Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate SM_b21344 SM_b21344 sugar uptake ABC transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Smeli:SM_b21344 Length = 497 Score = 360 bits (924), Expect = e-104 Identities = 200/499 (40%), Positives = 306/499 (61%), Gaps = 7/499 (1%) Query: 7 IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66 ++ M+GI F G+ AL L + EV AL+G+NGAGKST+IK LTG Y+ + G+++ Sbjct: 2 LLSMQGICKSFNGIPALRAASLEVGEAEVMALVGQNGAGKSTLIKILTGAYRRDEGAVVF 61 Query: 67 DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKK 126 G+ F+ ++Q GIAT+YQE+NL SV EN+ L E R ID + + A Sbjct: 62 AGEGVSFSMPAESQARGIATIYQEINLAPQRSVAENIYLSREPRRFGLIDRRAMRDGAAA 121 Query: 127 YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAI 186 L LE ID P++ S A +Q+VAIARA+ A+++I+DEPTSSLD EV LF Sbjct: 122 VLRAFNLE-IDVDQPVAGFSAATRQMVAIARAVTQKARLVIMDEPTSSLDEREVGILFDT 180 Query: 187 MRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAA 246 +R ++ GV+++F+ H L+++Y I DR+TI+R+G+ + D P+ L+ M+GK A Sbjct: 181 IRTLKRGGVSVVFIGHRLEELYRICDRVTIMRDGKTVATAAMADMPKLALVRHMLGKELA 240 Query: 247 ELSQIGAKKARREITPGEKPI-VDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTEL 305 I A+ ++P+ + V+ G + V + + +GE+ G AGLLGSGRTE Sbjct: 241 AFEAI----AKDADEGAQRPVRLSVRNAGAGVRVRDVSLTVREGEISGLAGLLGSGRTET 296 Query: 306 GRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIA 365 L++GAD+ G NG+ P A+ + I E+R+ +GII D+++R+N+ +A Sbjct: 297 ANLIFGADRLQRGEIRYNGEARAYRQPADAIADGIGLVAEDRKVDGIIPDMSIRENMTLA 356 Query: 366 LQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPE 425 L + + D IV++Y+ L ++ PD+P+K LSGGNQQKVL+GRWL T P+ Sbjct: 357 LLPKLARAGIVDRARQDEIVERYITALAIKCTSPDQPIKELSGGNQQKVLLGRWLCTDPK 416 Query: 426 LLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIA 485 LLI+DEPTRGIDIGAK+EI +++ LA +G+GV+ ISSELEE++ +D + VL D +A Sbjct: 417 LLIVDEPTRGIDIGAKSEILRLLRRLADEGLGVLMISSELEELLAAADRVTVLSDGTSVA 476 Query: 486 EIENDDTVSQATIVETIAN 504 + + +S+A + +A+ Sbjct: 477 VLPRKE-LSEAALFAAMAH 494 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: 631 Number of extensions: 28 Number of successful extensions: 7 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: 497 Length adjustment: 34 Effective length of query: 479 Effective length of database: 463 Effective search space: 221777 Effective search space used: 221777 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