Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_019894527.1 A377_RS0102365 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_000384235.1:WP_019894527.1 Length = 451 Score = 214 bits (544), Expect = 6e-60 Identities = 141/453 (31%), Positives = 221/453 (48%), Gaps = 8/453 (1%) Query: 27 NPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIE-RAGHLRRIAAKIRADAGRI 85 NPA GA + +E+ + A WA++ +E R L+R+ + D + Sbjct: 2 NPATGAHNAEFDLWDEATIEQTVTDAGMLWTQWAKEVPLEHRCQLLKRLGDVLLDDREPL 61 Query: 86 ARTITLEQGKIASLAEVEVNFTADYLDYMAEWARR-LEGEIIASDRPGENIFLFRKPLGV 144 A ITLE GK+ A EV+ A DY AE A L E + S G +L KPLGV Sbjct: 62 AELITLEMGKLYKEALAEVDKCAQLCDYYAEKAPEFLADEPLESG--GSRSYLTYKPLGV 119 Query: 145 VAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFARLVAETDLPRGVF-NV 203 V G++PWNFP + + R P + GN +VK + P + + P GV+ ++ Sbjct: 120 VLGVMPWNFPLWQVFRFAVPTITAGNIALVKHASNVPQCALAIEEVFRKAGYPEGVYQHM 179 Query: 204 VCGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLELGGKAPAIVLADAD 263 + A QV + + + +S TGS G ++ A A L K LELGG ++L D D Sbjct: 180 LISASQVEPVIRNKV-IKAVSLTGSEPAGRKVAAVAGSELKKCVLELGGSDAFVILDDVD 238 Query: 264 LELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAAT-RYGDPLAEPEVE 322 + V R N GQ C A+R V + F+ + A+ + + GDP+ + + Sbjct: 239 MATVVAGAVKGRFQNCGQSCIAAKRFIVDAYRHDEFVAQFKEAVESQLQAGDPM-DADTT 297 Query: 323 MGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVLTGCRADTRIMREEI 382 + P+ + LE++DA+V+ ++ GATLVTGG + PG +Y PT+LT + EE+ Sbjct: 298 LAPMARQDLLEELDAQVQKSVQMGATLVTGGYQLDCPGSYYAPTILTDVTSAMPAYHEEM 357 Query: 383 FGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALRELDFGETYINREHFEA 442 FGPV + + A+ LAN ++GL SV+ +D R ++ G +Y+N F Sbjct: 358 FGPVATVLKASEPAHAVGLANATDFGLGGSVWGKDAATCETIARNIESGASYVNSITFSD 417 Query: 443 MQGFHAGVRKSGIGGADGKHGLYEYTHTHVVYL 475 + G+R SG G + G+ E+T+ +Y+ Sbjct: 418 PRLPFGGIRHSGYGRELSREGIREFTNIKTIYI 450 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: 455 Number of extensions: 24 Number of successful extensions: 3 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: 451 Length adjustment: 33 Effective length of query: 444 Effective length of database: 418 Effective search space: 185592 Effective search space used: 185592 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: 51 (24.3 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