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 GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 440 bits (1132), Expect = e-128 Identities = 232/492 (47%), Positives = 336/492 (68%), Gaps = 3/492 (0%) Query: 4 ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63 +LE+ +I K FPGV AL V + PG V A++GENGAGKSTLMKIIAG+YQPD GEI Sbjct: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 Query: 64 EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYREAE 122 G+ + + P A AGI + QEL++M ++S+AENI++G E+ + +++++M+R Sbjct: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142 Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182 + + I +DPEE++G SIA +QMVEIA+AV + +LI+DEPTS++T+KE LF Sbjct: 143 ELL-ARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201 Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242 ++ LK +G I++I+H++ E+F I D+V+V RDG YIG +++ + ++ MMVGR+L Sbjct: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261 Query: 243 EKFYIKEAHEPGEVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFGF 301 + + G+++L V++L+ + F++VSF L GEILG AGL+G+GRT + ETIFG Sbjct: 262 SQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGI 321 Query: 302 RPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK 361 P G+I ++GK V I+ P AIE+G L+ EDRK GL +S++ N+ + L Sbjct: 322 TPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTG 381 Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421 FI K + L + K ++ ++ + LSGGNQQK +LA+WL P++LILDEP Sbjct: 382 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEP 441 Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481 TRGIDVGAKAEIYR+++ LA EG+ VIMISSELPEVL MSDR+ VM G+L G +D EA Sbjct: 442 TRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEA 501 Query: 482 SQEKVMKLAAGL 493 +QEKVM+LA+G+ Sbjct: 502 TQEKVMQLASGM 513 Score = 87.8 bits (216), Expect = 8e-22 Identities = 65/243 (26%), Positives = 117/243 (48%), Gaps = 10/243 (4%) Query: 257 VLEVKNLSGE-----RFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYI 311 +LE+ N+S +V +R G +L G GAG++ LM+ I G GEI + Sbjct: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 Query: 312 EGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREK 371 GK + PL A + GI ++ ++ L L+ MSI N+ + +++ ++ + Sbjct: 83 RGKPIVFETPLAAQKAGIAMIHQE---LNLMPHMSIAENIWI-GREQLNSLHMVNHREMH 138 Query: 372 ELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKA 431 + I P+ +V LS +Q V +AK ++ ILI+DEPT I A Sbjct: 139 RCTAELLARLRIN-LDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVA 197 Query: 432 EIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAA 491 ++ I++ L +G G++ I+ ++ EV ++D +AV G G+ A + + ++ + Sbjct: 198 HLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMV 257 Query: 492 GLE 494 G E Sbjct: 258 GRE 260 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: 608 Number of extensions: 26 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: 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 Apr 09 2024. 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