Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_029134446.1 A3GO_RS0117140 aldehyde dehydrogenase family protein
Query= BRENDA::P05091 (517 letters) >NCBI__GCF_000428045.1:WP_029134446.1 Length = 480 Score = 309 bits (792), Expect = 1e-88 Identities = 188/485 (38%), Positives = 272/485 (56%), Gaps = 33/485 (6%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 +IN +W D + +NPST E +A G + D D AV AAR AF W + D Sbjct: 8 YINGQWVDPIKPVELEVINPSTEEPCATIALGGQADTDAAVAAARNAF---GDWSQSDRE 64 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVIS----------YLVDLDMVLKCLRYY 149 R LL +LA++ + +A + + G P ++ ++ + LK + Sbjct: 65 QRLALLEKLAEIYQARSNEMAEAISSEMGAPISLAKTAQCGAGIWHIKNFIRALKTFEF- 123 Query: 150 AGWADKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMK 209 ++ G P D EPVGVCG I PWN+P+ K+ PALATG +V+K Sbjct: 124 ----ERRLGPHAPNDRILL-----EPVGVCGLITPWNWPMNQVTLKVIPALATGCTLVLK 174 Query: 210 VAEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRV 269 +E +PL+A+ A +I +AGFPPGV N+V G G G+ + +H DVD ++FTGST G Sbjct: 175 PSEISPLSAMLFAEMIDQAGFPPGVFNLVNGDGAGVGSQLTAHPDVDMISFTGSTRAGIA 234 Query: 270 IQVAAGSSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQE 329 I +A + +KRV+LELGGK N++ +DAD + A+++ F N GQ C A +R VQ Sbjct: 235 ISKSA-ADTVKRVSLELGGKGANLVFADADEN-AIKRGLRHCFNNSGQSCNAPTRMLVQR 292 Query: 330 DIYDEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGG- 388 +Y + VE + A+ V + + GP V + Q+ KI I G EGA+L+ GG Sbjct: 293 PLYQQAVETAAQLAEGTAVDHSANEGRHIGPVVSQAQYDKIQRLIQQGTDEGARLVAGGP 352 Query: 389 ----GIAADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGL 444 GI DRGYF++PTVF DV M IA+EEIFGPV+ I F + EE + AN++ YGL Sbjct: 353 GRPEGI--DRGYFVRPTVFADVGQDMQIAREEIFGPVLSITPFDSEEEAITIANDTVYGL 410 Query: 445 AAAVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTE 504 + T+D +A +++ L++G V +N + GA SPFGGYK SG+GRE G +GL+ + E Sbjct: 411 TNYIQTQDSARAKRVARQLRSGMVEINGHSP-GAGSPFGGYKQSGNGREGGVWGLEEFLE 469 Query: 505 VKTVT 509 VK V+ Sbjct: 470 VKAVS 474 Lambda K H 0.319 0.136 0.409 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: 598 Number of extensions: 32 Number of successful extensions: 7 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: 517 Length of database: 480 Length adjustment: 34 Effective length of query: 483 Effective length of database: 446 Effective search space: 215418 Effective search space used: 215418 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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