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_041936920.1 RL_RS31840 sugar ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >NCBI__GCF_000009265.1:WP_041936920.1 Length = 511 Score = 419 bits (1078), Expect = e-122 Identities = 225/491 (45%), Positives = 327/491 (66%), Gaps = 3/491 (0%) Query: 4 ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63 ILE++ I + FPGV AL VS+ +PG V A++GENGAGKSTL+KI+ G+Y+P+EGEI+ Sbjct: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79 Query: 64 EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYREAE 122 +G+ V + AI+AG+ + QE + D L+VAENIF+G + + ID++ M A Sbjct: 80 DGQPVTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRLRTIDWQAMNSRA- 138 Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182 K + IDP +L +SIA + +V IARA+ +A+++I+DEPT++L++KE + LF Sbjct: 139 KALLTALESNIDPTIRLKDFSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFR 198 Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242 +V+ LKEKG AI+FISH+ +E++EI D V RDG +G ++ +++IV MMVGR + Sbjct: 199 IVRGLKEKGKAILFISHKFDEVYEIADDFVVFRDGRAVGQGRLKETPQDEIVRMMVGRDV 258 Query: 243 EKFYIKEAHEPGEVVLEVKNLSGE-RFENVSFSLRRGEILGFAGLVGAGRTELMETIFGF 301 E + K G VLE++N S F ++SF+LR+GEILG GL+GAGR+EL +++FG Sbjct: 259 ENAFPKVDVAFGGPVLEIRNYSHRTEFRDISFTLRQGEILGIYGLIGAGRSELSQSLFGI 318 Query: 302 RPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK 361 G++ +EG+ + I+ P DAI GI VPE+R + GL L M I N++LPSL R + Sbjct: 319 TRPLSGKMMLEGREITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLTRTSR 378 Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421 F+ E LA + D+R A V LSGGNQQKVV+ KWLA PK++ILDEP Sbjct: 379 RGFLRAAEEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEP 438 Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481 T+GID+G+KA ++ +S+LA EG+ +IM+SSELPE++ MSDR+ VM G AGI + E Sbjct: 439 TKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLAAGIFERAEL 498 Query: 482 SQEKVMKLAAG 492 S E +++ A G Sbjct: 499 SPEALVRAATG 509 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: 651 Number of extensions: 25 Number of successful extensions: 7 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: 511 Length adjustment: 34 Effective length of query: 460 Effective length of database: 477 Effective search space: 219420 Effective search space used: 219420 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