GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Pseudomonas simiae WCS417

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate GFF3404 PS417_17420 alcohol dehydrogenase

Query= BRENDA::A4IP64
         (395 letters)



>FitnessBrowser__WCS417:GFF3404
          Length = 387

 Score =  193 bits (490), Expect = 8e-54
 Identities = 122/386 (31%), Positives = 199/386 (51%), Gaps = 6/386 (1%)

Query: 1   MSVARIVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGY 60
           +S+ R    P    G G    +    K  GA+ +LV++DP ++  G V  V + L+  G 
Sbjct: 5   LSLLRKFVSPEIIFGAGCRHNVGNYAKTFGARKVLVVSDPGVIAAGWVADVEASLQAIGI 64

Query: 61  SVHVYTDVVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADY 120
              +Y+ V P P +E         R+   D+++ +GGGS +D  K   ++  H   + ++
Sbjct: 65  DYCLYSAVSPNPRVEEVMLGAEVYRENHCDVIVAIGGGSPMDCGKAIGIVVAHGRCILEF 124

Query: 121 LNLTGTRTLEKKGLPKILIPTTSGTGSEVTNISVLS--LETTKDVVTHDYLLADVAIVDP 178
               G  T+     P ILIPTT+GT ++V+   ++S   E  K  +    ++ DV+++DP
Sbjct: 125 ---EGVDTIRVPSPPLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAVVPDVSLIDP 181

Query: 179 QLTVSVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDK 238
           + T S+ P ++A TGIDAL HA+EA+VS    P +D  A+ A+RLI+ +L + +AN  D 
Sbjct: 182 ETTASMDPFLSACTGIDALVHAIEAFVSTGHGPLTDPHALEAMRLINGNLVQMIANPGDI 241

Query: 239 QARIDMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCT 298
             R  +  GS  AGLAF NA +  VHA+++ LGG   + HG  NAVL+ +V+ +   S  
Sbjct: 242 ALREKIMLGSMQAGLAFSNAILGAVHAMSHSLGGFLDLPHGLCNAVLVEHVVAFNYNSAP 301

Query: 299 KRMADIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDA 358
           +R   I    G +   LS  +   R VE L      +G  +TLG  G+  + +  L++ A
Sbjct: 302 ERFKVIAETFGIDCRGLSHRQVCARLVEHLIALKHAIGFHETLGLHGVRVADIPFLSRHA 361

Query: 359 VQQKRLLARSPLPLLEADIRAIYEAA 384
           +    +L  +P    + D+  +Y  A
Sbjct: 362 MHDPCILT-NPRESSQRDVEVVYGEA 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: 408
Number of extensions: 16
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