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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR1154 IGR1153 IGR1159 IGR1158 IGR1156 IGR1157 IGR1155 HD1586 hisH, - HD1592 kicB,mukF, - HD1585 gyrA,parC, - HD1587 yfhC, - HD1591 HD1589 deaD, - HD1590 pnp, - HD1588 HD1586 hisH, - HD1592 kicB,mukF, - HD1585 gyrA,parC, - HD1587 yfhC, - HD1591 HD1589 deaD, - HD1590 pnp, - HD1588 HD1586 hisH, - HD1592 kicB,mukF, - HD1585 gyrA,parC, - HD1587 yfhC, - HD1591 HD1589 deaD, - HD1590 pnp, - HD1588
* Calculated from Protein Sequence

Gene ID: HD1588

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
pnp  

Definition:
polynucleotide phosphorylase (pnp)

Gene Start:
1308504

Gene Stop:
1310642

Gene Length:
2139

Molecular Weight*:
77269

pI*:
4.90

Net Charge*:
-20.59

EC:
2.7.7.8  

Functional Class:
Transcription; RNA synthesis, modification, and DNA transcription  

Pathway: pathway table
Purine metabolism
Pyrimidine metabolism

Secondary Evidence:
Jarrige A, Brechemier-Baey D, Mathy N, Duche O, Portier C.
Mutational analysis of polynucleotide phosphorylase from Escherichia coli.
J Mol Biol. 2002 Aug 16;321(3):397-409.
PMID: 12162954

Regnier,P., Grunberg-Manago,M. and Portier,C.
Nucleotide sequence of the pnp gene of Escherichia coli encoding polynucleotide phosphorylase. Homology of the primary structure of the protein with the RNA-binding domain of ribosomal protein S1. J. Biol. Chem. 262(1): 63-68.1987.
Medline: 87083499.

Evans,S. and Dennis,P.P. .
Promoter activity and transcript mapping in the regulatory region for genes encoding ribosomal protein S15 and polynucleotide phosphorylase of Escherichia coli.
Gene 40(1): 15-22.1985
Medline: 86137413.

Portier,C. and Regnier,P. .
Expression of the rpsO and pnp genes: structural analysis of a DNA fragment carrying their control regions.
Nucleic Acids Res. 12(15): 6091-6102.1984
Medline: 84297215.

Comment:


Blast Summary:  PSI-Blast Search
Numerous significant hits using gapped BLAST to polyribonucleotide nucleotidyltransferase proteins from H. influenzae (1172546), E. coli (1172545), Photorhabdus luminescens (730350), among others.

HD1588 is similar to predicted polyribonucleotide nucleotidyltransferases from C. pneumoniae (CPn0999), C. trachomatis (CT842), and T. pallidum (TP0886). It is also similar to predicted S1 ribosomal proteins from C. pneumoniae (CPn0315), C. trachomatis (CT098), and T. pallidum (TP0279). It is also similar to a hypothetical protein/possible Tex protein TP0924 from T. pallidum. No similarity to proteins from M. genitalium or M. pneumoniae.

COGS Summary:  COGS Search
BeTs to 11 clades of COG1185
COG name: Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase)
Functional Class: J
The phylogenetic pattern of COG1185 is -----qvcebrhuj--olinx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** PR00681 (Ribosomal protein S1 signature) with a combined E-value of 7.5e-08.
    PR00681A    461-479
    PR00681H    634-653
***** IPB003029 (S1 RNA binding domain) with a combined E-value of 6.6e-06.
    IPB003029A    626-637
    IPB003029B    668-679


ProDom Summary:  Protein Domain Search
Residues 3-87 are 96% similar to a (NUCLEOTIDYLTRANSFERASE POLYRIBONUCLEOTIDE) protein domain (PD005304) which is seen in Q9CLU1_PASMU.

Residues 393-439 are 93% similar to a (NUCLEOTIDYLTRANSFERASE POLYRIBONUCLEOTIDE) protein domain (PD111902) which is seen in PNP_PHOLU.

Residues 440-540 are 79% similar to a (NUCLEOTIDYLTRANSFERASE COMPLETE PROTEOME) protein domain (PD002075) which is seen in PNP_ECOLI.

Residues 626-691 are 77% similar to a (RIBOSOMAL COMPLETE PROTEOME RNA-BINDING 30S REPEAT) protein domain (PD000709) which is seen in Q9L6A4_PASMU.

Residues 544-610 are 65% similar to a (NUCLEOTIDYLTRANSFERASE POLYRIBONUCLEOTIDE) protein domain (PD023173) which is seen in PNP_HAEIN.

Residues 304-436 are 56% similar to a (NUCLEOTIDYLTRANSFERASE COMPLETE PROTEOME) protein domain (PD333034) which is seen in Q9KA83_BACHD.

