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 Dsui_0414 Dsui_0414 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__PS:Dsui_0414 Length = 352 Score = 272 bits (696), Expect = 8e-78 Identities = 138/331 (41%), Positives = 213/331 (64%), Gaps = 15/331 (4%) Query: 2 PFDQGGIKMKPLLQTVDLKKYFP-------QGKRILKAVDGISIEIKEGETLGLVGESGC 54 P D GG +PLL DLKK+FP + ++ + AVDG++ + +G+TLG+VGESGC Sbjct: 11 PHDMGG-PAQPLLIVRDLKKHFPVRSSPLDRERKFVHAVDGVNFSVPKGKTLGIVGESGC 69 Query: 55 GKSTLGRTILKLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVG 114 GKST R + +L+ D G++ F+G+ + +K +R+ +Q++FQD SLNP++T+ Sbjct: 70 GKSTTARLVARLMPADAGELIFDGEGVEEFRGLRLKEFRRNLQMVFQDSFASLNPRLTIA 129 Query: 115 RIIEDPLIIHKIGTKKERRKRVEELLDMVGIG-REFINSFPHEFSGGQQQRIGIARALAL 173 I +H I + + ELLD VG+ F +PHE SGGQ+QR+ IARALA Sbjct: 130 ETIAYGPRVHGIARADHQAR---ELLDRVGLDPSHFAGRYPHELSGGQRQRVNIARALAF 186 Query: 174 NPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLG 233 +P+ ++ DE V+ALD S+QAQ+++LL+E++ + ++YLFI+H+L VV ++S V VMYLG Sbjct: 187 DPRLVILDEAVAALDKSVQAQVLNLLQELKAERQLTYLFISHDLHVVHYLSDYVMVMYLG 246 Query: 234 KIVEYGDVDKIFLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQT 293 +++E G V++I+ P HPYTRALL +VP + + + Q L G+ P+PI+ P GCRF+ Sbjct: 247 QVIESGPVERIYGQPAHPYTRALLSAVPSMDPEHRTQA-SPLAGDPPNPINPPSGCRFRD 305 Query: 294 RCTEKKAICFEKEPELTEVEKN--HFVSCHL 322 RC A+C P L ++ ++ H +CHL Sbjct: 306 RCPHAHAVCASATPALRDMGRHSEHLAACHL 336 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: 348 Number of extensions: 18 Number of successful extensions: 4 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: 352 Length adjustment: 28 Effective length of query: 300 Effective length of database: 324 Effective search space: 97200 Effective search space used: 97200 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