Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Keio:16258 Length = 506 Score = 338 bits (868), Expect = 2e-97 Identities = 183/477 (38%), Positives = 296/477 (62%), Gaps = 11/477 (2%) Query: 7 IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66 ++ M GI FPGVKALD V+L + P +HALMGENGAGKST++K L G+Y+ ++G+I+ Sbjct: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 Query: 67 DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKK 126 GK F+ +A GI+ V+QE+NL SV +N+ LG +D K + K Sbjct: 73 QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKA 132 Query: 127 YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAI 186 ++ ++ IDP + ++S++ Q++ IA+A NAK++I+DEPTSSL EV LF I Sbjct: 133 IFDELDID-IDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191 Query: 187 MRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAA 246 +RK+++ G I+++SH +++I+++ D +T+LR+GQ+I D++I MM+G+S Sbjct: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS-- 249 Query: 247 ELSQIGAKKARREITPGEKPIVDVKGLG--KKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304 + + +E PGE I++V+ L ++ +I V D++KGE++G AGL+G+ RT+ Sbjct: 250 ----LNQRFPDKENKPGE-VILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTD 304 Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILI 364 + L+G + +GT TL+GK++N + A+ + A TE RR GI L + N LI Sbjct: 305 IVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLI 364 Query: 365 A-LQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423 + ++ + + + + + V+ + +LSGGNQQKV+IGRWL T Sbjct: 365 SNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQ 424 Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKD 480 PE+L+LDEPTRGID+GAK EI Q++ +LA +G G++ ISSE+ E++ ++D I V+ + Sbjct: 425 PEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSN 481 Score = 84.0 bits (206), Expect = 1e-20 Identities = 55/218 (25%), Positives = 112/218 (51%), Gaps = 6/218 (2%) Query: 26 VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIA 85 V L+ GE+ + G GA ++ +++ L G+ + +AG+I + GK + +A N G A Sbjct: 282 VSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFA 341 Query: 86 TVYQE---VNLCTNLSVGENVMLGHEK--RGPFGI-DWKKTHEAAKKYLAQMGLESIDPH 139 V +E + L +G N ++ + + + G+ D + + + M +++ Sbjct: 342 LVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHR 401 Query: 140 TPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILF 199 T + S+S QQ V I R ++ ++L+LDEPT +D +++ ++ ++ G I+ Sbjct: 402 TQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIII 461 Query: 200 VSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELI 237 +S + ++ ITDR+ ++ NG V TK T ++E++ Sbjct: 462 ISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEIL 499 Score = 83.2 bits (204), Expect = 2e-20 Identities = 59/225 (26%), Positives = 114/225 (50%), Gaps = 14/225 (6%) Query: 267 IVDVKGLGKK----GTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTL 322 ++++ G+ K ++ V++ + + G G+G++ L + L+G + DSGT Sbjct: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 Query: 323 NGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPK--KE 380 GK+++ AL+N I+ ++ ++ +V N+ + T+GMF K +E Sbjct: 73 QGKEIDFHSAKEALENGISMV---HQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRE 129 Query: 381 ADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGA 440 AI D EL++ DP V LS Q + I + + + +++I+DEPT + Sbjct: 130 TKAIFD----ELDI-DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKE 184 Query: 441 KAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIA 485 + ++ L +G G+V+IS ++EE+ +L D++ VL+D IA Sbjct: 185 VNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIA 229 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: 654 Number of extensions: 29 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 513 Length of database: 506 Length adjustment: 34 Effective length of query: 479 Effective length of database: 472 Effective search space: 226088 Effective search space used: 226088 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