Residues 88-127 are 97% similar to a (NUCLEOTIDYLTRANSFERASE POLYRIBONUCLEOTIDE) protein domain (PD005803) which is seen in PNP_HAEIN.

Residues 295-353 are 72% similar to a (NUCLEOTIDYLTRANSFERASE PROTEOME COMPLETE) protein domain (PD406609) which is seen in Q9K062_NEIMB.

Residues 226-298 are 75% similar to a (NUCLEOTIDYLTRANSFERASE POLYRIBONUCLEOTIDE) protein domain (PD384471) which is seen in PNP_HAEIN.

Residues 354-388 are 88% similar to a (NUCLEOTIDYLTRANSFERASE POLYRIBONUCLEOTIDE) protein domain (PD388019) which is seen in PNP_PHOLU.

Residues 299-354 are 92% similar to a (NUCLEOTIDYLTRANSFERASE POLYRIBONUCLEOTIDE) protein domain (PD379184) which is seen in PNP_HAEIN.

Residues 355-392 are 94% similar to a (NUCLEOTIDYLTRANSFERASE POLYRIBONUCLEOTIDE) protein domain (PD416000) which is seen in Q9L6A4_PASMU.



Paralogs:  Local Blast Search


HD1588 is paralogously related to HD1352 (1e-11), HD0317 (1e-10) and HD0301 (7e-05).


Pfam Summary:  Pfam Search
Residues 11 to 143 (E-value = 9.6e-42) place HD1588 in the RNase_PH family which is described as 3' exoribonuclease family, domain 1 (PF01138)
Residues 146 to 210 (E-value = 2e-16) place HD1588 in the RNase_PH_C family which is described as 3' exoribonuclease family, domain 2 (PF03725)
Residues 241 to 319 (E-value = 8.2e-33) place HD1588 in the PNPase family which is described as Polyribonucleotide nucleotidyltransferase, RNA binding domain (PF03726)
Residues 322 to 455 (E-value = 9.9e-52) place HD1588 in the RNase_PH family which is described as 3' exoribonuclease family, domain 1 (PF01138)
Residues 458 to 528 (E-value = 2.3e-22) place HD1588 in the RNase_PH_C family which is described as 3' exoribonuclease family, domain 2 (PF03725)
Residues 556 to 602 (E-value = 6.1e-12) place HD1588 in the KH family which is described as KH domain (PF00013)
Residues 617 to 689 (E-value = 1.3e-22) place HD1588 in the S1 family which is described as S1 RNA binding domain (PF00575)

PDB Hit:
pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibi... 523 3e-149
pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibiotic... 508 1e-144
pdb|1SRO| S1 Rna Binding Domain, Nmr, 20 Structures 105 2e-023

Gene Protein Sequence:
MTPIVKQFKYGQHTVTLETGAIARQATAAVMASMDDTTVFVSVVAKKEVK
EGQDFFPLTVNYQERTYAAGRIPGGFFKREGRPSENETLIARLIDRPIRP
LFPEGFFNEIQIVATVVSVNPQISPDLVAMIGASAALSLSGVPFNGPIGA
ARVGFINDQFVLNPTITEQKQSRLDLVVAGTDKAVLMVESEADILSEEQM
LAAVVFGHQQQQIVIENIKEFVKEAGKPRWDWQPAEANTALINQVKALAE
TRIGDAYRITEKQARYEQIDAIKADVIAQLTAQDETISEGAIIDIITALE
SSVVRGRILAGEPRIDGRTVDTVRALNICTGVLPRTHGSAIFTRGETQAL
AVATLGTERDAQIIDELTGEKSDRFLFHYNFPPYSVGETGMIGSPKRREI
GHGRLAKRGVLAVMPSAEEFPYVVRVVSEITESNGSSSMASVCGASLALM
DAGVPIKATVAGIAMGLVKEDEKFVVLSDILGDEDHLGDMDFKVAGTRKG
ITALQMDIKIEGITPEIMHIALNQAKGARMHILNVMEQALPAPRADLSDF
APRIHTMKIDPKKIKDVIGKGGAVIRSLTEETGTSIDIDDDGTVKIAATD
NNAAKMVMSRIEEIVAEVEVNAIYTGKVSRVVDFGAFVTILGGKEGLVHI
SQITDARVERVSDYLSVGQEVNVKVVEIDRQNRIRLTMKDLDNNLSTNVT
PEAVVQEESTEN$

