GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Lacinutrix algicola AKS293

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_055437269.1 ASC41_RS13975 3-oxoacyl-[acyl-carrier-protein] reductase

Query= BRENDA::Q4J702
         (264 letters)



>NCBI__GCF_001418085.1:WP_055437269.1
          Length = 248

 Score =  152 bits (384), Expect = 7e-42
 Identities = 94/245 (38%), Positives = 132/245 (53%), Gaps = 4/245 (1%)

Query: 9   VKGMNAVVLGASSGIGKAIAEMFSEMGGKVVLS-DIDEEGLKRLSDSLRSRGHEVNHMKC 67
           ++G  A++ GAS GIGK IAE+F++ G  V  +     E    L   L + G +    K 
Sbjct: 4   LEGKTAIITGASRGIGKGIAEVFAQQGANVAFTYSSSVEAANALEKELNALGVKAKGYKS 63

Query: 68  DITDLNQVKKLVNFSLSVYGNVDALYVTPSINVRKSIENYTYEDFEKVINVNLKGNFMVV 127
           +  + ++ +KL    L+ +G++D L     I     +      DF+KVI VNLK  F + 
Sbjct: 64  NAANFDESQKLAEDVLAEFGSIDILINNAGITKDNLLMRMGEADFDKVIEVNLKSVFNMT 123

Query: 128 KEFLSVMKNNKGGGSVVLFSSIRGTVVEPGQSVYAMTKAGIIQLAKVAAAEYGKYNIRVN 187
           K     M   + G S++  SS+ G     GQ+ YA +KAGII  +K  A E G  NIR N
Sbjct: 124 KAVQRTMLKQRKG-SIINMSSVVGVKGNAGQTNYAASKAGIIGFSKSVALELGSRNIRSN 182

Query: 188 VIAPGVVDTPLTRQIKSDPEWFKAYTEKTILKRWATPEEIANVALFLAMPASSYITGTVI 247
           VIAPG ++T +T   K D E  K++     LKR  TPE+IANV +FLA   S+Y+TG  I
Sbjct: 183 VIAPGFIETEMT--AKLDEETVKSWRNAIPLKRGGTPEDIANVCVFLASDMSAYVTGQTI 240

Query: 248 YVDGG 252
            VDGG
Sbjct: 241 NVDGG 245


Lambda     K      H
   0.317    0.134    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: 183
Number of extensions: 9
Number of successful extensions: 4
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: 264
Length of database: 248
Length adjustment: 24
Effective length of query: 240
Effective length of database: 224
Effective search space:    53760
Effective search space used:    53760
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 (21.6 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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