Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate SMc03815 SMc03815 ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Smeli:SMc03815 Length = 259 Score = 179 bits (455), Expect = 4e-50 Identities = 103/239 (43%), Positives = 145/239 (60%), Gaps = 5/239 (2%) Query: 12 LVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQ 71 +VK +G V ALD ++ GEIL ++GDNGAGKS+++K I+G P G LEGKP+ Sbjct: 22 IVKDFGAVRALDGVTLEINQGEILGLMGDNGAGKSTLVKTIAGNFQPSSGSYILEGKPVV 81 Query: 72 FRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQAR 131 F P EAR+ GIE VYQ+LA+ L+ + N+FLGRE+ + +G F+ LD M ++ Sbjct: 82 FSGPAEARRHGIEVVYQDLAICDNLTASANVFLGRELMRQ--VGP-FKVLDHKRMNARSA 138 Query: 132 AKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVL 191 EL T V +SGGQRQ VA+AR SK+V+MDEPTAA+ V++ VL Sbjct: 139 EIFKELKSET--RPADLVVRMSGGQRQAVAIARTRLARSKIVLMDEPTAAISVRQVAEVL 196 Query: 192 ELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTGA 250 LI ++ +GL ++LISH MP VFEV DR+ + R GR++ + + +TGA Sbjct: 197 ALIRRMKAQGLSVILISHRMPDVFEVCDRVVVMRRGRKVADKMIGQSSPEEVTGLITGA 255 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: 170 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: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 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