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 BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__BFirm:BPHYT_RS27185 Length = 516 Score = 408 bits (1049), Expect = e-118 Identities = 216/506 (42%), Positives = 322/506 (63%), Gaps = 3/506 (0%) Query: 8 PVTDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILT 67 P + + + IL+++G+S+ FPGV ALD + + L G V A+ GENGAGKSTL+KI++ Sbjct: 11 PAAEPEPPVSREILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIIS 70 Query: 68 GIYRPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFR 127 G YR +EG + G P F+S A AG+ IHQE L L+VAENI+L P+ R Sbjct: 71 GQYRADEGVVRYRGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPK-RGP 129 Query: 128 TIDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAA 187 +D++T+NS ++ L + N+ P+ + LS+AQ+ +V IA+ALS++AR++IMDEPT++ Sbjct: 130 FVDYRTLNSNAQRCLQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSS 189 Query: 188 LSRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQ 247 L+ E LFRI+R L+ G AIL+ISH+ DE+ EI D V R R T Sbjct: 190 LTESETVQLFRIIRELRAGGVAILYISHRLDEMAEIVDRVTVL-RDGRHIATSDFASTTV 248 Query: 248 DEIVRMMVGRDVENVFPKIDVAIGGPVL-EIRNYSHRTEFRDISFTLRKGEILGVYGLIG 306 +EIV MVGR +++ +P +L +R+ F +SF LRKGEILG GL+G Sbjct: 249 NEIVARMVGRPLDDAYPPRQSTPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMG 308 Query: 307 AGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIF 366 AGR+E ++++FG +P SG + L + +TI SP++AIR GI Y+ E+R + GLAL MP+ Sbjct: 309 AGRTETARAIFGAERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVS 368 Query: 367 QNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKW 426 N+TL ++ S RGFLR + E A+A +Y L +R + LSGGNQQK+VI KW Sbjct: 369 ANITLANVRAISSRGFLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKW 428 Query: 427 LATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMK 486 L +++ DEPT+GID+G+K A++G + LAA+G+ ++++SSELPE++GM+DR+ V Sbjct: 429 LYRGSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFH 488 Query: 487 EGLSAGIFERAELSPEALVRAATGNA 512 EG + E + S E ++ A+G + Sbjct: 489 EGRITAVLETRQTSQEEILHHASGRS 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: 610 Number of extensions: 31 Number of successful extensions: 8 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: 516 Length adjustment: 35 Effective length of query: 477 Effective length of database: 481 Effective search space: 229437 Effective search space used: 229437 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