GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frcC in Burkholderia phytofirmans PsJN

Align Fructose import permease protein FrcC (characterized)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease

Query= SwissProt::Q9F9B1
         (360 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS16055 BPHYT_RS16055 sugar ABC
           transporter permease
          Length = 335

 Score =  174 bits (441), Expect = 3e-48
 Identities = 111/315 (35%), Positives = 166/315 (52%), Gaps = 10/315 (3%)

Query: 43  LHSSPAAVPLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGI 102
           L  S    P I L++  I   V     F S   +  +L+QV+I  I+    T VILT GI
Sbjct: 31  LKRSTLFYPFIGLLVVCIVM-VFASDSFLSGANIENVLRQVSINAIIAVGMTCVILTGGI 89

Query: 103 DLSVGAIMVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTL 162
           DLSVG++M L+  +        G     ++  G+ VG   G  NG  VA   +PP IVTL
Sbjct: 90  DLSVGSVMALAGTLAAGLMVA-GMNAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVTL 148

Query: 163 GMWQIVLASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLW 222
               I      +Y+         I      + FFG    +G       VV+M ++  + W
Sbjct: 149 ATMGIARGLALIYTGG-----YPIDGLPDWVSFFGSGKILGVQA---PVVIMAVIYVIAW 200

Query: 223 YVLNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSP 282
            +L R  +GRYVYA+G + +A +L+GV V R+ + +YT++GL  A A   L  R+ S  P
Sbjct: 201 VLLERMPFGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSGQP 260

Query: 283 TAGQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIG 342
            AG    +++I AVV+GG S+ GGRGSI+G L GAL++GV + GL ++G +P    ++ G
Sbjct: 261 NAGVGFELDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVIKG 320

Query: 343 LLIIIAVAIDQWIRK 357
            +I++A+ I +  RK
Sbjct: 321 GIILLAIYISRDRRK 335


Lambda     K      H
   0.327    0.141    0.420 

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: 356
Number of extensions: 27
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: 360
Length of database: 335
Length adjustment: 29
Effective length of query: 331
Effective length of database: 306
Effective search space:   101286
Effective search space used:   101286
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 (21.7 bits)
S2: 49 (23.5 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