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Ureaplasma urealyticum Search Results

Record: 1 of 1  
MiniMap IGR317 IGR316 IGR315 IGR313 IGR314 UU380 UU379 UU376 mba, - UU375 UU378 polC, - UU377 UU380 UU379 UU376 mba, - UU375 UU378 polC, - UU377 Type: tandem, Name:  - 241 Type: tandem, Name:  - 238 Type: tandem, Name:  - 239 Type: tandem, Name:  - 240 Type: tandem, Name:  - 449 UU379 UU376 mba, - UU375 UU379.1 UU380 UU379.1 UU378 polC, - UU377
* Calculated from Protein Sequence

Gene ID: UU377

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
polC  

Definition:
DNA polymerase III alpha chain (epsilon function?)

Gene Start:
430144

Gene Stop:
434472

Gene Length:
4329

Molecular Weight*:
166233

pI*:
6.90

Net Charge*:
-2.40

EC:
2.7.7.7  

Functional Class:
replication; DNA replication, restriction, modification, recombination, and repair  

Pathway: pathway table
Purine metabolism
Pyrimidine metabolism

Comment:
UU019 is a predicted delta coding sequence. UU377 and UU415 appear to be alpha subunits. UU087 is a predicted gamma-tau sequence. Could UU377 serve as an epsilon sequence, since UU415 is not seen as a paralog?

This cds displays high A+T content at the 5' end; this observation coupled with the BLAST results suggests that the start site may be downstream from what is herein predicted.

See UU414, a predicted polA sequence.

Blast Summary:  PSI-Blast Search
Numerous hits in gapped BLAST to pol III alpha chain sequences, e.g. residues 270-1442 are 39% similar to DP31_MYCGE (MG031). Majority of strong similarities begin around residue 225, suggesting that the true start may be other than what has been proposed (see Comment). UU377 is also similar to CT545 and TP0669, predicted pol III alpha chain sequences. Best hits were to alpha sequences, weaker hits were to epsilon sequences.

COGS Summary:  COGS Search
The phylogenetic pattern of COG0587 is Ehgpc--u.
Cog name: DNA polymerase III epsilon subunit (3'-5' exonuclease).
Functional class: L.
BeTs to e-g-c---.
Number of proteins in this genome belonging to this COG is 1



Blocks Summary:  Blocks Search
Residues 842-1293 span seven regions of similarity to blocks PD2001A-F, which encompass pol II alpha chain sequences, e.g. DP3A_BACSU.



ProDom Summary:  Protein Domain Search
Residues 322-398, 409-495, 498-568, 607-876, and 877-1441 are 46%, 45%, 48%, 33%, and 49% similar to alpha and epsilon alpha chain domains of DP31 and DP3A sequences.

Paralogs:  Local Blast Search
No paralogs in U.u.

Pfam Summary:  Pfam Search
Residues 323 to 388 (E-value = 2.1e-11) place UU377 in the PHP_N family which is described as PHP domain N-terminal region (PF02231)
Residues 409 to 568 (E-value = 3.2e-42) place UU377 in the Exonuc_X-T family which is described as Exonuclease (PF00929)

Structural Feature(s):
Feature Type  Start  Stop
non-globular  
1  
256
coil-coil  
451  
482
coil-coil  
1400  
1427

PDB Hit:


