.5 bits (174), Expect = 2e-17
 Identities = 12/58 (20%), Positives = 27/58 (46%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58
                   +   Y++N +K    S+ V ++    +PL + + +   G+  +Y+AP+ E
Sbjct: 189 EGGDAESVYGLEYVVNTSKMRKPSDTVEIAFGSQIPLKLRYNLPQGGYADFYIAPRAE 246

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

 Score = 71.5 bits (174), Expect = 2e-17
 Identities = 11/57 (19%), Positives = 28/57 (49%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKI 57
           ++ P    ++   L +  K   +S  V +    ++P+ +E   D  G + +++AP++
Sbjct: 192 VESPSKAVYSIEVLKDVFKVTSISQNVTVGFGNNIPMKIEVPTDSGGQLIFWIAPRL 248

>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae} Length = 798

 Score = 72.7 bits (177), Expect = 2e-17
 Identities = 20/61 (32%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK   +
Sbjct: 739 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPKFNDE 797

Query: 61  D 61
           +
Sbjct: 798 E 798

>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae} Length = 798

 Score = 63.5 bits (153), Expect = 4e-14
 Identities = 20/62 (32%), Positives = 38/62 (61%), Gaps = 1/62 (1%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK   +
Sbjct: 472 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPKFNDE 530

Query: 61  DN 62
            +
Sbjct: 531 GS 532

>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae} Length = 798

 Score = 63.5 bits (153), Expect = 4e-14
 Identities = 20/62 (32%), Positives = 38/62 (61%), Gaps = 1/62 (1%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK   +
Sbjct: 205 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPKFNDE 263

Query: 61  DN 62
            +
Sbjct: 264 GS 265

>3p91_A Proliferating cell nuclear antigen; DNA binding protein, DNA replication, processivity, sliding; 2.40A {Entamoeba histolytica} Length = 265

 Score = 71.2 bits (173), Expect = 4e-17
 Identities = 24/61 (39%), Positives = 41/61 (67%), Gaps = 1/61 (1%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
             + V+ +FA + +  FAK+APL++ V LS+S   PL++EFK +    +++YLAPK + +
Sbjct: 202 HNKDVTASFALKQISEFAKSAPLADNVKLSLSGQAPLIMEFKGEA-CVLKFYLAPKFDEE 260

Query: 61  D 61
           D
Sbjct: 261 D 261

>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

 Score = 70.4 bits (171), Expect = 6e-17
 Identities = 15/58 (25%), Positives = 31/58 (53%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58
           +QE     +   YL +  K    +++V +    ++P+ +E+ I D G + + LAP++E
Sbjct: 191 VQEETKSAYGVSYLSDMVKGLGKADEVTIKFGNEMPMQMEYYIRDEGRLTFLLAPRVE 248

>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* Length = 244

 Score = 70.0 bits (170), Expect = 7e-17
 Identities = 15/57 (26%), Positives = 27/57 (47%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKI 57
             +    +++  YL +      LS+ V +S     PL + F ++  G + Y LAPK+
Sbjct: 188 FSKESKNSYSAEYLDDVLSLTKLSDYVKISFGNQKPLQLFFNMEGGGKVTYLLAPKV 244

>3ifv_A PCNA; processivity factor, sliding clamp, halophilic, replication; 2.00A {Haloferax volcanii} PDB: 3hi8_A Length = 247

 Score = 69.9 bits (170), Expect = 9e-17
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 3   EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKI-DDIGHIRYYLAPKIESD 60
                 F+  YL +  KA P   +V + +  + P+ + ++I + +G I Y LAP+I+SD
Sbjct: 189 GAADSLFSLDYLKDMNKAIPTDAEVTVELGEEFPVKLHYQIAEGMGTITYMLAPRIQSD 247

>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 Length = 245

 Score = 69.3 bits (168), Expect = 1e-16
 Identities = 15/57 (26%), Positives = 28/57 (49%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKI 57
             +  S  +   YL +      LS+ V ++ +   P+ +EF ++  G + Y LAPK+
Sbjct: 188 FNKESSSAYDVEYLNDIISLTKLSDYVKVAFADQKPMQLEFNMEGGGKVTYLLAPKL 244

>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

 Score = 69.0 bits (168), Expect = 2e-16
 Identities = 9/58 (15%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 1   MQEPVSLNFACRYLLNFAKAA-PLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKI 57
           +    S +++     +  K     S    +S   ++P+ ++ +    GH+ +++AP++
Sbjct: 192 IDTSASSSYSAEMFKDAVKGLRGFSAPTMVSFGENLPMKIDVEAVSGGHMIFWIAPRL 249

>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* Length = 245

 Score = 68.1 bits (165), Expect = 4e-16
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKI-DDIGHIRYYLAPKIES 59
                   F+  YL  F K A   + + + +  + P+ + F++      + Y LAP+IES
Sbjct: 185 NGGEARSMFSVDYLKEFCKVAGSGDLLTIHLGTNYPVRLVFELVGGRAKVEYILAPRIES 244

Query: 60  D 60
           +
Sbjct: 245 E 245

>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* Length = 245

 Score = 66.9 bits (162), Expect = 1e-15
 Identities = 15/56 (26%), Positives = 27/56 (48%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 56
               VS ++   Y+ N  K    S+ + L     +PL + FK+   G+  +Y+AP+
Sbjct: 189 SGADVSSSYGMEYVANTTKMRRASDSMELYFGSQIPLKLRFKLPQEGYGDFYIAPR 244

>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

 Score = 44.9 bits (106), Expect = 1e-07
 Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 4/58 (6%)

Query: 2   QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKID----DIGHIRYYLAP 55
            +     +    L    KA  LS +V +       L +++ I      I  + YY  P
Sbjct: 204 NQTQVNRYKISLLKPSTKALVLSCKVSIRTDNRGFLSLQYMIRNEDGQICFVEYYCCP 261

