Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_022949182.1 H035_RS0111795 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000421465.1:WP_022949182.1 Length = 506 Score = 344 bits (883), Expect = 4e-99 Identities = 200/475 (42%), Positives = 277/475 (58%), Gaps = 15/475 (3%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 +I ++ + + F ++P T +V + +EDI+ A++AA AA +W + P R Sbjct: 22 YIGGHWIAPVNGQYFENITPVTGTPFCEVARSTAEDIEKALDAAHAA-KDAWGKTSPAGR 80 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGSVI 142 +L K+AD +++ + LA E DNGK + + D+ L A +FR A + SV Sbjct: 81 ADLLLKIADRMEQQLEMLAVAETWDNGKPIRETLAADIPLAADHFRYFASAIRTQESSVC 140 Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 E Y EP+GV GQIIPWNFPLLMASWKL P L G VLK AE TP S L L Sbjct: 141 EIDADTIAYHFHEPLGVVGQIIPWNFPLLMASWKLAPALAAGNCVVLKPAEQTPASILVL 200 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 LI + PPGVVNVV+GFG AG P++ +I KVAFTG T TGR IM+ A++ NL Sbjct: 201 MELIGDL-IPPGVVNVVNGFGVEAGKPLARSSRIAKVAFTGETTTGRLIMQYASQ-NLIP 258 Query: 263 VTLELGGKSPNIVFDDADVKST--IQHLVTGIF---YNTGEVCCAGSRIYVQEGIYDKIV 317 VTLELGGKSPN+ F+D K + + G N GEVC SR +Q IYD + Sbjct: 259 VTLELGGKSPNLFFEDVTAKQDTFVDKALEGFASFALNQGEVCTCPSRALLQASIYDDFI 318 Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKG- 376 ++++ G+P +T +GAQ S Q++KIL YIDI ++EG + GGER +G Sbjct: 319 HRALERVKAIRQGNPLDTETMIGAQASAEQMEKILSYIDIARQEGTECLIGGERAQLQGE 378 Query: 377 ----YFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTT 432 Y+I+PTIF + ++ ++EIFGPV+ +T F+ EE + +AND+ YGL AGV T Sbjct: 379 LAGGYYIQPTIFKGHNQ-MRVFQEEIFGPVLAVTTFRDEEEALEIANDTLYGLGAGVWTR 437 Query: 433 NLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVK 487 +++TA + I +G +W N Y+ + FGGY QSGIGRE + LD+Y Q K Sbjct: 438 DMNTAYRMGRGIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRETHKMMLDHYQQTK 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: 571 Number of extensions: 25 Number of successful extensions: 8 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 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