Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_010959476.1 MCA_RS00530 cytochrome c550
Query= curated2:O29329 (290 letters) >NCBI__GCF_000008325.1:WP_010959476.1 Length = 283 Score = 162 bits (411), Expect = 6e-45 Identities = 99/277 (35%), Positives = 160/277 (57%), Gaps = 23/277 (8%) Query: 4 VYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEI 63 VY++GEF+P ++A+VS+ D GFL+GDGV+E I Y GR RL+EH+ RL DS + I + Sbjct: 6 VYLNGEFLPLDQARVSVLDRGFLFGDGVYEVIPVYGGRPLRLEEHLRRLDDSLRGIRMTS 65 Query: 64 PITKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLGLDPRKCQN------PSIIVITKP 117 P+ + E+ EII + + + Y++ VTRG+G P + + P++ + P Sbjct: 66 PLMRSEWSEIIGRLIDGVDDQSVYVQ--VTRGVG-----PARDHSIPVGVRPTVFAMASP 118 Query: 118 WGKLYGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDR 177 + G+ AIT+ R + NIK++ L N+L + +A +G EA+ L R Sbjct: 119 ----ITPVPVTGVRAITLEDIRWRW----CNIKAITLLPNVLLRQQAVDRGCAEAV-LVR 169 Query: 178 NGYVSEGSGDNIFVVKNGAITTPPT-INNLRGITREAVIEIINRLGIPFKETNIGLYDLY 236 G+V+EG+ N+F V G I TPP L GITR+ V+E++ G+P +E I L + Sbjct: 170 EGHVTEGTASNVFAVVGGTIVTPPKGPELLPGITRDLVLELVRAEGLPARERAISLEEFS 229 Query: 237 TADEVFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKL 273 A+E+++T + E+ P+V +DGR +G G PG + ++ Sbjct: 230 GAEEIWITSSTREVLPVVELDGRPVGRGSPGPVWERV 266 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: 239 Number of extensions: 15 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: 290 Length of database: 283 Length adjustment: 26 Effective length of query: 264 Effective length of database: 257 Effective search space: 67848 Effective search space used: 67848 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