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 Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410 Length = 514 Score = 368 bits (944), Expect = e-106 Identities = 203/490 (41%), Positives = 305/490 (62%), Gaps = 4/490 (0%) Query: 21 LEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILVD 80 L GI + FPGVKALD +S HPG V AL+GENGAGKSTL+KIL G Y P+ G++ + Sbjct: 16 LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIG 75 Query: 81 GRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSKA 140 + F S +I +GV IHQE L E+TVAEN+FLGH P + F I+ + ++ A Sbjct: 76 EQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPAS-FGLINRGVLRQQALA 134 Query: 141 LLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRIV 200 L L IDP ++ LS+ QR LV IA+ALS A ++ DEPT++LS +EID L I+ Sbjct: 135 CLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 Query: 201 RGLKEQGKAILFISHKFDELYEIADDFVVF-PRRSRRPVRGVSRKTPQDEIVRMMVGRDV 259 L+++GK +L++SH+ +E++ I + VF R R +S T D++V MVGRD+ Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALT-HDQLVTCMVGRDI 253 Query: 260 ENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGI 319 ++++ G L++ +SF KGEILG++GL+GAGR+EL + L G+ Sbjct: 254 QDIYDYRSRPRGAVALKVDGLLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFRMLSGL 313 Query: 320 TKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSR 379 T+ +G++ L G+E+ +HSP+DAI AGI+ PE+R + G+ + +N+ + + S Sbjct: 314 TRNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHST 373 Query: 380 RG-FLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDE 438 G LR E A K + L ++ + + LSGGNQQK ++G+WL+ KV++LDE Sbjct: 374 FGCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDE 433 Query: 439 PTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAE 498 PT+GIDIG+KA ++ I LAA G+++I+VSS+L E++G+SDR+LV+ EG G R + Sbjct: 434 PTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQ 493 Query: 499 LSPEALVRAA 508 + L++ A Sbjct: 494 ANESNLLQLA 503 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: 594 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: 514 Length adjustment: 35 Effective length of query: 477 Effective length of database: 479 Effective search space: 228483 Effective search space used: 228483 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 Apr 09 2024. 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