Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Burk376:H281DRAFT_02712 Length = 505 Score = 397 bits (1020), Expect = e-115 Identities = 218/501 (43%), Positives = 325/501 (64%), Gaps = 18/501 (3%) Query: 21 LEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEG-EILV 79 LEMR IS+ FPGVKALD V++ + G V AL GENGAGKSTL+KILTGIY P+ G ILV Sbjct: 10 LEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILV 69 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139 +G+ A + A GV I+QE + LTV ENIFL PRTR ID M ++ Sbjct: 70 EGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRMYREAR 129 Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199 +L ++ +IDP R+ +LS+ Q+ ++ IA+AL ++ +IMDEPTA+LS E L I Sbjct: 130 EVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLGI 189 Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRR----PVRGVSRKTPQDEIVRMMV 255 V+ L+E+ A+++ISH+ +E++E+AD V R R P+ ++R+T +VR+MV Sbjct: 190 VKRLRERNIAVVYISHRLEEIFELADRVTVL-RDGRTVGTAPIADMTRET----LVRLMV 244 Query: 256 GRDVENVFPKIDV-AIGGPVLEIRNYSHRT------EFRDISFTLRKGEILGVYGLIGAG 308 R++ ++ + A PVLE+R S + RDISFTL +GE+LG+ GL+G+G Sbjct: 245 ARELSELYGEPQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAGLVGSG 304 Query: 309 RSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQN 368 R+E+ + +FG+ + +G + +EG+ ++I +P DAIR+GI +V E+R GL L M + +N Sbjct: 305 RTEIMEMIFGM-RACTGSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVREN 363 Query: 369 MTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLA 428 +L L R S F++ A E R++ L ++ + V LSGGNQQK+VI KW+A Sbjct: 364 FSLTHLERYSPFQFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWVA 423 Query: 429 TAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEG 488 +PKV+I+DEPT+GID+G+KA VH I+ LAAEG+ +I++SS+L E++ +SDR+L ++EG Sbjct: 424 RSPKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVREG 483 Query: 489 LSAGIFERAELSPEALVRAAT 509 +G RA+ S E ++ AT Sbjct: 484 RISGELSRAQASQEKVMALAT 504 Lambda K H 0.320 0.137 0.382 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: 616 Number of extensions: 29 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: 512 Length of database: 505 Length adjustment: 34 Effective length of query: 478 Effective length of database: 471 Effective search space: 225138 Effective search space used: 225138 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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