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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR492 IGR491 IGR494 IGR488 IGR493 IGR489 IGR490 HD0697 oxyR, - HD0699 fbp, - HD0702 tyrS, - HD0693 vacB,rnr, - HD0695 grx, - HD0700 dnaG, - HD0690 rpoD, - HD0691 HD0697 oxyR, - HD0699 fbp, - HD0702 tyrS, - HD0693 vacB,rnr, - HD0695 grx, - HD0700 dnaG, - HD0690 rpoD, - HD0691 oxyR, - HD0699 fbp, - HD0702 tyrS, - HD0693 vacB,rnr, - HD0695 HD0694 HD0698 HD0694 HD0697 HD0698 grx, - HD0700 dnaG, - HD0690 rpoD, - HD0691
* Calculated from Protein Sequence

Gene ID: HD0695

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
vacB  rnr  

Definition:
ribonuclease r, virulence associated protein

Gene Start:
552572

Gene Stop:
550215

Gene Length:
2358

Molecular Weight*:
90047

pI*:
9.20

Net Charge*:
15.24

EC:
3.1.-.-  

Functional Class:
Transcription; Degradation of RNA  

Pathway: pathway table

Secondary Evidence:
Tobe,T., Sasakawa,C., Okada,N., Honma,Y. and Yoshikawa,M.
vacB, a novel chromosomal gene required for expression of virulence genes on the large plasmid of Shigella flexneri
J. Bacteriol. 174 (20), 6359-6367 (1992)
MEDLINE: 93015684

Cheng,Z.F., Zuo,Y., Li,Z., Rudd,K.E. and Deutscher,M.P.
The vacB gene required for virulence in Shigella flexneri and
Escherichia coli encodes the exoribonuclease RNase R
J. Biol. Chem. 273 (23), 14077-14080 (1998)
MEDLINE: 98269059



Comment:


Blast Summary:  PSI-Blast Search
Many very strong hits in gapped BLAST to ribonuclease R proteins and virulence-associated vacB proteins; e.g., residues 4-728 are 68% similar to RNR_HAEIN [1174933], residues 1-733 are 62% similar to RNR_ECOLI [731093], and residues 1-725 are 62% similar to RNR_SHIFL [7676163].

COGS Summary:  COGS Search
BeTs to 10 clades of COG0557
COG name: Exoribonucleases
Functional Class: K
The phylogenetic pattern of COG0557 is ----YqvCEb-Hujgp-lin-
Number of proteins in this genome belonging to this COG is 2

Blocks Summary:  Blocks Search
***** IPB001900 (Ribonuclease II domain) with a combined E-value of 3.6e-56.
    IPB001900A    270-282
    IPB001900B    294-333
    IPB001900C    457-466
    IPB001900D    562-581


ProDom Summary:  Protein Domain Search
Residues 648-722 are 68% similar to a (RIBOSOMAL COMPLETE PROTEOME RNA-BINDING 30S REPEAT) protein domain (PD000709) which is seen in Q9CJP2_PASMU.

Residues 86-231 are 76% similar to a (RIBONUCLEASE VACB PROTEOME COMPLETE) protein domain (PD220661) which is seen in RNR_HAEIN.

Residues 232-578 are 68% similar to a (RIBONUCLEASE HYDROLASE COMPLETE PROTEOME EXONUCLEASE) protein domain (PD003098) which is seen in Q9CJP2_PASMU.

Residues 86-224 are 41% similar to a (COMPLETE PROTEOME RIBONUCLEASE RNASE) protein domain (PD403247) which is seen in Q9HUM7_PSEAE.

Residues 582-643 are 63% similar to a (R RIBONUCLEASE EXONUCLEASE COMPLETE) protein domain (PD412683) which is seen in Q9KNY1_VIBCH.

Residues 4-85 are 71% similar to a (VACB PROTEOME COMPLETE RIBONUCLEASE) protein domain (PD344419) which is seen in Q9CJP2_PASMU.

Residues 87-198 are 37% similar to a (II HYDROLASE RNASE EXONUCLEASE) protein domain (PD139355) which is seen in RNR_AQUAE.

