Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate BWI76_RS14600 BWI76_RS14600 ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Koxy:BWI76_RS14600 Length = 260 Score = 194 bits (494), Expect = 1e-54 Identities = 111/248 (44%), Positives = 154/248 (62%), Gaps = 4/248 (1%) Query: 12 LVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQ 71 + K YG + +L + +L PGE+L ++GDNGAGKS++ K +SGAV P G IR++G+ Q Sbjct: 16 ITKTYGSIRSLRGVNLELAPGEVLGLVGDNGAGKSTLTKVLSGAVIPSGGTIRIDGEQQQ 75 Query: 72 FRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQAR 131 F +P ++R+ IE VYQ+L+L + +A N+F+GRE K ++G F LD A M AR Sbjct: 76 FANPADSRRCHIEMVYQDLSLCDTVDVAGNLFMGREPMK-SVLGIPF--LDEAKMHADAR 132 Query: 132 AKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVL 191 L LG+ +I + V LSGGQRQ +A+ARAAAF KV+IMDEPTAAL V E VL Sbjct: 133 EMLKGLGI-SIPDTRLLVRNLSGGQRQAIAIARAAAFDPKVLIMDEPTAALAVAEVEAVL 191 Query: 192 ELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTGAK 251 ELI V RG+ ++LI+H + +F V DRI + G + D ++SD V + G K Sbjct: 192 ELIRRVSARGVSVILITHRLQDLFLVCDRIMVMYEGTNVADRRVADTSLSDIVNLIVGEK 251 Query: 252 EPPREAIA 259 R A A Sbjct: 252 FTARSAAA 259 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: 180 Number of extensions: 6 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: 260 Length adjustment: 24 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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