Protein Info for Psest_1006 in Pseudomonas stutzeri RCH2

Annotation: dTDP-4-dehydrorhamnose reductase

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 50 100 150 200 250 306 PF04321: RmlD_sub_bind" amino acids 1 to 290 (290 residues), 358.5 bits, see alignment E=8e-111 TIGR01214: dTDP-4-dehydrorhamnose reductase" amino acids 2 to 288 (287 residues), 342.3 bits, see alignment E=9.6e-107 PF01370: Epimerase" amino acids 3 to 165 (163 residues), 88.4 bits, see alignment E=1.8e-28 PF01073: 3Beta_HSD" amino acids 34 to 176 (143 residues), 23.7 bits, see alignment E=8e-09 PF16363: GDP_Man_Dehyd" amino acids 34 to 138 (105 residues), 41.1 bits, see alignment E=5.8e-14 PF02719: Polysacc_synt_2" amino acids 36 to 103 (68 residues), 28.8 bits, see alignment E=2.5e-10 PF07993: NAD_binding_4" amino acids 46 to 152 (107 residues), 21.2 bits, see alignment E=4.9e-08

Best Hits

Swiss-Prot: 47% identical to RMLD_AGGAC: dTDP-4-dehydrorhamnose reductase (rmlD) from Aggregatibacter actinomycetemcomitans

KEGG orthology group: K00067, dTDP-4-dehydrorhamnose reductase [EC: 1.1.1.133] (inferred from 88% identity to psa:PST_3286)

MetaCyc: 47% identical to dTDP-6-deoxy-L-talose 4-dehydrogenase (NAD+) (Aggregatibacter actinomycetemcomitans)
RXN-13749 [EC: 1.1.1.339]

Predicted SEED Role

"dTDP-4-dehydrorhamnose reductase (EC 1.1.1.133)" in subsystem Rhamnose containing glycans or dTDP-rhamnose synthesis or linker unit-arabinogalactan synthesis (EC 1.1.1.133)

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 1.1.1.133

Use Curated BLAST to search for 1.1.1.133 or 1.1.1.339

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 L0GJK5 at UniProt or InterPro

Protein Sequence (306 amino acids)

>Psest_1006 dTDP-4-dehydrorhamnose reductase (Pseudomonas stutzeri RCH2)
MRILVCGAGGQVGRELVERAASFGLEVLAPARAQLDIAKPEQVAAAMQQRPGLIINAAAY
THVDNAESHGEQAYSVNRDGARNLAEAAERAGIPLFHISTDYVFSGEADHPYLESDETGP
TGIYGASKLAGEEAIRACLPAHLILRTSWVYGVHGHNFVKTMLRLARQRDALGVVSDQIG
CPTEAGTIASVLLELARRHATGTKLAWGVYHYSGAPACSWYDFAVEIFRQGEAAGLIVRQ
PSVSPIATAQYPTPARRPAWSVLDCSRFESTFGLAPHSWQDDLGDVIASLRQQEQRSAVR
ERTFRA