Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 140 bits (352), Expect = 7e-38 Identities = 84/225 (37%), Positives = 129/225 (57%), Gaps = 8/225 (3%) Query: 6 ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65 +LT + + K + V ALD +L G + A++G+NGAGKS+++K +SG +G I Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60 Query: 66 EGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAA 125 G P++F++ +A++ GI ++Q L L P LSI +N+FLGRE P MG LD A Sbjct: 61 NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETP--MG----LLDVAK 114 Query: 126 MEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVK 185 M K+A L L L + V L GQ+Q V +A+A + S+V+IMDEPT+A+ + Sbjct: 115 MHKEAAQLLHRLKLNV--DPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQ 172 Query: 186 ESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRL 230 E + +I +R G I ISH + +F +ADR + R G+ + Sbjct: 173 EVEILFGIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMI 217 Score = 97.4 bits (241), Expect = 5e-25 Identities = 68/255 (26%), Positives = 124/255 (48%), Gaps = 28/255 (10%) Query: 4 EPILTARGLVKRYGRVT---ALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60 E +L+ + L ++ ++ L +F+L GE+L + G GAG++ +++A+ G + Sbjct: 252 ETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTELMEALFGVLPHQG 311 Query: 61 GEIRLEGKPIQFRSPMEARQAGIETVYQN-----------LALSPALSIADNMFLGREIR 109 EI L GK +F+ P EA AG+ V ++ L + +L++ D++ G Sbjct: 312 AEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLTVVDSILSG---- 367 Query: 110 KPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFG 169 G+ LD + A+ + EL + + Q VE LSGG +Q V +A+ A Sbjct: 368 --GL-------LDDKKEKGLAQKYMGELKIKASSH-RQLVEKLSGGNQQKVVLAKWLATR 417 Query: 170 SKVVIMDEPTAALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRR 229 KV+++DEPT + + + +LI + GL ++++S +P + V+DR+ + GR Sbjct: 418 PKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRL 477 Query: 230 LCVINPKDYTMSDAV 244 I T D + Sbjct: 478 TANIPIDAQTSEDEI 492 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: 275 Number of extensions: 16 Number of successful extensions: 4 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: 502 Length adjustment: 29 Effective length of query: 231 Effective length of database: 473 Effective search space: 109263 Effective search space used: 109263 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