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_004124104.1 RHSP_RS23335 sugar ABC transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >NCBI__GCF_000359745.1:WP_004124104.1 Length = 492 Score = 394 bits (1012), Expect = e-114 Identities = 211/490 (43%), Positives = 310/490 (63%), Gaps = 1/490 (0%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 +LE+ G+ + F GV AL + L PG+V AL G NGAGKST +KIL GI++ + G I Sbjct: 4 LLEVEGLKKSFGGVAALRDGCFQLRPGSVHALCGGNGAGKSTFLKILMGIHKRDAGSIRR 63 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139 G+ +AS AA+ AG+ I QE +TVAENI+LG P RF ID++TMN ++ Sbjct: 64 RGKDVDYASPAAALAAGIAIIEQELSPIPHMTVAENIYLGREPSARFGGIDFKTMNRNAQ 123 Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199 ALL L NI T + +LS+AQ LV IA+ALS +A ++ MDEPT+A+ KE LF Sbjct: 124 ALLDRLRFNIRATQFMMNLSVAQIQLVEIAKALSHDAEVIFMDEPTSAIGEKEAQQLFST 183 Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDV 259 + LK +GK ++++SH+ E+++IAD + F R G + ++RM+VGR++ Sbjct: 184 IERLKAEGKGVVYVSHRLSEIFQIADSYTAF-RDGSYVGSGALADIDRPGLIRMIVGREL 242 Query: 260 ENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGI 319 + K +V P LE+ + + DISFT KGEI G+YGL+G+GR+E+ +FG+ Sbjct: 243 GEEYIKTNVPTATPGLEVAGLTAEGKLNDISFTAHKGEIFGIYGLMGSGRTEIFNCIFGL 302 Query: 320 TKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSR 379 SG++ L GQ IT+ P +A++ GI +V E+R GL L + N+ L SL S Sbjct: 303 DVLNSGQIKLAGQPITVGKPAEAMQHGIAFVTEDRKLTGLNLIDSVRNNICLASLPEMSP 362 Query: 380 RGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEP 439 R + + E + ++ ER ++AA S+PV LSGGNQQKVV+GKW PKV++LDEP Sbjct: 363 RFSMDSRAEASASQDMIERFGIKAARDSMPVSGLSGGNQQKVVLGKWFLRKPKVLLLDEP 422 Query: 440 TKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAEL 499 T+G+D+G+K ++ I + AAEG ++IM+SSE+ E++GMSDR+LVM++G SAGI +R E Sbjct: 423 TRGVDVGAKREIYRIICDFAAEGGTVIMISSEIDEVLGMSDRILVMRQGRSAGILKREEA 482 Query: 500 SPEALVRAAT 509 ++LV +T Sbjct: 483 DAQSLVHLST 492 Score = 76.3 bits (186), Expect = 2e-18 Identities = 66/226 (29%), Positives = 99/226 (43%), Gaps = 9/226 (3%) Query: 287 RDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAG 346 RD F LR G + + G GAG+S + L GI K +G + G+++ SP A+ AG Sbjct: 21 RDGCFQLRPGSVHALCGGNGAGKSTFLKILMGIHKRDAGSIRRRGKDVDYASPAAALAAG 80 Query: 347 IVYVPEERGRHGLALP-MPIFQNMTLPSLARTSRRGF-LRAANEFALARKYAERLDLRAA 404 I + +E +P M + +N+ L G + N A A R ++RA Sbjct: 81 IAIIEQELS----PIPHMTVAENIYLGREPSARFGGIDFKTMNRNAQALLDRLRFNIRAT 136 Query: 405 ALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLS 464 + LS Q V I K L+ +VI +DEPT I + I L AEG Sbjct: 137 QFMM---NLSVAQIQLVEIAKALSHDAEVIFMDEPTSAIGEKEAQQLFSTIERLKAEGKG 193 Query: 465 IIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510 ++ VS L EI ++D ++G G A++ L+R G Sbjct: 194 VVYVSHRLSEIFQIADSYTAFRDGSYVGSGALADIDRPGLIRMIVG 239 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: 22 Number of successful extensions: 6 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: 492 Length adjustment: 34 Effective length of query: 478 Effective length of database: 458 Effective search space: 218924 Effective search space used: 218924 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 24 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