Gene Protein Sequence:
METKNALFKKIVKISDQLLNKISIKKLTKDKKNNLFVYFDEFVDVTIIDE
LHQLSKTTLMHDLQIWYINNLKEVDHKKILTFFKKISEQNANLIFLEQIN
DLNTKIEYNSNLNSLILKINDKLIYDHFIANKLEILNILKVWSLPYSNFE
IHFENLSSLLNEKHEQAVNEIISHHIQQQKHLEQQISQQQNFYNNQKANF
NYYKNPSNKTITKLIDINPLMNNAKIRAYVFLKKIDILKSGAIAYKLNVI
DDSETLTIMTYLPSGEHPLKKFLDELKIDQLIEAEIDIVLDNMSKSGQVP
IGKIKKICCVEDKHVKKQITPRLELNFHTKMSSLDAIISTQELIDFAVKN
QLKTIGITDRNVVQAYPEIAKFSKKQDLKIIYGLETEELEDQIPLVLNVR
DQNLDNATYVIFDIETTGLFPNFDEIIEFGAVIMQNNKQIGEKIQFFIKP
IQQINENVTNLTNISQEMVNNAIDEKTALLKIKEIFDDHILVAHNGINFD
INFINQRLLKWGLEPLKNPSIDTLMISRAINPFKSHRLGAICKKYEVDYN
DESAHRADYDAIVLADVFKVMKNNLFNDFGITNLSEINTKLQTTMLKNRS
FGNWINLYIKNQANVKDMYELVSISHTDMYYTRPTITTSFLANKKDKLII
SNSIHESDLINALYSKNDEEIKRLIQRYDFITLPSLGSQKHLVYAKKITI
ENVQKAFKKLIYLALELNKIIIYSSSPYYFFKDDKKFYDVYVNTKGLEGK
AHRFANEVYVPDLEYIDQKNAIDELAYLEDEKLINLIINENPVHINSWFD
DSIQPLKEGLYAPKMEGVDQKTIDYVYHTAKKIYGENLPTIVEQRIKKEL
NSIIKHGFSVVYWISHLLVEKSMQDGYGVGSRGSVGSSLVATFLNITDVN
PLTPHYLCPNCKKCEFITNADDGFDLAPKSCEQCQTPMLTDGHNIPFETF
LGFDGDKVPDIDLNFSGVYQAVAHNFIKSIFGETHSYRAGTIGTMAQTSA
ENTVKKYFENRFNENKIIRDSTVSLYVQKCIDSKRTTGQHPGGIIIVPKE
YSIWDFSPYNFPANDINETWKTTHFAFEYLHDSLLKFDILGHDNPTILKL
LKDYTGIDERDVPMYDPLVMKSFSDISALNIKPSDVLNETTGAISIPEFG
TRFVRGMLVDTKPKSFADLIRISGLSHGESVWLGNAQSLIKSGKLLKDVI
ACRDDIMTYLIRQNVEPKTAFLIMEDVRKGKKIKPEHQIILKELKVPEWY
IESANKIKYMFPKAHATAYVMHAWKFAWYKIYYPLEYYAAFFSVRADNFD
LFVINQGKEFIEKTYNDIEQRSKSRDPQKKVSSRELALQPIYEIVIELLA
RGFKISNISIEQSQATSYVIDKENNAIIPPFIAIQGLGETVANSIIEARN
QKVFSTIEDLKNRTKISRTDLKNLRVLGVLDHLSETEQLTLF$

