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_523 Inositol transport system ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523 Length = 517 Score = 447 bits (1150), Expect = e-130 Identities = 238/492 (48%), Positives = 337/492 (68%), Gaps = 3/492 (0%) Query: 4 ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63 +LEV ++ K FPGV AL V + PG V A++GENGAGKSTLMKIIAG+YQPD GE+ Sbjct: 26 LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 85 Query: 64 EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYREAE 122 G+ V ++ P A+ AGI + QEL++M ++S+AENI++G E+ G+ +D+ +M+R Sbjct: 86 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRCTA 145 Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182 + + E I++DPEE++G SIA +QMVEIA+AV + +LI+DEPTS++T+ E LF Sbjct: 146 RLL-ERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFS 204 Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242 ++ LK +G II+I+H++ E+F I D+V+V RDG YIG +++ + ++ MMVGR+L Sbjct: 205 IIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 264 Query: 243 EKFYIKEAHEPGEVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFGF 301 + + G++VL V++LS + F+ VSF L GEILG AGL+G+GRT + E IFG Sbjct: 265 SQLFPVREQPIGDLVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGV 324 Query: 302 RPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK 361 P GGEI ++G+ V I+ P AIE+G L+ EDRK GL +S++ N+ + L Sbjct: 325 TPSTGGEILLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYVG 384 Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421 FI K + L + K ++ ++ + LSGGNQQK +LA+WL P+ILILDEP Sbjct: 385 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEP 444 Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481 TRGIDVGAKAEIYR++S LA EG+ VIMISSELPEVL MSDR+ VM G L G ++ EA Sbjct: 445 TRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLNRGEA 504 Query: 482 SQEKVMKLAAGL 493 +QE+VM+LA+GL Sbjct: 505 TQERVMQLASGL 516 Score = 89.4 bits (220), Expect = 3e-22 Identities = 67/243 (27%), Positives = 118/243 (48%), Gaps = 10/243 (4%) Query: 257 VLEVKNLSGE-----RFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYI 311 +LEV N+S +V +R G +L G GAG++ LM+ I G GE+ + Sbjct: 26 LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 85 Query: 312 EGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREK 371 GK V + PL A++ GI ++ ++ L L+ MSI N+ + +++ + Sbjct: 86 RGKPVTFDTPLAALQAGIAMIHQE---LNLMPHMSIAENIWI-GREQLNGLHMVDHGEMH 141 Query: 372 ELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKA 431 ++ I+ P+ +V LS +Q V +AK ++ ILI+DEPT I A Sbjct: 142 RCTARLLERLRIK-LDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVA 200 Query: 432 EIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAA 491 ++ I++ L +G G+I I+ ++ EV ++D +AV G G+ A + ++ + Sbjct: 201 HLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMV 260 Query: 492 GLE 494 G E Sbjct: 261 GRE 263 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: 641 Number of extensions: 26 Number of successful extensions: 8 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: 517 Length adjustment: 34 Effective length of query: 460 Effective length of database: 483 Effective search space: 222180 Effective search space used: 222180 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