Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000012965.1:WP_011373513.1 Length = 471 Score = 229 bits (584), Expect = 2e-64 Identities = 153/459 (33%), Positives = 239/459 (52%), Gaps = 17/459 (3%) Query: 27 VNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERASEI 86 VNP V S A+DA+KA++ A A E +R SWL +++ + + +I Sbjct: 21 VNPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKEDI 80 Query: 87 SALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPG---ENILLFKRA- 142 + I +E GK + +EV + + AE R GE + +D + I F R Sbjct: 81 AKTITDEVGKPITYSRIEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTISFFSRVP 140 Query: 143 LGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLP-RGV 201 GV I P+NFP LIA K+APAL+ GN +++KP+ P A FAK+ E + Sbjct: 141 CGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAIKDA 200 Query: 202 FNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVM 261 ++V G + VG L + ++S TGSV GE I T + I KV LELGG A + Sbjct: 201 LSVVYGDAD-VGGTLVTSEIPRVISFTGSVGVGEII--TKSAGIKKVSLELGGNAATFID 257 Query: 262 DDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERN 321 A+L+LA + +NSGQVC +R+YV K IY +F ++ EA + + G+P E Sbjct: 258 KSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPYE-E 316 Query: 322 DIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMH 381 D MGPL+N A +R + V A++EGA + VEG+ +Y P ++ DV+++M+I+ Sbjct: 317 DTFMGPLVNDEAAKRAMEWVQSAIKEGATPILEPR-VEGRVFY--PCVMADVKEDMAIVC 373 Query: 382 EETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYIN--- 438 +E F P++ ++ ++A+ M N+S YGL SI+T +LN+ +AI L G IN Sbjct: 374 QEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGGIVINDMP 433 Query: 439 RENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 F+ + G + SG+G + + E + + V + Sbjct: 434 TLRFDIQP--YGGVKLSGVGREGPRFAIEEMSEIKSVII 470 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: 468 Number of extensions: 22 Number of successful extensions: 6 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: 471 Length adjustment: 33 Effective length of query: 446 Effective length of database: 438 Effective search space: 195348 Effective search space used: 195348 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