Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate SMc02325 SMc02325 ABC transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Smeli:SMc02325 Length = 503 Score = 363 bits (933), Expect = e-105 Identities = 194/505 (38%), Positives = 314/505 (62%), Gaps = 14/505 (2%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 P + ++GI+ FPGV+AL V L LYPG V AL+GENGAGKST++K LTG+Y+ +AG+I Sbjct: 3 PAIALEGISKSFPGVRALSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGTIR 62 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKKTHEAA 124 + F L A AG+ ++QE L LSV EN+ LGH R FG IDWK+ + A Sbjct: 63 LGDTETTFPTALAASRAGVTAIHQETVLFDELSVAENIFLGHAPRNRFGLIDWKQLNADA 122 Query: 125 KKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLF 184 + L + G + DP L + IA + LVAIARA+ ++A+V+I+DEPT++L E+ +L+ Sbjct: 123 QALLGRAGAD-FDPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHELY 181 Query: 185 AIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKS 244 ++ +++ G A+LF+SH D+I+ I DR T+ R+G I E + D +D+L+ MM+G++ Sbjct: 182 DLIERLKADGKAVLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADVSQDDLVRMMVGRA 241 Query: 245 AAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304 +G+ ++E+T G+ P++ V G ++ ++ +GE++GF GL+G+GR+E Sbjct: 242 ------VGSVYPKKEVTIGQ-PVLTVSGYRHPTEFEDINFELRRGEILGFYGLVGAGRSE 294 Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILI 364 + L G +P +G L+G+ + I P A++ I Y E R +G I + + QN+ + Sbjct: 295 FMQSLIGITRPSAGAVKLDGEVLVIRSPAEAIRAGIVYVPEERGRQGAIIGMPIFQNVTL 354 Query: 365 ALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHP 424 + + E A+ +Y L++R A D+ V LSGGNQQKV+I +WLAT P Sbjct: 355 PSLSHTSRSGFLRLAEEFALAREYTSRLDLRAAALDQDVGTLSGGNQQKVVIAKWLATRP 414 Query: 425 ELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKD---- 480 +++ILDEPT+GIDIG+KA + + +LA+QG+ V+ +SSE+ E++ +SD + V+++ Sbjct: 415 KVIILDEPTKGIDIGSKAAVHAFMSELAAQGLSVIMVSSEIPEIMGMSDRVIVMREGRVA 474 Query: 481 -RHKIAEIENDDTVSQATIVETIAN 504 R++ +E+ + V A +ET A+ Sbjct: 475 GRYERSELTAEKLVRAAAGIETQAD 499 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: 617 Number of extensions: 35 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: 503 Length adjustment: 34 Effective length of query: 479 Effective length of database: 469 Effective search space: 224651 Effective search space used: 224651 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