GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Burkholderia phytofirmans PsJN

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate BPHYT_RS13905 BPHYT_RS13905 ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__BFirm:BPHYT_RS13905
          Length = 258

 Score =  185 bits (469), Expect = 9e-52
 Identities = 97/247 (39%), Positives = 152/247 (61%), Gaps = 3/247 (1%)

Query: 6   ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65
           IL    + K +G+V AL      L  GE+  ++GDNGAGKS++IK ++G   P  G+  +
Sbjct: 2   ILALENVNKYFGKVIALSGVTLRLKRGEVHCLLGDNGAGKSTLIKTLAGVHQPSSGQYLV 61

Query: 66  EGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAA 125
           +GKP+ F SP +A   GI TVYQ+LAL P LS+A N F+GRE +K   +  +   +D   
Sbjct: 62  DGKPVLFESPKDALDLGIATVYQDLALVPLLSVARNFFMGREPQKK--LFGFLSVMDLET 119

Query: 126 MEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVK 185
               AR KL+E+G+  +++ +Q + T+SGG++Q +A+ARA  FG++V+I+DEPTAALGVK
Sbjct: 120 SATTARDKLAEMGI-NVRDAHQPIGTMSGGEKQCLAIARAIHFGARVLILDEPTAALGVK 178

Query: 186 ESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVA 245
           +S  VL+LI   R +G+ ++ I+HN+ H + + D   +   G+ L     +  +  + + 
Sbjct: 179 QSFNVLKLIHKARAKGISVIFITHNVHHAYPIGDSFTVLNRGKSLGTFTKETISKDEVLD 238

Query: 246 FMTGAKE 252
            M G  E
Sbjct: 239 MMAGGAE 245


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: 164
Number of extensions: 3
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: 258
Length adjustment: 24
Effective length of query: 236
Effective length of database: 234
Effective search space:    55224
Effective search space used:    55224
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