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Porphyromonas gingivalis Search Results

Record: 1 of 1  
MiniMap tRNA-Ile-1 tRNA-Ala-1 rRNA-5S-1 rRNA-23S-1 IGR0083 IGR0082 IGR0081 IGR0080 IGR0079 PG0092 PG0093 wecC, - PG0094 PG0095 top3,topB, - PG0091 PG0092 PG0093 wecC, - PG0094 PG0095 top3,topB, - PG0091 PG0092 PG0093 PG0095 top3,topB, - PG0091 wecC, - PG0094


LANL Gene ID: PG0091

GenBank Locus Tag: PG0104

DNA Molecule Name:
1  

GenBank ID:
34539972

Gene Name:
top3  topB  

Definition:
DNA topoisomerase III

Cellular Location:
Cytoplasm [Evidence]

Gene Start:
125481

Gene Stop:
127505

Gene Length:
2025

Molecular Weight*:
75978

pI*:
8.20

Net Charge*:
7.45

EC:
5.99.1.2  

Functional Class:
DNA metabolism; DNA replication, recombination and repair  

Gene Ontology:
Biological process
  GO:0006265    DNA topological change
  GO:0006268    DNA unwinding during replication
  GO:0006304    DNA modification

Cellular component
  GO:0005694    chromosome

Molecular function
  GO:0003676    nucleic acid binding
  GO:0003677    DNA binding
  GO:0003916    DNA topoisomerase activity
  GO:0003917    DNA topoisomerase type I activity


Pathway: pathway table

Comment:
TIGR ID: PG0104

Proteomic Data: Proteomic Data Search
TIGR AnnotationDNA topoisomerase III, GroupF (DNA metabolism)
ORF #PG-PP/PG-PPC1PG-PP/PG-PPC2
Spectral CountPeptide IntensitySpectral CountPeptide Intensity
ProqValProqValProqValProqVal
TIGRPG0104-1.470.018-0.790.098-1.490.0053-0.790.098
LANLPG00910.360.580.360.33
ConsensusSP1IP1SP2IP2

Human Oral Microbiome Database:
View in HOMD Genome Viewer

 Blast Summary:  PSI-Blast Search
Numerous hits in gapped BLAST to DNA topoisomerase III sequences, e.g. residues 3-640 are 33% similar to emb|CAB12233.1| DNA topoisomerase III of Bacillus subtilis, residues 5-649 are 34% similar to gb|AAF72351.1|AF192329_12 DNA topoisomerase III-like protein of Enterococcus faecalis, residues 2-672 are 34% similar to dbj|BAB07106.1| DNA topoisomerase III of Bacillus halodurans.

This sequence is similar to BT2089.

 Top Blast Hits:  Updated monthly
Click here to view the entire PsiBlast results.
 gi|34539972|ref|NP_904451.1|  DNA topoisomerase III [Porphyr...  1367   0.0  
 gi|150008318|ref|YP_001303061.1|  putative DNA topoisomerase...   883   0.0  
 gi|154492552|ref|ZP_02032178.1|  hypothetical protein PARMER...   883   0.0  
 gi|150004505|ref|YP_001299249.1|  putative DNA topoisomerase...   841   0.0  
 gi|156861277|gb|EDO54708.1|  hypothetical protein BACUNI_016...   832   0.0  
 gi|53715082|ref|YP_101074.1|  DNA topoisomerase III [Bactero...   829   0.0  
 gi|60683041|ref|YP_213185.1|  putative DNA topoisomerase [Ba...   829   0.0  
 gi|29347499|ref|NP_811002.1|  DNA topoisomerase III [Bactero...   819   0.0  
 gi|156109641|gb|EDO11386.1|  hypothetical protein BACOVA_032...   818   0.0  
 gi|153808833|ref|ZP_01961501.1|  hypothetical protein BACCAC...   815   0.0


