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 PfGW456L13_7 ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_7 Length = 521 Score = 270 bits (689), Expect = 1e-76 Identities = 165/484 (34%), Positives = 259/484 (53%), Gaps = 15/484 (3%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P L+++ I KR+PG A + + PGE+HA++GENGAGKSTLMKII GV D GE+I Sbjct: 12 PRLQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVI 71 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122 ++G+ V +P++A GI VFQ S+ + LSVA+NI + G + RE Sbjct: 72 WQGQRVSLRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAGTPKQLEPKIREVS 131 Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182 + +G+ ++PE + SI +Q VEI R + + ++LILDEPTS LT +E + LF Sbjct: 132 R----RYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFV 187 Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242 ++ L +G +I+FISH+L E+ +C +VLR G G + +++ +MVG Sbjct: 188 TLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLARLMVGEAA 247 Query: 243 EKFYIKEAHEPGEVVLEVKNLS-------GERFENVSFSLRRGEILGFAGLVGAGRTELM 295 E G+ L+V+ LS G N+ +RRGEI+G AG+ G G+ EL+ Sbjct: 248 ELIADYPKVTGGDACLDVRGLSWHNPDPFGCSLANIDLEVRRGEIVGIAGVAGNGQDELL 307 Query: 296 ETIFG--FRPKRGGEIYIEGKRVEINHPLDAIEQ-GIGLVPEDRKKLGLILIMSIMHNVS 352 + G P+ GK + DA Q G+ VP +R G + +S+ N Sbjct: 308 ALLSGEALLPRNASATIRFGKEPVAHLRPDARRQLGLAFVPAERLGHGAVPELSLADNAL 367 Query: 353 LPSLDR-IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLAL 411 L + + I + + LA+ I+ F ++ LSGGN QK +L + + Sbjct: 368 LTAFQHGLVSNGLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKFILGREILQ 427 Query: 412 KPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGK 471 +P++L+ PT G+DVGA A I+R + L G +++IS +L E+ Q+SDR+ + G+ Sbjct: 428 QPRLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDRLGALCGGR 487 Query: 472 LAGI 475 L+ + Sbjct: 488 LSAL 491 Score = 84.0 bits (206), Expect = 1e-20 Identities = 62/222 (27%), Positives = 111/222 (50%), Gaps = 9/222 (4%) Query: 271 VSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIG 330 + ++ GEI G GAG++ LM+ I+G GE+ +G+RV + +P A GIG Sbjct: 32 IDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQGQRVSLRNPAQARGLGIG 91 Query: 331 LVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDR 390 +V + L +S+ N++L ++ P + +E++ T + P+R Sbjct: 92 MVFQH---FSLFETLSVAQNIAL-AMGAAAGTPKQLEPKIREVSRRYGMTLE-----PER 142 Query: 391 KVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMI 450 V LS G +Q+V + + L ++LILDEPT + +++ + +LA EG ++ I Sbjct: 143 LVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFVTLRRLAAEGCSILFI 202 Query: 451 SSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492 S +L EV + V+ G++AG E S +++ +L G Sbjct: 203 SHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLARLMVG 244 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: 589 Number of extensions: 24 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: 521 Length adjustment: 34 Effective length of query: 460 Effective length of database: 487 Effective search space: 224020 Effective search space used: 224020 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