GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Echinicola vietnamensis KMM 6221, DSM 17526

Align BadH (characterized)
to candidate Echvi_3928 Echvi_3928 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= metacyc::MONOMER-893
         (255 letters)



>FitnessBrowser__Cola:Echvi_3928
          Length = 252

 Score =  139 bits (350), Expect = 6e-38
 Identities = 87/254 (34%), Positives = 131/254 (51%), Gaps = 7/254 (2%)

Query: 1   MARLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAV 60
           M+ L  K AV+TGG  GIG +T ++  +EGA++ +   +   AEKV  A  + G T   +
Sbjct: 1   MSHLNGKVAVVTGGNSGIGYSTAKKLKEEGAQVIITGRS---AEKVNVAAAELGVTG--I 55

Query: 61  RCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALH 120
             D+ +  ++DAA+       G VDIL  NAG  +  P  +T    +++ + INL GA+ 
Sbjct: 56  TADVLELAAIDAAVNQVKADFGHVDILFVNAGIFLPAPIGQTTEDLFDQQMDINLKGAVF 115

Query: 121 MHHAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITV 180
                LP  + +  G I+N++S  A  G    ++Y A K  L ++++T A E A   I V
Sbjct: 116 TIEKFLP--ILKDGGSIINLSSINAYTGMPNTSIYGASKAALNSYTRTAATELAPRKIRV 173

Query: 181 NVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFI 240
           N V PGP  T + +           +  A    IPL R GKP+D+A  +AF  SD A FI
Sbjct: 174 NAVNPGPVYTPIFSKTGMSEDQLNGMAAAMQNRIPLKRYGKPEDIAELVAFLASDRASFI 233

Query: 241 TGQVLSVSGGLTMN 254
           TG   ++ GG  +N
Sbjct: 234 TGAEYNIDGGTNVN 247


Lambda     K      H
   0.318    0.135    0.398 

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: 169
Number of extensions: 9
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: 255
Length of database: 252
Length adjustment: 24
Effective length of query: 231
Effective length of database: 228
Effective search space:    52668
Effective search space used:    52668
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: 47 (22.7 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