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Porphyromonas gingivalis Search Results

Record: 1 of 1  
MiniMap IGR0063 IGR0061 IGR0066 IGR0060 IGR0062 IGR0064 IGR0065 IGR0067 IGR0068 PG0068 PG0076 abiPg, - PG0067 PG0074 PG0071 PG0070 sda,sdh, - PG0072 PG0077 melA, - PG0073 PG0069 PG0068 PG0076 abiPg, - PG0067 PG0074 PG0071 PG0070 sda,sdh, - PG0072 PG0077 melA, - PG0073 PG0069 PG0076 abiPg, - PG0067 PG0074 PG0068 PG0071 PG0070 sda,sdh, - PG0072 PG0077 melA, - PG0073 PG0069


LANL Gene ID: PG0072

GenBank Locus Tag: PG0084

DNA Molecule Name:
1  

GenBank ID:
34539954

Gene Name:
sda  sdh  

Definition:
L-serine dehydratase

Cellular Location:
Cytoplasm [Evidence]

Gene Start:
97972

Gene Stop:
99168

Gene Length:
1197

Molecular Weight*:
43271

pI*:
5.90

Net Charge*:
-6.95

EC:
4.2.1.13  

Functional Class:
Energy metabolism; Amino acids and amines  

Gene Ontology:

Pathway: pathway table
Cysteine metabolism
Glycine, serine and threonine metabolism

Comment:
TIGR ID: PG0084

Proteomic Data: Proteomic Data Search
TIGR AnnotationL-serine dehydratase, iron-sulfur-dependent, single chain form, GroupH (energy metabolism)
ORF #PG-PP/PG-PPC1PG-PP/PG-PPC2
Spectral CountPeptide IntensitySpectral CountPeptide Intensity
ProqValProqValProqValProqVal
TIGRPG0084-1.320.016-1.920.00065-0.010.38-1.920.00065
LANLPG00720.400.260.990.50
ConsensusSP1IP1SP2IP2

Human Oral Microbiome Database:
View in HOMD Genome Viewer

 Blast Summary:  PSI-Blast Search
Many hits in gapped BLAST to L-serine dehydratase sequences, e.g. residues 3-396 are 41% similar to the enzyme from P.aeruginosa (AE004671). Residues 1-395 are 40% similar to the enzyme from N. meningitidis (AE002378).

This sequence is similar to BT4678.

 Top Blast Hits:  Updated monthly
Click here to view the entire PsiBlast results.
 gi|34539954|ref|NP_904433.1|  L-serine dehydratase, iron-sul...   798   0.0  
 gi|150007978|ref|YP_001302721.1|  L-serine dehydratase, iron...   588   e-166
 gi|154492356|ref|ZP_02031982.1|  hypothetical protein PARMER...   587   e-166
 gi|150004980|ref|YP_001299724.1|  L-serine dehydratase [Bact...   554   e-156
 gi|156858563|gb|EDO51994.1|  hypothetical protein BACUNI_045...   553   e-156
 gi|29350086|ref|NP_813589.1|  L-serine dehydratase [Bacteroi...   552   e-155
 gi|153807815|ref|ZP_01960483.1|  hypothetical protein BACCAC...   551   e-155
 gi|156107928|gb|EDO09673.1|  hypothetical protein BACOVA_055...   548   e-154
 gi|53712557|ref|YP_098549.1|  L-serine dehydratase [Bacteroi...   548   e-154
 gi|78358151|ref|YP_389600.1|  L-serine dehydratase [Desulfov...   451   e-125


InterPro Summary:  InterProScan

InterPro
IPR005130
Domain
Serine dehydratase alpha chain
PF03313 [129-397]T 5.500017542664309E-102 PF03313 SDH_alpha SDH_alpha
InterPro
IPR005131
Domain
Serine dehydratase beta chain
PF03315 [3-120]T 1.0E-11 PF03315 SDH_beta SDH_beta


COGS Summary:  COGS Search
BeTs to 4 clades of COG1760
COG name: L-serine deaminase
Functional Class: E
The phylogenetic pattern of COG1760 is --------EBrhuj-------
Number of proteins in this genome belonging to this COG is 1
Blocks Summary:  Blocks Search
No significant hit to the Blocks database.

 ProDom Summary:  Protein Domain Search
Residues 142-396 are 46% similar to a (L-SERINE DEHYDRATASE DEAMINASE SDH LYASE IRON-SULFUR) protein domain (PD008627 which is seen in SDHL_STRCO.

Residues 1-73 are 49% similar to a (L-SERINE DEHYDRATASE DEAMINASE SDH LYASE IRON-SULFUR) protein domain (PD009440 which is seen in SDHX_ECOLI.


