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_RS18190 RR42_RS18190 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Cup4G11:RR42_RS18190 Length = 354 Score = 273 bits (697), Expect = 6e-78 Identities = 132/296 (44%), Positives = 199/296 (67%), Gaps = 2/296 (0%) Query: 27 KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLND 86 + ++ AVD + + I+ GE +GLVGESGCGKSTLGR + L G + G D+ L Sbjct: 57 EEVVHAVDRVDLSIRAGEVVGLVGESGCGKSTLGRMAVGLHSLTEGSRLWRGVDLDRLPP 116 Query: 87 KEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGIG 146 ++ + + +Q+IFQDP SLNP++ V I+ + ++H + E+++ VE++L VG+ Sbjct: 117 EKKREKQLAIQMIFQDPYASLNPRLRVMDIVGEAPVVHGMVPASEQKRYVEDMLVRVGMD 176 Query: 147 REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKM 206 + FPH+FSGGQ+ RIGIARALA+ P+F+VCDE V+ALDVSIQAQ+++L ++Q + Sbjct: 177 PTVLRRFPHQFSGGQRARIGIARALAVKPEFLVCDESVAALDVSIQAQVLNLFMRLRQDL 236 Query: 207 GISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPKIPWD 266 ++YLFI+H+L VV+HIS +V +MYLG++VE + +F +P HPYT+ALL PK+ + Sbjct: 237 NLTYLFISHDLGVVKHISDRVVIMYLGRVVESAPAEDVFASPNHPYTQALLAEAPKL--E 294 Query: 267 GQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKNHFVSCHL 322 K+ F ++KGE+PSP++ P GC F RC C E++P L E+ F +CHL Sbjct: 295 VGKKTFVAIKGEIPSPLNPPPGCHFHPRCPHAMPRCREEQPLLKEIAPMRFSACHL 350 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: 364 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: 328 Length of database: 354 Length adjustment: 28 Effective length of query: 300 Effective length of database: 326 Effective search space: 97800 Effective search space used: 97800 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