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 WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >NCBI__GCF_000017185.1:WP_011974043.1 Length = 238 Score = 132 bits (331), Expect = 1e-35 Identities = 79/232 (34%), Positives = 137/232 (59%), Gaps = 6/232 (2%) Query: 8 IKMKPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLL 67 I+ K L++ ++ K + G+ + GI+++IKEGE + ++G SGCGKSTL + L Sbjct: 12 IEKKELIEAKNIWKIYGGGEAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLD 71 Query: 68 RPDGGKIFFEGKDITNLNDKEMKPYRKKMQ-IIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126 P+ G ++ +GK T ++ + +R+K+ IFQ +L +T +E PL++ + Sbjct: 72 VPNKGMVYIKGKKTTMFSENDRAVFRRKISGFIFQQ--FNLINTLTALENVELPLVLDE- 128 Query: 127 GTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSA 186 K R K+ ++LL ++ +G N +P++ SGGQQQR+ IARAL+ NPK I DEP Sbjct: 129 KNKNYRIKKAKKLLKIINLGHRE-NYYPNQLSGGQQQRVAIARALSNNPKIIFADEPTGN 187 Query: 187 LDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEY 238 LD +++D+L+E+ +K GI+ + + H ++ S ++ M G+IVE+ Sbjct: 188 LDSKNSREVMDILKELNEKEGITVIMVTHEPEFAKYAS-RIINMKDGEIVEH 238 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: 190 Number of extensions: 11 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: 238 Length adjustment: 26 Effective length of query: 302 Effective length of database: 212 Effective search space: 64024 Effective search space used: 64024 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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