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.
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