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Porphyromonas gingivalis Search Results

Record: 1 of 1  
MiniMap IGR0014 IGR0011 IGR0013 IGR0010 IGR0015 IGR0012 PG0012 hisC, - PG0011 ISPg4, - PG0016 atoS,ntrB, - PG0014 ntrC, - PG0013 PG0015 nagA,ybbD, - PG0010 PG0012 hisC, - PG0011 ISPg4, - PG0016 atoS,ntrB, - PG0014 ntrC, - PG0013 PG0015 nagA,ybbD, - PG0010 Type: IS element, Name: ISPg4 - 7 PG0012 hisC, - PG0011 ISPg4, - PG0016 atoS,ntrB, - PG0014 ntrC, - PG0013 PG0015 nagA,ybbD, - PG0010


LANL Gene ID: PG0013

GenBank Locus Tag: PG0016

DNA Molecule Name:
1  

Genomic Island ID:
1

GenBank ID:
34539894

 Gene Name:
ntrC  

 Definition:
nitrogen assimilation regulatory protein NR-I (ntrC)

 Cellular Location:
Cytoplasm [Evidence]

 Gene Start:
17087

Gene Stop:
18433

Gene Length:
1347

Molecular Weight*:
49172

pI*:
7.00

Net Charge*:
0.00

EC:
 

 Functional Class:
Central intermediary metabolism; Nitrogen metabolism  

 Gene Ontology:
Biological process
  GO:0000160    two-component signal transduction system (phosphorelay)
  GO:0006355    regulation of transcription, DNA-dependent

Cellular component
  GO:0005622    intracellular

Molecular function
  GO:0000156    two-component response regulator activity
  GO:0000166    nucleotide binding
  GO:0003700    transcription factor activity
  GO:0005524    ATP binding
  GO:0008134    transcription factor binding
  GO:0017111    nucleoside-triphosphatase activity


 Pathway: pathway table

 Comment:
TIGR ID: PG0016

 Proteomic Data: Proteomic Data Search
TIGR Annotationsigma-54 dependent DNA-binding response regulator, GroupP (regulatory functions) ,GroupQ (signal transduction)
ORF #PG-PP/PG-PPC1PG-PP/PG-PPC2
Spectral CountPeptide IntensitySpectral CountPeptide Intensity
ProqValProqValProqValProqVal
TIGRPG00161.620.00622.445.1e-074.918.9e-092.445.1e-07
LANLPG00133.085.4230.03293.36
ConsensusSP1IP1SP2IP2

Human Oral Microbiome Database:
View in HOMD Genome Viewer

 Blast Summary:  PSI-Blast Search
Numerous significant hits in gapped BLAST to transcriptional regulatory proteins related to nitrogen metabolism; e.g. residues 6-446 are 39% similar to the transcriptional regulatory protein HYDG of Escherichia coli (U00006). Residues 5-449 are 35% similar to FrgC of Myxococcus xanthus (AF204400), residues 6-449 are 35% similar to the transcriptional regulator (NtrC family) of Aquifex aeolicus (AE000724).

This sequence is similar to BT0690.

 Top Blast Hits:  Updated monthly
Click here to view the entire PsiBlast results.
 gi|34539894|ref|NP_904373.1|  sigma-54 dependent DNA-binding...   849   0.0  
 gi|150005964|ref|YP_001300708.1|  two-component system respo...   488   e-136
 gi|156861046|gb|EDO54477.1|  hypothetical protein BACUNI_019...   475   e-132
 gi|60681686|ref|YP_211830.1|  putative two-component system,...   473   e-131
 gi|53713439|ref|YP_099431.1|  two-component system response ...   470   e-130
 gi|150008022|ref|YP_001302765.1|  two-component system respo...   469   e-130
 gi|156110148|gb|EDO11893.1|  hypothetical protein BACOVA_023...   468   e-130
 gi|29346100|ref|NP_809603.1|  two-component system response ...   468   e-130
 gi|153806548|ref|ZP_01959216.1|  hypothetical protein BACCAC...   464   e-129
 gi|154492708|ref|ZP_02032334.1|  hypothetical protein PARMER...   461   e-128


