Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate Ga0059261_3653 Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1)
Query= TCDB::P48243 (242 letters) >FitnessBrowser__Korea:Ga0059261_3653 Length = 276 Score = 145 bits (367), Expect = 6e-40 Identities = 88/241 (36%), Positives = 139/241 (57%), Gaps = 12/241 (4%) Query: 6 GVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRL-ETIE----EGTIEI 60 GV ++G+ A+ D+ +++ V +GPSG GKST RT+NR+ +T+ EG I + Sbjct: 33 GVNVFYGEKQAIRDVSIDVDMENVTAFIGPSGCGKSTFLRTLNRMNDTVASARVEGEITL 92 Query: 61 DGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAP-IKVRKMKKSEAEKLAMS 119 DG+ + ++ + LRA VGMVFQ N FP +I +NV P I K + +++ Sbjct: 93 DGENIYDKSMDVVQLRARVGMVFQKPNPFPK-SIYENVAYGPRIHGLARAKGDMDQIVER 151 Query: 120 LLERVG----IANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEV 175 L+R G + ++ + LSGGQQQR+ IARA+A++P+++L DEP SALDP ++ Sbjct: 152 SLKRAGLWEEVKDRLNDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDPIATAKI 211 Query: 176 LDVMASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDF 235 +++ L + +V VTH M A + + R F G +VE E D FT P+ +R KD+ Sbjct: 212 EELIHEL-RGRYAIVIVTHNMQQAARVSQRTAFFHLGTLVEYGETDQIFTAPRQERTKDY 270 Query: 236 L 236 + Sbjct: 271 I 271 Lambda K H 0.319 0.135 0.379 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: 145 Number of extensions: 7 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: 242 Length of database: 276 Length adjustment: 24 Effective length of query: 218 Effective length of database: 252 Effective search space: 54936 Effective search space used: 54936 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: 47 (22.7 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