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 WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >NCBI__GCF_001623255.1:WP_068005521.1 Length = 515 Score = 298 bits (762), Expect = 4e-85 Identities = 175/501 (34%), Positives = 293/501 (58%), Gaps = 14/501 (2%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P+L +++I K F + A V+++ + GE+ A++GENGAGK+TLM I+ G Y DEG ++ Sbjct: 9 PLLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVM 68 Query: 63 YEGRG-----VRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKM 117 + P A+ AGI V Q ++ +NL+ ENI +G E K Sbjct: 69 VRTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFARKFSRSKA 128 Query: 118 YREAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKET 177 + ++ M+ G+E+D + ++ K ++ +Q VEI +A+Y+ A++L+LDEPT+ LT +E+ Sbjct: 129 RAKLQELMQSS-GLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQES 187 Query: 178 EKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMM 237 + LF +K L KG+AIIFISH++ E+ D+V+VLR G + + K+ E+M Sbjct: 188 DSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAELM 247 Query: 238 VGRKLEKFYIKEAHEPGEVVLEVKNLSG----ERFENVSFSLRRGEILGFAGLVGAGRTE 293 VG ++ +E PGE +L K +S E ENV+ SLR+GEI+G AG+ G G++ Sbjct: 248 VGHAVQ-MAEREPGNPGEEILVFKGVSAGEGRELIENVNLSLRKGEIIGLAGVSGNGQSM 306 Query: 294 LMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSL 353 L + + G G + + + ++ N AI+ G+ +PEDR G++ MS+ N+ L Sbjct: 307 LAKVLSGLEEPTAGAVTLGSQPLKAN-AAAAIQSGVARIPEDRHHDGIVGAMSVEENLVL 365 Query: 354 PSLDR--IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLAL 411 + + ++ + F ++ A AIK +DIR + P LSGGN QK+VLA+ L Sbjct: 366 EEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIVLARTLDQ 425 Query: 412 KPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGK 471 +P I++ +P+RG+DVGA A+++R + + G GV++IS +L E+ Q+SDRIAV+ G Sbjct: 426 EPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRIAVIHRGH 485 Query: 472 LAGIIDAKEASQEKVMKLAAG 492 ++ + ++E +++V + AG Sbjct: 486 VSEPMASEELDKKQVGLMMAG 506 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: 642 Number of extensions: 39 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: 515 Length adjustment: 34 Effective length of query: 460 Effective length of database: 481 Effective search space: 221260 Effective search space used: 221260 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 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