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 Dsui_0415 Dsui_0415 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__PS:Dsui_0415 Length = 326 Score = 192 bits (489), Expect = 7e-54 Identities = 113/321 (35%), Positives = 179/321 (55%), Gaps = 12/321 (3%) Query: 12 PLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPD- 70 PL+ DL F G R A++ +S+E+ +GE LGL+GESG GKS RT+L+L P+ Sbjct: 4 PLVSIQDLTVQF-NGARRASALNQVSLELGQGEVLGLLGESGSGKSVTLRTLLRL-HPER 61 Query: 71 ----GGKIFFEGKDITNLNDKEMKPYRK-KMQIIFQDPLGSLNPQMTVGRIIEDPLIIHK 125 G+I +G+D+ L +E+ YR + ++FQ+P + +P T+G+ I + + +H+ Sbjct: 62 HTRTAGRIRVDGQDVLALRGRELDRYRGGTVSMVFQEPGLAFDPVYTIGQQISEAVRVHE 121 Query: 126 IGTKKERRKRVEELLDMVGI--GREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEP 183 + R +L+ V I R +++PHE SGG +QR IA ALA PK ++ DEP Sbjct: 122 GVDQATAAARALAMLERVQIPQARRRFDAYPHELSGGMRQRAMIALALACKPKLLLADEP 181 Query: 184 VSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDK 243 +ALD ++Q QI+ LL E+Q++ G+S +F+ H++ ++ ++AVMY G+IVE G V + Sbjct: 182 TTALDATVQIQILLLLRELQRETGMSVIFVTHDIGAAVEVADRIAVMYAGRIVEQGPVGQ 241 Query: 244 IFLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICF 303 + P HPYTR LL + + + + + ++ G P LP GC F RC+ C Sbjct: 242 LVRQPCHPYTRGLLAAT--VGHEHRGRPLEAIPGSPPDLAALPPGCSFAPRCSHASERCH 299 Query: 304 EKEPELTEVEKNHFVSCHLVR 324 P L + H VR Sbjct: 300 RDIPPLEQQGARTLACWHPVR 320 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: 270 Number of extensions: 11 Number of successful extensions: 5 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: 326 Length adjustment: 28 Effective length of query: 300 Effective length of database: 298 Effective search space: 89400 Effective search space used: 89400 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