GapMind for catabolism of small carbon sources

 

Protein WP_088754538.1 in Herbaspirillum aquaticum IEH 4430

Annotation: NCBI__GCF_002213425.1:WP_088754538.1

Length: 1187 amino acids

Source: GCF_002213425.1 in NCBI

Candidate for 5 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism ofo hi 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized) 58% 98% 1332.4 phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) 49% 1085.1
L-leucine catabolism ofo hi 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized) 58% 98% 1332.4 phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) 49% 1085.1
L-valine catabolism ofo hi 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized) 58% 98% 1332.4 phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) 49% 1085.1
L-phenylalanine catabolism iorAB med phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized) 49% 98% 1085.1 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) 58% 1332.4
L-phenylalanine catabolism iorB lo Indolepyruvate oxidoreductase subunit IorB; IOR; Indolepyruvate ferredoxin oxidoreductase subunit beta; EC 1.2.7.8 (characterized) 31% 95% 82.8 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) 58% 1332.4

Sequence Analysis Tools

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MDRTGNRTGTATDTSGLAPVSLDDKYTATEGAIYLSGIQALVRLPMLQQIRDRAAGLNTA
GFISGYRGSPLGGLDEALWHAQPHLAAHRVKFQPGVNEDMAATAVWGTQQVKLIGPSDYD
GVYAMWYGKGPGVDRCGDVLKHMNHAGTSAQGGVLLVAGDDHGAYSSTLPHQSDHIFSAS
MIPMLYPCNVQEYLDLGLHGWAMSRYSGCVVGFKALADTVESSASVDADPFRVEIRLPTD
FAMPAGGLNARLSTDTLGVQARKQEALMQDYKIYAALAYARANKLNRVMIDSPRARLGII
ASGKSYLDVLEALSELGIDEAFAAEIGLRVFKVSMPWPLEPDGVREFAQGLDEILVVEEK
RQMVEYQLKEQLYNWRDDVRPRVIGKFDEKGEWVAPRGEWLLTSKADFSVAQIARVIAAR
IARFHTSDLIKARLAFLDAKDAVLSKAVNTPPRPAYYCSGCPHNTSTRVPEGSFALAGIG
CHVMATAIYPEFNKLTTHMGGEGAPWIGQAPFSKVPHVFANLGDGTYFHSGYLAIRAAVA
ARVNMTYKILYNDAVAMTGGQPVDGTVSVPMIAQQMAAEGVQRIALVSEDISRYADRSGL
PQAVSLHDRRDMDAVQRELREIPGVSVIIYDQTCAAEKRRRRKKGEFPDPNERLFINAAV
CEGCGDCGVQSNCTSILPLETELGRKRVIDQSSCNKDYSCVKGFCPSFVTVTGGQLKKSR
NGVHKKGAPDDFRVLPEPAIPSCETPFNILINGIGGTGVITIGALMGMAAHLEGKGASVL
DMTGMSQKNGSVTSHVRIAARRDSIRAQRIATGEADLVLGCDMLTAGAFDAISKMRPGRT
RAVVNLHQQPPGQFAKNPDWQFPFEEVKALILESVDQQADFIDATRLATALMGDAIATNL
FMLGYAWQRGELPLTEAALLRAIELNGVAVEANQTAFRWGRRAAVDLRRVEQIALPAQPV
VVHLPQSLDQLIKRRVALLTGYQDASYAARFVEVVEAVRAAEAPLGSDKLALAVARNLSR
LMAYKDEYEVARLYTNGQFQKDLAQQFEGDFTLSFNLAPPIFARKDGQGRLVKARYGSWM
MTAFKLLARCKGLRGGVFDLFGRTAERRMERALIVQYREMVMELLPALTADNLAEAIALA
QLPEQVRGFGHVKEQAVQAMQVRQAQLLAAFAQAGTKPAPGATPAAA

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory