GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Acidovorax sp. GW101-3H11

Align aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized)
to candidate Ac3H11_1605 Aldehyde dehydrogenase B (EC 1.2.1.22)

Query= BRENDA::Q69P84
         (509 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1605 Aldehyde
           dehydrogenase B (EC 1.2.1.22)
          Length = 511

 Score =  454 bits (1169), Expect = e-132
 Identities = 238/482 (49%), Positives = 314/482 (65%), Gaps = 7/482 (1%)

Query: 33  SGPVVTSTNPTNNQVIAEVVEASAREYEEGMRACYDAAKTWMAIPAPKRGEIVRQIGDAL 92
           +G  + + +P   +V+A+V + SA +    +   + A   W  +PAP+RGE+VR +G+ L
Sbjct: 29  TGGTLAARSPITGEVLAQVPQQSAADATAAIGRAHAAFLAWRNVPAPRRGELVRLLGEEL 88

Query: 93  RAKLHHLGRLVSLEMGKILPEGIGEVQEIIDMCDYAVGLSRQLNGSIIPSERPNHMMMEV 152
           RA    LG LV++E GKI  EG+GEVQE+ID+CD+AVGLSRQL G  I +ERP H MME 
Sbjct: 89  RAAKGDLGLLVTIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMET 148

Query: 153 WNPLGVVGVITAFNFPCAVLGWNACIALVCGNCVVWKGAPTTPLITIAMTKIVASVLER- 211
           W+PLGV GVI+AFNFP AV  WNA +ALVCG+ VVWK +  TPL  +A   I    + R 
Sbjct: 149 WHPLGVCGVISAFNFPVAVWSWNAALALVCGDSVVWKPSEKTPLTALATHAIAQRAIARF 208

Query: 212 -NNLPGSIFTAFCGGADIGQAISLDTRIPLVSFTGSTKVGLMVQQQVNARFGKCLLELSG 270
             + P  +     G  DIG+ +  D R+P++S TGST +G  V  ++ ARF + +LEL G
Sbjct: 209 GTDAPEGLLELIVGQRDIGEVLVDDARVPVLSATGSTAMGRAVGPRLAARFARGILELGG 268

Query: 271 NNAIIVMDDADIQLAVRSVLFAAVGTAGQRCTTCRRLLLHESIYRTFLDQLVEVYKQVRI 330
           NNA IV   AD+ LA+R + FAA+GTAGQRCTT RRL +H SIY   + QL +VY  V++
Sbjct: 269 NNAAIVAPTADLNLALRGIAFAAMGTAGQRCTTLRRLFVHASIYDQLVPQLAKVYANVQV 328

Query: 331 GDPLENGTLLGPLHTPASRDAFLKGIQTIRSQGGKILYGGSAIESEGN----FVQPTIVE 386
           GDP   GTL+GPL    + D   K ++  R+ G  + +GG  +E  G     +V+P +VE
Sbjct: 329 GDPRTPGTLVGPLIDRMAFDGMQKALEQSRALGATV-HGGGRVEGVGGADAYYVRPALVE 387

Query: 387 ISPSAPVVREELFGPVLYVMKVQNLKEAVEINNSVPQGLSSSIFTKRPDIIFKWIGPHGS 446
           +         E F P+LYV++   + EA+ +NN+V  GLSSSIFT       +++   GS
Sbjct: 388 LQKHEGPALHETFAPILYVVRYSAIDEAIAMNNAVGAGLSSSIFTLNVREAEQFMSAAGS 447

Query: 447 DCGIVNVNIPTNGAEIGGAFGGEKATGGGREAGSDSWKQYMRRATCTINYGSELPLAQGI 506
           DCGI NVNI  +GAEIGGAFGGEK TGGGREAGSDSWK YMRRAT TINY + LPLAQG+
Sbjct: 448 DCGIANVNIGPSGAEIGGAFGGEKETGGGREAGSDSWKAYMRRATNTINYSTALPLAQGV 507

Query: 507 NF 508
            F
Sbjct: 508 TF 509


Lambda     K      H
   0.320    0.137    0.416 

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: 714
Number of extensions: 24
Number of successful extensions: 3
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: 509
Length of database: 511
Length adjustment: 34
Effective length of query: 475
Effective length of database: 477
Effective search space:   226575
Effective search space used:   226575
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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