Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Pf6N2E2_1751 Aldehyde dehydrogenase A (EC 1.2.1.22) / Glycolaldehyde dehydrogenase (EC 1.2.1.21)
Query= metacyc::MONOMER-16246 (477 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1751 Length = 477 Score = 724 bits (1869), Expect = 0.0 Identities = 363/473 (76%), Positives = 409/473 (86%), Gaps = 2/473 (0%) Query: 7 VHRNYIDGAFVESAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIE 66 +++NYI AFV S HLEV NPANG LL RVP S EVE+A+AAAR AQ+ WA +PAIE Sbjct: 5 IYQNYIANAFVASDEHLEVHNPANGQLLGRVPQGSTAEVEQAIAAARQAQRAWAARPAIE 64 Query: 67 RAGHLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEII 126 RAG+LR+IA+K+R R+ARTIT EQGK+ LA VEVNFTADYLDYMAEWARRLEGE++ Sbjct: 65 RAGYLRKIASKVREHGERLARTITAEQGKVLELARVEVNFTADYLDYMAEWARRLEGEVL 124 Query: 127 ASDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFE 186 +SDR GE+IFL RKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIV+KPSEETP NCFE Sbjct: 125 SSDRAGESIFLLRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVIKPSEETPINCFE 184 Query: 187 FARLVAETDLPRGVFNVVCGAG-QVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTK 245 FARLVAETDLP GVFNVVCG G VG ALS HPG+DLISFTGSV TG+RIMAAAAPN+TK Sbjct: 185 FARLVAETDLPAGVFNVVCGTGATVGHALSGHPGIDLISFTGSVGTGSRIMAAAAPNITK 244 Query: 246 LNLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAA 305 LNLELGGKAPAIVLADADL+LA++AI SR+IN+GQVCNCAERVYV+R+VA+ FI+ IAA Sbjct: 245 LNLELGGKAPAIVLADADLDLAIRAITASRVINTGQVCNCAERVYVERKVADAFIDGIAA 304 Query: 306 AMAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAE-RPGHHYQ 364 +MAATRYGDPLAE ++MGPLINR L+K+ VRTA QGA ++TGGA+A+ G HYQ Sbjct: 305 SMAATRYGDPLAEHGLDMGPLINRAALDKVAQMVRTASGQGAQIITGGAVADLGQGFHYQ 364 Query: 365 PTVLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHA 424 PTVL GC A IMR+EIFGPVLPIQIVDDLDEAIALAND EYGLTSS++T L+ AM A Sbjct: 365 PTVLAGCSAKMEIMRKEIFGPVLPIQIVDDLDEAIALANDSEYGLTSSIYTASLSAAMQA 424 Query: 425 LRELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHVVYLQS 477 R LDFGETYINRE+FEAMQGFHAG RKSGIGGADGKHGLYEYTHTHVVY+Q+ Sbjct: 425 TRLLDFGETYINRENFEAMQGFHAGTRKSGIGGADGKHGLYEYTHTHVVYIQA 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: 727 Number of extensions: 16 Number of successful extensions: 3 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