Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate Ga0059261_1321 Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::P48243 (242 letters) >FitnessBrowser__Korea:Ga0059261_1321 Length = 238 Score = 135 bits (339), Expect = 9e-37 Identities = 92/227 (40%), Positives = 127/227 (55%), Gaps = 12/227 (5%) Query: 1 MIKMTGVQKYFGD----FHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEG 56 +I++ + K FG+ F AL +DL+I V V+GPSGSGKST + L+ G Sbjct: 7 IIRLRNITKVFGEGATAFQALKGVDLDIAERDFVAVMGPSGSGKSTTMNILGCLDVPTSG 66 Query: 57 TIEIDG---KVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEA 113 G + L + + L R +G VFQ FNL +NV L P+ R K Sbjct: 67 EFLFKGVYIETLDRDQRALVR-RKYLGFVFQGFNLLSRTNALENVEL-PLLYRGEDKKVR 124 Query: 114 EKLAMSLLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVN 173 +L M+ LE+VG+A+ D PA+LSGGQ QRVAIARA+ +P ++L DEPT LD Sbjct: 125 HELGMAALEKVGLADWWDHTPAELSGGQPQRVAIARAIVTSPAVLLADEPTGNLDSARSV 184 Query: 174 EVLDVMASLAKE-GMTMVCVTHEMGFARKAADRVLFMADGLIVEDTE 219 E+++++ SL K+ G+T++ VTHE A A V F DGL VE TE Sbjct: 185 EIMELLTSLNKDSGITVLMVTHEPDMAAFARTIVHF-KDGL-VERTE 229 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: 6 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