Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1496 Length = 500 Score = 292 bits (747), Expect = 2e-83 Identities = 166/460 (36%), Positives = 255/460 (55%), Gaps = 8/460 (1%) Query: 23 WIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPE--WEALPAIERASWLRKISAGIR 80 W+ V +PATE V++ PD A D +A+ +A+RA W L +R L ++S I Sbjct: 38 WLPVTDPATEMVVAEAPDSDAADIARAVASAQRAFDSHVWRGLRPADREKLLFRLSELIE 97 Query: 81 ERASEISALIVEEGGKIQQLAE-VEVAFTADYIDYMAEWARRYEGEIIQSDRP--GENIL 137 A E+SAL + GK+Q +A ++V A+++ YMA WA + EG+ + + P G + Sbjct: 98 RHADELSALETLQSGKLQGIARAIDVQAGAEFVRYMAGWATKLEGQTLDNSIPIPGPQWV 157 Query: 138 LFKRA--LGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEI 195 + R +GV I+PWNFP + K+APAL G T+V+KPSE TP A+ A + E Sbjct: 158 TYTRREPVGVVGAIVPWNFPLAIALWKIAPALAAGCTVVLKPSEDTPLTALRLAHLALEA 217 Query: 196 GLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGK 255 G+P GV N+V GRG T G L +P V +S TGS + G+ + A +N+ + LELGGK Sbjct: 218 GIPEGVLNVVCGRGATAGAALIAHPGVRKLSFTGSTAVGKVVGHAAVENMARFTLELGGK 277 Query: 256 APAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFG 315 +PA+VM+DAD + I + GQVC + R+ V + +Y + ++ L Q ++ G Sbjct: 278 SPAVVMEDADPSQVAQGIATGIFFHQGQVCTASSRLLVHRSLYRRVLDELAGIAQGMRIG 337 Query: 316 NPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQ 375 + + GPL + A RV +A A EGA + GG+ V G + PT+ D Sbjct: 338 SGFDA-ATQFGPLTSKAHFARVMDFIASAKAEGATLVAGGERVHDAGCFVQPTIFADTTA 396 Query: 376 EMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGET 435 +M ++ EE FGPVL V FD +EDAI+ AND+ YGL +S++TQ+L+ A + + L+ G Sbjct: 397 QMRVVREEVFGPVLAVAPFDDVEDAIAAANDTPYGLAASLWTQSLSHAHRIVPRLQAGVV 456 Query: 436 YINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475 ++N N G ++SG G G+ + + + + V Sbjct: 457 WVNAHNVLDAGLPLGGIKQSGTGRDLGRAAVEGFTELKSV 496 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: 540 Number of extensions: 25 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: 500 Length adjustment: 34 Effective length of query: 445 Effective length of database: 466 Effective search space: 207370 Effective search space used: 207370 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