GapMind for catabolism of small carbon sources

 

Protein WP_012275835.1 in Shewanella halifaxensis HAW-EB4

Annotation: NCBI__GCF_000019185.1:WP_012275835.1

Length: 1517 amino acids

Source: GCF_000019185.1 in NCBI

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism pccA lo Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized) 38% 67% 312.4 pyruvate carboxylase subunit A (EC 6.4.1.1) 41% 334.0
propionate catabolism pccA lo Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized) 38% 67% 312.4 pyruvate carboxylase subunit A (EC 6.4.1.1) 41% 334.0
L-threonine catabolism pccA lo Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized) 38% 67% 312.4 pyruvate carboxylase subunit A (EC 6.4.1.1) 41% 334.0
L-valine catabolism pccA lo Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized) 38% 67% 312.4 pyruvate carboxylase subunit A (EC 6.4.1.1) 41% 334.0
L-leucine catabolism liuB lo Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized) 38% 68% 309.3 pyruvate carboxylase subunit A (EC 6.4.1.1) 41% 334.0
L-isoleucine catabolism pccA1 lo acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) 35% 96% 279.6 pyruvate carboxylase subunit A (EC 6.4.1.1) 41% 334.0
propionate catabolism pccA1 lo acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) 35% 96% 279.6 pyruvate carboxylase subunit A (EC 6.4.1.1) 41% 334.0
L-threonine catabolism pccA1 lo acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) 35% 96% 279.6 pyruvate carboxylase subunit A (EC 6.4.1.1) 41% 334.0
L-valine catabolism pccA1 lo acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) 35% 96% 279.6 pyruvate carboxylase subunit A (EC 6.4.1.1) 41% 334.0

Sequence Analysis Tools

View WP_012275835.1 at NCBI

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

MTSKNQPANMTQVQTADPLFLKAEQLAKDFSLFPEHSKQTLSEEIKGLLDDDAIQANLKD
LAQLDVDGYVTKVIQPTQDKNRPGAKRIIADLKGKLITETHIGPFYSAEIELNFGSRTRR
IGFVAQERTTANGAWMPEHHIACCKAIRHFAELSMPIVYLIDTPGADAGEVANSQNQAHS
ISKAIAESANVDVPTVGIVIGAGYSGGAIPLAAANILLSLRDGIFNTIQPQGLQSIARKY
NLSWQECAKSVGVSPEELYTSGCIDGIIDFSPSDKDERQHNLRRAIISSIEAVEKAAINF
VSESEDLREHYNRSLARFLNPSKSLEALELNAELAVANNPTMHLNLFGSAYRYLRYLTLR
SRIHSISLEQYGRLSKVSVPEGDLLARIQQEQDRVFQSWLSSPDKLVYDEDLNKLWGNFI
AKRDDVSTERNMLTRLILGEPKENYKKARKALIFNISWSLYHRWKGNAENNFKGLIHYLE
TLPSEVTQADWPELNKLTVLDVIVHDELREDFIWQCHNILVFDALYDNVVGNLASIAKEA
MMSKSLSRNSVDNLLHDSIDRALSTQNVANDKSKFYKWLKYFMSQSNRAELLTRTEQWKS
VGFPQLNDSLFVILTYFFERLLPEYFDSEEESGEYTGAINPVRIGRRKDFWNRLTMGYQD
LLIQKVLRDEKRTGKMGWESIVAKFFTEFEEINGDKISANLLNFPGFRLSIEDALDRGIR
PCGLITGLADFEHNGQPMRVGVAVSNTAFQAGAFDMAAAEKFSALLIECAKRKLPVICFI
SSGGMQTKEGAAALFSMAVVNDRITRFIRDNELPVLMFGFGDCTGGAQASFVTHPLVQTY
YLSGTNMPFAGQMVVPAYLPSTSTLSNYLSKVPGAMDALVTNPFSDTIDDQLQSIDPLMP
KPTAKIVDVIASAVSTLVPERLIAEEVIVQDDPRQLMKPIEKVLVHARGCTAVKLIRKAH
DNNIKVVLVASDPDMTSVPADMLKDNDKLVCIGGNTSDESYLNAYSVLKVAEYENVDALH
PGIGFLSESPQFAALCVNNGVNFVGPSVHSMTTMGNKSNAIKTSQAQNVPVVPGSHGILT
NAEQAVNVASEIGYPVLLKAVQGGGGKGIQVVERPGDMISLFQKTSTEAAAAFGNGDLYL
EKYVTSLRHIEVQLLRDQFGNTKVLGLRDCSVQRNNQKVVEESGSTMLPDELKQRVMEYT
RLLGDATDYMGAGTVEFIYNLDANEVYFMEMNTRLQVEHPVTEATSGIDIVSAGFDIAAG
RSIAELEPQNIGYAMEVRVTAEKAALDSHGVLQLLPYPGLITEYQMPERDDIEIISIAGE
GKEVSPYYDSLIAQIICRGESREDVIVKLHDYLANQVVIKGIATNIPLLTRILKDGTFNE
GVYDTNYLPRFMAELDVSEMIAEMEAAAETVGVDTASLRVGESNELKVMAQGAGIFYTSP
APGEADFVKEGDIVTVDQTLALTEAMKMFSQVTLAGFNRKNAVLYPEDQQYRIERILNSN
GQQVSQGELLFVVSPVA

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

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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