Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Smeli:SM_b20713 Length = 513 Score = 348 bits (892), Expect = e-100 Identities = 190/499 (38%), Positives = 314/499 (62%), Gaps = 11/499 (2%) Query: 7 IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66 ++ +G+ EFPGV ALD V+ L G VHALMGENGAGKST++K L G+Y + G + + Sbjct: 23 LLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKL 82 Query: 67 DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKKTHEAAK 125 G + LDA GIA ++QE+NL ++V EN+ + E + FG +D + Sbjct: 83 RGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRFGFVDHGEMRRMTA 142 Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185 K ++ ++ +DP + +S+A +Q+V IA+A+ + VLI+DEPTS+L EV LF Sbjct: 143 KLFERLKID-LDPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFE 201 Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245 I+R +R G+ I++++H +++++EI D ++ R+G++I ++ + RD++I MM+G+ Sbjct: 202 IIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMVGR-- 259 Query: 246 AELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTEL 305 E++Q+ K+ E+ G+ ++ VK L G V D+ GE++G AGL+GSGR+ + Sbjct: 260 -EITQMFPKE---EVPIGDV-VLSVKNLTLNGVFRDVSFDVRAGEILGVAGLVGSGRSNV 314 Query: 306 GRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIA 365 L+G SGT ++GK+V I A+++++A+ TE+R+D G + L + +N+ IA Sbjct: 315 AETLFGVTPASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDILENMQIA 374 Query: 366 LQATRGMFKP-IPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHP 424 + + + + + ++E A ++ ++L V+ + V+NLSGGNQQKVLIGRWL T+P Sbjct: 375 VLQDKFVKRGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGRWLLTNP 434 Query: 425 ELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKI 484 +LILDEPTRGID+GAKAEI ++V +LA G+ V+ ISSE+ EV+ +SD I V+ + ++ Sbjct: 435 RILILDEPTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVMHE-GRV 493 Query: 485 AEIENDDTVSQATIVETIA 503 I + +Q ++E A Sbjct: 494 TGILDRAEATQIKVMELAA 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: 632 Number of extensions: 30 Number of successful extensions: 8 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: 513 Length adjustment: 35 Effective length of query: 478 Effective length of database: 478 Effective search space: 228484 Effective search space used: 228484 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