GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Shewanella oneidensis MR-1

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized)
to candidate 201911 SO2776 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI ptt file)

Query= SwissProt::P0C0Y4
         (266 letters)



>FitnessBrowser__MR1:201911
          Length = 248

 Score =  130 bits (328), Expect = 2e-35
 Identities = 87/248 (35%), Positives = 130/248 (52%), Gaps = 10/248 (4%)

Query: 16  SLKGKVVIVTGASGPTGIGTEAARGCAEYGADLAITYNSRAEGAEKNAKEMSEKYGVKVK 75
           SL GKV +VTGAS   GIG   A    E GA +  T  S     EK A  + E  G K  
Sbjct: 6   SLAGKVALVTGAS--RGIGRAIAETLVEAGAVVIGTATS-----EKGAAAIQEYLGDKGF 58

Query: 76  AYKCQVNEYAQCEKLVQDVIKDFGKVDVFIANAGKTADNGILDATVEQWNEVIQTDLTGT 135
                V +      L   + +  G VD+ + NAG T DN ++    ++WN++I T+LT  
Sbjct: 59  GLVLNVTDSQSVTDLFDSIKEKAGDVDILVNNAGITRDNLLMRMKDDEWNDIIDTNLTSL 118

Query: 136 FNCARAVGLHFRERKTGSLVITSSMSGHIANFPQEQASYNVAKAGCIHLAKSLANEWRDF 195
           F  ++ V     +++ G ++   S+ G + N    Q +Y+ AKAG I   KSLA E    
Sbjct: 119 FRLSKPVMRTMMKKRFGRIINIGSVVGTMGN--AGQVNYSAAKAGLIGFTKSLAREVASR 176

Query: 196 A-RVNSISPGYIDTGLSDFVPQDIQKLWHSMIPMGRDAKATELKGAYVYFASDASSYCTG 254
              VN+I+PG+I T ++D + +D QK   S +PM R  +A E+  A ++ ASD+++Y TG
Sbjct: 177 QITVNAIAPGFIQTDMTDELTEDQQKAIMSQVPMERLGQAQEIANAVLFLASDSAAYITG 236

Query: 255 SDLLIDGG 262
             L ++GG
Sbjct: 237 ETLHVNGG 244


Lambda     K      H
   0.316    0.132    0.389 

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: 134
Number of extensions: 7
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: 266
Length of database: 248
Length adjustment: 24
Effective length of query: 242
Effective length of database: 224
Effective search space:    54208
Effective search space used:    54208
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 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