Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_046010388.1 OLEAN_RS18035 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000967895.1:WP_046010388.1 Length = 491 Score = 345 bits (885), Expect = 2e-99 Identities = 199/476 (41%), Positives = 274/476 (57%), Gaps = 10/476 (2%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FIN E++ + S KTF ++P+T QV E E I A ++ +WS R Sbjct: 13 FINGEYLDNASGKTFDVINPATGVLAYQV-EVADEKIRSAAIKSSQQGFETWSAMTGFER 71 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVALTAAYFRSCAGWTDKIKGSVI 142 ++L K +L+ E D LA IE +D GK S DV A I+G+ Sbjct: 72 NRILLKAVELLRERNDELAKIEVIDTGKPWQEASVVDVVTGTDSIEYFAALALSIEGTQQ 131 Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 + G F YTRREP+GVC I WN+PL +A WK P L G + + K +E TP AL L Sbjct: 132 DLGGD-FYYTRREPLGVCAGIGAWNYPLQIACWKAAPALACGNSMIFKPSEETPHGALKL 190 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 A + EAG P GV NVV G G GA +++H I KV+FTG TG+ +M AAA +NLK Sbjct: 191 AEIFFEAGVPAGVFNVVQGDGEV-GAWLTTHNDIAKVSFTGEVGTGKKVMAAAA-TNLKD 248 Query: 263 VTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKN 322 VT+ELGGKSP IVF DAD+ + + G FY GEVC +RI+VQ+ IY K +++ K Sbjct: 249 VTMELGGKSPLIVFSDADIDDAVSAAMLGNFYTQGEVCTNATRIFVQKDIYPKFITQLKE 308 Query: 323 AAE-SLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG----NKGY 377 E ++ GDP +T GA S+ +L YI+ G +EGA ++TGG+ GY Sbjct: 309 RTEKNIIAGDPMDPETNFGALISKNHQQLVLSYIEKGIQEGAFLLTGGQALQPPGVEGGY 368 Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437 F+ PTIF D +D IV++EIFGPV+++ F++ EEVI AN +E+GLAAGV T ++ A Sbjct: 369 FVAPTIFTDCTDDMTIVKEEIFGPVMSVLTFESEEEVIKRANGTEFGLAAGVFTNDIRRA 428 Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493 V ++ +G W+N Y +P GGY SGIGRE G ++ YTQ+K+V +G+ Sbjct: 429 HRVVKQLEAGICWINAYGASPAEMPVGGYKLSGIGRENGSSTMNQYTQIKSVYVGM 484 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: 630 Number of extensions: 35 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: 491 Length adjustment: 34 Effective length of query: 461 Effective length of database: 457 Effective search space: 210677 Effective search space used: 210677 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