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 PfGW456L13_7 ABC transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_7 Length = 521 Score = 222 bits (565), Expect = 3e-62 Identities = 146/474 (30%), Positives = 241/474 (50%), Gaps = 19/474 (4%) Query: 21 LEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILVD 80 L++R I++ +PG A D + + + PG + AL+GENGAGKSTL+KI+ G+ + GE++ Sbjct: 14 LQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQ 73 Query: 81 GRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFL--GHAPRTRFRTIDWQTMNSRS 138 G+ + + A G+ + Q LF+ L+VA+NI L G A T + + + Sbjct: 74 GQRVSLRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAGTP------KQLEPKI 127 Query: 139 KALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFR 198 + + ++P + LSI +R V I R L + R++I+DEPT+ L+ +E DDLF Sbjct: 128 REVSRRYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFV 187 Query: 199 IVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRD 258 +R L +G +ILFISHK E+ + V R R V + ++ R+MVG Sbjct: 188 TLRRLAAEGCSILFISHKLGEVRALCHSATVL-RGGRVAGHCVPAECSDQQLARLMVGEA 246 Query: 259 VENVFPKIDVAIGGPVLEIRNYSHRT------EFRDISFTLRKGEILGVYGLIGAGRSEL 312 E + V G L++R S +I +R+GEI+G+ G+ G G+ EL Sbjct: 247 AELIADYPKVTGGDACLDVRGLSWHNPDPFGCSLANIDLEVRRGEIVGIAGVAGNGQDEL 306 Query: 313 SQSLFG--ITKPLSGKMVLEGQEITIHSPQDAIR-AGIVYVPEERGRHGLALPMPIFQNM 369 L G + + + G+E H DA R G+ +VP ER HG + + N Sbjct: 307 LALLSGEALLPRNASATIRFGKEPVAHLRPDARRQLGLAFVPAERLGHGAVPELSLADNA 366 Query: 370 TLPSLAR-TSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLA 428 L + G ++ ALA + R ++ P +LSGGN QK ++G+ + Sbjct: 367 LLTAFQHGLVSNGLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKFILGREIL 426 Query: 429 TAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRV 482 P++++ PT G+D+G+ A +H + L G +I+++S +L E+ +SDR+ Sbjct: 427 QQPRLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDRL 480 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: 638 Number of extensions: 38 Number of successful extensions: 8 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: 521 Length adjustment: 35 Effective length of query: 477 Effective length of database: 486 Effective search space: 231822 Effective search space used: 231822 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