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 SMa2079 SMa2079 ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Smeli:SMa2079 Length = 314 Score = 330 bits (845), Expect = 4e-95 Identities = 158/311 (50%), Positives = 226/311 (72%), Gaps = 3/311 (0%) Query: 12 PLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG 71 PL+ +LK ++ +L++VDG+ + ++ GET+GLVGESGCGKSTLG+T+L+L+ P Sbjct: 2 PLISASNLKTHYKTRDGLLRSVDGVDLVVERGETVGLVGESGCGKSTLGKTLLRLVDPTA 61 Query: 72 GKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKE 131 G+I F+G+DIT L+ ++ RK +Q+IFQDP SLNP+ T+G I+E PLI+H+ G+ E Sbjct: 62 GRIEFKGEDITALDQGRLRNVRKSIQMIFQDPFASLNPRHTIGEILEAPLIVHQAGSPPE 121 Query: 132 RRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSI 191 RR V ++ VG+ + IN +PHEFSGGQ+QRIGIARAL LNP+ IVCDEPVSALD+SI Sbjct: 122 RRSTVASIVAKVGLPADAINRYPHEFSGGQRQRIGIARALLLNPELIVCDEPVSALDLSI 181 Query: 192 QAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHP 251 QAQI++LL E++++ G+SYLFI+H+L+VV + +V VMYLG++VE D + ++ +P HP Sbjct: 182 QAQILNLLVEMKKEFGLSYLFISHDLSVVRYFCDRVLVMYLGRVVESADNETLWSDPRHP 241 Query: 252 YTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTE 311 YTRAL+ +VP + ++ L GELPSP ++P GCRF TRC +C EPE Sbjct: 242 YTRALMAAVPD---PSRPRQAAPLGGELPSPSNIPPGCRFHTRCPLATELCRVAEPEFRS 298 Query: 312 VEKNHFVSCHL 322 ++ H V+CH+ Sbjct: 299 IKPGHRVACHV 309 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: 343 Number of extensions: 9 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: 314 Length adjustment: 28 Effective length of query: 300 Effective length of database: 286 Effective search space: 85800 Effective search space used: 85800 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