Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_011780059.1 MVAN_RS14295 ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >NCBI__GCF_000015305.1:WP_011780059.1 Length = 293 Score = 117 bits (292), Expect = 4e-31 Identities = 76/233 (32%), Positives = 122/233 (52%), Gaps = 9/233 (3%) Query: 4 EPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEI 63 E +L L ++G +TALD F++ GEIL +IG NGAGK++ AI+G P G + Sbjct: 37 EVLLQTTDLTVKFGGLTALDAVTFNIRRGEILGLIGPNGAGKTTCFNAITGVYRPTSGIV 96 Query: 64 RLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRK----PG--IMGKW 117 +G PI + + GI +QN+ L ++ +N+ +G + R PG I Sbjct: 97 TFDGAPIGRIKRHQITRLGIARTFQNIRLFGEMTALENVMVGTDARHHTSVPGALIRSPR 156 Query: 118 FRSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDE 177 R +R+A+E+ A A L +G+ + + LS G ++ + +ARA A K++ +DE Sbjct: 157 HRREERSAIERSA-ALLHFVGI--AHRGEEKAKNLSYGDQRRLEIARALATEPKLLCLDE 213 Query: 178 PTAALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRL 230 P A E ++ELI +R G ++LI H+M V V DRI + GR++ Sbjct: 214 PAAGFNPSEKSALIELIRKIRDDGYTVLLIEHDMRLVMGVTDRIVVLEFGRKI 266 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: 194 Number of extensions: 13 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: 293 Length adjustment: 25 Effective length of query: 235 Effective length of database: 268 Effective search space: 62980 Effective search space used: 62980 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 24 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