Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate CCNA_03695 CCNA_03695 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Caulo:CCNA_03695 Length = 506 Score = 341 bits (875), Expect = 3e-98 Identities = 201/485 (41%), Positives = 279/485 (57%), Gaps = 21/485 (4%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FI ++V + F SP +I ++ + + DI+ A++AA AA + W+ + R Sbjct: 22 FIGGQWVAPADGRYFDNSSPIHGRKICEIARSQAIDIERALDAAHAA-KAGWARTSAADR 80 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGSVI 142 ++L ++AD ++E+ LA E DNGK + + D+ L +FR AG +GS+ Sbjct: 81 SRILLRIADRMEENLAALATAETWDNGKPIRETLAADIPLAIDHFRYFAGCLRSQEGSIS 140 Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 E Y EP+GV GQIIPWNFPLLMA WKL P L G VLK AE TP S + Sbjct: 141 EIDHDTIAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPASIMVW 200 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 A +I + P GV+N+V+GFG AG P++S P+I K+AFTG T+TGR IM+ AA+ NL Sbjct: 201 AEMIGDL-LPAGVLNIVNGFGLEAGKPLASSPRIAKIAFTGETSTGRLIMQYAAQ-NLIP 258 Query: 263 VTLELGGKSPNIVFDDA-----DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317 VTLELGGKSPNI FDD D T N GEVC SR VQE IY+K + Sbjct: 259 VTLELGGKSPNIFFDDVAREDDDYLDKALEGFTMFALNQGEVCTCPSRALVQESIYEKFM 318 Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERF---GN 374 ++ G P T +GAQ S+ QL+KIL Y+DIG+ EGA ++ GG+R G Sbjct: 319 ERALKRVNAVVQGSPLDPATMIGAQASEEQLNKILGYMDIGRNEGAKLLAGGQRKILPGQ 378 Query: 375 --KGYFIKPTIFGDVKEDH---QIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGV 429 GY+++PT+F E H +I ++EIFGPV+ +T FKT EE + +AND+ +GL AGV Sbjct: 379 LADGYYVEPTVF----EGHNKMRIFQEEIFGPVLAVTTFKTEEEALEIANDTAFGLGAGV 434 Query: 430 HTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 + + + I +G +W N Y+ + FGGY QSG+GRE + LD+Y Q K + Sbjct: 435 WSRDANRCYRFGRGIEAGRVWTNCYHAYPAHAAFGGYKQSGVGRETHKMMLDHYQQTKNM 494 Query: 490 RIGLS 494 + S Sbjct: 495 LVSYS 499 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: 578 Number of extensions: 22 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