Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_012607209.1 AFE_RS08085 aldehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000021485.1:WP_012607209.1 Length = 506 Score = 248 bits (633), Expect = 3e-70 Identities = 160/478 (33%), Positives = 249/478 (52%), Gaps = 21/478 (4%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 +I G++V + DV+ P ++ AED A+DAA +W ERA Sbjct: 22 FIGGKWVAPVKGQYFDVITPINGKSYTQAARSTAEDIELALDAAHAIADKWGKTSPAERA 81 Query: 70 SWLRKISAGIRERASEIS-ALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128 + L K++ I ++ A V+ G I++ ++ D+ Y A R EG I Sbjct: 82 NILLKVADRIEANLELLAYAETVDNGKPIRETLNADIPLAVDHFRYFAGCVRAQEGGISD 141 Query: 129 SDRPGENILL--FKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAI 186 D EN + F LGV I+PWNFP + + K+APAL GN +V+KP+E TP + + Sbjct: 142 ID---ENTVAYHFHEPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAESTPISIL 198 Query: 187 AFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNIT 246 A+++ ++ LP GV N+V G G G LA + ++A ++ TGS + G I AA ++ Sbjct: 199 ILAELIADL-LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVIAQAAANSLI 257 Query: 247 KVCLELGGKAPAIVM------DDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQ 300 LELGGK+P I DD+ L+ A++ +V N G+VC C R +Q+ IYD+ Sbjct: 258 PATLELGGKSPNIFFADVMDKDDSFLDKAIEGLV-LFAFNQGEVCTCPSRALIQESIYDK 316 Query: 301 FVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKA--V 358 F+ R + ++A++ GNP + N + +G + L ++ + +EGA+V GG V Sbjct: 317 FMERCLDRIKAIKQGNPLDTNTM-IGAQASKEQLTKILSYLDLGKQEGAQVLIGGSQAIV 375 Query: 359 EGK---GYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSI 415 +G GYY PTL +M I EE FGPVL V F +A+S+AND+ YGL + + Sbjct: 376 DGDLDGGYYVQPTLFKG-HNKMRIFQEEIFGPVLAVTTFKDEAEALSIANDTLYGLGAGV 434 Query: 416 YTQNLNVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQ 473 +++N NVA + + +K G +IN + G+++SGIG K L Y QT+ Sbjct: 435 WSRNGNVAYRMGRAIKAGRVWINCYHAYPAHAAFGGYKESGIGRETHKVMLDHYQQTK 492 Lambda K H 0.318 0.135 0.392 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: 551 Number of extensions: 27 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: 479 Length of database: 506 Length adjustment: 34 Effective length of query: 445 Effective length of database: 472 Effective search space: 210040 Effective search space used: 210040 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