Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate CCNA_03047 CCNA_03047 4-amino-4-deoxychorismate lyase
Query= curated2:Q58414 (288 letters) >FitnessBrowser__Caulo:CCNA_03047 Length = 251 Score = 91.7 bits (226), Expect = 2e-23 Identities = 77/244 (31%), Positives = 122/244 (50%), Gaps = 16/244 (6%) Query: 17 VSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDIPLTKEEMIDVVLET 76 V + D GLL GDG+FE + A DG V L H+DR+ +A + +P +E +VL Sbjct: 7 VPLNDRGLLLGDGLFETMLAQDGAVAHLPAHLDRM--AAGCAVLGLPFDREAAQRLVLAA 64 Query: 77 LRVNNLRDAYIRLVVTRGVGDLGLDPRKCGKPTIFCIAIPMPPLLGEDGIRAITVSVRRL 136 R A IRL +T G G GLD + +F A P P+ + I + RR Sbjct: 65 APSQG-RFA-IRLTLTAGSGGRGLDRPEAPAVRLFATAAPSTPVTTPATL--IVAATRR- 119 Query: 137 PVDVLNPA--VKSLNYLNSVLAKIQANYAGVDEAFLLDDKGFVVEGTGDNIFIVKNGVLK 194 + +PA +K+L YL++VLA+ +A AG D+A +L+++G + N+F + G L Sbjct: 120 --NEGSPASRLKTLAYLDNVLARAEARAAGADDALMLNNRGEIACAAAANLFWLAGGRLF 177 Query: 195 TPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADELFITGTAAEIVPVFEID 254 TP + +L G TR +L E +E E + + L A+ + +T + + PV + Sbjct: 178 TPRLDCGVLAGTTR---ARLLAREAVE--EVAVGVEALEAAEAVVLTNSLIGVRPVSRLG 232 Query: 255 GRVI 258 R + Sbjct: 233 ERAL 236 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: 150 Number of extensions: 7 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: 251 Length adjustment: 25 Effective length of query: 263 Effective length of database: 226 Effective search space: 59438 Effective search space used: 59438 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 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