Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_012536996.1 AFE_RS09825 aldehyde dehydrogenase family protein
Query= BRENDA::P05091 (517 letters) >NCBI__GCF_000021485.1:WP_012536996.1 Length = 506 Score = 352 bits (903), Expect = e-101 Identities = 201/482 (41%), Positives = 280/482 (58%), Gaps = 18/482 (3%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 FI W V + F ++P G+ CQ+ ED++ A+ AA AA W R + Sbjct: 22 FIGGRWVAPVRGEYFDNISPINGKPFCQIPRSSAEDIELALDAAHAA---KDAWGRTSVT 78 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R +L ++AD I+ + LA ET DNGK + D+ + RY+AG G Sbjct: 79 ARSNILLKIADRIDANLEMLAVAETWDNGKAVRETLNADVPLSSDHFRYFAGCLRAQEGT 138 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 ID + +Y HEP+GV GQIIPWNFPLLM WKL PALA GN VV+K AEQTP + L Sbjct: 139 IGEIDENTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPASIL 198 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 + LI + P GV+N+V G+G AG A+A+ + + K+AFTGST +G +I A + N+ Sbjct: 199 VMMELIADL-LPAGVLNVVNGYGVEAGKALATSKRIAKIAFTGSTPVGSLIMKYA-AENI 256 Query: 280 KRVTLELGGKSPNIIMS------DADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYD 333 T+ELGGKSPNI + DA + AVE A A FFNQG+ C SR +QE IY+ Sbjct: 257 IPSTVELGGKSPNIFFADVLDQEDAFVSKAVEGAVLA-FFNQGEVCTCPSRLLIQESIYE 315 Query: 334 EFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGI--- 390 +F+ V R+ GNP D++ G Q + Q+ KIL YI GK EGA+++ GG + Sbjct: 316 KFIGMVVERSAQIKRGNPLDTEVMVGAQASQEQYDKILSYIQIGKDEGAEVITGGAVETM 375 Query: 391 AAD--RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAV 448 +AD GY+IQPT+ + M + +EEIFGPV+ + FK E + AN+ +GL A V Sbjct: 376 SADYCEGYYIQPTLLKGT-NNMRVFQEEIFGPVVSVTTFKDEAEALAIANDIEFGLGAGV 434 Query: 449 FTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTV 508 +T+D+++A + + +QAG VW NCY ++ A + FGGYK SG GRE + L Y + K + Sbjct: 435 WTRDMNRAYRMGRGIQAGRVWTNCYHMYPAHAAFGGYKKSGVGRETHKMMLDHYQQTKNL 494 Query: 509 TV 510 V Sbjct: 495 LV 496 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: 6 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: 506 Length adjustment: 35 Effective length of query: 482 Effective length of database: 471 Effective search space: 227022 Effective search space used: 227022 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