Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate PfGW456L13_2690 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2690 Length = 502 Score = 305 bits (782), Expect = 2e-87 Identities = 168/475 (35%), Positives = 268/475 (56%), Gaps = 9/475 (1%) Query: 9 MYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPE---WEALPA 65 M+I G +V DVV P+TE +I+RIP G +D +A+ AA RAQ + W Sbjct: 28 MFIGGAWVEASDGQTSDVVEPSTEGLITRIPMGTTDDLDRAVQAA-RAQFDGGAWRQAKP 86 Query: 66 IERASWLRKISAGIRERASEISAL-IVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEG 124 ER +++++ I + A+E++ + ++ G + +V++ T D + Y A WA + G Sbjct: 87 AERERMMQRLADLIEQNAAELAQIESIDMGKSVAFAKDVDIQGTVDTLRYFAGWATKLHG 146 Query: 125 EIIQSDRPGENILLF--KRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTP 182 ++ PG N L + K A+GV I+PWNFP +A K+ AL TG T+V+KP+E T Sbjct: 147 RTVEPSLPG-NYLAYTRKEAVGVVGAIVPWNFPLQTMAWKLGAALATGCTVVVKPAELTS 205 Query: 183 NNAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAA 242 +A+ FA++V E G+P GV N+V GRG VG +A +P + ++ TGS G+ + A Sbjct: 206 LSALRFAELVQEAGIPDGVINIVTGRGSVVGAAMATHPGIDKLTFTGSTPVGQTVGRAAL 265 Query: 243 KNITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFV 302 ++ ++ LELGGK+P IV DAD+ A +A+ + NSGQVC+ R Y+ +YD+F+ Sbjct: 266 DDMKRLTLELGGKSPVIVCADADIPAAAQAVANGVFFNSGQVCDAGTRAYIHSSVYDEFL 325 Query: 303 NRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKG 362 L + ++ P D +GPL++A +RV + + EGA + +GG+ V+G G Sbjct: 326 RELITYTRTLKMA-PGLDPDCFIGPLVSALQKQRVTEYIETGKAEGAELVYGGQPVDGPG 384 Query: 363 YYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNV 422 ++ PT+ + R +M I+ EE FGPVL FD E+A+++ANDS YGL +++Y+ +L Sbjct: 385 FFVEPTIFANCRNDMRIVQEEIFGPVLVTAPFDDEEEALALANDSPYGLAAALYSNDLGK 444 Query: 423 AMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 I LK G Y+N G+++SG G G L L+T+ V++ Sbjct: 445 VHSLIPRLKAGSVYVNAHGTLDPSMPFGGYKQSGFGKDLGAEQLDYLLETKAVWI 499 Lambda K H 0.318 0.135 0.392 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: 570 Number of extensions: 33 Number of successful extensions: 5 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: 479 Length of database: 502 Length adjustment: 34 Effective length of query: 445 Effective length of database: 468 Effective search space: 208260 Effective search space used: 208260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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