Residues 612-646 are 74% similar to a (PROTEOME VACB COMPLETE RIBONUCLEASE) protein domain (PD269263) which is seen in Q9CJP2_PASMU.

Residues 16-85 are 51% similar to a (R COMPLETE PROTEOME RIBONUCLEASE) protein domain (PD406748) which is seen in Q9KNY1_VIBCH.

Residues 451-589 are 34% similar to a (II EXORIBONUCLEASE HYDROLASE RNASE) protein domain (PD316878) which is seen in RNB_BUCAI.



Paralogs:  Local Blast Search

HD0695 is paralogously related to HD1264 (2e-44), HD0317 (7e-06) and HD1352 (0.001).


Pfam Summary:  Pfam Search
Residues 182 to 549 (E-value = 7.9e-129) place HD0695 in the RNB family which is described as RNB-like protein (PF00773)
Residues 639 to 723 (E-value = 1.8e-15) place HD0695 in the S1 family which is described as S1 RNA binding domain (PF00575)

PDB Hit:
No significant hits to the NCBI PDB database.

Gene Protein Sequence:
MITDPNYQQEREKYANPIPSREFILQTIRHFDAPMSREALLATFNINDEE
RSEAIRRRLHAMENDGQLIFTKRKSYALPEKMDLIKGTVIGHRNGYGFLQ
VDGSEKDWFIPNNQMNRIMHGDFVLAQPNGTDRHGRREVRIVRVLEAGKK
QIVGRFFIESGIAFVMPDDSRITRDILIPAEHCMGARMGQIVVVELQERK
ASLSRPIGFITEILGDNLAPGMEIEIALRNHDIPHHWSDDVKKQIRQYND
QVPEVAKQDRIDLRHLPLVTIDGESACDFDDAVFARKEGDQWRLWVAIAD
VSYYVRPKTALDLEAAKRGNSVYFPKRVIPMLPEVLSNGLCSLNPQVDRL
CLVAEMTVCQSGELTRYQFYEAVMNSHARLTYNKVWKILNGDQTLHSRYA
PLVPHLVELNNMFKSLTKARQKRGAIEFETIENQFIFNPQGRIERIEPLI
RNDAHKIIEECMILANVAAARFVTQANEPALFRIHDKPSEEKLTSFKSFI
RERGLVWNVGRDPTPKDYAELLAMLSERPDRELIQTMLLRSLKQAVYAAD
NIGHFGLALSEYAHFTSPIRRYPDLLLHRSIKYLIEKEKGNTRNYTDGGG
YHYKLDDIDQFGDQCSITERRADEASSEVADWLKCEFMQDHLGKEFKGVI
SSVTGFGLFVKLNDLLIDGLVHISTLDNDYYHYDADRQRLVGESGLIYRL
GDPVNVKVINVNLADKKIDFALLNNLRKGIAVGKTAKQKAKKATHQPRFK
ELNTLTTTNNSEKRTKKRKASTKYSKKASRIKKND$

