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 GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 404 bits (1039), Expect = e-117 Identities = 212/507 (41%), Positives = 332/507 (65%), Gaps = 5/507 (0%) Query: 6 QQPVTDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKI 65 Q P +T + P +LE+ IS+ FPGV AL +V + + PGTV AL+GENGAGKSTL+KI Sbjct: 9 QPPSLQPQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKI 68 Query: 66 LTGIYRPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTR 125 + GIY+P+ GEI + G+P F + AA AG+ IHQE L +++AENI++G Sbjct: 69 IAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNS 128 Query: 126 FRTIDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPT 185 ++ + M+ + LL L N+DP ++ +LSIA+R +V IA+A+S ++ I+IMDEPT Sbjct: 129 LHMVNHREMHRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPT 188 Query: 186 AALSRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKT 245 +A++ KE+ LF I+ LK QGK I++I+HK +E++ IAD+ VF R + G+ R Sbjct: 189 SAITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVF--RDGHYI-GLQRAD 245 Query: 246 PQ--DEIVRMMVGRDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYG 303 D ++ MMVGR++ +FP + IG +L +R+ + F+D+SF L GEILG+ G Sbjct: 246 SMNSDSLISMMVGRELSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAG 305 Query: 304 LIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPM 363 L+G+GR+ +++++FGIT SG++ L+G+ + I P AI G + E+R GL + Sbjct: 306 LMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCL 365 Query: 364 PIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVI 423 + +NM + L + GF++ AL ++L ++ +L + TLSGGNQQK ++ Sbjct: 366 SVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALL 425 Query: 424 GKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVL 483 +WL T P+++ILDEPT+GID+G+KA ++ I+ LA+EG+++IM+SSELPE++GMSDRV+ Sbjct: 426 ARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVM 485 Query: 484 VMKEGLSAGIFERAELSPEALVRAATG 510 VM EG G +R+E + E +++ A+G Sbjct: 486 VMHEGELMGTLDRSEATQEKVMQLASG 512 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: 578 Number of extensions: 32 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: 517 Length adjustment: 35 Effective length of query: 477 Effective length of database: 482 Effective search space: 229914 Effective search space used: 229914 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 Apr 09 2024. 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