Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Putida:PP_2759 Length = 512 Score = 313 bits (802), Expect = 9e-90 Identities = 177/508 (34%), Positives = 290/508 (57%), Gaps = 20/508 (3%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 P++ ++GI F +ALDG L + G VH L+GENGAGKST+IK L G+++ +AGS++ Sbjct: 4 PVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLL 63 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKR-GPFGIDWKKTHEAA 124 +DG+P + GI ++QE L +VGE + GHE+R GP + EAA Sbjct: 64 LDGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQREAA 123 Query: 125 KKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLF 184 + GL + + + +S A QQ+V I RA++I +VL+ DEP+ +L EV L Sbjct: 124 RLLDDYFGLR-LPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLL 182 Query: 185 AIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKS 244 I++++RD G+AI+++SH+L +I + DR+T+LRNG+ + EV ++T +++ +M+ + Sbjct: 183 RIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNRE 242 Query: 245 AAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304 EL + P ++DV+GLG+ +D+ + +GE+VG GL+GSG E Sbjct: 243 VGELYP-------KVAVPAGALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKE 295 Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILI 364 L R L+G PDSG L+G+ +++ P A+ +A E RR +G+ DL+V++N + Sbjct: 296 LLRSLFGLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTL 355 Query: 365 ALQA---TRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLA 421 A + G+ P ++ + ++ L ++ V+ LSGGNQQKV + +W A Sbjct: 356 AALSRFVRLGLLSPARERHTTL---ELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFA 412 Query: 422 THPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEV---- 477 L +LDEP+ GID+GAK EI +++ +L +G GV+ +SS+L E++ L D I V Sbjct: 413 RCSSLYLLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRG 472 Query: 478 -LKDRHKIAEIENDDTVSQATIVETIAN 504 + R E +D ++ AT + N Sbjct: 473 AIAARFAAGEANSDRLLAVATGAQRAQN 500 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: 609 Number of extensions: 28 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: 512 Length adjustment: 35 Effective length of query: 478 Effective length of database: 477 Effective search space: 228006 Effective search space used: 228006 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