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 PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 298 bits (762), Expect = 4e-85 Identities = 180/476 (37%), Positives = 277/476 (58%), Gaps = 5/476 (1%) Query: 36 LDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILVDGRPTTFASAQAAIDA 95 L VS++L G V AL GENGAGKSTL K+++G+ P G + G+ S A Sbjct: 31 LGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYRGQAYAPGSRGEAERL 90 Query: 96 GVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSKALLTALESN-IDPTIR 154 GV + QE L LTVAEN+FL + P +RF I + + + A + + + IDP Sbjct: 91 GVRMVMQELNLLPTLTVAENLFLDNLP-SRFGWISHKRLRQLATAAMARVGLDAIDPDTP 149 Query: 155 LKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRIVRGLKEQGKAILFIS 214 + +L I + +V IAR L + ++I+DEPTA L+ +E+ LF + L+ +G AI++IS Sbjct: 150 VGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQIERLRARGVAIVYIS 209 Query: 215 HKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDVENVFPKIDVAIGGPV 274 H+ +EL +A VV R + ++ E+V +MVGR++ +G P+ Sbjct: 210 HRLEELQRVAQRIVVL-RDGKLVCDEPIQRYSSAELVNLMVGRELGEHIDLGRRQLGAPL 268 Query: 275 LEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVL--EGQ 332 L++ + R++SF +R GEI G+ GLIGAGR+EL + ++G + SG + L Q Sbjct: 269 LKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQ 328 Query: 333 EITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALA 392 ++I SP+ A+RAGI + E+R GL L I N+ L +L SR G L + E ALA Sbjct: 329 AVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDSEAEKALA 388 Query: 393 RKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVH 452 + + + +R+A VG LSGGNQQKVVIG+WL +V++ DEPT+GID+G+K ++ Sbjct: 389 ERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIY 448 Query: 453 GFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAA 508 G ++ELA +G ++++VSS+L E++ + DR+ V+ G F R S + L+ AA Sbjct: 449 GLLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLLAAA 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: 584 Number of extensions: 37 Number of successful extensions: 7 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: 524 Length adjustment: 35 Effective length of query: 477 Effective length of database: 489 Effective search space: 233253 Effective search space used: 233253 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