Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000746085.1:WP_036262823.1 Length = 506 Score = 346 bits (887), Expect = 1e-99 Identities = 203/485 (41%), Positives = 280/485 (57%), Gaps = 21/485 (4%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FI ++V + +TF +SP I V + +ED++ A++AA AA +W + P R Sbjct: 22 FIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAA-RGAWGRTSPAER 80 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGSVI 142 L ++AD I++ D LA +E +DNGK + +K D+ L +FR AG +G + Sbjct: 81 SLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEGGIS 140 Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 E Y EP+GV QIIPWNFPLLMA WKL P L G +LK AE TP+S + L Sbjct: 141 EIDHDTVAYHFHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQTPMSVMVL 200 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 +I + PPGV+NV++GFG AG P++ + +I KVAFTG T TGR IM+ A+E N+ Sbjct: 201 VDMIGDL-LPPGVLNVINGFGVEAGKPLAQNKRIAKVAFTGETTTGRLIMQYASE-NIIP 258 Query: 263 VTLELGGKSPNIVF-----DDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317 VTLELGGKSPNI F +D D + N GEVC SR VQE IYD+ + Sbjct: 259 VTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFALNQGEVCTCPSRALVQEKIYDRFM 318 Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG---- 373 + +K G+P T +GAQ S QL+KIL Y+DIG++EGA V+ GG R Sbjct: 319 ERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAGGGRADVGPE 378 Query: 374 -NKGYFIKPTIFGDVKEDH---QIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGV 429 G++++PTI E H +I ++EIFGPV+++T FK EE + +AND+ YGL AGV Sbjct: 379 LAGGFYVQPTIL----EGHNKMRIFQEEIFGPVLSVTSFKDDEEALEIANDTLYGLGAGV 434 Query: 430 HTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 T N + A I +G +W N Y+ + FGGY QSGIGRE + LD+Y + K + Sbjct: 435 WTRNGTRAYRFGRAIEAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQKTKNM 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: 581 Number of extensions: 25 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 Apr 09 2024. 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