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_040659554.1 ON16_RS03945 sugar ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >NCBI__GCF_000307265.1:WP_040659554.1 Length = 511 Score = 329 bits (843), Expect = 2e-94 Identities = 190/497 (38%), Positives = 294/497 (59%), Gaps = 14/497 (2%) Query: 4 ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63 +L V++I K F LKG+S++ PGE+ A+VG NGAGKSTLMKII G+Y D G+I Sbjct: 13 LLSVQNIRKSFGLNAVLKGISLDVAPGEILALVGGNGAGKSTLMKIIMGIYTQDGGDIYI 72 Query: 64 EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEK 123 +G V N P++A+ GI V QE + N++V ENI +G + + +++RE Sbjct: 73 KGEHVVLNKPAQALAKGIYMVPQEPLLFPNMTVEENITIGFSQNKA------ELHRELVA 126 Query: 124 FMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEV 183 M +E G ++ + SIA QQ+VEI R + + A++LILDEPTS+LT E E LF+ Sbjct: 127 TM-DEIGWHLNLTRRASSLSIAEQQLVEILRGLLRHAQILILDEPTSALTFDEVESLFKC 185 Query: 184 VKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLE 243 V+ L+ KG+ II+I+HRL E+FE+ V+++RDG ++ T+E +V ++ ++ Sbjct: 186 VRDLQSKGIGIIYITHRLTEVFELATHVAIMRDGIIAVKGAVSGFTREDLVRGLLPPDMD 245 Query: 244 KFYIKEAHEPGEV------VLEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRTELMET 297 P V VLE++N G F ++ + GEILG AG+VGAGRTEL T Sbjct: 246 ACKDGGCPVPTAVDYTKAPVLELQNFGGYGFSGINLKIYPGEILGMAGVVGAGRTELATT 305 Query: 298 IFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLD 357 IFG GG++ + G+ + I+ G+ VPEDR GL I + N S L Sbjct: 306 IFGMDKVLGGKVLLNGRDITGLKTRAVIQAGLNYVPEDRHLNGLFKISDVACNTSSALLG 365 Query: 358 RIKKGPFI-SFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKIL 416 G F+ + K+E+ L + F + ++ V LSGGNQQKVV+A+ L+ P+++ Sbjct: 366 DGSLGKFLLNRKKEQTLTQRYVDDFRTKITGQEQAVGSLSGGNQQKVVIARSLSTSPRVI 425 Query: 417 ILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGII 476 ILDEPTRGID A+ ++YRI+ QL +GV +++ISS++ E+++++DR + G++ G Sbjct: 426 ILDEPTRGIDAAARGDVYRIIHQLRDQGVSILLISSDMEEIVELADRAVTVFQGRVNGEF 485 Query: 477 DAKEASQEKVMKLAAGL 493 + +Q+++M A G+ Sbjct: 486 KGADINQDRLMAAAFGV 502 Score = 93.6 bits (231), Expect = 1e-23 Identities = 62/249 (24%), Positives = 124/249 (49%), Gaps = 13/249 (5%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P+LE+++ G + G++++ YPGE+ + G GAG++ L I G+ + G+++ Sbjct: 264 PVLELQNF-----GGYGFSGINLKIYPGEILGMAGVVGAGRTELATTIFGMDKVLGGKVL 318 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQE------LSVMDNLSVAENIFMGDEEKRGIFIDYKK 116 GR + I AG+ V ++ + D + +GD ++ KK Sbjct: 319 LNGRDITGLKTRAVIQAGLNYVPEDRHLNGLFKISDVACNTSSALLGDGSLGKFLLNRKK 378 Query: 117 MYREAEKFMKEEFGIEIDPEEK-LGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQK 175 ++++ ++F +I +E+ +G S QQ V IAR++ +V+ILDEPT + Sbjct: 379 EQTLTQRYV-DDFRTKITGQEQAVGSLSGGNQQKVVIARSLSTSPRVIILDEPTRGIDAA 437 Query: 176 ETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVE 235 ++ ++ L+++GV+I+ IS +EEI E+ D+ + G G ++ +++++ Sbjct: 438 ARGDVYRIIHQLRDQGVSILLISSDMEEIVELADRAVTVFQGRVNGEFKGADINQDRLMA 497 Query: 236 MMVGRKLEK 244 G EK Sbjct: 498 AAFGVSEEK 506 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: 661 Number of extensions: 38 Number of successful extensions: 8 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: 511 Length adjustment: 34 Effective length of query: 460 Effective length of database: 477 Effective search space: 219420 Effective search space used: 219420 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