Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >NCBI__GCF_003046325.1:WP_069332735.1 Length = 499 Score = 302 bits (774), Expect = 2e-86 Identities = 176/503 (34%), Positives = 296/503 (58%), Gaps = 15/503 (2%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 P++ ++ ++ F V+ L VD L PGEVHAL+GENGAGKST +K L G +AG ++ Sbjct: 4 PVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVL 63 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHE-KRGPFGIDWKKTHEAA 124 +DG+P F + +A+ AG+ ++QE NL T L+V EN+ LG E KRGPF +D + + Sbjct: 64 LDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPF-LDHRAMQAES 122 Query: 125 KKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLF 184 ++ L ++ ++DP +S++S+ +Q+V IA+A+ + A+VLI+DEPT+ L E L Sbjct: 123 RRLLERLHC-AVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLL 181 Query: 185 AIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKS 244 + ++R +G AIL+ SH LD++ I DR+T+LR+G+ + K D + M+G+ Sbjct: 182 EQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGR- 240 Query: 245 AAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304 ELS + K+ +P +P+++V GL G + + +GEV+GFAGL+GSGRTE Sbjct: 241 --ELSGLFPPKS----SPAPEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTE 294 Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNI-L 363 L + G +P +G + G + + A + Y TE+R+++G++ + +N+ L Sbjct: 295 LMEGIVGL-RPATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTL 353 Query: 364 IALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423 +AL + I K + + + + + ++R D +LSGGNQQK+L+ + + Sbjct: 354 LALDRFGRVL--IDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAE 411 Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHK 483 P ++I+DEPTRGID+G K +I + LA++G V+ +SSEL EV+ L++ + V+ Sbjct: 412 PRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRI 471 Query: 484 IAEIENDDTVSQATIVETIANTN 506 E+E + +++ IV N Sbjct: 472 AGEVEG-EAITEENIVRLAMGLN 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: 602 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: 499 Length adjustment: 34 Effective length of query: 479 Effective length of database: 465 Effective search space: 222735 Effective search space used: 222735 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 24 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