Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_093429006.1 BM272_RS11855 branched-chain amino acid transaminase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_900112605.1:WP_093429006.1 Length = 306 Score = 285 bits (728), Expect = 1e-81 Identities = 144/299 (48%), Positives = 195/299 (65%), Gaps = 2/299 (0%) Query: 9 IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68 IW++GE+V W DA HV++H LHYG VFEG R Y + G +FR +H RL SA I Sbjct: 10 IWYDGELVPWRDATTHVLTHTLHYGMGVFEGERAYAADGGTAIFRLADHTDRLFRSAHIM 69 Query: 69 RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWG 128 P+ + + EA R +R+N L SAYIRP+ F G GMG+ VIIAA+ WG Sbjct: 70 GMPMPYDRETINEATRQAVRENGLESAYIRPMAFYGSEGMGLR-ATNLQVHVIIAAWGWG 128 Query: 129 AYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDV 188 AYLG E +E+GI SS +R N+ AKA GNY++S+L EA GY E + LD Sbjct: 129 AYLGEEGMERGIRVRTSSHSRHHVNSSMCKAKANGNYINSMLALQEAVSCGYDEALLLDT 188 Query: 189 NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLY 248 G+++EG+GENLF V++GVL+TP T +AL GITR+ I+ LA+E GI VRE+ ++R+ +Y Sbjct: 189 EGFVAEGSGENLFVVRNGVLYTPELT-AALEGITRETIVHLAEEAGIPVREKRMTRDEVY 247 Query: 249 LADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLDQV 307 +ADE F +GTAAE+TPVR +DG +G GR GP+T+++Q +F L G E WLD+V Sbjct: 248 VADEAFFTGTAAEVTPVRELDGRTIGAGRRGPITEQLQTMYFELVHGRREPHHDWLDRV 306 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: 302 Number of extensions: 13 Number of successful extensions: 3 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: 306 Length adjustment: 27 Effective length of query: 282 Effective length of database: 279 Effective search space: 78678 Effective search space used: 78678 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