Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 382 bits (980), Expect = e-110 Identities = 220/506 (43%), Positives = 324/506 (64%), Gaps = 18/506 (3%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEG-EI 61 P+L +++I K FPGV AL+ V + Y GEVHA++GENGAGKSTLMKI++G Y D G E Sbjct: 9 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 68 Query: 62 IYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREA 121 +G+ V+ + P A + G+ ++QELS+ NLSVAENI++G +R + M R Sbjct: 69 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 128 Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181 + G + P + SIA +Q+VEIARAV+ +A++L++DEPT+ L+ ET++LF Sbjct: 129 APTLAR-LGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 187 Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241 +++ L+ +G+AI++ISHR+ EI E+ D+V+VLRDG ++GT +L++ +V+MMVGR Sbjct: 188 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 247 Query: 242 LEKFYIKEAHE--PGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETI 298 L FY K + EV+L V++++ G R + SF LR GE+LG AGLVGAGRTEL + Sbjct: 248 LSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLV 307 Query: 299 FGFRPKRGGEIYIEGK-------RVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNV 351 FG + GE+ I + P AI+ GI + EDRK GL L S+ N+ Sbjct: 308 FGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENI 367 Query: 352 SL--PSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWL 409 +L + D + G + + AI T IR A+ V LSGGNQQKV+L++ L Sbjct: 368 NLIVAARDALGLGRLNRTAARRRTTE-AIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLL 426 Query: 410 ALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSF 469 ++P++LILDEPTRG+D+GAK+EIYR+++ LA+ GV ++MISSELPEV+ + DR+ VM Sbjct: 427 EIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMRE 486 Query: 470 GKLAGII---DAKEASQEKVMKLAAG 492 G LAG + + +QE+++ LA G Sbjct: 487 GTLAGEVRPAGSAAETQERIIALATG 512 Lambda K H 0.318 0.138 0.385 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: 647 Number of extensions: 34 Number of successful extensions: 10 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: 494 Length of database: 537 Length adjustment: 35 Effective length of query: 459 Effective length of database: 502 Effective search space: 230418 Effective search space used: 230418 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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