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 SM_b20503 SM_b20503 sugar ABC transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Smeli:SM_b20503 Length = 512 Score = 375 bits (964), Expect = e-108 Identities = 203/494 (41%), Positives = 311/494 (62%), Gaps = 6/494 (1%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 +LE+R +S+ F VKAL V L G V AL GENGAGKSTL+ ++ G+ +P+EGE+L+ Sbjct: 6 VLEIRNVSKHFGAVKALTAVDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSEGEVLI 65 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139 +G P AS A G+ +HQE L + T+AEN+F+ R R +++ + ++ Sbjct: 66 EGAPVKIASPAVAQSLGIALVHQEIALCPDATIAENMFMAATNRRRSALMNYAQLERDAQ 125 Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199 A++ L + ID + ++ DL I+ + LV IA+AL+++ R++I DEPTAAL+ E LF I Sbjct: 126 AVMNRL-APIDVSQKVGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETEAQVLFGI 184 Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDV 259 +R LK +G +I++ISH+ E++ + D VF VS TP D++VR+MVGR++ Sbjct: 185 IRDLKARGISIIYISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTP-DDVVRLMVGREI 243 Query: 260 ENVFPKIDVA---IGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSL 316 ++P + +G P+L +R+ FRD+SF LR GEILGV GLIG+GR+E+++ + Sbjct: 244 SQLYPDKQPSSERLGEPILSVRDLGGE-RFRDVSFELRYGEILGVGGLIGSGRTEIAEGI 302 Query: 317 FGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLAR 376 + G++ L + + + DA +AG+VY+ E+R G+ L + I QN+ L Sbjct: 303 CALRPVTQGEIRLHDKVLRLRRYSDAAKAGVVYLSEDRKGSGVFLDLSIAQNIAALDLKA 362 Query: 377 TSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIIL 436 + G L + E ALA RL +R + +PV +LSGGNQQKV I K LA PKVI++ Sbjct: 363 LTSLGLLNSREERALAEDLTRRLGVRMGGVDMPVSSLSGGNQQKVAIAKQLAVDPKVILM 422 Query: 437 DEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFER 496 DEPT+GID+G+K+ +H + ELA G+ I+++SSELPE+IG+ DRVLV++EG AG Sbjct: 423 DEPTRGIDVGAKSEIHRLLRELARAGIGILVISSELPELIGLCDRVLVVREGRIAGEVSG 482 Query: 497 AELSPEALVRAATG 510 E++ E ++R A+G Sbjct: 483 NEMTEEVIMRLASG 496 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: 594 Number of extensions: 28 Number of successful extensions: 8 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: 512 Length adjustment: 35 Effective length of query: 477 Effective length of database: 477 Effective search space: 227529 Effective search space used: 227529 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