Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_015820520.1 TERTU_RS09270 PLP-dependent aminotransferase family protein
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >NCBI__GCF_000023025.1:WP_015820520.1 Length = 401 Score = 205 bits (522), Expect = 2e-57 Identities = 138/399 (34%), Positives = 212/399 (53%), Gaps = 23/399 (5%) Query: 13 VAGMGASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYT 72 V + S IRE+L+ + +S AGG+PDP +FP A A A + + S S G QY Sbjct: 7 VESLPTSYIREILQAATAADCLSLAGGLPDPKYFPLDATAEALQLVADSPSVHGHLFQYA 66 Query: 73 ISEGFTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYL 132 + G+ PL + + L + AG E+L+T+GSQQ ++ + + G+++ + P YL Sbjct: 67 STRGYQPLIDHLQTQLS---VGAG-HELLMTNGSQQGIDLAVRTYLNQGDEVALEVPAYL 122 Query: 133 GALQAFSPYEPQYLSVPGDAEGPDLAAVEAALEQ-KPKFFYLVPDFQNPNGTTISLARRE 191 GALQ F+ + +P GPDL A+ E + K FY VPDF NP G SL R Sbjct: 123 GALQVFALAGVRVRPIPQLPNGPDLEALRKVFETGRCKMFYTVPDFHNPTGCCWSLEVRT 182 Query: 192 ALLDLCAKHGVPIVEDAAYTELRYEGE--PIPSMVALDAARNGGKITNVLFCGSFSKTMV 249 + LC KHGV ++EDA Y ++R+ GE P+ S D A + SFSKT + Sbjct: 183 EVARLCRKHGVLLLEDAPYRDIRFHGENLPLVSDFCSDVA---------IVLSSFSKTAM 233 Query: 250 PALRVGWINGPAEVINRLVLMKQAGDLHTSTINQIVLHD-VVSQNFDSHIRRLRAGYKER 308 P LR+G + +++ ++ +KQA DLHT+T+ Q +L + +V N+ +HI L Y + Sbjct: 234 PGLRLGAVVAGKKLLAPMLRVKQAVDLHTNTLGQFLLAEFLVKGNYVAHIANLCRNYHAK 293 Query: 309 RDAMLTALSEFAPAGVTWTKP-EGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFH 367 +A+ AL E A + +P +GGMF+W L E L+A+ + +A VPG F Sbjct: 294 YEALHAAL-ELHTAEFGFHRPVQGGMFIWFVLHE--LDATLVAQRCLERGLAVVPGGVFF 350 Query: 368 --ADRSGKNTLRLSFSNNNPERIREGIRRLCGLLQTVAA 404 ++ N LRL+FS ++ E RL +L+ ++A Sbjct: 351 PAGEKHSINALRLNFSYLAISQLEEAAARLAAVLRELSA 389 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: 437 Number of extensions: 23 Number of successful extensions: 6 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: 401 Length adjustment: 31 Effective length of query: 373 Effective length of database: 370 Effective search space: 138010 Effective search space used: 138010 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