Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 296 bits (758), Expect = 1e-84 Identities = 164/482 (34%), Positives = 284/482 (58%), Gaps = 13/482 (2%) Query: 10 MKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGK 69 ++ IT + GV ALD VD T+ PGE L GENG+GKST+IK ++GV AG++ + G+ Sbjct: 12 LRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAGQ 71 Query: 70 PQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGI-DWKKTHEAAKKYL 128 + AG+ ++Q+ +L NLSV EN+ + + ++ + A+ L Sbjct: 72 EHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARAAL 131 Query: 129 AQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMR 188 ++G++ ID + ++ +A +QLVAI RA+ A+++I+DEPT++L EVR L I+R Sbjct: 132 DRIGVQ-IDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGIIR 190 Query: 189 KVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAEL 248 +++ GVA++FVSH L ++ E+++++ +LRNG+ + E + L M G+ E+ Sbjct: 191 MLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDVPEV 250 Query: 249 SQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRL 308 ++ G + ++ V+GLGK G+ + + D+ GEV+G GLLG GRT + + Sbjct: 251 PP-------SDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKA 303 Query: 309 LYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIA-LQ 367 L+G PD+G+ ++G V + DP A +I Y E+R EG+ ++ +N+ + L Sbjct: 304 LFGLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLD 363 Query: 368 A-TRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPEL 426 A T G F + +A +++ L V+ D + PV++LSGGNQQ+V + RWL+ P + Sbjct: 364 AHTSGGFLDMTGLAKEA--SDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRV 421 Query: 427 LILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAE 486 LIL+ P+ G+D+G+KA+I ++ +LA +G+GV+ IS +L E++ + V+++ I Sbjct: 422 LILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDA 481 Query: 487 IE 488 +E Sbjct: 482 LE 483 Score = 84.3 bits (207), Expect = 9e-21 Identities = 60/216 (27%), Positives = 106/216 (49%), Gaps = 5/216 (2%) Query: 26 VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIA 85 + L GEV + G G G++++ KAL G+ +AGSI+VDG P A A I Sbjct: 277 ISFDLRTGEVLGITGLLGCGRTSVAKALFGLVTPDAGSILVDGSPVPLGDPQAASLARIG 336 Query: 86 TVYQE---VNLCTNLSVGENVMLGHEKRGPFG--IDWKKTHEAAKKYLAQMGLESIDPHT 140 V ++ L + S+ NV +G G +D + A +L ++ +++ D Sbjct: 337 YVPEDRLTEGLFLSQSILRNVAVGRLDAHTSGGFLDMTGLAKEASDWLRRLKVKAPDVEA 396 Query: 141 PLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILFV 200 P+ S+S QQ VA+AR + +VLIL+ P+ +D D+ I+R++ G+ ++ + Sbjct: 397 PVQSLSGGNQQRVALARWLSRAPRVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVI 456 Query: 201 SHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDEL 236 S L ++ R+ ++R G+ I + D+L Sbjct: 457 SDDLPELLATCHRVLVMREGRIIDALEGTALTEDDL 492 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: 560 Number of extensions: 25 Number of successful extensions: 9 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: 498 Length adjustment: 34 Effective length of query: 479 Effective length of database: 464 Effective search space: 222256 Effective search space used: 222256 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