Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Caulo:CCNA_00903 Length = 515 Score = 333 bits (854), Expect = 9e-96 Identities = 190/503 (37%), Positives = 305/503 (60%), Gaps = 17/503 (3%) Query: 13 ITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKP-Q 71 ++ FPGV+ALD VDL + GEVHAL+GENGAGKST+IK L+ + +AG++ G+ Sbjct: 9 VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68 Query: 72 QFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKKYLAQM 131 + L Q GIAT+YQE NL LSV EN+ LG E R +DW + A+ L + Sbjct: 69 PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128 Query: 132 GLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVR 191 GL ++P P+ +++A QQ+V IA+AM +NA+++I+DEPT++L EV L AI+ ++ Sbjct: 129 GLP-LNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLK 187 Query: 192 DSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELSQI 251 V++++VSH L ++ + DR T++R+G+F+ D +++ +M+G+ + Sbjct: 188 ARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV----EF 243 Query: 252 GAKKARREITPGEKPIVDVKG-------LGKKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304 +K RR P ++ V+G L G + V GE+VG AGL+G+GRT+ Sbjct: 244 ERRKRRR---PPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300 Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNI-L 363 L RL++GAD +G ++ K + + P A++ I E+R+ +G D ++R+N+ L Sbjct: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360 Query: 364 IALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423 +L+A + + + ++ +V+ Y ++L ++ AD + + LSGGNQQKVL+GR +A Sbjct: 361 PSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420 Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHK 483 P++LI+DEPTRGIDIGAKAE+ QV+ DLA G+ VV ISSEL EV+ +SD I V ++ Sbjct: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480 Query: 484 IAEIENDDTVSQATIVETIANTN 506 +A+++ + + T+ Sbjct: 481 VADLDAQTATEEGLMAYMATGTD 503 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: 648 Number of extensions: 31 Number of successful extensions: 9 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: 515 Length adjustment: 35 Effective length of query: 478 Effective length of database: 480 Effective search space: 229440 Effective search space used: 229440 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