Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_024851875.1 N745_RS0109415 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_000526715.1:WP_024851875.1 Length = 456 Score = 236 bits (601), Expect = 2e-66 Identities = 151/454 (33%), Positives = 232/454 (51%), Gaps = 8/454 (1%) Query: 27 NPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIE-RAGHLRRIAAKIRADAGRI 85 NPA G L++ ++ + DWA+ +E R L+R+A +R D + Sbjct: 7 NPATGELIAEFDTWDQATLDDVVTQVGYGFGDWAKLTTMEERCLLLKRLADVLRDDQDVL 66 Query: 86 ARTITLEQGKIASLAEVEVNFTADYLDYMAEWA-RRLEGEIIASDRPGENIFLFRKPLGV 144 A ITLE GK+ S A+ EV A DY AE A +L EII S ++ PLGV Sbjct: 67 AELITLEMGKLYSEAQAEVEKCATLCDYYAEHAPAQLADEIIESG--ASKSYVAYLPLGV 124 Query: 145 VAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFARLVAETDLPRGVF-NV 203 V G++PWN+PF+ + R PA+ GN ++K + P + + P GVF + Sbjct: 125 VLGVMPWNYPFWQVFRFAVPAVTAGNMALLKHASNVPQCALAIQEVFRKAGYPDGVFTTL 184 Query: 204 VCGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLELGGKAPAIVLADAD 263 + GA +V + HP V +S TGS G ++ A A L K LELGG IV+ DAD Sbjct: 185 MIGADKVESVI-RHPAVKSVSLTGSEPAGRKVAAIAGEELKKTVLELGGSDAFIVMDDAD 243 Query: 264 LELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAATRY-GDPLAEPEVE 322 +++AV R +N GQ C ++R V + FIE AA+ GDP+ + E Sbjct: 244 IKVAVAGAVKGRFVNMGQSCISSKRFIVDSMIYAEFIEAFKAAIEDKFIAGDPM-DKETS 302 Query: 323 MGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVLTGCRADTRIMREEI 382 + P+ + L+++ A+VR ++ GA +VTGG +RPG +Y PT+L ++ EE Sbjct: 303 LAPMARQDLLDELHAQVRASVELGAEIVTGGYQLDRPGCYYAPTILANISSNMPAFNEEF 362 Query: 383 FGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALRELDFGETYINREHFEA 442 FGPV + + A+ LAN ++GL S+++ D+ A R ++ G TYIN F Sbjct: 363 FGPVAIVLKATEPAHALGLANATDFGLGGSIWSNDMATAETMARGMESGATYINSITFSD 422 Query: 443 MQGFHAGVRKSGIGGADGKHGLYEYTHTHVVYLQ 476 + GV+ SG G +HG+ E+T+ ++++ Sbjct: 423 PRLPFGGVKNSGYGRELSEHGIREFTNIKTIWIK 456 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: 443 Number of extensions: 25 Number of successful extensions: 2 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: 456 Length adjustment: 33 Effective length of query: 444 Effective length of database: 423 Effective search space: 187812 Effective search space used: 187812 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