Gene Nucleotide Sequence:  Sequence Viewer
ATGACACCCATTGTTAAACAATTTAAATACGGCCAACATACCGTAACTCT
AGAAACAGGCGCTATCGCGCGTCAAGCCACTGCTGCGGTTATGGCAAGTA
TGGACGATACGACAGTCTTTGTAAGTGTGGTAGCGAAAAAAGAAGTAAAA
GAAGGTCAAGACTTCTTCCCATTAACAGTAAACTATCAAGAACGTACTTA
TGCAGCTGGCCGTATTCCCGGTGGTTTTTTCAAACGTGAAGGACGCCCGT
CCGAAAATGAAACGTTAATTGCACGGCTAATCGACCGCCCAATTCGTCCG
CTTTTCCCAGAAGGCTTCTTTAATGAAATTCAAATTGTTGCTACTGTTGT
TTCTGTTAATCCACAAATTAGCCCGGATTTAGTCGCAATGATCGGCGCTT
CTGCAGCATTATCACTGTCTGGTGTACCATTTAATGGCCCAATTGGTGCA
GCACGTGTCGGCTTTATTAATGATCAATTTGTCCTTAATCCAACGATTAC
TGAGCAAAAACAAAGCCGTTTAGATTTAGTGGTTGCAGGTACAGATAAAG
CGGTCTTAATGGTCGAATCTGAAGCAGATATCCTTTCAGAAGAACAAATG
TTAGCGGCGGTGGTATTTGGTCATCAGCAACAACAAATAGTGATTGAAAA
TATCAAAGAATTTGTAAAAGAAGCGGGAAAACCACGTTGGGATTGGCAAC
CAGCAGAAGCAAATACTGCATTAATTAATCAAGTAAAAGCATTGGCAGAA
ACGCGTATTGGTGATGCCTACCGCATTACAGAAAAACAAGCACGTTATGA
GCAAATTGATGCGATTAAAGCTGACGTTATCGCACAATTAACCGCTCAAG
ATGAAACAATTAGCGAAGGTGCTATTATTGATATTATCACCGCATTAGAA
AGTTCGGTCGTGCGTGGGCGTATCTTAGCGGGTGAGCCTCGTATTGATGG
TCGTACAGTGGACACGGTTCGTGCATTAAATATTTGCACCGGCGTATTAC
CTCGCACCCATGGTTCGGCAATTTTCACGCGTGGTGAAACTCAGGCATTA
GCAGTCGCTACTTTAGGGACTGAGCGTGATGCACAAATTATTGATGAATT
AACTGGCGAAAAATCCGACCGCTTCTTATTCCATTATAATTTCCCTCCAT
ATTCTGTCGGAGAGACAGGTATGATCGGCTCACCAAAACGTCGCGAAATT
GGTCACGGTCGTTTAGCAAAACGTGGGGTATTAGCCGTTATGCCAAGCGC
AGAAGAATTTCCTTATGTCGTACGTGTTGTATCAGAAATTACTGAATCAA
ATGGTTCTTCCTCAATGGCTTCCGTATGTGGTGCGTCTTTAGCGTTAATG
GATGCAGGTGTGCCAATTAAAGCTACTGTAGCGGGTATTGCTATGGGATT
AGTTAAAGAAGACGAAAAATTTGTTGTGCTTTCTGATATTTTGGGCGATG
AAGATCACTTAGGCGATATGGACTTTAAAGTAGCCGGTACGCGCAAAGGT
ATAACTGCACTACAAATGGATATCAAAATTGAAGGCATTACGCCAGAGAT
TATGCATATTGCATTAAACCAAGCTAAAGGTGCACGTATGCATATTCTGA
ACGTAATGGAACAAGCACTCCCTGCTCCGCGTGCGGATCTTTCTGATTTT
GCACCTCGTATTCACACTATGAAGATTGATCCTAAAAAAATCAAAGATGT
GATTGGTAAAGGCGGTGCCGTTATTCGTTCTTTAACTGAAGAAACCGGTA
CATCCATCGATATTGATGATGACGGTACAGTAAAAATTGCAGCAACAGAT
AATAATGCGGCTAAAATGGTTATGTCTCGTATTGAAGAGATCGTAGCTGA
AGTAGAAGTGAATGCAATTTATACCGGTAAAGTTTCCCGTGTTGTCGATT
TTGGCGCATTCGTGACGATTTTAGGTGGCAAAGAAGGTTTAGTGCATATT
TCACAAATTACAGATGCTCGTGTTGAACGCGTTTCTGATTACCTATCGGT
CGGTCAAGAAGTTAATGTAAAAGTAGTCGAAATTGACCGCCAAAACCGTA
TCCGCCTAACGATGAAAGATCTGGATAATAACCTTTCGACAAACGTTACT
CCGGAAGCTGTCGTTCAAGAAGAATCTACTGAGAACTAA


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