Align Xanthosine permease; Xanthosine transporter (characterized)
to candidate CA265_RS15375 CA265_RS15375 MFS transporter
Query= SwissProt::P45562 (418 letters) >FitnessBrowser__Pedo557:CA265_RS15375 Length = 405 Score = 253 bits (645), Expect = 1e-71 Identities = 138/406 (33%), Positives = 234/406 (57%), Gaps = 18/406 (4%) Query: 6 RLKVMSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKGIAAIIMPGIMGIIADKW 65 +L M FL++FIWG+W VT+G+Y+ L +G YS++ + AII P I+G+IADK+ Sbjct: 8 KLSAMMFLEFFIWGAWFVTMGTYLGKNLLANDVQIGSAYSTQSLGAIIAPFIIGLIADKF 67 Query: 66 LRAERAYMLCHLVCAGVLFYAASVTDPDMMFWVMLVNAMAFMPTIALSNSVSYSCLAQAG 125 A++ + HLV +L+ A + + D F +L +A+MPT+AL NS+S+ + Sbjct: 68 FSAQKVLGVLHLVGGALLWVAGTSLNFDSFFPFILGYMIAYMPTLALVNSISFKQMK--- 124 Query: 126 LDPVTAFPPIRVFGTVGFIVAMWAVSLLHLELSSLQLY---IASGASLLLSAYALTLPKI 182 DP FP IRVFGT+G+I+A + L+ E S ++ +AS AS++L + LP Sbjct: 125 -DPGKEFPSIRVFGTIGWIIAGLVIGWLNWEQSGNLVFTFKMASVASIILGLLSFFLPNT 183 Query: 183 PVAEKKATTSLASKLGLDAFVLFKNPRMAIFFLFAMMLGAVLQITNVFGNPFLHDFARNP 242 P +K T+ +GLDA L KN +FFL ++ + L F NPFL++ Sbjct: 184 PPVKKGEKTTFGEIIGLDAIGLLKNKSYLLFFLASVAICIPLAFYYNFTNPFLNEVG--- 240 Query: 243 EFADSFVVKYPSILLSVSQMAEVGFILTIPFFLKRFGIKTVMLMSMVAWTLRFGFFAYGD 302 +K + + S+ Q++E F+L +P F R G+K ++ + M+AW +R+ FFA+G+ Sbjct: 241 -------MKGAAGVQSLGQVSETLFMLLMPLFFARLGVKKMLAIGMIAWVVRYLFFAFGN 293 Query: 303 PSTTGFILLLLSMIVYGCAFDFFNISGSVFVEQEVDSSIRASAQGLFMTMVNGVGAWVGS 362 + + + +L+ ++++G +DFF ++G ++ ++ +++AQG GVG +GS Sbjct: 294 -ADSNYWMLIGGIVLHGICYDFFFVTGQIYTDRLAGEKFKSAAQGFITLATYGVGMLIGS 352 Query: 363 ILSGMAVDYFSVDGVKDWQTIWLVFAGYALFLAVIFFFGFKYNHDP 408 I+SGM V+ + V+G WQ+IW++ AG A +A++F F + P Sbjct: 353 IISGMVVNKYVVEGGHIWQSIWIIPAGIAGLVALLFLLFFSDKNKP 398 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: 526 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: 405 Length adjustment: 31 Effective length of query: 387 Effective length of database: 374 Effective search space: 144738 Effective search space used: 144738 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