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Porphyromonas gingivalis Search Results

Record: 1 of 1  
MiniMap IGR0033 IGR0035 IGR0031 IGR0034 IGR0036 IGR0032 dnaE, - PG0031 PG0037 rl19, - PG0032 ISPg5, - PG0033 ISPg5, - PG0034 glyA, - PG0035 htpG, - PG0038 PG0036 dnaE, - PG0031 PG0037 rl19, - PG0032 ISPg5, - PG0033 ISPg5, - PG0034 glyA, - PG0035 htpG, - PG0038 PG0036 Type: IS element, Name: ISPg5 - 8 dnaE, - PG0031 PG0037 rl19, - PG0032 ISPg5, - PG0033 ISPg5, - PG0034 glyA, - PG0035 htpG, - PG0038 PG0036


LANL Gene ID: PG0035

GenBank Locus Tag: PG0042

DNA Molecule Name:
1  

Genomic Island ID:
20

GenBank ID:
34539916

 Gene Name:
glyA  

 Definition:
serine hydroxymethyltransferase

 Cellular Location:
Cytoplasm [Evidence]

 Gene Start:
49769

Gene Stop:
51046

Gene Length:
1278

Molecular Weight*:
46663

pI*:
6.80

Net Charge*:
-1.22

EC:
2.1.2.1  

 Functional Class:
Amino acid biosynthesis; Serine family  

 Gene Ontology:
Biological process
  GO:0006544    glycine metabolic process
  GO:0006563    L-serine metabolic process

Molecular function
  GO:0003824    catalytic activity
  GO:0004372    glycine hydroxymethyltransferase activity
  GO:0030170    pyridoxal phosphate binding


 Pathway: pathway table
Cyanoamino acid metabolism
Glycine, serine and threonine metabolism
Lysine degradation
Methane metabolism
One carbon pool by folate

 Comment:
TIGR ID: PG0042

 Proteomic Data: Proteomic Data Search
TIGR Annotationserine hydroxymethyltransferase, GroupA (amino acid biosynthesis) ,GroupE (central intermediary metabolism)
ORF #PG-PP/PG-PPC1PG-PP/PG-PPC2
Spectral CountPeptide IntensitySpectral CountPeptide Intensity
ProqValProqValProqValProqVal
TIGRPG00420.343e-06-0.270.0450.323.8e-08-0.270.045
LANLPG00351.270.831.240.75
ConsensusSP1IP1SP2IP2

Human Oral Microbiome Database:
View in HOMD Genome Viewer

 Blast Summary:  PSI-Blast Search
Numerous significant hits in gapped BLAST to serine hydroxymethyltransferase; e.g. residues 1-424 are 57% similar to (AE000692) serine hydroxymethyl transferase of Aquifex aeolicus, residues 4-424 are 56% similar to (AE001743) serine hydroxymethyltransferase of Thermotoga maritima, residues 4-425 are 57% similar to (J01620) serine hydroxymethyltransferase of Escherichia coli.

This sequence is similar to BT0738.

 Top Blast Hits:  Updated monthly
Click here to view the entire PsiBlast results.
 gi|34539916|ref|NP_904395.1|  serine hydroxymethyltransferas...   862   0.0  
 gi|150005845|ref|YP_001300589.1|  serine hydroxymethyltransf...   726   0.0  
 gi|28274156|gb|AAO33831.1|  GlyA [Tannerella forsythensis]        723   0.0  
 gi|156110201|gb|EDO11946.1|  hypothetical protein BACOVA_024...   720   0.0  
 gi|53713493|ref|YP_099485.1|  serine hydroxymethyltransferas...   719   0.0  
 gi|29346148|ref|NP_809651.1|  serine hydroxymethyltransferas...   718   0.0  
 gi|153806511|ref|ZP_01959179.1|  hypothetical protein BACCAC...   718   0.0  
 gi|156860035|gb|EDO53466.1|  hypothetical protein BACUNI_027...   715   0.0  
 gi|154492187|ref|ZP_02031813.1|  hypothetical protein PARMER...   714   0.0  
 gi|150007910|ref|YP_001302653.1|  serine hydroxymethyltransf...   712   0.0


InterPro Summary:  InterProScan

InterPro
IPR001085
Family
Glycine hydroxymethyltransferase
PIRSF000412 [1-426]T 0.0 PIRSF000412 SHMT SHMT
PTHR11680 [2-426]T 0.0 PTHR11680 Gly_HO-Metrfase Gly_HO-Metrfase
PF00464 [1-394]T 0.0 PF00464 SHMT SHMT
PS00096 [214-230]T 8.0E-5 PS00096 SHMT SHMT
InterPro
IPR015421
Domain
Pyridoxal phosphate-dependent transferase, major region, subdomain 1
G3DSA:3.40.640.10 [29-295]T 4.100013996988709E-109 G3DSA:3.40.640.10 PyrdxlP-dep_Trfase_major_sub1 PyrdxlP-dep_Trfase_major_sub1
InterPro
IPR015424
Domain
Pyridoxal phosphate-dependent transferase, major region
SSF53383 [2-424]T 0.0 SSF53383 PyrdxlP-dep_Trfase_major PyrdxlP-dep_Trfase_major


COGS Summary:  COGS Search
BeTs to 17 clades of COG0112
COG name: Glycine hydroxymethyltransferase
Functional Class: E
The phylogenetic pattern of COG0112 is amtkYqvcebRhujgpolinx
Number of proteins in this genome belonging to this COG is 2
Blocks Summary:  Blocks Search
***** IPB001085 (Serine hydroxymethyltransferase (SHMT)) with a combined E-value of 6.2e-147.
    IPB001085A    22-74
    IPB001085B    93-118
    IPB001085C    143-174
    IPB001085D    175-218
    IPB001085E    257-293
    IPB001085F    328-360
    IPB001085G    367-387


 ProDom Summary:  Protein Domain Search
Residues 4-387 are 59% similar to a (HYDROXYMETHYLTRANSFERASE SERINE TRANSFERASE METHYLASE) protein domain (PD001547 which is seen in GLYA_AQUAE.


