Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_027456704.1 K420_RS0102760 D-amino acid aminotransferase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000519045.1:WP_027456704.1 Length = 291 Score = 135 bits (341), Expect = 8e-37 Identities = 91/276 (32%), Positives = 143/276 (51%), Gaps = 10/276 (3%) Query: 4 VYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEI 63 VY++G F+P EA +S D FLYGDGV+E I Y+ + FR+ EH+ RL + I + Sbjct: 9 VYLNGRFLPLAEAAISPLDRAFLYGDGVYEVIPVYSRKPFRIDEHLKRLQATLDGIQMAN 68 Query: 64 PITKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLGLD---PRKCQNPSIIVITKPWGK 120 P++ + +I + + D I VTRG D D P P+ P Sbjct: 69 PLSAGAWQAVICKLIEAAPWDDQSIYLQVTRG-ADNKRDHAFPPASVPPTAFAFASPLVT 127 Query: 121 LYGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGY 180 D+ KG+ AITV R S ++K ++ L N+LA+ +A + EA+ + R+G+ Sbjct: 128 APADVRAKGVAAITVPDLRWS----RCDLKVVSLLANVLARQQAVEQDCAEALLI-RDGF 182 Query: 181 VSEGSGDNIFVVKNGAITTPP-TINNLRGITREAVIEIINRLGIPFKETNIGLYDLYTAD 239 + EG+ NIF+VK+G + PP T L GIT + ++E+ + P I +L AD Sbjct: 183 MKEGAASNIFIVKDGVLIAPPKTHLMLPGITYDVILELAEQHQQPLVVREISEAELRAAD 242 Query: 240 EVFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLME 275 EV++T + EI I +DG+ +G G PG ++ + Sbjct: 243 EVWMTSSTKEILAITTLDGKPVGTGTPGPYAAQMWQ 278 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: 214 Number of extensions: 14 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: 291 Length adjustment: 26 Effective length of query: 264 Effective length of database: 265 Effective search space: 69960 Effective search space used: 69960 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 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