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	62
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	99.92
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.91
3fds_C	249	DNA polymerase sliding clamp B; protein-protein co	99.84
3p91_A	265	Proliferating cell nuclear antigen; DNA binding pr	99.84
3ifv_A	247	PCNA; processivity factor, sliding clamp, halophil	99.81
3k4x_A	798	PCNA, proliferating cell nuclear antigen; DNA repl	99.8
3k4x_A	798	PCNA, proliferating cell nuclear antigen; DNA repl	99.78
3lx2_A	259	DNA polymerase sliding clamp 2; PCNA, DNA processi	99.77
3fds_D	245	DNA polymerase sliding clamp C; protein-protein co	99.75
1plq_A	258	Proliferating cell nuclear antigen (PCNA); DNA-bin	99.69
1u7b_A	261	PCNA, cyclin, proliferating cell nuclear antigen;	99.68
3a1j_C	263	Cell cycle checkpoint protein RAD1; DNA damage, DN	99.67
2zvv_A	276	PCNA 1, proliferating cellular nuclear antigen 1;	99.61
1rwz_A	245	DNA polymerase sliding clamp; torus, processivity	99.54
1iz5_A	249	Proliferating cell nuclear antigen; DNA, replicati	99.53
3aiz_C	246	DNA polymerase sliding clamp C; protein-protein co	99.52
1ud9_A	245	DNA polymerase sliding clamp A; DNA-binding, DNA r	99.5
3aiz_A	248	DNA polymerase sliding clamp B; protein-protein co	99.49
2ijx_A	244	DNA polymerase sliding clamp A; PCNA3 subunit, pro	99.48
3a1j_B	281	HHUS1, checkpoint protein HUS1; DNA damage, DNA re	99.21
3a1j_A	266	Cell cycle checkpoint control protein RAD9A; DNA d	98.97
3g65_A	296	Cell cycle checkpoint control protein RAD9A; PCNA,	98.26
1vpk_A	378	DNA polymerase III, beta subunit; TM0262, structur	97.65
3d1g_A	366	DNA polymerase III subunit beta; chemical probe, D	97.51
2avt_A	378	DNA polymerase III beta subunit; beta clamp, slidi	97.44
3t0p_A	371	DNA polymerase III, beta subunit; DNA clamp, struc	95.58
3p16_A	408	DNA polymerase III subunit beta; DNA polymerase II	92.04
3p91_A	265	Proliferating cell nuclear antigen; DNA binding pr	90.78
1plq_A	258	Proliferating cell nuclear antigen (PCNA); DNA-bin	81.19

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

Probab=99.92  E-value=2e-25  Score=146.93  Aligned_cols=60  Identities=33%  Similarity=0.786  Sum_probs=55.2

Q ss_pred             CCCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCC
Q psy5572           1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD   61 (62)
Q Consensus         1 ~~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~   61 (62)
                      +++|++++||++||++|+||+++|++|+|+|++++||+++|+++ +|+|+|||||||++|+
T Consensus       141 ~~e~v~~~fsl~YL~~f~Ka~~ls~~V~l~l~~~~Pl~l~y~i~-~G~l~f~LAPrie~~~  200 (200)
T 3pge_A          141 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLK-SGFLQFFLAPKFNDEE  200 (200)
T ss_dssp             ESSCEEEEEEHHHHHHHGGGGGGCSEEEEEECSSSCEEEEEEET-TEEEEEEECCCCC---
T ss_pred             eCCcceeeEhHHHHHHHhccccCCCeEEEEEcCCCCEEEEEEEC-CEEEEEEECCccCCCC
Confidence            36899999999999999999999999999999999999999997 8999999999999875

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

Probab=99.91  E-value=1.4e-24  Score=138.50  Aligned_cols=57  Identities=35%  Similarity=0.793  Sum_probs=54.8

Q ss_pred             CCCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCC
Q psy5572           1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE   58 (62)
Q Consensus         1 ~~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie   58 (62)
                      +++|++++||++||++|+||+++|++|+|+|++|+||+++|+++ +|+|+||||||+|
T Consensus       113 ~~~~~~~~fsl~yl~~~~ka~~~s~~v~l~~~~~~Pl~~~~~~~-~g~~~~~lAPri~  169 (169)
T 3l0w_B          113 MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLK-SGFLQFFLAPKFN  169 (169)
T ss_dssp             ESSCEEEEEEHHHHHHHGGGGGGCSEEEEEECSSSCEEEEEEET-TEEEEEEECCCCC
T ss_pred             cCCcceEEEhHHHHHHHhccccCCCeEEEEEcCCCCEEEEEEEC-CEEEEEEEccccC
Confidence            36899999999999999999999999999999999999999997 8999999999996

>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*

Probab=99.84  E-value=2.8e-21  Score=128.62  Aligned_cols=56  Identities=16%  Similarity=0.401  Sum_probs=54.6

Q ss_pred             CCceeeEEehHHHHhhhc-ccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecC
Q psy5572           2 QEPVSLNFACRYLLNFAK-AAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKI   57 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~K-a~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPri   57 (62)
                      ++|++++|+++||++|+| |+++|++|+|+|++++||+++|.++++|+|+||||||+
T Consensus       193 ~~~~~~~fsl~yL~~~~K~a~~ls~~V~i~~~~~~Pl~l~y~i~~~G~l~f~lAPri  249 (249)
T 3fds_C          193 DTSASSSYSAEMFKDAVKGLRGFSAPTMVSFGENLPMKIDVEAVSGGHMIFWIAPRL  249 (249)
T ss_dssp             SSCCEEEEEHHHHHHHHHTTTTCCSCEEEEECTTCCEEEEEECTTSCEEEEEECCBC
T ss_pred             CCceEEEEEHHHHHHHHhhhcccCCEEEEEecCCcCEEEEEEeCCCcEEEEEEeccC
Confidence            689999999999999999 99999999999999999999999999999999999997

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

Probab=99.84  E-value=4.8e-21  Score=127.83  Aligned_cols=60  Identities=40%  Similarity=0.710  Sum_probs=53.8

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDDN   62 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~~   62 (62)
                      .++++.+|+++||++++||+++|++|+|+|+++.||+++|.+ ++|+++||||||+++||+
T Consensus       203 ~e~~~~~F~~~YL~~~~Ka~~ls~~V~i~~~~~~Pl~l~~~i-~~g~~~f~lAPri~~~~~  262 (265)
T 3p91_A          203 NKDVTASFALKQISEFAKSAPLADNVKLSLSGQAPLIMEFKG-EACVLKFYLAPKFDEEDE  262 (265)
T ss_dssp             SSCEEEEEEHHHHHHHGGGGGGCSEEEEEECSSSCEEEEEEE-TTEEEEEEECCBC-----
T ss_pred             CCcEEEEEEHHHHHHhhcccccCCEEEEEeCCCccEEEEEEE-CCEEEEEEEcCCCCCccC
Confidence            588999999999999999999999999999999999999999 889999999999998864

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

Probab=99.81  E-value=3.6e-20  Score=122.29  Aligned_cols=58  Identities=31%  Similarity=0.606  Sum_probs=52.2

