Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_068465118.1 APY04_RS16460 branched-chain amino acid aminotransferase
Query= BRENDA::P54691 (305 letters) >NCBI__GCF_001541235.1:WP_068465118.1 Length = 297 Score = 137 bits (345), Expect = 3e-37 Identities = 90/271 (33%), Positives = 141/271 (52%), Gaps = 21/271 (7%) Query: 7 IAYFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKS 66 + + + K VP+ +A I V THALHYG+ F GLR +F+L H RL S Sbjct: 13 LIWLDGKMVPWREANIHVLTHALHYGSGVFEGLRAYGGE-------IFKLSEHSQRLIDS 65 Query: 67 AKFLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVY--SSGLGIAPRLHNLEKDFLV 122 AK L +DI +A +I ++ D V N YIRP+ + S +G+A + + Sbjct: 66 AKTLDFDIPYTAAEIDQICRDVVAANNLSDC-YIRPIAWRGSEQIGVAAQATKIHLSVAA 124 Query: 123 YGLEMGDYLAAD----GVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDE 178 + E G Y + G+ ++ + R + + P K + Y+ + K A +GF + Sbjct: 125 W--EWGSYFPMEQRLKGIKITMAKYRRPDPATAPSTSKAAGLYMICTIEKHRAENAGFAD 182 Query: 179 AILMNSQGKVCEATGMNVFMVRNGQIVTPGNEQD-ILEGITRDSILTIAADLGIPTCQRP 237 A++++ +G+V E TG N+F V++G I TP E D L GITR +++ +A G +R Sbjct: 183 ALMLDWRGRVAECTGANIFFVKDGVIHTP--EADCFLNGITRRTVIDLAKKRGYQVIERA 240 Query: 238 IDKSELMIADEVFLSGTAAKITPVKRIENFT 268 I EL EVF++GTAA++TPV +I T Sbjct: 241 IMPDELKDFSEVFVTGTAAEVTPVSQIGEHT 271 Lambda K H 0.320 0.138 0.406 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: 200 Number of extensions: 11 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: 305 Length of database: 297 Length adjustment: 27 Effective length of query: 278 Effective length of database: 270 Effective search space: 75060 Effective search space used: 75060 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