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 8501090 DvMF_1826 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Miya:8501090 Length = 333 Score = 225 bits (573), Expect = 1e-63 Identities = 129/332 (38%), Positives = 187/332 (56%), Gaps = 18/332 (5%) Query: 10 MKPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRP 69 M+PLL +L F L AV+ +S + +GE LGLVGESG GKS G +IL L+ Sbjct: 1 MQPLLDVSNLTVKFALRDTALTAVNDVSFTLAKGERLGLVGESGAGKSVTGFSILNLVSK 60 Query: 70 DG----GKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124 G G + FEGKD+T + + ++ R ++ +IFQDP+ +LNP +TVG + + ++ H Sbjct: 61 PGFIAGGSVLFEGKDLTRADAETLRDIRGNRISMIFQDPMMTLNPVLTVGTQMIETILAH 120 Query: 125 KIGTKKERRKRVEELLDMVGIG--REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDE 182 K T+KE + L V I + +PHEFSGG +QRI IA AL +P I+ DE Sbjct: 121 KKVTRKEAEAIALDKLRKVYIPSPERRLAQYPHEFSGGMRQRIVIAIALLTSPSLIIADE 180 Query: 183 PVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVD 242 P +ALDV+IQA+I+DLL E+ Q + + I H+L VV ++ K+AVMY G IVE GD Sbjct: 181 PTTALDVTIQAEIMDLLLELCQSEDMGLILITHDLGVVSQVTQKIAVMYAGGIVEMGDTA 240 Query: 243 KIFLNPIHPYTRALLKSVPK-----------IPWDGQKQRFYSLKGELPSPIDLPKGCRF 291 + P+HPYTR LL ++P+ + ++R + G +PS D+P+GC F Sbjct: 241 MVVGEPLHPYTRGLLGALPQCADKADCGLEDVAAPRVRRRLNQIPGSMPSLSDVPRGCPF 300 Query: 292 QTRCTEKKAICFEKEPELTEVEKNHFVSCHLV 323 RC + +C P L +CH+V Sbjct: 301 NNRCELCETVCTTTRPLLEVKSDGRMAACHMV 332 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: 280 Number of extensions: 10 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: 333 Length adjustment: 28 Effective length of query: 300 Effective length of database: 305 Effective search space: 91500 Effective search space used: 91500 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