Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000504245.1:WP_034273599.1 Length = 496 Score = 287 bits (734), Expect = 7e-82 Identities = 170/475 (35%), Positives = 258/475 (54%), Gaps = 8/475 (1%) Query: 9 MYIDGQFVTWRGDAWIDVV-NPATEAVISRIPDGQAEDARKAIDAAERAQPE--WEALPA 65 ++IDG++V G A VV NPA A ++ + + +D A+ AA RA + W A A Sbjct: 4 LFIDGRWVDTTGTAPARVVLNPANAAELATVCEADEKDVDAAVAAARRAFDDSPWRATTA 63 Query: 66 IERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGE 125 ER LR+I+ ++ ++ + GK V+V Y A A G Sbjct: 64 RERGELLREIARLLQRDKEHLARTESLDTGKTMAEGRVDVDDVTSVFRYYANLADNEAGR 123 Query: 126 IIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNA 185 ++ + + +GV + I PWN+P ++ K+APAL GNT+V+KPSE TP Sbjct: 124 VVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTPLTT 183 Query: 186 IAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNI 245 I ++V+E G+P GV NLVLG G VG + +P V +VS TG + G+KIMA AA+ + Sbjct: 184 IELMRLVEEAGVPAGVVNLVLGGGANVGAPMVSHPDVDLVSFTGGLETGKKIMAMAAEGV 243 Query: 246 TKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRL 305 +V LELGGK P +V DAD + AV + + +SGQVC+ R+ V+ I+D+FV L Sbjct: 244 KRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEFVAEL 303 Query: 306 GEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGG----KAVEGK 361 A++ G+ + GPL +A ++VE+ + A EGAR+ GG + Sbjct: 304 ARRADAIRLGDGLD-PATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPTEPELAD 362 Query: 362 GYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLN 421 GY+ PT+ D +EM I+ +E FGPV+ V FDT ++AI +AND++YGL +++T + + Sbjct: 363 GYFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWTSDAS 422 Query: 422 VAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVY 476 A + L+ G +IN + Q G+ KSGIG G GL EY +T+ +Y Sbjct: 423 RAQRVAGALRHGTVWINDFHPYLPQAEWGGFGKSGIGRELGPSGLEEYRETKHIY 477 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: 551 Number of extensions: 22 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: 496 Length adjustment: 34 Effective length of query: 445 Effective length of database: 462 Effective search space: 205590 Effective search space used: 205590 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 24 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