Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 337 bits (864), Expect = 6e-97 Identities = 188/497 (37%), Positives = 294/497 (59%), Gaps = 6/497 (1%) Query: 7 IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66 ++ +K IT EF GVKALD V L L G V A++GENGAGKST++K L+GVY G+I Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60 Query: 67 DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGI-DWKKTHEAAK 125 +G P +F T DAQ GI ++QE+NL LS+ EN+ LG E P G+ D K H+ A Sbjct: 61 NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAA 120 Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185 + L ++ L ++DP TP+S + + QQLV IA+A+ + ++V+I+DEPTS++ EV LF Sbjct: 121 QLLHRLKL-NVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFG 179 Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245 I+R +R G AI ++SH LD+++ I DR +LR+G+ I+ + + LI M+G+ Sbjct: 180 IIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREI 239 Query: 246 AELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTEL 305 ++ + + V + K + ++ ++ KGEV+G GL+G+GRTEL Sbjct: 240 VIERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTEL 299 Query: 306 GRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGII--GDLTVRQNIL 363 L+G TL GK P A+ +A E+R+ +G++ DL ++ Sbjct: 300 MEALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLT 359 Query: 364 IALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423 + G + K+ + KYM EL ++ + + V+ LSGGNQQKV++ +WLAT Sbjct: 360 VVDSILSGGL--LDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATR 417 Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHK 483 P++L+LDEPTRGIDI AK EI +++ LA++G+G++ +SSEL E++ +SD + V+ + Sbjct: 418 PKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRL 477 Query: 484 IAEIENDDTVSQATIVE 500 A I D S+ I++ Sbjct: 478 TANIPIDAQTSEDEILQ 494 Score = 78.6 bits (192), Expect = 5e-19 Identities = 63/239 (26%), Positives = 110/239 (46%), Gaps = 13/239 (5%) Query: 265 KPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNG 324 K V VK L + V +++ G V G G+G++ L ++L G GT NG Sbjct: 9 KEFVGVKAL------DDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYYNG 62 Query: 325 KKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGM-FKPIPKKEADA 383 V + A + I ++ +I L++R+NI + + M + K +A Sbjct: 63 DPVKFQNTRDAQEKGINII---HQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEA 119 Query: 384 IVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAE 443 + +LNV DP+ PV L G QQ V I + L+ +++I+DEPT I Sbjct: 120 AQLLHRLKLNV---DPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEI 176 Query: 444 IQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVETI 502 + ++ L ++G + +IS +L+E+ ++D VL+D I E + +A I + + Sbjct: 177 LFGIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMV 235 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: 28 Number of successful extensions: 8 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: 513 Length of database: 502 Length adjustment: 34 Effective length of query: 479 Effective length of database: 468 Effective search space: 224172 Effective search space used: 224172 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