PSCA Target Info

YP_164873.1;PJ05853H	Protein Sequence Comparative Analysis (PSCA)

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YP_164873.1 PJ05853H JCSG 374753 PDB Deposition 08-MAR-10 PDB id: 3chv

Protein Sequence Information

TOPSAN

JCSG Internal annotations

ACCESSION	YP_164873.1
DESCRIPTION	Protein of unknown function [TIM beta/alpha-barrel] that belongs to DUF849 family.
ORGANISM	Silicibacter pomeroyi dss-3
COMMENT	This protein, YP_164873.1(PJ05843H), is from Silicibacter Pomeroyi with the length of 285 residues. A sequence search of PJ05843H against the PFAM database reveals that this target is a prokaryotic protein with unknown function (PF05853) (e-value: 6.2e-73). Additionally, this protein shares sequence similarity with COG3246: Uncharacterized conserved protein. It has a TIM barrel fold and as such shares structural similarity with many proteins. Of structures solved to date (March 5, 2008), this protein seems to be the most similar (sequence similarity from ffas score -96.700, from a structurally superimposition from VAST: RMSD: 1.6 A, 30.3% sequence identity, with 264 residues aligned) to 3-Keto-5-Aminohexanoate Cleavage Enzyme (Yp_293392.1) from Ralstonia Eutropha Jmp134 (PDB code:3c6c which also has a TOPSAN page). Additionally this protein is a structural homolog to D-Ribulose 5-Phosphate 3-Epimerase (PDB ID: 1TQX) which has a conserved active site. Based on the results of calculations of surface interaction, the biomolecule of this protein should be a dimer.

DR	UNIPROT; Q5LLI5_SILPO
DR	SPTR;
DR	GenBank; YP_164873
DR	Pfam; PF05853; DUF849;
DR	PDB; 3CHV; Identical; 01-APR-08; PROKARYOTIC DOMAIN OF UNKNOWN FUNCTION (DUF849) W BARREL FOL;
DR	PDB; 3FA5; Highly similar; 02-DEC-08; PROTEIN OF UNKNOWN FUNCTION (DUF849);
DR	PDB; 3NO5; Highly similar; 25-AUG-10; UNCHARACTERIZED PROTEIN;
DR	PDB; 2Y7D; Highly similar; 01-JUN-11; 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME;
DR	PDB; 2Y7E; Highly similar; 01-JUN-11; 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME;
DR	PDB; 2Y7F; Highly similar; 01-JUN-11; 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME;
DR	PDB; 2Y7G; Highly similar; 01-JUN-11; 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME;
DR	FFAS; 374753; Fold and function assignment.
DR	TVPC; YP_164873.1; Homologs in PDB, JCSG and SG center.
DR	OVP; YP_164873.1; Ortholog view popup.
DR	TPM; YP_164873.1; Target PDB monitor.
DR	FSS; YP_164873.1; Target function coverage.

PROPERTY

Residues: 283 aa
Molecule Weight: 30784.27 Dalton
Isoelectric Point: 6.39
Extinction Coefficient: 30940
Gravy Index: -.25
Number of Met residues: 10
Percentage of Met residues: 3.53 %
Number of Cys residues: 6
Percentage of Cys residues: 2.12 %

SEQUENCE  amino acids 283 aa
>YP_164873.1  gi|56708832|ref|YP_164873.1| hypothetical protein SPOA0042 [Silicibacter pomeroyi DSS-3]
MDTPANKPCIICVAITGSVPTKADNPAVPITVSEQVESTQEAFEAGAAIAHCHVRNDDGT
PSSDPDRFARLTEGLHTHCPGMIVQFSTGGRSGAGQARGGMLPLKPDMASLSVGSNNFPS
RVYENPPDLVDWLAAQMRSYRVTPEIEAFDLSHILRAIDMHGRGLLYGKLYVQFVMGVKN
AMPADREVFDFYVRMMRTRAPQAEWCAAGIGANQLTVNEWAIAAGGHTRTGLEDNIRLDR
QTLAPSNAALVRRSVELCDKYQRPVASWQQAREILGLPAAARN

CDS  cDNA 852 bp
   1 atggacacgc ccgccaacaa gccctgcatc atctgcgtcg cgatcaccgg gtcggttccc    60
  61 accaaggccg acaatccggc ggtgcccatc acggtcagcg aacaggtcga aagcacgcaa   120
 121 gaggcgttcg aggccggcgc cgccatcgcc cattgccatg tgcgcaacga cgacggcacc   180
 181 ccatccagcg accccgaccg ctttgcgcgg ctgacggagg ggctgcacac acattgcccg   240
 241 ggcatgatcg tacaattctc gaccggcggg cgctcgggcg ccgggcaggc gcgcggcggc   300
 301 atgctgccac tgaaacctga catggcctcg ctctcggtgg gctccaacaa ctttccctcc   360
 361 cgggtctatg agaacccgcc cgacctggtc gactggctgg ccgcccagat gcgcagctat   420
 421 cgcgtcaccc cggaaatcga ggccttcgac ctcagccata tcctgcgcgc cattgacatg   480
 481 cacgggcgcg ggctgctcta cggcaagctc tatgtgcaat tcgtgatggg ggtgaagaac   540
 541 gcgatgcccg ccgaccgcga ggtgttcgat ttctatgtcc ggatgatgcg gacccgggcc   600
 601 ccccaggccg aatggtgcgc cgccggcatc ggcgccaatc aactgaccgt caacgaatgg   660
 661 gccatcgctg cgggcggaca cacacgcacg gggctcgagg acaacatccg cctcgaccgg   720
 721 caaacgctgg ccccctcaaa cgctgcactc gtccgacgca gcgtcgaact ctgtgacaaa   780
 781 taccagcgcc cagtcgccag ctggcaacag gcgcgtgaga tcctcgggct gccagccgcg   840
 841 gcgcggaatt ga   852

Target constructs
Download sequence in PIR or FASTA format
Chemical properties of sequence with tag

GENE PREDICTION

PREDICTOR	SCORE
Glimmer3 score	-	-
Genemark probabilities	- -	-
GenemarkHMM class	-	-

Notes

The start codon is a ATG/Methionine in most of sequences, but the GTG/V, TTG/L, CTG/I can be the start codons in some cases as expressing in E.coli. The start codon warning is labelled by RED color in sequence(sample: 10174951).

Protein sequence information contains the annotation contents from both of JCSG and SWISS-PROT. The SWISS-PROT/TrEMBL annotation is accessed from SWALL(SPTR) on the EBI SRS server. PDB homologes show both identical and highly similar proteins with released date and protein function.

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