Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate AZOBR_RS26825 AZOBR_RS26825 aldehyde dehydrogenase
Query= BRENDA::Q402C7 (499 letters) >FitnessBrowser__azobra:AZOBR_RS26825 Length = 494 Score = 373 bits (957), Expect = e-108 Identities = 204/474 (43%), Positives = 282/474 (59%), Gaps = 6/474 (1%) Query: 22 IGGEWVSGDSGKTIDLINPATGAVLTKIQAGNAKDIQRAVAAAKAAFPKWSESSPAERQE 81 IGGE +GKT D++NPATG V+ G +D+ AV AA AA W+ S ER Sbjct: 20 IGGELRPAATGKTFDVVNPATGDVIATAADGGERDVDAAVRAAVAAQGAWARLSARERGR 79 Query: 82 ILIEVARRLKARHQHYATLETLNNGKPIRESMYFDMPQAISQFEVFAGAAYGLHGQTLDY 141 +L+E RRL + L L GK IR + + G A L G+T+ + Sbjct: 80 LLVECGRRLVGHAEEIGRLLALETGKAIRTESRVEASLVADTLTFYGGLASELKGETVPF 139 Query: 142 -PDAIGIVHREPLGVCAQIIPWNVPILMMACKIAPALASGNTVVLKPAETVCLSVIEFFV 200 P + REP+GV IIPWNVP+ +MA KIAPAL +GN V++K AE L+ + Sbjct: 140 HPKMLTFTQREPIGVVGAIIPWNVPLYLMALKIAPALVAGNAVIVKSAEEAPLAALRVIQ 199 Query: 201 EMADLLPPGVINVVTGYGADVGEALVTHEDVRKVAFTGSVATARRIIQYASSNIIPQTLE 260 M LLPPGV+N+++G G G LVTH V KV FTGSV T + I A+ +IP TLE Sbjct: 200 VMNQLLPPGVLNILSGDGPGCGAPLVTHPGVGKVTFTGSVETGKIISHLAADKLIPVTLE 259 Query: 261 LGGKSAHIVCADADIDAAVESATMSTVFNK-GEVCLAGSRLFLHQSIQDEFLAKFKVALE 319 LGGKS IV DAD+D A++ A F + G+ C A SR+F+H+S+ D F+ K K ++ Sbjct: 260 LGGKSPMIVMGDADLDKAIDGAVAGMRFTRQGQSCTASSRIFVHESLHDAFIDKLKAKVD 319 Query: 320 GIRQGDPLDFATQLGAQASQMQMDKVQSYLQLA-TEEGATV--LTGGSRNESLADGHFIK 376 + GDPLD AT +G S Q ++VQSY+ L T GA + +E LA G F++ Sbjct: 320 AMTMGDPLDEATDIGTIISPQQFERVQSYIALGETTAGAIAHRCSALPTDERLARGLFVQ 379 Query: 377 PTVFTNVSNSMRIAREEIFGPVTSVLTWNDEDDMMALANDTTYGLAGGVWTRDISRAHRI 436 P +FT ++N R+AREEIFGPVT V+ + D +D +A+AND+ +GLA +WTRD+ A Sbjct: 380 PVLFTGLANDHRLAREEIFGPVTCVIAFRDYEDALAMANDSDFGLAATIWTRDLRTALDA 439 Query: 437 ARKLETGTVWVNRYYNLKPNMPLGGYKQSGFGREFSHE-VLHHYTQTKSVVINL 489 R+L+ G V VN+ ++P + GG+KQSG G+E S E +L H+T K+V+IN+ Sbjct: 440 TRRLQAGFVQVNQNLVVQPGLSYGGFKQSGLGKEASLEAMLDHFTHKKTVIINM 493 Lambda K H 0.318 0.133 0.390 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: 555 Number of extensions: 21 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: 499 Length of database: 494 Length adjustment: 34 Effective length of query: 465 Effective length of database: 460 Effective search space: 213900 Effective search space used: 213900 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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