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

Pfam Summary:  Pfam Search
Residues 3 to 120 (E-value = 8.2e-15) place PG0072 in the SDH_beta family which is described as Serine dehydratase beta chain (PF03315)
Residues 129 to 397 (E-value = 4.9e-105) place PG0072 in the SDH_alpha family which is described as Serine dehydratase alpha chain (PF03313)

 Structural Feature(s):
Feature Type  Start  Stop
transmembrane  
229  
245
non-globular  
260  
326

Top PDB Hits:
-45% similar to PDB:2IQQ The Crystal Structure of Iron, Sulfur-Dependent L-serine dehydratase from Legionella pneumophila subsp. pneumophila (E_value = 2.2E_15);
-45% similar to PDB:2IAF Crystal structure of a fragment (residues 11 to 161) of L-serine dehydratase from Legionella pneumophila (E_value = 2.4E_14);
-44% similar to PDB:1PCI PROCARICAIN (E_value = 2.4E_14);
-63% similar to PDB:1O6B Crystal structure of phosphopantetheine adenylyltransferase with ADP (E_value = 2.4E_14);
-41% similar to PDB:2D6F Crystal structure of Glu-tRNA(Gln) amidotransferase in the complex with tRNA(Gln) (E_value = 2.4E_14);

Gene Protein Sequence:
MESITQIYRIGYGPSSSHTIGPRRAAEMFLDRNPRATSFRVTLYGSLAAT
GKGHLTDAAILAVLEAKAPTEIVWKPEIFQNFHPNGMLFESFDKEGKQLD
DWLIYSIGGGVLANEHFNEQRGREVYPLSKMADILDELNRRGLSYWEYVE
ENEDPDIWDYLAEVWSVMRSAIQEGLDAEGVLPGGLGVRRKAASYLIRAQ
GYSPGVRSRGNVYAYALAVSEQNASGGKIVTAPTCGSCGVVPAVLHHLQQ
TRDFSDKRILRALATAGLFANVVRTNASISGAEVGCQGEVGVACAMGAAA
SSQLFGGTLSQIEYAAEMALEHHLGLTCDPVCGLVQVPCIERNAFAAARA
LDANTYANFSDGRHRISFDQVVEVMRQTGKDLPSLYKETSQGGLAIVHC

Gene Nucleotide Sequence:  Sequence Viewer
ATGGAATCGATAACCCAAATATATCGCATCGGCTACGGTCCGAGCAGTAG
CCACACGATTGGCCCACGTCGGGCTGCTGAGATGTTTCTCGATCGGAACC
CCCGGGCGACCTCTTTCCGTGTTACGCTATACGGCAGCCTTGCTGCCACG
GGCAAAGGACACCTCACGGATGCAGCTATCCTTGCCGTCTTGGAAGCAAA
GGCTCCGACCGAAATCGTTTGGAAACCGGAGATCTTCCAAAATTTTCACC
CCAACGGCATGCTCTTCGAGAGCTTCGACAAAGAGGGCAAGCAGCTCGAC
GACTGGCTCATCTATAGCATCGGCGGCGGAGTCTTGGCCAACGAACACTT
CAACGAACAGCGAGGTCGCGAGGTATATCCGCTCAGCAAGATGGCAGATA
TTCTCGACGAACTGAACAGGCGCGGCCTAAGCTATTGGGAGTATGTGGAA
GAAAACGAAGATCCCGATATATGGGACTATTTGGCTGAGGTCTGGTCGGT
AATGCGGAGCGCCATTCAGGAGGGGCTCGATGCTGAGGGGGTGCTGCCGG
GTGGACTGGGCGTTCGCCGGAAGGCAGCCAGCTATCTGATTCGTGCGCAG
GGGTATTCGCCGGGTGTACGAAGCCGAGGCAATGTATATGCCTATGCTTT
GGCTGTGAGCGAACAGAATGCATCGGGTGGCAAGATCGTAACGGCGCCGA
CATGTGGGTCGTGCGGCGTTGTACCGGCGGTACTCCACCACCTCCAACAG
ACTCGTGACTTCAGCGATAAGCGCATATTGCGTGCACTGGCTACGGCCGG
CCTTTTTGCTAATGTGGTACGCACCAATGCTTCTATTTCGGGTGCAGAAG
TCGGCTGTCAGGGCGAAGTGGGAGTGGCTTGTGCCATGGGAGCGGCAGCC
AGCAGCCAGCTATTCGGGGGTACCCTGTCCCAAATCGAATATGCTGCAGA
GATGGCTTTGGAGCATCACCTCGGACTGACCTGCGACCCTGTATGCGGAT
TGGTGCAGGTACCTTGTATCGAACGAAATGCCTTTGCGGCAGCACGAGCT
TTGGATGCCAATACTTATGCCAATTTCAGCGATGGCAGACACCGCATTTC
GTTCGATCAGGTCGTGGAAGTGATGCGTCAGACGGGCAAGGATTTGCCGA
GTCTATATAAGGAAACCTCTCAGGGTGGATTGGCCATAGTACACTGC

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