Align Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::Q8GAK7 (458 letters) >FitnessBrowser__Cola:Echvi_3822 Length = 453 Score = 394 bits (1013), Expect = e-114 Identities = 207/452 (45%), Positives = 286/452 (63%), Gaps = 3/452 (0%) Query: 5 TIDPTTGITLKTFDAHTPEEVENRIARAEAAFRSLQNTSFEERARWMHKAADILESEADE 64 +I+P TG L+ F HT ++VE I + + A+ S + +RA M KA +L D+ Sbjct: 3 SINPYTGELLEEFTDHTEQQVEAAIQKGQEAYLSWRELPISQRADLMKKAGQVLRDNTDK 62 Query: 65 VARLIATEMGKTLTTAKYEALKSATGMRHFADHAQRYLSPETPVPASEVNASNLHVQFDP 124 ++I+ EMGK +T +K E K A ++A++A+ L+ P + + V ++P Sbjct: 63 YGKIISLEMGKVITESKSEVEKCAWVCEYYAENAEEMLAD---APIALPDGKEAKVVYNP 119 Query: 125 LGVVLAVMPWNYPLWQAVRFAAPALMAGNTGLLKHASNVPQCALYLGDLFARGGFPEGAF 184 LG+VLAVMPWN+P WQ RFAAP L AGN GLLKHASNVPQCAL + ++F + GFPEG F Sbjct: 120 LGIVLAVMPWNFPFWQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGFPEGVF 179 Query: 185 QTLLVEGKDVIPLVDDARIRAVTLTGSVAAGSAIAEAAGRNIKRSVLELGGMDVFIVMPS 244 Q+LL+ V ++ ++A TLTGS AG IA AG IK++VLELGG D FIV+ Sbjct: 180 QSLLIGSDKVANIIAHPDVKAATLTGSEKAGQKIAAQAGEQIKKTVLELGGSDPFIVLKD 239 Query: 245 ADIEKAAAQAVIARLQNSGQSCIAAKRFYVHEDVYDRFEHLFVTGMAEAVAGDPLDESTS 304 AD+++AA A R+ N GQSCIAAKRF + ++VYD F F + + V GDPLDE Sbjct: 240 ADVKEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDPLDEKAG 299 Query: 305 FGPLATERGRQDVHELVRDAREKGAAVQCGGEIPEGEGWYYPATVLTGVTEDMRIYREEC 364 + +A +++E V + +KGA V G PE + +L +T DM YREE Sbjct: 300 YACMARPDLAMELYEQVEASIQKGAEVILEGTKPEKGKAFIKPYILGKLTPDMPAYREEL 359 Query: 365 FGPVACLYKVSSLQEAIALSNDSDFGLSSSVWTNDETEATEAARSIEAGGVFINGLTASF 424 FGPVA ++K + + EAIA++NDS FGL +S+WT D +A +R IE+G VFIN + AS Sbjct: 360 FGPVASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIESGAVFINSMVASN 419 Query: 425 PAVPFGGLKDSGYGRELSAYGIREFVNIKTVW 456 P +PFGG+K SGYGREL+ GI+EF+NIKTV+ Sbjct: 420 PYLPFGGIKKSGYGRELAENGIKEFMNIKTVY 451 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: 463 Number of extensions: 19 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: 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 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