Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_057687530.1 ABB28_RS16890 betaine-aldehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_001431535.1:WP_057687530.1 Length = 490 Score = 270 bits (689), Expect = 1e-76 Identities = 165/483 (34%), Positives = 261/483 (54%), Gaps = 9/483 (1%) Query: 2 SVPVQHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWE 61 ++P+Q +YI G+ V +NPAT VI+ + D +A+ +A Q W Sbjct: 3 TLPLQQ-LYIHGKLVDATSGKTFQSINPATGKVIAEVQIANQADVERAVASAAEGQKVWA 61 Query: 62 ALPAIERASWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEVAFTADYIDYMAEWAR 120 A+ A+ER+ LR+ +RER ++ L + GK + + V++ AD ++Y A A Sbjct: 62 AMTAMERSRILRRAVDLLRERNDALAQLETLDTGKALSETTTVDIVTGADVLEYYAGLAT 121 Query: 121 RYEGEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEF 180 EG + R + LGV GI WN+P + K APAL GN +V KPSE Sbjct: 122 AIEGNQVPL-RESSFFYTRREPLGVVAGIGAWNYPVQIALWKSAPALAAGNAMVFKPSEV 180 Query: 181 TPNNAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMAT 240 TP I AKI E G+P GVFN+V G G VGQ L +P + +S TG V G+K+MA+ Sbjct: 181 TPLTVIELAKIYTEAGVPDGVFNVVQGPGREVGQWLTEHPVIEKISFTGGVETGKKVMAS 240 Query: 241 AA-KNITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYD 299 AA ++ +V +ELGGK+P ++ DDA LE A V + +SGQVC RV+V + + Sbjct: 241 AASSSLKEVTMELGGKSPLVICDDAQLERAADIAVMANFFSSGQVCTNGTRVFVPRPMLA 300 Query: 300 QFVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGAR-VAFGGKAV 358 F + E ++ ++ G+P + GP+ + A ++ V + + EGAR + GG+A Sbjct: 301 AFEAAVVERVKRIRIGDPQDA-QTNFGPMTSFAHMDNVLRLIETGKREGARLLTGGGRAT 359 Query: 359 EG---KGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSI 415 +G KG Y PT+ D R +M+I+ EE FGPV+ ++A+D E+ I+ AND+ +GL + + Sbjct: 360 DGALAKGAYVLPTVFSDCRDDMTIVREEIFGPVMSILAYDDEEEVIARANDTHFGLAAGV 419 Query: 416 YTQNLNVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475 + ++ A + I L+ G +IN + G+++SG+G +G L Y + + V Sbjct: 420 VSNDIARAHRIIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGISTLAHYTRIKSV 479 Query: 476 YLQ 478 ++ Sbjct: 480 QVE 482 Lambda K H 0.318 0.135 0.392 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: 543 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 479 Length of database: 490 Length adjustment: 34 Effective length of query: 445 Effective length of database: 456 Effective search space: 202920 Effective search space used: 202920 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 (21.7 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