Align TM1748, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate CA265_RS18010 CA265_RS18010 peptide transporter
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__Pedo557:CA265_RS18010 Length = 380 Score = 192 bits (488), Expect = 1e-53 Identities = 98/222 (44%), Positives = 146/222 (65%), Gaps = 1/222 (0%) Query: 67 FIFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIV 126 +I GTD GRDL SR++ +R + +G + + L IG LGA+AG+ GG +D I + Sbjct: 155 YILGTDIYGRDLLSRLILGIRVSLSVGLMAVLISLFIGVSLGAIAGYFGGRVDAAISWFM 214 Query: 127 DIMFAFPTFLFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKA 186 +++++ P+ L + + ALG+G + IF+A+GL+ W +ARLVRGQV+ LK EFVEAA+A Sbjct: 215 NVVWSLPSLLLVIAISFALGKGFWQIFIAVGLSTWVDVARLVRGQVMALKEVEFVEAARA 274 Query: 187 AGASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEG 246 G ST I KHILPN+ GPILV + A++ E+GL+ +G G +PPMPSWG++I E Sbjct: 275 LGFSTSRTIIKHILPNIAGPILVVASSNFASAILLETGLSFLGFGAQPPMPSWGSMIKEH 334 Query: 247 IG-MMMAFPHLLIFPAVTFAFTLISFTFLADGLRDAFNPRSE 287 G ++M +L + P + FT+ +F LA GLRDAF+ + + Sbjct: 335 YGYIIMDAAYLAVLPGLAIMFTVYAFNVLAIGLRDAFDVKGQ 376 Score = 37.4 bits (85), Expect = 5e-07 Identities = 17/35 (48%), Positives = 23/35 (65%) Query: 14 KAFWLRFKKNKMAVIGGVFVLILIALAILAPYIAP 48 K WL+FK+NK A G VF+L+L+ + IL I P Sbjct: 7 KKVWLKFKRNKFAFGGLVFILLLMVMGILGYLIMP 41 Lambda K H 0.331 0.147 0.457 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: 301 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 289 Length of database: 380 Length adjustment: 28 Effective length of query: 261 Effective length of database: 352 Effective search space: 91872 Effective search space used: 91872 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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