GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Pseudomonas fluorescens GW456-L13

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate PfGW456L13_3512 Alcohol dehydrogenase (EC 1.1.1.1); Acetaldehyde dehydrogenase (EC 1.2.1.10)

Query= BRENDA::A4IP64
         (395 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3512
          Length = 387

 Score =  198 bits (504), Expect = 2e-55
 Identities = 123/372 (33%), Positives = 199/372 (53%), Gaps = 6/372 (1%)

Query: 15  GWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPL 74
           G G+   +    K  GA+ +LV++DP ++  G V  V + L+  G    +Y+DV P P +
Sbjct: 19  GAGSRHSVGNYAKTFGARKVLVVSDPGVIAAGWVADVEASLQALGIEYCLYSDVSPNPRV 78

Query: 75  ETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGL 134
           E         R+   D+++ VGGGS +D  K   ++  H  S+ D+    G  T+     
Sbjct: 79  EEVMLGAEMYRENHCDVIVAVGGGSPMDCGKGIGIVVAHGRSILDF---EGVDTIRVPSP 135

Query: 135 PKILIPTTSGTGSEVTNISVLS--LETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAAT 192
           P ILIPTT+GT ++V+   ++S   E  K  +    ++ DV+++DP+ T+S+ P ++A T
Sbjct: 136 PLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAVVPDVSLIDPETTLSMDPFLSACT 195

Query: 193 GIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAG 252
           GIDAL HA+EA+VS    P +D  A+ A+RLI+ +L + +AN +D   R  +  GS  AG
Sbjct: 196 GIDALVHAIEAFVSTGHGPLTDPHALEAMRLINGNLVQMIANPTDIALREKIMLGSMQAG 255

Query: 253 LAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALGGNS 312
           LAF NA +  VHA+++ LGG   + HG  NAVL+ +V+ +   S  +R   I    G + 
Sbjct: 256 LAFSNAILGAVHAMSHSLGGFLDLPHGLCNAVLVEHVVAFNYNSAPERFKVIAETFGIDC 315

Query: 313 SFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPL 372
             L+  +   R VE L      +G  +TLG  G+  S +  L++ A+    +L  +P   
Sbjct: 316 RGLNHRQICGRLVEHLIALKHAIGFHETLGLHGVRTSDIPFLSQHAMHDPCILT-NPRES 374

Query: 373 LEADIRAIYEAA 384
            + D+  +Y  A
Sbjct: 375 SQRDVEVVYGEA 386


Lambda     K      H
   0.318    0.135    0.381 

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: 396
Number of extensions: 17
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: 395
Length of database: 387
Length adjustment: 31
Effective length of query: 364
Effective length of database: 356
Effective search space:   129584
Effective search space used:   129584
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: 50 (23.9 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