GapMind for Amino acid biosynthesis

 

Protein Pf1N1B4_4430 in Pseudomonas fluorescens FW300-N1B4

Annotation: Cystathionine beta-lyase (EC 4.4.1.8)

Length: 919 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 5 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-methionine biosynthesis metC hi Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; Osteotoxin; EC 4.4.1.13 (characterized) 43% 99% 309.3 cystathionine γ-lyase (EC 2.5.1.48) 37% 240.7
L-methionine biosynthesis metB lo cystathionine γ-lyase (EC 2.5.1.48) (characterized) 37% 99% 240.7 Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; Osteotoxin; EC 4.4.1.13 43% 309.3
L-cysteine biosynthesis CGL lo cystathionine gamma-lyase (EC 4.4.1.1); cystathionine beta-lyase (EC 4.4.1.8) (characterized) 34% 98% 219.2 Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; Osteotoxin; EC 4.4.1.13 43% 309.3
L-methionine biosynthesis metZ lo O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized) 34% 93% 195.7 Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; Osteotoxin; EC 4.4.1.13 43% 309.3
L-methionine biosynthesis metY lo Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized) 32% 86% 173.3 Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; Osteotoxin; EC 4.4.1.13 43% 309.3

Sequence Analysis Tools

View Pf1N1B4_4430 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNRTVTPGQLQQWLFDGQEIALFDVREHGQYGEAHLFHGVNLPYSRLELEVRRLAPNPQV
RLVIYDQNGGDVVARAAQRLQALGYGRVHILDGGADGWQAAGLQLFAGVHVPSKAFGELV
EEVSHTPHVTARQLAEWQARGESLVVLDGRPFDEYRKMTIPGSVCCPNGELGYRVHDLVP
DDSTPIVVNCAGRTRSIIGAQTLINLGLKNPVYALENGTQGWDLEDLQLEHGSTRRYADE
VSSKTLPLQRLAAAQLAERAGVKTVATAQVEQWAGEAERSLFLCDVRTAEEFAAGSLPGA
QHTPGGQLIQSTDLYIGVRQARVVLIDSDGVRAPIIASWLRQLGHEAYVLADGVSSGLAL
PAVETPAHEALPVITAQALSDALKDNAVALIDLRPSMTWRKGHIAGSRWSIRSLLATEVM
GEQRPLVLLADDPLLAAFATLELPNAQRTQTRLLDGGVEAWRAAGFALQEDANTPPDHQC
IDFLFFTHDRHSGNKDAARQYLAWEIGLLAQMSADEIASLKPLRAQSQATRDARIRTRLV
HSARTEKGSGGRAVNVPVTRLSTVLFDNLAQMRDARARRDSERVLSYGARGNPTAFALED
LVTELEGGYRTRLYGTGLAAVAQTFLAYLRPGDHVLITDAVYAPVRRLARELLEPFGIQV
SYFAPDGSGLQAQLQANTKMVYTEVPGSLLYELCDLPAIAALCKPRGILLAVDNTWGSGY
LYRPLTLGADISIMALTKYLCGHSDVVMGSVCTRQEVWQPLSSMSDTFGIAVSPDDAYLV
LRGARTLAPRLDVHERQALEIAQWLQAQPQVKRVFHPALPDHPHHALWRRDFNGSNGLLS
FELREADATYVERFIDALQVFGLGASWGGYESLVTVADTKDRNSAADRALNPVLRLHIGL
EDVDALIEDLQRGFAAAVD

This GapMind analysis is from Mar 30 2021. The underlying query database was built on Mar 30 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, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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