Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_012975915.1 AZL_RS17990 aminotransferase class IV
Query= curated2:O29329 (290 letters) >NCBI__GCF_000010725.1:WP_012975915.1 Length = 303 Score = 155 bits (393), Expect = 8e-43 Identities = 101/283 (35%), Positives = 149/283 (52%), Gaps = 5/283 (1%) Query: 4 VYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEI 63 ++++G VP +A VSIFD GF GDGV+EGIR +GR L +H+ RL AKAI L+I Sbjct: 22 IWLNGRLVPRAQATVSIFDAGFGLGDGVWEGIRYVDGRFVFLDDHLGRLEAGAKAIALDI 81 Query: 64 PITKEEFMEIILETLRKNNLRDA-YIRPIVTRGIGD-LGLDPRKCQNPSIIVITKPWGKL 121 ++++ E + +T+ N + D +IR +VTRG + DPR I I Sbjct: 82 GLSRDGVREALQQTIDANGMTDGVHIRLMVTRGEKTTIHQDPRNALGRPTIAIVAEHKLP 141 Query: 122 YGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYV 181 + GL T VR + D + S + LN I A + A A G EA+ LD +G+V Sbjct: 142 DPQVKRDGLALATTPVRCSPPDMFDMRLNSHSRLNLIQALLPAIAAGAQEALMLDPHGFV 201 Query: 182 SEGSGDNIFVVKNGAITTPPTINNLRGITREAVIEIINRLGIPFKETNIGLYDLYTADEV 241 S + N+F V G + T GITR+ V+++ GIP ++ + L + Y ++E Sbjct: 202 SSCNSTNLFFVSGGTVLTSTGRYCFNGITRQKVLDLCAAHGIPLRQADFTLAEAYASEEA 261 Query: 242 FVTGTAAEIAPIVVIDGRKIGD-GKPGEITRKLMEEFSKLTES 283 FVTGT I P+ +DGR G G+P +T +L + LT S Sbjct: 262 FVTGTFGGITPVSRLDGRPFGGAGRP--VTERLCTLYEALTRS 302 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: 248 Number of extensions: 14 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: 303 Length adjustment: 26 Effective length of query: 264 Effective length of database: 277 Effective search space: 73128 Effective search space used: 73128 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: 48 (23.1 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