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

Pfam Summary:  Pfam Search
Residues 1 to 394 (E-value = 5.2e-233) place PG0035 in the SHMT family which is described as Serine hydroxymethyltransferase (PF00464)

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

Top PDB Hits:
-72% similar to PDB:1DFO CRYSTAL STRUCTURE AT 2.4 ANGSTROM RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE AND 5-FORMYL TETRAHYDROFOLATE (E_value = 5.0E_130);
-72% similar to PDB:1EQB X-RAY CRYSTAL STRUCTURE AT 2.7 ANGSTROMS RESOLUTION OF TERNARY COMPLEX BETWEEN THE Y65F MUTANT OF E-COLI SERINE HYDROXYMETHYLTRANSFERASE, GLYCINE AND 5-FORMYL TETRAHYDROFOLATE (E_value = 1.5E_129);
-69% similar to PDB:1KKJ Crystal Structure of Serine Hydroxymethyltransferase from B.stearothermophilus (E_value = 1.7E_125);
-69% similar to PDB:1KKP Crystal Structure of Serine Hydroxymethyltransferase complexed with Serine (E_value = 1.7E_125);
-69% similar to PDB:1KL1 Crystal Structure of Serine Hydroxymethyltransferase Complexed with Glycine (E_value = 1.7E_125);

Gene Protein Sequence:
MKKDSVIFDLIEKEHQRQLKGIELIASENFVSEQVMQAMGSCMTNKYAEG
YPGKRYYGGCEVVDQSEQIAIDRIKQLYGAEWANVQPHSGAQANMAVLLA
CLEAGDTFMGLNLEHGGHLSHGSLVNSSGILYRPIGYNLSEETGMVDYDH
MEKMAIEHKPKLIIGGGSAYSREWDYKRMREIADKVGALLMIDMAHPAGL
IAAGLLENPVKYAHIVTSTTHKTLRGPRGGIILMGKDFDNPWGKKTPKGE
IKKMSALLDSAVFPGVQGGPLEHVIAAKAVAFGEALDPSFKEYQTQVKKN
AAVLAQAFMDKGYKVISGGTDNHSMLIDLRPKFPELTGKVAEKALVAADI
TVNKNMVPFDSRSAFQTSGFRVGTPAITTRGVKEDKMGYIVELIDRVLSA
PEDEAVIASVRTEVNRMMADYPLFAW

Gene Nucleotide Sequence:  Sequence Viewer
ATGAAAAAAGACAGCGTAATTTTCGATCTGATCGAAAAAGAACATCAGCG
CCAGCTCAAAGGCATCGAGCTGATCGCATCGGAAAACTTTGTAAGCGAAC
AAGTTATGCAGGCTATGGGTAGCTGTATGACCAATAAGTATGCCGAAGGT
TATCCCGGCAAACGCTATTACGGTGGTTGTGAAGTGGTAGACCAAAGCGA
GCAAATCGCCATCGACCGTATCAAACAACTCTACGGAGCCGAATGGGCCA
ACGTACAGCCTCACTCCGGAGCACAGGCCAATATGGCCGTTCTTCTGGCT
TGCCTCGAAGCAGGCGATACGTTCATGGGACTGAACCTCGAACACGGCGG
CCACCTATCGCACGGCTCACTCGTCAATAGCTCGGGTATCCTCTACCGTC
CCATCGGCTACAATCTGAGCGAAGAGACGGGAATGGTGGATTACGACCAC
ATGGAGAAAATGGCCATCGAGCACAAACCCAAGCTGATCATCGGCGGTGG
TTCGGCCTATTCTCGTGAGTGGGACTACAAGCGTATGCGTGAGATCGCTG
ACAAGGTGGGTGCCTTGTTGATGATCGATATGGCACACCCTGCCGGTCTG
ATCGCTGCCGGTCTGCTGGAGAACCCCGTGAAGTATGCTCATATCGTTAC
TTCTACGACTCACAAGACACTGCGTGGCCCCCGTGGCGGTATCATCCTTA
TGGGCAAGGACTTCGACAATCCTTGGGGCAAGAAAACCCCGAAGGGCGAG
ATCAAGAAGATGAGCGCACTCCTCGACTCTGCCGTATTCCCCGGTGTACA
GGGTGGTCCGCTCGAGCACGTTATAGCTGCTAAGGCTGTAGCTTTCGGAG
AAGCACTGGATCCTTCGTTCAAGGAATACCAAACGCAGGTGAAAAAGAAT
GCTGCCGTTTTGGCTCAGGCTTTCATGGACAAAGGCTATAAAGTGATTTC
CGGTGGTACGGACAACCACAGTATGCTGATCGATCTTCGTCCGAAGTTCC
CCGAACTGACAGGTAAAGTGGCAGAGAAAGCCCTCGTGGCAGCGGATATT
ACCGTCAATAAGAACATGGTACCGTTCGATTCTCGCTCTGCATTCCAGAC
ATCGGGCTTCCGCGTGGGTACTCCGGCCATCACCACTCGTGGCGTAAAAG
AAGATAAGATGGGCTATATCGTGGAGTTGATAGACCGTGTGCTCTCCGCA
CCGGAGGACGAAGCCGTAATAGCATCGGTTCGTACCGAAGTCAACCGGAT
GATGGCCGATTATCCTCTCTTTGCTTGG

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