GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mt2d in Bacteroides thetaiotaomicron VPI-5482

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate 349658 BT0130 putative oxidoreductase (NCBI ptt file)

Query= SwissProt::Q8NK50
         (266 letters)



>lcl|FitnessBrowser__Btheta:349658 BT0130 putative oxidoreductase
           (NCBI ptt file)
          Length = 271

 Score =  104 bits (260), Expect = 2e-27
 Identities = 83/270 (30%), Positives = 132/270 (48%), Gaps = 24/270 (8%)

Query: 13  DLFSLKGKVVVVTGASGPRGMGIEAARGCAEMGADLAITYSSRKEGAEKNAEELTKEYGV 72
           +LFS+ GKV V+TGA G  G  I  A+   + GA + +    R+E  +    EL K+YG 
Sbjct: 3   ELFSIAGKVAVITGAGGVLGGNI--AQHFVQQGAKV-VAIDIRQEQLDNRVAEL-KQYGQ 58

Query: 73  KVKVYKVNQSDYNDVERFVNQVVSDFGKIDAFIANAGAT-------ANSGVVDGSASDWD 125
            V     +  D   +E+   ++V+ +G+ID  +  AG         ++    D   S W+
Sbjct: 59  DVIGIIGDVLDIASLEKVAEEIVAQWGQIDILLNIAGGNMPGATLESDQNFYDMDISCWE 118

Query: 126 HVIQVDLSGTAYCAKAVGAHFKKQGHGSLVITASMSGHVANYPQEQTSYNVAKAGCIHLA 185
            V  ++++GT Y +   G    +Q  G ++  +SM+ + A        Y+ AK    +  
Sbjct: 119 KVTSLNMNGTVYPSMIFGKVMAEQKKGCIINVSSMAAYSAI--TRVPGYSAAKTAVANFT 176

Query: 186 RSLANE----WRDFARVNSISPGYI--DTGLSDFIDEKTQELWRSM-----IPMGRNGDA 234
           + LA+E    + D  RVN+I+PG+   D      I+       RS       PM R GD 
Sbjct: 177 QWLASEMALKYGDGIRVNAIAPGFFIGDQNRRVLINPDGSLTDRSKKVLAKTPMNRFGDI 236

Query: 235 KELKGAYVYLVSDASSYTTGADIVIDGGYT 264
           KEL GA  +L S+A+S+ TGA + IDGG++
Sbjct: 237 KELNGAVQFLCSEAASFVTGAMLPIDGGFS 266


Lambda     K      H
   0.314    0.131    0.379 

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: 147
Number of extensions: 8
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: 271
Length adjustment: 25
Effective length of query: 241
Effective length of database: 246
Effective search space:    59286
Effective search space used:    59286
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: 42 (22.0 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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