GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_02703
          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:

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