Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Keio:17809 Length = 501 Score = 150 bits (380), Expect = 4e-41 Identities = 89/248 (35%), Positives = 138/248 (55%), Gaps = 8/248 (3%) Query: 4 EPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEI 63 E +L +G+ K + V AL A ++YPG ++A++G+NGAGKS+M+K ++G T D G + Sbjct: 2 EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61 Query: 64 RLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDR 123 GK F P +++AGI ++Q L L P L+IA+N+FLGRE F +D Sbjct: 62 LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNR------FGKIDW 115 Query: 124 AAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALG 183 M +A L++L L ++ V LS G +Q V +A+ +F SKV+IMDEPT AL Sbjct: 116 KTMYAEADKLLAKLNLRF--KSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALT 173 Query: 184 VKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDA 243 E+ + +I +++ +G IV ISH M +FE+ D + + R G+ + T Sbjct: 174 DTETESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSL 233 Query: 244 VAFMTGAK 251 + M G K Sbjct: 234 IEMMVGRK 241 Score = 97.1 bits (240), Expect = 7e-25 Identities = 67/204 (32%), Positives = 105/204 (51%), Gaps = 8/204 (3%) Query: 27 FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIETV 86 F L GEIL V G GAG++ ++K + GA+ G + L+G + RSP + GI + Sbjct: 273 FTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYI 332 Query: 87 YQNL---ALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQ 143 ++ L +S+ +NM L +R G + D E+QA + L + Sbjct: 333 SEDRKRDGLVLGMSVKENMSL-TALRYFSRAGGSLKHAD----EQQAVSDFIRLFNVKTP 387 Query: 144 NINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGLP 203 ++ QA+ LSGG +Q VA+AR KV+I+DEPT + V + + +LI + GL Sbjct: 388 SMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLS 447 Query: 204 IVLISHNMPHVFEVADRIHIHRLG 227 I+L+S MP V ++DRI + G Sbjct: 448 IILVSSEMPEVLGMSDRIIVMHEG 471 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: 13 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: 501 Length adjustment: 29 Effective length of query: 231 Effective length of database: 472 Effective search space: 109032 Effective search space used: 109032 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