GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Echinicola vietnamensis KMM 6221, DSM 17526

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::V4GH04
         (496 letters)



>lcl|FitnessBrowser__Cola:Echvi_3822 Echvi_3822 NAD-dependent
           aldehyde dehydrogenases
          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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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