Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_012756602.1 RLEG_RS04700 branched-chain amino acid aminotransferase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_000023185.1:WP_012756602.1 Length = 295 Score = 123 bits (309), Expect = 5e-33 Identities = 92/302 (30%), Positives = 147/302 (48%), Gaps = 16/302 (5%) Query: 2 TTKKADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRL 61 T + + +GE + SHA+ G++VF+G R +D + H QR+ Sbjct: 6 TPRSTTWTHVDGEWFPGNPPLIGPTSHAMWLGSTVFDGARWFDGIAPDLDL----HCQRI 61 Query: 62 HDSAKIYRFPVSQSIDELME-ACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPA--GYST 118 + SA +S +E++ A V + + T+ YI+P+ + G+ G + A G ST Sbjct: 62 NRSALAMGLKPVKSAEEIVALAWEGVAKFDGATAIYIKPMYW-GEHGSPGSVVAVDGEST 120 Query: 119 DVIIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRH 178 + F A +G G VS + R +P T T AK G Y +S + +EAR Sbjct: 121 RFALCLFE--APMGGHG---GTSLTVSPYRRPSPETAMTEAKTGSLYPNSGRMIAEARSR 175 Query: 179 GYQEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVR 238 G+ + D+NG + E A N+F VKDGV+ TP + L GITR +I L ++ G +V Sbjct: 176 GFDNALVRDLNGNVVETASSNVFMVKDGVVMTPAANRTFLAGITRARVIDLLRKAGFDVH 235 Query: 239 EQVLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETE 298 E LS E ADE+F +G +++ V +DG + E GPVT++ + + G +E Sbjct: 236 EAALSVEDFMQADEIFTTGNYSKVVGVTRLDGRDLQE---GPVTRKALELYMDWAFGRSE 292 Query: 299 DK 300 + Sbjct: 293 SE 294 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: 261 Number of extensions: 12 Number of successful extensions: 2 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: 295 Length adjustment: 27 Effective length of query: 282 Effective length of database: 268 Effective search space: 75576 Effective search space used: 75576 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 10 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