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Porphyromonas gingivalis Search Results

Record: 1 of 1  
MiniMap tRNA-Gln-1 IGR0022 IGR0028 IGR0027 IGR0025 IGR0021 IGR0023 IGR0026 IGR0024 PG0027 spoU, - PG0025 PG0029 PG0028 PG0026.1 cdd, - PG0026 ispF, - PG0024 PG0023 PG0022 PG0027 spoU, - PG0025 PG0029 PG0028 PG0026.1 cdd, - PG0026 ispF, - PG0024 PG0023 PG0022 PG0027 spoU, - PG0025 PG0029 PG0028 cdd, - PG0026 ispF, - PG0024 PG0023 PG0022 PG0026.1


LANL Gene ID: PG0026

GenBank Locus Tag: PG0030

DNA Molecule Name:
1  

GenBank ID:
34539906

Gene Name:
cdd  

Definition:
cytidine deaminase

Cellular Location:
Cytoplasm [Evidence]

Gene Start:
35986

Gene Stop:
36459

Gene Length:
474

Molecular Weight*:
17175

pI*:
5.10

Net Charge*:
-2.95

EC:
3.5.4.5  

Functional Class:
Purines, pyrimidines, nucleosides and nucleotides; Salvage of nucleosides and nucleotides  

Gene Ontology:
Biological process
  GO:0046087    cytidine metabolic process

Molecular function
  GO:0004126    cytidine deaminase activity
  GO:0008270    zinc ion binding
  GO:0016787    hydrolase activity


Pathway: pathway table
Pyrimidine metabolism

Comment:
TIGR ID: PG0030

Proteomic Data: Proteomic Data Search
TIGR Annotationcytidine deaminase, GroupO (purines, pyrimidines, nucleosides and nucleotides)
ORF #PG-PP/PG-PPC1PG-PP/PG-PPC2
Spectral CountPeptide IntensitySpectral CountPeptide Intensity
ProqValProqValProqValProqVal
TIGRPG0030-0.790.0380.200.19-0.970.00440.200.19
LANLPG00260.581.150.510.29
ConsensusSP1IP1SP2IP2

Human Oral Microbiome Database:
View in HOMD Genome Viewer

 Blast Summary:  PSI-Blast Search
Numerous significant hits in gapped BLAST to cytidine deaminase
proteins; e.g. residues 31-144 are 41% similar to CDD_MOUSE;
residues 23-156 are 40% similar to the cytidine deaminase of
Bacillus caldolyticus (AJ237979).

 Top Blast Hits:  Updated monthly
Click here to view the entire PsiBlast results.
 gi|34539906|ref|NP_904385.1|  cytidine deaminase [Porphyromo...   293   2e-78
 gi|150008708|ref|YP_001303451.1|  cytidine deaminase [Paraba...   167   2e-40
 gi|146299314|ref|YP_001193905.1|  cytidine deaminase [Flavob...   136   4e-31
 gi|150004871|ref|YP_001299615.1|  cytidine deaminase [Bacter...   135   6e-31
 gi|53712787|ref|YP_098779.1|  cytidine deaminase [Bacteroide...   135   9e-31
 gi|154490833|ref|ZP_02030774.1|  hypothetical protein PARMER...   134   2e-30
 gi|60680936|ref|YP_211080.1|  putative cytidine deaminase [B...   133   4e-30
 gi|86134148|ref|ZP_01052730.1|  cytidine deaminase [Tenaciba...   129   7e-29
 gi|156108155|gb|EDO09900.1|  hypothetical protein BACOVA_042...   129   7e-29
 gi|29346949|ref|NP_810452.1|  cytidine deaminase [Bacteroide...   128   9e-29


