Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_123809403.1 BTUS_RS06175 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000092905.1:WP_123809403.1 Length = 501 Score = 380 bits (977), Expect = e-110 Identities = 200/472 (42%), Positives = 287/472 (60%), Gaps = 6/472 (1%) Query: 23 LFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WSTSDPQ 81 + I+ + V+ + + T +P+T E + +V + ED+D AV+AA A WS Sbjct: 17 MLIDGQHVEGSTGEWMDTYNPATGEVLAKVAKGTREDVDRAVKAARRALEEGKWSRWTAA 76 Query: 82 VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSV 141 R +VL ++A ++ E D L IE L++GK+L +KG V F A + G Sbjct: 77 RRAQVLNRIAGIMRERYDELCRIEVLNSGKTLSAAKGQVMQAIEDFELYAAAAMMLDGRT 136 Query: 142 IETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALY 201 F+YT +EP+GVC QI+PWN+PL+MA+WKL P L GCT VLK A TP++AL Sbjct: 137 KPVPHGFFHYTVKEPVGVCAQIVPWNYPLMMAAWKLAPALAAGCTVVLKPASLTPITALI 196 Query: 202 LASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLK 261 L + +EAG P GVVN++ G G GA + HP + KVAFTG T TG+ IM A+E+ LK Sbjct: 197 LGDICQEAGVPEGVVNILVGGGSDVGAYLVEHPGVDKVAFTGETGTGKDIMARASET-LK 255 Query: 262 KVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFK 321 +VTLELGGKSPN++F+DAD+ + + + GI+YNTG+ C A SR++V E IY++ + F Sbjct: 256 RVTLELGGKSPNVIFEDADLDAAVNGSLFGIYYNTGQSCEARSRLFVHESIYEEFLDRFV 315 Query: 322 NAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN----KGY 377 A LKIGDP +T +GA S+ Q I Y+ +G +EGA V GG R KG+ Sbjct: 316 EKASRLKIGDPLDPNTHIGAIISENQEKVIDSYVKLGVQEGARVALGGRRPEGQEFAKGH 375 Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437 + PT+ DV ++ ++EIFGPV+ T+FK E + LAND+ YGLAA + T + + A Sbjct: 376 WYLPTLLADVDNRTRVAQEEIFGPVLVATRFKDEAEAVRLANDTRYGLAASLWTRDFARA 435 Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 V+ K+ +G + +N P +PFGGY QSG GRE+ E+L+ YT+ K+V Sbjct: 436 HRVAGKLKAGVVLINNPFSAFPGLPFGGYKQSGFGRELAAESLELYTETKSV 487 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: 634 Number of extensions: 18 Number of successful extensions: 4 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: 501 Length adjustment: 34 Effective length of query: 461 Effective length of database: 467 Effective search space: 215287 Effective search space used: 215287 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