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 RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 405 bits (1041), Expect = e-117 Identities = 217/493 (44%), Positives = 325/493 (65%), Gaps = 10/493 (2%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P+ E++ I K FPGV AL VS YPGEVH ++GENGAGKS+LMK++ GVY D GE Sbjct: 9 PLFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFY 68 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI--FIDYKKMYRE 120 ++G V P++ + GI +FQE S++ L +A+NIF+G E + I +D +M+ E Sbjct: 69 HDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHAE 128 Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180 A + + + G+E+ + + +A QQMVEIA+A+ + A++L+LDEPT++L+ +ETEKL Sbjct: 129 ARRIL-DILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKL 187 Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240 F V+ LK GV++I+ISHR+ E+F + D++++LRDG +G + T +++V MVGR Sbjct: 188 FAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVGR 247 Query: 241 KLEKFYIKE-AHEPGEVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETI 298 K++ Y +E + +PGEV L+V+N+S + +++ +R GEI+G AGLVG+GR+E+ + Sbjct: 248 KVDMSYSRERSAQPGEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVARAV 307 Query: 299 FGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDR 358 FG P R GEIYI GKR+ P A E G L+PE RK GL LI ++ N+ L L R Sbjct: 308 FGADPIRQGEIYIFGKRLT-GGPDRARELGAALIPESRKSEGLALIRTVRDNLLLAGLRR 366 Query: 359 IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVL--YLSGGNQQKVVLAKWLALKPKIL 416 + + + LA+ I +R A PD L +LSGGNQQK+V+ KWL + K+ Sbjct: 367 AFPARWYRADKAEALAEREIAR--LRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKLF 424 Query: 417 ILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGII 476 I DEPTRGIDVGAKAEI+ ++ L K+G GV++ISSELPE++ + DR VM G++AG + Sbjct: 425 IFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGEV 484 Query: 477 DAKEASQEKVMKL 489 E ++E++++L Sbjct: 485 AHAEMTEERILQL 497 Score = 85.1 bits (209), Expect = 5e-21 Identities = 64/235 (27%), Positives = 112/235 (47%), Gaps = 9/235 (3%) Query: 261 KNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEIN 319 KN G + ++VSF++ GE+ G GAG++ LM+ + G GE Y +G V I Sbjct: 18 KNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFYHDGSPVAIT 77 Query: 320 HPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIK 379 P D + GI ++ ++ L+ + I N+ L R +G + A + Sbjct: 78 SPADTMGLGIAVIFQE---FSLVPYLDIAQNIFL---GREPRGRIPGSVDAARMHAEARR 131 Query: 380 TFDIRPAYPDRK--VLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIM 437 DI + V L QQ V +AK L+ +IL+LDEPT + +++ ++ Sbjct: 132 ILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKLFAVI 191 Query: 438 SQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492 ++L +GV +I IS + EV + DRI ++ G+ G +A+ ++++ G Sbjct: 192 ARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVG 246 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: 683 Number of extensions: 34 Number of successful extensions: 9 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