GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Phaeobacter inhibens BS107

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate GFF3641 PGA1_262p00450 sugar ABC transporter, ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__Phaeo:GFF3641
          Length = 260

 Score =  190 bits (483), Expect = 2e-53
 Identities = 102/253 (40%), Positives = 154/253 (60%), Gaps = 7/253 (2%)

Query: 5   PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64
           P++  + +   +G + A+D    DLYPGE++ ++G NGAGKS++IK +SGA   D GEIR
Sbjct: 14  PLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIR 73

Query: 65  LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124
           + G  ++  +P +AR   IET+YQ LAL+  L  A N+FLGRE+  P      F  +D +
Sbjct: 74  VNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTP------FGLVDDS 127

Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184
           AME + R  ++ L     Q  ++ V  LSGGQRQ VA+ARA  F +K++IMDEPTAALG 
Sbjct: 128 AMEAECRKIMNRLN-PNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGP 186

Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244
            E++ V ELI  ++ +G+ I LI H++  V E+ DR  + + G+ +  ++  D T  D +
Sbjct: 187 HETQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDVTDDDLL 246

Query: 245 AFMTGAKEPPREA 257
           + +   K P   A
Sbjct: 247 SMIILGKRPGEAA 259


Lambda     K      H
   0.321    0.136    0.383 

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: 166
Number of extensions: 6
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: 260
Length of database: 260
Length adjustment: 24
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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