Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_050750381.1 ALVIN_RS14285 cytochrome c
Query= curated2:Q58414 (288 letters) >NCBI__GCF_000025485.1:WP_050750381.1 Length = 266 Score = 137 bits (346), Expect = 2e-37 Identities = 86/265 (32%), Positives = 143/265 (53%), Gaps = 11/265 (4%) Query: 21 DHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDIPLTKEEMIDVVLETLRVN 80 D G L+GDGV+E I +Y G L+ H+DRL S ++ ++ PL +E+ V+ + Sbjct: 2 DRGFLFGDGVYEVIPSYGGHFLGLEPHLDRLDASLAAMRLEAPLAREDWRAVLRRLIGEP 61 Query: 81 NLRDAYIRLVVTRGVGDLGLDPRKCG-KPTIFCIAIPMPP---LLGEDGIRAIT-VSVRR 135 D Y+ L VTRG G +PT+ A P+ P + E G+ IT +R Sbjct: 62 PAADQYVYLQVTRGTAPERDHLCPAGVRPTVLAFAKPIKPRAPAIAEQGVACITHPDIRW 121 Query: 136 LPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEAFLLDDKGFVVEGTGDNIFIVKNGVLKT 195 L D+ KS++ +VL + +A A E + D G+V EG N+F+V G L T Sbjct: 122 LRGDI-----KSISLAAAVLMRREAADADALETIMHRD-GWVTEGAVSNVFVVAGGALMT 175 Query: 196 PPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADELFITGTAAEIVPVFEIDG 255 PP + +L GITR++ + LA E G+E VE P+ L L ADE++++ + E++PV +DG Sbjct: 176 PPKSRLLLSGITRELALTLAHEHGLEFVERPVALDILRAADEIWLSSSTREVLPVTRLDG 235 Query: 256 RVINNKQVGEITKKLKEKFKDIRTK 280 ++ + + G + +++ ++D + + Sbjct: 236 ELVGDGRPGLLWRRMDALYQDYKAR 260 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: 203 Number of extensions: 10 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: 266 Length adjustment: 25 Effective length of query: 263 Effective length of database: 241 Effective search space: 63383 Effective search space used: 63383 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