Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Dino:3609044 Length = 510 Score = 142 bits (359), Expect = 1e-38 Identities = 83/238 (34%), Positives = 130/238 (54%), Gaps = 8/238 (3%) Query: 12 LVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQ 71 + K + V AL LYPG++ A+IG+NGAGKS+++K ++G PD G I ++G+P+ Sbjct: 26 ITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVDGQPVP 85 Query: 72 FRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQAR 131 F +P A G+ ++Q L LS+A+N+FLG R F +D + AR Sbjct: 86 FSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGA------FGLIDWKKTTENAR 139 Query: 132 AKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVL 191 A L+ +G + + ++ L + VA+ARA + ++VVIMDEPTAAL KE + Sbjct: 140 ALLTSIGAEL--DPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELY 197 Query: 192 ELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTG 249 EL+ ++ +G I+ ISH +F +AD + R G+ + D T +D V M G Sbjct: 198 ELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVG 255 Score = 90.5 bits (223), Expect = 6e-23 Identities = 65/231 (28%), Positives = 112/231 (48%), Gaps = 19/231 (8%) Query: 4 EPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEI 63 + +LT +G Y T D F L GEIL G GAG+S ++++ G P G + Sbjct: 271 DTVLTVQG----YAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFGITRPSAGSV 326 Query: 64 RLEGKPIQFRSPMEARQAGIETVYQNLALSPA---LSIADNMFL---GREIRKPGIMGKW 117 + G + SP +A GI V ++ A L I N+ L GR RK + Sbjct: 327 EIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRISRKG-----F 381 Query: 118 FRSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDE 177 R + A+ ++ +L + +++ V LSGG +Q V +A+ A +V+I+DE Sbjct: 382 LRLAEEFALAREYTERLD----LRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDE 437 Query: 178 PTAALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGR 228 PT + + V + + ++ +GL ++++S +P V ++DR+ + R GR Sbjct: 438 PTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGR 488 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: 299 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: 510 Length adjustment: 29 Effective length of query: 231 Effective length of database: 481 Effective search space: 111111 Effective search space used: 111111 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