Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.118 (uncharacterized)
to candidate WP_013721656.1 ALIDE2_RS06730 aspartate aminotransferase family protein
Query= curated2:Q9RW75 (429 letters) >NCBI__GCF_000204645.1:WP_013721656.1 Length = 442 Score = 156 bits (395), Expect = 1e-42 Identities = 115/350 (32%), Positives = 172/350 (49%), Gaps = 30/350 (8%) Query: 34 QGATVWDENGRSYIDCVVGYGVATLGHSHPDVVKAVQEQAGKLMVMPQTVPNDKRAEFLQ 93 +G V D+ GR +D G AT+GH+HP +V+AVQE K M + + A Q Sbjct: 29 KGCVVTDDTGREILDFTSGQMCATIGHNHPAIVQAVQEAGEKAYHMFSGMIPEVVARLAQ 88 Query: 94 ELV-GVLPQGLDRVFLCNSGTEAMEAAKK--------FAITATGRS-----------RFV 133 + +PQGL + N+G+E+ E A + F I A G S F Sbjct: 89 TMARDWMPQGLSKSIFINTGSESNEVALRMAKMYTQGFEILAVGGSWHGVTGAASAASFA 148 Query: 134 SMKRGFSGRSLGALSFTWEPKYREPFGDAVDNKSVDFVTYG-NLDELRAAVTEQTAAVIM 192 S ++G+ G EP P+ +D ++ L A T + +A+I+ Sbjct: 149 SDRKGYGVHVPGVFVMP-EPNMYRPYIQGMDGEASALACLEIGLKMYDMASTGRRSAIII 207 Query: 193 EPVQGEGGVRPASAEFIQEARRITREKGALLILDEIQTGFCRTGKMFACEHFGVIPDGMT 252 EP+ GGV ++Q R+ E+G LLI DE QT F R G A + FGV PD M Sbjct: 208 EPIISAGGVLVPPKSYMQALRKAADERGMLLIFDEAQTAFGRIGHRHAADFFGVTPDIMA 267 Query: 253 LAKAIAGGTPTAAFAMMSEVADRMPAGGHG--TTFGGNPLSMAAGVASLRAMKREGLAEQ 310 ++K + GG P AA + E+ + + A G T+ +PL G+A LR +++E L E+ Sbjct: 268 VSKTMGGGLPLAAVSTTPEIEEDIHAKGFTFYTSHVSDPLPATVGLAVLRTIQQERLIER 327 Query: 311 AREKGAYMMDKLRAIQS--PKIREVRGLGLMIGVEL---KEKSAPYIHAM 355 A+ GAY+ +L +QS I +VRG G+++GVEL +E PY HA+ Sbjct: 328 AQSMGAYLRRRLEELQSRYEAIGDVRGEGMLLGVELVKSRETREPY-HAL 376 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: 441 Number of extensions: 23 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: 429 Length of database: 442 Length adjustment: 32 Effective length of query: 397 Effective length of database: 410 Effective search space: 162770 Effective search space used: 162770 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 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