Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 15218 b1096 4-amino-4-deoxychorismate lyase (NCBI)
Query= BRENDA::E6TUA8 (302 letters) >FitnessBrowser__Keio:15218 Length = 269 Score = 102 bits (255), Expect = 7e-27 Identities = 73/242 (30%), Positives = 118/242 (48%), Gaps = 5/242 (2%) Query: 15 KQEAVISVYDHGFLYGDGVFEGIRVYDGNIFKLTEHLKRLYESAQSIMLEIPYSKEDFQQ 74 KQE+ ++V D +GDG F RV DG + L+ H++RL ++ Q +M+ + + Q+ Sbjct: 8 KQES-LAVSDRATQFGDGCFTTARVIDGKVSLLSAHIQRLQDACQRLMISCDFWPQLEQE 66 Query: 75 IIVDTVRKNQLESGYIRVVVSRGPGNLGLDPSRCSAPHVIVIAEELALFPKELYELGLTV 134 + T+ Q ++G ++VV+SRG G G I+ L G+T+ Sbjct: 67 M--KTLAAEQ-QNGVLKVVISRGSGGRGYSTLNSGPATRILSVTAYPAHYDRLRNEGITL 123 Query: 135 ASVASRRNRPDVLSPQIKSLNYLNNILVKLEANQAGAHEALMLNDQGYVTEGSADNIFIV 194 A R R L+ IK LN L +L++ Q A EAL+L+ +G+VTE A N+F Sbjct: 124 ALSPVRLGRNPHLAG-IKHLNRLEQVLIRSHLEQTNADEALVLDSEGWVTECCAANLFWR 182 Query: 195 KNNTIITPPVYLGALEGITRNAIIDLAKECGYEMKETPFTRHDVYVADEVFLTGTAAEVI 254 K N + TP + + GI R I L + Y++ E + + ADE+ + V+ Sbjct: 183 KGNVVYTPRLDQAGVNGIMRQFCIRLLAQSSYQLVEVQASLEESLQADEMVICNALMPVM 242 Query: 255 AV 256 V Sbjct: 243 PV 244 Lambda K H 0.318 0.136 0.385 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: 154 Number of extensions: 6 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: 302 Length of database: 269 Length adjustment: 26 Effective length of query: 276 Effective length of database: 243 Effective search space: 67068 Effective search space used: 67068 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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