Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate BPHYT_RS30865 BPHYT_RS30865 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__BFirm:BPHYT_RS30865 Length = 256 Score = 176 bits (445), Expect = 6e-49 Identities = 100/223 (44%), Positives = 144/223 (64%), Gaps = 6/223 (2%) Query: 7 LTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLE 66 L +VKR+G VTALD L GEIL V+GDNGAGKS++IK ++G G++ + Sbjct: 8 LRGEDIVKRFGAVTALDGVSLTLKQGEILGVLGDNGAGKSTLIKILTGFHQQTSGKLFVG 67 Query: 67 GKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAM 126 G+ RS AR GIE VYQ+LAL+ +LSI NMFL REI + G FR LD AM Sbjct: 68 GEETMLRSVDHARSLGIECVYQDLALANSLSIYHNMFLNREIIRRGP----FRLLDNRAM 123 Query: 127 EKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKE 186 ++A L E+G + + +++ VE LSGGQRQ +AVARA +K++++DEP AA+G +E Sbjct: 124 RERAAECLEEIG-VHVPSVDLPVEQLSGGQRQAIAVARAVNSNAKILLLDEPLAAMGARE 182 Query: 187 SRRVLELILDVRRR-GLPIVLISHNMPHVFEVADRIHIHRLGR 228 + +++LIL ++ + GL IV+I HN ++ADR+ + + GR Sbjct: 183 AGLIIDLILRLKAKGGLSIVMIMHNYAQTLDIADRVMLMQRGR 225 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: 153 Number of extensions: 6 Number of successful extensions: 3 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: 256 Length adjustment: 24 Effective length of query: 236 Effective length of database: 232 Effective search space: 54752 Effective search space used: 54752 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