Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate WP_089136612.1 CES79_RS05995 amino acid ABC transporter ATP-binding protein
Query= TCDB::P48243 (242 letters) >NCBI__GCF_002217945.1:WP_089136612.1 Length = 246 Score = 247 bits (630), Expect = 2e-70 Identities = 125/238 (52%), Positives = 176/238 (73%), Gaps = 3/238 (1%) Query: 1 MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60 +IK+ ++KY+ H L DI+ I +G+VV +LGPSGSGKSTL R +N LE + GT+ Sbjct: 5 VIKVEHLEKYYQKDHILHDINFSIDQGEVVALLGPSGSGKSTLIRCLNGLEPYQNGTVSF 64 Query: 61 DG-KVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEKLAMS 119 +G +V+P E K LR +GMVFQS++LFP+LT+ DN+ L P+KV+K + A+ A Sbjct: 65 NGDQVVPTE-KNWQKLRQKIGMVFQSYDLFPNLTVLDNILLGPVKVQKQSRETAKAAAEK 123 Query: 120 LLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEVLDVM 179 LL++VG+ + YP QLSGGQ+QR+AI RALA+NP++MLFDE T++LDPEMV VL+++ Sbjct: 124 LLDQVGLREYENVYPRQLSGGQKQRIAIVRALALNPELMLFDEVTASLDPEMVRGVLNII 183 Query: 180 ASLAKEG-MTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDFL 236 + LA++ MTM+ VTHEM FA++ ADRVLF+ DG I+E T+ D FF P++DRAK+FL Sbjct: 184 SKLAQDSDMTMIVVTHEMNFAQQIADRVLFLEDGKILEQTKGDQFFKQPQTDRAKEFL 241 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: 176 Number of extensions: 3 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: 242 Length of database: 246 Length adjustment: 24 Effective length of query: 218 Effective length of database: 222 Effective search space: 48396 Effective search space used: 48396 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 24 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