Protein Info for b1440 in Escherichia coli BW25113

Name: ydcS
Annotation: predicted spermidine/putrescine transporter subunit (NCBI)

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 50 100 150 200 250 300 350 381 signal peptide" amino acids 1 to 23 (23 residues), see Phobius details PF01547: SBP_bac_1" amino acids 55 to 312 (258 residues), 78.8 bits, see alignment E=1.2e-25 PF13416: SBP_bac_8" amino acids 56 to 326 (271 residues), 83.4 bits, see alignment E=3.7e-27 PF13343: SBP_bac_6" amino acids 215 to 325 (111 residues), 27.9 bits, see alignment E=2.5e-10

Best Hits

Swiss-Prot: 100% 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 100% identity to eco:b1440)

MetaCyc: 100% 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)

Search 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 P76108 at UniProt or InterPro

Protein Sequence (381 amino acids)

>b1440 predicted spermidine/putrescine transporter subunit (NCBI) (Escherichia coli BW25113)
MSKTFARSSLCALSMTIMTAHAAEPPTNLDKPEGRLDIIAWPGYIERGQTDKQYDWVTQF
EKETGCAVNVKTAATSDEMVSLMTKGGYDLVTASGDASLRLIMGKRVQPINTALIPNWKT
LDPRVVKGDWFNVGGKVYGTPYQWGPNLLMYNTKTFPTPPDSWQVVFVEQNLPDGKSNKG
RVQAYDGPIYIADAALFVKATQPQLGISDPYQLTEEQYQAVLKVLRAQHSLIHRYWHDTT
VQMSDFKNEGVVASSAWPYQANALKAEGQPVATVFPKEGVTGWADTTMLHSEAKHPVCAY
KWMNWSLTPKVQGDVAAWFGSLPVVPEGCKASPLLGEKGCETNGFNYFDKIAFWKTPIAE
GGKFVPYSRWTQDYIAIMGGR