Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate BPHYT_RS22735 BPHYT_RS22735 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__BFirm:BPHYT_RS22735 Length = 265 Score = 332 bits (850), Expect = 6e-96 Identities = 169/255 (66%), Positives = 206/255 (80%), Gaps = 1/255 (0%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64 P+L ARGL+KRYG VTALD DF++ PGEI+AVIGDNGAGKSS+IKA+SGA PDEGEI Sbjct: 12 PVLQARGLIKRYGNVTALDGCDFEVMPGEIMAVIGDNGAGKSSLIKALSGATVPDEGEIL 71 Query: 65 LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124 L+GKP++FRSP++AR GIETVYQ LA++PA+SIA+N+FL RE+ KPG G F+ +D+ Sbjct: 72 LDGKPVKFRSPLDARAQGIETVYQELAVAPAMSIAENLFLARELLKPGWRGSIFKMIDKR 131 Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184 M +A A + +L + I+++ QAVETLSGGQRQGVAVAR+AAF VVI+DEPTAALGV Sbjct: 132 RMLDEATAHMKDLQI-GIRSMRQAVETLSGGQRQGVAVARSAAFARHVVILDEPTAALGV 190 Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244 KE VLELI VR RGLP++LISHNMPHVFE+ADRIHI RLGRR ++N D MS+AV Sbjct: 191 KEGNMVLELIRRVRDRGLPVILISHNMPHVFEIADRIHIQRLGRRAALVNRADIHMSEAV 250 Query: 245 AFMTGAKEPPREAIA 259 A MTGAKE +AIA Sbjct: 251 AIMTGAKEADVKAIA 265 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: 236 Number of extensions: 5 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: 265 Length adjustment: 25 Effective length of query: 235 Effective length of database: 240 Effective search space: 56400 Effective search space used: 56400 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