Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate H281DRAFT_02174 H281DRAFT_02174 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Burk376:H281DRAFT_02174 Length = 550 Score = 396 bits (1018), Expect = e-115 Identities = 208/497 (41%), Positives = 316/497 (63%), Gaps = 2/497 (0%) Query: 7 IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66 ++ M+ I I F GV AL G +L++ GEVHAL+G+NGAGKSTMIK LTG Y+ +GS+ Sbjct: 24 LLEMQDIGISFGGVPALRGANLSVAAGEVHALIGQNGAGKSTMIKILTGAYRRGSGSVRF 83 Query: 67 DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKK 126 +G+ F A+ AGI+T+YQE+NL SV EN+ LG E R IDW+ A Sbjct: 84 EGREVDFRTPKQAREAGISTIYQEINLVPFRSVAENIFLGREPRRFGLIDWRTVQHRAAA 143 Query: 127 YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAI 186 L GL ID P+ S A+QQ+VA+ARA+ +AK++I+DE TSSLD EV LF + Sbjct: 144 LLDSFGLH-IDVKKPVGRYSTAIQQMVALARAVSSDAKMVIMDESTSSLDEREVELLFTV 202 Query: 187 MRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAA 246 +RK+RD G A++FVSH LD++Y + DR+T++R+GQ + + + + +L+ M+G++ A Sbjct: 203 VRKLRDDGRAVIFVSHRLDELYALCDRVTVMRDGQTVAQSTMAEMDKLQLVTTMLGRTLA 262 Query: 247 ELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELG 306 + + K + + LG ++ V ++++ GE VG AGLLGSGRTE Sbjct: 263 AVVHDDPAAREANLARRGKQAIAARDLGAHPKVSDVSLEVHAGEAVGLAGLLGSGRTETM 322 Query: 307 RLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIAL 366 RL++GAD + G+ +++G V + P A+ +AY TE+R+ EGI+ +L+VR N+ + Sbjct: 323 RLMFGADPLERGSVSIDGATVTLKSPQDAIARGLAYLTEDRKAEGIVPELSVRDNLTLVC 382 Query: 367 QATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPEL 426 T + K+ AIVD+++ L ++ D+P++ LSGGNQQKVL+ RWLA P L Sbjct: 383 LRTLTRNGIVDVKKQQAIVDRFIASLGIKLRSADQPIRELSGGNQQKVLLARWLAAEPSL 442 Query: 427 LILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAE 486 L+LDEPTRGID+GAKA++ ++V +L G+ V+ +SELEE+ +SD V++D +AE Sbjct: 443 LLLDEPTRGIDVGAKADVAKIVRELRDAGLAVLMSASELEELTAVSDRAVVIRDGRTVAE 502 Query: 487 IENDDTVSQATIVETIA 503 + N +S++ I++ IA Sbjct: 503 L-NGAEMSESAIMDAIA 518 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: 674 Number of extensions: 28 Number of successful extensions: 6 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: 550 Length adjustment: 35 Effective length of query: 478 Effective length of database: 515 Effective search space: 246170 Effective search space used: 246170 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