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Porphyromonas gingivalis Search Results

Record: 1 of 1  
MiniMap IGR0055 IGR0057 IGR0058 IGR0060 IGR0056 IGR0059 PG0068 lpxA, - PG0059 pyrF,ura3, - PG0062 prfA, - PG0063 PG0064 abiPg, - PG0067 fabZ, - PG0060 PG0058 PG0068 lpxA, - PG0059 pyrF,ura3, - PG0062 prfA, - PG0063 PG0064 abiPg, - PG0067 fabZ, - PG0060 PG0058 pyrF,ura3, - PG0062 prfA, - PG0063 PG0064 abiPg, - PG0067 fabZ, - PG0060 PG0058 PG0066 PG0065 firA,lpxD, - PG0061 PG0066 PG0065 firA,lpxD, - PG0061 PG0068 lpxA, - PG0059


LANL Gene ID: PG0063

GenBank Locus Tag: PG0074

DNA Molecule Name:
1  

GenBank ID:
34539945

Gene Name:
prfA  

Definition:
peptide chain release factor

Cellular Location:
Cytoplasm [Evidence]

Gene Start:
89262

Gene Stop:
88180

Gene Length:
1083

Molecular Weight*:
40356

pI*:
5.00

Net Charge*:
-12.36

EC:
 

Functional Class:
Translation; Translation factors  

Gene Ontology:
Biological process
  GO:0006415    translational termination

Cellular component
  GO:0005737    cytoplasm

Molecular function
  GO:0003747    translation release factor activity
  GO:0016149    translation release factor activity, codon specific


Pathway: pathway table

Comment:
TIGR ID: PG0074

Proteomic Data: Proteomic Data Search
TIGR Annotationpeptide chain release factor 1, GroupN (protein synthesis)
ORF #PG-PP/PG-PPC1PG-PP/PG-PPC2
Spectral CountPeptide IntensitySpectral CountPeptide Intensity
ProqValProqValProqValProqVal
TIGRPG00743.330.00247.889.9e-054.035.7e-057.889.9e-05
LANLPG006310.08235.0016.38397.48
ConsensusSP1IP1SP2IP2

Human Oral Microbiome Database:
View in HOMD Genome Viewer

 Blast Summary:  PSI-Blast Search
Numerous hits in gapped BLAST to peptide chain release sequences, e.g. residues 5-348 are 72% similar to RF1_PSEAE (AE004880).

This sequence is similar to CT023 and BT4210.

 Top Blast Hits:  Updated monthly
Click here to view the entire PsiBlast results.
 gi|34539945|ref|NP_904424.1|  peptide chain release factor 1...   667   0.0  
 gi|149280703|ref|ZP_01886814.1|  peptide chain release facto...   463   e-129
 gi|150008712|ref|YP_001303455.1|  peptide chain release fact...   456   e-126
 gi|156107454|gb|EDO09199.1|  hypothetical protein BACOVA_050...   451   e-125
 gi|29349618|ref|NP_813121.1|  peptide chain release factor 1...   451   e-125
 gi|53712203|ref|YP_098195.1|  peptide chain release factor 1...   450   e-125
 gi|153807530|ref|ZP_01960198.1|  hypothetical protein BACCAC...   450   e-125
 gi|156859247|gb|EDO52678.1|  hypothetical protein BACUNI_034...   443   e-122
 gi|150002702|ref|YP_001297446.1|  peptide chain release fact...   431   e-119
 gi|154490829|ref|ZP_02030770.1|  hypothetical protein PARMER...   424   e-117


InterPro Summary:  InterProScan

InterPro
IPR000352
Domain
Class I peptide chain release factor
PF00472 [211-324]T 3.99998544139379E-60 PF00472 RF-1 RF-1
PS00745 [231-247]T 8.0E-5 PS00745 RF_PROK_I RF_PROK_I
InterPro
IPR004373
Family
Peptide chain release factor 1
PTHR11075:SF9 [1-361]T 0.0 PTHR11075:SF9 PrfA PrfA
TIGR00019 [1-360]T 0.0 TIGR00019 prfA prfA
InterPro
IPR005139
Domain
PCRF
PF03462 [69-182]T 5.20000089003276E-56 PF03462 PCRF PCRF
InterPro
IPR012086
Family
Protein chain release factor, RF-1/RF-2
PIRSF003056 [6-361]T 0.0 PIRSF003056 Release_factor Release_factor
noIPR
unintegrated
unintegrated
PIRSF500105 [6-361]T 0.0 PIRSF500105 PrfA PrfA
PTHR11075 [1-361]T 0.0 PTHR11075 PTHR11075 PTHR11075
SSF75620 [29-360]T 5.0E-101 SSF75620 SSF75620 SSF75620


COGS Summary:  COGS Search
BeTs to 13 clades of COG0216
COG name: Protein chain release factor A
Functional Class: J
The phylogenetic pattern of COG0216 is ----YqvcEbrhujgpolinx
Number of proteins in this genome belonging to this COG is 1
Blocks Summary:  Blocks Search
***** IPB000352 (Class I peptide chain release factor) with a combined E-value of 2.8e-109.
    IPB000352A    117-152
    IPB000352B    162-212
    IPB000352C    224-270
    IPB000352D    297-324
    IPB000352D    310-337


 ProDom Summary:  Protein Domain Search
Residues 248-350 are 56% similar to a (PEPTIDE CHAIN FACTOR RELEASE) protein domain (PD002191 which is seen in RF1_TREPA.

Residues 98-152 are 65% similar to a (PEPTIDE CHAIN FACTOR RELEASE) protein domain (PD088320 which is seen in RF1_BACSU.

