GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ngcG in Dyella japonica UNC79MFTsu3.2

Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate N515DRAFT_3133 N515DRAFT_3133 carbohydrate ABC transporter membrane protein 2, CUT1 family (TC 3.A.1.1.-)

Query= TCDB::Q8RJU8
         (307 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3133
          Length = 273

 Score =  145 bits (367), Expect = 8e-40
 Identities = 86/267 (32%), Positives = 141/267 (52%), Gaps = 7/267 (2%)

Query: 43  HGILVLWAFMVVLPLLWAVMTSFK--DDASIFGSPWSLPDKLHFDNWSRAWTEAHMGDYF 100
           +G+L+    + V PLLW +  SF    +AS    P  LP      N+   +  A MG Y 
Sbjct: 11  NGLLIGSTLVAVFPLLWMLSVSFMRPGEASALPPPL-LPTHATLANYHELFERAGMGRYL 69

Query: 101 LNTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVN 160
           LN++ V     + +L    MA Y  A+  F G   ++ + +GG+  P  +A++PLF ++ 
Sbjct: 70  LNSLGVSSAITLLSLAFNLMAGYAFAKLRFSGRERLFQVLLGGLVIPAQVAMLPLFLLLK 129

Query: 161 NMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPM 220
            +GL+N+   +++   A +  F +F +  + R +P  + EAA +DGA   R F QI+LP+
Sbjct: 130 YLGLVNSYAAVVVP--AMATIFGIFLVRQYARGIPDDLMEAARIDGAGELRIFVQIVLPL 187

Query: 221 AKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLV 280
            KP ++++ IF FL  WN +M P +  T  +   L   L  L  S+ +  D   + AG V
Sbjct: 188 LKPIMVTLAIFTFLTAWNDFMWPLIALTGQEHYTLPIALASL--SREHVQDSELMMAGSV 245

Query: 281 MAMLPVLAAYIIFQRQVVQGLTAGALK 307
           + +LPVL  ++  QR  +QGL  G++K
Sbjct: 246 VTVLPVLVLFLALQRYYLQGLLLGSVK 272


Lambda     K      H
   0.326    0.141    0.440 

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: 257
Number of extensions: 17
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: 307
Length of database: 273
Length adjustment: 26
Effective length of query: 281
Effective length of database: 247
Effective search space:    69407
Effective search space used:    69407
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 (21.6 bits)
S2: 48 (23.1 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