GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Weissella oryzae SG25

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_027699119.1 TT13_RS05830 glucose 1-dehydrogenase

Query= BRENDA::Q4J702
         (264 letters)



>NCBI__GCF_000691805.2:WP_027699119.1
          Length = 270

 Score =  132 bits (331), Expect = 1e-35
 Identities = 76/246 (30%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 11  GMNAVVLGASSGIGKAIAEMFSEMGGKVVLSDI--DEEGLKRLSDSLRSRGHEVNHMKCD 68
           G  AVV G+SSGIG+AIA      G  VV++    D++ +  +   +   G     +K D
Sbjct: 15  GKTAVVTGSSSGIGEAIARHMGAEGMNVVINYFSPDDKAIDGIIYLIEQSGGHAVAIKAD 74

Query: 69  ITDLNQVKKLVNFSLSVYGNVDALYVTPSINVRKSIENYTYEDFEKVINVNLKGNFMVVK 128
           +     V+ + + ++  +G++D         ++ +     Y D+++VI+V+L G F+  K
Sbjct: 75  VGTEAGVQAIYDKAIEAFGDLDVWVNNAGFEIQSATHLTDYRDWQRVIHVDLDGVFLGTK 134

Query: 129 EFLSVMKNNKGGGSVVLFSSIRGTVVEPGQSVYAMTKAGIIQLAKVAAAEYGKYNIRVNV 188
             ++    +   G ++  SSI   +  P  + YA  KAG++   K +A EY    IR+N 
Sbjct: 135 IAINHFLTHNKVGQILNTSSIHDKIPWPTYASYATAKAGVLMFTKTSALEYADKGIRINA 194

Query: 189 IAPGVVDTPLTRQIKSDPEWFKAYTEKTILKRWATPEEIANVALFLAMPASSYITGTVIY 248
           I+PG ++TP+  +  +DP   K  T+   +KR   P ++AN A++L    +SYITGT +Y
Sbjct: 195 ISPGALETPINAERFADPAVRKDTTDMIPMKRIGDPLDVANAAVWLISSEASYITGTTLY 254

Query: 249 VDGGWT 254
           +DGG T
Sbjct: 255 IDGGIT 260


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: 189
Number of extensions: 6
Number of successful extensions: 2
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: 270
Length adjustment: 25
Effective length of query: 239
Effective length of database: 245
Effective search space:    58555
Effective search space used:    58555
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