Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_077279545.1 B1C78_RS12570 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_002000365.1:WP_077279545.1 Length = 452 Score = 242 bits (617), Expect = 2e-68 Identities = 159/452 (35%), Positives = 226/452 (50%), Gaps = 6/452 (1%) Query: 27 NPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAGHLRRIAAKIRADAGRIA 86 NPANGA + R +E ALA A A WA+ ERA L+ A +R + Sbjct: 5 NPANGAQMGRFEPWDDSRIESALAQAGEAAPAWAKLHMAERARFLQGAARVLREREPEFS 64 Query: 87 RTITLEQGKIASLAEVEVNFTADYLDYMAEWARR-LEGEIIASDRPGENIFLFRKPLGVV 145 R IT E GK+ S A E+ A DY A A R L E++ASD + +PLG V Sbjct: 65 RLITEEMGKLISEASAEIEKCAKVCDYYAAEAERFLTDEVLASD--ASRSLVAWQPLGTV 122 Query: 146 AGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFARLVAETDLPRGVFN-VV 204 ++PWNFPF+ + R APAL+ GNT ++K + P + PRGVF ++ Sbjct: 123 LAVMPWNFPFWQVFRFAAPALMAGNTALLKHASNVPRCALAIESVFEAAGFPRGVFRTLM 182 Query: 205 CGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLELGGKAPAIVLADADL 264 GA QV G + V ++ TGS G + A A L K LELGG P +VL DADL Sbjct: 183 IGASQVEGVIRDRR-VHAVTLTGSEPAGRAVAAVAGEVLKKTVLELGGSDPFVVLEDADL 241 Query: 265 ELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAATRYGDPLAEPEVEMG 324 EL V+ SR +N+GQ C A+R V VAE F+E+ A+ A R GDP+ E + Sbjct: 242 ELTVEQAVASRYMNAGQSCIAAKRFVVVEPVAETFLEQFREAVRALRPGDPMDE-STTLA 300 Query: 325 PLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVLTGCRADTRIMREEIFG 384 P+ + + A+V ++ GA ++ GG E G+ YQ ++L G EE+FG Sbjct: 301 PMARGDLRDALHAQVHESVKHGAQVLEGGQPVEGKGNWYQASILDGVGPGMPAYEEEMFG 360 Query: 385 PVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALRELDFGETYINREHFEAMQ 444 PV I D D+A+ +AND +GL SV++RD + R L G ++N + Sbjct: 361 PVAAILRARDEDDAVRIANDTRFGLGGSVWSRDAARGEAVARRLACGCAFVNGLVKSDPR 420 Query: 445 GFHAGVRKSGIGGADGKHGLYEYTHTHVVYLQ 476 G++ SG G G+ E+ + V+++ Sbjct: 421 LPFGGIKDSGYGRELSLLGIREFVNAKTVWIR 452 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: 478 Number of extensions: 19 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: 452 Length adjustment: 33 Effective length of query: 444 Effective length of database: 419 Effective search space: 186036 Effective search space used: 186036 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