Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate 3610820 Dshi_4206 aminotransferase class IV (RefSeq)
Query= curated2:O29329 (290 letters) >FitnessBrowser__Dino:3610820 Length = 307 Score = 160 bits (405), Expect = 3e-44 Identities = 91/268 (33%), Positives = 149/268 (55%), Gaps = 12/268 (4%) Query: 4 VYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEI 63 +Y++G +EA VS++D GF+ GDG++EG+R Y+G L +H+DR Y+S KA+ L++ Sbjct: 20 IYINGALKHRSEAMVSVYDSGFMLGDGMWEGLRLYDGVWAFLDDHMDRFYNSCKAVSLDV 79 Query: 64 PITKEEFMEIILETLRKNNLR-DAYIRPIVTRGIGDLGLDPRKCQNPSI------IVITK 116 + + + + T R N++ D + R ++TRG+ R Q+P++ +VI Sbjct: 80 GMDRAALFDALETTRRANDMHTDVHCRLMLTRGV-----KVRPFQHPALSRSGPTLVILM 134 Query: 117 PWGKLYGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLD 176 K L++KG+ TV R + S + LN ++A ++A G DEA+ LD Sbjct: 135 EHSKPVDRLHDKGIRLATVPQVRGLPMSQDAKYNSHSKLNCVIACLQAEQAGADEALMLD 194 Query: 177 RNGYVSEGSGDNIFVVKNGAITTPPTINNLRGITREAVIEIINRLGIPFKETNIGLYDLY 236 +G+V+ + N F+V+ G + T + G+TR+ VI++ GIP +E N LY+ Sbjct: 195 PHGFVNTTNACNFFIVRKGEVWTSTGDYCMNGVTRQKVIDLCRANGIPVREKNYSLYEAI 254 Query: 237 TADEVFVTGTAAEIAPIVVIDGRKIGDG 264 ADE F+TGT P+ IDG+ IGDG Sbjct: 255 GADEAFLTGTFGAQTPVASIDGKPIGDG 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: 262 Number of extensions: 15 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: 290 Length of database: 307 Length adjustment: 27 Effective length of query: 263 Effective length of database: 280 Effective search space: 73640 Effective search space used: 73640 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