Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 3609638 Dshi_3021 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Dino:3609638 Length = 485 Score = 301 bits (771), Expect = 4e-86 Identities = 180/485 (37%), Positives = 265/485 (54%), Gaps = 13/485 (2%) Query: 28 PNQQPEVFCNQIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAF 87 P P ++I I W T ++PS G + Q+A G ++D+AV AARAA Sbjct: 5 PTYDPGFPGDEILIGGVWQRCAD--TLEVIDPSDGTPLAQIARGGAAEIDRAVAAARAA- 61 Query: 88 QLGSPWRRMDASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLR 147 L W RM A+ RGR L RL L+ + LA +E D GKP + D + + L Sbjct: 62 -LDGDWGRMSATERGRCLTRLGALVAGEVDRLAEMEARDVGKP-LSQARADALALARYLE 119 Query: 148 YYAGWADKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVV 207 +Y G ADK G+TIP + YT EP GV G I+PWN+P+ + +G ALA GN V Sbjct: 120 FYGGAADKVMGETIPYQSGYTVYTLREPHGVTGHIVPWNYPMQIIGRSVGAALAMGNACV 179 Query: 208 MKVAEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIG 267 +K AE LTAL A L + AG PPG +N+V G G AGAA++ H VD ++FTGS +G Sbjct: 180 LKPAEDACLTALAFARLAEAAGLPPGALNVVTGLGAEAGAALSDHPGVDHLSFTGSVPVG 239 Query: 268 RVIQVAAGSSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFV 327 +Q A + ++ VTLELGGKSP I+ +DAD+D A+ N GQ C A +R V Sbjct: 240 AEVQ-ATAARHITPVTLELGGKSPQIVFADADLDAALPFLVKGGVQNAGQTCSAAARILV 298 Query: 328 QEDIYDEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCG 387 Q D++D +R ++ VG P S GP + Q ++ + + + ++L Sbjct: 299 QTDVFDAVADRMAEAYRALTVG-PALSDPAVGPLISPKQKARVSAMLAQAQPD--QILAT 355 Query: 388 GGI---AADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGL 444 G + A + G ++ P + G + +A++EIFGPV +++F+T +E + AN + +GL Sbjct: 356 GHLLPEAPEGGCYVLPHLLGGIAADHPLAQQEIFGPVQILMRFETEQEAIALANGTEFGL 415 Query: 445 AAAVFTKDLDKANYLSQALQAGTVWVNCYDV-FGAQSPFGGYKMSGSGRELGEYGLQAYT 503 A ++T+D + + + L+AG V+VN Y G + PFGG SG GRE G L ++ Sbjct: 416 VAGIWTRDGARQMRMPKRLRAGQVFVNTYGAGGGVELPFGGVGKSGHGREKGFEALFGFS 475 Query: 504 EVKTV 508 ++KTV Sbjct: 476 QLKTV 480 Lambda K H 0.319 0.136 0.409 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: 619 Number of extensions: 36 Number of successful extensions: 7 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: 517 Length of database: 485 Length adjustment: 34 Effective length of query: 483 Effective length of database: 451 Effective search space: 217833 Effective search space used: 217833 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: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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