GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Marinobacter adhaerens HP15

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized)
to candidate GFF2840 HP15_2784 3-ketoacyl-(acyl-carrier-protein) reductase

Query= SwissProt::P0C0Y4
         (266 letters)



>FitnessBrowser__Marino:GFF2840
          Length = 247

 Score =  142 bits (359), Expect = 5e-39
 Identities = 87/247 (35%), Positives = 139/247 (56%), Gaps = 7/247 (2%)

Query: 17  LKGKVVIVTGASGPTGIGTEAARGCAEYGADLAITYNSRAEGAEKNAKEMSEKYGVKVKA 76
           LKGKV +VTGAS   GIG   A   A+ GAD+AI Y SR    E+ AKE+ E  GV+  +
Sbjct: 4   LKGKVALVTGAS--RGIGRHIALQLAQRGADVAINYRSRQSEGEEVAKEI-EATGVRALS 60

Query: 77  YKCQVNEYAQCEKLVQDVIKDFGKVDVFIANAGKTADNGILDATVEQWNEVIQTDLTGTF 136
           +K  +++  +   LV+ V + +G++D+ + NAG T D  +   T + WN+V+ T+L   +
Sbjct: 61  FKADLSKMPEARSLVRQVQEQWGRIDILVNNAGITKDKSMKKLTDDDWNDVLDTNLGSVY 120

Query: 137 NCARAVGLHFRERKTGSLVITSSMSGHIANFPQEQASYNVAKAGCIHLAKSLANEWRDF- 195
                V     ++K G ++  +S  G   NF   QA+Y  +K G I   K+LA E   + 
Sbjct: 121 ATCSEVLKIMMDQKYGRIINITSFVGQAGNF--GQANYAASKGGIIAFTKTLALEMAKYN 178

Query: 196 ARVNSISPGYIDTGLSDFVPQDIQKLWHSMIPMGRDAKATELKGAYVYFASDASSYCTGS 255
             VN+I+PG+ +T +   VP++I++   + +PMGR  K  E+  A V+ A++   Y TG 
Sbjct: 179 ITVNAIAPGFTETEMLAQVPENIREQIIARVPMGRFGKPEEIARAVVFLAAE-GDYITGQ 237

Query: 256 DLLIDGG 262
            + ++GG
Sbjct: 238 QINVNGG 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: 173
Number of extensions: 8
Number of successful extensions: 5
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: 247
Length adjustment: 24
Effective length of query: 242
Effective length of database: 223
Effective search space:    53966
Effective search space used:    53966
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