InterPro Summary:  InterProScan

InterPro
IPR001789
Domain
Response regulator receiver
PD000039 [6-125]T 0.0 PD000039 Response_reg Response_reg
PF00072 [5-122]T 2.3999979815724097E-20 PF00072 Response_reg Response_reg
SM00448 [5-121]T 7.400000000000411E-17 SM00448 REC REC
PS50110 [6-125]T 0.0 PS50110 RESPONSE_REGULATORY RESPONSE_REGULATORY
InterPro
IPR002078
Domain
RNA polymerase sigma factor 54, interaction
PF00158 [144-365]T 0.0 PF00158 Sigma54_activat Sigma54_activat
PS00676 [230-245]T 8.0E-5 PS00676 SIGMA54_INTERACT_2 SIGMA54_INTERACT_2
PS00688 [357-366]T 8.0E-5 PS00688 SIGMA54_INTERACT_3 SIGMA54_INTERACT_3
PS50045 [144-373]T 0.0 PS50045 SIGMA54_INTERACT_4 SIGMA54_INTERACT_4
InterPro
IPR002197
Domain
Helix-turn-helix, Fis-type
PR01590 [413-430]T 1.3E-11 PR01590 HTHFIS[430-449]T 1.3E-11 PR01590 HTHFIS HTHFIS
PF02954 [407-447]T 1.2000011745814E-13 PF02954 HTH_8 HTH_8
InterPro
IPR003593
Domain
AAA+ ATPase, core
SM00382 [164-307]T 7.40000000000006E-9 SM00382 AAA AAA
InterPro
IPR009057
Domain
Homeodomain-like
SSF46689 [357-449]T 1.8E-20 SSF46689 Homeodomain_like Homeodomain_like
InterPro
IPR011006
Domain
CheY-like
SSF52172 [2-189]T 1.1E-30 SSF52172 CheY_like CheY_like
noIPR
unintegrated
unintegrated
G3DSA:1.10.1680.10 [407-449]T 2.5000008644594E-5 G3DSA:1.10.1680.10 G3DSA:1.10.1680.10 G3DSA:1.10.1680.10
G3DSA:1.10.8.60 [317-392]T 3.09999945899376E-18 G3DSA:1.10.8.60 G3DSA:1.10.8.60 G3DSA:1.10.8.60
G3DSA:3.40.50.2300 [7-129]T 1.50000306971087E-21 G3DSA:3.40.50.2300 G3DSA:3.40.50.2300 G3DSA:3.40.50.2300
G3DSA:3.40.50.300 [144-316]T 7.40000780398385E-62 G3DSA:3.40.50.300 G3DSA:3.40.50.300 G3DSA:3.40.50.300
PTHR23283 [6-130]T 1.1000002989614901E-4 PTHR23283 PTHR23283 PTHR23283
SSF52540 [143-385]T 4.3999999999999997E-66 SSF52540 SSF52540 SSF52540


COGS Summary:  COGS Search
BeTs to 7 clades of COG2204
COG name: AAA superfamily ATPases with N-terminal receiver domain
Functional Class: T
The phylogenetic pattern of COG2204 is -----Q--E---uj--olinx
Number of proteins in this genome belonging to this COG is 2
Blocks Summary:  Blocks Search
***** IPB002078 (Sigma-54 transcription factor family) with a combined E-value of 1.6e-61.
    IPB002078A    168-202
    IPB002078B    221-270
    IPB002078C    295-322
    IPB002078D    357-366


 ProDom Summary:  Protein Domain Search
Residues 7-117 are 32% similar to a (PROTEIN SENSORY TRANSDUCTION) protein domain (PD000039 which is seen in ATOC_ECOLI.

Residues 145-372 are 27% similar to a (NITROGEN ASSIMILATION REGULATORY PROTEIN) protein domain (PD082887 which is seen in P74210_SYNY3.

Residues 145-373 are 48% similar to a (PROTEIN ATP-BINDING PROTEASE SUBUNIT REGULATORY HOMOLOG) protein domain (PD000092 which is seen in HYDG_ECOLI.


Paralogs:  Local Blast Search
Residues 1-449 are 42% similar to PG0675, two-component sensor system regulatory subunit.
Residues 128-386 and 397-449 are 40% and 45% similar respectively to PG0136, a nitrogen assimilation regulatory protein.

Pfam Summary:  Pfam Search
Residues 5 to 129 (E-value = 2e-18) place PG0013 in the Response_reg family which is described as Response regulator receiver domain (PF00072)
Residues 145 to 365 (E-value = 2.8e-112) place PG0013 in the Sigma54_activat family which is described as Sigma-54 interaction domain (PF00158)
Residues 407 to 447 (E-value = 3.7e-16) place PG0013 in the HTH_8 family which is described as Bacterial regulatory protein, Fis family (PF02954)

 Structural Feature(s):
Feature Type  Start  Stop
non-globular  
1  
75

Top PDB Hits:
-57% similar to PDB:1NY5 Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state (E_value = 1.2E_65);
-60% similar to PDB:1OJL CRYSTAL STRUCTURE OF A SIGMA54-ACTIVATOR SUGGESTS THE MECHANISM FOR THE CONFORMATIONAL SWITCH NECESSARY FOR SIGMA54 BINDING (E_value = 4.3E_63);
-64% similar to PDB:1NY6 Crystal structure of sigm54 activator (AAA+ ATPase) in the active state (E_value = 1.6E_54);
-58% similar to PDB:2BJW PSPF AAA DOMAIN (E_value = 1.4E_42);
-58% similar to PDB:2C96 STRUCTURAL BASIS OF THE NUCLEOTIDE DRIVEN CONFORMATIONAL CHANGES IN THE AAA DOMAIN OF TRANSCRIPTION ACTIVATOR PSPF (E_value = 1.4E_42);

