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_RS19720 BPHYT_RS19720 arabinose ABC transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__BFirm:BPHYT_RS19720 Length = 515 Score = 385 bits (988), Expect = e-111 Identities = 199/488 (40%), Positives = 309/488 (63%), Gaps = 1/488 (0%) Query: 21 LEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILVD 80 L + GI+ FPGV ALD VS+ + G V L+GENGAGKSTL+K+L+G+ +P G + +D Sbjct: 26 LRLDGITVRFPGVLALDQVSLEVRRGEVHGLMGENGAGKSTLLKVLSGVNQPAAGTLSLD 85 Query: 81 GRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSKA 140 G F + +AAI AGV I+QE L ELTVAEN+ LG P RF +D + + +R+ Sbjct: 86 GVEQQFITTKAAIAAGVAIIYQELHLVPELTVAENLMLGALPN-RFGILDEKALVARAVR 144 Query: 141 LLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRIV 200 L L IDP+ ++K+LSI QR ++ I +AL +AR++ DEPT++LS +E LFRI+ Sbjct: 145 ELERLGEKIDPSQQVKNLSIGQRQMIEIGKALMRDARVIAFDEPTSSLSSRETTQLFRII 204 Query: 201 RGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDVE 260 R LK +G+AI++++H+ DE+YE+ D VF R +D ++ MVGR + Sbjct: 205 RALKAEGRAIIYVTHRMDEVYELCDRVTVFRDGRRIDTFEAGEGLDRDRLISCMVGRSIA 264 Query: 261 NVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGIT 320 +V+ +G L+++ R SFT RKGEI+G +GL+GAGRSEL + ++G Sbjct: 265 DVYGYRSRDLGDVQLDVKEMMGRGLREPASFTARKGEIVGFFGLVGAGRSELMKLIYGAV 324 Query: 321 KPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSRR 380 KP +G++ L+G+ + +P+DA+RAG+ PE+R + G+ + N+ + SR Sbjct: 325 KPDAGEIALKGKRVRFATPRDAVRAGVALCPEDRKQEGIVSIASVSDNLNISCRRHFSRF 384 Query: 381 GFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPT 440 L E A+++ +L ++ P+GTLSGGNQQKV++ +WLA V ++DEPT Sbjct: 385 NVLNGRKEAQTAKEFIGKLAIKTRNGDTPIGTLSGGNQQKVILSRWLAEDIDVFLMDEPT 444 Query: 441 KGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELS 500 +GID+G+++ ++G + LA G ++I+VSS+L E+IG++DRV+VMKEG G +A+ + Sbjct: 445 RGIDVGARSEIYGLLYGLAEAGRTVIVVSSDLAEVIGVADRVIVMKEGRIVGDLPKAQAT 504 Query: 501 PEALVRAA 508 P+AL++ A Sbjct: 505 PDALIKLA 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: 648 Number of extensions: 31 Number of successful extensions: 6 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: 515 Length adjustment: 35 Effective length of query: 477 Effective length of database: 480 Effective search space: 228960 Effective search space used: 228960 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