Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_090447986.1 BLS63_RS22155 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_900100495.1:WP_090447986.1 Length = 502 Score = 390 bits (1001), Expect = e-113 Identities = 206/475 (43%), Positives = 297/475 (62%), Gaps = 5/475 (1%) Query: 23 LFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHS-SWSTSDPQ 81 +FI ++ + + + PSTE +T++ D+D AV+AA F +W P Sbjct: 28 MFIGGAWLDASDGGSAEVIEPSTEGLLTRIPMGTVADLDRAVQAARGQFDGGAWRQLKPL 87 Query: 82 VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGS 140 R ++L++LADL++ +A LA IE++D GKSL+ + D+ + FR AGW KI G Sbjct: 88 QRERLLHRLADLLEANAAELAEIESIDMGKSLVQAGAVDIQGSIDTFRYFAGWASKIHGR 147 Query: 141 VIETG--DTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLS 198 +E + YTR+EP+GV G I+PWNFPL +WKLG L GC+ V+K AE T LS Sbjct: 148 SVEPSLPGNYLAYTRKEPVGVVGVIVPWNFPLQTLAWKLGAALAVGCSVVVKPAELTSLS 207 Query: 199 ALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAES 258 AL A L+++AG P GVVN+V+G G GA ++SHP I K++FTGST G + KAA E Sbjct: 208 ALRFAELVQQAGIPDGVVNIVTGRGSVVGAAMASHPGIDKLSFTGSTPVGCSVGKAALEQ 267 Query: 259 NLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVS 318 +K++TLELGGKSP IVF DAD+K+ Q + G+F+N+G+VC AG+R Y+Q IY + + Sbjct: 268 -MKRLTLELGGKSPVIVFADADLKAAAQAVANGVFFNSGQVCDAGTRAYIQRSIYPQFLR 326 Query: 319 EFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYF 378 E SLKI D F+ S+ Q +++L YI GK EGA + GGE GYF Sbjct: 327 ELAAYTASLKIAPGLDPDCFISPLVSRQQQERVLGYIAAGKAEGAELYYGGEAVEGPGYF 386 Query: 379 IKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAI 438 ++PTIF + + D +IV++EIFGPV+ F EE +ALANDS +GLAA +++ +L Sbjct: 387 VQPTIFANCRNDMRIVQEEIFGPVLVTAPFDDEEEALALANDSPFGLAAALYSNDLGRVH 446 Query: 439 SVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493 S+ ++ +G+++VN ++ P +PFGGY QSG G+++G E LD + KAV I L Sbjct: 447 SLIPRLRAGSVYVNAHSTIDPAMPFGGYKQSGYGKDLGAEQLDYLLETKAVWITL 501 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: 565 Number of extensions: 25 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: 502 Length adjustment: 34 Effective length of query: 461 Effective length of database: 468 Effective search space: 215748 Effective search space used: 215748 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