GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Bacteroides clarus YIT 12056

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate WP_004289114.1 BUB52_RS00875 SDR family oxidoreductase

Query= SwissProt::Q8NK50
         (266 letters)



>NCBI__GCF_900129655.1:WP_004289114.1
          Length = 271

 Score =  108 bits (271), Expect = 9e-29
 Identities = 88/268 (32%), Positives = 130/268 (48%), Gaps = 24/268 (8%)

Query: 15  FSLKGKVVVVTGASGPRGMGIEAARGCAEMGADLAITYSSRKEGAEKNAEELTKEYGVKV 74
           FS+ GKV V+TGA G  G  I  A+   + GA + +    R+E  +K  EEL K YG  V
Sbjct: 5   FSIAGKVAVITGAGGVLGGSI--AKCFMQQGAKV-VAVDIRQEQLDKRVEEL-KTYGEDV 60

Query: 75  KVYKVNQSDYNDVERFVNQVVSDFGKIDAFIANAGATANSGVV-------DGSASDWDHV 127
                N  D   +E+  + +V+ +G+ID  +  AG       +       D   S W+ V
Sbjct: 61  IGIVGNVLDIASLEKLADDIVAKWGRIDILLNIAGGNMPGATLAPDQHFYDMDISCWEKV 120

Query: 128 IQVDLSGTAYCAKAVGAHFKKQGHGSLVITASMSGHVANYPQEQTSYNVAKAGCIH---- 183
             ++++GT Y +        KQG G +V  +SM+ + A        Y+ AK    +    
Sbjct: 121 TNLNMNGTVYPSLVFSKVMAKQGKGCIVNVSSMAAYSAI--TRVPGYSAAKTAVANFTQW 178

Query: 184 LARSLANEWRDFARVNSISPGYI--DTGLSDFIDEKTQELWRSM-----IPMGRNGDAKE 236
           LA  LA ++ D  RVN+I+PG+   D   +  I+       RS       PM R GD  E
Sbjct: 179 LASELALKYGDGIRVNAIAPGFFIGDQNRAVLINPDGSLTDRSKKVLAKTPMKRFGDINE 238

Query: 237 LKGAYVYLVSDASSYTTGADIVIDGGYT 264
           L GA  +L SDA+S+ TGA + IDGG++
Sbjct: 239 LNGAVQFLCSDAASFVTGALLPIDGGFS 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: 148
Number of extensions: 11
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 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