Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_013721656.1 ALIDE2_RS06730 aspartate aminotransferase family protein
Query= curated2:Q9YBY6 (388 letters) >NCBI__GCF_000204645.1:WP_013721656.1 Length = 442 Score = 142 bits (358), Expect = 2e-38 Identities = 117/344 (34%), Positives = 176/344 (51%), Gaps = 35/344 (10%) Query: 17 RIVKGSMQYVWDDSGRKYLDCHAGHGAAFLGHSNPAIVEAVVRQARELVAASSSFSTPSL 76 R KG + V DD+GR+ LD +G A +GH++PAIV+AV ++A E S P + Sbjct: 26 RSAKGCV--VTDDTGREILDFTSGQMCATIGHNHPAIVQAV-QEAGEKAYHMFSGMIPEV 82 Query: 77 EEALTEFSRIAPPWAEE----IVFLNTGTEAVEAALKAAWLATGKRGIVALKNSFHGRTL 132 L + +A W + +F+NTG+E+ E AL+ A + T I+A+ S+HG T Sbjct: 83 VARLAQ--TMARDWMPQGLSKSIFINTGSESNEVALRMAKMYTQGFEILAVGGSWHGVTG 140 Query: 133 ASLSVTW-NPRYRRGVPVLDTRFLSPSTD---------PGEVEKLVPEDT---------- 172 A+ + ++ + R GV V F+ P + GE L + Sbjct: 141 AASAASFASDRKGYGVHVPGV-FVMPEPNMYRPYIQGMDGEASALACLEIGLKMYDMAST 199 Query: 173 ---AAIIVEPIQGEGGLTKIYAELAKALREAADRVGALLIFDEIQTGFGRTGRVWAHESL 229 +AII+EPI GG+ +ALR+AAD G LLIFDE QT FGR G A + Sbjct: 200 GRRSAIIIEPIISAGGVLVPPKSYMQALRKAADERGMLLIFDEAQTAFGRIGHRHAADFF 259 Query: 230 GVEPDIMTAGKSIAGGLPASAVLSREGVLATL-ASG-RHGSTHAANPLSMAAVAAASRFL 287 GV PDIM K++ GGLP +AV + + + A G ++H ++PL A R + Sbjct: 260 GVTPDIMAVSKTMGGGLPLAAVSTTPEIEEDIHAKGFTFYTSHVSDPLPATVGLAVLRTI 319 Query: 288 REEGVPDKARAAGALLEGLLRDRIEGLRLVRGVRGEGLMLGVEL 331 ++E + ++A++ GA L L + + VRGEG++LGVEL Sbjct: 320 QQERLIERAQSMGAYLRRRLEELQSRYEAIGDVRGEGMLLGVEL 363 Lambda K H 0.319 0.136 0.398 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: 364 Number of extensions: 22 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 388 Length of database: 442 Length adjustment: 31 Effective length of query: 357 Effective length of database: 411 Effective search space: 146727 Effective search space used: 146727 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