Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_083769223.1 AFER_RS11545 4-amino-4-deoxychorismate lyase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000023265.1:WP_083769223.1 Length = 276 Score = 128 bits (322), Expect = 1e-34 Identities = 91/287 (31%), Positives = 144/287 (50%), Gaps = 17/287 (5%) Query: 1 MLYVYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAID 60 M ++DG V E +A+V +FDHG + GDGVFE + GR F ++ H++RL SA+ + Sbjct: 1 MAVAWIDGALVDEADARVPVFDHGLVVGDGVFETLVVVGGRAFAIRRHLERLARSAQGMG 60 Query: 61 LEIPITKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGK 120 + +P + I + N A +R T G G+LG + P+ ++ + + Sbjct: 61 ITLP-DLDALRGAIEAVVSTNGYERAKVRVTYTAGDGELG--SGRVGGPTRAIVAEAPIE 117 Query: 121 LYGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGY 180 L E A+ VA + + IK+ +Y N++ A A+G E +F + G Sbjct: 118 L-----EPATCAVAVAPWPRNERGVLAGIKTTSYAENVVGLAWARARGASEVLFGNLAGN 172 Query: 181 VSEGSGDNIFVVKNGAITTPP-TINNLRGITREAVIEIINRLGIPFKETNIGLYDLY--T 237 + EGSG N+FVV++G + TPP L G+TR +IE R + KETNI L DL+ Sbjct: 173 LCEGSGSNVFVVRDGDVLTPPLDAGPLAGVTRALLIE---RFAV--KETNIPLDDLFDER 227 Query: 238 ADEVFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLMEEFSKLTESE 284 EVFVT T + + +D R+ + PG +T + + L S+ Sbjct: 228 VSEVFVTSTLRFVQGVHRLDDREF-EQAPGPVTARAQALLADLVASD 273 Lambda K H 0.319 0.142 0.409 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 208 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 290 Length of database: 276 Length adjustment: 26 Effective length of query: 264 Effective length of database: 250 Effective search space: 66000 Effective search space used: 66000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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:
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