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Ureaplasma urealyticum Search Results

Record: 1 of 1  
MiniMap IGR155 IGR150 IGR153 IGR152 IGR151 IGR154 UU191 UU190 UU189 UU192 prsA,kprS, - UU193 rpoC, - UU188 rpoB, - UU187 UU191 UU190 UU189 UU192 prsA,kprS, - UU193 rpoC, - UU188 rpoB, - UU187 Type: tandem, Name:  - 125 Type: tandem, Name:  - 122 Type: tandem, Name:  - 123 Type: tandem, Name:  - 124 UU190 UU191 UU189 UU192 prsA,kprS, - UU193 rpoC, - UU188 rpoB, - UU187
* Calculated from Protein Sequence

Gene ID: UU188

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
rpoC  

Definition:
DNA-directed RNA polymerase beta prime chain

Gene Start:
229931

Gene Stop:
233848

Gene Length:
3918

Molecular Weight*:
147973

pI*:
9.30

Net Charge*:
20.70

EC:
2.7.7.6  

Functional Class:
transcription; DNA-dependent RNA polymerase  

Pathway: pathway table
Purine metabolism
Pyrimidine metabolism

Comment:
DNA-dependent RNA polymerase catalyzes the transcription of DNA
into RNA using the four ribnucleoside triphosphates as substrates.

Activity: N nucleoside triphosphate = N pyrophosphate + RNA(N).

Bacterial RNA polymerase consists of a sigma factor and a core enzyme composed of two alpha, one beta and one beta' chains. The alpha, beta, and beta' chains in U.u. are UU257, UU187, and UU188 respectively. The sigma factor is UU349. There is also a probable delta sequence: UU597.

Reference: Eur J Biochem. 1981 Jun 1;116(3):621-9.

Blast Summary:  PSI-Blast Search
A gapped BLAST reveals significant similarity to proteins described as: DNA-directed RNA Polymerase Beta' Chain (RpoC). For example: UU188 residues 4-1305 are 56% similar to RPOC_MYCPN. Other significant alignments are seen against (but not limited to): RPOC_BACSU, RPOC_MYCTU, RPOC_MYCLE, RPOC_BORBU and RPOC_STAAU.

A BLAST against the STDPRO database reveals significant hits to the RpoC proteins of M.genitalium (MG340), C.trachomatis (CT314) and T.pallidum (TP0242). For example: residues 4-1305 are 57% similar to MG340.

COGS Summary:  COGS Search
The phylogenetic pattern of COG0086 is ehgpCMYu.
Cog name: DNA-dependent RNA polymerase beta' subunit.
Functional class: K.
BeTs to -hg-cmyu.
Number of proteins in this genome belonging to this COG is 1



Blocks Summary:  Blocks Search
Residues 271-311 (D-8), 344-372(E-26), 372-402(F-4), 403-420(G-5), 475-529(I-2), 530-555(J-6), 556-597(K-17), 869-898(Q-3), 899-925(R-63), 1020-1053(T-1) and 1139-1184(Y-13) rank in the 100.ooth percentile to Block BL00115(block and rank given next to each stretch of amino acids), described as Eukaryotic RNA polymerase II heptapeptide repeat proteins.


ProDom Summary:  Protein Domain Search
Residues 9-141 are 73% similar to a defined domain of RPOC_MYCPN.
Residues 705-874 are 57% similar to a defined domain of RPOC_MYCGE.
Residues 318-469 are 32% similar to a defined domain of RPOC_PLAFA.

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

Pfam Summary:  Pfam Search
Residues 3 to 400 (E-value = 6.4e-179) place UU188 in the RNA_pol_Rpb1_1 family which is described as RNA polymerase Rpb1, domain 1 (PF04997)
Residues 402 to 553 (E-value = 1e-80) place UU188 in the RNA_pol_Rpb1_2 family which is described as RNA polymerase Rpb1, domain 2 (PF00623)
Residues 556 to 752 (E-value = 1.9e-37) place UU188 in the RNA_pol_Rpb1_3 family which is described as RNA polymerase Rpb1, domain 3 (PF04983)
Residues 777 to 872 (E-value = 1.5e-24) place UU188 in the RNA_pol_Rpb1_4 family which is described as RNA polymerase Rpb1, domain 4 (PF05000)
Residues 874 to 1246 (E-value = 8.5e-19) place UU188 in the RNA_pol_Rpb1_5 family which is described as RNA polymerase Rpb1, domain 5 (PF04998)

