Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_046008427.1 OLEAN_RS05680 aldehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_000967895.1:WP_046008427.1 Length = 453 Score = 218 bits (555), Expect = 3e-61 Identities = 152/456 (33%), Positives = 228/456 (50%), Gaps = 13/456 (2%) Query: 19 SAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAGHLRRIAAKI 78 SA LE +P+NG ++ V + ++ + A AQ +W ++P ER+ +++ A + Sbjct: 8 SAQILESIDPSNGEVVGSVAITNEAALKTIVERAAQAQVNWGQRPLHERSSLVQQAYAAL 67 Query: 79 RADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEIIASDRPGENIFLF 138 +A I+ E GK A E + T Y+A + AS R N + Sbjct: 68 EDAEESMAMLISREMGKDTRRAGYEASGTLHGGRYLAAETAKA----FASQRLAGNSEIQ 123 Query: 139 RKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFARLVAETDLPR 198 +P+G VA I PWN+P + + PAL+ GN++++KPSEETP ++ ET LP Sbjct: 124 YRPVGTVAVISPWNYPLAMANNLIVPALVAGNSVILKPSEETPLVADMLVNILNET-LPS 182 Query: 199 GVFNVVCGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLELGGKAPAIV 258 GV + G G VG AL +++++FTGS++TG IMA AAP L +L +ELGG P IV Sbjct: 183 GVLQIAHGGGDVGEALVKS-NINMVAFTGSLQTGRNIMANAAPQLKRLVMELGGNDPMIV 241 Query: 259 LADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAATRYGDPLAE 318 L DAD+ A + S N+GQ+C ERVYV ++AE F + + + + + G + Sbjct: 242 LDDADVFAAAQFAVASSFENAGQMCTSTERVYVDEKIAEQFEQAVVSIASQYKVGS-WRD 300 Query: 319 PEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVLTGCRADTRIM 378 V +GPL+N K+ + + AL +GATL+ G P PTV++ I Sbjct: 301 SRVNIGPLVNAKQHAKVVSHIEDALDKGATLLFGERKPLLP--FIPPTVISNINPTMIIE 358 Query: 379 REEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVF-TRDLNKAMHALRELDFGETYINR 437 EE FGPV+ I LD+ I AND YGL + VF RD K ++L G IN+ Sbjct: 359 SEETFGPVVAIDRFGSLDDVIKRANDSVYGLGAVVFGDRDAKK---VAQQLQAGMIGINQ 415 Query: 438 EHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHVV 473 G ++SG G G ++ V+ Sbjct: 416 GVGAGGDAPWVGAKQSGFGFHGSVEGHRQFAQVTVI 451 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: 423 Number of extensions: 18 Number of successful extensions: 6 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: 453 Length adjustment: 33 Effective length of query: 444 Effective length of database: 420 Effective search space: 186480 Effective search space used: 186480 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