Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_066920129.1 ACG33_RS07760 aminodeoxychorismate lyase
Query= curated2:Q58414 (288 letters) >NCBI__GCF_001579945.1:WP_066920129.1 Length = 272 Score = 114 bits (285), Expect = 2e-30 Identities = 83/249 (33%), Positives = 120/249 (48%), Gaps = 5/249 (2%) Query: 3 IYLNGKFVDEKDAKVSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDI 62 I ++G+ E+ + + G YGDGVFE D V L +H+ RL KSL I Sbjct: 5 ILIDGQPPLEEARALHASERGFHYGDGVFETALVRDERVRFLDDHLSRLAHGCKSLNIQA 64 Query: 63 PLTKEEMIDVVLETLRVNNLRDAYIRLVVTRGVGDLGLDP-RKCGKPTIFCIAIPMPPLL 121 P D+ + ++++V+RG G G P G+PT F P P Sbjct: 65 PRRAVLQADIARLS---TGCAMGILKIIVSRGAGTRGYRPDAHAGEPTRFVAMYPALPRA 121 Query: 122 GEDGIRAITVSVRRLPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEAFLLDDKGFVVEGT 181 IR + RL + +K LN L VLA+ + + E +LD +G +V GT Sbjct: 122 PARPIR-LRWCETRLSRNARLAGIKHLNRLEQVLAQAEWRDDRIAEGLMLDTEGELVSGT 180 Query: 182 GDNIFIVKNGVLKTPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADELFIT 241 NIF++++G+L TP + ++G+ R VI+ A GI VVEEPL HDL A E+F+T Sbjct: 181 ASNIFLLRDGMLATPDLRFCGVQGVMRAQVIRAAAGLGIAVVEEPLWPHDLEQASEVFVT 240 Query: 242 GTAAEIVPV 250 I PV Sbjct: 241 NAVRGIRPV 249 Lambda K H 0.321 0.143 0.411 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: 174 Number of extensions: 7 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: 288 Length of database: 272 Length adjustment: 26 Effective length of query: 262 Effective length of database: 246 Effective search space: 64452 Effective search space used: 64452 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 (21.8 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