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 HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__HerbieS:HSERO_RS03640 Length = 502 Score = 427 bits (1098), Expect = e-124 Identities = 219/494 (44%), Positives = 334/494 (67%), Gaps = 7/494 (1%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P+L+++ I K F AL + + PGE+HA++GENGAGKSTLMK+++GV+ PD+GEI+ Sbjct: 9 PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 68 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYREA 121 +GR V P + AGI ++QEL+V N+SVA N+FMG E + + ID+ M Sbjct: 69 LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 128 Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181 + ++ + G + G+ SIA QQ VEIARA+ +++++I+DEPT++L+++ETE+LF Sbjct: 129 DAVLR-QLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 187 Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241 VV+ L+++G+AII+ISHR+ E++ + D+V+VLRDG ++G + + E+IV+MMVGR Sbjct: 188 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 247 Query: 242 LEKFYIKEAHEPGE-----VVLEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRTELME 296 L +FY + P + V++V+ L+G + SF +R GE+LGFAGLVGAGRTEL Sbjct: 248 LSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELAR 307 Query: 297 TIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356 +FG P+ GG+I +EG+ V I+ P A+ GI VPEDRK GL L M++ N ++ Sbjct: 308 LLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVA 367 Query: 357 DRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKIL 416 R + + + +A AI+ +++ A+P+ V LSGGNQQKV+LA+WL + PK+L Sbjct: 368 SRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 427 Query: 417 ILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGII 476 ILDEPTRG+D+ AK+EIY+++ +LA +GV V++ISSELPEV+ + DR+ VM G + G + Sbjct: 428 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 487 Query: 477 DAKEASQEKVMKLA 490 +QE +M+LA Sbjct: 488 AGAAITQENIMRLA 501 Score = 84.7 bits (208), Expect = 7e-21 Identities = 59/223 (26%), Positives = 110/223 (49%), Gaps = 5/223 (2%) Query: 270 NVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGI 329 ++ ++R GEI G GAG++ LM+ + G GEI ++G+ V + P + GI Sbjct: 28 DMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGI 87 Query: 330 GLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPD 389 L+ ++ L + +S+ NV + S R + G I + D ++ D Sbjct: 88 NLIYQE---LAVAPNISVAANVFMGSELRTRLG-LIDHAAMRSRTDAVLRQLGAGFGASD 143 Query: 390 RKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIM 449 LS QQ+V +A+ L + +I+I+DEPT + +++ ++ +L EG+ +I Sbjct: 144 LAGR-LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIY 202 Query: 450 ISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492 IS + EV ++DR+ V+ G G + E E+++++ G Sbjct: 203 ISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 245 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: 678 Number of extensions: 19 Number of successful extensions: 6 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: 502 Length adjustment: 34 Effective length of query: 460 Effective length of database: 468 Effective search space: 215280 Effective search space used: 215280 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