GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_3133
          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:

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