Align Probable branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42 (uncharacterized)
to candidate WP_011937544.1 GURA_RS03090 aminodeoxychorismate synthase, component I
Query= curated2:P74921 (273 letters) >NCBI__GCF_000016745.1:WP_011937544.1 Length = 574 Score = 70.5 bits (171), Expect = 8e-17 Identities = 68/226 (30%), Positives = 107/226 (47%), Gaps = 25/226 (11%) Query: 6 RGKFRRADEISLDFSLFEKSLQGAVYETLRTYSRAPFAAYKHYTRLKRSADFFNLPLSLS 65 +G+F R E +F L E L ++ + Y F +H RLKRSA +F L Sbjct: 360 KGRFAR--EKPREFHLIESLL----FDEGKGY----FLLERHMERLKRSAAYFAFTLEAG 409 Query: 66 FDEFTKVLKAGADEF--KQEVRIKVYLFPDSGEVLFVFSPLNIPDLETGVEVKISNVRRI 123 E K L+ KQ+VR+ L +GE+ +P+ G E+ ++ RR Sbjct: 410 GAE--KALEEIGSHLIGKQKVRL---LLSRTGEIACEAAPIGAES--GGKELTVTFARRT 462 Query: 124 PDLSTPPAL-KITGRTDIVLARREIVDCYDVILLGLNGQVCEGSFSNVFLVKEGKLITPS 182 D + P K T R+ DC DV+ + G+V EG+ SN+ G+L+TP Sbjct: 463 ADSADPFLYHKTTSRSLYAEEAALRPDCADVLFINERGEVTEGTISNIVARIGGELVTPP 522 Query: 183 LDSGILDGITRENVIKLAKSLEIPVEERVVWVWELFEADEMFLTHT 228 L G+L G+ RE +++ + + ERV+ EL A+E+FL ++ Sbjct: 523 LCCGLLPGVFREELLENGE-----IRERVICREELETAEEIFLVNS 563 Lambda K H 0.322 0.140 0.415 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: 320 Number of extensions: 17 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: 273 Length of database: 574 Length adjustment: 31 Effective length of query: 242 Effective length of database: 543 Effective search space: 131406 Effective search space used: 131406 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 (21.9 bits) S2: 50 (23.9 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