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_041937034.1 RL_RS36695 sugar ABC transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >NCBI__GCF_000009265.1:WP_041937034.1 Length = 512 Score = 378 bits (970), Expect = e-109 Identities = 206/495 (41%), Positives = 310/495 (62%), Gaps = 6/495 (1%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 +LE+R +S+ F VKAL VS +L G V AL GENGAGKSTL+ I+ G+ +P EG++LV Sbjct: 6 VLEIRNVSKHFGAVKALTEVSFSLEKGEVHALCGENGAGKSTLMNIIAGVLQPTEGDVLV 65 Query: 80 DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139 DG P S A G+ +HQE L + TVAEN+F+ R R +++ + ++ Sbjct: 66 DGAPVKVTSPAVAQSLGLGLVHQEIALCPDATVAENMFMAATNRRRSPFMNYGRLERDAQ 125 Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199 ++ L + ID ++ DLSI+ + LV IA+AL+++ R++I DEPTAAL+ E LF I Sbjct: 126 VVMNRL-APIDVRRKVGDLSISSQQLVEIAKALTLDCRVLIFDEPTAALTESETQVLFAI 184 Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDV 259 +R LK QG +I++ISH+ E++ + D VF + V+ TP D++VR MVGR++ Sbjct: 185 IRDLKAQGISIIYISHRMAEIFSLCDRVTVFRDGRYVSMEKVADVTP-DDVVRRMVGREI 243 Query: 260 ENVFPKIDVAIGGP---VLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSL 316 ++P+ +L +RN + F D++F LRKGEILGV GLIG+GR+E+++ + Sbjct: 244 TQLYPEKQAPAERTDEIILSVRNLGDGSRFTDVNFDLRKGEILGVGGLIGSGRTEIAEGI 303 Query: 317 FGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSL-A 375 G+ + GK+ L GQ + S A +AG+VY+ E+R G+ L + I QN+ + L + Sbjct: 304 CGLRPVIDGKVQLHGQRLRARSYAQAAQAGVVYLSEDRKGSGIFLDLSIAQNIAVLDLKS 363 Query: 376 RTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVII 435 T G L + E A RL +R + +PV +LSGGNQQKV I K LA PKVI+ Sbjct: 364 LTGPLGLLNSKAEADRAHNLVRRLGVRMGGIDMPVSSLSGGNQQKVAIAKQLAVDPKVIL 423 Query: 436 LDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFE 495 +DEPT+GID+G+K+ +H + +LA G+ I+++SSELPE++G+ DRVLV+ EG AG E Sbjct: 424 MDEPTRGIDVGAKSEIHRLLRDLARSGIGIVVISSELPELLGLCDRVLVIHEGTVAGEVE 483 Query: 496 RAELSPEALVRAATG 510 ++ EA++R A+G Sbjct: 484 GEAMTEEAIMRLASG 498 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: 605 Number of extensions: 32 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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 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