Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_092487738.1 BM299_RS18000 D-amino-acid transaminase
Query= curated2:Q58414 (288 letters) >NCBI__GCF_900115975.1:WP_092487738.1 Length = 283 Score = 159 bits (402), Expect = 7e-44 Identities = 95/279 (34%), Positives = 155/279 (55%), Gaps = 7/279 (2%) Query: 3 IYLNGKFVDEKDAKVSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDI 62 +YLNG +DA +SV D G +GDGV+E + AYDGV+F L +H+ RL SA ++ +D+ Sbjct: 5 VYLNGWIGSFEDAYISVNDRGYNFGDGVYEVVMAYDGVMFALDDHLKRLAASAAAVEMDL 64 Query: 63 PLTKEEMIDVVLETLRVNNLRDAYIRLVVTRGVGDLGLDPRKCGKPTIFCIAIPMP---P 119 P +++ + + L ++++ A I + VTRG +P + P P Sbjct: 65 PWDLQQLKSIAEDVLVKSSIKRAMIYIQVTRGTAPRNHFFEPDIRPNLLVTVRYAPETDP 124 Query: 120 LLGEDGIRAITVSVRRLPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEAFLLDDKGFVVE 179 + +G++ IT R + VK+++ +++AK +A AGV E + G V E Sbjct: 125 AMYREGVKVITHPDFRWQMC----HVKTISLQANIMAKNRARRAGVAEVVFVLPDGTVTE 180 Query: 180 GTGDNIFIVKNGVLKTPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADELF 239 NIFI ++GVLKT P IL G+TR V+++A G+++ EEP + +L+ A+E+F Sbjct: 181 CGSSNIFIYQDGVLKTHPANNKILAGVTRQYVLQVAGSLGLDIKEEPFNVSELFKANEVF 240 Query: 240 ITGTAAEIVPVFEIDGRVINNKQVGEITKKLKEKFKDIR 278 T T E++PV +DG VI N + G +T +L + F +R Sbjct: 241 YTNTVIEVMPVVNVDGHVIGNGKPGPVTTQLHQGFITLR 279 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: 228 Number of extensions: 5 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: 283 Length adjustment: 26 Effective length of query: 262 Effective length of database: 257 Effective search space: 67334 Effective search space used: 67334 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