Align Xanthosine permease; Xanthosine transporter (characterized)
to candidate WP_017260342.1 B176_RS0118540 nucleoside permease
Query= SwissProt::P45562 (418 letters) >NCBI__GCF_000302595.1:WP_017260342.1 Length = 409 Score = 229 bits (583), Expect = 1e-64 Identities = 133/410 (32%), Positives = 226/410 (55%), Gaps = 25/410 (6%) Query: 6 RLKVMSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKGIAAIIMPGIMGIIADKW 65 +L +M FL++F+WG+W VTLG+++ L+ TGA +S++ AII P I+G+IAD++ Sbjct: 8 KLSLMMFLEFFVWGAWFVTLGTFLNANLNATGAQTAAAFSTQSFGAIIAPFIIGLIADRY 67 Query: 66 LRAERAYMLCHLVCAGVLFYAASVTDPDMMFWVMLVNAMAFMPTIALSNSVSYSCLAQAG 125 AE+ + HL+ A ++++ ++ + + +L +AFMPT+AL NS+S++ + Sbjct: 68 FNAEKILGILHLIGALLMYFMFKASNFEDFYPYVLGYMIAFMPTLALVNSISFNQMN--- 124 Query: 126 LDPVTAFPPIRVFGTVGFIVAMWAVS-LLHLELSSL--------QLYIASGASLLLSAYA 176 DP F IRV+GTVG+I A +S H + ++ +A SL+L ++ Sbjct: 125 -DPEKEFSTIRVWGTVGWIAAGLTISYFFHWDSATSISSGFLKNTFAMAGIGSLILGVFS 183 Query: 177 LTLPKI-PVAEKKATTSLASKLGLDAFVLFKNPRMAIFFLFAMMLGAVLQITNVFGNPFL 235 LP P A K +L+ LGL+A L K+ IFF+ ++++ L NPFL Sbjct: 184 FALPLTPPKAIKGEKVTLSDILGLEALKLLKSKDFLIFFISSVLICIPLAFYYQNANPFL 243 Query: 236 HDFARNPEFADSFVVKYPSILLSVSQMAEVGFILTIPFFLKRFGIKTVMLMSMVAWTLRF 295 ++ P+ +++ Q++EV F+L +P F K+FG K +L+ M+AW R+ Sbjct: 244 SGIG----------LENPTGKMTLGQISEVLFMLLLPVFFKKFGFKITLLLGMLAWVARY 293 Query: 296 GFFAYGDPSTTGFILLLLSMIVYGCAFDFFNISGSVFVEQEVDSSIRASAQGLFMTMVNG 355 FAYG+ F +LL + ++G +DFF +SG ++ R++AQGL G Sbjct: 294 LLFAYGNAGELTF-MLLTGIALHGICYDFFFVSGQIYTNARAGEKNRSAAQGLITLATYG 352 Query: 356 VGAWVGSILSGMAVDYFSVDGVKDWQTIWLVFAGYALFLAVIFFFGFKYN 405 VG +G ++G+ D + V+G+ +W+ +WL+ AG A + V+F F N Sbjct: 353 VGMLIGFWVAGLITDTYQVNGIINWKMVWLIPAGIAAAVLVLFALLFSEN 402 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: 514 Number of extensions: 26 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: 409 Length adjustment: 31 Effective length of query: 387 Effective length of database: 378 Effective search space: 146286 Effective search space used: 146286 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 24 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