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeC-CCeEEEEEEeecCCCC
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKID-DIGHIRYYLAPKIESD   60 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~-~~g~l~~~lAPrie~e   60 (62)
                      ++++.+|+++||++++||+++|++|+|+|++++||+++|.++ ++|+++||||||+|+|
T Consensus       189 e~~~~~F~~~YL~~~~Ka~~~s~~V~i~~~~~~Pl~l~~~i~~~~g~~~~~lAPri~~~  247 (247)
T 3ifv_A          189 GAADSLFSLDYLKDMNKAIPTDAEVTVELGEEFPVKLHYQIAEGMGTITYMLAPRIQSD  247 (247)
T ss_dssp             CCCEEEEEHHHHHHHHHHSCTTCEEEEEECBSSCEEEEEEEGGGTEEEEEEECCC----
T ss_pred             CeEEEEEeHHHHHHhhhhccCCCEEEEEecCCccEEEEEEEcCCcEEEEEEEeecccCC
Confidence            688999999999999999999999999999999999999998 5799999999999986

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

Probab=99.80  E-value=6.8e-20  Score=137.16  Aligned_cols=60  Identities=32%  Similarity=0.753  Sum_probs=53.0

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDDN   62 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~~   62 (62)
                      ++|++++|+++||+.|+||+++|++|+|+|++++||+++|.+ ++|+|+||||||+++||+
T Consensus       206 ~e~~~~~ysl~yL~~~~Ka~~ls~~V~l~~~~~~PL~l~y~i-~~G~l~f~lAPri~~~~~  265 (798)
T 3k4x_A          206 DQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDL-KSGFLQFFLAPKFNDEGS  265 (798)
T ss_dssp             SSCEEEEEEHHHHHHHGGGGGTCSEEEEEECSSSCEEEEEEE-TTEEEEEEECCC------
T ss_pred             CCceeEEEEHHHHHHhhcccccCCEEEEEeCCCCcEEEEEEE-CCeEEEEEEccCCCCccc
Confidence            689999999999999999999999999999999999999999 889999999999998873

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

Probab=99.78  E-value=4.5e-19  Score=132.76  Aligned_cols=59  Identities=32%  Similarity=0.776  Sum_probs=52.9

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD   61 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~   61 (62)
                      +++++.+|+++||++|+||+++|++|+|+|++++||+++|.+ ++|+|+||||||+++|+
T Consensus       740 ~e~~~~~f~l~YL~~~~Ka~~ls~~V~i~~~~~~Pl~~~y~i-~~G~i~fylAPki~~~~  798 (798)
T 3k4x_A          740 DQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDL-KSGFLQFFLAPKFNDEE  798 (798)
T ss_dssp             SSCEEEEEEHHHHHHHGGGGGTCSEEEEEECSSSCEEEEEEE-TTEEEEEEECCC-----
T ss_pred             CCceEEEEEHHHHHHHhhhccCCCeEEEEeCCCccEEEEEEE-cceEEEEEECcCCCCCC
Confidence            589999999999999999999999999999999999999999 88999999999999875

>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}

Probab=99.77  E-value=1.1e-18  Score=115.73  Aligned_cols=59  Identities=19%  Similarity=0.553  Sum_probs=54.0

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCC
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD   61 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~   61 (62)
                      ++++.+|+++||++++||+++|++|+|+|++++|++++|.++++|+++||||||+++..
T Consensus       194 e~~~~~F~~~YL~~~~Ka~~~s~~V~l~~~~~~Pl~l~~~i~~~g~~~y~laP~~~~~~  252 (259)
T 3lx2_A          194 TKAKSAYGVAYLEDILRSLADADEVIIRFGFDIPLLLKYMVRDAGEVSFLIAPRVEEGR  252 (259)
T ss_dssp             SCEEEEEEHHHHHHHHSSSCTTSEEEEEECTTSCEEEEEEETTTEEEEEEECCCC----
T ss_pred             ceEEEEEEHHHHHhhhccccCCCeEEEEeCCCCCEEEEEEeCCCeEEEEEEccccCCCc
Confidence            79999999999999999999999999999999999999999989999999999998753

>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*

Probab=99.75  E-value=2.6e-18  Score=113.10  Aligned_cols=56  Identities=27%  Similarity=0.460  Sum_probs=53.8

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKI   57 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPri   57 (62)
                      .++++..|+++||++++||+++|++|+|+|+++.|++++|.++++|+++||||||+
T Consensus       190 ~e~~~~~F~~~YL~~~~ka~~~s~~V~i~~~~~~Pl~l~~~i~~~g~~~y~laPr~  245 (245)
T 3fds_D          190 GADVSSSYGMEYVANTTKMRRASDSMELYFGSQIPLKLRFKLPQEGYGDFYIAPRA  245 (245)
T ss_dssp             ECCCEEEEEHHHHHHGGGGGGTCSEEEEEECTTSCEEEEEECSTTCEEEEEECCCC
T ss_pred             cceEEEEEEHHHHHHHhhhcccCCEEEEEecCCccEEEEEEeCCCeEEEEEEeecC
Confidence            36889999999999999999999999999999999999999999999999999996

>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

Probab=99.69  E-value=1.2e-16  Score=104.78  Aligned_cols=59  Identities=32%  Similarity=0.776  Sum_probs=55.9

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD   61 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~   61 (62)
                      .++++..|+++||.+++||.++|++|+|+|+++.|+.++|.++ +|+++||||||+++||
T Consensus       200 ge~~~i~f~~~yL~~~lka~~~s~~V~i~~~~~~Pl~l~~~~~-~~~~~y~l~P~~~~e~  258 (258)
T 1plq_A          200 DQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLK-SGFLQFFLAPKFNDEE  258 (258)
T ss_dssp             SSCEEEEEEHHHHHHHGGGGGTCSEEEEEECSSSCEEEEEEET-TEEEEEEECCCSSSCC
T ss_pred             CCcEEEEEEHHHHHHHhccccCCceEEEEECCCCCEEEEEEEC-CeEEEEEECCcCCCCC
Confidence            4678999999999999999999999999999999999999998 7899999999999875

>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*

Probab=99.68  E-value=1.1e-16  Score=104.99  Aligned_cols=60  Identities=67%  Similarity=1.082  Sum_probs=53.5

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD   61 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~   61 (62)
                      .++++..|+++||.+|+||.+++++|+|+|+++.|+.++|.++++|+++||||||+++||
T Consensus       200 ~e~~~i~f~~~yL~~~lka~~~s~~V~i~~~~~~P~~l~~~~~~~~~~~y~l~P~i~~e~  259 (261)
T 1u7b_A          200 NEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEE  259 (261)
T ss_dssp             SSCEEEEEEHHHHHHHGGGGGGCSEEEEEECTTSCEEEEEEETTTEEEEEEECCBC----
T ss_pred             CCcEEEEEeHHHHHHHhCcccCCCeEEEEECCCCCEEEEEEeCCCcEEEEEECCcCcccC
Confidence            467899999999999999999999999999999999999999767899999999999876

