Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate Pf6N2E2_3404 Multi antimicrobial extrusion protein (Na(+)/drug antiporter), MATE family of MDR efflux pumps
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3404 Length = 227 Score = 91.3 bits (225), Expect = 3e-23 Identities = 72/225 (32%), Positives = 116/225 (51%), Gaps = 17/225 (7%) Query: 217 PEVDSDQFGGFLL----ALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRG 272 PE SD LL + + +T ++ LG LLA +S + +K +V I+ +R Sbjct: 9 PEYWSDWSARLLLGARVSAELSLTGFALAAMLGALLAWAMKSHSVWLKHAAVFFIQGMRA 68 Query: 273 VPLITLLFTASLLLQYFLPP-GTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYE 331 VPL+ LL L L + LP G I + L +AY+AE++RGGL +L RGQ E Sbjct: 69 VPLLALL----LALYFTLPSLGLTLSGYWAGAIGLGLQGSAYVAEILRGGLDSLHRGQRE 124 Query: 332 AADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVR 391 AA A GL QA +I PQA++ +P ++++++ + KD++L A + D L + + Sbjct: 125 AAIATGLTPLQAFTAVIFPQAIRGMLPPLLNAYVSILKDSSLCALIAT-DELMLAARAIA 183 Query: 392 SDMAWKGTYWEPYIF--VALIFFLFNFSMSRYSMYLERKLKRDHR 434 S+ ++ +IF V L +F+ F +S S LE + R + Sbjct: 184 SE-----SFLPMHIFLLVGLFYFVIAFPLSLLSRALEARFSRGRK 223 Lambda K H 0.329 0.143 0.457 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: 273 Number of extensions: 19 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: 434 Length of database: 227 Length adjustment: 27 Effective length of query: 407 Effective length of database: 200 Effective search space: 81400 Effective search space used: 81400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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