GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS16055
          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:

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