Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate PfGW456L13_3932 Aldehyde dehydrogenase A (EC 1.2.1.22)
Query= metacyc::MONOMER-16246 (477 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3932 Length = 477 Score = 798 bits (2062), Expect = 0.0 Identities = 393/475 (82%), Positives = 441/475 (92%), Gaps = 1/475 (0%) Query: 3 SSVPVHRNYIDGAFVESAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARK 62 SSVPV+ N+IDG FV SAAHL+V NPA GA+LS+VPA++AE+VERALAAA AAQK WARK Sbjct: 2 SSVPVYENFIDGQFVASAAHLDVINPATGAVLSKVPASTAEDVERALAAACAAQKGWARK 61 Query: 63 PAIERAGHLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLE 122 PA +RAG+LRRIAAK+R + +ARTITLEQGKI+ LAEVEVNFTADYLDYMAEWARR+E Sbjct: 62 PANDRAGYLRRIAAKLRENVAHLARTITLEQGKISGLAEVEVNFTADYLDYMAEWARRIE 121 Query: 123 GEIIASDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPN 182 GEII SDR ENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIV+KPSEETPN Sbjct: 122 GEIITSDRQNENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVIKPSEETPN 181 Query: 183 NCFEFARLVAETDLPRGVFNVVCGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPN 242 NCFEFARLVAETDLP GVFNVVCG G+VG ALSSH GVD+ISFTGSV+TG+RIMAAAAPN Sbjct: 182 NCFEFARLVAETDLPPGVFNVVCGDGKVGAALSSHKGVDMISFTGSVDTGSRIMAAAAPN 241 Query: 243 LTKLNLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIER 302 +TKLNLELGGKAPAIVLADADL+LAV+AIRDSRIINSGQVCNCAERVYV+R+VA+ FIER Sbjct: 242 ITKLNLELGGKAPAIVLADADLDLAVRAIRDSRIINSGQVCNCAERVYVERKVADQFIER 301 Query: 303 IAAAMAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERP-GH 361 IAAAM+ATRYGDP+A+P+VEMGPLINR GL+ ++ KVRTAL+QGA+L++GG +A+ P G Sbjct: 302 IAAAMSATRYGDPIAQPDVEMGPLINRQGLDSVNRKVRTALSQGASLISGGQMADLPNGF 361 Query: 362 HYQPTVLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKA 421 H+QPTVL GCRAD IMREEIFGPVLPIQI+DDLDEAIALANDC+YGLTSS++TRDL+K Sbjct: 362 HFQPTVLAGCRADMEIMREEIFGPVLPIQIIDDLDEAIALANDCDYGLTSSIYTRDLSKT 421 Query: 422 MHALRELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHVVYLQ 476 M A+RELDFGETY+NRE+FEAMQGFHAGVRKSGIGGADGKHGLYEYTHTH VYLQ Sbjct: 422 MQAMRELDFGETYVNRENFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHAVYLQ 476 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: 749 Number of extensions: 17 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: 477 Length adjustment: 33 Effective length of query: 444 Effective length of database: 444 Effective search space: 197136 Effective search space used: 197136 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 17 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