Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_041099671.1 SUTH_RS12545 methylmalonate-semialdehyde dehydrogenase (CoA acylating)
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_000828635.1:WP_041099671.1 Length = 505 Score = 180 bits (456), Expect = 1e-49 Identities = 133/420 (31%), Positives = 201/420 (47%), Gaps = 11/420 (2%) Query: 24 EVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAGHLRRIAAKIRADAG 83 EVFNPA G + +V A+ +V+RA+AAARAA DW RA + + + + Sbjct: 30 EVFNPAEGRVARQVALATRADVDRAVAAARAAFADWGSAAPQRRARVMFKFRDLVDQYST 89 Query: 84 RIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEIIASDRPGENIFLFRKPLG 143 IA+ ++ E GK A EV + +++ + L+G+ G + + R PLG Sbjct: 90 DIAKLLSAEHGKTLPDALGEVQRGLEVIEFACGIPQLLKGQHSHGIGGGIDHWNQRMPLG 149 Query: 144 VVAGILPWNFPFFLIARKMAP-ALLTGNTIVVKPSEETPNNCFEFARLVAETDLPRGVFN 202 V AGI P+NFP F++ MAP AL GNT ++KPSE P+ A L+ E LP G FN Sbjct: 150 VTAGITPFNFP-FMVPMWMAPMALACGNTFILKPSERDPSPSLFAAELLREAGLPAGAFN 208 Query: 203 VVCGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLELGGKAPAIVLADA 262 V+ G + AL HP V +SF GS I A + ++ G K +V+ DA Sbjct: 209 VIQGDKEAVDALLEHPFVSAVSFVGSTPIAKYIQAHGIAHGKRVQALGGAKNHMVVMPDA 268 Query: 263 DLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAATRYGDPLAEPEVE 322 DL+ A A+ + ++G+ C A+ + R+ A + G A VE Sbjct: 269 DLDGAADALIGAAYGSAGERCMAISVAVAVGSCADDLVARVLARAKKLKVGAGDA-ANVE 327 Query: 323 MGPLINRLGLEKIDAKVRTALAQGATLVTG------GAIAERPGHHYQPTVLTGCRADTR 376 MGPL+ + +K+ + + +GA LV G +A+ G PT+ + Sbjct: 328 MGPLVTAVHRDKVAGYIAAGVQEGAKLVLDGREGLTGELAQ--GFFINPTLFDNVTPNMS 385 Query: 377 IMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALRELDFGETYIN 436 I +EEIFGPVL + V A+ L N + + FTRD A +++++ G IN Sbjct: 386 IYQEEIFGPVLCVVRVPTFAAAVELINRHTFANGVACFTRDGGTAQAFIQKIEVGMVGIN 445 Lambda K H 0.320 0.136 0.395 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: 526 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: 477 Length of database: 505 Length adjustment: 34 Effective length of query: 443 Effective length of database: 471 Effective search space: 208653 Effective search space used: 208653 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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