Protein Info for GFF281 in Hydrogenophaga sp. GW460-11-11-14-LB1

Annotation: ABC transporter, periplasmic spermidine putrescine-binding protein PotD (TC 3.A.1.11.1)

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 50 100 150 200 250 300 350 395 signal peptide" amino acids 1 to 32 (32 residues), see Phobius details PF13416: SBP_bac_8" amino acids 65 to 338 (274 residues), 69.6 bits, see alignment E=4e-23 PF13343: SBP_bac_6" amino acids 102 to 337 (236 residues), 44.4 bits, see alignment E=1.5e-15

Best Hits

Swiss-Prot: 61% identical to YDCS_ECOLI: Bifunctional polyhydroxybutyrate synthase / ABC transporter periplasmic binding protein (ydcS) from Escherichia coli (strain K12)

KEGG orthology group: K02055, putative spermidine/putrescine transport system substrate-binding protein (inferred from 74% identity to sno:Snov_0497)

MetaCyc: 61% identical to putative ABC transporter periplasmic binding protein / polyhydroxybutyrate synthase (Escherichia coli K-12 substr. MG1655)
RXN1-42 [EC: 2.3.1.304]

Predicted SEED Role

"ABC transporter, periplasmic spermidine putrescine-binding protein PotD (TC 3.A.1.11.1)" in subsystem Polyamine Metabolism (TC 3.A.1.11.1)

MetaCyc Pathways

Isozymes

No predicted isozymes

Use Curated BLAST to search for 2.3.1.304

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

Find the best match in UniProt

Protein Sequence (395 amino acids)

>GFF281 ABC transporter, periplasmic spermidine putrescine-binding protein PotD (TC 3.A.1.11.1) (Hydrogenophaga sp. GW460-11-11-14-LB1)
MKLAQRPLARTVAGLLTTALTLATLAPAAQAQSALKKLGKGEGQVDIVAWAGYIERGQTD
KNFDWVTDFEKKTSCKVNVKTAGTSDEMVALMNEGGFDLVTASGDASMRLIAGKRVQPVN
VDLIPSYKTVDPRLQKAPWHYVNNTHYGTPYQWGWNVLMYNTTVFKDKPPTSWNVVFEET
TLPDGKSNKGRVQAFDGPIYIADAALYLMKKNPALGIKDPYELNEAQYKAALDLLRGQRK
LVGKYWHDAFVQIDDFTNEGVVASSSWQFMANILKSKNRPVATVVPAEGATGWADTTMLH
ADAKHPNCAYMWMEHSLNTKLQGDLAAWFGSVPSVPAACKGNKLLGDQGCANQGYNSFEK
ISFWKTPTSKCTTQNNNCVPYHKWVSDYIAVLGGR