Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Dino:3607686 Length = 506 Score = 343 bits (879), Expect = 1e-98 Identities = 199/476 (41%), Positives = 281/476 (59%), Gaps = 17/476 (3%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FI +FV + F V+P T E + Q+ + + D++ A++AA AA +W + R Sbjct: 22 FIGGKFVPPVEGRYFDNVTPITGEVVGQIARSSAADVELALDAAHAA-KDAWGKTSVTER 80 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVALTAAYFRSCAGWTDKIKGSVI 142 ++ K+AD I+E+ D +A E DNGK + + D+ L +FR AG +GS+ Sbjct: 81 ANIVLKIADRIEENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLRGQEGSMS 140 Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 E + Y EP+GV GQIIPWNF +LMA+WKL P + G VLK AE TP + + L Sbjct: 141 EIDNDTVAYHFHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQTPAAIMVL 200 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 LI + P GV+N+V+G+G GA +++ +I K+AFTGSTATGR IM+AA NL Sbjct: 201 VELISDL-LPAGVLNIVNGYGGEVGAALATSDRIAKIAFTGSTATGRKIMEAATV-NLIP 258 Query: 263 VTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316 VTLELGGKSPNI F DDA + ++ V F N GEVC SR + E IY++ Sbjct: 259 VTLELGGKSPNIFFKDVMAEDDAFLDKAVEGFVLFAF-NQGEVCTCPSRALIHEDIYEEF 317 Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG--- 373 ++ +++ GDP K +T +GAQ S+ Q DKIL Y IG +EGA V+TGG+ Sbjct: 318 IARAIARVKAIVQGDPRKMETMVGAQASKEQKDKILSYFQIGVEEGAEVLTGGKVADVSD 377 Query: 374 --NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHT 431 G++I+PTI + ++ ++EIFGPVV++T FKT EE + LAND+ YGL AGV + Sbjct: 378 DLKDGFYIEPTILKGHNK-MRVFQEEIFGPVVSVTTFKTEEEALELANDTMYGLGAGVWS 436 Query: 432 TNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVK 487 + +T + +G +WVN Y+ + FGGY QSGIGRE + LD+Y Q K Sbjct: 437 RDQNTCYRFGRGVQAGRVWVNNYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTK 492 Lambda K H 0.316 0.133 0.389 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: 614 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: 495 Length of database: 506 Length adjustment: 34 Effective length of query: 461 Effective length of database: 472 Effective search space: 217592 Effective search space used: 217592 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: 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