Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Koxy:BWI76_RS07240 Length = 494 Score = 356 bits (914), Expect = e-103 Identities = 197/492 (40%), Positives = 313/492 (63%), Gaps = 14/492 (2%) Query: 11 KGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKP 70 +GI+ FPGVKALD V L + PG VHALMGENGAGKST++K L G+Y+ + G+I V G+P Sbjct: 9 EGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVKGEP 68 Query: 71 QQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKKYLAQ 130 QF T+DA +GI+ ++QE+NL +++V EN+ LG E +D ++ + L + Sbjct: 69 VQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLARQTQDLLDK 128 Query: 131 MGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKV 190 + + + + +SIA QQ+V IA+A+ NA ++I+DEPTS+L +EV LF I+R + Sbjct: 129 LNIR-LSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIRDL 187 Query: 191 RDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELSQ 250 R G AI+++SH +D+I+ ITD +++ R+G ++ T + R LI M+G+ EL+Q Sbjct: 188 RQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGR---ELTQ 244 Query: 251 IGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLY 310 + K GE+ ++ V+ L +KG + ++ + +GE++G AGL+G+GR+E+ L+ Sbjct: 245 LFPKFNN---AIGEE-VLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLF 300 Query: 311 GADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQAT- 369 G +K DSG ++G VNI P TA++ +A TE+R+ G+ L+V +N+ I Sbjct: 301 GMEKADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEY 360 Query: 370 --RGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELL 427 + F K D + + ++ LN++ D+ + NLSGGNQQKVLI RWL P++L Sbjct: 361 IGKTGFVQHLKMAEDCM--EQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKIL 418 Query: 428 ILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEI 487 ILDEPTRGID+GAKAEI ++ +LA++G+ V+ +SSEL E++ +SD + V+ + +I I Sbjct: 419 ILDEPTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHE-GRITGI 477 Query: 488 ENDDTVSQATIV 499 + + Q TI+ Sbjct: 478 LDKEDADQETIL 489 Score = 87.4 bits (215), Expect = 1e-21 Identities = 54/224 (24%), Positives = 113/224 (50%), Gaps = 6/224 (2%) Query: 279 INPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKN 338 ++ V + + G V G G+G++ L + L G +PD G + G+ V D AL++ Sbjct: 21 LDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVKGEPVQFQDTMDALRS 80 Query: 339 KIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPAD 398 I+ ++ ++ +TV +NI + + + F + ++ + +LN+R Sbjct: 81 GISMI---HQELNLVPHMTVAENIWLGREPMKYGF--VDHRQLARQTQDLLDKLNIR-LS 134 Query: 399 PDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGV 458 DR V LS +QQ V I + ++ + +++I+DEPT + A + ++ DL QG + Sbjct: 135 ADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIRDLRQQGKAI 194 Query: 459 VFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVETI 502 ++IS +++E+ ++D+I V +D + + + Q+ I + + Sbjct: 195 IYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMV 238 Score = 87.4 bits (215), Expect = 1e-21 Identities = 56/224 (25%), Positives = 120/224 (53%), Gaps = 6/224 (2%) Query: 22 ALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQN 81 A ++ ++ GE+ + G GAG+S ++++L G+ K ++G +++DG P + A Sbjct: 268 AFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGMEKADSGEVLIDGMPVNIDSPSTAIE 327 Query: 82 AGIATVYQE---VNLCTNLSVGENVMLGH--EKRGPFG-IDWKKTHEAAKKYLAQMGLES 135 G+A + ++ L LSV EN+ + E G G + K E + + ++ +++ Sbjct: 328 KGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIGKTGFVQHLKMAEDCMEQIRRLNIKT 387 Query: 136 IDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGV 195 ++++S QQ V IAR ++ K+LILDEPT +D +++ ++ ++ + GV Sbjct: 388 PTMDQIINNLSGGNQQKVLIARWLLAQPKILILDEPTRGIDVGAKAEIYHLISELANRGV 447 Query: 196 AILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGM 239 A++ VS L +I ++DR+ ++ G+ + +D ++ ++ + Sbjct: 448 AVIMVSSELPEILGMSDRVMVMHEGRITGILDKEDADQETILSL 491 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: 639 Number of extensions: 29 Number of successful extensions: 9 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: 494 Length adjustment: 34 Effective length of query: 479 Effective length of database: 460 Effective search space: 220340 Effective search space used: 220340 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