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 AZOBR_RS06625 AZOBR_RS06625 heme ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__azobra:AZOBR_RS06625 Length = 511 Score = 305 bits (781), Expect = 2e-87 Identities = 175/505 (34%), Positives = 285/505 (56%), Gaps = 17/505 (3%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P LE + ++K F HA + VS+ G +H ++GENGAGKST+M I+ G D G I+ Sbjct: 6 PALETRGVNKWFGANHANRDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPADGGTIL 65 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122 +GR V P +A+ AGI V Q ++D +V EN+ +G E + + E Sbjct: 66 VDGRPVAVRSPRDALAAGIGMVHQHFMLVDPFTVLENVLLGAEGGVTLAAGMARARTELT 125 Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182 + ++ +G+E+D + +G+ + QQ VEI +A+Y+ A +LILDEPT LT +ET+ LF Sbjct: 126 RLARD-YGLEVDLDRPVGELPVGAQQRVEILKALYRGADILILDEPTGVLTPQETDHLFR 184 Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242 ++++L+E+G ++ I+H+L EI E+ D V+V+R G+ + + ++E++ E+MVGRK+ Sbjct: 185 ILRALREQGKTVVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMVGRKV 244 Query: 243 EKFYIKEAHEPGEVVLEVKNL------SGERFENVSFSLRRGEILGFAGLVGAGRTELME 296 K PG VLEV L ER + + ++R GEI+G AG+ G G++EL+E Sbjct: 245 LLRVEKVPATPGPAVLEVSGLCVRDGAGVERVKGIGLTVRAGEIVGIAGVSGNGQSELLE 304 Query: 297 TIFGFRPKRGGEIYIEGKRVEIN------HPLDAIEQGIGLVPEDRKKLGLILIMSIMHN 350 + G RP G + + G+ + L A+ G+G VPEDR+++GL+ Sbjct: 305 ALAGMRPPAEGSVRLRGEELTATPDRFTARGLRAL--GVGHVPEDRQRVGLVTGFEAQEC 362 Query: 351 VSLPSL-DRIKKGPFISFKREK-ELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKW 408 L D G + +R + + +D+RP P SGGNQQK+VLA+ Sbjct: 363 AILGHQGDPAFNGRLLMDRRALFDRCASEMDAYDVRPRDPRLPAANFSGGNQQKIVLARE 422 Query: 409 LALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMS 468 + P +L++ +PTRG+D+GA I+R + L +G ++++S EL E+ +SDRI VM Sbjct: 423 MERNPDLLLVGQPTRGVDIGAIEFIHRRLVALRDQGKAILLVSVELDEIRALSDRILVMF 482 Query: 469 FGKLAGIIDAKEASQEKVMKLAAGL 493 G+L G + EA + ++ + AG+ Sbjct: 483 DGRLVGEVAPGEADERRLGLMMAGV 507 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: 657 Number of extensions: 42 Number of successful extensions: 9 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 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