Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Cola:Echvi_3822 Length = 453 Score = 217 bits (553), Expect = 6e-61 Identities = 137/451 (30%), Positives = 224/451 (49%), Gaps = 2/451 (0%) Query: 27 VNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERASEI 86 +NP T ++ D + AI + A W LP +RA ++K +R+ + Sbjct: 4 INPYTGELLEEFTDHTEQQVEAAIQKGQEAYLSWRELPISQRADLMKKAGQVLRDNTDKY 63 Query: 87 SALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPGENILLFKRALGVT 146 +I E GK+ ++ EV A +Y AE A + + G+ + LG+ Sbjct: 64 GKIISLEMGKVITESKSEVEKCAWVCEYYAENAEEMLADAPIALPDGKEAKVVYNPLGIV 123 Query: 147 TGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGVFNLVL 206 ++PWNFPF+ + R AP L GN ++K + P A+A ++ + G P GVF +L Sbjct: 124 LAVMPWNFPFWQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGFPEGVFQSLL 183 Query: 207 GRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVMDDADL 266 + V +A +P V ++TGS AG+KI A A + I K LELGG P IV+ DAD+ Sbjct: 184 IGSDKVANIIA-HPDVKAATLTGSEKAGQKIAAQAGEQIKKTVLELGGSDPFIVLKDADV 242 Query: 267 ELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERNDIAMG 326 + A K R+IN GQ C A+R +++ +YD+F+ A+++ G+P + Sbjct: 243 KEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDPLDEKAGYAC 302 Query: 327 PLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMHEETFG 386 A+E EQ V ++++GA V G E + P +L + +M EE FG Sbjct: 303 MARPDLAMELYEQ-VEASIQKGAEVILEGTKPEKGKAFIKPYILGKLTPDMPAYREELFG 361 Query: 387 PVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRENFEAMQ 446 PV V + +++AI++ANDS +GL +S++TQ+ A + ++ G +IN Sbjct: 362 PVASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIESGAVFINSMVASNPY 421 Query: 447 GFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 G +KSG G ++G+ E++ + VYL Sbjct: 422 LPFGGIKKSGYGRELAENGIKEFMNIKTVYL 452 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: 425 Number of extensions: 19 Number of successful extensions: 4 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: 453 Length adjustment: 33 Effective length of query: 446 Effective length of database: 420 Effective search space: 187320 Effective search space used: 187320 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