Structural Feature(s):
Feature Type  Start  Stop
coil-coil  
169  
197
non-globular  
349  
420
coil-coil  
440  
474
non-globular  
906  
992

PDB Hit:


Gene Protein Sequence:
MSQKGIKSLTISIASPEQILNWSKGEITKPETINYKSLKPEPNGLFDESI
FGPSKDYECYCGKYRKVKHKGKICERCHVEITESIVRRERMGHIELAAPV
AHIWFTKELPSPSKISLLLDITYKEVDQVVYFVNYIVLDEGNNVYDGKSI
FNKKEVLDLTSPKNSIRSRNKLRRTLRNIQERIEDELNHEREALIQDFDY
RLAVTYDQMLKDSNIPFSVKDVMAFIEKHTGVRFGIGAEAIRELLEKLNL
EEEHEKIKQAIQNSPNAYDQKTKRLLRRLECVRWIKDSGSKPEWMVMTRI
PVTPSETRPIISLDGGRFTTSDTNNFYRKIIIRNERLKQMQATDAPEILL
DNEKRLLQEAVDSLFDNNSRKKPVVGKDKRPLKSLSNHLKGKQGLFRQNL
LGKRVDYSGRSVIVVGPELKMYEVGIPALMILKLFRPYIISELIRKRDEL
GNEIQPICANIKLAEQKILAQDNEIWPVVEKVIKQRPVILNRAPTLHRLG
IQAFEPKMVDGKAIRLHPLVTTAFNADFDGDQMAVHIPLSKEAVAEARSI
LLASWHILGPKDGKPIITPTQDMILGIYYLTKEKFPQVIEEMMAKDPTQA
RVEFINNFHIFSTQDEAIRAYKLKTIRINDVIGITTKAFNNKTFSKEGIL
VTTVGKIIFNQAFPVNFPYINDVKNLYGENQFEIIGMHESILDYLKAYNL
KEPLTKKTLSTVIDYLYKVSEIEVVPQTMDKIKALGFKYSMISATSISAF
DIPSYDQKYEYFKETDELVSKLREFYLDGKLTDDERYTKVVQAWSQTKDK
VTHDIEKLINSNEYKDNPIVIMAKSGARGNTSNFTQLAGMRGLMSKSYNY
DQKNNNGVIKDTIEIPIKHSFIEGLSVSEYFNSSFGARKGMTDTAMKTAK
SGYMTRKLVDSTQAVVIKDHDCGTKEGIIVREIRNTKDNTSIESLKDRIV
GRYSINTIYDTKNKLIIESDKLITSEIANIIQNSGIREVEVRSPLHCASL
YGVCQKCFGLDLSTNKLIETGTAIGVIAAQSIGEPGTQLTMRTFHTGGVA
GDTNITQGFERIKQLFDCIQPQENEKAVISQVKGTVERIEKDSNTNGYNV
VIKYNKDNYVNYPTRSNAVLRVKTGDEIIAGQKITEGSIDVNDLLKYAGI
ENVRHYIIKEVQKVYRMQGIEISDKYIEVIISQLTNKITITNPGDSGLFV
GETISINEFTEVAQNMLVNKKKPPSAINQVFGLDHAPSKSGSFLSAASFQ
DTKKILTDAAARSQKDMLIGLKENVILGNLIPAGTGLKDVEEVIAYGEEM
YKKQY$

