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 GFF717 PGA1_c07320 sugar ABC transporter, ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__Phaeo:GFF717
          Length = 261

 Score =  186 bits (472), Expect = 4e-52
 Identities = 100/250 (40%), Positives = 155/250 (62%), Gaps = 6/250 (2%)

Query: 4   EPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEI 63
           +P++  +G+ K +G V AL     D++PGE   ++GDNGAGKS+ IK +SG   P +G+I
Sbjct: 5   QPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDI 64

Query: 64  RLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGRE-IRKPGIMGKWFRSLD 122
             EG+P+ F  P +A  AGI TV+Q+LA+ P +S++ N F+G E IRK G +    +  D
Sbjct: 65  LFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPL----KLFD 120

Query: 123 RAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAAL 182
                +    ++ ++G+  ++  +QAV TLSGG+RQ VA+ARA  FG+KV+I+DEPT+AL
Sbjct: 121 HDYANRITMEEMRKMGI-NLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSAL 179

Query: 183 GVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSD 242
           GV+++  VL  I  VR++G+ +V I+HN+ H   V DR  +   G+ L      D +  +
Sbjct: 180 GVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEE 239

Query: 243 AVAFMTGAKE 252
               M G +E
Sbjct: 240 LQDMMAGGQE 249


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: 154
Number of extensions: 7
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: 261
Length adjustment: 25
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
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