InterPro Summary:  InterProScan

InterPro
IPR000380
Family
DNA topoisomerase, type IA
PR00417 [98-111]T 3.3E-24 PR00417 PRTPISMRASEI[187-205]T 3.3E-24 PR00417 PRTPISMRASEI[300-309]T 3.3E-24 PR00417 PRTPISMRASEI[378-394]T 3.3E-24 PR00417 PRTPISMRASEI[499-513]T 3.3E-24 PR00417 PRTPISMRASEI PRTPISMRASEI
PTHR11390 [21-480]T 0.0 PTHR11390 Topo_IA[497-574]T 0.0 PTHR11390 Topo_IA Topo_IA
InterPro
IPR003601
Domain
DNA topoisomerase, type IA, domain 2
SM00436 [124-217]T 7.300000000000739E-38 SM00436 TOP1Bc TOP1Bc
InterPro
IPR003602
Domain
DNA topoisomerase, type IA, DNA-binding
SM00437 [258-536]T 6.69999999999959E-77 SM00437 TOP1Ac TOP1Ac
InterPro
IPR005738
Family
DNA topoisomerase III, bacterial-type
TIGR01056 [1-673]T 0.0 TIGR01056 topB topB
InterPro
IPR006154
Domain
Toprim subdomain
SM00493 [1-124]T 2.59999999999989E-12 SM00493 TOPRIM TOPRIM
InterPro
IPR006171
Domain
TOPRIM
PF01751 [1-131]T 3.7999986264479004E-10 PF01751 Toprim Toprim
InterPro
IPR013497
Domain
DNA topoisomerase, type IA, central
PF01131 [147-542]T 3.3999997243776603E-102 PF01131 Topoisom_bac Topoisom_bac
InterPro
IPR013824
Domain
DNA topoisomerase, type IA, central region, subdomain 1
G3DSA:1.10.460.10 [153-218]T 1.29999924468183E-14 G3DSA:1.10.460.10 Topo_IA_cen_sub1[458-587]T 7.900030794430431E-35 G3DSA:1.10.460.10 Topo_IA_cen_sub1 Topo_IA_cen_sub1
InterPro
IPR013826
Domain
DNA topoisomerase, type IA, central region, subdomain 3
G3DSA:1.10.290.10 [268-392]T 2.10000267834025E-34 G3DSA:1.10.290.10 Topo_IA_cen_sub3 Topo_IA_cen_sub3
InterPro
IPR014396
Family
DNA topoisomerase IA
PIRSF001508 [1-674]T 0.0 PIRSF001508 TopA TopA
noIPR
unintegrated
unintegrated
G3DSA:3.40.50.140 [1-152]T 1.0E-43 G3DSA:3.40.50.140 G3DSA:3.40.50.140 G3DSA:3.40.50.140
SSF56712 [1-588]T 0.0 SSF56712 SSF56712 SSF56712


COGS Summary:  COGS Search
BeTs to 17 clades of COG0550
COG name: Topoisomerase IA
Functional Class: L
The phylogenetic pattern of COG0550 is amtkyqvcEBrHUJgpolinx
Number of proteins in this genome belonging to this COG is 3
Blocks Summary:  Blocks Search
***** IPB000380 (Prokaryotic DNA topoisomerase I) with a combined E-value of 1.7e-58.
    IPB000380A    17-46
    IPB000380B    98-115
    IPB000380C    148-184
    IPB000380D    187-218
    IPB000380E    269-296
    IPB000380F    301-310
    IPB000380G    352-364
    IPB000380H    378-394
    IPB000380I    483-519


 ProDom Summary:  Protein Domain Search
Residues 371-582 are 35% similar to a (TOPOISOMERASE ISOMERASE DNA ENZYME DNA-BINDING I) protein domain (PD001411 which is seen in Q60149_STRPY.

Residues 3-179 are 43% similar to a (TOPOISOMERASE ISOMERASE DNA ENZYME DNA-BINDING I) protein domain (PD001285 which is seen in P96583_BACSU.

Residues 239-309 are 41% similar to a (TOPOISOMERASE ISOMERASE DNA ENZYME I DNA-BINDING) protein domain (PD001593 which is seen in O87222_BBBBB.

