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 RR42_RS07940 RR42_RS07940 ABC transporter permease
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__Cup4G11:RR42_RS07940 Length = 295 Score = 185 bits (470), Expect = 9e-52 Identities = 99/274 (36%), Positives = 152/274 (55%), Gaps = 1/274 (0%) Query: 9 SIGYWKAFWLRFKKNKMAVIGGVFVLILIALAILAPYIAPY-PYDEPHYIRAFEGPSKDF 67 S GYW R +NK+A++ + VL L+ +AI AP + P PY R ++ + Sbjct: 17 SPGYWATVGKRLLRNKVAMLAALIVLALVLMAIFAPVLMPADPYAASIMKRLKPIGTEHY 76 Query: 68 IFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVD 127 + GTD LGRDL SR++ R + +G + +IG LG VAG+ GGW + IM +VD Sbjct: 77 LLGTDELGRDLLSRLMLGARLSLFMGITPVLIAFVIGSALGIVAGYAGGWTNTVIMRLVD 136 Query: 128 IMFAFPTFLFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAA 187 I++AFP+ L + L LG G+ L++ + + R+ ++N EFV+AA+A+ Sbjct: 137 ILYAFPSVLLAIALSGTLGAGVGNALLSLTIVFVPQIVRVAESVTTQVRNREFVDAARAS 196 Query: 188 GASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGI 247 GAS+ I+R H+L N++GPI V + +M+ SGL+ +G+GV+PP P WG ++ Sbjct: 197 GASSLTIVRAHVLNNVLGPIFVYATSLISVSMILASGLSFLGLGVKPPEPEWGLMLNTLR 256 Query: 248 GMMMAFPHLLIFPAVTFAFTLISFTFLADGLRDA 281 + P + P T ISF LADG+R A Sbjct: 257 TAIYTQPLVAALPGAMIFLTSISFNLLADGIRSA 290 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: 188 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: 289 Length of database: 295 Length adjustment: 26 Effective length of query: 263 Effective length of database: 269 Effective search space: 70747 Effective search space used: 70747 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: 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