Gene Nucleotide Sequence:  Sequence Viewer
ATGAGTCAAAAAGGGATTAAATCATTAACGATTTCCATTGCTTCACCTGA
ACAAATTTTAAATTGATCAAAAGGTGAAATCACTAAACCTGAAACAATTA
ATTACAAATCATTAAAACCAGAACCTAATGGGTTGTTTGATGAAAGTATT
TTTGGGCCTTCAAAAGATTATGAATGTTATTGTGGAAAATATCGTAAAGT
AAAACATAAAGGTAAAATTTGTGAACGTTGTCATGTTGAAATTACTGAAT
CAATTGTACGTCGTGAACGAATGGGACATATTGAGTTAGCTGCTCCTGTT
GCCCATATTTGATTTACAAAAGAATTACCTTCGCCATCAAAAATCTCATT
ATTATTAGATATTACATATAAAGAAGTTGATCAGGTAGTTTATTTTGTTA
ATTACATTGTTTTAGATGAAGGAAATAATGTATATGATGGTAAATCAATT
TTTAATAAAAAAGAAGTTTTAGATTTAACATCACCAAAAAATTCAATTCG
ATCACGTAATAAATTACGTCGAACATTACGTAATATTCAAGAACGAATTG
AAGATGAATTAAATCATGAACGTGAAGCATTAATTCAAGATTTTGATTAT
CGTTTAGCTGTAACATATGATCAAATGTTAAAAGATTCTAATATTCCTTT
TTCAGTGAAAGATGTAATGGCTTTTATTGAAAAACATACAGGCGTTCGTT
TTGGTATTGGTGCTGAAGCTATTCGTGAATTATTAGAAAAACTAAATCTT
GAAGAAGAACATGAAAAGATTAAACAAGCAATTCAAAATTCACCTAATGC
TTATGATCAAAAAACAAAACGCTTATTGCGTCGTTTAGAATGTGTAAGAT
GAATTAAGGATTCAGGTTCAAAACCAGAATGAATGGTAATGACAAGAATC
CCTGTCACACCATCTGAAACAAGACCAATTATTTCTTTAGATGGCGGTCG
TTTTACGACCTCTGACACAAATAATTTTTATCGTAAAATCATTATTCGTA
ATGAACGTTTAAAACAAATGCAAGCAACAGATGCTCCTGAAATTTTATTA
GATAATGAAAAACGTTTATTACAAGAAGCAGTTGATTCATTATTTGATAA
TAATTCACGTAAAAAACCAGTTGTAGGTAAAGATAAACGTCCTTTAAAAT
CATTGTCAAATCATCTTAAAGGAAAACAAGGATTATTTAGACAAAATTTA
TTAGGAAAACGTGTTGACTATTCAGGTCGTTCTGTAATTGTTGTTGGTCC
TGAATTAAAAATGTATGAAGTAGGAATTCCTGCTTTAATGATTTTAAAAT
TATTTAGACCATATATTATTTCTGAATTAATACGTAAACGTGATGAATTA
GGTAATGAAATTCAACCAATTTGTGCCAATATTAAATTAGCAGAACAAAA
AATTCTTGCGCAAGATAATGAGATTTGACCCGTTGTTGAAAAAGTTATTA
AGCAACGTCCTGTAATTTTAAACCGTGCACCAACCTTACACCGTTTAGGG
ATCCAAGCTTTTGAACCAAAAATGGTGGACGGTAAAGCTATTCGTTTACA
TCCTCTAGTTACAACCGCTTTTAATGCGGATTTTGACGGAGACCAAATGG
CTGTTCATATCCCCTTATCCAAAGAAGCAGTGGCTGAAGCACGATCAATT
TTATTAGCCTCATGACATATTCTTGGTCCAAAAGATGGGAAACCTATCAT
TACACCCACACAGGATATGATTTTAGGTATTTATTATTTAACAAAAGAAA
AATTTCCACAAGTAATTGAAGAAATGATGGCTAAAGATCCAACGCAAGCG
AGAGTTGAATTTATTAATAATTTTCACATTTTTTCAACACAAGACGAAGC
TATTCGTGCTTATAAATTAAAAACAATTCGTATTAATGACGTAATTGGAA
TTACAACAAAAGCTTTTAACAATAAAACATTTAGTAAAGAAGGTATTTTG
