Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 200454 SO1276 4-aminobutyrate aminotransferase (NCBI ptt file)
Query= curated2:Q5SHH5 (395 letters) >FitnessBrowser__MR1:200454 Length = 425 Score = 203 bits (516), Expect = 9e-57 Identities = 140/394 (35%), Positives = 197/394 (50%), Gaps = 34/394 (8%) Query: 22 GVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMP 81 GV H + R + A VWD EG E+ID GG V N GH +P+V AV Q E Sbjct: 19 GVGQIHPIFTARAENASVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFS--- 75 Query: 82 QTLPTPMRGEFY----RTLTAILPPELNRVFPV-NSGTEANEAALKFARAHTGRKKFVAA 136 T + E Y L ++P + + + SG+EA E A+K ARA+T R +A Sbjct: 76 HTCFMVLGYESYIQVCEKLNQLVPGDFAKKTALFTSGSEAVENAVKVARAYTKRAGVIAF 135 Query: 137 MRGFSGRTMGSLSVTWEPKYREPFLPLVE--------PVEFIPYNDVEALKR-------- 180 G+ GRTM +L++T + + L+ P +D +A+ Sbjct: 136 TSGYHGRTMAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGVSDDDAMASIERIFKND 195 Query: 181 AVDEETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAF 240 A + AA+ILEPVQGEGG +P F++ R + +G +LI DE+QTG GRTG FA Sbjct: 196 AEPSDIAAIILEPVQGEGGFYAVSPAFMQRLRALCDREGIMLIADEVQTGAGRTGTFFAM 255 Query: 241 EHFGIVPDILTLAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRY 300 E G+ DI T AK++ GG PL R +V ++ GG G T+GGNPLA AA +A + Sbjct: 256 EQMGVSADITTFAKSIAGGFPLSGITGRAQVMDAIGPGGLGGTYGGNPLACAAALAVLEV 315 Query: 301 LERTRLWERAAELGPWFMEKLRA--IPSPKIREVRGMGLMVGLELKEKAAP---YIARLE 355 E +L ERA +G L + P+I +VRG+G M +EL E P Y A++ Sbjct: 316 FEEEKLLERANAIGDRIKSALNTMQVEHPQIADVRGLGAMNAIELMEDGKPAPQYCAQIL 375 Query: 356 KEHR---VLALQAGP--TVIRFLPPLVIEKEDLE 384 E R ++ L G V+R L PL + L+ Sbjct: 376 AEARNRGLILLSCGTYGNVLRILVPLTVSDTQLD 409 Lambda K H 0.319 0.137 0.402 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: 363 Number of extensions: 15 Number of successful extensions: 4 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: 395 Length of database: 425 Length adjustment: 31 Effective length of query: 364 Effective length of database: 394 Effective search space: 143416 Effective search space used: 143416 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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