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_RS04800 RR42_RS04800 ABC transporter
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Cup4G11:RR42_RS04800 Length = 529 Score = 268 bits (686), Expect = 3e-76 Identities = 176/507 (34%), Positives = 276/507 (54%), Gaps = 18/507 (3%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P L + I KR+PGV A VS+ PGE+HA++GENGAGKSTLMKII G +PD G++ Sbjct: 7 PRLALAHISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGDMH 66 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFM----GDEEKRGIFIDYKKMY 118 + G ++P +A N GI VFQ S+ D L+VAENI + G + G M Sbjct: 67 FNGARAAIHNPHDARNLGIAMVFQHFSLFDTLTVAENIALGLPRGSKTAAGSPHAGTNMK 126 Query: 119 REAEKFMKE--EFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKE 176 + AE+ + +G+ ++P + S+ +Q VEI RA+ K ++LILDEPTS LT + Sbjct: 127 QLAEQIRETALRYGLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLTPQA 186 Query: 177 TEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEM 236 + LF ++ L +G +I++ISH+L+EI E+C +V+R G G + + + Sbjct: 187 VQTLFITLRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAASLSRL 246 Query: 237 MVGRKLEKFYIKEAHEPGEVVLEVKNLSGER-------FENVSFSLRRGEILGFAGLVGA 289 M+G + + + EPG L V+ LS R +S LR GEI+G AG+ G Sbjct: 247 MIGGEPPR-EARVQTEPGVCRLAVRELSLPRSHAFATELAGISLDLRAGEIVGIAGVSGN 305 Query: 290 GRTELMETIFGFRPKRGGE-IYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIM 348 G+ EL+ + G + + I ++ K V G+ VPE+R G + MS+ Sbjct: 306 GQQELLAALSGEDVRAARDAITLDNKPVGKLDARQRRRAGLAFVPEERLGRGAVPGMSLA 365 Query: 349 HNVSL--PSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLA 406 N+ L S +++G IS K LA I ++ + P LSGGN QK ++ Sbjct: 366 ANILLSHQSAPYVQRG-MISPKAAAGLAQAVIARLRVKASGPHALAKSLSGGNLQKFIVG 424 Query: 407 KWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAV 466 + + PK+LI+ +PT G+DVGA A+I+ + L G ++++S EL E+ + DR+ V Sbjct: 425 REIESGPKVLIVAQPTWGVDVGAAAQIHNELLALKATGCALLVVSEELDELFAICDRLHV 484 Query: 467 MSFGKLAGIIDAKEASQEKVMKLAAGL 493 ++ G+L+ I ++A++E+V +GL Sbjct: 485 IAKGRLSPSIPTRDATREQVGLWMSGL 511 Score = 103 bits (256), Expect = 2e-26 Identities = 72/231 (31%), Positives = 120/231 (51%), Gaps = 9/231 (3%) Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQG 328 ++VS + GEI G GAG++ LM+ IFG G+++ G R I++P DA G Sbjct: 25 DDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGDMHFNGARAAIHNPHDARNLG 84 Query: 329 IGLVPEDRKKLGLILIMSIMHNVSL--PSLDRIKKGPFISFKREKELADWAIKTFDIR-- 384 I +V + L +++ N++L P + G + K+LA+ I+ +R Sbjct: 85 IAMVFQH---FSLFDTLTVAENIALGLPRGSKTAAGSPHAGTNMKQLAE-QIRETALRYG 140 Query: 385 -PAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKE 443 P P+R V LS G +Q+V + + L KP++LILDEPT + A ++ + QLA E Sbjct: 141 LPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLTPQAVQTLFITLRQLAAE 200 Query: 444 GVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494 G ++ IS +L E+ ++ VM G++ G+ D ++ S + +L G E Sbjct: 201 GTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAASLSRLMIGGE 251 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: 584 Number of extensions: 33 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: 529 Length adjustment: 35 Effective length of query: 459 Effective length of database: 494 Effective search space: 226746 Effective search space used: 226746 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