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 WP_083441123.1 NITAL_RS01685 sugar ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >NCBI__GCF_000969705.1:WP_083441123.1 Length = 532 Score = 325 bits (832), Expect = 3e-93 Identities = 191/495 (38%), Positives = 297/495 (60%), Gaps = 16/495 (3%) Query: 4 ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63 +LEV+ + + F GV AL+GV F G VHA++GENGAGKSTL+++ +G + D GE+ Sbjct: 46 VLEVRQVTRSFSGVRALRGVDTAFRRGRVHALLGENGAGKSTLVRVCSGAVEADGGELWL 105 Query: 64 EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIF--IDYKKMYREA 121 +G VR+ P A GI V QE ++ + LSV +NIF+ R + ++ E Sbjct: 106 DGGVVRFASPFVAAQEGIAVVNQEPALAEQLSVLKNIFLPRLSLRRPLGRLRSDELRDEG 165 Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181 E+ + E G ID + + ++A +Q+VE+A+A+ + ++L +DEP S+LT ETE++ Sbjct: 166 EQLLAE-LGASIDLDAPVSSLTVAERQLVELAKALATRPRLLFMDEPNSALTSGETERML 224 Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVG-R 240 ++ L+E+GVA++ ++HRL E F++ D V+VLRDG+ + + ++++ +M G Sbjct: 225 GLIGRLREQGVAVVLVTHRLREAFQVADDVTVLRDGQTVLRAPAAETSIDEVIRIMAGDA 284 Query: 241 KLEKFYIKEAHEPGEVVLEVKNLSGE-RFENVSFSLRRGEILGFAGLVGAGRTELMETIF 299 L + G+V L+ + L+ RF +V+ LR EI+G AGLVGAGR++L ET+F Sbjct: 285 PLHEHQGPPDLPAGKVALKAEGLTVRGRFADVNLELRESEIVGLAGLVGAGRSDLAETLF 344 Query: 300 GFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRI 359 G R G +Y+ G+ V + P DA+ GI LVPEDRK L +SI N+ S+ Sbjct: 345 GLRKPDAGRLYVNGQAVTWSGPSDAMRAGIALVPEDRKVQALFAGLSIDWNLRAASVA-- 402 Query: 360 KKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILD 419 I +A+ A++ F ++ + LSGGNQQK V+A+W+AL P+ L+LD Sbjct: 403 -----IGRDDRHRIAE-AVRKFRVKFDSLRAPISTLSGGNQQKAVIARWMALGPRTLLLD 456 Query: 420 EPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAK 479 EPTRGIDV AKAE++ ++ + A EGV +++ISSEL EVL +S RI VM G+ ++ Sbjct: 457 EPTRGIDVAAKAEVHELVRRTAAEGVAILLISSELDEVLDLSHRIIVMRDGR---VVTEL 513 Query: 480 EASQEKVMKLAAGLE 494 A+ E+ +AA E Sbjct: 514 PANAERSAVVAAAFE 528 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: 591 Number of extensions: 26 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 494 Length of database: 532 Length adjustment: 35 Effective length of query: 459 Effective length of database: 497 Effective search space: 228123 Effective search space used: 228123 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 24 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