Align Xanthosine permease; Xanthosine transporter (characterized)
to candidate N515DRAFT_1323 N515DRAFT_1323 nucleoside transporter
Query= SwissProt::P45562 (418 letters) >FitnessBrowser__Dyella79:N515DRAFT_1323 Length = 401 Score = 239 bits (609), Expect = 1e-67 Identities = 131/399 (32%), Positives = 225/399 (56%), Gaps = 16/399 (4%) Query: 6 RLKVMSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKGIAAIIMPGIMGIIADKW 65 RL++M +Y IWG+W VT+G+++ TLHF+G +G + + I A+I P +G++AD+ Sbjct: 4 RLRLMMLFEYAIWGAWYVTVGTWLGKTLHFSGQEIGAIAGTTAIGAMISPLFVGLLADRL 63 Query: 66 LRAERAYMLCHLVCAGVLFYAASVTDPDMMFWVMLVNAMAFMPTIALSNSVSYSCLAQAG 125 R H++ A +L +AA + +++ +L ++ +MPT+AL+ S++ + Sbjct: 64 FDTRRVLAALHVLGAVLLMFAARQSSFPLLYGTLLAYSLCYMPTLALTTSLAMRHIR--- 120 Query: 126 LDPVTAFPPIRVFGTVGFIVAMWAVSLLHLELSSLQLYIASGASLLLSAYALTLPKIPVA 185 DP F IRV GT+G+IV V +E ++ L +A+G S++ + Y LTLP P Sbjct: 121 -DPQEEFGGIRVLGTIGWIVVGLIVGAWGVEATATPLQLAAGLSVVTALYCLTLPPTPPL 179 Query: 186 EKKATTSLASKLGLDAFVLFKNPRMAIFFLFAMMLGAVLQITNVFGNPFLHDFARNPEFA 245 + L L L++ L ++ MA+F L + ++ LQ F N FL++ Sbjct: 180 ARNQRFELRHALPLESLHLLRDRSMAVFALASFLICIPLQFYYAFTNLFLNEVG------ 233 Query: 246 DSFVVKYPSILLSVSQMAEVGFILTIPFFLKRFGIKTVMLMSMVAWTLRFGFFAYGDPST 305 V + ++ QM+E+ +L IP+F +R G+K ++ + M+AW LR+ FA+G P Sbjct: 234 ----VVNAAGKMTGGQMSEILCMLLIPWFFRRLGVKYMLAVGMLAWVLRYVLFAFGAPGD 289 Query: 306 TGFILLLLSMIVYGCAFDFFNISGSVFVEQEVDSSIRASAQGLFMTMVNGVGAWVGSILS 365 + +L L ++++G FDFF + G +++++E S++RA+ QGL + G+G +VGS LS Sbjct: 290 LMW-MLWLGIVLHGICFDFFFVVGQIYIDREAPSALRAATQGLITFLTYGLGMFVGSWLS 348 Query: 366 GMAVD-YFSVDGVKDWQTIWLVFAGYALFLAVIFFFGFK 403 G+ VD Y DW++IWL+ G A + V+F FK Sbjct: 349 GVVVDTYAGAQNAHDWRSIWLIAGGCAAAVLVLFVLAFK 387 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: 501 Number of extensions: 22 Number of successful extensions: 6 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: 401 Length adjustment: 31 Effective length of query: 387 Effective length of database: 370 Effective search space: 143190 Effective search space used: 143190 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 Apr 09 2024. 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