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 Pf6N2E2_1008 Inositol transport system ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008 Length = 485 Score = 367 bits (943), Expect = e-106 Identities = 208/476 (43%), Positives = 314/476 (65%), Gaps = 18/476 (3%) Query: 35 IVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRG-VRWNH--PSEAINAGIVTVFQELSVM 91 ++GENGAGKST++KI+AG D G+ E G V H P GI+T++QE +++ Sbjct: 1 LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60 Query: 92 DNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVE 151 ++SVAEN+++G E R F+D+K+M+ +A+ + ++ G+ I P + K S+A QQMVE Sbjct: 61 ADMSVAENMYLGREPLRHGFVDWKQMFSDAQHVL-DDLGLHITPRTMVRKLSVAEQQMVE 119 Query: 152 IARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKV 211 IA+A+ AK++I+DEPT++L+ +E +KL E++ LK KG++II++SH+L E+ CD+ Sbjct: 120 IAKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACCDRY 179 Query: 212 SVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEKFYIKEAHEPGEVVLEVKNLS-----GE 266 ++ RDG YI + + +++ + IV +MVGR +E PGEV+L+V+++S G Sbjct: 180 TIFRDGAYITSGDVCDVSVDDIVRLMVGRDVEFVRKPLTGAPGEVMLKVQSVSRTAAGGG 239 Query: 267 R------FENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVE-IN 319 R ++S +R GEI+GFAGLVGAGRTEL IFG G IY+ G++V Sbjct: 240 RSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQVSPFK 299 Query: 320 HPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK-GPFISFKREKELADWAI 378 P + I G+ LVPEDRK+ L SI N+SLPSL +++ G FI + E +L Sbjct: 300 SPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQLIQDYQ 359 Query: 379 KTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMS 438 K I+ + + LSGGNQQKV+LA+ +ALKPK+LI+DEPTRGIDVGAKAE+++++ Sbjct: 360 KRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVHQLLF 419 Query: 439 QLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVM-KLAAGL 493 +A+ GV VI+ISSELPEV+ +SDRI G++ GI+ A EA++E +M ++A G+ Sbjct: 420 DMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLMARMAQGV 475 Score = 91.7 bits (226), Expect = 5e-23 Identities = 72/250 (28%), Positives = 122/250 (48%), Gaps = 19/250 (7%) Query: 4 ILEVKSIHKRFPG----VHA--LKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPD 57 +L+V+S+ + G +HA L +S++ GE+ G GAG++ L ++I G D Sbjct: 225 MLKVQSVSRTAAGGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCD 284 Query: 58 EGEIIYEGRGVR-WNHPSEAINAGIVTV---------FQELSVMDNLSVAENIFMGDEEK 107 EG I GR V + P E I AG+ V F S+ N+S+ +G ++ Sbjct: 285 EGMIYVNGRQVSPFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPS---LGGLQR 341 Query: 108 RGIFIDYKKMYREAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDE 167 G+FID + + + + K + +G S QQ V +AR + K KVLI+DE Sbjct: 342 WGMFIDDRAETQLIQDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDE 401 Query: 168 PTSSLTQKETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIEN 227 PT + ++ +++ + GVA+I IS L E+ + D++ R+G+ G S + Sbjct: 402 PTRGIDVGAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADE 461 Query: 228 LTKEKIVEMM 237 T+E ++ M Sbjct: 462 ATEELLMARM 471 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: 620 Number of extensions: 26 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: 485 Length adjustment: 34 Effective length of query: 460 Effective length of database: 451 Effective search space: 207460 Effective search space used: 207460 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