Align ABC transporter for D-glucosamine, permease component 2 (characterized)
to candidate Pf6N2E2_3404 Multi antimicrobial extrusion protein (Na(+)/drug antiporter), MATE family of MDR efflux pumps
Query= reanno::pseudo3_N2E3:AO353_21720 (220 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3404 Length = 227 Score = 132 bits (332), Expect = 5e-36 Identities = 70/205 (34%), Positives = 118/205 (57%), Gaps = 2/205 (0%) Query: 12 WVARDTLWSGFLTSVQCSVLAIMLGTLIGIVAGLVLTYGTLWMRAPFRFYVDLIRGTPVF 71 W AR L G S + S+ L ++G + + ++W++ F++ +R P+ Sbjct: 15 WSAR--LLLGARVSAELSLTGFALAAMLGALLAWAMKSHSVWLKHAAVFFIQGMRAVPLL 72 Query: 72 VLVLACFYMAPALGWQIDAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASKAIGLT 131 L+LA ++ P+LG + + AG +GL L ++VAEI+RG L +L RGQ EA+ A GLT Sbjct: 73 ALLLALYFTLPSLGLTLSGYWAGAIGLGLQGSAYVAEILRGGLDSLHRGQREAAIATGLT 132 Query: 132 FYQALAYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEF 191 QA V+ PQA+R +LP +N+ I+K S+L ++I EL+L+ + I + +F+ + Sbjct: 133 PLQAFTAVIFPQAIRGMLPPLLNAYVSILKDSSLCALIATDELMLAARAIASESFLPMHI 192 Query: 192 YLFAGFLFFIINYAIELLGRHIEKR 216 +L G +F+I + + LL R +E R Sbjct: 193 FLLVGLFYFVIAFPLSLLSRALEAR 217 Lambda K H 0.330 0.142 0.440 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: 147 Number of extensions: 8 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 (21.9 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