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 RR42_RS11235 RR42_RS11235 peptide ABC transporter substrate-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Cup4G11:RR42_RS11235 Length = 330 Score = 314 bits (805), Expect = 2e-90 Identities = 163/320 (50%), Positives = 221/320 (69%), Gaps = 11/320 (3%) Query: 12 PLLQTVDLKKYFPQGKRIL-------KAVDGISIEIKEGETLGLVGESGCGKSTLGRTIL 64 PLL+ LKK++ +R L +AVDG+S ++ GETL LVGESGCGK+T +++L Sbjct: 10 PLLKVDRLKKHYIAPQRWLAPRKPPIQAVDGVSFTVERGETLSLVGESGCGKTTTAKSVL 69 Query: 65 KLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124 +L+ P G + +G+++ L+ M+ R+ +QIIFQDP SL+P++T G I+ +PL Sbjct: 70 RLVEPTSGSVQLDGEELLGLSANAMRLRRRDLQIIFQDPYASLSPRLTAGEIVSEPLRNF 129 Query: 125 KIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184 + ++ ER +RV+ L VG+ E FPHEFSGGQ+QR+GIARALALNPK IVCDEPV Sbjct: 130 GMRSRTERSERVQWLFAKVGLRPEAARKFPHEFSGGQRQRLGIARALALNPKLIVCDEPV 189 Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244 SALDVS+QAQ+++LL ++Q ++GI+YLF+AH+LAVV HISH+VAVMYLG+IVE D D + Sbjct: 190 SALDVSVQAQVVNLLMDLQAELGIAYLFVAHDLAVVRHISHRVAVMYLGQIVELADRDTL 249 Query: 245 FLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFE 304 F P HPYT LL +VP +P R L+G+ PSP + P GCRF TRC +AIC E Sbjct: 250 FSAPRHPYTEILLSAVP-VPNPRTPARRLLLQGDPPSPANPPPGCRFHTRCPLAQAICKE 308 Query: 305 KEPELTE---VEKNHFVSCH 321 + P LTE H V+CH Sbjct: 309 QAPALTERPSAGGGHQVACH 328 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: 338 Number of extensions: 10 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: 330 Length adjustment: 28 Effective length of query: 300 Effective length of database: 302 Effective search space: 90600 Effective search space used: 90600 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: 49 (23.5 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