Align Xanthosine permease; Xanthosine transporter (characterized)
to candidate Pf1N1B4_4098 Putative nucleoside transporter yegT
Query= SwissProt::P45562 (418 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4098 Length = 400 Score = 239 bits (610), Expect = 1e-67 Identities = 139/406 (34%), Positives = 222/406 (54%), Gaps = 29/406 (7%) Query: 10 MSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKGIAAIIMPGIMGIIADKWLRAE 69 M FLQ+FIWG W VTLG+++ + L +G +GM +S++ AII P ++G+IAD++ AE Sbjct: 1 MMFLQFFIWGGWFVTLGTFLSSNLGASGGQIGMAFSTQSWGAIIAPFVIGLIADRYFNAE 60 Query: 70 RAYMLCHLVCAGVLFYAASVTDPDMMFWVMLVNAMAFMPTIALSNSVSYSCLAQAGLDPV 129 R + HL+ A +L D + +L M +MPT+AL NSV++ + DP Sbjct: 61 RILAVLHLIGAVLLLQLYRAPDFSAFYPFVLAYMMIYMPTLALVNSVAFRQMR----DPA 116 Query: 130 TAFPPIRVFGTVGFIVAMWAVSLLHLELSSLQLYIASG-----------ASLLLSAYALT 178 F IRV+GT+G+IVA +S + S Q I+SG AS +L Y+ + Sbjct: 117 LEFSRIRVWGTIGWIVAGVVISFVFAWDS--QQAISSGGLRNTFLMSAIASFVLGIYSFS 174 Query: 179 LPK-IPVAEKKATTSLASKLGLDAFVLFKNPRMAIFFLFAMMLGAVLQITNVFGNPFLHD 237 LP+ P+ + + L LGLDA L K+ +FF+ ++++ L NPFL + Sbjct: 175 LPRTAPLKPEPGSVGLKQMLGLDALGLLKDRSYLVFFIASILICIPLAFYYQNANPFLAE 234 Query: 238 FARNPEFADSFVVKYPSILLSVSQMAEVGFILTIPFFLKRFGIKTVMLMSMVAWTLRFGF 297 V P+ +++ Q++EV F+L +P F++RFGIK +L+ M+AW LR+ Sbjct: 235 IG----------VTNPTAKMAIGQVSEVLFMLLLPLFIQRFGIKIALLVGMLAWALRYLL 284 Query: 298 FAYGDPSTTGFILLLLSMIVYGCAFDFFNISGSVFVEQEVDSSIRASAQGLFMTMVNGVG 357 FAYG+ F +L + ++G +DFF +SG ++ + + R+SAQGL G+G Sbjct: 285 FAYGNNGDLAF-MLFTGIALHGICYDFFFVSGQIYTDAKASERFRSSAQGLITLATYGLG 343 Query: 358 AWVGSILSGMAVDYFSVDGVKDWQTIWLVFAGYALFLAVIFFFGFK 403 +G ++G D+++ DW++IWL AG+AL + F FK Sbjct: 344 MLIGFWVAGAVTDHYASADSHDWKSIWLFPAGFALAIFFCFSLAFK 389 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: 513 Number of extensions: 22 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: 400 Length adjustment: 31 Effective length of query: 387 Effective length of database: 369 Effective search space: 142803 Effective search space used: 142803 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