Gene Protein Sequence:
MKKSGNIIVVDDNKHVLTALKLLLTGSFETVTLLPSPKTLLSTIVEVHPD
VLLLDMNFSTGINTGNEGLYWLDQVRSRFPDLPVVLFTAYADIRLAVEAL
KRGASDFVVKPWNNTELLESLRMAMNKAASTQVTATPKEGDSVFLSKSKA
MCEVLELAGRIGDTAAHVLITGENGTGKGVLAEYIHARSPRSRQPMLTVD
MGALSETLFESELFGHVKGAFTDAKSDRAGKFETASGGTIFMDEIGNLSL
ALQAKLLAVLQQKVVTRVGSNTPIPVDVRVISATNSDLPLSVAEGRFRED
LLYRLNTIHIEMPPLRRRREDIVPMAVFFLHRYARQYGKEVPELTPEAEA
LLSDYPWPGNVRELQHCIEKAVILSRSSSLSAADLSLPKSVDAHPTATGV
ASTPQTLDEMEKTAIEQALARNGSNLSNVARELGISRQTLYNKMKRYGL

Gene Nucleotide Sequence:  Sequence Viewer
ATGAAGAAAAGCGGCAATATCATCGTGGTCGATGATAACAAACATGTACT
GACGGCTTTGAAATTGCTCCTGACGGGGAGTTTCGAGACCGTGACGCTCC
TACCTTCCCCCAAGACACTGCTTTCCACGATCGTAGAGGTGCATCCGGAT
GTACTCCTGCTGGATATGAATTTTTCTACCGGCATCAATACGGGTAATGA
AGGATTATATTGGCTGGATCAGGTCCGTAGCCGTTTCCCTGACCTCCCTG
TGGTACTCTTTACCGCTTATGCGGACATTCGTCTGGCAGTGGAAGCCTTG
AAGCGTGGAGCAAGCGATTTCGTAGTCAAGCCGTGGAACAACACCGAGCT
GTTGGAGTCGCTTCGCATGGCGATGAATAAGGCCGCAAGCACTCAAGTGA
CGGCTACACCTAAAGAAGGCGATTCGGTATTTCTCAGCAAAAGCAAGGCC
ATGTGTGAGGTGTTGGAGCTGGCTGGTCGTATCGGCGATACTGCAGCCCA
TGTCCTCATTACGGGTGAGAATGGTACCGGCAAGGGCGTTTTAGCCGAGT
ATATCCATGCCCGTTCTCCTCGTAGCCGGCAGCCGATGCTGACTGTGGAT
ATGGGAGCTTTGAGCGAGACGCTGTTCGAGAGCGAACTGTTCGGCCATGT
GAAAGGAGCCTTTACCGATGCCAAAAGCGATCGCGCCGGCAAGTTCGAGA
CGGCGTCCGGCGGCACGATCTTCATGGACGAGATTGGCAATCTGAGCCTT
GCCTTGCAAGCCAAGTTGTTGGCTGTACTACAGCAAAAAGTGGTGACCCG
TGTGGGCAGCAATACACCGATCCCTGTGGATGTTCGTGTCATCTCTGCCA
CGAATAGCGATTTGCCCCTCTCCGTGGCAGAAGGCCGGTTTCGAGAAGAT
TTGCTTTATCGTCTCAATACGATTCATATCGAGATGCCGCCGCTACGTCG
TCGCAGGGAAGATATAGTGCCGATGGCCGTATTCTTCCTGCATCGTTATG
CACGACAGTATGGAAAAGAGGTGCCGGAATTGACTCCCGAAGCAGAGGCC
CTACTCTCCGATTATCCGTGGCCGGGCAATGTGCGTGAGCTTCAGCATTG
CATAGAGAAGGCTGTGATCCTTAGCCGTAGCAGTAGCCTTTCTGCTGCGG
ATCTGTCGTTGCCGAAGTCGGTCGATGCACATCCGACTGCTACCGGTGTA
GCAAGCACTCCTCAGACGTTGGATGAAATGGAAAAGACCGCTATCGAGCA
AGCCTTGGCACGAAACGGCAGCAACCTTTCGAATGTGGCAAGGGAATTAG
GCATCAGCCGCCAGACTCTGTATAATAAGATGAAACGCTACGGGCTG

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