Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_029134950.1 A3GO_RS0120300 phenylacetaldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >NCBI__GCF_000428045.1:WP_029134950.1 Length = 480 Score = 327 bits (839), Expect = 5e-94 Identities = 188/481 (39%), Positives = 277/481 (57%), Gaps = 10/481 (2%) Query: 38 QIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMD 97 ++FIN EW + + +NPSTGEV +V + +DV+ A+ AA AA W + Sbjct: 5 RLFINGEWVETQDGEVLDDINPSTGEVFARVHQAGPKDVEHAITAASAA---SVAWGKTQ 61 Query: 98 ASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYH 157 + R +L + AD ++ R + A +D + + V+ LR AG A + Sbjct: 62 PAVREEILIKAADCLQA-RIHEIADVLIDEAGSTFGKAMFEASFVVNLLRSAAGEARRIF 120 Query: 158 GKTIPIDG-DFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPL 216 G+T+P DG D FS + P+GV I P+NFP L+ K+ A+A GN V+K +E+T + Sbjct: 121 GETMPSDGPDIFSMSVRRPLGVIAGIAPFNFPFLLACKKVALAIAAGNAFVLKPSEETAV 180 Query: 217 TALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGS 276 T L +A + ++AG P GV+N++PG GP G + V + FTGST +G+ + V A + Sbjct: 181 TGLKIAEIFEQAGLPKGVLNVIPGSGPEVGGRLVDDPRVKMITFTGSTVVGKKLAVQA-A 239 Query: 277 SNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFV 336 LK++TLELGGKSP I+++DAD+D+AV+ A F +F +QGQ C A S+ V+ +YD F Sbjct: 240 QQLKKITLELGGKSPLIVLADADLDYAVDAACFGIFLHQGQVCMANSKLIVEAAVYDAFC 299 Query: 337 ERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGY 396 ++ A+ KS VG+P T GP + Q + I ++ +GA+LL GG + Sbjct: 300 DKFAAKVKSLKVGDPRQPNTVIGPLIRGAQCQVIDRHVQDALDKGARLLTGG---SSESN 356 Query: 397 FIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKA 456 F QPTV DV M I +EE FGPV+ I+K E + AN+S YGL++AV T DL KA Sbjct: 357 FYQPTVMADVGPDMQIYREESFGPVVSIIKADDHEAALYIANDSEYGLSSAVITNDLQKA 416 Query: 457 NYLSQALQAGTVWVNCYDVFG-AQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKVPQK 515 LS L+AG V +N VF PFGG K SG GRE G Y ++ TEVK +T+++ ++ Sbjct: 417 MELSLRLEAGMVHINDCTVFDEPHVPFGGVKKSGFGREGGRYSMEEMTEVKWITIQMGKR 476 Query: 516 N 516 + Sbjct: 477 H 477 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: 617 Number of extensions: 29 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: 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