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 3610414 Dshi_3795 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Dino:3610414 Length = 331 Score = 258 bits (659), Expect = 1e-73 Identities = 134/316 (42%), Positives = 205/316 (64%), Gaps = 10/316 (3%) Query: 13 LLQTVDLKKYFPQG-----KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLL 67 +L +L K+FP G +R+++AVD ++ E+ GETLG+VGESGCGKST R +++LL Sbjct: 10 VLSAHNLVKHFPLGGWGKNRRVVRAVDDVTFEVAPGETLGVVGESGCGKSTTARLLVQLL 69 Query: 68 RPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIG 127 D G++ F+G + +K +R+ +Q++FQD SLNP+M++ I +H + Sbjct: 70 GADSGEVRFQGHVAGT--EMPLKEFRRHVQMVFQDSYASLNPRMSMLDAIAFGPTVHGV- 126 Query: 128 TKKERRKRVEELLDMVGIG-REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSA 186 ++ E ++ +LLD VG+ F +PHE SGGQ+QR+ IARALA P+ IV DE VSA Sbjct: 127 SEAEAQRIARDLLDRVGLDPSRFGPRYPHELSGGQRQRVNIARALAFQPEVIVLDEAVSA 186 Query: 187 LDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFL 246 LD S++AQ+++LL +++++ ++Y+FI+H+L VV H+S +V VMYLG++ E G +++ Sbjct: 187 LDKSVEAQVLNLLMDLKRERNLTYVFISHDLNVVRHVSDRVMVMYLGEVAEIGPTAEMYA 246 Query: 247 NPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKE 306 +P HPYTRALL ++P + D ++ L G+ P+PID P GCRF TRC E C + Sbjct: 247 DPRHPYTRALLAAMPSLDPD-RRTTEAPLSGDPPNPIDPPSGCRFHTRCAEAFGACSAQR 305 Query: 307 PELTEVEKNHFVSCHL 322 P V H+ SCHL Sbjct: 306 PSNLRVGAGHYASCHL 321 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: 276 Number of extensions: 14 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: 331 Length adjustment: 28 Effective length of query: 300 Effective length of database: 303 Effective search space: 90900 Effective search space used: 90900 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