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 AO356_20250 AO356_20250 L-arabinose transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20250 Length = 514 Score = 367 bits (942), Expect = e-106 Identities = 203/504 (40%), Positives = 311/504 (61%), Gaps = 4/504 (0%) Query: 7 QPVTDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKIL 66 Q T ++ + L GI + FPGV+AL N+S HPG V AL+GENGAGKSTL+KIL Sbjct: 2 QAQTATRQHNIGGSLRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKIL 61 Query: 67 TGIYRPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRF 126 G Y P+ G++ + + F +I +GV IHQE L E+TVAEN+FLGH P RF Sbjct: 62 GGAYIPSSGDLQIGEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLP-ARF 120 Query: 127 RTIDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTA 186 ++ + ++ LL L IDP ++ LS+ QR LV IA+ALS A ++ DEPT+ Sbjct: 121 GLVNRGVLRQQALTLLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTS 180 Query: 187 ALSRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVF-PRRSRRPVRGVSRKT 245 +LS +EID L I+ L+++GK +L++SH+ +E++ I + VF R R +S T Sbjct: 181 SLSAREIDRLMAIIARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELT 240 Query: 246 PQDEIVRMMVGRDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLI 305 D++V MVGRD+++++ G L++++ +SF + KGEILG++GL+ Sbjct: 241 -HDQLVTCMVGRDIQDIYDYRPRERGDVALQVKSLLGPGLREPVSFQVHKGEILGLFGLV 299 Query: 306 GAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPI 365 GAGR+EL + L G+ + G +VL G+E+ + SP+DAI AG++ PE+R + G+ + Sbjct: 300 GAGRTELFRLLSGLERQSEGSLVLHGKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSV 359 Query: 366 FQNMTLPSLARTSRRG-FLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIG 424 +N+ + + S G LR E A K + L ++ A S + LSGGNQQK ++G Sbjct: 360 GENINISARPAHSALGCLLRGDWERGNADKQIKSLKVKTPAASQKIMYLSGGNQQKAILG 419 Query: 425 KWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLV 484 +WL+ KV++LDEPT+GIDIG+KA ++ I LAA+G+++I+VSS+L E++G+SDR+LV Sbjct: 420 RWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILV 479 Query: 485 MKEGLSAGIFERAELSPEALVRAA 508 + EG G R + + L++ A Sbjct: 480 LCEGAMRGELSRDQANESNLLQLA 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: 579 Number of extensions: 33 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: 514 Length adjustment: 35 Effective length of query: 477 Effective length of database: 479 Effective search space: 228483 Effective search space used: 228483 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