Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate Pf6N2E2_3404 Multi antimicrobial extrusion protein (Na(+)/drug antiporter), MATE family of MDR efflux pumps
Query= TCDB::P48245 (273 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3404 Length = 227 Score = 92.8 bits (229), Expect = 6e-24 Identities = 64/211 (30%), Positives = 105/211 (49%), Gaps = 3/211 (1%) Query: 22 WTTYILPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIPVLIL 81 W+ +L G + + ++ LA ++G L S L+ I+ RA+P+L L Sbjct: 15 WSARLLLGARVSAELSLTGFALAAMLGALLAWAMKSHSVWLKHAAVFFIQGMRAVPLLAL 74 Query: 82 MIFAYQMFAQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAIALGM 141 ++ Y + S A A GL + + +AEILR G+ SL +GQ+EAAIA G+ Sbjct: 75 LLALYFTLPSLGLTLSGYWAGA---IGLGLQGSAYVAEILRGGLDSLHRGQREAAIATGL 131 Query: 142 SSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSASVNRNYLA 201 + Q +++ PQA+ MLP L++ V LKDS+L I E++ + AS + + Sbjct: 132 TPLQAFTAVIFPQAIRGMLPPLLNAYVSILKDSSLCALIATDELMLAARAIASESFLPMH 191 Query: 202 ALFVVALIMIVLNFSLTALASRIERQLRAGR 232 +V L V+ F L+ L+ +E + GR Sbjct: 192 IFLLVGLFYFVIAFPLSLLSRALEARFSRGR 222 Lambda K H 0.323 0.136 0.395 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: 154 Number of extensions: 5 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: 273 Length of database: 227 Length adjustment: 24 Effective length of query: 249 Effective length of database: 203 Effective search space: 50547 Effective search space used: 50547 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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