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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap tRNA-Val-4 IGR922 IGR921 IGR924 IGR920 IGR927 IGR926 IGR925 IGR923 HD1259 HD1261 HD1267 fabI,envM, - HD1266 ybfF, - HD1268 apaH, - HD1263 perM, - HD1258 queA, - HD1257 rnb, - HD1264 seqA, - HD1270 menE, - HD1271 HD1259 HD1261 HD1267 fabI,envM, - HD1266 ybfF, - HD1268 apaH, - HD1263 perM, - HD1258 queA, - HD1257 rnb, - HD1264 seqA, - HD1270 menE, - HD1271 HD1261 HD1267 fabI,envM, - HD1266 ybfF, - HD1268 apaH, - HD1263 perM, - HD1258 queA, - HD1257 rnb, - HD1264 HD1259 seqA, - HD1270 menE, - HD1271
* Calculated from Protein Sequence

Gene ID: HD1264

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
rnb  

Definition:
exoribonuclease II (ribonuclease II)

Gene Start:
1028064

Gene Stop:
1026085

Gene Length:
1980

Molecular Weight*:
75967

pI*:
6.20

Net Charge*:
-9.02

EC:
3.1.13.1  

Functional Class:
Transcription; Degradation of RNA  

Pathway: pathway table

Secondary Evidence:
Cheng ZF, Deutscher MP.
Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II.
J Biol Chem. 2002 Jun 14;277(24):21624-9.
PMID: 11948193

Cannistraro VJ, Kennell D.
Escherichia coli ribonuclease II.
Methods Enzymol. 2001;342:309-30.
PMID: 11586905

Zilhao,R., Camelo,L. and Arraiano,C.M.
DNA sequencing and expression of the gene rnb encoding Escherichia coli ribonuclease II.
Mol. Microbiol. 8(1):43-51.
Medline: 93268098



Comment:


Blast Summary:  PSI-Blast Search
Numerous significant hits in gapped BLAST to ribonuclease II and ribonuclease R proteins; e.g., residues 1-659 are 62% similar to ribonuclease II protein (U32846) of Haemophilus influenzae Rd, residues 1-654 are 47% similar to a ribonuclease II protein ((AE000226) of Escherichia coli, residues 23-653 are 27% similar to a virulence-associated VacB protein (U32767) of Haemophilus influenzae Rd, and residues 21-653 are 25% to a VacB protein (AJ242786) of Burkholderia sp.Swi

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 3.4e-43.
    IPB001900A    199-211
    IPB001900B    228-267
    IPB001900C    393-402
    IPB001900D    507-526


ProDom Summary:  Protein Domain Search
Residues 565-654 are 50% similar to a (II EXORIBONUCLEASE EXONUCLEASE) protein domain (PD042374) which is seen in RNB_HAEIN.

Residues 173-564 are 47% similar to a (RIBONUCLEASE HYDROLASE COMPLETE PROTEOME EXONUCLEASE) protein domain (PD003098) which is seen in RNB_ECOLI.

Residues 1-168 are 70% similar to a (II HYDROLASE RNASE EXONUCLEASE) protein domain (PD139355) which is seen in Q9CP74_PASMU.

Residues 385-564 are 67% similar to a (II EXORIBONUCLEASE HYDROLASE RNASE) protein domain (PD316878) which is seen in RNB_HAEIN.



Paralogs:  Local Blast Search

HD1264 is paralogously related to HD0695 (2e-44).


Pfam Summary:  Pfam Search
Residues 118 to 489 (E-value = 7e-104) place HD1264 in the RNB family which is described as RNB-like protein (PF00773)

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

Gene Protein Sequence:
MFQNNPLLAQLKQQIEANKEYVEGKVKASDKNFGFLEADKKSYFIPPLEM
KKVMHGDNVKAVIKREGDKESVEIDSLIDPMLDRFIARVRFNKDGKLQLA
VDHPQIRLNIPATTHKKVTEQLANDDWVVAQLKSHPLRDDRFFFAQVTEF
ICKADDHFAPWWVTLARHQQPRESVKTEQSYTLQDQSPREDLSHLYFTTI
DSPSTQDMDDALFIEPITENAIQQGWRLVVAIADPTAYIAEDSNIEHAAR
QRCFTNYLPGFNIPMLPRELSDDLCSLVPNKKRPALVVYIETDLNGNLIK
DASFHTAWVESKAKLAYDNVSDYLEGVEQAWQPDCAELKQQIYWLHQFTQ
ARIQWRSKNALLFKEQMDYNFELNADGSVKSIQIQYHRIANQIIEEAMII
ANICCAQFLAKHAKTGIFNSHAGFDPKNYEAVQTFLLNTLATDENRSELT
DLFSPTQLATLDGYCAMRRYIEDFPEKFLELRLRRYLTFAEFKAEVAPHF
GLGISHYATWTSPIRKYGDIVNHRLIKQVLLNQPIKHIESTILARLQEAR
RQNRLVERDIADWLYARYLLPIATQGVEFDCEITDISRGGIRAKVLENGA
QIFIPCSTLHENKDEIDFIPEEIALYTKGEKIYQIGQATRVKLTDVRLET
RSVLGNIIK$

