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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR1270 IGR1264 IGR1267 IGR1266 IGR1268 IGR1269 IGR1265 HD1730 HD1733 phoH,psiH, - HD1726 fadR, - HD1727 mrp, - HD1734 oppA, - HD1735 dsbB, - HD1729 nrdB, - HD1732 nhaB, - HD1728 nrdA, - HD1731 HD1730 HD1733 phoH,psiH, - HD1726 fadR, - HD1727 mrp, - HD1734 oppA, - HD1735 dsbB, - HD1729 nrdB, - HD1732 nhaB, - HD1728 nrdA, - HD1731 HD1730 HD1733 phoH,psiH, - HD1726 fadR, - HD1727 mrp, - HD1734 oppA, - HD1735 dsbB, - HD1729 nrdB, - HD1732 nhaB, - HD1728 nrdA, - HD1731
* Calculated from Protein Sequence

Gene ID: HD1731

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
nrdA  

Definition:
ribonucleoside-diphosphate reductase alpha chain (large subunit)

Gene Start:
1442317

Gene Stop:
1444587

Gene Length:
2271

Molecular Weight*:
85131

pI*:
6.60

Net Charge*:
-4.88

EC:
1.17.4.1  

Functional Class:
Purines, pyrimidines, nucleosides, and nucleotides; 2'-Deoxyribonucleotide metabolism  

Pathway: pathway table
Purine metabolism
Pyrimidine metabolism

Secondary Evidence:
Guzman EC, Caballero JL, Jimenez-Sanchez A.
Ribonucleoside diphosphate reductase is a component of the replication hyperstructure in Escherichia coli.
Mol Microbiol. 2002 Jan;43(2):487-95.
PMID: 11985724

Gallardo-Madueno R, Leal JF, Dorado G, Holmgren A, Lopez-Barea J, Pueyo C.
In vivo transcription of nrdAB operon and of grxA and fpg genes is triggered in Escherichia coli lacking both thioredoxin and
glutaredoxin 1 or thioredoxin and glutathione, respectively.
J Biol Chem. 1998 Jul 17;273(29):18382-8.
PMID: 9660805

Comment:
0

Blast Summary:  PSI-Blast Search
Numerous significant hits in gapped BLAST to ribonucleoside-diphosphate reductase - alpha chain; i.e. residues 1-756 are 81% similar to (U32839) ribonucleoside-diphosphate reductase - alpha chain of H.influenzae, residues 1-756 are 76% similar to (AE000313) ribonucleoside-diphosphate reductase - alpha chain of E.coli, residues 1-756 are 76% similar to (X72948) ribonucleoside-diphosphate reductase of Salmonella typhimurium.

COGS Summary:  COGS Search
BeTs to 15 clades of COG0209
COG name: Ribonucleotide reductase alpha subunit
Functional Class:  F
The phylogenetic pattern of COG0209 is a-tKYqvcEBRhujgp-linx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB000788 (Ribonucleotide reductase large subunit) with a combined E-value of 2.7e-114.
    IPB000788A    12-22
    IPB000788B    145-156
    IPB000788C    197-227
    IPB000788D    247-283
    IPB000788E    298-320
    IPB000788F    374-383
    IPB000788G    431-450
    IPB000788H    549-577
    IPB000788I    599-637
    IPB000788J    722-731


ProDom Summary:  Protein Domain Search
Residues 313-421 are 87% similar to a (REDUCTASE CHAIN) protein domain (PD001074) which is seen in Q9CMU1_PASMU.

Residues 433-565 are 75% similar to a (REDUCTASE CHAIN) protein domain (PD000706) which is seen in Q9CMU1_PASMU.

Residues 568-672 are 88% similar to a (REDUCTASE RIBONUCLEOSIDE-DIPHOSPHATE DNA) protein domain (PD024116) which is seen in RIR1_HAEIN.

Residues 461-563 are 68% similar to a (REDUCTASE RIBONUCLEOSIDE-DIPHOSPHATE REPLICATION) protein domain (PD001915) which is seen in Q9JZ50_NEIMB.

Residues 129-177 are 75% similar to a (REDUCTASE CHAIN DNA) protein domain (PD002419) which is seen in Q9JZ50_NEIMB.

Residues 233-296 are 79% similar to a (REDUCTASE CHAIN) protein domain (PD001775) which is seen in RIR1_ECOLI.

