Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_035239120.1 Q366_RS11805 branched chain amino acid aminotransferase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000745975.1:WP_035239120.1 Length = 286 Score = 159 bits (401), Expect = 9e-44 Identities = 103/286 (36%), Positives = 165/286 (57%), Gaps = 16/286 (5%) Query: 5 YMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEIP 64 Y+DG+FV E++A +S+ D L G GVF+ + YN R FRL++H+ RL +SA+ I LE+ Sbjct: 9 YIDGKFVSEDKATLSVKDITVLRGFGVFDFLITYNKRPFRLEKHVARLENSARHIGLELN 68 Query: 65 ITKEEFMEIILETLRKN-NLRDAYIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGKLYG 123 + +E +I+++T+ +N + ++ IR + T GI G+ P+ N ++V+ P +L Sbjct: 69 HSNKEICDIVMQTIERNPHHKEDNIRIVYTGGISPDGVTPQ--GNGILMVMVTPKHELPD 126 Query: 124 DLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYVSE 183 Y +G ITV + R P KS NYL+ I A+ +A++ G EAI+ D++ + E Sbjct: 127 WWYTQGAKIITVDIER-----FIPQAKSTNYLSAIFAQQKASSLGAVEAIYKDKDNRLLE 181 Query: 184 GSGDNIFVVKNGAITTPPTINNLRGITREAVIEIINR---LGIPFKETNIGLYDLYTADE 240 G+ NIF K + TPP L G+TR AV+E++ + + + F I DL DE Sbjct: 182 GTTTNIFAFKGTTLITPPD-GILPGVTRGAVLELLEKKYDIVLDF----IPQADLADIDE 236 Query: 241 VFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLMEEFSKLTESEGV 286 VF+ + EI P++ +D I DGKPGE T LM +++ T + G+ Sbjct: 237 VFIAASNKEIVPVIQVDDTVISDGKPGEKTLALMADWNAYTTAYGL 282 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: 206 Number of extensions: 11 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: 286 Length adjustment: 26 Effective length of query: 264 Effective length of database: 260 Effective search space: 68640 Effective search space used: 68640 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