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 Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410 Length = 514 Score = 375 bits (964), Expect = e-108 Identities = 197/489 (40%), Positives = 313/489 (64%), Gaps = 4/489 (0%) Query: 5 LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64 L I K FPGV AL G+S +PG+VHA++GENGAGKSTL+KI+ G Y P G++ Sbjct: 16 LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIG 75 Query: 65 GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKF 124 + + +++I +G+ + QEL ++ ++VAEN+F+G I+ + ++A Sbjct: 76 EQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRGVLRQQALAC 135 Query: 125 MKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVV 184 +K EIDP+EK+G+ S+ +Q+VEIA+A+ + A V+ DEPTSSL+ +E ++L ++ Sbjct: 136 LKG-LADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 Query: 185 KSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGT-DSIENLTKEKIVEMMVGRKLE 243 L+++G ++++SHR+EE+F IC+ V+V +DG ++ T + + LT +++V MVGR ++ Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDIQ 254 Query: 244 KFYIKEAHEPGEVVLEVKNLSGERF-ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFR 302 Y + G V L+V L G E VSF +GEILG GLVGAGRTEL + G Sbjct: 255 DIYDYRSRPRGAVALKVDGLLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFRMLSGLT 314 Query: 303 PKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK- 361 G + + G+ ++++ P DAI GI L PEDRKK G++ + S+ N+++ + Sbjct: 315 RNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTF 374 Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421 G + EK+ AD IK ++ +K++YLSGGNQQK +L +WL++ K+L+LDEP Sbjct: 375 GCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434 Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481 TRGID+GAKAEIY+I+ LA G+ VI++SS+L EV+ +SDRI V+ G + G + ++A Sbjct: 435 TRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQA 494 Query: 482 SQEKVMKLA 490 ++ +++LA Sbjct: 495 NESNLLQLA 503 Score = 83.2 bits (204), Expect = 2e-20 Identities = 57/225 (25%), Positives = 114/225 (50%), Gaps = 6/225 (2%) Query: 23 VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAGIV 82 VS E + GE+ + G GAG++ L ++++G+ + G + GR ++ + P +AI AGI+ Sbjct: 283 VSFEAHKGEILGLFGLVGAGRTELFRMLSGLTRNTAGRLELRGRELKLHSPRDAIAAGIL 342 Query: 83 TVFQELS---VMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMKEEFGIEI---DPE 136 ++ ++ SVAENI + F + E + K+ +++ + Sbjct: 343 LCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNADKQIKALKVKTPNAA 402 Query: 137 EKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAIIF 196 +K+ S QQ + R + KVL+LDEPT + ++++++ +L G+A+I Sbjct: 403 QKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIV 462 Query: 197 ISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241 +S L E+ I D++ VL +G G + E + ++++ + R+ Sbjct: 463 VSSDLMEVMGISDRILVLCEGAMRGELTREQANESNLLQLALPRQ 507 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: 647 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: 514 Length adjustment: 34 Effective length of query: 460 Effective length of database: 480 Effective search space: 220800 Effective search space used: 220800 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 Apr 09 2024. 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