Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate WP_036258213.1 DL86_RS03210 aldehyde dehydrogenase
Query= CharProtDB::CH_018413 (862 letters) >NCBI__GCF_000746085.1:WP_036258213.1 Length = 477 Score = 264 bits (674), Expect = 1e-74 Identities = 161/448 (35%), Positives = 246/448 (54%), Gaps = 16/448 (3%) Query: 8 ELDEKLKVIKEAQKKFSCYSQEMVDEIFRNAAMAAIDARIELAKAAVLETGMGLVEDKVI 67 E++ + + AQ Y+QE D + +R LAK AV E G G V+DKV Sbjct: 20 EIEAMVGRARVAQAAIEHYAQEEADALVTAVGWQVYKSREALAKLAVEEGGFGNVQDKVA 79 Query: 68 KNHFAGEYI--YNKYKDEKTCGIIERNEPYGITKIAEPIGVVAAIIPVTNPTSTTIFKSL 125 K FA + KTCG++E + G+ KIA+P+GV+AA+IP T P +T K+L Sbjct: 80 K--FANRVMGTLTDMASIKTCGVVEEDPARGLIKIAKPVGVIAALIPTTGPDATPPVKAL 137 Query: 126 ISLKTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIGWIDEPSIELTQYLMQKA 185 +LK RN I +PHPR +K++ + + ++ GAP ++I I+ PSI T+ LM+ + Sbjct: 138 GALKARNAIIIAPHPRTRKTSAAVVEVMRKGCLQVGAPADLIQVIERPSIAKTELLMRMS 197 Query: 186 DITLATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMAVSSIILSKTYDNGVICA 245 D+ +ATGG +VK+AYSSG PA GVG GN ++DE+A + A I +KT+D C Sbjct: 198 DLIVATGGAGMVKAAYSSGTPAYGVGVGNAVHVVDETADLDDAAQMIANAKTFDYATSCL 257 Query: 246 SEQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIFKDGSVNP--KIVGQSAYTIA 303 ++ SV SIY +K + ERG ++ E +++ ++ G P ++V +SA IA Sbjct: 258 ADNSVAAHSSIYEALKRKLVERGGHVCAPAEKARLQAAMWPKGEHIPSIEVVAKSAARIA 317 Query: 304 AMAGIKVPKTTRILIGEVTSLGEEEPFAHEKLSPVLAMYE-ADNFDDALKKAVTLINLGG 362 +AGI++ L+ E +GE PF+ EKLS VLA+Y + D A+ + + G Sbjct: 318 ELAGIELAPDRTFLMVEEDGVGEAHPFSGEKLSVVLALYRYSGGIDGAVDLVNRITSYQG 377 Query: 363 LGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLGCGFW 422 GHT GI++ D + + +T R VN ++GA G + N +P + +L CG W Sbjct: 378 AGHTCGIHSSR---DDHVRTLAFGTRTARVIVNQSLNEGA-GSVRN-GLPYTLSLSCGTW 432 Query: 423 GGNSVSENVGPKHLLNI----KTVAERR 446 GGN +ENV +H +N+ + VA RR Sbjct: 433 GGNITTENVNVRHFVNLTWVSRPVAPRR 460 Lambda K H 0.317 0.134 0.378 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: 838 Number of extensions: 35 Number of successful extensions: 4 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: 862 Length of database: 477 Length adjustment: 38 Effective length of query: 824 Effective length of database: 439 Effective search space: 361736 Effective search space used: 361736 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 (21.6 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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