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 RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Cup4G11:RR42_RS30800 Length = 530 Score = 265 bits (678), Expect = 2e-75 Identities = 170/491 (34%), Positives = 268/491 (54%), Gaps = 23/491 (4%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 PIL + I KRF + A +S+E GEV A++GENGAGKSTL+ I+ G Y D G + Sbjct: 4 PILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVE 63 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122 +G+ + P A+ AGI V Q ++ DNLSV +NI +G + +D R Sbjct: 64 VDGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAA-RGKV 122 Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182 + E FG+ + P+ ++G+ S+ +Q VEI +A+Y+ A+VLILDEPT+ LT E E LF Sbjct: 123 LALAERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFS 182 Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242 + L +G+++IFISH+L+E+ + D+++VLR G+ + + TK ++ E+MVGR + Sbjct: 183 TLAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRVV 242 Query: 243 ---EKFYIKEAHE-------PGEVVLE---VKNLSGER-FENVSFSLRRGEILGFAGLVG 288 E+ + A + P + LE + +G VS +R GEI+G AG+ G Sbjct: 243 AMPERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVSG 302 Query: 289 AGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIM 348 G+ L E G G I + GK + P I G+ VPEDR +G++ +++ Sbjct: 303 NGQAALAELASGMLEASEGRITLAGKPMSAK-PRAWIGAGVARVPEDRHAIGVVGDLAVW 361 Query: 349 HNVSLPSLD--RIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLA 406 N L R + I + A + FD+R A D +SGGN QK++L Sbjct: 362 ENAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKLILG 421 Query: 407 KWLALK-----PKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMS 461 + L+++ P++++ +PT G+D+GA A + + A+EG V++IS +L E+ ++ Sbjct: 422 RALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISEDLDELHALA 481 Query: 462 DRIAVMSFGKL 472 DRIAVM G L Sbjct: 482 DRIAVMHAGHL 492 Score = 100 bits (249), Expect = 1e-25 Identities = 70/229 (30%), Positives = 118/229 (51%), Gaps = 16/229 (6%) Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQG 328 +++S L+RGE+L G GAG++ L+ +FG G + ++G+ + P A+ G Sbjct: 22 DDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEVDGQPLPPGQPRAALTAG 81 Query: 329 IGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKG--PFISFKREKELADWAIKTFDIR-- 384 IG+V + ++ N+S+ LD I G P ++ + A + R Sbjct: 82 IGMVHQH---------FTLADNLSV--LDNIMLGTQPLWQWRLDGHAARGKVLALAERFG 130 Query: 385 -PAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKE 443 P +V LS G +Q+V + K L ++LILDEPT + ++ ++QL E Sbjct: 131 LAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFSTLAQLIAE 190 Query: 444 GVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492 G+ VI IS +L EVL++SDRIAV+ GKL + A + ++ ++ +L G Sbjct: 191 GLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVG 239 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: 614 Number of extensions: 38 Number of successful extensions: 9 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: 530 Length adjustment: 35 Effective length of query: 459 Effective length of database: 495 Effective search space: 227205 Effective search space used: 227205 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