GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1605
          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 (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:

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