Gene Nucleotide Sequence:  Sequence Viewer
ATGTTCCAAAACAATCCACTGTTAGCTCAGCTAAAACAACAAATTGAAGC
AAATAAAGAATATGTTGAGGGTAAAGTAAAGGCCTCAGATAAAAATTTTG
GCTTTTTAGAAGCTGATAAAAAAAGCTACTTTATTCCACCGCTTGAAATG
AAAAAAGTGATGCATGGAGATAATGTCAAAGCGGTTATAAAACGAGAAGG
CGATAAGGAATCGGTCGAAATAGATAGCTTAATTGATCCTATGTTAGATC
GTTTTATTGCACGAGTTCGTTTTAATAAAGATGGTAAGCTACAATTAGCA
GTTGACCATCCACAAATCAGATTAAATATTCCCGCGACTACGCATAAAAA
AGTAACAGAACAATTAGCAAATGACGACTGGGTGGTCGCACAATTAAAAA
GCCATCCATTACGAGATGATCGTTTTTTCTTTGCACAAGTCACTGAATTT
ATCTGTAAAGCGGATGATCATTTTGCGCCTTGGTGGGTTACACTTGCTCG
CCATCAACAACCACGTGAATCAGTAAAAACTGAACAATCCTATACTTTAC
AAGATCAATCACCTCGTGAAGATTTATCGCATTTATATTTTACCACCATC
GATAGCCCATCTACGCAAGATATGGACGATGCATTATTCATTGAGCCGAT
CACTGAAAATGCTATCCAACAAGGCTGGCGTTTAGTGGTTGCAATTGCAG
ATCCCACTGCCTATATTGCCGAAGACTCAAACATTGAACACGCAGCCCGC
CAACGTTGTTTCACAAACTACTTACCAGGGTTCAACATTCCTATGTTGCC
ACGTGAGCTTTCTGATGATCTTTGTTCCCTCGTACCAAACAAAAAACGCC
CTGCGTTAGTTGTTTATATTGAAACCGATCTTAACGGCAATCTAATCAAA
GACGCTAGTTTCCATACCGCTTGGGTAGAATCGAAAGCAAAATTAGCATA
TGACAATGTTTCTGACTATTTAGAAGGCGTAGAGCAAGCGTGGCAACCTG
ACTGTGCTGAACTAAAACAACAAATCTATTGGCTACACCAATTTACACAA
GCTCGCATTCAATGGCGATCAAAAAATGCTTTATTGTTTAAAGAACAAAT
GGATTATAACTTTGAGTTAAATGCAGATGGTTCCGTCAAAAGCATTCAGA
TTCAATATCATCGCATTGCTAACCAAATTATTGAAGAAGCGATGATTATT
GCTAATATTTGCTGTGCACAATTCTTAGCTAAACATGCCAAAACAGGTAT
CTTTAACAGTCATGCAGGTTTTGATCCTAAAAATTATGAAGCGGTACAAA
CATTCTTACTCAATACTTTAGCAACTGATGAAAATCGTTCTGAGTTAACA
GATCTCTTTAGCCCAACACAATTAGCAACACTCGATGGCTATTGTGCAAT
GCGACGTTATATTGAAGATTTTCCGGAAAAATTCCTCGAATTACGTTTAC
GCCGTTACTTGACGTTTGCTGAATTTAAGGCTGAAGTCGCCCCTCATTTT
GGTCTAGGTATTAGCCATTATGCCACTTGGACTTCACCTATCCGTAAATA
TGGTGATATAGTCAACCACCGTTTAATCAAACAAGTATTACTAAATCAGC
CAATTAAGCACATAGAGAGTACAATTTTAGCCCGCTTACAAGAAGCACGC
CGCCAAAATCGTTTAGTCGAACGCGATATCGCAGATTGGTTATATGCACG
CTATTTGCTCCCAATCGCAACACAAGGGGTAGAATTTGACTGCGAAATTA
CCGATATTTCACGTGGTGGTATTCGTGCTAAAGTACTAGAAAATGGCGCA
CAAATTTTCATTCCTTGTTCAACATTACACGAAAATAAAGATGAAATTGA
TTTTATCCCTGAAGAAATTGCACTTTACACTAAAGGGGAAAAAATTTATC
AAATAGGGCAAGCTACCCGTGTAAAACTAACCGATGTGCGGTTAGAAACA
CGTTCGGTGTTAGGTAATATTATTAAATAG


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