Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate SMc02689 SMc02689 aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Smeli:SMc02689 Length = 502 Score = 374 bits (959), Expect = e-108 Identities = 217/488 (44%), Positives = 285/488 (58%), Gaps = 20/488 (4%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 FI EW + V+ + F P TG +C+VA D D++ A+ AA AA + W R + Sbjct: 18 FIGGEWREPVAGRYFDNTTPITGGTLCEVARSDAADIEIALDAAHAARE---KWGRTSTT 74 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R +L ++A +E + LA ET DNGKP + D+ + + RY+A G Sbjct: 75 ERSNILMKIAARMEDNLELLARAETWDNGKPIRETMAADIPLAIDHFRYFAACIRAQEGS 134 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 ID D +Y HEP+GV GQIIPWNFP+LM AWKL PALA GN VV+K AEQTP + L Sbjct: 135 IGEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQTPGSIL 194 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 A LI + PPGV+NIV GFG AG +A+ + K+AFTG T GR+I A S NL Sbjct: 195 VWAELIGDL-LPPGVLNIVNGFGLEAGKPLATSPRIAKIAFTGETTTGRLIMQYA-SQNL 252 Query: 280 KRVTLELGGKSPNIIMSDAD------MDWAVEQAHFALF-FNQGQCCCAGSRTFVQEDIY 332 VTLELGGKSPNI +D D A+E FA+F NQG+ C SR VQE IY Sbjct: 253 IPVTLELGGKSPNIFFADVASEDDDFFDKALE--GFAMFALNQGEVCTCPSRALVQESIY 310 Query: 333 DEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGG--- 389 D F+ER+V R ++ GNP D T G Q Q +KIL YI GK+EGA++L GGG Sbjct: 311 DRFMERAVKRVEAIRQGNPLDEATMIGAQASSEQLEKILAYIEIGKEEGAEVLTGGGRNV 370 Query: 390 IAAD--RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAA 447 + D GY+++PTVF + M I +EEIFGPV+ + FKT E + AN++ YGL A Sbjct: 371 LEGDLSGGYYVKPTVFHG-HNRMRIFQEEIFGPVVSVTTFKTEAEALEIANDTLYGLGAG 429 Query: 448 VFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKT 507 V+++D ++ +A++AG VW NCY + A + FGGYK SG GRE + L Y + K Sbjct: 430 VWSRDANRCYRFGRAIEAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKN 489 Query: 508 VTVKVPQK 515 + V K Sbjct: 490 MLVSYSPK 497 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: 630 Number of extensions: 31 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: 502 Length adjustment: 34 Effective length of query: 483 Effective length of database: 468 Effective search space: 226044 Effective search space used: 226044 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