>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

Probab=99.67  E-value=3.7e-17  Score=108.73  Aligned_cols=55  Identities=22%  Similarity=0.304  Sum_probs=52.9

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCC-CeE---EEEEEeec
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDD-IGH---IRYYLAPK   56 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~-~g~---l~~~lAPr   56 (62)
                      +++++++|+++||+.|+||+++|++|+|+++++.||+++|.+.+ +|+   |+||||||
T Consensus       204 ~~~~~~~y~l~yL~~~~ka~~~s~~v~i~~~~~~pL~l~~~i~~~~g~~~~v~f~laP~  262 (263)
T 3a1j_C          204 NQTQVNRYKISLLKPSTKALVLSCKVSIRTDNRGFLSLQYMIRNEDGQICFVEYYCCPD  262 (263)
T ss_dssp             CSCEEEEEEHHHHTTHHHHHHHCSEEEEEEETTCCEEEEEEEECTTSCEEEEEEEECCC
T ss_pred             CChhhcEEeHHHHHHHHhhhhhcCEEEEEECCCeeEEEEEEEecCCCCEEEEEEEEEEC
Confidence            57899999999999999999999999999999999999999987 788   99999998

>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

Probab=99.61  E-value=1.9e-15  Score=100.63  Aligned_cols=57  Identities=60%  Similarity=1.046  Sum_probs=53.3

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE   58 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie   58 (62)
                      .++++..|+++||.+++||.+++++|+|+|+++.|+.++|.++++|+++||||||+|
T Consensus       220 ge~~~i~fn~~YL~d~lka~~ls~~V~i~l~~~~Pl~l~~~~~~~g~~~y~laP~i~  276 (276)
T 2zvv_A          220 KEPVSLSFALRYMNSFTKATPLSDTVTISLSSELPVVVEYKVAEMGYIRYYLAPKIE  276 (276)
T ss_dssp             SSCEEEEEEHHHHHHHGGGGGGCSEEEEEECTTSCEEEEEEETTTEEEEEEECCBC-
T ss_pred             CCcEEEEEEHHHHHHHhccccCCCEEEEEEcCCceEEEEEEeCCCcEEEEEEccccC
Confidence            467899999999999999999999999999999999999999767899999999986

>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*

Probab=99.54  E-value=3.7e-14  Score=92.48  Aligned_cols=58  Identities=26%  Similarity=0.472  Sum_probs=53.4

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCC-eEEEEEEeecCCCC
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDI-GHIRYYLAPKIESD   60 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~-g~l~~~lAPrie~e   60 (62)
                      ++++..|+++||.++.|+.+++++|+|+|+++.|+.++|.++++ |++.|||+||+++|
T Consensus       187 ~~~~i~Fn~~yL~d~lk~~~~s~~V~l~~~~~~p~~i~~~~~~~~~~~~y~i~P~~~~~  245 (245)
T 1rwz_A          187 GEARSMFSVDYLKEFCKVAGSGDLLTIHLGTNYPVRLVFELVGGRAKVEYILAPRIESE  245 (245)
T ss_dssp             CCEEEEEEHHHHHHHGGGCCTTCEEEEEECSSSCEEEEEEETTTTEEEEEEECCBCCC-
T ss_pred             eeEEEEEeHHHHHHHhhhccCCCeEEEEECCCCCEEEEEEECCCcEEEEEEEccccCCC
Confidence            34899999999999999999999999999999999999999766 89999999999965

>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*

Probab=99.53  E-value=3.2e-14  Score=92.84  Aligned_cols=58  Identities=26%  Similarity=0.556  Sum_probs=52.4

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIES   59 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~   59 (62)
                      .++++..|+++||.++.|+.+++++|+|+|+++.|+.++|.++++|++.||||||+++
T Consensus       192 ge~~~i~Fn~~yL~d~lk~~~~s~~V~l~~~~~~p~~i~~~~~~~~~~~y~i~P~~~~  249 (249)
T 1iz5_A          192 QEETKSAYGVSYLSDMVKGLGKADEVTIKFGNEMPMQMEYYIRDEGRLTFLLAPRVEE  249 (249)
T ss_dssp             SSCEEEEEEHHHHHHHHTTSCTTCEEEEEECTTCCEEEEEEETTTEEEEEEECCC---
T ss_pred             CCceEEEEeHHHHHHHhhhccCCCeEEEEEcCCCCEEEEEEeCCCcEEEEEEccccCC
Confidence            4679999999999999999999999999999999999999997678999999999974

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

Probab=99.52  E-value=5.6e-14  Score=91.52  Aligned_cols=56  Identities=21%  Similarity=0.452  Sum_probs=53.2

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCC
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE   58 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie   58 (62)
                      ++++..|+++||.++.|+.+++++|+|+|+++.|+.++|.++++|++.||||||+|
T Consensus       191 e~~~i~Fn~~yL~d~lk~~~~s~~V~l~~~~~~p~~i~~~~~~~~~~~y~i~P~~~  246 (246)
T 3aiz_C          191 GDAESVYGLEYVVNTSKMRKPSDTVEIAFGSQIPLKLRYNLPQGGYADFYIAPRAE  246 (246)
T ss_dssp             CCEEEEEEHHHHHTTGGGTTTCSEEEEEEETTEEEEEEEEETTTEEEEEEECBCCC
T ss_pred             eeEEEEEEHHHHHHHhhhccCCCeEEEEecCCCcEEEEEEeCCCCEEEEEEcccCC
Confidence            57899999999999999999999999999999999999999777999999999986

>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

Probab=99.50  E-value=4.7e-14  Score=91.86  Aligned_cols=57  Identities=26%  Similarity=0.496  Sum_probs=53.5

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE   58 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie   58 (62)
                      .++++..|+++||.++.|+.+++++|+|+|+++.|+.++|.+.++|.+.||||||++
T Consensus       189 ge~~~i~Fn~~yL~d~lk~~~~s~~V~l~~~~~~p~~i~~~~~~~~~~~y~i~P~~~  245 (245)
T 1ud9_A          189 NKESSSAYDVEYLNDIISLTKLSDYVKVAFADQKPMQLEFNMEGGGKVTYLLAPKLS  245 (245)
T ss_dssp             SSCEEEEEEHHHHHHTGGGGGGCSEEEEEECTTSCEEEEEECGGGCEEEEEECCBCC
T ss_pred             CCceeEEEEHHHHHHHhhhcccCCEEEEEEcCCCCEEEEEEeCCCcEEEEEEcccCC
Confidence            467999999999999999999999999999999999999998666899999999986

