Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_037572571.1 BS73_RS14690 branched-chain amino acid aminotransferase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_000744815.1:WP_037572571.1 Length = 359 Score = 134 bits (338), Expect = 2e-36 Identities = 105/320 (32%), Positives = 149/320 (46%), Gaps = 36/320 (11%) Query: 10 WFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPV-VFRHREHMQRLHDSAKIY 68 W + ++V + ++ + LHY +FEG++ Y G V +FR + R SA+ Sbjct: 45 WHDAQLVPYGPLEMDPANMTLHYAQEIFEGLKAYRQPDGGVALFRPERNALRFQHSARTL 104 Query: 69 RFPVSQSIDELMEACRDVIRKN--------NLTSAYIRPLIFVGDVGMGVNPPAGYSTDV 120 P ++ +EAC ++ ++ S Y+RP + +VG+GV P Y Sbjct: 105 AMP-ELPVETFIEACDALVAQDVEWVPPHGGEASLYLRPFMIASEVGLGVKPANEYL--F 161 Query: 121 IIAAFPWGAYLGAEALEQGIDAMVSSWN-----RAAPNTIPTAAKAGGNYLSSLLVGSEA 175 ++ A P G Y G VS W RA P + A K GGNY +SLL +EA Sbjct: 162 LVIASPAGPYF------PGGVKPVSIWISQDRVRAVPGGMGDA-KTGGNYAASLLAQAEA 214 Query: 176 RRHGYQEGIALDV--NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKEL 233 G + LD ++ E G NL+ V + TP T S L G+TRD+++ LA++L Sbjct: 215 AEQGCAQVAYLDAVERRWVEELGGMNLYFVYGDRIVTPALTGSLLEGVTRDSLLTLARDL 274 Query: 234 GIEVREQVLS----RESLYLAD--EVFMSGTAAEITPVRSVD----GIQVGEGRCGPVTK 283 G E E +S RE EVF GTAA ITPV V G G GPVT Sbjct: 275 GYESEEARISVDQWREDTANGSLTEVFACGTAAVITPVGEVKTKGAAWTQGSGEPGPVTL 334 Query: 284 RIQQAFFGLFTGETEDKWGW 303 R+++A L TG ED GW Sbjct: 335 RLREALLSLQTGNAEDPHGW 354 Lambda K H 0.319 0.136 0.413 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: 317 Number of extensions: 22 Number of successful extensions: 6 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: 309 Length of database: 359 Length adjustment: 28 Effective length of query: 281 Effective length of database: 331 Effective search space: 93011 Effective search space used: 93011 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: 49 (23.5 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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