Gene Nucleotide Sequence:  Sequence Viewer
ATGATCACTGATCCAAATTATCAACAAGAACGCGAAAAATACGCCAACCC
TATCCCTTCTCGTGAATTTATTTTACAAACTATCCGCCATTTTGATGCAC
CGATGAGCCGTGAAGCATTATTAGCTACGTTTAATATCAATGATGAAGAA
CGCAGTGAAGCAATCCGCCGTCGTTTACATGCAATGGAAAATGATGGGCA
ACTGATTTTCACTAAACGAAAATCTTACGCATTGCCTGAAAAAATGGATT
TAATCAAAGGCACCGTAATCGGCCATCGTAACGGCTATGGCTTTTTACAA
GTTGACGGCAGTGAAAAAGATTGGTTTATCCCCAATAATCAAATGAATCG
CATTATGCACGGTGACTTTGTATTAGCACAACCCAATGGCACAGATCGCC
ATGGTCGCCGTGAAGTGCGTATAGTTCGCGTGCTTGAAGCCGGTAAAAAA
CAAATTGTCGGCCGCTTTTTCATAGAAAGCGGTATCGCTTTCGTTATGCC
CGATGATAGCCGTATTACCCGCGATATTCTCATTCCTGCCGAACATTGTA
TGGGGGCAAGAATGGGGCAAATTGTAGTGGTTGAATTACAAGAGCGTAAA
GCCAGTTTAAGCCGTCCTATTGGCTTTATTACCGAAATATTAGGTGACAA
TCTCGCGCCGGGTATGGAAATCGAAATCGCCTTACGTAATCACGATATTC
CACATCATTGGAGTGACGACGTCAAAAAACAAATTCGGCAATATAATGAT
CAGGTTCCTGAAGTCGCCAAACAAGACAGAATAGACTTACGCCACTTACC
CTTAGTCACCATTGATGGTGAAAGTGCCTGCGATTTTGACGATGCCGTAT
TCGCAAGAAAAGAAGGCGATCAATGGCGTTTATGGGTAGCTATCGCTGAT
GTAAGCTATTATGTTCGCCCTAAAACAGCATTAGATTTAGAAGCCGCTAA
GCGCGGTAACTCCGTTTATTTTCCTAAACGTGTGATTCCAATGCTACCTG
AAGTATTATCAAATGGTTTATGTTCGCTTAACCCACAAGTTGACCGCCTC
TGTTTAGTAGCAGAAATGACCGTTTGCCAGAGTGGTGAATTAACCCGTTA
TCAATTTTATGAAGCCGTGATGAATTCACACGCCCGTTTAACTTATAACA
AAGTTTGGAAAATATTAAATGGCGATCAAACACTACACAGCCGTTATGCC
CCATTAGTACCGCATTTAGTAGAATTGAATAATATGTTCAAAAGCCTAAC
TAAAGCACGCCAAAAACGTGGTGCCATTGAATTTGAAACCATCGAAAATC
AGTTTATCTTTAATCCACAAGGCAGAATTGAACGAATTGAACCACTGATC
CGTAATGATGCACATAAAATCATTGAAGAATGTATGATTTTAGCCAACGT
TGCCGCTGCACGCTTTGTAACACAAGCAAATGAACCTGCGTTATTCCGTA
TTCACGATAAACCAAGTGAAGAAAAGCTCACTAGCTTTAAATCCTTCATT
CGTGAGCGTGGCTTAGTATGGAATGTAGGGCGTGATCCCACCCCCAAAGA
TTATGCTGAATTACTAGCCATGCTAAGCGAACGACCTGATCGGGAACTGA
TTCAAACAATGCTATTACGTTCATTAAAACAGGCCGTTTATGCTGCCGAT
AATATTGGTCATTTTGGTTTAGCCTTGAGTGAATATGCTCATTTCACCTC
TCCTATTCGTCGTTACCCAGATCTCCTATTACATCGTTCAATTAAATATT
TAATTGAAAAAGAAAAAGGCAACACACGCAATTACACCGATGGTGGTGGC
TATCACTATAAACTAGATGATATTGATCAATTTGGCGATCAATGTTCTAT
TACTGAACGGCGAGCTGATGAAGCCTCCAGTGAAGTTGCTGATTGGCTGA
AATGTGAATTTATGCAAGATCATCTCGGCAAAGAATTTAAAGGCGTTATT
TCAAGCGTTACTGGCTTTGGTTTATTCGTCAAACTCAATGATTTACTGAT
TGATGGCTTAGTCCATATTTCTACACTAGATAATGACTACTACCATTATG
ATGCAGATCGCCAACGACTCGTCGGTGAAAGCGGGCTAATTTATCGTTTA
GGCGACCCAGTTAACGTCAAAGTTATCAACGTTAATCTAGCGGATAAAAA
GATTGATTTTGCTTTACTGAATAACTTACGCAAAGGCATTGCTGTAGGTA
AAACCGCGAAACAAAAAGCGAAAAAGGCTACTCATCAACCAAGGTTTAAA
GAACTTAACACATTGACCACAACGAACAATAGCGAAAAACGAACAAAAAA
AAGAAAAGCAAGTACCAAATATTCAAAAAAAGCTTCACGAATTAAAAAGA
ATGATTAA


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