Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_012708832.1 NGR_RS22740 aldehyde dehydrogenase family protein
Query= BRENDA::P05091 (517 letters) >NCBI__GCF_000018545.1:WP_012708832.1 Length = 502 Score = 379 bits (973), Expect = e-109 Identities = 217/486 (44%), Positives = 288/486 (59%), Gaps = 16/486 (3%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 FI EW + V+ + F P TG +CQ+A D D++ A+ AA AA + W R + Sbjct: 18 FIGGEWREPVAGRYFDNTTPVTGGSLCQIARSDAADIELALDAAHAAKE---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 AWK+ PALA GN VV+K AEQTP + L Sbjct: 135 IGEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKVAPALAAGNCVVLKPAEQTPASIL 194 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 +A LI + PPGV+NIV GFG AG +A+ + K+AFTG T GR+I A S NL Sbjct: 195 ILAELIADL-LPPGVLNIVNGFGLEAGKPLATSPRIAKIAFTGETTTGRLIMQYA-SQNL 252 Query: 280 KRVTLELGGKSPNIIMSDA---DMDWAVEQAH-FALF-FNQGQCCCAGSRTFVQEDIYDE 334 VTLELGGKSPNI +D D D+ + FA+F NQG+ C SR VQE IYD Sbjct: 253 IPVTLELGGKSPNIFFADVLNEDDDYFDKALEGFAMFALNQGEVCTCPSRALVQESIYDR 312 Query: 335 FVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGG---IA 391 F+ER+V R ++ GNP DS T G Q Q +KIL YI+ GKQEGA++L GGG + Sbjct: 313 FMERAVKRVEAIRQGNPLDSATMIGAQASGEQLEKILSYIDIGKQEGAEVLAGGGRNVLE 372 Query: 392 AD--RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVF 449 D GY+++PTVF + M I +EEIFGPV+ + FKT +E + AN++ YGL A V+ Sbjct: 373 GDLAGGYYVKPTVFRG-HNKMRIFQEEIFGPVVSVTTFKTEDEALEIANDTLYGLGAGVW 431 Query: 450 TKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVT 509 ++D ++ + +QAG VW NCY + A + FGGYK SG GRE + L Y + K + Sbjct: 432 SRDANRCYRFGREIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNML 491 Query: 510 VKVPQK 515 V K Sbjct: 492 VSYSPK 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: 615 Number of extensions: 28 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 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