Align Xanthosine permease; Xanthosine transporter (characterized)
to candidate Pf6N2E2_326 Putative nucleoside transporter YegT
Query= SwissProt::P45562 (418 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_326 Length = 410 Score = 259 bits (661), Expect = 1e-73 Identities = 147/408 (36%), Positives = 233/408 (57%), Gaps = 25/408 (6%) Query: 6 RLKVMSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKGIAAIIMPGIMGIIADKW 65 RL VM FLQ+FIWG W VTLG+++ +TL +G +GM +S++ AII P ++G+IAD++ Sbjct: 7 RLSVMMFLQFFIWGGWFVTLGTFLSSTLGASGGQIGMAFSTQSWGAIIAPFVIGLIADRF 66 Query: 66 LRAERAYMLCHLVCAGVLFYAASVTDPDMMFWVMLVNAMAFMPTIALSNSVSYSCLAQAG 125 AER + HL+ A +L+ S D + + +LV + +MPT+AL NSV++ + Sbjct: 67 FNAERILAVLHLLGAVLLYQLYSAADFSVFYPYVLVYMVVYMPTLALVNSVAFRQMR--- 123 Query: 126 LDPVTAFPPIRVFGTVGFIVAMWAVSLLH-------LELSSLQ--LYIASGASLLLSAYA 176 DP F IRV+GT+G+IVA +S + + L+ +A+ ASL+L Y+ Sbjct: 124 -DPALEFSRIRVWGTIGWIVAGVVISFVFAWDSREAISAGGLRNTFLMAAVASLVLGLYS 182 Query: 177 LTLP-KIPVAEKKATTSLASKLGLDAFVLFKNPRMAIFFLFAMMLGAVLQITNVFGNPFL 235 TLP P+ E+ + LGLDA L K+ +FF+ ++++ L NPFL Sbjct: 183 FTLPATAPLKEQARAGGVRQLLGLDALGLLKDRSYLVFFIASILICIPLAFYYQNANPFL 242 Query: 236 HDFARNPEFADSFVVKYPSILLSVSQMAEVGFILTIPFFLKRFGIKTVMLMSMVAWTLRF 295 + + P+ +++ Q++EV F+L +P F++RFGIK +L+ M+AW LR+ Sbjct: 243 AETG----------MTNPTAKMAIGQVSEVLFMLLLPLFIQRFGIKLALLVGMLAWALRY 292 Query: 296 GFFAYGDPSTTGFILLLLSMIVYGCAFDFFNISGSVFVEQEVDSSIRASAQGLFMTMVNG 355 FAYG+ F +L + ++G +DFF +SG ++ + + R+SAQGL G Sbjct: 293 LLFAYGNNGDLAF-MLFTGIALHGICYDFFFVSGQIYTDAKAPERFRSSAQGLITLATYG 351 Query: 356 VGAWVGSILSGMAVDYFSVDGVKDWQTIWLVFAGYALFLAVIFFFGFK 403 VG +G ++G D+F V G DWQ+IWL AG+AL + + F F F+ Sbjct: 352 VGMLIGFWVAGQVTDHFVVAGGHDWQSIWLFPAGFALLVLLCFLFTFR 399 Lambda K H 0.330 0.141 0.435 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: 496 Number of extensions: 25 Number of successful extensions: 5 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: 418 Length of database: 410 Length adjustment: 31 Effective length of query: 387 Effective length of database: 379 Effective search space: 146673 Effective search space used: 146673 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: 50 (23.9 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