Align Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized)
to candidate Ga0059261_1006 Ga0059261_1006 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::Q8GAK7 (458 letters) >FitnessBrowser__Korea:Ga0059261_1006 Length = 453 Score = 374 bits (959), Expect = e-108 Identities = 208/452 (46%), Positives = 270/452 (59%), Gaps = 7/452 (1%) Query: 5 TIDPTTGITLKTFDAHTPEEVENRIARAEAAFRSLQNTSFEERARWMHKAADILESEADE 64 +I+P TG TF A + +E + RAEAAFRS + + +R + AD E+ Sbjct: 4 SINPATGEAGATFAALDDDAIEAALTRAEAAFRSWRASDIAQRTALLTAIADRFEANKRH 63 Query: 65 VARLIATEMGKTLTTAKYEALKSATGMRHFADHAQRYLSP-ETPVPASEVNASNLHVQFD 123 +A EMGKTL +A E K G RH+AD YL+P ET + L Sbjct: 64 LAETATKEMGKTLASAIAEVEKCIAGFRHYADKGPGYLAPIETKTASGRAVGHWL----- 118 Query: 124 PLGVVLAVMPWNYPLWQAVRFAAPALMAGNTGLLKHASNVPQCALYLGDLFARGGFPEGA 183 PLG +LAVMPWN+P WQ VR+ AP ++AGN GLLKHAS CA + + + G P+G Sbjct: 119 PLGPILAVMPWNFPYWQVVRWLAPTILAGNVGLLKHASLTQGCAALIQQMVSAAGAPDGL 178 Query: 184 FQTLLVEGKDVIPLVDDARIRAVTLTGSVAAGSAIAEAAGRNIKRSVLELGGMDVFIVMP 243 FQ L ++ V ++ D R+ AVTLTGS AG+ +AEAAGR +K+ VLELGG D FIVMP Sbjct: 179 FQNLPIKSDKVSRIIADTRVAAVTLTGSEGAGAKVAEAAGRALKKVVLELGGSDPFIVMP 238 Query: 244 SADIEKAAAQAVIARLQNSGQSCIAAKRFYVHEDVYDRFEHLFVTGMAEAVAGDPLDEST 303 SAD++KA A AV AR+QN+GQSCI AKR VH DVYD F F M GDP+++ Sbjct: 239 SADLDKAVATAVKARVQNAGQSCICAKRMIVHADVYDAFLDKFTAAMLAVKIGDPMEDGV 298 Query: 304 SFGPLATERGRQDVHELVRDAREKGAAVQCGGEIPEGEGWYYPATVLTGVTEDMRIYREE 363 GPL++ R V E V A GA + G +I E +G + A VLT V D +EE Sbjct: 299 EMGPLSSVEQRDTVLEQVERAVADGATLAGGAKI-ERDGAWMEAGVLTHVHPDADFAQEE 357 Query: 364 CFGPVACLYKVSSLQEAIALSNDSDFGLSSSVWTNDETEATEAARSIEAGGVFINGLTAS 423 FGPVA +++ + AIAL+ND FGL SSVWT+D+ E R IE+G +N L AS Sbjct: 358 IFGPVAMVFRADDIDAAIALANDVPFGLGSSVWTSDQAEIDRFVRDIESGMTAVNQLLAS 417 Query: 424 FPAVPFGGLKDSGYGRELSAYGIREFVNIKTV 455 P PFGG+K SG+GREL +G+ EF+N+K V Sbjct: 418 TPEAPFGGVKLSGHGRELGPWGLHEFMNLKAV 449 Lambda K H 0.317 0.132 0.386 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: 474 Number of extensions: 14 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: 458 Length of database: 453 Length adjustment: 33 Effective length of query: 425 Effective length of database: 420 Effective search space: 178500 Effective search space used: 178500 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