Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_041666743.1 SULKU_RS04655 PLP-dependent aminotransferase family protein
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >NCBI__GCF_000183725.1:WP_041666743.1 Length = 379 Score = 214 bits (545), Expect = 3e-60 Identities = 137/378 (36%), Positives = 210/378 (55%), Gaps = 19/378 (5%) Query: 16 MGASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYTISE 75 M S IRE+L+++ + +SFAGG+PD FP + +A +++F + GALQY+IS Sbjct: 1 MKRSFIREILEVIGS-DTVSFAGGLPDESLFPIEEMQKASQEVFATP----GALQYSISS 55 Query: 76 GFTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYLGAL 135 G LRE + +Y G++ + +L+T+G+QQAL+ + ++ G +V P YLGAL Sbjct: 56 GIPSLREKLASYYSAMGLETKSENILITTGAQQALDLISRIYFTAGT--VVEAPAYLGAL 113 Query: 136 QAFSPYEPQYLSVPGDAEGPDLAAVEAALEQKPKFFYLVPDFQNPNGTTISLARREALLD 195 AFS V + G D+ A E +Q K YL+ DFQNP G + + A R+ L Sbjct: 114 NAFSANGCPLHPVTLNPTGLDMDAFEEKYKQT-KRAYLMCDFQNPTGISYTDAVRQELAR 172 Query: 196 LCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNVLFCGSFSKTMVPALRVG 255 + ++ IVED AY EL +E P ++L A N L GSFSKT+ P LR+G Sbjct: 173 ISVENDGIIVEDGAYMELFFEERRAP--LSLYAPHN------TLHVGSFSKTLAPGLRLG 224 Query: 256 WINGPAEVINRLVLMKQAGDLHTSTINQIVLHDV-VSQNFDSHIRRLRAGYKERRDAMLT 314 WI G +++ ++ +K+ DLHTST++Q++ S F H+R++RA YK + DA+ Sbjct: 225 WIRGDTKLLQPILALKERSDLHTSTLSQLLADRFWESGFFGKHLRKIRAAYKRKCDALAD 284 Query: 315 ALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFHADRSGKN 374 L+ + + KP+GGMF++ P+ D +L R +K+ V FVPG F++ Sbjct: 285 ELTS-QLSDFCFIKPKGGMFIYGTFPDEIDAKELAMRCLKNGAV-FVPGGEFYSGAPLSA 342 Query: 375 TLRLSFSNNNPERIREGI 392 R +FSN E +R GI Sbjct: 343 EARFNFSNATSEEMRRGI 360 Lambda K H 0.320 0.138 0.410 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: 402 Number of extensions: 26 Number of successful extensions: 8 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: 404 Length of database: 379 Length adjustment: 31 Effective length of query: 373 Effective length of database: 348 Effective search space: 129804 Effective search space used: 129804 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: 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