Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011812614.1 VEIS_RS24010 aldehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_000015565.1:WP_011812614.1 Length = 478 Score = 620 bits (1600), Expect = 0.0 Identities = 312/473 (65%), Positives = 376/473 (79%), Gaps = 3/473 (0%) Query: 8 HRNYIDGAFV-ESAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIE 66 ++NYIDG FV A + V NPA+ L++ VP A V+ A++AAR AQ W R PAI+ Sbjct: 5 YQNYIDGRFVPHRGATIAVHNPADHRLIAEVPDGDAAAVDAAVSAARRAQPAWERLPAIQ 64 Query: 67 RAGHLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEII 126 RAG+LR+I+ K+R A +A TI EQGK+ LA VEVNFTADY+DYMAEWARRLEGE++ Sbjct: 65 RAGYLRQISVKLREHAEALATTIAREQGKVMPLARVEVNFTADYIDYMAEWARRLEGEVL 124 Query: 127 ASDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFE 186 SDRP E++FL RKP+GV AGILPWNFPFFLIARKMAPAL+TGNT+V+KPSEETP N F Sbjct: 125 TSDRPNEHMFLLRKPIGVAAGILPWNFPFFLIARKMAPALITGNTVVIKPSEETPLNAFA 184 Query: 187 FARLVAETDLPRGVFNVVCGAG-QVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTK 245 F +L+A+TDLP GVFN+V G G G L +H GV+LI+FTGSV TG RIM AAAPNLT+ Sbjct: 185 FTQLLAQTDLPPGVFNLVSGKGASTGAELVAHKGVNLITFTGSVTTGVRIMQAAAPNLTR 244 Query: 246 LNLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAA 305 +NLELGGKAPAIVL DADL+LA +A+ SRIIN+GQVCNCAERVYVQR+V ++I Sbjct: 245 VNLELGGKAPAIVLKDADLDLAAQALVASRIINTGQVCNCAERVYVQREVLGALTDKIVQ 304 Query: 306 AMAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAE-RPGHHYQ 364 MAATR+G+PL + ++MGPLIN+ GL+K+ V A A GA ++TGG A+ G+HY Sbjct: 305 RMAATRFGNPLLDETLDMGPLINQAGLDKVARLVDEARAAGAEVLTGGRRADVGHGYHYL 364 Query: 365 PTVLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHA 424 PTV+ GCR D IMR+EIFGPVLP+Q VDD+DEAIALAND +YGLTSS+FTRDLN AM A Sbjct: 365 PTVVAGCRQDMSIMRDEIFGPVLPLQAVDDMDEAIALANDSDYGLTSSIFTRDLNAAMKA 424 Query: 425 LRELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHVVYLQS 477 REL FGETYINREHFEAMQGFHAG +KSGIGGADG+HGL E+T THVVY+Q+ Sbjct: 425 CRELQFGETYINREHFEAMQGFHAGRKKSGIGGADGRHGLLEFTETHVVYMQT 477 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: 658 Number of extensions: 23 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: 478 Length adjustment: 34 Effective length of query: 443 Effective length of database: 444 Effective search space: 196692 Effective search space used: 196692 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