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

Probab=99.49  E-value=5.7e-14  Score=91.57  Aligned_cols=56  Identities=20%  Similarity=0.491  Sum_probs=53.0

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKI   57 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPri   57 (62)
                      .++++..|+++||.+++|+.+++++|+|+|+++.|+.++|.++++|++.||||||+
T Consensus       193 ge~~~i~fn~~yL~d~lk~~~~s~~V~l~~~~~~p~~i~~~~~~~~~~~y~i~P~i  248 (248)
T 3aiz_A          193 ESPSKAVYSIEVLKDVFKVTSISQNVTVGFGNNIPMKIEVPTDSGGQLIFWIAPRL  248 (248)
T ss_dssp             SSCEEEEEEHHHHHHHHHHGGGCSSEEEEEETTEEEEEEEECTTSCEEEEEECCCC
T ss_pred             CCceEEEEEHHHHHHHhhhccCCCeEEEEEcCCCCEEEEEEeCCCcEEEEEECCcC
Confidence            46899999999999999999999999999999999999999977789999999996

>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*

Probab=99.48  E-value=8.4e-14  Score=90.61  Aligned_cols=56  Identities=27%  Similarity=0.466  Sum_probs=52.8

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKI   57 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPri   57 (62)
                      .++++..|+++||.+++|+.+++++|+|+|+++.|+.++|.++++|++.||||||+
T Consensus       189 ge~~~i~Fn~~yL~d~lk~~~~s~~V~l~~~~~~p~~i~~~~~~~~~~~y~i~P~~  244 (244)
T 2ijx_A          189 SKESKNSYSAEYLDDVLSLTKLSDYVKISFGNQKPLQLFFNMEGGGKVTYLLAPKV  244 (244)
T ss_dssp             SSCEEEEEEHHHHHHTGGGGGGCSEEEEEEETTEEEEEEEECGGGCEEEEEECCCC
T ss_pred             CCceEEEEEHHHHHHHhhhccCCCEEEEEEcCCCCEEEEEEeCCCcEEEEEECccC
Confidence            46799999999999999999999999999999999999999976689999999996

>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

Probab=99.21  E-value=5.2e-11  Score=80.15  Aligned_cols=52  Identities=12%  Similarity=0.213  Sum_probs=49.6

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEE-eeCCCcEEEEEEeCCCeEEEEEEe
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLS-MSLDVPLVVEFKIDDIGHIRYYLA   54 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~-l~~~~Pl~l~~~l~~~g~l~~~lA   54 (62)
                      +++++.+|+++||+.|+||.+++++|.+. ++++.||.+ |.+.++|+|+|||+
T Consensus       226 ~~~~sv~~~~k~l~~f~k~~~ls~~v~~~~i~~~~~l~~-y~~~~~g~l~yylp  278 (281)
T 3a1j_B          226 EHMAEVHIDIRKLLQFLAGQQVNPTKALCNIVNNKMVHF-DLLHEDVSLQYFIP  278 (281)
T ss_dssp             CCCEEEEEEHHHHHHHHHHCCSCCSEEEEEEETTTEEEE-EEESSSCEEEEEEE
T ss_pred             CccEEEEEEHHHHHHhhCcccCCCcEEEEEEeCCceEEE-EEeCCcEEEEEEee
Confidence            47899999999999999999999999999 999999999 99999999999996

>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

Probab=98.97  E-value=1.1e-09  Score=72.63  Aligned_cols=52  Identities=25%  Similarity=0.404  Sum_probs=43.5

Q ss_pred             CCCceeeEEehHHHHh---hhcccCCCceEEEEee-CCCcEEEEEEeCCCeEEEEEEee
Q psy5572           1 MQEPVSLNFACRYLLN---FAKAAPLSNQVCLSMS-LDVPLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         1 ~~~~~~~~ysl~YL~~---~~Ka~~ls~~V~l~l~-~~~Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      +++|++.+|+++||+.   |+|+++++  |+|.|+ .+.|+.++|. +++++++|+||-
T Consensus       209 ~~~~~~~tFslkyl~~~l~f~~~~~~~--v~i~~~~~g~Pl~~~~~-~~~~~~~f~LAT  264 (266)
T 3a1j_A          209 AQEGVAITFCLKEFRGLLSFAESANLN--LSIHFDAPGRPAIFTIK-DSLLDGHFVLAT  264 (266)
T ss_dssp             CCTTCEEEEEHHHHHHHHHHHHHTTCE--EEEEECSTTSCEEEEEE-CSSEEEEEEECC
T ss_pred             cCCCCEEEEEHHHHHHHHHHHHhcCCc--EEEEECCCCccEEEEEe-CCcEEEEEEEee
Confidence            3578999999999999   88887665  999996 5999999993 333499999993

>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}

Probab=98.26  E-value=3.3e-06  Score=57.40  Aligned_cols=60  Identities=18%  Similarity=0.293  Sum_probs=52.1

Q ss_pred             CCCceeeEEehHHHHhhhc-ccCCCceEEEEeeC-CCcEEEEEEeCCCeEEEEEEeecCCCCC
Q psy5572           1 MQEPVSLNFACRYLLNFAK-AAPLSNQVCLSMSL-DVPLVVEFKIDDIGHIRYYLAPKIESDD   61 (62)
Q Consensus         1 ~~~~~~~~ysl~YL~~~~K-a~~ls~~V~l~l~~-~~Pl~l~~~l~~~g~l~~~lAPrie~e~   61 (62)
                      ++++++.+|++++|+.|.. |-.++..|++.|+. +.|+.++|+ .++....|.||++.+++.
T Consensus       209 v~~~~~itf~lKefrail~~ae~~~~~i~i~f~~pG~Pl~~~~~-~~~~~~~fvLaT~~~~~~  270 (296)
T 3g65_A          209 AQEGVAITFCLKEFRGLLSFAESANLNLSIHFDAPGRPAIFTIK-DSLLDGHFVLATLSDTDS  270 (296)
T ss_dssp             CCTTCEEEEEHHHHHHHHHHHHHTTCEEEEECCSTTSCEEEEEE-CSSCEEEEEECCCCSSSC
T ss_pred             cCCCcEEEEEHHHHHHHHHHHHhcCCeEEEEECCCCCcEEEEEe-CCcEEEEEEEEECCCCCC
Confidence            3578899999999999996 55678899999995 999999999 467899999999998664

