Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate 3609919 Dshi_3301 branched-chain amino acid aminotransferase (RefSeq)
Query= CharProtDB::CH_024500 (309 letters) >FitnessBrowser__Dino:3609919 Length = 289 Score = 166 bits (419), Expect = 8e-46 Identities = 92/263 (34%), Positives = 147/263 (55%), Gaps = 12/263 (4%) Query: 9 IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68 IW +G++V W A VH+++HA+HY +SVFEG R Y+ +F R H +RLH SA Sbjct: 12 IWMDGKLVDWRAANVHILTHAMHYASSVFEGERAYNGK----IFESRRHSERLHFSAGEL 67 Query: 69 RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVG---DVGMGVNPPAGYSTDVIIAAF 125 + ++DE+ A +V++ N L+ AY+R + + G D+G+ A + IA + Sbjct: 68 DIEIPFTVDEIEAAKYEVMKVNGLSDAYVRAVAWRGAGPDMGVA---SARNPVHLAIACW 124 Query: 126 PWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIA 185 WG+Y G +A +G ++ W R +P TIP AKA G Y+ A G + + Sbjct: 125 EWGSYYG-DAKTRGAKLDIAKWKRPSPETIPVHAKAAGLYMICTTSKHAAEAKGCSDALF 183 Query: 186 LDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRE 245 +D GY++E G N+F VKDG + TP L GITR +I + ++ ++V E+ + E Sbjct: 184 MDYRGYVAEATGANIFFVKDGEVHTPD-PDCFLNGITRQTVIGMLRDKQVKVHERHIMPE 242 Query: 246 SLYLADEVFMSGTAAEITPVRSV 268 L ++ +++GTAAE+TPV + Sbjct: 243 ELEGFEQCWLTGTAAEVTPVGQI 265 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: 259 Number of extensions: 12 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: 289 Length adjustment: 27 Effective length of query: 282 Effective length of database: 262 Effective search space: 73884 Effective search space used: 73884 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 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