Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Keio:17809 Length = 501 Score = 342 bits (878), Expect = 1e-98 Identities = 192/502 (38%), Positives = 295/502 (58%), Gaps = 11/502 (2%) Query: 7 IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66 ++ +KGI FPGVKAL G L +YPG V AL+GENGAGKSTM+K LTG+Y +AG+++ Sbjct: 4 LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63 Query: 67 DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKKTHEAAK 125 GK F G +Q AGI ++QE+NL L++ EN+ LG E FG IDWK + A Sbjct: 64 LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123 Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185 K LA++ L + +SI QQ+V IA+ + +KV+I+DEPT +L E LF Sbjct: 124 KLLAKLNLR-FKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFR 182 Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245 ++R+++ G I+++SH + +I+EI D +T+ R+GQFI E D LI MM+G+ Sbjct: 183 VIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKL 242 Query: 246 AELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTEL 305 + + + PG+ + V L G +N V + KGE++G +GL+G+GRTEL Sbjct: 243 ED------QYPHLDKAPGDIRL-KVDNLCGPG-VNDVSFTLRKGEILGVSGLMGAGRTEL 294 Query: 306 GRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNI-LI 364 ++LYGA SG TL+G +V P L N I Y +E+R+ +G++ ++V++N+ L Sbjct: 295 MKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLT 354 Query: 365 ALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHP 424 AL+ + + V +++ NV+ ++ + LSGGNQQKV I R L T P Sbjct: 355 ALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRP 414 Query: 425 ELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKI 484 ++LILDEPTRG+D+GAK EI Q++ + G+ ++ +SSE+ EV+ +SD I V+ + H Sbjct: 415 KVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLS 474 Query: 485 AEIENDDTVSQATIVETIANTN 506 E + + + + N Sbjct: 475 GEFTREQATQEVLMAAAVGKLN 496 Lambda K H 0.316 0.135 0.376 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: 629 Number of extensions: 34 Number of successful extensions: 8 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: 513 Length of database: 501 Length adjustment: 34 Effective length of query: 479 Effective length of database: 467 Effective search space: 223693 Effective search space used: 223693 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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