Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate Echvi_2909 Echvi_2909 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::P48243 (242 letters) >FitnessBrowser__Cola:Echvi_2909 Length = 218 Score = 150 bits (378), Expect = 3e-41 Identities = 86/220 (39%), Positives = 133/220 (60%), Gaps = 5/220 (2%) Query: 1 MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60 M++ G+ KY+GD H L +D+EI G++V ++G SG+GKSTL + L+ ++G + I Sbjct: 1 MLRAKGIHKYYGDLHVLKGVDVEIAAGEIVSIVGASGAGKSTLLHILGTLDDADKGLVSI 60 Query: 61 DGKVLPE-EGKGLANLR-ADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEKLAM 118 D K L +G LA R +VG +FQ NL P T ++N+ + + +K +K EK A Sbjct: 61 DDKSLTALKGDKLAAYRNQEVGFIFQFHNLLPEFTAEENIIIPGLIAKKDEKYLTEK-AK 119 Query: 119 SLLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEVLDV 178 L +GI ++ P++LSGG+QQRVA+ARAL +PKI+ DEP+ LD + + ++ Sbjct: 120 ELARLLGIMDRLGHKPSELSGGEQQRVAVARALINDPKIIFADEPSGNLDTQSAESLHEL 179 Query: 179 MASLA-KEGMTMVCVTHEMGFARKAADRVLFMADGLIVED 217 +L + G + V VTH A + ADR+L M DG+IV + Sbjct: 180 FFTLRDRFGQSFVIVTHNQQLA-QMADRMLTMQDGVIVSE 218 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: 136 Number of extensions: 12 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: 218 Length adjustment: 23 Effective length of query: 219 Effective length of database: 195 Effective search space: 42705 Effective search space used: 42705 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