Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_014148502.1 MEALZ_RS09945 aminodeoxychorismate lyase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000968535.2:WP_014148502.1 Length = 276 Score = 109 bits (273), Expect = 6e-29 Identities = 79/262 (30%), Positives = 128/262 (48%), Gaps = 14/262 (5%) Query: 18 VSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEIPITKEEFMEIILET 77 + + D GF YGDG+FE I GR+ HI RL + + L+IP+ E+ ++ E Sbjct: 12 IDVSDRGFQYGDGLFETIEINKGRLVFFDRHIRRLKEGCRR--LQIPL--EDTGNLVAEA 67 Query: 78 LRKNNLRDA---YIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGKLYGDLYEKGLTAIT 134 +N +D ++ I+TRG G G P+ ++ P+ + G+TA Sbjct: 68 --ENAAKDVDRGVLKIILTRGTGGRGYRQPDSIKPTRVISVYPFPDYSENYTRNGITARV 125 Query: 135 VAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYVSEGSGDNIFVVKN 194 + R AL IK LN L ILA+ E N G E + LD +G V EG+ N+F V N Sbjct: 126 CSTRLGLNPALA-GIKHLNRLEQILARAEWNDPGIQEGLMLDADGNVIEGTMTNLFYVIN 184 Query: 195 GAITTPPTINN-LRGITREAVIEIINRLGIPFKETNIGLYDLYTADEVFVTGTAAEIAPI 253 + T +++ + GI RE ++E+ + + GL +L ADE+FV + + P+ Sbjct: 185 RQLYTSEILHSGVAGIMREIILELAESNALTLSKRYFGLDELLNADEIFVCNSVIGLWPV 244 Query: 254 VVIDGRKIGDGKPGEITRKLME 275 +DG+ G +TR++ + Sbjct: 245 TQVDGKPFA---VGPVTREITD 263 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: 200 Number of extensions: 8 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: 276 Length adjustment: 26 Effective length of query: 264 Effective length of database: 250 Effective search space: 66000 Effective search space used: 66000 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: 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