Residues 131-178 are 89% similar to a (REDUCTASE RIBONUCLEOSIDE-DIPHOSPHATE DNA) protein domain (PD207516) which is seen in RIR1_SALTY.

Residues 405-457 are 50% similar to a (REDUCTASE ALPHA B1 OXIDOREDUCTASE) protein domain (PD013963) which is seen in RIR1_BPT4.

Residues 673-756 are 89% similar to a (REDUCTASE OXIDOREDUCTASE DNA CHAIN) protein domain (PD013964) which is seen in RIR1_HAEIN.

Residues 5-129 are 79% similar to a (REDUCTASE REPLICATION OXIDOREDUCTASE) protein domain (PD008187) which is seen in Q9CMU1_PASMU.

Residues 179-232 are 90% similar to a (REDUCTASE OXIDOREDUCTASE DNA CHAIN) protein domain (PD378944) which is seen in Q9KSK0_VIBCH.



Paralogs:  Local Blast Search
HD1731 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 5 to 94 (E-value = 7.1e-22) place HD1731 in the ATP-cone family which is described as ATP cone domain (PF03477)
Residues 141 to 220 (E-value = 2.8e-22) place HD1731 in the Ribonuc_red_lgN family which is described as Ribonucleotide reductase, all-alpha domain (PF00317)
Residues 222 to 736 (E-value = 8.6e-246) place HD1731 in the Ribonuc_red_lgC family which is described as Ribonucleotide reductase, barrel domain (PF02867)

PDB Hit:
pdb|2R1R|A Chain A, Ribonucleotide Reductase R1 Protein With Dt... 1213 0.0
pdb|7R1R|A Chain A, Ribonucleotide Reductase E441q Mutant R1 Pr... 1212 0.0
pdb|6R1R|A Chain A, Ribonucleotide Reductase E441d Mutant R1 Pr... 1212 0.0

Gene Protein Sequence:
MQSQLMVTKRNGQQEPLDLEKIHRVITWAAEGLANVSVSQVELSAHIQFY
QGIRTSDIHETIIKAAADLISKETPDYQYLAARLAVFHLRKKAYGTFYPP
HLFEHIQKLVKLGKYDNLLLKQYSEEEWDIMNGFLVHERDMNFSYAAVKQ
LEGKYLVQNRVTGEIYESAQFLYILVAACLFSSYPKATRLDYIHRFYDAT
STFKISLPTPIMAGVRTPTRQFSSCVLIECGDSLDSINATSSAVIKYVSQ
RAGIGINAGAIRALGSPIRNGEAFHTGCIPFYKHFQTAVKSCSQGGVRGG
AATVFYPIWHLEVESLVVLKNNRGVEDNRCRHMDYGVQINKLIYQRLIKG
SDITLFSPSDVPGLYEAFFADQEKFELLYLQYEQDPSIRKKSIKAIELFS
LLMQERASTGRIYIHNVDHSNTHSPFDPSVAPIRQSNLCLEIALPTKPLN
NINDEQGEIALCTLSAFNLGTLQNLDELEPLADLAVRALDALLDYQNYPV
KAAEKGAIARRSLGIGVINYAYYLAKHGVRYSDGSANDLTHRTFEAVQYY
LLKASMNLAKELGPCKGFNETTYAKGILPIDSYKKDIDQLTQEPSHYDWE
ALRADIKQFGLRNSTLTALMPSETSSQISNATNGIEPPRGYVSIKASKDG
ILKQVVPEYETLKDQYELLWDIPNMDGYLHLVGIMQKFVDQAISANTNYD
PKRFEDDKVPMKILLKDLLTAYKYGLKTLYYQNTRDGAEDSQEDLDANCA
DGACRI$