InterPro Summary:  InterProScan

InterPro
IPR002125
Domain
CMP/dCMP deaminase, zinc-binding
PF00383 [19-131]T 1.8999985986586497E-9 PF00383 dCMP_cyt_deam_1 dCMP_cyt_deam_1
PS00903 [72-117]? 0.0 PS00903 CYT_DCMP_DEAMINASES CYT_DCMP_DEAMINASES
InterPro
IPR006262
Family
Cytidine deaminase, homotetrameric
PIRSF001250 [21-157]T 2.39999999999997E-29 PIRSF001250 Cyd_deaminase Cyd_deaminase
PTHR11644:SF2 [28-157]T 4.90001027782408E-35 PTHR11644:SF2 Cyt_deam_tetra Cyt_deam_tetra
TIGR01354 [23-156]T 7.086523666575042E-67 TIGR01354 cyt_deam_tetra cyt_deam_tetra
noIPR
unintegrated
unintegrated
G3DSA:3.40.140.10 [12-157]T 1.9999963603453604E-31 G3DSA:3.40.140.10 G3DSA:3.40.140.10 G3DSA:3.40.140.10
PTHR11644 [28-157]T 4.90001027782408E-35 PTHR11644 PTHR11644 PTHR11644
SSF53927 [22-157]T 3.5E-31 SSF53927 SSF53927 SSF53927


COGS Summary:  COGS Search
BeTs to 7 clades of COG0295
COG name: Cytidine deaminase
Functional Class: F
The phylogenetic pattern of COG0295 is ----y-v-ebrh--gpo----
Number of proteins in this genome belonging to this COG is 1
Blocks Summary:  Blocks Search
***** BP03466 (CYTIDINE DEAMINASE HYDROLASE ZINC AMINOHYDROLA) with a combined E-value of 2.7e-24.
    BP03466A    36-47
    BP03466B    59-85
    BP03466C    108-120
    BP03466D    142-156


 ProDom Summary:  Protein Domain Search
Residues 31-151 are 42% similar to a (DEAMINASE CYTIDINE HYDROLASE ZINC) protein domain (PD003466 which is seen in CDD_HUMAN.


Paralogs:  Local Blast Search
No paralogs found in P. gingivalis.

Pfam Summary:  Pfam Search
Residues 20 to 131 (E-value = 6.9e-10) place PG0026 in the dCMP_cyt_deam family which is described as Cytidine and deoxycytidylate deaminase zinc-binding region (PF00383)

 Structural Feature(s):
Feature Type  Start  Stop
No predicted structural features.  
  

Top PDB Hits:
-58% similar to PDB:1ZAB Crystal Structure of Mouse Cytidine Deaminase Complexed with 3-Deazauridine (E_value = 2.8E_20);
-58% similar to PDB:2FR5 Crystal Structure of Mouse Cytidine Deaminase Complexed with Tetrahydrouridine (E_value = 2.8E_20);
-58% similar to PDB:2FR6 Crystal Structure of Mouse Cytidine Deaminase Complexed with Cytidine (E_value = 2.8E_20);
-56% similar to PDB:1MQ0 Crystal Structure of Human Cytidine Deaminase (E_value = 1.1E_19);
-58% similar to PDB:2D30 Crystal Structure of Cytidine Deaminase Cdd-2 (BA4525) from Bacillus Anthracis at 2.40A Resolution (E_value = 1.2E_18);

Gene Protein Sequence:
MLRKTLSTPYDIIPRSDFSADVLRLEGAAIEAARSAYAPYSRFSVGAAVL
LDNGEILSGSNQENAAYPSGLCAERTVLFYAGARYPEAAVREMVLVAFSA
SGRVPLITPCGACRQVMLEVCSRHRPFPILMVGEEEAVRVSDVRLLLPFS
FDGSDLER

Gene Nucleotide Sequence:  Sequence Viewer
ATGCTCCGTAAAACTCTTTCCACTCCTTATGATATAATTCCCCGATCGGA
TTTCTCTGCCGATGTGCTCCGTCTGGAAGGTGCCGCCATCGAGGCAGCCC
GGTCGGCATATGCACCTTATAGTCGCTTTTCGGTGGGAGCGGCTGTTTTG
CTCGACAATGGGGAGATCCTTTCAGGCAGCAATCAGGAGAATGCAGCCTA
TCCGTCCGGACTATGTGCCGAGCGTACGGTGCTTTTCTATGCCGGAGCCA
GATATCCGGAGGCAGCCGTGAGAGAGATGGTGCTCGTGGCTTTTTCCGCT
TCGGGACGTGTGCCGCTGATTACGCCGTGCGGGGCTTGCCGTCAGGTGAT
GCTGGAGGTTTGTAGTCGCCATCGTCCTTTTCCCATCTTGATGGTCGGGG
AAGAGGAGGCTGTCAGAGTGTCGGATGTGCGTCTGCTGCTGCCCTTTTCT
TTCGACGGTAGCGACTTGGAACGA

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