GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtsC in Dyella japonica UNC79MFTsu3.2

Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate N515DRAFT_3133 N515DRAFT_3133 carbohydrate ABC transporter membrane protein 2, CUT1 family (TC 3.A.1.1.-)

Query= TCDB::Q72KX4
         (268 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3133 N515DRAFT_3133
           carbohydrate ABC transporter membrane protein 2, CUT1
           family (TC 3.A.1.1.-)
          Length = 273

 Score =  144 bits (363), Expect = 2e-39
 Identities = 85/207 (41%), Positives = 124/207 (59%), Gaps = 7/207 (3%)

Query: 65  NSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMKS 124
           NS+ ++ + TLLS     + GY  AK  F G   LF ++L G+ IP Q  ++PLF  +K 
Sbjct: 71  NSLGVSSAITLLSLAFNLMAGYAFAKLRFSGRERLFQVLLGGLVIPAQVAMLPLFLLLKY 130

Query: 125 IGLYGSLFGLVL--VHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILP 182
           +GL  S   +V+  +  I+GI +V    R Y   IPD+L+EAARIDGAG   IF  ++LP
Sbjct: 131 LGLVNSYAAVVVPAMATIFGIFLV----RQYARGIPDDLMEAARIDGAGELRIFVQIVLP 186

Query: 183 LSVPAFVVVAIWQFTQIWNEFLF-AVTLTRPESQPITVALAQLAGGEAVKWNLPMAGAIL 241
           L  P  V +AI+ F   WN+F++  + LT  E   + +ALA L+        L MAG+++
Sbjct: 187 LLKPIMVTLAIFTFLTAWNDFMWPLIALTGQEHYTLPIALASLSREHVQDSELMMAGSVV 246

Query: 242 AALPTLLVYILLGRYFLRGLLAGSVKG 268
             LP L++++ L RY+L+GLL GSVKG
Sbjct: 247 TVLPVLVLFLALQRYYLQGLLLGSVKG 273


Lambda     K      H
   0.330    0.146    0.461 

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: 222
Number of extensions: 10
Number of successful extensions: 3
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: 268
Length of database: 273
Length adjustment: 25
Effective length of query: 243
Effective length of database: 248
Effective search space:    60264
Effective search space used:    60264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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