Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein
Query= BRENDA::P05091 (517 letters) >NCBI__GCF_000504245.1:WP_034273599.1 Length = 496 Score = 389 bits (999), Expect = e-112 Identities = 214/477 (44%), Positives = 286/477 (59%), Gaps = 9/477 (1%) Query: 38 QIFINNEWHDAVSRKTFPTV-NPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRM 96 ++FI+ W D V NP+ + V E D++DVD AV AAR AF SPWR Sbjct: 3 ELFIDGRWVDTTGTAPARVVLNPANAAELATVCEADEKDVDAAVAAARRAFD-DSPWRAT 61 Query: 97 DASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKY 156 A RG LL +A L++RD+ +LA E+LD GK + VD+D V RYYA AD Sbjct: 62 TARERGELLREIARLLQRDKEHLARTESLDTGKT-MAEGRVDVDDVTSVFRYYANLADNE 120 Query: 157 HGKTIPI-DGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTP 215 G+ + D S HEPVGVC I PWN+PLL +WKL PALA GN VVMK +E TP Sbjct: 121 AGRVVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTP 180 Query: 216 LTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAG 275 LT + + L++EAG P GVVN+V G G GA + SH DVD V+FTG E G+ I +A Sbjct: 181 LTTIELMRLVEEAGVPAGVVNLVLGGGANVGAPMVSHPDVDLVSFTGGLETGKKI-MAMA 239 Query: 276 SSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEF 335 + +KRV LELGGK+PN++ +DAD D AV+ A A F + GQ C AGSR V+ DI+DEF Sbjct: 240 AEGVKRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEF 299 Query: 336 VERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAAD-- 393 V RA + +G+ D TE GP K+ +I K EGA+L+ GG + Sbjct: 300 VAELARRADAIRLGDGLDPATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPTEPE 359 Query: 394 --RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTK 451 GYF++PTVF D M I ++E+FGPV+ + +F T +E + AN++ YGLA AV+T Sbjct: 360 LADGYFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWTS 419 Query: 452 DLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTV 508 D +A ++ AL+ GTVW+N + + Q+ +GG+ SG GRELG GL+ Y E K + Sbjct: 420 DASRAQRVAGALRHGTVWINDFHPYLPQAEWGGFGKSGIGRELGPSGLEEYRETKHI 476 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: 662 Number of extensions: 29 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: 517 Length of database: 496 Length adjustment: 34 Effective length of query: 483 Effective length of database: 462 Effective search space: 223146 Effective search space used: 223146 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