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 BWI76_RS00660 BWI76_RS00660 ABC transporter
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Koxy:BWI76_RS00660 Length = 503 Score = 436 bits (1122), Expect = e-127 Identities = 228/494 (46%), Positives = 333/494 (67%), Gaps = 4/494 (0%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P+L +K I K FPGV AL+ V ++ +PG+V A++GENGAGKSTL+K++ G+YQP+EGEI+ Sbjct: 6 PLLSLKGITKVFPGVRALENVQLDLWPGKVTALIGENGAGKSTLVKVMTGIYQPEEGEIL 65 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIF--IDYKKMYRE 120 Y+ ++ +P A GI + QE + D LSV ENIF+G G+ +D+ M+R+ Sbjct: 66 YKAIPIQLPNPESAHKVGITAIHQETVLFDELSVTENIFVGQYLHTGLLKKLDWPAMHRK 125 Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180 A + + ++IDP L SIA + MV IARA+ +A+V+ILDEPT++L+Q E + Sbjct: 126 ASEILTR-LEVQIDPRATLKTLSIAQRHMVAIARALSFEAQVVILDEPTAALSQHEILEF 184 Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240 +++V+ LK+ G AI+FISH+ +EIFE+ D ++LRDG Y+ + +I ++T+E++V MMVGR Sbjct: 185 YQIVERLKQDGKAILFISHKFDEIFELADYYTILRDGVYVSSGAINDITEERMVAMMVGR 244 Query: 241 KLEKFYIKEAHEPGEVVLEVKNLSGE-RFENVSFSLRRGEILGFAGLVGAGRTELMETIF 299 + + Y K PGE VLEVK+L F ++SFSLR+GEILGF GLVGAGRTELM+ + Sbjct: 245 AITQTYPKVDCIPGETVLEVKDLCHPTEFAHISFSLRKGEILGFYGLVGAGRTELMQALS 304 Query: 300 GFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRI 359 G G+I ++GK + P DAI GI VPE+R+K G I+ + I N+SLP L ++ Sbjct: 305 GVSHPSSGDIVLKGKPMRFRQPADAISAGIVCVPEERQKQGAIIALPIAQNISLPQLSKL 364 Query: 360 KKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILD 419 G ++ RE LAD ++ + V LSGGNQQKVV+ KWLA P+++ILD Sbjct: 365 NPGGVLNDAREWRLADEYASRLQVKAFSWRQAVETLSGGNQQKVVIGKWLATHPEVIILD 424 Query: 420 EPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAK 479 EPT+GID+G+KA +++ MS+L +G+ VIM+SSELPEV+ M+DRI VM G + A Sbjct: 425 EPTKGIDIGSKAAVHQFMSELVSQGLAVIMVSSELPEVMGMADRIIVMHEGLMVAEYRAG 484 Query: 480 EASQEKVMKLAAGL 493 EA+ E ++ A+G+ Sbjct: 485 EATAETIVSAASGI 498 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: 664 Number of extensions: 33 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: 503 Length adjustment: 34 Effective length of query: 460 Effective length of database: 469 Effective search space: 215740 Effective search space used: 215740 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