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 Echvi_1095 Echvi_1095 nitrate transport ATP-binding subunits C and D
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Cola:Echvi_1095 Length = 272 Score = 108 bits (270), Expect = 1e-28 Identities = 76/235 (32%), Positives = 125/235 (53%), Gaps = 13/235 (5%) Query: 8 IKMKPLLQTVD-LKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKL 66 +K +P + D LKK +P K +D +++ I++GE + ++G SGCGKSTL I L Sbjct: 15 LKDQPEMLVCDQLKKVYPTPKGDYVVLDDLNLSIRKGEFVSIIGHSGCGKSTLLTMIAGL 74 Query: 67 LRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMT-VGRIIEDPLIIHK 125 GGKI +G + E P R ++FQ P SL P ++ + ++ + Sbjct: 75 NDISGGKIKVDGTPVI-----EAGPDRA---VVFQSP--SLLPWLSALDNVMIGVKQVFP 124 Query: 126 IGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVS 185 ++ +++ + LD VG+G +F + H S G QQR+GIARA AL PK ++ DEP Sbjct: 125 HASRAQKQDICKYYLDKVGLGADF-DKKAHSLSQGMQQRVGIARAFALKPKLLLLDEPFG 183 Query: 186 ALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGD 240 LD + ++ D+L EI Q+ I+ + I H++ ++ +V +M G + GD Sbjct: 184 MLDSLTRGELQDVLLEIWQREKITAVAITHDVDESIFLADRVIMMTSGPYAKIGD 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: 243 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: 272 Length adjustment: 27 Effective length of query: 301 Effective length of database: 245 Effective search space: 73745 Effective search space used: 73745 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: 48 (23.1 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