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 Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 352 bits (903), Expect = e-101 Identities = 199/502 (39%), Positives = 311/502 (61%), Gaps = 17/502 (3%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNE--GEI 77 +LEMR I + FPGV AL+ V++ + G + A++GENGAGKSTL+K+L+G+Y G+I Sbjct: 2 LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61 Query: 78 LVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSR 137 L DG+ FA + + G+ IHQE L L++AENIFLG+ R IDW +SR Sbjct: 62 LFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNET-ARHGVIDWMAAHSR 120 Query: 138 SKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLF 197 ++ALL + P + L + ++ LV IA+ALS + R++I+DEPTA+L+ + L Sbjct: 121 AQALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQALL 180 Query: 198 RIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVS-RKTP--QDEIVRMM 254 ++ LK QG + ISHK +E+ +AD V R V+ + R+ P +D +++ M Sbjct: 181 DLLLELKAQGITCILISHKLNEISRVADAITVL--RDGSTVQMLDCREGPVSEDRVIQAM 238 Query: 255 VGRDVENVFPKIDVAIGGPVLEIRNY-------SHRTEFRDISFTLRKGEILGVYGLIGA 307 VGR++ + +P+ +G V E+RN+ S R + I +R+GEI+G+ GL+GA Sbjct: 239 VGREMSDRYPQRQPQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLMGA 298 Query: 308 GRSELSQSLFGIT--KPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPI 365 GR+EL+ S+FG + + +SG++ L GQ I + + + A+ G+ YV E+R +GL L I Sbjct: 299 GRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNEDI 358 Query: 366 FQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGK 425 N +L +L S + + E +A+ Y E+L +R + + LSGGNQQKVV+ K Sbjct: 359 QFNTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKVVLSK 418 Query: 426 WLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVM 485 WL T+P+V+ILDEPT+GID+G+K ++ I++LAAEG +I++SSE+PE++G++DR+ VM Sbjct: 419 WLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDRIYVM 478 Query: 486 KEGLSAGIFERAELSPEALVRA 507 EG +E S E ++RA Sbjct: 479 NEGRFVAEMPTSEASQEKIMRA 500 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: 589 Number of extensions: 32 Number of successful extensions: 11 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: 505 Length adjustment: 34 Effective length of query: 478 Effective length of database: 471 Effective search space: 225138 Effective search space used: 225138 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