Residues 183-364 are 26% similar to a (DNA TOPOISOMERASE I EC) protein domain (PD112610 which is seen in TOP1_BACAN.


Paralogs:  Local Blast Search
Residues 5-669 are 34% similar to PG1310, a predicted DNA topoisomerase III and residues 27-570 are 26% similar to PG0680, DNA topoisomerase I.

Pfam Summary:  Pfam Search
Residues 1 to 131 (E-value = 3.1e-16) place PG0091 in the Toprim family which is described as Toprim domain (PF01751)
Residues 147 to 542 (E-value = 7.1e-103) place PG0091 in the Topoisom_bac family which is described as DNA topoisomerase (PF01131)

 Structural Feature(s):
Feature Type  Start  Stop
No predicted structural features.  
  

Top PDB Hits:
-52% similar to PDB:1D6M CRYSTAL STRUCTURE OF E. COLI DNA TOPOISOMERASE III (E_value = 2.4E_84);
-52% similar to PDB:1I7D NONCOVALENT COMPLEX OF E.COLI DNA TOPOISOMERASE III WITH AN 8-BASE SINGLE-STRANDED DNA OLIGONUCLEOTIDE (E_value = 7.1E_84);
-40% similar to PDB:2GAI Structure of Full Length Topoisomerase I from Thermotoga maritima in triclinic crystal form (E_value = 5.2E_26);
-40% similar to PDB:2GAJ Structure of Full Length Topoisomerase I from Thermotoga maritima in monoclinic crystal form (E_value = 5.2E_26);
-40% similar to PDB:1CY0 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 3'-5'-ADENOSINE DIPHOSPHATE (E_value = 9.1E_23);

Gene Protein Sequence:
MIVCIAEKPSVGREIAAVLGATKAYKGYMEGNGYQVTWTFGHLCALKEPH
DYAPEWKRWSISSLPMIPLRFGIKLIDSDSIREQFGTIERLVHEADMVVN
CGDAGQEGELIQRWVLQKTGCTCPVRRLWISSLTEESIREGFARLRDSEE
FHSLYEAGLARAIGDWLLGMNATRLYTLRFGGNRQVLSIGRVQTPTLALI
VRRQHEIEHFTPEVYWEVKTIYRDTVFNATKGRFSSIEDARREVEVVAGS
PFAVTSVATKKGRELPPRLFDLTGLQVECNKRFAMTADATLRTIQSLYEK
KITTYPRVDTTYLSDDVFEKVPNILQGLSDYTLLTAPLRSSKLKKSKKVF
DNSKITDHHAIIPTGQPSHGMSEDERRVFDLVARRFIAVFYPDCIFSQTT
VLGQAAKVEFKTTGKQILEPGWRTVFTDPQTDDDGENKDEEKKLPIFSEG
ESGVHTPEVQEKTTQPPKFYTEATLLRAMETAGKSVKDEELRDALKENGI
GRPSTRAAIIETLFKRNYIYKEKKNLKATPTGMSLIATIDYDLLKSAELT
GQWEYKLRRIERGDYSAADFINELKVLLTHLIPNVLKSNSSVLLSEPIPA
ASPAPGKKKKADKPMQKQLDLTCPVCGKGIIVRGREAFGCNAFREGCTFR
LPYSEYPASLSDNELVDLLSSQKGH

