Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate WP_011383782.1 AMB_RS06945 phosphate ABC transporter ATP-binding protein
Query= TCDB::P48243 (242 letters) >NCBI__GCF_000009985.1:WP_011383782.1 Length = 259 Score = 154 bits (389), Expect = 2e-42 Identities = 92/246 (37%), Positives = 145/246 (58%), Gaps = 14/246 (5%) Query: 2 IKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEE-----G 56 I G+ ++G+ AL DIDL+IP G+V ++GPSG GKST R INR+ + + G Sbjct: 12 ISARGLNVHYGEKQALHDIDLDIPAGEVTALIGPSGCGKSTFLRCINRMNDMVDGAKVTG 71 Query: 57 TIEIDGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAE-- 114 ++ +DG + + + LRA VGMVFQ N FP +I DNV P ++ + + +AE Sbjct: 72 SLTLDGSDVYDRSLDVVQLRARVGMVFQKPNPFPK-SIYDNVAYGP-RIHGLARDQAELD 129 Query: 115 KLAMSLLERVGIANQADKYPAQ----LSGGQQQRVAIARALAMNPKIMLFDEPTSALDPE 170 ++ M+ LE+ G+ + + ++ LSGGQQQR+ IARA+A+ P+++L DEP SALDP Sbjct: 130 EIVMNSLEKAGLLAEVESRLSESGTGLSGGQQQRLCIARAIAVAPEVILMDEPCSALDPI 189 Query: 171 MVNEVLDVMASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSD 230 +V +++ L ++ T+V VTH M A + + R F G ++E + FTNPK Sbjct: 190 ATAKVEELIDEL-RDNYTIVIVTHSMQQAARVSQRTAFFHLGKLIEVGGTEEIFTNPKEP 248 Query: 231 RAKDFL 236 + ++ Sbjct: 249 LTQGYI 254 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: 149 Number of extensions: 10 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: 259 Length adjustment: 24 Effective length of query: 218 Effective length of database: 235 Effective search space: 51230 Effective search space used: 51230 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: 46 (22.3 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