Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.118 (uncharacterized)
to candidate 200454 SO1276 4-aminobutyrate aminotransferase (NCBI ptt file)
Query= curated2:Q9RW75 (429 letters) >FitnessBrowser__MR1:200454 Length = 425 Score = 183 bits (464), Expect = 1e-50 Identities = 134/405 (33%), Positives = 193/405 (47%), Gaps = 28/405 (6%) Query: 21 GVYNKHDVVMVRGQGATVWDENGRSYIDCVVGYGVATLGHSHPDVVKAVQEQAGKLM-VM 79 GV H + R + A+VWD GR +ID G V GH HP V AV Q Sbjct: 19 GVGQIHPIFTARAENASVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFSHTC 78 Query: 80 PQTVPNDKRAEFLQELVGVLPQGL-DRVFLCNSGTEAMEAAKKFAITATGRSRFVSMKRG 138 + + + ++L ++P + L SG+EA+E A K A T R+ ++ G Sbjct: 79 FMVLGYESYIQVCEKLNQLVPGDFAKKTALFTSGSEAVENAVKVARAYTKRAGVIAFTSG 138 Query: 139 FSGRSLGALSFTWEPK-------------YREPFGDAVDNKSVDFVTYGNLDEL--RAAV 183 + GR++ AL+ T + +R F A+ S D +++ + A Sbjct: 139 YHGRTMAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGVSDDDAM-ASIERIFKNDAE 197 Query: 184 TEQTAAVIMEPVQGEGGVRPASAEFIQEARRITREKGALLILDEIQTGFCRTGKMFACEH 243 AA+I+EPVQGEGG S F+Q R + +G +LI DE+QTG RTG FA E Sbjct: 198 PSDIAAIILEPVQGEGGFYAVSPAFMQRLRALCDREGIMLIADEVQTGAGRTGTFFAMEQ 257 Query: 244 FGVIPDGMTLAKAIAGGTPTAAFAMMSEVADRMPAGGHGTTFGGNPLSMAAGVASLRAMK 303 GV D T AK+IAGG P + ++V D + GG G T+GGNPL+ AA +A L + Sbjct: 258 MGVSADITTFAKSIAGGFPLSGITGRAQVMDAIGPGGLGGTYGGNPLACAAALAVLEVFE 317 Query: 304 REGLAEQAREKGAYMMDKLRAIQ--SPKIREVRGLGLMIGVELKEKSAP------YIHAM 355 E L E+A G + L +Q P+I +VRGLG M +EL E P I A Sbjct: 318 EEKLLERANAIGDRIKSALNTMQVEHPQIADVRGLGAMNAIELMEDGKPAPQYCAQILAE 377 Query: 356 EHDEGVLCLAATPL--VVRFLPPAVISKEQIDQVVAAFERVLNNV 398 + G++ L+ V+R L P +S Q+D + + N V Sbjct: 378 ARNRGLILLSCGTYGNVLRILVPLTVSDTQLDAGLGILKTSFNAV 422 Lambda K H 0.317 0.132 0.380 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: 406 Number of extensions: 16 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: 429 Length of database: 425 Length adjustment: 32 Effective length of query: 397 Effective length of database: 393 Effective search space: 156021 Effective search space used: 156021 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 (21.7 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