>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

Probab=97.65  E-value=8.9e-05  Score=51.01  Aligned_cols=50  Identities=16%  Similarity=0.315  Sum_probs=44.7

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      ++.+..|+.+||.++.|+.. +++|+|+|++. .|+.++..  +++...|+|.|
T Consensus       324 ~~~~i~fN~~yL~d~L~~~~-~~~v~l~~~~~~~p~~i~~~--~~~~~~~limP  374 (378)
T 1vpk_A          324 EDLVIAFNPKFIEDVLKHIE-TEEIEMNFVDSTSPCQINPL--DISGYLYIVMP  374 (378)
T ss_dssp             CCEEEEECHHHHHHHHHHCC-SSEEEEEESCTTSCEEEEET--TCCSEEEEECC
T ss_pred             CeEEEEEcHHHHHHHHhcCC-CCEEEEEECCCCCCEEEEcC--CCCceEEEEEe
Confidence            46788999999999999998 99999999998 79999986  34678999999

>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*

Probab=97.51  E-value=0.00028  Score=48.59  Aligned_cols=50  Identities=16%  Similarity=0.297  Sum_probs=45.0

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      ++.+-.|+.+||.++.++.. +++|+|+|++. .|+.++..  +++...|+|.|
T Consensus       313 e~~~I~fN~~YL~d~L~~~~-~~~v~l~~~~~~~p~~i~~~--~~~~~~ylvmP  363 (366)
T 3d1g_A          313 AEMEIGFNVSYVLDVLNALK-CENVRMMLTDSVSSVQIEDA--ASQSAAYVVMP  363 (366)
T ss_dssp             CCEEEEEEHHHHHHHHHHCC-SSEEEEEECCTTSCEEEEET--TEEEEEEEECC
T ss_pred             CcEEEEEcHHHHHHHHhcCC-CCEEEEEECCCCCCEEEEcC--CCCceEEEEEE
Confidence            56789999999999999998 99999999998 79999876  45789999999

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

Probab=97.44  E-value=0.00041  Score=47.97  Aligned_cols=51  Identities=20%  Similarity=0.293  Sum_probs=44.3

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      ++.+-.|+.+||.++.++.. +++|+|+|++. .|+.++.. ++.+...|+|.|
T Consensus       323 e~~~I~FN~~YL~d~L~~~~-~~~v~l~~~~~~~p~~i~~~-~~~~~~~ylvmP  374 (378)
T 2avt_A          323 SDLTISFNPTYLIESLKAIK-SETVKIHFLSPVRPFTLTPG-DEEESFIQLITP  374 (378)
T ss_dssp             CCEEEEECHHHHHHHHHTCC-SSEEEEEECCTTSCEEEEET-TCCSEEEEEECC
T ss_pred             CeEEEEEcHHHHHHHHhcCC-CCEEEEEECCCCCCEEEEcC-CCCCceEEEEEe
Confidence            46788999999999999998 99999999998 79999876 332379999999

>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}

Probab=95.58  E-value=0.034  Score=38.30  Aligned_cols=53  Identities=17%  Similarity=0.396  Sum_probs=43.0

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee-cCCC
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP-KIES   59 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP-rie~   59 (62)
                      ++.+-.|..+||.++.++.. +++|+|+|.+. .|+.++=   +++...|.|-| |+.+
T Consensus       314 e~~~I~FN~~yLld~L~~~~-~~~v~l~~~~~~~p~~i~~---~~~~~~~lvMPvrl~~  368 (371)
T 3t0p_A          314 KDIMIGFNPKFFIDALRVID-EEEVNLYMVNPKAPCFIKD---DEGKFIYLILPVNFNT  368 (371)
T ss_dssp             CCEEEEECHHHHHHHHTTCC-CSEEEEEESCTTSCEEEEC---TTSCEEEEECCCCC--
T ss_pred             CcEEEEEchHHHHHHHhCCC-CCeEEEEECCCCCcEEEEc---CCCCeEEEEcceeccc
Confidence            56788999999999999988 78999999665 6998863   45678999999 6544

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

Probab=92.04  E-value=0.46  Score=33.26  Aligned_cols=52  Identities=25%  Similarity=0.406  Sum_probs=40.9

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCC---------e-------EEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDI---------G-------HIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~---------g-------~l~~~lAP   55 (62)
                      ++.+-.|..+||.++.++.. +++|+|+|.+. .|+.++=.-++.         |       ...|+|=|
T Consensus       335 e~l~I~FN~~YLlD~L~~i~-~e~V~l~~~~~~~P~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~limP  403 (408)
T 3p16_A          335 EPLTIAFNPTYLTDGLSSLR-SERVSFGFTTAGKPALLRPVSGDDRPVAGLNGNGPFPAVSTDYVYLLMP  403 (408)
T ss_dssp             SCCEEEECHHHHHHHHHHSC-SSEEEEEESCTTSCEEEEEECCC--------------CCSSSEEEEECC
T ss_pred             CcEEEEEeHHHHHHHHhccC-CCeEEEEECCCCCcEEEEeCCCCccccccccccccccCCCCcEEEEEEE
Confidence            46788999999999999998 79999999766 799996432221         1       57888888

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

Probab=90.78  E-value=2  Score=27.94  Aligned_cols=55  Identities=13%  Similarity=0.120  Sum_probs=40.3

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEeecCC
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAPKIE   58 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAPrie   58 (62)
                      ++++-..+++-|..+.|...-.+.|+|.+..+ -++.+.|.=.+.+.+.|++. -+|
T Consensus        69 ~~~~igi~l~~L~kiLk~~~~~d~v~i~~~~~~~~l~~~~e~~~~~~i~~~lr-Lid  124 (265)
T 3p91_A           69 KPITLGINLTHLSKILKALDNDCGLILDVKKVDDAVLSITSEGTNKTMKFGLN-LVD  124 (265)
T ss_dssp             SCEEEEEEHHHHHHHHTTSCTTSEEEEEECSSSSEEEEEEEC--CCEEEEEEE-CCC
T ss_pred             CCeEEEEEHHHHHHHHhhcCCCCEEEEEEcCCCCeEEEEEEeCCCceEEEEEE-ecc
Confidence            45667888999999999888899999999865 48888877443345666654 444

>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

Probab=81.19  E-value=8.1  Score=24.40  Aligned_cols=58  Identities=16%  Similarity=0.219  Sum_probs=41.6

