Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__PS:Dsui_0105 Length = 476 Score = 309 bits (792), Expect = 1e-88 Identities = 184/471 (39%), Positives = 270/471 (57%), Gaps = 9/471 (1%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 YI GQ+V G+A+IDV NPATE VI+R+P+G A DA +A AA A P W AL ER Sbjct: 8 YIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPAWAALSGAERG 67 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129 ++L+KI+ G++ R E+ LI E G +LA V + A R E Sbjct: 68 AFLQKIADGLKARQDELGRLIASEVGMPVKLA-TRVQAGNPIFTFAA--CARIAAEGFAE 124 Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189 +R G++++L K G I PWNFP IA K+ AL G T+V+KPSE P NA A Sbjct: 125 ERIGQSLVL-KVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLNAFLLA 183 Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249 ++++ GLP GVFNLV G G VG+ LA +P +A VS TGS +AG+++ A AA + +V Sbjct: 184 EVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATVKRVS 243 Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309 LELGGK+ ++V+ DADL AVK V +NSGQ C+ R+ V + Y + +A Sbjct: 244 LELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALAVQAA 303 Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAV-EG--KGYYYP 366 A G+P +GPL++ +RV + +AV +GA + GG A EG GYY Sbjct: 304 AAYTLGDPLAEGS-RLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAPEGLPTGYYVR 362 Query: 367 PTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKA 426 PT+ VR + ++ EE FGPVL ++ + +A ++AN +DYGL +++++ A+ Sbjct: 363 PTVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEEARALAF 422 Query: 427 IKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 + L+ G+ IN F + F G+++SG G G+HG+ ++L+TQ + L Sbjct: 423 ARRLRAGQVDINGAFFNLLAPF-GGFKQSGYGRELGRHGVEDFLETQSIQL 472 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: 531 Number of extensions: 19 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: 476 Length adjustment: 34 Effective length of query: 445 Effective length of database: 442 Effective search space: 196690 Effective search space used: 196690 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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