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 WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 255 bits (652), Expect = 2e-72 Identities = 157/481 (32%), Positives = 273/481 (56%), Gaps = 17/481 (3%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 ++ ++G+++ F V A D++S+ ++PG V AL+GENGAGKSTL+ +L G Y+P+ G I + Sbjct: 24 LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139 DG+P F+SA+ AI+AG+ ++Q +L + +TVAEN+ LG ++ + M +R + Sbjct: 84 DGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQEGSF---FLNPKEMRNRVQ 140 Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199 L +IDP R+ DLS+ ++ V I + L ++R++I DEPTA L+ +E LF Sbjct: 141 ELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEA 200 Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDV 259 + + EQGK+I+FISHK +E+ +AD+ + + S T + ++ MVG++V Sbjct: 201 LWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVGKEV 260 Query: 260 ENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGI 319 + + G VL++RN + DI+F L +GE++ V G+ G G+ L +++ G+ Sbjct: 261 LLEVDREAMPHGDAVLQVRNLT-GIGLEDITFDLHQGEVVAVVGVAGNGQKALVEAICGL 319 Query: 320 TKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTL-PSLARTS 378 KP M + G+ + + + + Y+PE+R L + +N+ L +L T+ Sbjct: 320 RKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDR------LGLATCRNLNLVDNLLLTT 373 Query: 379 RRGFLRA--ANEFALARKYAE---RLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKV 433 R+GF R ++ AR E + D+R ++ LSGGN QK V+ + L P++ Sbjct: 374 RQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRL 433 Query: 434 IILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGI 493 I+ ++PT+G+DI + V + A E I++V+ +L E + ++DRV V+ G + Sbjct: 434 IVAEQPTQGLDIAATEQVWNHLL-AAREMAGILLVTGDLNEALQLADRVAVIYRGRFMDV 492 Query: 494 F 494 F Sbjct: 493 F 493 Score = 48.5 bits (114), Expect = 6e-10 Identities = 53/245 (21%), Positives = 103/245 (42%), Gaps = 15/245 (6%) Query: 19 AILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEIL 78 A+L++R ++ I L++++ LH G V A++G G G+ LV+ + G+ +P + Sbjct: 274 AVLQVRNLTGI-----GLEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMF 328 Query: 79 VDGRPTTFASAQAAIDAGVTAIHQETV---LFDELTVAENIFLGHAPRTRFRTIDWQTMN 135 + G+ A+ + + I ++ + L + +N+ L R F W Sbjct: 329 IMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLL--TTRQGFARGPWLDKK 386 Query: 136 SRSKALLTALES-NIDP---TIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRK 191 ++ ++ +I P LS +AR L R+++ ++PT L Sbjct: 387 KAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIA 446 Query: 192 EIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIV 251 + ++ + +E IL ++ +E ++AD V R V VS K + I Sbjct: 447 ATEQVWNHLLAAREMA-GILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIG 505 Query: 252 RMMVG 256 MM G Sbjct: 506 LMMAG 510 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: 540 Number of extensions: 31 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 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