Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate N515DRAFT_1821 N515DRAFT_1821 putative ABC transport system ATP-binding protein
Query= TCDB::P48243 (242 letters) >FitnessBrowser__Dyella79:N515DRAFT_1821 Length = 238 Score = 165 bits (418), Expect = 7e-46 Identities = 95/229 (41%), Positives = 142/229 (62%), Gaps = 8/229 (3%) Query: 1 MIKMTGVQKYFG----DFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEG 56 M+KMT + K + + +AL D ++++ G+ V V GPSGSGK+T LET G Sbjct: 1 MLKMTHLSKVYRTEVVETYALRDFNIDVKEGEFVAVTGPSGSGKTTFLTIAGLLETFTGG 60 Query: 57 TIEIDG-KVLPEEGKGLANLRAD-VGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAE 114 +DG +V + +R + +G +FQ+FNL P L + DNV + P++ R MK E + Sbjct: 61 EYHLDGVEVSNLNDNARSKIRNEKIGFIFQAFNLIPDLNVYDNVEV-PLRYRGMKALERK 119 Query: 115 KLAMSLLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNE 174 + M LERVG+A++A YPA+LSGGQQQRVAIARALA +P+++L DEPT LD +M Sbjct: 120 QRIMDALERVGLASRAKHYPAELSGGQQQRVAIARALAGSPRLLLADEPTGNLDTQMARG 179 Query: 175 VLDVMASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSF 223 V++++ + +EG T+V VTH+ A + A R + + DG +V+ E F Sbjct: 180 VMELLEEIHREGATIVMVTHDPELATR-AQRNVHVIDGQVVDLAEDPRF 227 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: 151 Number of extensions: 5 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: 242 Length of database: 238 Length adjustment: 23 Effective length of query: 219 Effective length of database: 215 Effective search space: 47085 Effective search space used: 47085 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