Align Xanthosine permease; Xanthosine transporter (characterized)
to candidate 353856 BT4330 xanthosine permease (NCBI ptt file)
Query= SwissProt::P45562 (418 letters) >lcl|FitnessBrowser__Btheta:353856 BT4330 xanthosine permease (NCBI ptt file) Length = 416 Score = 475 bits (1222), Expect = e-138 Identities = 239/414 (57%), Positives = 301/414 (72%), Gaps = 7/414 (1%) Query: 1 MSIAMRLKVMSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKGIAAIIMPGIMGI 60 MSI +RL +M+FLQ+F+WGSWL++LG YM LHF G +G ++++ GIA+++MPGI+GI Sbjct: 1 MSIKVRLIIMNFLQFFVWGSWLISLGGYMGRELHFEGGQIGAIFATMGIASLVMPGIIGI 60 Query: 61 IADKWLRAERAYMLCHLVCAGVLFYAASVTDPDMMFWVMLVNAMAFMPTIALSNSVSYSC 120 IADKW AER Y LCH+ A LFYA++VT+ D M+W ML+N + +MPT++L+N+VSY+ Sbjct: 61 IADKWFNAERLYGLCHIAGAACLFYASTVTNYDQMYWAMLLNLLVYMPTLSLANTVSYNA 120 Query: 121 LAQAGLDPVTAFPPIRVFGTVGFIVAMWAVSLLHLELSSLQLYIASGASLLLSAYALTLP 180 L Q D + FPPIRV+GT+GFI AMWAV L + SS QLY+ ++LLL Y+ TLP Sbjct: 121 LEQYKCDLIKDFPPIRVWGTIGFICAMWAVDLTGFKNSSAQLYVGGASALLLGLYSFTLP 180 Query: 181 KIPVAEKKATTSLASKLGLDAFVLFKNPRMAIFFLFAMMLGAVLQITNVFGNPFLHDFAR 240 A+ + T L S GLDAFVLFK +MAIFFLF+M+LGA LQITN +G+ FL FA Sbjct: 181 ACKPAKTEKKT-LLSSFGLDAFVLFKRKKMAIFFLFSMLLGAALQITNTYGDLFLGSFAS 239 Query: 241 NPEFADSFVVKYPSILLSVSQMAEVGFILTIPFFLKRFGIKTVMLMSMVAWTLRFGFFAY 300 PEFADSF VK+ ILLS+SQM+E FIL IPFFL+ FGIK VML+SM AW RFG F + Sbjct: 240 IPEFADSFGVKHSVILLSISQMSETLFILAIPFFLRHFGIKQVMLISMFAWVFRFGLFGF 299 Query: 301 GDPSTTGFILLLLSMIVYGCAFDFFNISGSVFVEQEVDSSIRASAQGLFMTMVNGVGAWV 360 GDP +G +L+LSMIVYG AFDFFNISGS+FVEQE SSIRASAQGLF M NG+GA + Sbjct: 300 GDPG-SGLWMLILSMIVYGMAFDFFNISGSLFVEQETSSSIRASAQGLFFMMTNGLGAII 358 Query: 361 GSILSGMAVDYFSV--DG---VKDWQTIWLVFAGYALFLAVIFFFGFKYNHDPE 409 G SG VD FSV DG ++W IW +FA YAL + ++F FKY H E Sbjct: 359 GGYASGAVVDAFSVYADGKLVSREWPDIWFIFAAYALVIGILFALVFKYKHQRE 412 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: 565 Number of extensions: 36 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: 416 Length adjustment: 31 Effective length of query: 387 Effective length of database: 385 Effective search space: 148995 Effective search space used: 148995 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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