Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_041434172.1 THAL_RS02350 branched-chain-amino-acid transaminase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_000025605.1:WP_041434172.1 Length = 305 Score = 221 bits (563), Expect = 2e-62 Identities = 122/305 (40%), Positives = 182/305 (59%), Gaps = 8/305 (2%) Query: 7 DYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCY--DSHKGPVVFRHREHMQRLHDS 64 +Y +F G +V E+AK+ + +++ HYGT+VFEGIR Y + H + REH QRL + Sbjct: 2 EYAFFEGRIVPIEEAKISIKTNSFHYGTAVFEGIRAYWNEEHHQLYILFAREHYQRLLAN 61 Query: 65 AKIYRFPVSQSIDELMEACRDVIRKNNLT-SAYIRPLIFVGDVGMGVNPPAGYSTDVIIA 123 + + S+D+L+ +++RKNN+ YIRP+ + D+ + G++ ++ I Sbjct: 62 CRAMFMELPYSVDDLVNITVELLRKNNIKHDVYIRPIAYFKDLAL-TPKLIGFTPEIAIY 120 Query: 124 AFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEG 183 + +G YL +GI SSW R N+IP+ K G Y++S L +EA GY E Sbjct: 121 TYSFGRYLDTS---KGIRVKTSSWIRNDDNSIPSRWKVAGAYVNSALAKTEAILAGYDEA 177 Query: 184 IALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAK-ELGIEVREQVL 242 I L+ NG+++EG+GEN+F V+ + TPP L GITR A+IKL K EL +EV E+ + Sbjct: 178 IMLNQNGFVAEGSGENIFLVRGRKVVTPPCWDHILEGITRSAVIKLIKNELVLEVEERSI 237 Query: 243 SRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWG 302 SR LY ADEVF++GTAAEITPV +D ++G G GP+T+ +Q+ +F G E G Sbjct: 238 SRSELYSADEVFLTGTAAEITPVVEIDNRKIGSGDIGPITRELQKIYFDAVRGNIERYKG 297 Query: 303 WLDQV 307 WL V Sbjct: 298 WLTPV 302 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: 253 Number of extensions: 13 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: 309 Length of database: 305 Length adjustment: 27 Effective length of query: 282 Effective length of database: 278 Effective search space: 78396 Effective search space used: 78396 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: 48 (23.1 bits)
This GapMind analysis is from Jul 25 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