Protein Info for PP_3343 in Pseudomonas putida KT2440

Annotation: nickel ABC transporter permease subunit

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

1 50 100 150 200 250 313 transmembrane" amino acids 7 to 29 (23 residues), see Phobius details amino acids 99 to 124 (26 residues), see Phobius details amino acids 138 to 164 (27 residues), see Phobius details amino acids 173 to 194 (22 residues), see Phobius details amino acids 232 to 260 (29 residues), see Phobius details amino acids 279 to 302 (24 residues), see Phobius details PF19300: BPD_transp_1_N" amino acids 1 to 103 (103 residues), 30.4 bits, see alignment E=3.9e-11 TIGR02789: nickel ABC transporter, permease subunit NikB" amino acids 1 to 312 (312 residues), 538.1 bits, see alignment E=3.9e-166 PF00528: BPD_transp_1" amino acids 117 to 307 (191 residues), 146.3 bits, see alignment E=8.6e-47

Best Hits

Swiss-Prot: 62% identical to NIKB_ECOLI: Nickel transport system permease protein NikB (nikB) from Escherichia coli (strain K12)

KEGG orthology group: K02033, peptide/nickel transport system permease protein (inferred from 100% identity to ppu:PP_3343)

MetaCyc: 62% identical to nickel ABC transporter membrane subunit NikB (Escherichia coli K-12 substr. MG1655)
7.2.2.i [EC: 7.2.2.i]; 7.2.2.- [EC: 7.2.2.i]

Predicted SEED Role

"Nickel transport system permease protein NikB (TC 3.A.1.5.3)" in subsystem Transport of Nickel and Cobalt (TC 3.A.1.5.3)

Isozymes

No predicted isozymes

Use Curated BLAST to search for 7.2.2.i

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Compare to protein structures

Predict protein localization: PSORTb (Gram-negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the current SEED with FIGfam search

Find homologs in fast.genomics or the ENIGMA genome browser

See Q88HL3 at UniProt or InterPro

Protein Sequence (313 amino acids)

>PP_3343 nickel ABC transporter permease subunit (Pseudomonas putida KT2440)
MLRYILLRLALLVPVMLGASLLVFVLLHLGSTDPALDYLRLSHIPPTDAAIAEVRHTLGL
DRPLYAQYLSWLWNAVHLDFGISYITGRPVLDDLLYYLPATLQLGGLALACTLLLSIPLG
LLAARWQGRWPDHAVRAVTFLGVSMPNFWLAFLLIALFSLWLGWLPPLGRGGAGHLVMPV
LAIALMSMSINARLLRASLLDAGGQRHVTYARARGLPERHVWRDHILRNAWLPLVTATGM
HIGELLGGALVIETIFAWPGVGRFAVSAVLNRDFPVMQCFTLLLTGLLMICNLIVDVCYA
WLDPRSRLEGVNA