Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_104913141.1 C3B54_RS02765 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_002950575.1:WP_104913141.1 Length = 507 Score = 347 bits (889), Expect = e-100 Identities = 200/483 (41%), Positives = 275/483 (56%), Gaps = 15/483 (3%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 +I ++ + F +SP + ++ +EDID A++AA AA +W + R Sbjct: 23 WIGGQWTKPVKGNYFEDISPVNGKPFCEIARGTAEDIDAALDAAHAAA-PAWGKASTTER 81 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGSVI 142 VL K+AD+ID + + LA E DNGK + + D+ L A +FR G Sbjct: 82 AAVLNKIADVIDANVEMLAVAETWDNGKPIRETLNADIPLAADHFRYFVAAVRAQDGDFQ 141 Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 E Y EP+GV GQIIPWNFP+LMA+WKL P L G VLK AE TP S L L Sbjct: 142 EMDGDTTAYHYHEPLGVVGQIIPWNFPILMAAWKLAPALSAGNAVVLKPAEQTPASILVL 201 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 A LI + PPGV+N+V+GFG AG P++S P+I+K+AFTG T TGR I++ A+ +N+ Sbjct: 202 AELIGDI-LPPGVLNIVNGFGAEAGKPLASSPRIRKIAFTGETTTGRLILQYAS-ANIIP 259 Query: 263 VTLELGGKSPNIVFDDA-----DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317 TLELGGKSPNI FDD D Q +N GEVC SR +Q+ YD + Sbjct: 260 TTLELGGKSPNIFFDDVSQEKDDFYDKAQEGFVLFAFNQGEVCTCPSRALIQKSHYDSFL 319 Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG---- 373 + + G+P DT +GAQ S QL+KIL YIDIGK+EGAT++ GG+R Sbjct: 320 GDAVERTKKAIQGNPLDTDTQVGAQASNDQLEKILSYIDIGKQEGATLVCGGDRVDLGGD 379 Query: 374 -NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTT 432 GY+++P IF + ++ ++EIFGPVV +T F ++ I +AND+ YGL AGV + Sbjct: 380 LADGYYVEPAIF-EGNNKMRLFQEEIFGPVVAVTSFDDYDDAIQIANDTLYGLGAGVWSR 438 Query: 433 NLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIG 492 N +TA I +G +WVN Y+ + FGGY SGIGRE + AL +Y Q K + + Sbjct: 439 NGNTAYRAGRDIQAGRVWVNNYHAYPAGAAFGGYKSSGIGRENNKLALSHYQQTKNLLVS 498 Query: 493 LSQ 495 S+ Sbjct: 499 YSE 501 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: 642 Number of extensions: 33 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: 507 Length adjustment: 34 Effective length of query: 461 Effective length of database: 473 Effective search space: 218053 Effective search space used: 218053 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