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_00427 H281DRAFT_00427 monosaccharide ABC transporter membrane protein, CUT2 family

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__Burk376:H281DRAFT_00427
          Length = 341

 Score =  219 bits (557), Expect = 1e-61
 Identities = 125/310 (40%), Positives = 177/310 (57%), Gaps = 3/310 (0%)

Query: 46  SPAAVPLIVLVLSLI---AFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGI 102
           SP A+  ++   SLI    F       F     +  ILQ  A+ G++  A T VI+T GI
Sbjct: 25  SPTALQKLLAFASLILLLVFFSFASPAFMQMDNILGILQATAVNGVLAIASTFVIITGGI 84

Query: 103 DLSVGAIMVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTL 162
           DLSVG +M  ++VI G F   +  P  L VI  +G GA+CG I+GTL A+MK+PPFI TL
Sbjct: 85  DLSVGTLMTFTAVICGVFLTYWHLPMWLGVIAAIGTGAICGTISGTLTAKMKIPPFIATL 144

Query: 163 GMWQIVLASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLW 222
           GM  ++   + + SA++ I   D      I Q     + + +      V+++  L  +  
Sbjct: 145 GMMLLLKGLSLVVSADKPIYFTDTENFYMISQDSLIGYLVPSLPIPNAVLILFFLAIVSS 204

Query: 223 YVLNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSP 282
             LNRTA GRY +A+G + EA +L+GVNV R  I+IY L G IC +AG  +  R+ S  P
Sbjct: 205 VTLNRTALGRYTFALGSNEEAVRLSGVNVDRWKIAIYGLGGAICGIAGLLIASRLNSAQP 264

Query: 283 TAGQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIG 342
             GQ   +E+I AVVIGG SL GG G+I+G + GA I+ V + GLR+M    +W  ++ G
Sbjct: 265 ALGQGYELEAIAAVVIGGTSLSGGSGTILGTIIGAFIMSVLTNGLRIMSVAQEWQIVVTG 324

Query: 343 LLIIIAVAID 352
           L+II+AV  D
Sbjct: 325 LIIILAVYAD 334


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: 379
Number of extensions: 22
Number of successful extensions: 2
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: 341
Length adjustment: 29
Effective length of query: 331
Effective length of database: 312
Effective search space:   103272
Effective search space used:   103272
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