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 3609044 Dshi_2433 ABC transporter related (RefSeq)
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Dino:3609044 Length = 510 Score = 438 bits (1126), Expect = e-127 Identities = 232/492 (47%), Positives = 332/492 (67%), Gaps = 5/492 (1%) Query: 5 LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64 L + I K FPGV AL VS+ YPG+V A++GENGAGKST++KI+ G+YQPD G I+ + Sbjct: 21 LALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVD 80 Query: 65 GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIF--IDYKKMYREAE 122 G+ V ++ P A + G+ + QE + D LSVAENIF+G RG F ID+KK A Sbjct: 81 GQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLG-HAPRGAFGLIDWKKTTENAR 139 Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182 + G E+DP+ KL IA + +V IARA+ +A+V+I+DEPT++L+ KE E+L+E Sbjct: 140 ALL-TSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYE 198 Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242 +V+SLK +G AI+FISH+ +EIF I D +V RDG+ IG +I ++T+ +V+MMVGR + Sbjct: 199 LVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDV 258 Query: 243 EKFYIKEAHEPGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGF 301 + + + A G+ VL V+ + F+++SF+LR GEILGF GLVGAGR+E M+++FG Sbjct: 259 SQIFPQRAPNVGDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFGI 318 Query: 302 RPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK 361 G + I G R EI+ P DA++ GI VPEDR K G IL + I NV+LPSL RI + Sbjct: 319 TRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRISR 378 Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421 F+ E LA + D+R A D V LSGGNQQKVV+AKWLA +P+++ILDEP Sbjct: 379 KGFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDEP 438 Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481 T+G+D+G+KA ++ M++LA +G+ VIM+SSE+PEVL MSDR+ VM G++ + + Sbjct: 439 TKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELAGDDL 498 Query: 482 SQEKVMKLAAGL 493 E +++ AAG+ Sbjct: 499 QPETLVRHAAGI 510 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: 622 Number of extensions: 32 Number of successful extensions: 7 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: 494 Length of database: 510 Length adjustment: 34 Effective length of query: 460 Effective length of database: 476 Effective search space: 218960 Effective search space used: 218960 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