Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate SM_b21588 SM_b21588 sugar uptake ABC transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Smeli:SM_b21588 Length = 505 Score = 466 bits (1198), Expect = e-135 Identities = 249/512 (48%), Positives = 348/512 (67%), Gaps = 10/512 (1%) Query: 2 TDKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINA 61 T + I+ I FPG KALD VD L GEVHAL+GENGAGKST+IK LTG Y+ + Sbjct: 3 TSSDNILSATRIEKGFPGTKALDRVDFHLRRGEVHALLGENGAGKSTLIKCLTGAYRRDG 62 Query: 62 GSIMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTH 121 GS+++DG T DAQ GI TVYQEVNL NL+V EN+ LG + R +D + + Sbjct: 63 GSMLLDGAEADPRDTFDAQRLGIGTVYQEVNLLPNLTVAENLFLGRQPRRFGMVDTRTMN 122 Query: 122 EAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVR 181 A++ LA+ L+ ID L+S S+A+QQ+VAIARA+ ++ KVLILDEPT+SLDA+EV Sbjct: 123 RKARELLAEYELD-IDVTRDLASYSVAIQQVVAIARAVDLSGKVLILDEPTASLDAHEVE 181 Query: 182 DLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241 LF I+R++++ G+ I+F++HFL+Q+Y I+DR+T+LRNGQ + D R ELI MMI Sbjct: 182 MLFRIVRRLKERGLGIIFITHFLEQVYAISDRITVLRNGQLVGTRNAADLDRRELIAMMI 241 Query: 242 GKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSG 301 G+ A A + GE P + G++G I+P D+D+ GEVVG AGLLGSG Sbjct: 242 GRELAT----EIHSAHSDAVAGE-PRYRFRNFGRRGKIDPFDLDVRAGEVVGMAGLLGSG 296 Query: 302 RTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQN 361 RTE +L+GA + DSGT ++G+ V++S P A++ K + E+R+ GI+GDL+VR+N Sbjct: 297 RTETAEILFGAHRADSGTAEIDGRSVDLSSPRAAIRQKFGFCPEDRKTAGIVGDLSVREN 356 Query: 362 ILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLA 421 I++ALQA RG +PIP+ E + + D Y++ L++R AD ++P++ LSGGNQQK ++ RWLA Sbjct: 357 IVLALQARRGWTRPIPRAEQNRLADHYIRALDIRTADREKPIRLLSGGNQQKAILARWLA 416 Query: 422 THPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDR 481 T PELLILDEPTRGID+GA AEI +++ L +GM ++ ISSE+EE+V S + VL+D Sbjct: 417 TEPELLILDEPTRGIDVGAHAEIIRLIESLREKGMSLIVISSEIEELVAYSTRVVVLRDH 476 Query: 482 HKIAEIENDDTVSQATIVETIANTNVNTGKEA 513 +AE++ + IVE IA TN G+EA Sbjct: 477 AHVAELDGAQLTAH-RIVEAIAATN---GREA 504 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: 711 Number of extensions: 38 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: 505 Length adjustment: 34 Effective length of query: 479 Effective length of database: 471 Effective search space: 225609 Effective search space used: 225609 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