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 GFF4164 PS417_21330 L-arabinose transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__WCS417:GFF4164 Length = 499 Score = 355 bits (912), Expect = e-102 Identities = 198/493 (40%), Positives = 298/493 (60%), Gaps = 6/493 (1%) Query: 19 AILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEIL 78 A L GI + FPGVKAL +S P V AL+GENGAGKSTL+KIL G Y P+ G + Sbjct: 4 AALRFNGIGKEFPGVKALSQISFEARPREVHALMGENGAGKSTLLKILGGAYLPSSGTLQ 63 Query: 79 VDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRS 138 + + F SA +I GV IHQE L E+TVAEN+FLGH P TRF ++ + ++ Sbjct: 64 IGEQTMDFKSAADSIACGVAVIHQELHLVPEMTVAENLFLGHLP-TRFGVVNRSQLRKQA 122 Query: 139 KALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFR 198 A L L IDP +L LS+ QR LV IA+ALS A ++ DEPT++LS +EID L Sbjct: 123 LACLKGLADEIDPDEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMA 182 Query: 199 IVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVS--RKTPQDEIVRMMVG 256 I+ L+++GK +L++SH+ +E++ I + VF + R VR D++V MVG Sbjct: 183 IITRLRDEGKVVLYVSHRMEEVFRICNAVTVF--KDGRYVRTFDDMNALSHDQLVTCMVG 240 Query: 257 RDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSL 316 RD+++++ G L++ +S + KGEILG++GL+GAGR+EL + L Sbjct: 241 RDIQDIYDYRQREQGEVALKVEGLLGPGLREPVSLNVHKGEILGLFGLVGAGRTELFRLL 300 Query: 317 FGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLAR 376 G+T+ +G + L GQ + + SP+DAI AG++ PE+R + G+ + +N+ + + Sbjct: 301 SGLTRSTAGSLALCGQTLQLRSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGA 360 Query: 377 TSRRGF-LRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVII 435 S G+ LR E A + + + ++ + LSGGNQQK ++G+WL+ KV++ Sbjct: 361 HSTFGWLLRDGWETTNADRQIKAMKVKTPNAEQKIMYLSGGNQQKAILGRWLSMPMKVLL 420 Query: 436 LDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFE 495 LDEPT+GIDIG+K+ ++ I LAA G+++I+VSS+L E++G+SDR+LVM EG G Sbjct: 421 LDEPTRGIDIGAKSEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVMSEGALTGELT 480 Query: 496 RAELSPEALVRAA 508 R + L++ A Sbjct: 481 RDQADEARLLQLA 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: 576 Number of extensions: 26 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: 499 Length adjustment: 34 Effective length of query: 478 Effective length of database: 465 Effective search space: 222270 Effective search space used: 222270 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