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 HSERO_RS22220 HSERO_RS22220 D-ribose transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__HerbieS:HSERO_RS22220 Length = 505 Score = 398 bits (1022), Expect = e-115 Identities = 214/498 (42%), Positives = 330/498 (66%), Gaps = 11/498 (2%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P+L + I KRF GV AL+ V PGEV A++GENGAGKSTL+KI+ G++QPDEG I Sbjct: 11 PVLSLSGIGKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEGSIH 70 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI--FIDYKKMYRE 120 GR VR+ +A+ GI V QE + + LSVAENI++G + G ID+++M E Sbjct: 71 LGGREVRFASAQDAMRGGITAVHQETVMFEELSVAENIWIGRQPLCGTPRRIDWRRMEDE 130 Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180 A +++ ++ S+A + VEIARA+ ++A+V+I+DEPT++L+ E +L Sbjct: 131 ARALFAR-LEVDLPVRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALSHHEIGEL 189 Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240 + ++ L+ G A+IFISH+ +EI+ + D+ +VLRDG +I + + ++T++++V +MVGR Sbjct: 190 YRIIGQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQLVALMVGR 249 Query: 241 KLEKFYIKEAHEPGEV---VLEVKNLSG-ERFENVSFSLRRGEILGFAGLVGAGRTELME 296 ++ + + + A + VLEVK+LS F++VSF++R GEILGF GLVGAGR+E+M Sbjct: 250 EVGQVFSRAASNTEDQTAPVLEVKHLSHPSEFDDVSFAVRPGEILGFYGLVGAGRSEVMH 309 Query: 297 TIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356 +FG P+ G ++I+G+ V++ P AI G+ VPEDR++ G +L + I N++LP L Sbjct: 310 ALFGLSPEAQGAVWIDGREVKLCSPAQAIAHGLAYVPEDRQRQGALLSLPIFQNITLPVL 369 Query: 357 DRIKKGPFISFKREKEL--ADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPK 414 I G F+ R +E+ A + +++ ++ + V LSGGNQQKVVLAKWLA +P+ Sbjct: 370 PGI--GFFLRRHRRREIDIARRLCEQLELKASHFHQHVAQLSGGNQQKVVLAKWLATQPR 427 Query: 415 ILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAG 474 +LILDEPT+GID+G+KA ++R + +L +G+ VI++SSELPEV+ MSDRI VM G++ Sbjct: 428 VLILDEPTKGIDIGSKAAVHRFIGELVAQGLAVILVSSELPEVMGMSDRIVVMHQGRVQQ 487 Query: 475 IIDAKEASQEKVMKLAAG 492 + EAS E + A+G Sbjct: 488 VFSRAEASAEALAAAASG 505 Score = 81.6 bits (200), Expect = 6e-20 Identities = 60/237 (25%), Positives = 117/237 (49%), Gaps = 12/237 (5%) Query: 265 GERFE------NVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEI 318 G+RF+ +V F++R GE++ G GAG++ L++ + G G I++ G+ V Sbjct: 19 GKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEGSIHLGGREVRF 78 Query: 319 NHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAI 378 DA+ GI V ++ + +S+ N+ + I ++R ++ A Sbjct: 79 ASAQDAMRGGITAVHQETV---MFEELSVAENIWIGRQPLCGTPRRIDWRRMEDEARALF 135 Query: 379 KTFDIRPAYPDR-KVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIM 437 ++ P R +V LS + V +A+ L+ + +++I+DEPT + E+YRI+ Sbjct: 136 ARLEVD--LPVRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALSHHEIGELYRII 193 Query: 438 SQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494 QL + G VI IS + E+ ++DR V+ G+ + + ++++++ L G E Sbjct: 194 GQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQLVALMVGRE 250 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: 600 Number of extensions: 32 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: 505 Length adjustment: 34 Effective length of query: 460 Effective length of database: 471 Effective search space: 216660 Effective search space used: 216660 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