Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 7025500 Shewana3_2654 ABC transporter related (RefSeq)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__ANA3:7025500 Length = 261 Score = 198 bits (504), Expect = 1e-55 Identities = 101/252 (40%), Positives = 170/252 (67%), Gaps = 8/252 (3%) Query: 12 PLLQTVDLKKYFPQG-----KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKL 66 PLL+ DL K + G ++ A+ +S E+ GETL +VGE+G GKSTL R ++ Sbjct: 4 PLLKVNDLFKRYDTGYKGFTRQYNDALAPVSFELNRGETLAIVGEAGSGKSTLARILVGA 63 Query: 67 LRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126 GG+I+FEG+ L+ + +K + +++IFQDP SLNP++T+G+++++PL + Sbjct: 64 EPRSGGEIYFEGEA---LDSRNIKQRCRLIRMIFQDPNTSLNPRLTIGQLLDEPLRFNTE 120 Query: 127 GTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSA 186 + KER +V + L VG+ E + +PH S GQ+QR+ +ARAL LNPK I+ DE ++A Sbjct: 121 LSAKERSGQVIDTLRKVGLLPEHADFYPHMISEGQKQRVAVARALMLNPKIIIADEALTA 180 Query: 187 LDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFL 246 LD+S+++QI++LL ++Q+ +G+SY+F++HNL ++ H+S K+ V++ G +VE ++IF Sbjct: 181 LDLSVRSQILNLLLKLQKDLGLSYIFVSHNLNIIRHVSDKIMVLHKGVMVEKAPTEQIFN 240 Query: 247 NPIHPYTRALLK 258 +P H YT+ L++ Sbjct: 241 SPQHEYTQRLIQ 252 Lambda K H 0.321 0.142 0.417 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: 245 Number of extensions: 18 Number of successful extensions: 2 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: 328 Length of database: 261 Length adjustment: 26 Effective length of query: 302 Effective length of database: 235 Effective search space: 70970 Effective search space used: 70970 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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