Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_086509188.1 BZY95_RS06660 PLP-dependent aminotransferase family protein
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >NCBI__GCF_002151265.1:WP_086509188.1 Length = 476 Score = 164 bits (414), Expect = 7e-45 Identities = 115/387 (29%), Positives = 191/387 (49%), Gaps = 17/387 (4%) Query: 16 MGASEIRELLKLLERP----EIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQY 71 + S+ ++L+L+ R ++ GIPD + R + + + G L Y Sbjct: 86 LDVSQWDQVLELVTRSPDEDRLLMLGRGIPDLAAASLRPLQRQLGTLHRHVAAHG--LNY 143 Query: 72 TISEGFTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTY 131 +G LR + + G D+VL+T+G Q+AL + L PG+ + V P++ Sbjct: 144 DSLQGSLALRRQVVRLAAKSGCLLHPDDVLITTGCQEALSLALRTLTEPGDVVAVDSPSF 203 Query: 132 LGALQAFSPYEPQYLSVPGDAE-GPDLAAVEAALEQKP-KFFYLVPDFQNPNGTTISLAR 189 G +Q + + L +P D G L A+E ALEQ P K + P NP G T+ AR Sbjct: 204 YGTMQILKAQKLKALEIPTDPRTGISLEALELALEQWPIKAIQITPTCNNPLGYTMPEAR 263 Query: 190 REALLDLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNVLFCGSFSKTMV 249 + AL+ L + V IVED Y +L +E P L + + G+ VL C +FSKT+V Sbjct: 264 KRALVALAQRFDVAIVEDDIYGDLSFEA---PRPRTLKSFDDDGR---VLLCSAFSKTLV 317 Query: 250 PALRVGWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQ-NFDSHIRRLRAGYKER 308 P LRVGW+ P ++ + MK ++T+ Q+ + + V +++ H+R + Y+ Sbjct: 318 PGLRVGWM-APGRYRDQALHMKYVSTGASATLPQLAVAEFVEHGHYERHLREMLRQYRRH 376 Query: 309 RDAMLTALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFHA 368 RD M+ ++ + PAG + P+GG +W+ELP D V L + + + PGS F A Sbjct: 377 RDIMIDWVTRYFPAGTGVSFPQGGFLLWLELPGDIDCV-RLKEQLANEGLHITPGSLFSA 435 Query: 369 DRSGKNTLRLSFSNNNPERIREGIRRL 395 ++ LRL+++ + GI+R+ Sbjct: 436 SGKFRHCLRLNYAAAMTPTVEAGIKRV 462 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: 457 Number of extensions: 26 Number of successful extensions: 5 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: 476 Length adjustment: 32 Effective length of query: 372 Effective length of database: 444 Effective search space: 165168 Effective search space used: 165168 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: 51 (24.3 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