Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate YP_004134387.1 Mesci_6218 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000185905.1:YP_004134387.1 Length = 492 Score = 360 bits (925), Expect = e-104 Identities = 191/461 (41%), Positives = 278/461 (60%), Gaps = 7/461 (1%) Query: 37 TFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WSTSDPQVRMKVLYKLADLID 95 TF + P T + + +D AV +A AAF S W+ R K+L ++ADLI Sbjct: 20 TFESHDPFTGRPWALIPRGGAAQVDAAVASAKAAFRSKEWAGITATARGKLLVRMADLIA 79 Query: 96 EHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIETGDTH-FNYTRR 154 ++A+ +A IE DNGK L + +FR G DKI+G+V+ F +TR Sbjct: 80 DNAERIAAIETRDNGKLLTEMTAQLRYIPEWFRYFGGLADKIEGAVLPIDKAGMFAFTRH 139 Query: 155 EPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPG 214 EP+GV I+PWN PLL+ +WKL P+L G T V+K +E S L L +AG PPG Sbjct: 140 EPLGVIAAIVPWNSPLLLLTWKLAPLLAAGNTVVIKPSEHASASTLEFVKLFAQAGFPPG 199 Query: 215 VVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNI 274 VVN V+G G P+ +HP + K+AFTG G + +AAAE LK VTLELGGKS NI Sbjct: 200 VVNTVTGMPLDVGVPLVAHPDVAKIAFTGGEPGGIAVYRAAAEQ-LKTVTLELGGKSANI 258 Query: 275 VFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFK 334 VFDDAD++S + ++GIF +G+ C AGSR+ V I+D+ V A S ++G+P Sbjct: 259 VFDDADIESAVNGAISGIFAASGQTCIAGSRLLVHRKIHDRFVEGVITLAASARLGNPAL 318 Query: 335 EDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN----KGYFIKPTIFGDVKED 390 +T +G T+Q Q +K+L Y+ I ++EGA + GG + + +G+F++PTIF V Sbjct: 319 AETQVGPITTQAQREKVLSYLGIARREGALCVLGGGKPASSELAEGWFVEPTIFTGVNNT 378 Query: 391 HQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIW 450 +I R+E+FGP++++ F +E A+ANDS YGLAAG+ T+++ A+ + + +G +W Sbjct: 379 MRIAREEVFGPILSVIPFDDEDEAFAIANDSPYGLAAGIWTSDMGRALRGAAVMEAGMVW 438 Query: 451 VNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRI 491 +N+Y M PFGGY +SGIGRE G+EA+++Y Q K V I Sbjct: 439 INSYRAVSYMAPFGGYKRSGIGRESGQEAINSYLQTKTVWI 479 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: 585 Number of extensions: 20 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: 492 Length adjustment: 34 Effective length of query: 461 Effective length of database: 458 Effective search space: 211138 Effective search space used: 211138 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