Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate BPHYT_RS01820 BPHYT_RS01820 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__BFirm:BPHYT_RS01820 Length = 544 Score = 403 bits (1036), Expect = e-117 Identities = 210/500 (42%), Positives = 320/500 (64%), Gaps = 2/500 (0%) Query: 4 KNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGS 63 ++P++ M+ I I F GV AL +L++ GEVHAL+G+NGAGKSTMIK LTG Y+ +GS Sbjct: 15 RSPLLEMQDIGISFGGVPALRSANLSVAAGEVHALIGQNGAGKSTMIKILTGAYRRGSGS 74 Query: 64 IMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEA 123 + +G+ F A+ AGI+T+YQE+NL SV EN+ LG E R IDW + Sbjct: 75 VRFEGREVDFRTPKQAREAGISTIYQEINLVPFRSVAENIFLGREPRRFGLIDWHAVQQR 134 Query: 124 AKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDL 183 A L GL+ ID P+ S A+QQ+VA+ARA+ +AK++I+DE TSSLD EV L Sbjct: 135 AAALLESFGLQ-IDVKKPVGRYSTAIQQMVALARAVSSDAKMVIMDESTSSLDEREVELL 193 Query: 184 FAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGK 243 F ++RK+RD G A++FVSH LD++Y + DR+T++R+GQ + + D + +L+ M+G+ Sbjct: 194 FTVVRKLRDDGRAVIFVSHRLDELYALCDRVTVMRDGQTVAQSTMADMDKLQLVTTMLGR 253 Query: 244 SAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303 + A + Q A+ + K ++ L ++ V ++++ GE VG AGLLGSGRT Sbjct: 254 TLAAVVQDDAEAREANLARRGKQMIAATQLSAHPKVSDVSLEVHAGEAVGLAGLLGSGRT 313 Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363 E RL++GAD + G+ ++ G+ V + P A+ +AY TE+R+ EGI+ +L+VR N+ Sbjct: 314 ETMRLMFGADPLERGSLSIGGETVALKSPQDAISRGLAYLTEDRKAEGIVPELSVRDNLT 373 Query: 364 IALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423 + T + K+ AIVD+++ L ++ D+P++ LSGGNQQKVL+ RWLA Sbjct: 374 LVCLRTLAKNGVVDVKKQQAIVDRFIASLGIKLRSADQPIRELSGGNQQKVLLARWLAAE 433 Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHK 483 P LL+LDEPTRGID+GAKAE+ ++V +L G+ V+ +SELEE+ ++D V++D Sbjct: 434 PSLLLLDEPTRGIDVGAKAEVAKIVRELRDAGLAVLLSASELEELTAVADRAVVIRDGRT 493 Query: 484 IAEIENDDTVSQATIVETIA 503 +AE+ D +S+ I++ IA Sbjct: 494 VAELNGAD-MSETAIMDAIA 512 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: 671 Number of extensions: 29 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: 544 Length adjustment: 35 Effective length of query: 478 Effective length of database: 509 Effective search space: 243302 Effective search space used: 243302 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