Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_008509302.1 BIBO1_RS15485 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000182725.1:WP_008509302.1 Length = 492 Score = 342 bits (876), Expect = 2e-98 Identities = 193/479 (40%), Positives = 275/479 (57%), Gaps = 6/479 (1%) Query: 20 PTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHS-SWSTS 78 P LFIN + + +SP ++T + A + D+D A AA +F +W+ + Sbjct: 15 PQSLFINGRWQPAADGNVMAVISPIDGTQLTTIAAATAIDVDRAAAAARQSFEKGTWAKA 74 Query: 79 DPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSL-MCSKGDVALTAAYFRSCAGWTDKI 137 P R KVL K+A+LI+ +A LA + DNG + M K + A FR A DK+ Sbjct: 75 APAERRKVLLKIAELIERNALELAVLGVRDNGTEISMALKAEPGSAANSFRYYAEAIDKV 134 Query: 138 KGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPL 197 G + T + R P+GV G I+PWNFP+++ +WK+ P L G + VLK AE L Sbjct: 135 YGEIAPTAENILGLVHRAPVGVVGAIVPWNFPMMIGAWKIAPALAAGNSIVLKPAEGASL 194 Query: 198 SALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAE 257 S L LA L EAG P GV+NVV+G GP G + HP I +AFTGS GR +++ +A Sbjct: 195 SLLRLAELCAEAGLPEGVLNVVTGAGPVTGEALGLHPDIDVLAFTGSGFVGRKLLEYSAR 254 Query: 258 SNLKKVTLELGGKSPNIVFDDA-DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316 SNLK+V LELGGKSPNIVF DA D+ + GIF N+G+VC AGSR+ V+ I + Sbjct: 255 SNLKRVYLELGGKSPNIVFADAPDLAQAAKVSAYGIFRNSGQVCVAGSRLLVERSIAGEF 314 Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNK- 375 + A ++K+GDP T GA +S++QL K L + + EGA + TGG+R + Sbjct: 315 AEKVSAIAAAIKVGDPLNLATEAGAISSEVQLRKNLGFAEQALSEGAGLRTGGKRILEET 374 Query: 376 -GYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNL 434 G++++PT+F +V+ + R+E+FGP+++I F E+ + +ANDS+YGLA+ V T+NL Sbjct: 375 GGFYMQPTVF-NVEPGMTLAREEVFGPILSIIPFDNEEDALKIANDSDYGLASAVWTSNL 433 Query: 435 STAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493 S A + I +G + VNTY VP GG QSG G + ALD Y +K I L Sbjct: 434 SRAHRMVRGIRAGVVHVNTYGGADNTVPLGGVKQSGNGHDKSLHALDKYIDLKTAWIQL 492 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: 540 Number of extensions: 28 Number of successful extensions: 5 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