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 Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 404 bits (1039), Expect = e-117 Identities = 221/497 (44%), Positives = 335/497 (67%), Gaps = 11/497 (2%) Query: 4 ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63 +L VK+I K F GV AL VS+E G V AI+GENGAGKSTLMKI++GVY +G I Y Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60 Query: 64 EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYREAE 122 G V++ + +A GI + QEL+++ LS+ ENIF+G E + + +D KM++EA Sbjct: 61 NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAA 120 Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182 + + + +DPE + + + QQ+VEIA+A+ +++V+I+DEPTS+++ +E E LF Sbjct: 121 QLL-HRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFG 179 Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242 ++++L+ +G AI +ISH+L+E+F I D+ VLRDG+ I + +E +T+E +++ MVGR++ Sbjct: 180 IIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREI 239 Query: 243 EKFYIKEAHEPGEVVLEVKNLS------GERF--ENVSFSLRRGEILGFAGLVGAGRTEL 294 + E VL VK+L+ ++F ++++F L +GE+LG GL+GAGRTEL Sbjct: 240 VIERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTEL 299 Query: 295 METIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLP 354 ME +FG P +G EI + GK E P +A++ G+ LVPEDRK+ GL+L M + N SL Sbjct: 300 MEALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLT 359 Query: 355 SLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPK 414 +D I G + K+EK LA + I+ + + V LSGGNQQKVVLAKWLA +PK Sbjct: 360 VVDSILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATRPK 419 Query: 415 ILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKL-A 473 +L+LDEPTRGID+ AK EIY+++ QLA EG+G+I++SSELPE+L +SDR+ VM+ G+L A Sbjct: 420 VLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRLTA 479 Query: 474 GIIDAKEASQEKVMKLA 490 I + S++++++ A Sbjct: 480 NIPIDAQTSEDEILQAA 496 Score = 97.1 bits (240), Expect = 1e-24 Identities = 73/244 (29%), Positives = 120/244 (49%), Gaps = 12/244 (4%) Query: 257 VLEVKNLSGE-----RFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYI 311 +L VKN++ E ++VS L+ G + G GAG++ LM+ + G P G IY Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60 Query: 312 EGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREK 371 G V+ + DA E+GI ++ ++ L LI +SI N+ L G K K Sbjct: 61 NGDPVKFQNTRDAQEKGINIIHQE---LNLIPYLSIRENIFLGREPETPMGLLDVAKMHK 117 Query: 372 ELADWAIKT-FDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAK 430 E A + ++ P P V L G QQ V +AK L+L+ +++I+DEPT I Sbjct: 118 EAAQLLHRLKLNVDPETP---VSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEV 174 Query: 431 AEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLA 490 ++ I+ L EG + IS +L E+ ++DR V+ GK+ + + ++E +++ Sbjct: 175 EILFGIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKM 234 Query: 491 AGLE 494 G E Sbjct: 235 VGRE 238 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: 655 Number of extensions: 32 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: 502 Length adjustment: 34 Effective length of query: 460 Effective length of database: 468 Effective search space: 215280 Effective search space used: 215280 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