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 Ga0059261_3653 Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Korea:Ga0059261_3653 Length = 276 Score = 108 bits (270), Expect = 2e-28 Identities = 75/234 (32%), Positives = 121/234 (51%), Gaps = 17/234 (7%) Query: 31 KAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG-----GKIFFEGKDITNLN 85 +A+ +SI++ +G SGCGKST RT+ ++ G+I +G+ N+ Sbjct: 42 QAIRDVSIDVDMENVTAFIGPSGCGKSTFLRTLNRMNDTVASARVEGEITLDGE---NIY 98 Query: 86 DKEMK--PYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMV 143 DK M R ++ ++FQ P + P+ + P I K + + VE L Sbjct: 99 DKSMDVVQLRARVGMVFQKP--NPFPKSIYENVAYGPRIHGLARAKGDMDQIVERSLKRA 156 Query: 144 GIGREF---INSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLE 200 G+ E +N SGGQQQR+ IARA+A++P+ I+ DEP SALD A+I +L+ Sbjct: 157 GLWEEVKDRLNDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDPIATAKIEELIH 216 Query: 201 EIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTR 254 E++ + I + + HN+ +S + A +LG +VEYG+ D+IF P T+ Sbjct: 217 ELRGRYAI--VIVTHNMQQAARVSQRTAFFHLGTLVEYGETDQIFTAPRQERTK 268 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: 211 Number of extensions: 11 Number of successful extensions: 3 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: 276 Length adjustment: 27 Effective length of query: 301 Effective length of database: 249 Effective search space: 74949 Effective search space used: 74949 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