Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_028999950.1 H537_RS0124485 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000430725.1:WP_028999950.1 Length = 503 Score = 387 bits (995), Expect = e-112 Identities = 204/478 (42%), Positives = 295/478 (61%), Gaps = 10/478 (2%) Query: 23 LFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WSTSDPQ 81 L+I+ +V + S T + P+T ++I+ + E +D+D AV AA AF W Sbjct: 28 LYIDGRWVDASSGATRPVLDPATGQQISVMAEGNVQDVDAAVRAARKAFDGGEWRRLSTN 87 Query: 82 VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGD-VALTAAYFRSCAGWTDKIKGS 140 R ++++K+ +LID HA LA +E LD G K V L A +FR AGW +K+ G Sbjct: 88 ERSRIVWKIGELIDVHAQELAELEVLDEGAPFAVVKDFWVRLAADHFRYYAGWPNKLNGD 147 Query: 141 VIET---GDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPL 197 I G+ H YT REP+GV GQIIPWN P LMA+WKL P L GCT VLK AE TPL Sbjct: 148 TIPVNMPGEWHA-YTVREPVGVVGQIIPWNVPFLMAAWKLAPALAAGCTVVLKPAEDTPL 206 Query: 198 SALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAE 257 +AL LA L +EAG P GVVNV++G G AGA + +HP I K+AFTGST TG+ I++AAA+ Sbjct: 207 TALRLAELCREAGVPDGVVNVITG-GGDAGAALVAHPDIDKIAFTGSTETGKAIVRAAAQ 265 Query: 258 SNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317 NLK+V+LELGGKSP VF DAD+ + I + + N G+ C AGSR+Y+ E +YD+++ Sbjct: 266 -NLKRVSLELGGKSPVFVFPDADLANVIPGVAQAVLLNAGQACTAGSRLYIHEDVYDRVI 324 Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGY 377 A SLK+G + +G S Q ++ + + G EGA ++ GG++ G++GY Sbjct: 325 DGVAQYASSLKLGHGLDPASQLGPLISARQFSRVSRMLQTGLDEGAQLVVGGQQHGDRGY 384 Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKF--KTVEEVIALANDSEYGLAAGVHTTNLS 435 F++PT+ V+ + RDEIFGPV+ K + ++ + AN++ YGL A + T ++ Sbjct: 385 FMQPTLLTGVRPGMSVYRDEIFGPVIAAMKISGENLDALAREANNTTYGLGASIWTNDVK 444 Query: 436 TAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493 A ++ +I +G IW+N ++ PFGG+ QSG GREMG+ ++ YT++K+V I L Sbjct: 445 RAHQLAARIRAGVIWINAHHSIDAAFPFGGFKQSGWGREMGKPGIELYTELKSVAINL 502 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: 589 Number of extensions: 29 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: 503 Length adjustment: 34 Effective length of query: 461 Effective length of database: 469 Effective search space: 216209 Effective search space used: 216209 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