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 GFF2162 PS417_11030 L-arabinose transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__WCS417:GFF2162 Length = 500 Score = 358 bits (919), Expect = e-103 Identities = 200/492 (40%), Positives = 307/492 (62%), Gaps = 4/492 (0%) Query: 19 AILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEIL 78 A L GI + FPGVKALD +S + HPG V AL+GENGAGKSTL+KIL G Y PN G + Sbjct: 4 AALRFDGIGKTFPGVKALDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPNSGTLH 63 Query: 79 VDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRS 138 + + F SA +I +GV IHQE L E++VAEN+FLGH P +RF ++ + ++ Sbjct: 64 IGEQVMAFKSAADSIASGVAVIHQELHLVPEMSVAENLFLGHLP-SRFGVVNRGLLRKQA 122 Query: 139 KALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFR 198 A L L IDP +L LS+ QR LV IA+ALS A ++ DEPT++LS +EID L Sbjct: 123 LACLKGLADEIDPAEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMA 182 Query: 199 IVRGLKEQGKAILFISHKFDELYEIADDFVVF-PRRSRRPVRGVSRKTPQDEIVRMMVGR 257 I+ L+++GK +L++SH+ +E++ I + VF R R +S T D++V MVGR Sbjct: 183 IIARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFEDMSALT-HDQLVTCMVGR 241 Query: 258 DVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLF 317 D+++++ G L++ +SF +RKGEILG++GL+GAGR+EL + L Sbjct: 242 DIQDIYDYRPREHGEVALKVDGLLGPGLREPVSFNVRKGEILGLFGLVGAGRTELFRLLS 301 Query: 318 GITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLART 377 G+ + +G++ L G+ + + SP+DAI AG++ PE+R + G+ + +N+ + + Sbjct: 302 GLERASAGQLELCGEPLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAH 361 Query: 378 SRRGF-LRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIIL 436 S G+ LR E A + + ++ + + LSGGNQQK ++G+WL+ KV++L Sbjct: 362 STFGWLLREGWEKGNADQQINAMKVKTPNAAQKIMYLSGGNQQKSILGRWLSMPMKVLLL 421 Query: 437 DEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFER 496 DEPT+GIDIG+KA ++ I LAA+G+++I+VSS+L E++G++DR+LV+ EG G R Sbjct: 422 DEPTRGIDIGAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQTR 481 Query: 497 AELSPEALVRAA 508 + L++ A Sbjct: 482 EHATESNLLQLA 493 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: 581 Number of extensions: 29 Number of successful extensions: 9 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: 500 Length adjustment: 34 Effective length of query: 478 Effective length of database: 466 Effective search space: 222748 Effective search space used: 222748 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