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 Ac3H11_1109 ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1109 Length = 513 Score = 290 bits (742), Expect = 8e-83 Identities = 174/492 (35%), Positives = 276/492 (56%), Gaps = 14/492 (2%) Query: 10 IHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVR 69 I KR+P V A GVS+ PGE+HA++GENGAGKSTLMKII G +PDEG + + G+ V+ Sbjct: 3 ITKRYPAVVANSGVSLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGSVFFNGQAVQ 62 Query: 70 WNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMKEEF 129 +P EA GI VFQ S+ D L+VAEN+++G ++ + +++ +A E+ Sbjct: 63 VRNPQEARALGIAMVFQHFSLFDTLTVAENVWLGLDKSLTLAEVTQRISAKA-----AEY 117 Query: 130 GIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKE 189 G++IDP + S+ Q VEI RA+ KVLILDEPTS LT + EKLF V++ L Sbjct: 118 GLDIDPLRPVHTLSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKLFVVLRKLAS 177 Query: 190 KGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEKFYIKE 249 +G +I++ISH+L EI +C +VLR G+ G + T + +M+G + Sbjct: 178 EGCSILYISHKLHEIRALCTACTVLRGGKVTGVCNPSEETNASLSRLMIGAEPPALE-HR 236 Query: 250 AHEPGEVVLEVKNLSGERFE-------NVSFSLRRGEILGFAGLVGAGRTELMETIFGFR 302 A + G VL VK LS R + ++ F ++ GE++G AG+ G G+ EL+ + G Sbjct: 237 AVQTGATVLRVKGLSLPRADQFGVDLIDLQFEVKAGEVVGIAGVSGNGQKELLYALSGED 296 Query: 303 PK-RGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK 361 + I + G+ P G+ VPE+R G + M + HN+ L + + Sbjct: 297 QRAEPASIQVTGQNAGRMGPGQRRALGLHFVPEERLGRGAVPTMGLAHNLLLTRKNAVGG 356 Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421 +I ++ A+ I+ F+++ P LSGGN QK ++ + + PK+LI+ +P Sbjct: 357 SGWIKVGALQKHAEDIIQRFNVKAGGPHSAAKSLSGGNLQKFIVGREIDANPKLLIVSQP 416 Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481 T G+DVGA A+I + L G V+++S EL E+ ++ DR+ V++ G+L+ + EA Sbjct: 417 TWGVDVGAAAQIRGSILALRDAGCAVLVVSEELDELFEICDRLHVVAKGRLSPSVQRAEA 476 Query: 482 SQEKVMKLAAGL 493 + E++ + +GL Sbjct: 477 TVERIGEWMSGL 488 Score = 92.8 bits (229), Expect = 3e-23 Identities = 62/224 (27%), Positives = 113/224 (50%), Gaps = 10/224 (4%) Query: 271 VSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIG 330 VS ++ GEI G GAG++ LM+ I+G G ++ G+ V++ +P +A GI Sbjct: 16 VSLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGSVFFNGQAVQVRNPQEARALGIA 75 Query: 331 LVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDR 390 +V + L +++ NV L LD+ ++ + + A++ + +RP + Sbjct: 76 MVFQH---FSLFDTLTVAENVWL-GLDKSLTLAEVTQRISAKAAEYGLDIDPLRPVHT-- 129 Query: 391 KVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMI 450 LS G Q+V + + L PK+LILDEPT + A +++ ++ +LA EG ++ I Sbjct: 130 ----LSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKLFVVLRKLASEGCSILYI 185 Query: 451 SSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494 S +L E+ + V+ GK+ G+ + E + + +L G E Sbjct: 186 SHKLHEIRALCTACTVLRGGKVTGVCNPSEETNASLSRLMIGAE 229 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: 554 Number of extensions: 30 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: 2 Length of query: 494 Length of database: 513 Length adjustment: 34 Effective length of query: 460 Effective length of database: 479 Effective search space: 220340 Effective search space used: 220340 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