Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::V4GH04 (496 letters) >FitnessBrowser__Cola:Echvi_3822 Length = 453 Score = 226 bits (577), Expect = 1e-63 Identities = 147/460 (31%), Positives = 227/460 (49%), Gaps = 13/460 (2%) Query: 36 NPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPPSARERILLRLADLLEVHGDE 95 NP TG++L E D + V AA++ S WR +P S R ++ + +L + D+ Sbjct: 5 NPYTGELLEEFTDHTEQQVEAAIQKGQEAYLS--WRELPISQRADLMKKAGQVLRDNTDK 62 Query: 96 LARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATKLTGSTLDLSLPLPPEVRSRASTQ 155 ++ +L GK++ SK EV A Y A A ++ D + LP ++ Sbjct: 63 YGKIISLEMGKVITESK-SEVEKCAWVCEYYAENAEEMLA---DAPIALPDGKEAKVVYN 118 Query: 156 RVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAEETPLTALRLAELAMEAGLPA 215 P+G+V A++PWNFP AP L GN +LK A P AL + E+ +AG P Sbjct: 119 --PLGIVLAVMPWNFPFWQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGFPE 176 Query: 216 GAL-NVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIGSACGRSLKAVSLELGGKSPV 274 G +++ G + A ++ HP V TGS + G+ I + G +K LELGG P Sbjct: 177 GVFQSLLIGSDKVAN--IIAHPDVKAATLTGSEKAGQKIAAQAGEQIKKTVLELGGSDPF 234 Query: 275 IVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIYEDVIQRLAVIGESIVVGSGL 334 IVL D D +EAA+ AA N GQ C A R + + +Y++ I ES V G L Sbjct: 235 IVLKDADVKEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDPL 294 Query: 335 EQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTEAPCAQGFFVKPTIFANREKKDI 394 ++ M + + I+ GA++I GT+ P F+KP I + D+ Sbjct: 295 DEKAGYACMARPDLAMELYEQVEASIQKGAEVILEGTK-PEKGKAFIKPYIL-GKLTPDM 352 Query: 395 RLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASIWTNDLSAALRINDELEAGTVWV 454 +E+FGPV +D+ E + AN S +GLGAS+WT D A ++ ++E+G V++ Sbjct: 353 PAYREELFGPVASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIESGAVFI 412 Query: 455 NTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTRSLVI 494 N+ +P LPFGG K SG GRE I+ + +++ + Sbjct: 413 NSMVASNPYLPFGGIKKSGYGRELAENGIKEFMNIKTVYL 452 Lambda K H 0.317 0.134 0.395 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: 455 Number of extensions: 27 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: 496 Length of database: 453 Length adjustment: 33 Effective length of query: 463 Effective length of database: 420 Effective search space: 194460 Effective search space used: 194460 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 Sep 17 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