Align [amino group carrier protein]-C-terminal-L-glutamyl-γ-L-lysine aminotransferase (EC 2.6.1.118; EC 2.6.1.124) (characterized)
to candidate 200454 SO1276 4-aminobutyrate aminotransferase (NCBI ptt file)
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__MR1:200454 Length = 425 Score = 182 bits (461), Expect = 2e-50 Identities = 125/389 (32%), Positives = 193/389 (49%), Gaps = 32/389 (8%) Query: 16 KGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISILSTSFSTPIKDEM 75 + E VWD+EGR ++DF GI V GH +P + + QLE+ S T F + Sbjct: 30 RAENASVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFS--HTCFMVLGYESY 87 Query: 76 LQALDK----VKPDKMDNAMLLNSGTEAVEAALKTARKITGRKKIIAFKNAFHGRTAGSL 131 +Q +K V D L SG+EAVE A+K AR T R +IAF + +HGRT +L Sbjct: 88 IQVCEKLNQLVPGDFAKKTALFTSGSEAVENAVKVARAYTKRAGVIAFTSGYHGRTMAAL 147 Query: 132 SVTWN-------------KKYREPFE-PLVGPVEFLTFNNIEDLSKIDNET---AAVIVE 174 ++T +R F L G + +IE + K D E AA+I+E Sbjct: 148 ALTGKVAPYSKGMGLMSANVFRAEFPCALHGVSDDDAMASIERIFKNDAEPSDIAAIILE 207 Query: 175 PIQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTA 234 P+QGE G + FM+ L+ + G +LI DE+QTG GRTG +A + + DI T Sbjct: 208 PVQGEGGFYAVSPAFMQRLRALCDREGIMLIADEVQTGAGRTGTFFAMEQMGVSADITTF 267 Query: 235 GKAIGGGFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACKVIEKENVVEQANQ 294 K+I GGFP+S + + + + G G TYGGNP+A AA A +V E+E ++E+AN Sbjct: 268 AKSIAGGFPLSGITGRAQVMDAIGPGGLGGTYGGNPLACAAALAVLEVFEEEKLLERANA 327 Query: 295 KGQQFSNILVKNLADLKVVREVRGKGLMIGIDIRFQP-------GQVLKYLQEKGILAVK 347 G + + L + + +VRG G M I++ Q+L + +G++ + Sbjct: 328 IGDRIKSALNTMQVEHPQIADVRGLGAMNAIELMEDGKPAPQYCAQILAEARNRGLILLS 387 Query: 348 AGS--TVIRFLPSYLITYENMEEASNVLR 374 G+ V+R L ++ ++ +L+ Sbjct: 388 CGTYGNVLRILVPLTVSDTQLDAGLGILK 416 Lambda K H 0.317 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: 374 Number of extensions: 9 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: 387 Length of database: 425 Length adjustment: 31 Effective length of query: 356 Effective length of database: 394 Effective search space: 140264 Effective search space used: 140264 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 (21.6 bits) S2: 50 (23.9 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