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 AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21385 Length = 521 Score = 446 bits (1147), Expect = e-130 Identities = 236/492 (47%), Positives = 335/492 (68%), Gaps = 3/492 (0%) Query: 4 ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63 +LE+ ++ K FPGV AL V + PG V A++GENGAGKSTLMKIIAG+YQPD GE+ Sbjct: 27 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86 Query: 64 EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYREAE 122 G+ V ++ P A+ AGI + QEL++M ++S+AENI++G E+ G ID+++M+R Sbjct: 87 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146 Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182 + + E I +DPEE++G SIA +QMVEIA+AV + +LI+DEPTS++T KE LF Sbjct: 147 QLL-ERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFS 205 Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242 ++ LK +G II+I+H++ E+F I D+V+V RDG YIG +++ + ++ MMVGR+L Sbjct: 206 IIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 265 Query: 243 EKFYIKEAHEPGEVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFGF 301 + + G++++ V++L + F+ VSF L GEILG AGL+G+GRT + E IFG Sbjct: 266 SQLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGI 325 Query: 302 RPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK 361 P GGEI ++G+ V I+ P AIE+G L+ EDRK GL +S++ N+ + L Sbjct: 326 TPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAG 385 Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421 FI K + L + K ++ ++ + LSGGNQQK +LA+WL P+ILILDEP Sbjct: 386 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEP 445 Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481 TRGIDVGAKAEIYR++S LA EG+ VIMISSELPEVL MSDR+ VM G L G +D EA Sbjct: 446 TRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEA 505 Query: 482 SQEKVMKLAAGL 493 +QE+VM+LA+G+ Sbjct: 506 TQERVMQLASGM 517 Score = 90.1 bits (222), Expect = 2e-22 Identities = 63/225 (28%), Positives = 111/225 (49%), Gaps = 5/225 (2%) Query: 270 NVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGI 329 +V +R G +L G GAG++ LM+ I G GE+ + GK V + PL A++ GI Sbjct: 45 DVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGI 104 Query: 330 GLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPD 389 ++ ++ L L+ MSI N+ + +++ I + ++ I P+ Sbjct: 105 AMIHQE---LNLMPHMSIAENIWI-GREQLNGFHMIDHREMHRCTAQLLERLRIN-LDPE 159 Query: 390 RKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIM 449 +V LS +Q V +AK ++ ILI+DEPT I A ++ I++ L +G G+I Sbjct: 160 EQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGKGIIY 219 Query: 450 ISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494 I+ ++ EV ++D +AV G G+ A + ++ + G E Sbjct: 220 ITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRE 264 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: 636 Number of extensions: 29 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