GapMind for catabolism of small carbon sources

 

Protein 5210426 in Shewanella loihica PV-4

Annotation: Shew_2867 pyruvate carboxylase, propionyl-CoA carboxylase (RefSeq)

Length: 1094 amino acids

Source: PV4 in FitnessBrowser

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism pccB med propionyl-CoA carboxylase β subunit (EC 6.4.1.3) (characterized) 31% 98% 242.7
propionate catabolism pccB med propionyl-CoA carboxylase β subunit (EC 6.4.1.3) (characterized) 31% 98% 242.7
L-threonine catabolism pccB med propionyl-CoA carboxylase β subunit (EC 6.4.1.3) (characterized) 31% 98% 242.7
L-valine catabolism pccB med propionyl-CoA carboxylase β subunit (EC 6.4.1.3) (characterized) 31% 98% 242.7
L-leucine catabolism liuB lo methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized) 39% 71% 314.3 pyruvate carboxylase (EC 6.4.1.1) 38% 367.9
L-isoleucine catabolism pccA lo Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized) 33% 95% 305.1 pyruvate carboxylase (EC 6.4.1.1) 38% 367.9
propionate catabolism pccA lo Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized) 33% 95% 305.1 pyruvate carboxylase (EC 6.4.1.1) 38% 367.9
L-threonine catabolism pccA lo Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized) 33% 95% 305.1 pyruvate carboxylase (EC 6.4.1.1) 38% 367.9
L-valine catabolism pccA lo Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized) 33% 95% 305.1 pyruvate carboxylase (EC 6.4.1.1) 38% 367.9
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) 39% 87% 301.2 pyruvate carboxylase (EC 6.4.1.1) 38% 367.9
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) 39% 87% 301.2 pyruvate carboxylase (EC 6.4.1.1) 38% 367.9
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) 39% 87% 301.2 pyruvate carboxylase (EC 6.4.1.1) 38% 367.9
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) 39% 87% 301.2 pyruvate carboxylase (EC 6.4.1.1) 38% 367.9

Sequence Analysis Tools

View 5210426 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTRVFNRILIANRGEIAIRIAQTCADMGIDSLAIYAEDDSQSLHTKKADQAVALKGRGVK
AYLDIEQLIAVAKAHGCDAVHPGYGFLSENSSFSKRCHEEGICFIGSSAELLDLLGNKAT
ARETALRSDTPLTGGINKPCSLEEVQAFFTSLGDGAAVMIKALAGGGGRGMRPVSRYEDL
AEAYRQCREEAIIAFGSGELYVEQLVQHARHIEVQILGDGTGAAVHAWERECTLQRRNQK
LLEIAPSPSLDDATRMPIIESALQLASDVKYQGLGTFEFLLDADDHSKFYFMEINPRIQV
EHTITEEITGLNLVKLQILLGAGKTLAELSLTEAPIKRGCAIQARINLEQMLPDGSTKPA
SGVIKAYQVPNGHNVRVDDYLYAGYKVSPSYDSLGAKIIAKGEDFSAALNKVYLSLKALN
IDGVQSNKALLMNLLQREEVQHNRLSTRFVEAHMAELLADDDHHEHFFNIASDQQETVQA
VNIPAGCEGVKSPTAGVLVQVNIESGDEVFAGQEIAVIEAMKMEIPVKSEHAGIVTEVLT
GNIGEVIDEHQILAVIQPGEVSVTGGQTEMEIDLDYIRANLAEFFDRRDKTLDESRSEAV
AKRHSEGKRTARENLNDLLDEGSFNEYGQLAIAAQRQKHAIDKLVEISPADGKITGIGTV
NADSFGEEAARCAVMSYDYTVMAGSQGLVNHKKTDRLLELCKKWKLPLVIFAEGAGGRPS
DTDYPGVAFLNLHTFSSLGELSGLVPTVGIAAGNCFAGNAALYGVCDLTIATRQASIGMA
GPAMIEGGGLGVFKPEEVGPPSVLSPNGVIDILVEDEAEAVAVTKKYLSYFQGDLSEWQV
ADQRRLRHLIPENRMAIYDIREVIDTLCDKDSVLELRREFAKNMITAMVRIEGKAYGLYA
NDPRFLGGAIDADAGDKLARFIQLCDAHDIPMISLCDTPGFMVGPESEKRATVRHISRLF
VHGANSTVPLFALVLRKGYGLGVMGMTGGGFTAPVFTASWPSGEFGAMGIEGAVRIAAKR
QLEAIADPDEREATFKAMVDKLYSHGSAINTASYLELDAVIDPMESRDWIVRGLACLPKP
EKRSGKKRNCIDTW

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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