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 Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 339 bits (869), Expect = 2e-97 Identities = 193/493 (39%), Positives = 293/493 (59%), Gaps = 6/493 (1%) Query: 21 LEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILVD 80 +E R +++ F V+ L V AL PG V L+GENGAGKSTL+KIL G P GE++VD Sbjct: 5 VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVD 64 Query: 81 GRPTTFASAQAAIDA-GVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139 G A +A G+ IHQE L D+LT+A+NIFLGH + R +D + M +++ Sbjct: 65 GAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIK-RGLFLDDKAMREKTR 123 Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199 L + +DP R++ L +A++ LV IARAL+ AR++IMDEPTA L+ E + LF + Sbjct: 124 EALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFAL 183 Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDV 259 + GLK G I++ISHK DE+ D+ VV R R + + ++ +MVGR++ Sbjct: 184 MAGLKAAGVTIIYISHKLDEVERTTDEVVVM-RDGLLVAREATASVTRRQMANLMVGREL 242 Query: 260 ENVFPKIDVAI--GGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLF 317 ++FP A G P + +R + + F +R+GEILG GL+GAGR+EL + L Sbjct: 243 ADLFPPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTELFEGLL 302 Query: 318 GITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLART 377 G+ +G + + GQ + + SP+DA R G+ Y+ E+R GL + + N+TL +L R Sbjct: 303 GLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMALERY 362 Query: 378 SRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILD 437 ++ AA + AL R+ + +R +L V +LSGGNQQK+ + K L P V++LD Sbjct: 363 AKPWLDPAAEQAAL-REAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVVVLD 421 Query: 438 EPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERA 497 EPT+G+D+G+K ++ + LA +GL++I++SSEL E+IG+ RV VM+ G + Sbjct: 422 EPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQTTLQEP 481 Query: 498 ELSPEALVRAATG 510 L+ E L+ ATG Sbjct: 482 HLTEEELIAHATG 494 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: 617 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: 496 Length adjustment: 34 Effective length of query: 478 Effective length of database: 462 Effective search space: 220836 Effective search space used: 220836 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