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 7024900 Shewana3_2074 ABC transporter related (RefSeq)
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__ANA3:7024900 Length = 499 Score = 387 bits (993), Expect = e-112 Identities = 204/499 (40%), Positives = 324/499 (64%), Gaps = 10/499 (2%) Query: 1 MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60 M ILE+K I K +PGV AL+ VS+ + GEVHA++GENGAGKSTL+K++ G D G+ Sbjct: 1 MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD 60 Query: 61 IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYRE 120 I++ G +N P +A AGI TV+QE++++ NL+VA+N+F+G E +R I +KKMY + Sbjct: 61 ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYAD 120 Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180 A + + F ++ID L YSIA+QQ++ IAR V AKVL+LDEPT+SL KE + L Sbjct: 121 ARAVLTQ-FKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVL 179 Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240 F ++ LK KGVAI+FI+H L+++++I D+++VLR+G++IG L + K++E M+GR Sbjct: 180 FGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239 Query: 241 KLEKFYIKEAHEPGEVV--------LEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRT 292 L++ + + + V LE ++ G ++++ ++ +G+ +G AGL+G+GR+ Sbjct: 240 SLQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGS-IQSMNLTVPKGQAVGLAGLLGSGRS 298 Query: 293 ELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVS 352 E+ +FG G I++ G+++ ++ P+DAI GI L PEDRK G+I +SI N+ Sbjct: 299 EVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENII 358 Query: 353 LPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALK 412 L RI ++S R++E+A + I I D+ + LSGGNQQKV+LA+WLA++ Sbjct: 359 LALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIE 418 Query: 413 PKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKL 472 P +L+LDEPTRGID+GA AEI +++ L EG+ +++ SSEL E++ S+++ V+ Sbjct: 419 PILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYA 478 Query: 473 AGIIDAKEASQEKVMKLAA 491 + E + + VM+ A Sbjct: 479 VRELSGAELTSQHVMQAIA 497 Score = 92.8 bits (229), Expect = 2e-23 Identities = 70/246 (28%), Positives = 123/246 (50%), Gaps = 19/246 (7%) Query: 256 VVLEVKNLSG-----ERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIY 310 ++LE+K +S + E+VS L GE+ G GAG++ L++ + G + K G+I Sbjct: 3 LILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62 Query: 311 IEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKRE 370 G+ N P+DA + GI V ++ + L+ +++ N+ L R + I FK+ Sbjct: 63 FLGEPQHFNTPMDAQKAGISTVYQE---VNLVPNLTVAQNLFLGYEPR--RLGLIHFKKM 117 Query: 371 KELADWAIKTF----DIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGID 426 A + F D+ D + QQ + +A+ +A+ K+L+LDEPT +D Sbjct: 118 YADARAVLTQFKLDIDVSAPLSDYSIAV-----QQLIAIARGVAMSAKVLVLDEPTASLD 172 Query: 427 VGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKV 486 ++ I++QL +GV ++ I+ L +V Q+SDRI V+ G+ G E Q K+ Sbjct: 173 AKEVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKL 232 Query: 487 MKLAAG 492 ++ G Sbjct: 233 IEAMLG 238 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: 596 Number of extensions: 28 Number of successful extensions: 7 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: 499 Length adjustment: 34 Effective length of query: 460 Effective length of database: 465 Effective search space: 213900 Effective search space used: 213900 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