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_RS35215 RR42_RS35215 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Cup4G11:RR42_RS35215 Length = 329 Score = 318 bits (816), Expect = 9e-92 Identities = 163/321 (50%), Positives = 224/321 (69%), Gaps = 12/321 (3%) Query: 13 LLQTVDLKKYFP--QGKRI------LKAVDGISIEIKEGETLGLVGESGCGKSTLGRTIL 64 +L+ +LK +FP QG I +KAVDG+S ++ GETLGLVGESGCGKST G I+ Sbjct: 5 ILRVENLKVHFPVTQGVFIKRQVGSVKAVDGVSFTLRRGETLGLVGESGCGKSTTGLAII 64 Query: 65 KLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124 K+L GG+I F+G D + + K +R+ +Q+++QDP GSLNP+M V II +PL +H Sbjct: 65 KMLAASGGRIAFDGDDFATFSKAQEKNFRRSVQMVYQDPFGSLNPRMKVCDIIGEPLEVH 124 Query: 125 KIGTKKER-RKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEP 183 + +E R R+ ELL MVG+ + +PHEFSGGQ+QRIGIARALA+ P IVCDEP Sbjct: 125 GMANDREHYRARIAELLQMVGLLPYMADRYPHEFSGGQRQRIGIARALAVEPSLIVCDEP 184 Query: 184 VSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDK 243 VSALDVSIQAQ++++ E+Q+++G++Y+FIAH+LAVV HIS ++AVMYLG+IVE D Sbjct: 185 VSALDVSIQAQVVNVFMELQRRLGLTYIFIAHDLAVVRHISDRIAVMYLGRIVEIASRDA 244 Query: 244 IFLNPIHPYTRALLKSVP--KIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAI 301 ++ NP HPYT+ALL +VP + + ++QR LKGE+PSP++ P GCRF RC + Sbjct: 245 LYANPRHPYTKALLSAVPVASVEAEAKRQRIV-LKGEVPSPLNPPSGCRFHPRCAQATQR 303 Query: 302 CFEKEPELTEVEKNHFVSCHL 322 C ++P L E V+CHL Sbjct: 304 CRVEDPVLRERGDGQMVACHL 324 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: 334 Number of extensions: 12 Number of successful extensions: 3 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: 329 Length adjustment: 28 Effective length of query: 300 Effective length of database: 301 Effective search space: 90300 Effective search space used: 90300 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