Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_012591341.1 MSIL_RS11965 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000021745.1:WP_012591341.1 Length = 506 Score = 341 bits (874), Expect = 4e-98 Identities = 197/485 (40%), Positives = 276/485 (56%), Gaps = 21/485 (4%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FI ++ ++F +SP + + + +ED++ A++AA AA SW + P R Sbjct: 22 FIGGKWTPPVKGQSFENISPIDGNVVCTIARSTAEDVELALDAAHAA-RESWGNASPATR 80 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGSVI 142 VL ++AD I+E D LA +E +DNGK + +K D+ L +FR AG +GS+ Sbjct: 81 SLVLLRIADRIEEKLDVLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGVLRAQEGSIS 140 Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 E Y EP+GV QIIPWNFPLLMA WK+ P L G V+K AE TP+S + L Sbjct: 141 EIDHDTIAYHFHEPLGVVAQIIPWNFPLLMAVWKIAPALAAGNCIVMKPAEQTPMSIMVL 200 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 +I + PPGV+NV++GFG G P++ P+I KVAFTG T TGR IM+ A+E N+ Sbjct: 201 MDVIGDL-LPPGVLNVINGFGVECGKPLAQSPRIAKVAFTGETTTGRLIMQYASE-NIIP 258 Query: 263 VTLELGGKSPNIVFDDA-----DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317 VTLELGGKSPNI F+D D N GEVC SR V E IYD+ + Sbjct: 259 VTLELGGKSPNIFFEDVADEDDDYFDKALEGFAMFALNQGEVCTCPSRALVHEKIYDRFM 318 Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG---- 373 ++K G+P T +GAQ S QL+KIL Y+DIG++EGA V+ GG R Sbjct: 319 ERAIKRVNAIKQGNPLDPSTMIGAQASNDQLEKILSYMDIGRQEGAKVLAGGGRADLGPE 378 Query: 374 -NKGYFIKPTIFGDVKEDH---QIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGV 429 G++++PT+ E H +I ++EIFGPV+++T FK + + +AND+ YGL +GV Sbjct: 379 LANGFYVQPTVL----EGHNKMRIFQEEIFGPVLSVTTFKDDAQALEIANDTLYGLGSGV 434 Query: 430 HTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 T N + A I +G +W N Y+ + FGGY +SGIGRE + LD+Y Q K + Sbjct: 435 WTRNGTRAYRFGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGIGRENHKMMLDHYQQTKNM 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: 596 Number of extensions: 26 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