Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 314 bits (804), Expect = 6e-90 Identities = 190/495 (38%), Positives = 297/495 (60%), Gaps = 19/495 (3%) Query: 4 KNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKIN-AG 62 K P++ ++ I FPGV+AL V+LT Y GEVHALMGENGAGKST++K L+G Y + G Sbjct: 7 KAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGG 66 Query: 63 SIMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHE 122 +DG+ Q +G A++ G+A +YQE++L NLSV EN+ LG + + Sbjct: 67 ECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVR 126 Query: 123 AAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRD 182 A LA++G + P ++S+SIA +QLV IARA+ A++L++DEPT+ L +E Sbjct: 127 ACAPTLARLGAD-FSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDR 185 Query: 183 LFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIG 242 LFA++R++R G+AIL++SH + +I E+ DR+T+LR+G F+ + + L+ MM+G Sbjct: 186 LFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVG 245 Query: 243 KSAAEL-SQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSG 301 + + ++ + RE+ + + D G++ + D+ GEV+G AGL+G+G Sbjct: 246 RDLSGFYTKTHGQAVEREVMLSVRDVAD----GRR--VKGCSFDLRAGEVLGLAGLVGAG 299 Query: 302 RTELGRLLYGADKPDSGTYTL-----NGKKVNI--SDPYTALKNKIAYSTENRRDEGIIG 354 RTEL RL++GAD G + +G V + P A+ IAY TE+R+ +G+ Sbjct: 300 RTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFL 359 Query: 355 DLTVRQNI--LIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQ 412 D +V +NI ++A + G+ + + + A + + L +R A V LSGGNQQ Sbjct: 360 DQSVHENINLIVAARDALGLGR-LNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQ 418 Query: 413 KVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLS 472 KV++ R L P +LILDEPTRG+DIGAK+EI +++ LA G+ ++ ISSEL EVV L Sbjct: 419 KVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLC 478 Query: 473 DDIEVLKDRHKIAEI 487 D + V+++ E+ Sbjct: 479 DRVLVMREGTLAGEV 493 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: 633 Number of extensions: 34 Number of successful extensions: 10 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: 537 Length adjustment: 35 Effective length of query: 478 Effective length of database: 502 Effective search space: 239956 Effective search space used: 239956 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