Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 154 bits (389), Expect = 4e-42 Identities = 88/246 (35%), Positives = 141/246 (57%), Gaps = 10/246 (4%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEG-EI 63 P+L R + K + V AL + + Y GE+ A++G+NGAGKS+++K +SGA T D G E Sbjct: 9 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 68 Query: 64 RLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDR 123 ++G+ +Q P AR G+ +YQ L+L+P LS+A+N++LGR +++ G++ R Sbjct: 69 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVA-------R 121 Query: 124 AAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALG 183 M + L+ LG N V +LS QRQ V +ARA F +++++MDEPT L Sbjct: 122 GDMVRACAPTLARLGADFSPAAN--VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLS 179 Query: 184 VKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDA 243 E+ R+ LI +R G+ I+ ISH M + E+ADR+ + R G + ++ + + Sbjct: 180 THETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAAL 239 Query: 244 VAFMTG 249 V M G Sbjct: 240 VKMMVG 245 Score = 78.6 bits (192), Expect = 3e-19 Identities = 63/237 (26%), Positives = 109/237 (45%), Gaps = 18/237 (7%) Query: 27 FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKP-------IQFRSPMEAR 79 FDL GE+L + G GAG++ + + + GA GE+R+ + P +A Sbjct: 282 FDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAI 341 Query: 80 QAGIETVYQNLALSPAL---SIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSE 136 AGI + ++ L S+ +N+ L R +G+ L+R A ++ + Sbjct: 342 DAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGR----LNRTAARRRTTEAIDT 397 Query: 137 LGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILD 196 LG+ + + V LSGG +Q V ++R +V+I+DEPT + + + LI Sbjct: 398 LGIR-VAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINA 456 Query: 197 VRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKD---YTMSDAVAFMTGA 250 + + G+ I++IS +P V + DR+ + R G + P T +A TGA Sbjct: 457 LAQSGVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGA 513 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: 284 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 260 Length of database: 537 Length adjustment: 30 Effective length of query: 230 Effective length of database: 507 Effective search space: 116610 Effective search space used: 116610 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: 49 (23.5 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