Align Xanthosine permease; Xanthosine transporter (characterized)
to candidate Pf1N1B4_4098 Putative nucleoside transporter yegT
Query= SwissProt::P45562 (418 letters) >lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4098 Putative nucleoside transporter yegT 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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