Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_018231665.1 THITHI_RS0103365 aminodeoxychorismate lyase
Query= curated2:Q58414 (288 letters) >NCBI__GCF_000378965.1:WP_018231665.1 Length = 269 Score = 104 bits (259), Expect = 2e-27 Identities = 82/256 (32%), Positives = 128/256 (50%), Gaps = 12/256 (4%) Query: 3 IYLNGKFVDEKDAKVSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDI 62 I +NG+ ++ V V D GL YGDG+FE + + H+ R+ +A +D+ Sbjct: 2 ILVNGEARED----VPVTDRGLAYGDGLFETLAVQRREPGHWQRHMTRM--AAGCARLDL 55 Query: 63 PLTKEEMIDVVLETLRVNNLRDAYIRLVVTRGVGDLGLDPRKCGKPTIFCIAIPMPPLLG 122 P+ + T+ + A ++L++TRG G G P +PT +A+ +P Sbjct: 56 PMPDPALWLTEARTVLASGTHGA-LKLMLTRGSGPRGYRPPPSPEPTRILMALDIPAYPA 114 Query: 123 ---EDGIRAITVSVRRLPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEAFLLDDKGFVVE 179 E+G+ + V RL L +K LN L VLA+ + G E +LD + VVE Sbjct: 115 AWREEGV-PVRVCRTRLARHPLLAGIKHLNRLEQVLARNEWQ-DGFQEGIMLDTEDHVVE 172 Query: 180 GTGDNIFIVKNGVLKTPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADELF 239 GT N+F++++G L TP + Q + G+TR V+ A+ GI V E L DL+ AD L Sbjct: 173 GTMSNLFLIRDGALHTPLLDQCGVAGVTRARVMACARGLGIPVHEGRYGLDDLFGADGLL 232 Query: 240 ITGTAAEIVPVFEIDG 255 +T T + PV +DG Sbjct: 233 LTNTLIGLWPVQALDG 248 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: 228 Number of extensions: 12 Number of successful extensions: 3 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: 269 Length adjustment: 25 Effective length of query: 263 Effective length of database: 244 Effective search space: 64172 Effective search space used: 64172 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 Jul 25 2024. The underlying query database was built on Jul 25 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