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 BWI76_RS07535 BWI76_RS07535 dipeptide/oligopeptide/nickel ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Koxy:BWI76_RS07535 Length = 347 Score = 266 bits (679), Expect = 7e-76 Identities = 140/323 (43%), Positives = 213/323 (65%), Gaps = 11/323 (3%) Query: 4 DQGGIKMKPLLQTVDLKKYFPQG----KRILKAVDGISIEIKEGETLGLVGESGCGKSTL 59 D GG +PLL+ +L K+FP G + +++AVD +S + +GETLG+VGESGCGKST Sbjct: 8 DLGG-PAQPLLKVNNLLKHFPAGGGKAREVVQAVDDVSFAVIKGETLGVVGESGCGKSTT 66 Query: 60 GRTILKLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIED 119 R +++LL+ D G++ F+G ++ + + MK YR+++Q++FQD SLNP+MT+ I Sbjct: 67 ARLLMQLLKQDSGELIFDGLEVGS-SRLPMKAYRRQVQMVFQDSYASLNPRMTMEESIAF 125 Query: 120 PLIIHKIGTKKERRKRVEELLDMVGIGRE-FINSFPHEFSGGQQQRIGIARALALNPKFI 178 +H + K E + LL VG+ E F + +PH SGGQ+QR+ IARALA+ P+ + Sbjct: 126 GQRVHGVSAK-EASEYARYLLAHVGLEPERFAHRYPHALSGGQRQRVNIARALAMKPRLV 184 Query: 179 VCDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEY 238 + DE VSALD S++AQ++ LL+E+++ + ++Y+FI+H+L VV +S ++ VMYLG++VE Sbjct: 185 ILDEAVSALDKSVEAQVLQLLQELKRTLALTYVFISHDLHVVRWLSDRILVMYLGEVVEI 244 Query: 239 GDVDKIFLNPIHPYTRALLKSVPKIPWDGQKQRFYS-LKGELPSPIDLPKGCRFQTRCTE 297 G +++F HPYTRALL S+P + D + S L G+ PSPI P GCRF TRC Sbjct: 245 GPAEQLFTASAHPYTRALLSSMPSM--DPHNRTLTSALNGDPPSPISPPSGCRFHTRCPH 302 Query: 298 KKAICFEKEPELTEVEKNHFVSC 320 +A+C E +P L V + H +C Sbjct: 303 ARAVCAEVKPTLQSVGEGHQSAC 325 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: 318 Number of extensions: 18 Number of successful extensions: 5 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: 347 Length adjustment: 28 Effective length of query: 300 Effective length of database: 319 Effective search space: 95700 Effective search space used: 95700 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