GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpQ in Cupriavidus basilensis 4G11

Align ABC transporter for Glycerol, permease component 2 (characterized)
to candidate RR42_RS13775 RR42_RS13775 sugar ABC transporter permease

Query= reanno::acidovorax_3H11:Ac3H11_794
         (270 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS13775 RR42_RS13775 sugar ABC
           transporter permease
          Length = 277

 Score =  468 bits (1205), Expect = e-137
 Identities = 223/262 (85%), Positives = 246/262 (93%)

Query: 9   RTLFLIAYLLFALLPIYWMVNMSFKTNAEILSTFSFFPQHFTWDNYKTIFTDESWYSGYI 68
           R +FL+ YL+FA+LPIYWM+NMSFK+N EI+ST S +P  FT ++YKTIFTD SWYSGYI
Sbjct: 16  RAVFLVVYLVFAILPIYWMLNMSFKSNEEIVSTLSLWPNDFTLEHYKTIFTDPSWYSGYI 75

Query: 69  NSLIYVSINMVITLTVALPAAYAFSRYSFLGDKHVFFWLLTNRMTPPAVFLLPFFQLYTT 128
           NS+IYV++N VI++TVALPAAYAFSRY F+GDKHVFFWLLTNRMTPPAVFLLPFFQLYTT
Sbjct: 76  NSMIYVAMNTVISITVALPAAYAFSRYRFIGDKHVFFWLLTNRMTPPAVFLLPFFQLYTT 135

Query: 129 VGLMDTHIAVALAHLLFSVPLAVWILEGFMSGIPREIDETAYIDGYSFPRFFMTIFLPLI 188
           +GLMDTH+ VALAHL+F+VPLAVWILEGFMSG+PREIDETAY+DGYSF RFF+TIFLPLI
Sbjct: 136 IGLMDTHLGVALAHLVFNVPLAVWILEGFMSGVPREIDETAYVDGYSFGRFFITIFLPLI 195

Query: 189 KAGVGVAAFFCFMFSWVELLLARTLTSVNAKPIVATMTRTVSASGMDWATLAAAGVLTIV 248
           KAGVGVAAFFCFMFSWVELLLARTLTSVNAKPIVATMTRTVSASGMDW  LAAAGVLTIV
Sbjct: 196 KAGVGVAAFFCFMFSWVELLLARTLTSVNAKPIVATMTRTVSASGMDWGVLAAAGVLTIV 255

Query: 249 PGAIVIWFVRHYIAKGFAMGRV 270
           PG IVIWFVRHYIAKGFAMGRV
Sbjct: 256 PGGIVIWFVRHYIAKGFAMGRV 277


Lambda     K      H
   0.332    0.141    0.451 

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: 386
Number of extensions: 14
Number of successful extensions: 1
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: 270
Length of database: 277
Length adjustment: 25
Effective length of query: 245
Effective length of database: 252
Effective search space:    61740
Effective search space used:    61740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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