Gene Nucleotide Sequence:  Sequence Viewer
ATGGAAACAAAGAATGCATTATTTAAAAAGATTGTAAAAATTTCTGATCA
ATTATTAAATAAAATTAGTATCAAAAAATTAACTAAAGATAAAAAAAATA
ATTTATTTGTTTATTTTGACGAATTTGTTGATGTAACAATTATTGATGAA
TTACATCAATTATCAAAAACAACATTAATGCATGATTTACAAATTTGATA
TATTAATAATTTAAAAGAAGTTGATCATAAAAAAATATTAACTTTTTTTA
AAAAAATTAGTGAACAAAATGCTAATTTAATCTTTTTAGAACAAATAAAT
GATTTAAATACAAAAATAGAATATAACTCTAATTTAAATTCATTAATTTT
AAAAATTAATGATAAATTAATTTATGATCATTTTATAGCAAATAAATTAG
AAATTTTAAACATCTTAAAAGTTTGATCACTACCTTATAGTAATTTTGAA
ATTCATTTTGAAAATCTTAGTTCATTATTAAATGAAAAGCATGAACAAGC
AGTAAATGAAATTATTAGTCATCATATTCAACAACAAAAACATTTAGAAC
AACAAATTAGTCAGCAGCAAAATTTTTATAATAATCAAAAGGCAAATTTT
AATTATTATAAAAATCCTTCAAATAAAACAATTACAAAATTAATTGATAT
TAATCCTTTAATGAATAATGCAAAAATTCGAGCTTATGTTTTTTTAAAAA
AGATTGATATATTAAAAAGTGGAGCAATAGCTTATAAACTAAATGTTATT
GATGATAGTGAAACCTTAACAATTATGACTTATTTACCAAGCGGTGAACA
TCCTTTAAAAAAGTTTTTAGATGAACTGAAAATTGATCAATTAATCGAGG
CTGAAATTGATATTGTTTTAGATAATATGAGTAAGAGTGGTCAAGTTCCT
ATTGGTAAAATTAAAAAAATTTGTTGCGTTGAAGATAAACATGTAAAAAA
ACAAATCACACCTCGTTTAGAACTAAATTTTCATACAAAAATGTCATCAC
TTGATGCAATTATTTCGACACAAGAATTAATTGATTTTGCGGTTAAGAAT
CAATTAAAAACAATTGGCATCACTGATCGAAATGTTGTACAAGCATATCC
TGAAATCGCTAAATTTTCTAAAAAACAAGATTTAAAAATTATTTATGGTT
TAGAAACAGAAGAATTAGAAGATCAAATCCCATTAGTTTTAAATGTTCGG
GATCAAAATTTAGATAATGCTACATATGTTATTTTTGATATTGAAACAAC
AGGATTATTTCCTAATTTTGATGAAATTATTGAATTTGGGGCCGTGATTA
TGCAAAATAATAAGCAAATTGGGGAAAAAATTCAATTTTTTATAAAACCT
ATTCAACAAATTAATGAGAATGTTACTAATCTAACTAATATTAGTCAAGA
AATGGTCAATAATGCAATTGATGAAAAAACAGCATTATTAAAAATTAAAG
AAATTTTTGATGACCATATTTTAGTTGCACATAATGGAATTAATTTTGAT
ATTAATTTTATTAATCAGAGACTGTTAAAATGAGGATTAGAACCTCTTAA
AAATCCTAGTATTGATACATTAATGATATCACGAGCAATAAATCCATTTA
AAAGTCATCGATTAGGAGCGATTTGTAAAAAATATGAAGTTGATTATAAT
GATGAAAGTGCACACCGTGCAGACTATGATGCCATAGTTTTAGCTGATGT
TTTTAAAGTTATGAAAAATAACTTATTTAATGATTTTGGAATTACTAATT
TAAGTGAAATTAATACTAAATTACAAACAACAATGTTAAAAAATCGTAGT
TTTGGTAATTGAATTAATCTTTATATTAAAAATCAAGCAAATGTTAAAGA
TATGTATGAATTAGTGTCTATATCTCATACTGATATGTATTATACAAGAC
CAACAATTACGACAAGCTTTTTAGCAAATAAAAAAGATAAATTAATTATT
TCTAACTCGATTCACGAATCAGATTTAATCAATGCTTTATATTCAAAAAA
CGATGAAGAAATTAAAAGGTTAATTCAACGTTATGATTTTATAACATTAC
CATCATTAGGTTCACAAAAACACTTAGTATATGCTAAAAAAATTACAATT
GAAAATGTACAAAAAGCTTTTAAAAAATTGATCTATTTAGCTTTAGAATT
