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 H281DRAFT_03878 H281DRAFT_03878 xylose ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Burk376:H281DRAFT_03878 Length = 519 Score = 419 bits (1077), Expect = e-121 Identities = 223/501 (44%), Positives = 330/501 (65%), Gaps = 12/501 (2%) Query: 2 KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPD--EG 59 +P+L ++ I K F GV AL G+ + PGE + GENGAGKSTLMK+++GVY +G Sbjct: 3 QPLLTMRGIVKAFSGVKALDGIDLTVSPGECVGLCGENGAGKSTLMKVLSGVYPHGTWDG 62 Query: 60 EIIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDE-EKRGIFIDYKKMY 118 EI +EG+ ++ + AGI+ + QEL ++ LSVAENIF+G+E G ++Y MY Sbjct: 63 EITWEGKPLKATSIRDTERAGIIIIHQELMLVPELSVAENIFLGNEITLPGGRMNYAAMY 122 Query: 119 REAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETE 178 + A++ ++E I+ + + Y QQ++EIA+A+ K+AK+LILDEP+SSLT E Sbjct: 123 QRADELLRELGISGINAAQPVMNYGGGHQQLIEIAKALNKQAKLLILDEPSSSLTSSEIA 182 Query: 179 KLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238 L ++V+ LK +GVA ++ISH+L+E+ +CD +SV+RDG ++ T+ + LT ++I+ +MV Sbjct: 183 ILLDIVRDLKRRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMHALTTDRIISLMV 242 Query: 239 GRKLEKFYIKEAHEPGEVVLEVKNLS--------GERFENVSFSLRRGEILGFAGLVGAG 290 GR+++ + +E H G+V+ E +N++ +R +VSF LRRGEILG AGLVGAG Sbjct: 243 GREIKNLFPREPHPIGDVIFEARNVTCFDVTNPRRKRVSDVSFELRRGEILGVAGLVGAG 302 Query: 291 RTELMETIFGFRPKRG-GEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMH 349 RTELM+ IFG P + +EGK V+I P+DAI GIG+VPEDRK+ G++ +S+ H Sbjct: 303 RTELMQAIFGAYPGVSEATVVMEGKTVKIRAPIDAIRAGIGMVPEDRKRHGIVPGLSVGH 362 Query: 350 NVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWL 409 N++L L R G I E + +K +R A+P + LSGGNQQK VL + L Sbjct: 363 NITLAVLQRFSSGGRIDSAAELDTIHTEMKRLSVRAAHPMLSIASLSGGNQQKAVLTRML 422 Query: 410 ALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSF 469 PK+LILDEPTRG+DVGAK EIY+++ QLA+ G+ ++M+SSELPEVL +SDR+ V+ Sbjct: 423 LTDPKVLILDEPTRGVDVGAKFEIYKLIFQLAQRGMSIVMVSSELPEVLGISDRVLVIGE 482 Query: 470 GKLAGIIDAKEASQEKVMKLA 490 G+L G +QE ++ A Sbjct: 483 GELRGDFVNDGLTQEDILSAA 503 Score = 88.2 bits (217), Expect = 6e-22 Identities = 66/222 (29%), Positives = 107/222 (48%), Gaps = 6/222 (2%) Query: 23 VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQP-DEGEIIYEGRGVRWNHPSEAINAGI 81 VS E GE+ + G GAG++ LM+ I G Y E ++ EG+ V+ P +AI AGI Sbjct: 283 VSFELRRGEILGVAGLVGAGRTELMQAIFGAYPGVSEATVVMEGKTVKIRAPIDAIRAGI 342 Query: 82 VTVFQELS---VMDNLSVAENIFMGDEEK--RGIFIDYKKMYREAEKFMKEEFGIEIDPE 136 V ++ ++ LSV NI + ++ G ID MK P Sbjct: 343 GMVPEDRKRHGIVPGLSVGHNITLAVLQRFSSGGRIDSAAELDTIHTEMKRLSVRAAHPM 402 Query: 137 EKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAIIF 196 + S QQ + R + KVLILDEPT + ++++++ L ++G++I+ Sbjct: 403 LSIASLSGGNQQKAVLTRMLLTDPKVLILDEPTRGVDVGAKFEIYKLIFQLAQRGMSIVM 462 Query: 197 ISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238 +S L E+ I D+V V+ +GE G + LT+E I+ + Sbjct: 463 VSSELPEVLGISDRVLVIGEGELRGDFVNDGLTQEDILSAAI 504 Score = 82.8 bits (203), Expect = 3e-20 Identities = 65/238 (27%), Positives = 116/238 (48%), Gaps = 7/238 (2%) Query: 260 VKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKR--GGEIYIEGKRV 316 VK SG + + + ++ GE +G G GAG++ LM+ + G P GEI EGK + Sbjct: 12 VKAFSGVKALDGIDLTVSPGECVGLCGENGAGKSTLMKVLSGVYPHGTWDGEITWEGKPL 71 Query: 317 EINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADW 376 + D GI ++ ++ L L+ +S+ N+ L + + G +++ + AD Sbjct: 72 KATSIRDTERAGIIIIHQE---LMLVPELSVAENIFLGNEITLPGGR-MNYAAMYQRADE 127 Query: 377 AIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRI 436 ++ I + V+ GG+QQ + +AK L + K+LILDEP+ + A + I Sbjct: 128 LLRELGISGINAAQPVMNYGGGHQQLIEIAKALNKQAKLLILDEPSSSLTSSEIAILLDI 187 Query: 437 MSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494 + L + GV + IS +L EV + D I+V+ G+ + ++++ L G E Sbjct: 188 VRDLKRRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMHALTTDRIISLMVGRE 245 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: 686 Number of extensions: 28 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 494 Length of database: 519 Length adjustment: 34 Effective length of query: 460 Effective length of database: 485 Effective search space: 223100 Effective search space used: 223100 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