GTTACAACGGTTGGAAAAATTATCTTCAACCAAGCTTTTCCTGTTAATTT
TCCATATATTAATGATGTTAAAAATCTATATGGCGAAAATCAATTTGAAA
TTATTGGAATGCATGAAAGTATTTTAGATTATTTAAAAGCCTATAATTTA
AAAGAACCATTAACTAAAAAAACTTTATCAACAGTAATTGATTATTTATA
TAAAGTTTCTGAAATCGAAGTCGTACCACAAACAATGGATAAAATTAAAG
CTTTAGGATTTAAATATTCAATGATTTCAGCGACAAGCATTTCTGCCTTT
GATATTCCATCTTATGATCAAAAATATGAATATTTTAAAGAAACTGATGA
ATTGGTTTCAAAACTTCGTGAATTCTATTTAGATGGTAAATTAACTGATG
ATGAGCGATATACTAAAGTTGTTCAAGCTTGATCACAAACAAAAGATAAA
GTTACTCATGATATTGAAAAACTAATTAATTCTAATGAATATAAAGATAA
TCCGATTGTGATTATGGCAAAATCAGGAGCTCGTGGAAACACGTCAAACT
TTACACAGTTAGCAGGAATGCGTGGTTTAATGTCAAAATCATATAACTAT
GACCAAAAAAATAATAATGGTGTTATTAAAGATACAATTGAAATTCCAAT
TAAGCATTCATTTATTGAAGGATTATCAGTTAGTGAATACTTTAATTCAT
CATTTGGAGCACGTAAAGGGATGACTGATACGGCGATGAAAACCGCAAAA
TCAGGTTATATGACACGTAAGTTAGTTGATTCAACACAGGCTGTTGTAAT
TAAAGATCATGATTGTGGCACAAAAGAAGGTATTATTGTTCGTGAAATTC
GAAATACAAAAGATAATACATCAATTGAATCACTAAAAGATCGTATTGTT
GGAAGATATAGTATTAATACAATTTATGATACAAAAAATAAATTAATTAT
CGAAAGTGATAAATTAATTACAAGCGAAATAGCTAATATCATTCAAAATT
CAGGTATTCGTGAAGTTGAGGTTCGTTCTCCATTACATTGTGCATCACTT
TATGGTGTTTGTCAAAAATGTTTTGGTTTAGATCTATCAACAAATAAATT
AATTGAAACCGGTACAGCGATTGGAGTAATTGCAGCGCAATCAATTGGTG
AACCTGGAACACAGTTAACAATGCGTACTTTCCATACTGGAGGGGTTGCT
GGTGATACGAATATTACTCAAGGGTTTGAAAGAATTAAACAATTATTTGA
TTGCATTCAACCACAAGAAAATGAGAAAGCAGTTATTTCACAAGTAAAAG
GAACTGTTGAACGAATCGAAAAAGATTCAAACACCAATGGTTATAATGTT
GTAATTAAATATAATAAAGATAATTATGTAAATTATCCAACACGTTCGAA
TGCTGTATTACGTGTTAAAACAGGAGATGAAATTATTGCTGGTCAAAAAA
TTACTGAAGGATCAATTGATGTTAATGATTTACTAAAATATGCAGGTATT
GAAAATGTGCGTCATTACATTATTAAAGAAGTTCAAAAAGTTTATCGTAT
GCAAGGAATTGAGATTTCAGATAAGTATATTGAAGTAATCATTTCACAAC
TTACAAATAAAATTACAATTACAAATCCAGGAGATTCAGGATTATTTGTT
GGAGAAACAATTAGTATTAATGAATTTACTGAAGTGGCTCAAAATATGCT
TGTTAATAAGAAAAAACCACCAAGTGCAATTAATCAAGTATTTGGTTTAG
ACCATGCGCCAAGTAAATCAGGTTCATTCTTATCTGCTGCTTCGTTCCAA
GATACTAAGAAAATATTAACTGACGCTGCTGCGCGTTCACAAAAAGATAT
GTTAATCGGCTTGAAAGAAAACGTTATTCTAGGAAATTTAATTCCTGCTG
GAACAGGATTAAAGGATGTTGAAGAAGTGATTGCTTATGGTGAAGAAATG
TATAAAAAGCAATACTAA


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