AAACAAGATTATTATTTATTCAAGCTCGCCTTATTATTTCTTTAAAGATG
ATAAAAAATTTTATGATGTTTATGTTAATACGAAAGGTCTCGAAGGTAAA
GCACACCGATTTGCTAATGAAGTTTATGTTCCTGATTTAGAATATATTGA
TCAAAAAAATGCCATTGATGAATTAGCTTATTTAGAAGATGAAAAGTTAA
TTAACTTGATTATTAATGAGAATCCTGTGCATATTAATAGTTGATTTGAT
GATAGCATACAACCTTTAAAAGAAGGATTGTATGCTCCAAAAATGGAAGG
TGTTGATCAAAAAACAATCGATTATGTTTATCATACTGCTAAAAAAATAT
ATGGAGAGAATTTACCAACAATTGTTGAACAGCGCATTAAAAAAGAATTA
AATTCAATTATTAAACATGGTTTTAGTGTTGTTTATTGAATTTCACATTT
ATTAGTAGAAAAATCAATGCAAGATGGTTATGGTGTTGGTAGTCGTGGTT
CGGTTGGCTCATCACTTGTCGCAACGTTTTTAAATATTACTGACGTTAAT
CCGCTTACACCACATTATTTATGTCCTAATTGTAAAAAATGTGAATTTAT
AACAAACGCTGATGATGGATTTGATTTAGCTCCTAAAAGTTGTGAGCAGT
GTCAAACTCCAATGTTAACTGATGGACATAATATTCCTTTTGAAACTTTT
TTAGGTTTTGATGGGGATAAAGTACCAGATATTGATCTTAATTTTTCTGG
AGTTTATCAAGCAGTTGCACATAATTTTATTAAAAGTATTTTTGGAGAAA
CACATTCTTATCGTGCTGGTACAATTGGTACTATGGCCCAAACAAGCGCT
GAAAATACGGTTAAGAAGTATTTTGAAAACCGTTTTAATGAAAATAAAAT
TATTCGTGATTCAACGGTTAGTTTATATGTACAAAAGTGCATTGATTCTA
AACGCACAACTGGTCAACATCCTGGGGGTATTATTATTGTTCCTAAAGAA
TATAGTATTTGGGATTTTTCACCTTATAATTTTCCAGCTAATGATATTAA
TGAAACTTGAAAAACAACTCATTTTGCGTTTGAATATCTACATGATAGTT
TATTAAAATTTGATATTTTAGGACATGATAATCCAACAATTTTAAAACTT
TTAAAAGATTATACGGGGATTGATGAACGTGATGTACCAATGTATGATCC
ATTAGTTATGAAATCATTTAGCGATATTAGTGCGCTAAATATTAAACCGT
CTGATGTTTTAAATGAAACAACAGGAGCAATTTCTATTCCTGAATTTGGG
ACACGCTTTGTACGTGGTATGCTAGTGGATACTAAACCAAAATCATTTGC
TGACTTAATTCGTATTTCAGGATTATCACATGGAGAAAGTGTTTGATTAG
GAAATGCACAGTCATTAATTAAATCTGGTAAATTGCTAAAGGATGTTATT
GCTTGTCGTGATGATATTATGACATATTTAATTCGTCAAAATGTTGAACC
AAAAACTGCCTTTTTAATTATGGAAGATGTTAGAAAAGGTAAAAAGATCA
AACCAGAACACCAAATCATTTTAAAAGAATTAAAGGTTCCTGAATGATAC
ATTGAATCAGCTAATAAAATTAAATATATGTTTCCCAAAGCACATGCCAC
AGCTTATGTTATGCATGCATGAAAATTTGCTTGATATAAAATTTATTATC
CACTAGAATACTATGCAGCATTTTTTAGTGTTCGTGCTGATAATTTTGAT
TTATTTGTAATTAATCAAGGTAAAGAATTTATTGAAAAAACTTATAATGA
TATCGAACAACGTTCTAAATCACGCGATCCACAAAAAAAAGTTAGTTCAC
GTGAACTTGCTTTACAACCAATTTATGAAATTGTGATTGAATTATTAGCT
CGAGGTTTTAAAATTTCAAATATTAGTATTGAACAATCACAGGCGACTAG
TTATGTAATTGATAAAGAAAACAATGCTATTATTCCACCATTTATTGCGA
TTCAAGGATTGGGTGAAACAGTAGCTAATTCAATCATTGAAGCTCGTAAT
CAAAAAGTTTTTTCAACAATTGAGGATTTAAAAAACCGTACAAAAATTTC
GCGTACAGATTTAAAAAATTTACGAGTATTAGGCGTTTTAGATCATTTAA
GTGAAACTGAACAACTAACATTATTTTAA


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