Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate 8501549 DvMF_2268 branched-chain amino acid aminotransferase (RefSeq)
Query= CharProtDB::CH_024500 (309 letters) >FitnessBrowser__Miya:8501549 Length = 307 Score = 291 bits (745), Expect = 1e-83 Identities = 152/302 (50%), Positives = 199/302 (65%), Gaps = 3/302 (0%) Query: 4 KKADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYD-SHKGPVVFRHREHMQRLH 62 +KA+ IWF+G+ V W++A VHV++H LHYG VFEGIR Y + G VFR REHMQRL Sbjct: 3 QKAETIWFDGKQVPWDEANVHVLTHTLHYGVGVFEGIRAYKCADGGSAVFRLREHMQRLL 62 Query: 63 DSAKIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVII 122 +SAKI R + ++D+L++A + +++N L YIRPL FVG MGV P II Sbjct: 63 NSAKILRMVIPYTVDQLVDAVEETLKRNKLAEGYIRPLSFVGAGAMGVYP-GDNPVQTII 121 Query: 123 AAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQE 182 A +PWGAYLGAEALE GI SS+ R N + T AKA GNY++S+L EA+ GY E Sbjct: 122 ATWPWGAYLGAEALEHGIRVKTSSFCRHHVNAMMTKAKACGNYVNSVLAKMEAKADGYDE 181 Query: 183 GIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVL 242 G+ LD G++SE GEN+F V+ ++ T P T S L GITR+++I LA+ELG EV EQ Sbjct: 182 GLMLDTQGFVSEATGENIFIVRGKLIKTTPLT-SVLDGITRNSLITLARELGYEVVEQQF 240 Query: 243 SRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWG 302 +R+ LY+ADE F GTAAE+TP+R VD +G+G GPVTK +Q +F GE Sbjct: 241 TRDELYIADEAFFCGTAAELTPIREVDLRVIGQGTAGPVTKHLQGEYFKAVKGENPAYAH 300 Query: 303 WL 304 WL Sbjct: 301 WL 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: 295 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: 307 Length adjustment: 27 Effective length of query: 282 Effective length of database: 280 Effective search space: 78960 Effective search space used: 78960 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