Residues 6-96 are 31% similar to a (PEPTIDE CHAIN FACTOR RELEASE) protein domain (PD004306 which is seen in RF1_BACSU.

Residues 161-247 are 67% similar to a (PEPTIDE CHAIN FACTOR RELEASE) protein domain (PD002273 which is seen in RF1_SYNY3.

Residues 202-307 are 35% similar to a (CHROMOSOME XII COSMID 8003) protein domain (PD092301 which is seen in Q05863_YEAST.

Residues 1-97 are 31% similar to a (PROTEIN COILED COIL REPEAT FILAMENT HEPTAD PATTERN) protein domain (PD000002 which is seen in RF1_AQUAE.


Paralogs:  Local Blast Search
Residues 84-349 share 39% identity with PG1027, a peptide chain release factor.

Pfam Summary:  Pfam Search
Residues 69 to 182 (E-value = 2.5e-59) place PG0063 in the PCRF family which is described as PCRF domain (PF03462)
Residues 213 to 324 (E-value = 4.8e-62) place PG0063 in the RF-1 family which is described as Peptidyl-tRNA hydrolase domain (PF00472)

 Structural Feature(s):
Feature Type  Start  Stop
coil-coil  
36  
99

Top PDB Hits:
-72% similar to PDB:2B3T Molecular basis for bacterial class 1 release factor methylation by PrmC (E_value = 1.2E_97);
-68% similar to PDB:1ZBT Crystal structure of Peptide chain release factor 1 (RF-1) (SMU.1085) from Streptococcus mutans at 2.34 A resolution (E_value = 4.7E_94);
-67% similar to PDB:2B64 30S ribosomal subunit, tRNAs, mRNA and release factor RF1 from a crystal structure of the whole ribosomal complex. This file contains the 30S subunit, tRNAs, mRNA and release factor RF1 from a crystal structure of the whole ribosomal complex". The entire crystal structure contains one 70S ribosome, tRNAs, mRNA and release factor RF1 and is described in remark 400. (E_value = 8.3E_91);
-65% similar to PDB:1RQ0 Crystal structure of peptide releasing factor 1 (E_value = 1.9E_82);
-65% similar to PDB:2FVO Docking of the modified RF1 X-ray structure into the Low Resolution Cryo-EM map of E.coli 70S Ribosome bound with RF1 (E_value = 1.9E_82);

Gene Protein Sequence:
MSENNLLDRLDGLESRFEEISTLITDPAVIADMKRFTKLSKEYRDLEKIH
TAGRDYRNLLANIEEAKHTMAKESDEELREMAREMLAEANERLPILEEEI
KMLLIPANPEDDKNAIVEIRGGTGGDEAALFAGDLYRMYVKYCESKGWQV
EVTDLSEGATGGYKEIVFSVKGEGVYGILKYESGVHRVQRVPATETQGRI
HTSAATVAVLPEAEEVDVEINPADIEMQTSRSGGAGGQNVNKVETKVQLT
HKPTGMVVVCQQARSQIANRELAMQMLRSKLYDIELSKHNEAIAARRKTM
VSTGDRSAKIRTYNYPQGRVTDHRINMTVYNLSAVMDGEVQPFIDALIIA
ENVERMKEAAL

Gene Nucleotide Sequence:  Sequence Viewer
ATGTCAGAGAATAACCTATTAGACCGATTGGATGGCTTGGAGAGCCGTTT
CGAAGAGATTTCCACGCTTATCACGGATCCGGCCGTAATCGCGGACATGA
AGCGTTTCACGAAGTTGAGCAAGGAGTATCGCGATCTGGAAAAGATCCAT
ACGGCCGGGCGCGACTATCGCAATCTGCTCGCCAACATCGAGGAAGCAAA
GCATACCATGGCCAAAGAGAGCGACGAGGAGTTGCGCGAGATGGCTCGCG
AGATGCTGGCCGAGGCTAACGAACGCTTGCCCATTTTGGAGGAGGAGATC
AAGATGCTACTCATTCCGGCCAATCCGGAGGATGACAAGAATGCCATCGT
GGAAATTCGCGGAGGAACGGGGGGCGATGAGGCTGCACTTTTTGCCGGCG
ACCTCTACCGCATGTACGTCAAGTATTGCGAGAGCAAAGGCTGGCAGGTG
GAGGTCACCGACCTGAGCGAAGGAGCTACGGGTGGTTACAAAGAGATCGT
CTTCTCGGTCAAGGGGGAAGGAGTGTATGGTATCCTGAAATATGAGAGCG
GTGTGCACCGTGTCCAGCGCGTACCTGCGACCGAGACACAGGGGCGCATA
CATACCTCGGCAGCTACCGTGGCTGTCTTGCCCGAAGCCGAAGAAGTGGA
CGTGGAGATCAATCCGGCAGACATCGAGATGCAGACGTCCCGTTCAGGCG
GTGCCGGAGGTCAGAATGTAAACAAGGTGGAGACTAAGGTGCAGCTTACG
CACAAGCCTACGGGTATGGTGGTGGTTTGCCAGCAGGCTCGTTCGCAGAT
TGCCAACCGCGAACTGGCTATGCAAATGCTGCGCTCCAAGCTCTACGACA
TAGAGCTGTCCAAGCATAACGAAGCTATTGCAGCCCGACGCAAGACGATG
GTATCGACCGGCGACCGTTCGGCCAAGATTCGTACCTACAACTATCCGCA
AGGACGGGTGACGGATCACCGCATCAATATGACGGTCTACAACCTGTCGG
CCGTAATGGACGGTGAGGTACAGCCTTTTATCGATGCCTTGATAATAGCA
GAAAATGTTGAGCGGATGAAAGAAGCCGCCTTA

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