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 RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 339 bits (869), Expect = 2e-97 Identities = 194/495 (39%), Positives = 289/495 (58%), Gaps = 4/495 (0%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 + EMRGI + FPGVKALD+VS A++PG V L+GENGAGKS+L+K+L G+Y + GE Sbjct: 10 LFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFYH 69 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRF-RTIDWQTMNSRS 138 DG P S + G+ I QE L L +A+NIFLG PR R ++D M++ + Sbjct: 70 DGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHAEA 129 Query: 139 KALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFR 198 + +L L + + L +AQ+ +V IA+ALS ARI+++DEPTAALS +E + LF Sbjct: 130 RRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKLFA 189 Query: 199 IVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRD 258 ++ LK G ++++ISH+ E++ + D + R R+ + DE+V MVGR Sbjct: 190 VIARLKADGVSMIYISHRMAEVFALGDRITIL-RDGRKVGACLPGDATPDELVARMVGRK 248 Query: 259 VENVFPKIDVAIGGPV-LEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLF 317 V+ + + A G V L++RN S + DI+ +R GEI+G+ GL+G+GRSE+++++F Sbjct: 249 VDMSYSRERSAQPGEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVARAVF 308 Query: 318 GITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLART 377 G G++ + G+ +T P A G +PE R GLAL + N+ L L R Sbjct: 309 GADPIRQGEIYIFGKRLT-GGPDRARELGAALIPESRKSEGLALIRTVRDNLLLAGLRRA 367 Query: 378 SRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILD 437 + RA ALA + RL + + LSGGNQQK+VIGKWL K+ I D Sbjct: 368 FPARWYRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKLFIFD 427 Query: 438 EPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERA 497 EPT+GID+G+KA + I L +G ++++SSELPEII + DR VM+ G AG A Sbjct: 428 EPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGEVAHA 487 Query: 498 ELSPEALVRAATGNA 512 E++ E +++ +A Sbjct: 488 EMTEERILQLGMNDA 502 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: 592 Number of extensions: 28 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: 502 Length adjustment: 34 Effective length of query: 478 Effective length of database: 468 Effective search space: 223704 Effective search space used: 223704 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