Gene Nucleotide Sequence:  Sequence Viewer
ATGATAGTCTGTATTGCCGAAAAGCCCAGTGTGGGGCGTGAGATCGCTGC
TGTACTCGGTGCCACCAAAGCCTATAAAGGCTATATGGAGGGCAACGGTT
ATCAGGTGACATGGACTTTCGGACATCTCTGTGCCCTCAAAGAACCTCAC
GACTATGCACCCGAATGGAAGCGATGGAGTATCAGTTCTCTACCGATGAT
ACCACTGCGATTTGGCATCAAACTCATCGATAGCGATAGTATTCGGGAGC
AATTCGGCACCATCGAAAGGCTTGTCCATGAAGCGGATATGGTCGTGAAC
TGCGGTGATGCCGGACAGGAGGGAGAGCTGATCCAGCGTTGGGTATTGCA
GAAAACGGGCTGCACATGTCCCGTGCGGCGACTTTGGATATCTTCTCTTA
CTGAGGAGTCTATCCGTGAAGGCTTTGCGAGGCTGCGCGACAGCGAAGAA
TTTCATTCCCTATATGAGGCCGGACTGGCTCGTGCCATAGGCGACTGGCT
ATTGGGTATGAACGCTACGCGTCTTTATACGCTCCGCTTCGGGGGCAACC
GACAGGTACTTTCCATCGGACGTGTACAGACTCCGACTCTCGCCCTTATT
GTCAGGAGACAGCACGAGATCGAGCACTTCACCCCTGAAGTCTACTGGGA
GGTGAAGACCATCTACCGCGATACGGTGTTCAATGCCACCAAGGGACGCT
TTTCCTCGATCGAGGATGCTCGTCGGGAAGTGGAGGTCGTAGCTGGCAGC
CCATTTGCTGTTACCTCCGTGGCTACGAAGAAAGGTCGGGAGCTGCCGCC
TCGACTTTTCGACCTCACCGGCCTACAGGTAGAATGCAATAAGAGGTTTG
CCATGACGGCCGATGCTACGCTACGCACCATCCAATCGCTGTATGAGAAG
AAGATCACCACCTATCCGCGCGTGGATACCACCTATCTGAGCGACGATGT
ATTCGAAAAAGTGCCGAATATCCTCCAAGGACTCTCCGACTATACCCTGC
TCACAGCTCCACTTCGAAGTAGCAAACTAAAAAAAAGCAAGAAGGTATTC
GACAATAGCAAGATCACTGACCACCATGCCATCATTCCCACCGGTCAGCC
ATCCCATGGTATGTCGGAGGATGAGCGACGTGTATTCGATCTGGTGGCCC
GCCGATTTATAGCCGTTTTCTATCCGGACTGCATATTCAGCCAGACCACG
GTCTTGGGACAAGCAGCTAAGGTAGAGTTCAAAACCACGGGGAAACAGAT
ACTGGAGCCCGGCTGGCGCACTGTCTTCACCGATCCGCAGACGGACGATG
ATGGAGAGAACAAGGACGAGGAGAAAAAACTGCCAATATTCTCCGAGGGC
GAAAGTGGAGTACACACCCCCGAGGTGCAGGAGAAAACGACACAGCCGCC
CAAATTCTATACCGAAGCTACACTCCTGCGTGCCATGGAGACGGCCGGCA
AGTCGGTCAAGGACGAAGAGCTCCGCGATGCCCTCAAAGAAAATGGCATC
GGCCGGCCGTCTACGCGAGCAGCCATCATTGAGACTCTCTTCAAGCGCAA
CTACATTTATAAAGAGAAGAAGAATCTCAAAGCTACTCCTACGGGTATGT
CTTTGATAGCGACGATCGACTATGACCTGCTCAAGAGTGCCGAGCTGACC
GGCCAATGGGAATACAAGCTTCGTCGCATCGAGCGAGGCGACTATTCAGC
AGCCGATTTTATCAATGAATTGAAAGTACTCCTGACCCATCTGATTCCTA
ATGTACTCAAGAGCAACTCTTCCGTACTCCTGTCAGAGCCGATACCTGCT
GCTTCGCCTGCTCCCGGCAAAAAGAAAAAGGCTGATAAACCCATGCAGAA
GCAGCTCGATCTCACCTGTCCGGTATGTGGCAAGGGAATCATTGTCCGCG
GTCGGGAAGCTTTCGGTTGCAATGCCTTTCGCGAAGGCTGCACCTTCCGA
CTTCCATACTCTGAGTATCCTGCATCTCTGTCCGACAACGAATTGGTTGA
TCTCCTTTCTTCGCAAAAAGGACAC

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