GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frcC in Paraburkholderia bryophila 376MFSha3.1

Align Fructose import permease protein FrcC (characterized)
to candidate H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family

Query= SwissProt::Q9F9B1
         (360 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02703 H281DRAFT_02703
           monosaccharide ABC transporter membrane protein, CUT2
           family
          Length = 333

 Score =  179 bits (453), Expect = 1e-49
 Identities = 117/351 (33%), Positives = 187/351 (53%), Gaps = 42/351 (11%)

Query: 18  LADSSTDVASFDAHDKTLLQKLQHFLHSSPAAVPLIVLVLSLIAFGVILGGKFFSAFTMT 77
           +  ++ + A  +A  + ++++L+  +    AA+ +I + LS      I   +F +  T+T
Sbjct: 1   MTSTAANRADTEALSRRVIRQLRSGIGPLFAALVIICIALS------IASPEFLTTSTLT 54

Query: 78  LILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVLSSVIMGQFTFRYGFPPA-----LSV 132
            I+ QV++VGI     T VI+T+GIDLSVG+++ L+ ++    T   G  P      ++ 
Sbjct: 55  NIMVQVSVVGIAAVGGTFVIITSGIDLSVGSLVALTGMVAA--TVMAGSSPGAIGLGIAG 112

Query: 133 ICG-LGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLASNFLYSANETIRAQDISANAS 191
           +C  L VGA  G +NG  VA ++L PFIVTL M  +        S   T           
Sbjct: 113 LCAALAVGAAAGALNGLAVAWLRLVPFIVTLAMMAMARGLTLAISDGRT----------- 161

Query: 192 ILQFFGQNFRIGNAVFTYG----------VVVMVLLVCLLWYVLNRTAWGRYVYAVGDDP 241
                   F   NA   +G          ++VM+++  +   +L +T +G  V+AVG + 
Sbjct: 162 -------KFDFPNAFTAFGAKTVAGLPMPMIVMLVIFVIGHVLLRKTTFGHQVFAVGGNQ 214

Query: 242 EAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANIESITAVVIGGI 301
           EAA+LAG+ V R++   Y L+G+  A+AG  L GR+ S  P+A     ++ I AVVIGG 
Sbjct: 215 EAARLAGIPVHRVVFLTYMLAGVTAAIAGIVLAGRLNSALPSAANGLELQVIAAVVIGGT 274

Query: 302 SLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVAID 352
           SL GGRGSI+G   G +++GV ++GL L+G +P WT  + G +I  AV +D
Sbjct: 275 SLAGGRGSIVGTFIGVVLIGVINVGLSLLGVNPFWTQFIQGGVIFAAVLLD 325


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: 362
Number of extensions: 16
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: 333
Length adjustment: 29
Effective length of query: 331
Effective length of database: 304
Effective search space:   100624
Effective search space used:   100624
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