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.
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:
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