Align Xanthosine permease; Xanthosine transporter (characterized)
to candidate Echvi_1845 Echvi_1845 Nucleoside H+ symporter.
Query= SwissProt::P45562 (418 letters) >FitnessBrowser__Cola:Echvi_1845 Length = 410 Score = 235 bits (599), Expect = 2e-66 Identities = 139/412 (33%), Positives = 229/412 (55%), Gaps = 32/412 (7%) Query: 6 RLKVMSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKGIAAIIMPGIMGIIADKW 65 +L M FL++FIWG W VTLG ++ N L GA V+S++ + AII P I+G+IADK+ Sbjct: 8 KLSFMMFLEFFIWGGWFVTLGLFLGNNLGTNGAQDAAVFSTQSLGAIIAPFIIGLIADKY 67 Query: 66 LRAERAYMLCHLVCAGVLFYAASVTDPDMMFWVMLVNAMAFMPTIALSNSVSYSCLAQAG 125 AER + HL+ A +++ + TD + + + +A+MPT+AL NSVS++ ++ Sbjct: 68 FNAERILGILHLIGAVLMYLMYTATDFESFYPYVFAYMVAYMPTLALVNSVSFNQMS--- 124 Query: 126 LDPVTAFPPIRVFGTVGFIVAMWAVSLLH------------LELSSLQLYIASGASLLLS 173 +P F IRV+GT+G+IVA +SL+ L+ + L I ASL+L Sbjct: 125 -NPEKEFGVIRVWGTIGWIVAGLVISLVFAWDSTENAAAGMLKYTFLMTCI---ASLVLG 180 Query: 174 AYALTLPKI-PVAEKKATTSLASKLGLDAFVLFKNPRMAIFFLFAMMLGAVLQITNVFGN 232 Y+ LPK P K S++ LGLDAF L K+ +FFL ++++ Sbjct: 181 VYSFMLPKTPPKIAKGEKKSISEILGLDAFTLLKDRNYLVFFLSSVLICI---------- 230 Query: 233 PFLHDFARNPEFADSFVVKYPSILLSVSQMAEVGFILTIPFFLKRFGIKTVMLMSMVAWT 292 P + +F + + +++ Q +EV F+L +P F +FG+K +L+ M+AW Sbjct: 231 PLAFYYQNASKFFGEIGMTNLTSKMALGQGSEVLFMLLLPIFFGKFGVKKTLLVGMLAWV 290 Query: 293 LRFGFFAYGDPSTTGFILLLLSMIVYGCAFDFFNISGSVFVEQEVDSSIRASAQGLFMTM 352 +R+ FA+G+ F +LL + ++G +DFF +SG ++ + + +++AQG+ Sbjct: 291 VRYALFAFGNVGELSF-MLLTGIALHGICYDFFFVSGQIYTDSKAGEKFKSAAQGMITLA 349 Query: 353 VNGVGAWVGSILSGMAVDYFSV-DGVKDWQTIWLVFAGYALFLAVIFFFGFK 403 GVG +G ++G A D + + D V DW+TIWL+ +G A+ +A+IF FK Sbjct: 350 TYGVGMLIGFWVAGWAYDTYEMSDKVHDWKTIWLIPSGIAVLVALIFAVAFK 401 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: 527 Number of extensions: 29 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: 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