Align ABC transporter for D-Glucosamine Hydrochloride, permease component 2 (characterized)
to candidate Pf6N2E2_3404 Multi antimicrobial extrusion protein (Na(+)/drug antiporter), MATE family of MDR efflux pumps
Query= reanno::pseudo6_N2E2:Pf6N2E2_2052 (220 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3404 Length = 227 Score = 131 bits (329), Expect = 1e-35 Identities = 76/208 (36%), Positives = 114/208 (54%), Gaps = 1/208 (0%) Query: 11 WRDFDT-LLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVTVIRNTPI 69 W D+ LL G + L+L A+ ++G +A+A+ S L+ A ++ +R P+ Sbjct: 12 WSDWSARLLLGARVSAELSLTGFALAAMLGALLAWAMKSHSVWLKHAAVFFIQGMRAVPL 71 Query: 70 LVLILLIYFALPSLGIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQREAGLAIGL 129 L L+L +YF LPSLG+ L + I L L AY+ E+ RGGL S+H+GQREA +A GL Sbjct: 72 LALLLALYFTLPSLGLTLSGYWAGAIGLGLQGSAYVAEILRGGLDSLHRGQREAAIATGL 131 Query: 130 GEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESYRVIE 189 Q V P +R +LP L N ++S+ KD+SL A IA EL AR I ES+ + Sbjct: 132 TPLQAFTAVIFPQAIRGMLPPLLNAYVSILKDSSLCALIATDELMLAARAIASESFLPMH 191 Query: 190 TWLVTTALYVAACYLIAMLLRYFEQRLA 217 +L+ Y + +++L R E R + Sbjct: 192 IFLLVGLFYFVIAFPLSLLSRALEARFS 219 Lambda K H 0.330 0.142 0.414 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: 139 Number of extensions: 4 Number of successful extensions: 1 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: 220 Length of database: 227 Length adjustment: 22 Effective length of query: 198 Effective length of database: 205 Effective search space: 40590 Effective search space used: 40590 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: 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