Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_034995716.1 DL88_RS10695 aldehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_000745425.1:WP_034995716.1 Length = 475 Score = 638 bits (1646), Expect = 0.0 Identities = 320/475 (67%), Positives = 385/475 (81%), Gaps = 4/475 (0%) Query: 7 VHRNYIDGAFVESAAH--LEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPA 64 +H N+++G F+E+ A + VFNPA G +S +P +SA V++A+AAARAAQK+WA+ P Sbjct: 1 MHHNFVNGQFLETKAAETIAVFNPATGKQISEIPDSSAAVVDQAVAAARAAQKEWAKLPP 60 Query: 65 IERAGHLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGE 124 I RAG+LR IA+KIR IARTI+ EQGK+ LAEVEV FTADY DYMAEWARRLEGE Sbjct: 61 IARAGYLRTIASKIRERVDVIARTISEEQGKLLGLAEVEVRFTADYFDYMAEWARRLEGE 120 Query: 125 IIASDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNC 184 IIASDRPGE I LFR+PLGVVAGILPWNFPFFLIARKMAPAL+TGNTIV+KPSEETPNN Sbjct: 121 IIASDRPGETILLFRQPLGVVAGILPWNFPFFLIARKMAPALVTGNTIVIKPSEETPNNA 180 Query: 185 FEFARLVAETDLPRGVFNVVCGAG-QVGGALSSHPGVDLISFTGSVETGARIMAAAAPNL 243 FA LVAETDLP G+FN+V G G VG A++SHP V+LISFTGSV G+ IMA+AA N+ Sbjct: 181 ALFAGLVAETDLPPGLFNLVYGRGTTVGEAMTSHPDVNLISFTGSVRAGSAIMASAAKNI 240 Query: 244 TKLNLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERI 303 TK+NLELGGKAPAIV+ D D++LAV+A+ SR+INSGQVCNCAER+YVQ +A+ F + Sbjct: 241 TKVNLELGGKAPAIVMKDCDIDLAVRAVTGSRVINSGQVCNCAERIYVQEDIADEFTAKF 300 Query: 304 AAAMAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGH-H 362 AAAM+AT YGDPL V MGPLIN + +IDA V+ A+++GA +VTGG E+ G + Sbjct: 301 AAAMSATTYGDPLGNEPVGMGPLINAAAMHRIDAIVQRAVSEGAQIVTGGKPDEKAGGVY 360 Query: 363 YQPTVLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAM 422 +QPTVL CR D IMR+E+FGPV P+ IV DLDEAIA AND YGLTSS++TRDL+ AM Sbjct: 361 FQPTVLVNCRQDMEIMRDEVFGPVAPVNIVKDLDEAIARANDSVYGLTSSIYTRDLSTAM 420 Query: 423 HALRELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHVVYLQS 477 A E+ FGETY+NRE+FEAMQGFHAGVR+SGIGGADGKHGLYE+THTHVVY+Q+ Sbjct: 421 RACNEIHFGETYVNRENFEAMQGFHAGVRRSGIGGADGKHGLYEFTHTHVVYIQN 475 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: 643 Number of extensions: 18 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: 475 Length adjustment: 33 Effective length of query: 444 Effective length of database: 442 Effective search space: 196248 Effective search space used: 196248 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