Gene Nucleotide Sequence:  Sequence Viewer
ATGCAAAGCCAATTAATGGTAACTAAACGTAATGGACAACAAGAACCTTT
AGATTTAGAGAAAATCCATCGTGTTATTACTTGGGCTGCCGAGGGTTTAG
CTAATGTTTCAGTTTCGCAAGTAGAATTAAGCGCTCATATCCAATTTTAT
CAAGGCATTCGCACGTCAGATATTCATGAAACCATTATTAAGGCCGCTGC
TGATTTAATCAGTAAAGAAACTCCTGACTATCAATATCTGGCCGCGCGTT
TAGCCGTATTTCATCTGCGTAAAAAAGCTTATGGTACTTTTTATCCACCC
CATTTATTTGAACATATACAAAAATTAGTTAAATTGGGTAAATATGATAA
TTTATTGCTAAAGCAATATAGCGAAGAAGAATGGGATATCATGAATGGCT
TTTTAGTGCATGAACGTGATATGAATTTTTCCTATGCTGCCGTCAAACAA
TTGGAAGGAAAATACTTAGTCCAAAACCGTGTTACCGGTGAAATTTACGA
ATCGGCACAATTCTTATATATTTTAGTTGCTGCATGTTTATTTTCTAGTT
ACCCCAAAGCAACTCGTTTAGACTATATCCATCGTTTTTATGATGCAACA
TCGACCTTTAAAATCTCACTCCCGACTCCAATTATGGCGGGCGTTCGAAC
ACCAACTCGTCAATTTAGTTCTTGTGTACTAATTGAATGTGGAGATAGTT
TAGACTCAATTAATGCAACGTCTTCAGCGGTAATTAAATATGTATCTCAA
CGTGCAGGAATAGGCATTAATGCAGGCGCTATTCGCGCATTAGGCAGTCC
AATTCGAAATGGTGAGGCATTCCATACCGGTTGTATTCCATTTTATAAAC
ATTTCCAAACAGCGGTGAAATCTTGTTCACAAGGTGGCGTTCGTGGTGGT
GCAGCAACGGTTTTCTATCCGATTTGGCATTTAGAAGTAGAAAGTTTAGT
TGTGCTTAAAAATAATCGCGGAGTGGAAGATAACCGCTGTCGCCATATGG
ATTACGGCGTTCAAATCAATAAATTAATCTACCAACGCCTCATTAAAGGA
TCAGATATCACTTTATTCAGTCCTTCTGATGTACCAGGTCTATATGAGGC
CTTTTTTGCGGATCAAGAAAAATTTGAACTACTTTATCTGCAATATGAAC
AAGATCCTAGCATCAGGAAGAAAAGCATAAAAGCTATTGAGTTATTCTCG
TTATTAATGCAAGAAAGAGCATCAACCGGTCGAATTTATATTCATAATGT
CGATCACTCTAATACTCATTCGCCTTTTGATCCAAGCGTAGCGCCTATTC
GTCAATCGAATTTGTGTTTAGAAATTGCCTTGCCAACCAAACCATTGAAT
AATATAAACGATGAGCAAGGTGAAATTGCACTTTGTACACTCTCAGCATT
TAACTTAGGCACGTTACAAAATTTAGATGAATTGGAACCGCTTGCTGATT
TAGCCGTACGAGCATTAGATGCGTTATTAGATTATCAAAATTATCCGGTA
AAAGCGGCTGAAAAAGGGGCAATAGCACGTCGTTCACTTGGTATTGGGGT
AATTAACTATGCTTACTATCTAGCCAAACATGGGGTACGTTATTCAGATG
GGAGTGCGAATGATTTAACACATCGCACTTTTGAAGCAGTCCAATACTAT
TTACTCAAAGCTTCCATGAACTTAGCCAAAGAACTAGGCCCTTGTAAAGG
CTTTAATGAAACCACTTATGCTAAAGGTATTTTACCGATTGATAGCTACA
AAAAAGATATTGATCAACTTACTCAAGAACCATCCCACTATGATTGGGAA
GCATTACGTGCTGACATTAAACAATTTGGATTGCGCAATTCAACCTTGAC
CGCATTAATGCCATCAGAAACTTCATCGCAAATCTCAAATGCAACCAATG
GTATTGAACCGCCACGTGGTTACGTTAGTATTAAAGCTTCTAAAGATGGT
ATTTTAAAACAAGTTGTTCCTGAATATGAAACATTGAAAGATCAATATGA
ATTACTTTGGGATATTCCTAACATGGATGGCTACTTACATTTAGTTGGTA
TTATGCAAAAATTTGTTGACCAAGCTATTTCAGCCAATACTAACTACGAT
CCGAAACGCTTTGAAGATGATAAAGTGCCAATGAAAATCTTACTTAAAGA
CTTATTAACCGCCTATAAATATGGTTTAAAAACACTTTATTATCAAAATA
CACGTGATGGCGCAGAAGACTCACAAGAAGATTTAGATGCCAACTGTGCT
GATGGTGCGTGTAGAATTTAA


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