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_2759 PP_2759 ribose ABC transporter - ATP-binding subunit
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Putida:PP_2759 Length = 512 Score = 355 bits (910), Expect = e-102 Identities = 194/493 (39%), Positives = 299/493 (60%), Gaps = 5/493 (1%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 +LE+RGI + F +ALD S+ + G+V L+GENGAGKSTL+K+L GI+RP+ G +L+ Sbjct: 5 VLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLLL 64 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139 DG+P S + G+ IHQE +L TV E +F GH R +D ++ + Sbjct: 65 DGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFG-PLLDRRSQQREAA 123 Query: 140 ALLTALES-NIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFR 198 LL + + +LS A++ +V I RAL I+ R+++ DEP+ AL ++E++ L R Sbjct: 124 RLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLR 183 Query: 199 IVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVS-RKTPQDEIVRMMVGR 257 IV+ L++ G AI++ISH E+ + D V R+ R V VS R T ++I R+MV R Sbjct: 184 IVQRLRDDGLAIVYISHYLQEIEALCDRVTVL--RNGRDVAEVSPRNTSLEQITRLMVNR 241 Query: 258 DVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLF 317 +V ++PK+ V G +L++R ++ I +R+GEI+G+ GL+G+G EL +SLF Sbjct: 242 EVGELYPKVAVPAGALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSLF 301 Query: 318 GITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLART 377 G+ P SG++ L+GQ +++ SP++A+ G+ +PEER R G+AL + + +N TL +L+R Sbjct: 302 GLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAALSRF 361 Query: 378 SRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILD 437 R G L A E + ERL ++A V LSGGNQQKV + KW A + +LD Sbjct: 362 VRLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLYLLD 421 Query: 438 EPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERA 497 EP+ GID+G+K ++ I EL EG ++++SS+LPE+IG+ DR+ VM G A F Sbjct: 422 EPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARFAAG 481 Query: 498 ELSPEALVRAATG 510 E + + L+ ATG Sbjct: 482 EANSDRLLAVATG 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: 570 Number of extensions: 29 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: 512 Length adjustment: 35 Effective length of query: 477 Effective length of database: 477 Effective search space: 227529 Effective search space used: 227529 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