Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_245566311.1 B076_RS0103825 D-amino acid aminotransferase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000483485.1:WP_245566311.1 Length = 296 Score = 186 bits (471), Expect = 7e-52 Identities = 95/277 (34%), Positives = 166/277 (59%), Gaps = 8/277 (2%) Query: 4 VYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEI 63 VY++GE++P ++K+S D GFL+GDG++E I Y ++F EH+ RL +S +A+ + Sbjct: 13 VYLNGEYLPMADSKISTQDRGFLFGDGIYEVIPVYQRKLFAWPEHLQRLKNSLQAVSIPN 72 Query: 64 PITKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLGLD--PRKCQNPSIIVITKPWGKL 121 P+T EE+++++ ++K+ + +I VTRGI + D P C +P+I T P L Sbjct: 73 PLTDEEWLDLLTGLVKKHPWENQFIYLQVTRGI-QMQRDHMPADCLHPTIYAYTNPLKPL 131 Query: 122 YGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYV 181 + G+ +++ L + K++ L N++ K+ A +G D+AI + R+G V Sbjct: 132 DAKILSHGIKVVSL----EDIRWLRCDTKAITLLPNVMMKLAAKQQGADDAILISRDGKV 187 Query: 182 SEGSGDNIFVVKNGAITTPPTINN-LRGITREAVIEIINRLGIPFKETNIGLYDLYTADE 240 +EGS N+ +VK G + TPP + L G+TR + ++ N+ IPF E + L DL TADE Sbjct: 188 TEGSASNVVIVKEGKLLTPPNSQHILPGVTRLVIEKVANQHHIPFIERELSLADLQTADE 247 Query: 241 VFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLMEEF 277 +++T + E P+ +DG+++GDG+PG + +KL + + Sbjct: 248 IWLTSSTKEAVPVTQLDGKEVGDGRPGPVWQKLHQHY 284 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: 232 Number of extensions: 11 Number of successful extensions: 4 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: 296 Length adjustment: 26 Effective length of query: 264 Effective length of database: 270 Effective search space: 71280 Effective search space used: 71280 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 09 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