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEeecCCCC
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAPKIESD   60 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAPrie~e   60 (62)
                      +++.-..+++-|..+.|...-.+.|+|.+..+ -++.+.+.-.+.|..+-+-.+-+|.+
T Consensus        64 ~~~~~~i~l~~l~kil~~~~~~d~v~i~~~~~~~~l~~~~~~~~~~~~~~~~~rlie~~  122 (258)
T 1plq_A           64 HPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDID  122 (258)
T ss_dssp             SCEEEEEEHHHHHHHTTCSTTTSEEEEEECSSCSEEEEEEECSSSSCEEEEEEECBCCC
T ss_pred             CCeEEEEEHHHHHHHHhcCCCCCEEEEEecCCCCeEEEEEEcCCCCeEEEEEEEcccCC
Confidence            34567778899999998776688899999764 57777776544566666666666543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	62
d1u7ba2	129	d.131.1.2 (A:127-255) Proliferating cell nuclear a	1e-19
d1plqa2	132	d.131.1.2 (A:127-258) Proliferating cell nuclear a	9e-19
d1ud9a2	119	d.131.1.2 (A:127-245) Proliferating cell nuclear a	1e-18
d1rwza2	122	d.131.1.2 (A:123-244) Proliferating cell nuclear a	1e-17
d1iz5a2	121	d.131.1.2 (A:126-246) Proliferating cell nuclear a	1e-17

>d1u7ba2 d.131.1.2 (A:127-255) Proliferating cell nuclear antigen (PCNA) {Human (Homo sapiens) [TaxId: 9606]} Length = 129

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: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.9 bits (181), Expect = 1e-19
 Identities = 40/57 (70%), Positives = 45/57 (78%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKI 57
           M EPV L FA RYL  F KA PLS+ V LSMS DVPLVVE+KI D+GH++YYLAPKI
Sbjct: 73  MNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKI 129

>d1plqa2 d.131.1.2 (A:127-258) Proliferating cell nuclear antigen (PCNA) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 132

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]

 Score = 71.5 bits (175), Expect = 9e-19
 Identities = 20/61 (32%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESD 60
           M +PV L F  +YLL+  K + LS++V + +S + P + +F +   G ++++LAPK   +
Sbjct: 73  MDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPKFNDE 131

Query: 61  D 61
           +
Sbjct: 132 E 132

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

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 = 70.7 bits (173), Expect = 1e-18
 Identities = 15/57 (26%), Positives = 28/57 (49%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKI 57
             +  S  +   YL +      LS+ V ++ +   P+ +EF ++  G + Y LAPK+
Sbjct: 62  FNKESSSAYDVEYLNDIISLTKLSDYVKVAFADQKPMQLEFNMEGGGKVTYLLAPKL 118

>d1rwza2 d.131.1.2 (A:123-244) Proliferating cell nuclear antigen (PCNA) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 122

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 Archaeoglobus fulgidus [TaxId: 2234]

 Score = 68.4 bits (167), Expect = 1e-17
 Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 3   EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKI-DDIGHIRYYLAPKIES 59
                 F+  YL  F K A   + + + +  + P+ + F++      + Y LAP+IES
Sbjct: 65  GEARSMFSVDYLKEFCKVAGSGDLLTIHLGTNYPVRLVFELVGGRAKVEYILAPRIES 122

>d1iz5a2 d.131.1.2 (A:126-246) Proliferating cell nuclear antigen (PCNA) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 121

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]

 Score = 68.0 bits (166), Expect = 1e-17
 Identities = 14/56 (25%), Positives = 29/56 (51%)

Query: 1   MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 56
           +QE     +   YL +  K    +++V +    ++P+ +E+ I D G + + LAP+
Sbjct: 66  VQEETKSAYGVSYLSDMVKGLGKADEVTIKFGNEMPMQMEYYIRDEGRLTFLLAPR 121

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	62
d1plqa2	132	Proliferating cell nuclear antigen (PCNA) {Baker's	99.91
d1rwza2	122	Proliferating cell nuclear antigen (PCNA) {Archaeo	99.9
d1ud9a2	119	Proliferating cell nuclear antigen (PCNA) {Archaeo	99.88
d1iz5a2	121	Proliferating cell nuclear antigen (PCNA) {Archaeo	99.88
d1u7ba2	129	Proliferating cell nuclear antigen (PCNA) {Human (	99.87
d1vpka3	123	DNA polymerase III, beta subunit {Thermotoga marit	95.81
d1ok7a3	122	DNA polymerase III, beta subunit {Escherichia coli	93.97
d1rwza1	122	Proliferating cell nuclear antigen (PCNA) {Archaeo	86.02
d1ud9a1	119	Proliferating cell nuclear antigen (PCNA) {Archaeo	85.01

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

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=99.91  E-value=1.9e-24  Score=130.28  Aligned_cols=59  Identities=32%  Similarity=0.789  Sum_probs=56.3

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD   61 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~   61 (62)
                      +++++++|+++||+.|+|++++|+.|+|+|++++||+++|++++ |+|+||||||+++||
T Consensus        74 ~~~~~~~ysl~yL~~~~K~~~ls~~V~i~~~~~~Pl~~~y~i~~-g~l~fyLAPkieddd  132 (132)
T d1plqa2          74 DQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKS-GFLQFFLAPKFNDEE  132 (132)
T ss_dssp             SSCEEEEEEHHHHHHHGGGGGTCSEEEEEECSSSCEEEEEEETT-EEEEEEECCCSSSCC
T ss_pred             ccceeeEEEHHHHHHHhCcccCCCEEEEEEeCCCCEEEEEEeCC-EEEEEEECccCCCCC
Confidence            47789999999999999999999999999999999999999966 999999999999886

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

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 Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.90  E-value=6.2e-24  Score=126.81  Aligned_cols=57  Identities=26%  Similarity=0.477  Sum_probs=54.2

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCC-CeEEEEEEeecCCC
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDD-IGHIRYYLAPKIES   59 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~-~g~l~~~lAPrie~   59 (62)
                      ++++++|+++||+.|+||+++|+.|+|+|++++||+++|++.+ .|+|+||||||+|+
T Consensus        65 ~~~~~~fsl~YL~~~~K~~~ls~~v~i~~~~~~Pl~l~y~i~~~~g~i~fylAPries  122 (122)
T d1rwza2          65 GEARSMFSVDYLKEFCKVAGSGDLLTIHLGTNYPVRLVFELVGGRAKVEYILAPRIES  122 (122)
T ss_dssp             CCEEEEEEHHHHHHHGGGCCTTCEEEEEECSSSCEEEEEEETTTTEEEEEEECCBCCC
T ss_pred             cceeEEEeHHHHHHHhhhccCCCEEEEEEcCCCCEEEEEEEcCCcEEEEEEEccccCC
Confidence            5788999999999999999999999999999999999999976 59999999999985

