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 AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__azobra:AZOBR_RS31245 Length = 518 Score = 345 bits (885), Expect = 2e-99 Identities = 193/505 (38%), Positives = 305/505 (60%), Gaps = 17/505 (3%) Query: 17 APAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPN--E 74 A ILEM+GI++ FPGVKALD+V++++ G + ALIGENGAGKSTL+K+L+G+Y + Sbjct: 2 AMPILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFD 61 Query: 75 GEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTM 134 GEI G+P F + G+ IHQE L L++ EN+FLG+ +R IDW Sbjct: 62 GEIRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASR-GVIDWDAA 120 Query: 135 NSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEID 194 R++ LL + + P + D+ + ++ LV IA+ALS E +++I+DEPTA+L+ + D Sbjct: 121 TLRARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSD 180 Query: 195 DLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRK---TPQDEIV 251 L ++ K +G A + ISHK +E+ ++AD + R V + + QD I+ Sbjct: 181 ALLELLLQFKARGIASILISHKLNEIAKVADRVTIL--RDGTTVETLDCREAVVSQDRII 238 Query: 252 RMMVGRDVENVFPKIDVAIGGPVLEIRNYSH-------RTEFRDISFTLRKGEILGVYGL 304 R MVGR + + +P+ G + E++ +S R RD++ T+R+GE++G+ GL Sbjct: 239 RGMVGRALSDRYPRRTTVPGDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAGL 298 Query: 305 IGAGRSELSQSLFGIT--KPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALP 362 +GAGR+E + SLFG + + + G+ L+G+EI + + A+ G+ Y E+R GL L Sbjct: 299 MGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLVLD 358 Query: 363 MPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVV 422 I N+TL +L ++R + E +A ++ RL +R A + LSGGNQQKVV Sbjct: 359 NDIRHNVTLANLRGVAKRWVIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGNQQKVV 418 Query: 423 IGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRV 482 + KWL P+V+ILDEPT+GID+G+K ++ I++L AEG ++++SSE+PE++G++DR+ Sbjct: 419 LSKWLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGVADRI 478 Query: 483 LVMKEGLSAGIFERAELSPEALVRA 507 VM G AE S E ++ A Sbjct: 479 YVMNAGEMVAEMPAAEASQEKIMGA 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: 644 Number of extensions: 34 Number of successful extensions: 10 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: 518 Length adjustment: 35 Effective length of query: 477 Effective length of database: 483 Effective search space: 230391 Effective search space used: 230391 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