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_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 330 bits (847), Expect = 6e-95 Identities = 214/518 (41%), Positives = 304/518 (58%), Gaps = 22/518 (4%) Query: 12 SKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYR 71 S T +L +R I + FPGV+AL V + + G V AL+GENGAGKSTL+KIL+G Y Sbjct: 2 SDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYT 61 Query: 72 PNEG-EILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTID 130 + G E +DG+ Q+A D GV I+QE L L+VAENI+LG A + R Sbjct: 62 ADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVAR 121 Query: 131 WQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSR 190 + + + L L ++ P + LSIAQR LV IARA+ EARI++MDEPT LS Sbjct: 122 GDMVRACAPTL-ARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLST 180 Query: 191 KEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRK-TPQDE 249 E D LF ++R L+ +G AIL+ISH+ E+ E+AD V R V + R Q Sbjct: 181 HETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVL--RDGCFVGTLDRAHLSQAA 238 Query: 250 IVRMMVGRDVENVFPKID-VAIGGPV-LEIRNYSHRTEFRDISFTLRKGEILGVYGLIGA 307 +V+MMVGRD+ + K A+ V L +R+ + + SF LR GE+LG+ GL+GA Sbjct: 239 LVKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGA 298 Query: 308 GRSELSQSLFGITKPLSGKMVL-----EGQEITIHS--PQDAIRAGIVYVPEERGRHGLA 360 GR+EL++ +FG G++ + G +T+ + P+ AI AGI Y+ E+R GL Sbjct: 299 GRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLF 358 Query: 361 LPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLD---LRAAALSVPVGTLSGGN 417 L + +N+ L AR + L N A R+ E +D +R A V VG LSGGN Sbjct: 359 LDQSVHENINLIVAARDALG--LGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGN 416 Query: 418 QQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIG 477 QQKV++ + L P+V+ILDEPT+G+DIG+K+ ++ I+ LA G++I+M+SSELPE++G Sbjct: 417 QQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVG 476 Query: 478 MSDRVLVMKEGLSAGIFE---RAELSPEALVRAATGNA 512 + DRVLVM+EG AG A + E ++ ATG A Sbjct: 477 LCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAA 514 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: 31 Number of successful extensions: 12 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: 537 Length adjustment: 35 Effective length of query: 477 Effective length of database: 502 Effective search space: 239454 Effective search space used: 239454 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