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

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]

Probab=99.88  E-value=3.6e-23  Score=122.65  Aligned_cols=57  Identities=26%  Similarity=0.496  Sum_probs=55.1

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE   58 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie   58 (62)
                      +++++++|+++||+.|+|++++|+.|+|+|++|+||+++|+++++|+++|||||||.
T Consensus        63 ~~~~~~~ysl~yL~~~~K~~~ls~~v~i~~~~d~Pl~l~y~l~~~g~i~f~lAPri~  119 (119)
T d1ud9a2          63 NKESSSAYDVEYLNDIISLTKLSDYVKVAFADQKPMQLEFNMEGGGKVTYLLAPKLS  119 (119)
T ss_dssp             SSCEEEEEEHHHHHHTGGGGGGCSEEEEEECTTSCEEEEEECGGGCEEEEEECCBCC
T ss_pred             CCceEEEEEHHHHHHHHhhccCCCEEEEEECCCcCEEEEEEeCCCeEEEEEEeeccC
Confidence            578999999999999999999999999999999999999999999999999999984

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

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=1.2e-22  Score=121.04  Aligned_cols=55  Identities=25%  Similarity=0.545  Sum_probs=53.7

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeec
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK   56 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPr   56 (62)
                      +++++++|+++||+.|+|++++|+.|+|+|++|+||+++|+++++|+|+||||||
T Consensus        67 ~~~~~~~ysl~yL~~~~K~~~ls~~V~i~~~~~~Pl~l~y~~~~~g~i~f~LAPr  121 (121)
T d1iz5a2          67 QEETKSAYGVSYLSDMVKGLGKADEVTIKFGNEMPMQMEYYIRDEGRLTFLLAPR  121 (121)
T ss_dssp             SSCEEEEEEHHHHHHHHTTSCTTCEEEEEECTTCCEEEEEEETTTEEEEEEECCC
T ss_pred             CCceEEEEEHHHHHHHhhhccCCCEEEEEEcCCCCEEEEEEeCCCcEEEEEEccC
Confidence            5789999999999999999999999999999999999999999999999999998

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

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: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.7e-22  Score=121.04  Aligned_cols=56  Identities=70%  Similarity=1.102  Sum_probs=54.2

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecC
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKI   57 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPri   57 (62)
                      +++++++|+++||+.|+|++++|++|+|+|++|+||+++|+++++|+|+|||||||
T Consensus        74 ~~~~~~~fsl~YL~~~~K~~~ls~~v~i~~~~~~Pl~i~y~~~~~g~l~fyLAPki  129 (129)
T d1u7ba2          74 NEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKI  129 (129)
T ss_dssp             SSCEEEEEEHHHHHHHGGGGGGCSEEEEEECTTSCEEEEEEETTTEEEEEEECCBC
T ss_pred             CccceeEEEHHHHHHHhchhcCCCeEEEEEcCCCCEEEEEEeCCCcEEEEEEcccC
Confidence            47789999999999999999999999999999999999999999999999999997

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

class: Alpha and beta proteins (a+b)
fold: DNA clamp
superfamily: DNA clamp
family: DNA polymerase III, beta subunit
domain: DNA polymerase III, beta subunit
species: Thermotoga maritima [TaxId: 2336]

Probab=95.81  E-value=0.017  Score=32.61  Aligned_cols=50  Identities=16%  Similarity=0.321  Sum_probs=40.8

Q ss_pred             CceeeEEehHHHHhhhcccCCCceEEEEeeC-CCcEEEEEEeCCCeEEEEEEee
Q psy5572           3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSL-DVPLVVEFKIDDIGHIRYYLAP   55 (62)
Q Consensus         3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~-~~Pl~l~~~l~~~g~l~~~lAP   55 (62)
                      ++.+-.|..+||.++.++.+ +++|+|.|.+ ..|+.+. . .++....|.|.|
T Consensus        69 e~~~i~fN~~yL~d~L~~~~-~~~V~l~~~~~~~p~~i~-~-~~~~~~~~liMP  119 (123)
T d1vpka3          69 EDLVIAFNPKFIEDVLKHIE-TEEIEMNFVDSTSPCQIN-P-LDISGYLYIVMP  119 (123)
T ss_dssp             CCEEEEECHHHHHHHHHHCC-SSEEEEEESCTTSCEEEE-E-TTCCSEEEEECC
T ss_pred             CCeEEEECHHHHHHHHhhCC-CCEEEEEEcCCCCCEEEe-c-CCCCceEEEEEe
Confidence            46788999999999999997 7889999985 5699885 2 344567889988

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

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 Archaeoglobus fulgidus [TaxId: 2234]

Probab=86.02  E-value=1.3  Score=24.50  Aligned_cols=40  Identities=18%  Similarity=0.271  Sum_probs=32.8

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEE
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEF   41 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~   41 (62)
                      +++.+--.+++.|..+.|..+-.+.++++..++--+.+.+
T Consensus        62 ~~~~~iGv~~~~l~kilk~~~~~d~l~l~~~~~~~l~i~~  101 (122)
T d1rwza1          62 DEEKTIGVDMDRIFDISKSISTKDLVELIVEDESTLKVKF  101 (122)
T ss_dssp             SSCEEEEEEHHHHHHHHTTSCTTSEEEEEESSSSEEEEEE
T ss_pred             CCCEEEEEEHHHHHHHHhhCCCCCEEEEEEcCCCEEEEEE
Confidence            4677788899999999999999999999987655454444

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

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]

Probab=85.01  E-value=1.7  Score=23.88  Aligned_cols=40  Identities=15%  Similarity=0.282  Sum_probs=33.6

Q ss_pred             CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEE
Q psy5572           2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEF   41 (62)
Q Consensus         2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~   41 (62)
                      +++..--..++-|.++.|..+-.+.++++..++--+.+.+
T Consensus        62 ~~~~~igv~~~~l~kilk~~~~~d~l~l~~~~~~~l~i~~  101 (119)
T d1ud9a1          62 PEEFKFGFNTQYMSKLLKAAKRKEEIIIDADSPEVVKLTL  101 (119)
T ss_dssp             SSCEEEEEEHHHHHHHHTTCCSCCCEEEEEEETTEEEEEE
T ss_pred             CCCEEEEEEHHHHHHHHhhCCCCCEEEEEeCCCCEEEEEE
Confidence            5677888999999999999999999999997765555555