Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Dsui_1109 Dsui_1109 ABC-type branched-chain amino acid transport systems, ATPase component
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__PS:Dsui_1109 Length = 266 Score = 118 bits (296), Expect = 1e-31 Identities = 83/238 (34%), Positives = 127/238 (53%), Gaps = 4/238 (1%) Query: 4 EPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEI 63 E IL + + R+G V AL F++ EI A+IG NGAGKSSM+ I+G P EG I Sbjct: 13 EVILDLQNISLRFGGVKALTDISFNVKEHEIRAIIGPNGAGKSSMLNVINGVYHPQEGRI 72 Query: 64 RLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDR 123 G+ + P A GI +QN+AL +S+ DN+ GR + + L R Sbjct: 73 VFHGEERKKMEPHMAATQGIARTFQNIALFKGMSVLDNIMTGRITKMKCGFLEQALYLGR 132 Query: 124 AAMEKQA-RAKLSE-LGLMTIQNINQA-VETLSGGQRQGVAVARAAAFGSKVVIMDEPTA 180 A E+ A R K+ E + + IQ+I + V L G ++ V + RA A ++++DEP A Sbjct: 133 AQKEELAHREKVEEVIDFLEIQHIRKTPVGRLPYGLQKRVELGRALAAEPSLLLLDEPMA 192 Query: 181 ALGVKESRRVLELILDVRRR-GLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKD 237 + V+E + + ILDV + G IVLI H+M V +++DR+ + G+++ P D Sbjct: 193 GMNVEEKQDMCRFILDVNDQFGTTIVLIEHDMGVVMDISDRMVVLDYGKKIGDGTPDD 250 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: 156 Number of extensions: 8 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: 266 Length adjustment: 25 Effective length of query: 235 Effective length of database: 241 Effective search space: 56635 Effective search space used: 56635 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