Align Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized)
to candidate WP_012384805.1 BIND_RS09220 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q8GAK7 (458 letters) >NCBI__GCF_000019845.1:WP_012384805.1 Length = 463 Score = 333 bits (854), Expect = 7e-96 Identities = 182/455 (40%), Positives = 261/455 (57%), Gaps = 1/455 (0%) Query: 1 MAIATIDPTTGITLKTFDAHTPEEVENRIARAEAAFRSLQNTSFEERARWMHKAADILES 60 MA +++P TG TL +F T +EV + I +A F + TSF ER + KAADIL Sbjct: 1 MAYESVNPYTGQTLASFSEATDDEVRHAIGKAHDTFLRWRLTSFSERGVILQKAADILRR 60 Query: 61 EADEVARLIATEMGKTLTTAKYEALKSATGMRHFADHAQRYLSPETPVPASEVNASNLHV 120 ++D ARL+ EMGK + AK E SA ++ +A+ L P+ +P + + + Sbjct: 61 DSDAYARLLTLEMGKLIGEAKAEVELSAKIFEYYVRNAEELLKPQK-LPVLDPAEGDALL 119 Query: 121 QFDPLGVVLAVMPWNYPLWQAVRFAAPALMAGNTGLLKHASNVPQCALYLGDLFARGGFP 180 +PLGV+LA+ PWN+P +Q R AP L AGNT LLKHASNVPQ A L A G P Sbjct: 120 VHEPLGVLLAIEPWNFPYYQIARILAPQLSAGNTLLLKHASNVPQSAAAFEKLMAEAGLP 179 Query: 181 EGAFQTLLVEGKDVIPLVDDARIRAVTLTGSVAAGSAIAEAAGRNIKRSVLELGGMDVFI 240 GAF+ L + +++D R+ V LTGS AG+ +A AG+ +K+S LELGG D FI Sbjct: 180 AGAFKNLYATRSQIELILNDDRVHGVALTGSEGAGAVVAAQAGKALKKSTLELGGADAFI 239 Query: 241 VMPSADIEKAAAQAVIARLQNSGQSCIAAKRFYVHEDVYDRFEHLFVTGMAEAVAGDPLD 300 V+ AD+EK AV R N GQ C+++KR + + VYD F + G+A +AGDP D Sbjct: 240 VLADADLEKTTKWAVFGRHWNGGQVCVSSKRMIIVDPVYDDFLTRYRKGVAGLIAGDPFD 299 Query: 301 ESTSFGPLATERGRQDVHELVRDAREKGAAVQCGGEIPEGEGWYYPATVLTGVTEDMRIY 360 T+ PL+++ +V + +R+A + GA + G +G + T+LT + ED Sbjct: 300 AKTTLAPLSSKGAADEVKDKIREAVKLGAKAEEVGPPVPNQGSFVQPTILTDIGEDNPAR 359 Query: 361 REECFGPVACLYKVSSLQEAIALSNDSDFGLSSSVWTNDETEATEAARSIEAGGVFINGL 420 E FGPV+ L++ +A+ ++NDS FGL SV+T + E A+ + G VF+N Sbjct: 360 YWEFFGPVSMLFRAKDEDDAVRIANDSPFGLGGSVFTGNPAHGAEVAKRVSTGMVFVNHP 419 Query: 421 TASFPAVPFGGLKDSGYGRELSAYGIREFVNIKTV 455 T +PFGG++ SGYGREL G+ EFVN K + Sbjct: 420 TKVEADLPFGGIRRSGYGRELIGLGLTEFVNHKLI 454 Lambda K H 0.317 0.132 0.386 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: 484 Number of extensions: 14 Number of successful extensions: 2 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: 458 Length of database: 463 Length adjustment: 33 Effective length of query: 425 Effective length of database: 430 Effective search space: 182750 Effective search space used: 182750 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 Sep 24 2021. The underlying query database was built on Sep 17 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