Align Xanthosine permease; Xanthosine transporter (characterized)
to candidate N515DRAFT_2002 N515DRAFT_2002 MFS transporter, NHS family, xanthosine permease
Query= SwissProt::P45562 (418 letters) >FitnessBrowser__Dyella79:N515DRAFT_2002 Length = 420 Score = 471 bits (1212), Expect = e-137 Identities = 232/412 (56%), Positives = 303/412 (73%), Gaps = 4/412 (0%) Query: 1 MSIAMRLKVMSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKGIAAIIMPGIMGI 60 MSI +RL +M FLQYF+WGSWL+T+G+Y H+ G G ++S+ GIA++ MP I G+ Sbjct: 1 MSIKLRLVIMYFLQYFVWGSWLLTIGAYWFQNKHWPGTQFGAIFSTMGIASLFMPSIAGV 60 Query: 61 IADKWLRAERAYMLCHLVCAGVLFYAASVTDPDMMFWVMLVNAMAFMPTIALSNSVSYSC 120 IADKW+ AE+ L H+ A +LF ++ P +MFWVML+N M +MPTI+LS +V+Y+ Sbjct: 61 IADKWINAEKLLGLMHIGGAIMLFVVPAIDSPGLMFWVMLLNMMFYMPTISLSIAVAYNA 120 Query: 121 LAQAGLDPVTAFPPIRVFGTVGFIVAMWAVSLLHLELSSLQLYIASGASLLLSAYALTLP 180 L +G D VT FPPIRV+GTVGFI A+W VSLLHLE ++ Q ++A A+LLL YA TLP Sbjct: 121 LKSSGEDIVTVFPPIRVWGTVGFIAALWTVSLLHLETTAGQFHVAGAAALLLGLYAFTLP 180 Query: 181 KIPVA-EKKATTSLASKLGLDAFVLFKNPRMAIFFLFAMMLGAVLQITNVFGNPFLHDFA 239 K P E+K SL LGL +F L +N +MAIFF+FAM+LGA LQ+TN +G+ FLHDFA Sbjct: 181 KCPPRFERKEQQSLLDTLGLTSFALLRNTQMAIFFMFAMLLGAALQLTNAYGDTFLHDFA 240 Query: 240 RNPEFADSFVVKYPSILLSVSQMAEVGFILTIPFFLKRFGIKTVMLMSMVAWTLRFGFFA 299 + + V+YP+I++S+SQ++E FIL IPFFLKRFGIKTVML+SM+AWTLRFG FA Sbjct: 241 AMEPYKNLIAVRYPAIIMSISQISETLFILAIPFFLKRFGIKTVMLISMLAWTLRFGLFA 300 Query: 300 YGDPSTTGFILLLLSMIVYGCAFDFFNISGSVFVEQEVDSSIRASAQGLFMTMVNGVGAW 359 YGDP G +++LS IVYG AFDFFNISGS+FVE + D SIRASAQGLFM M NG+GA Sbjct: 301 YGDPG-AGLWMIVLSCIVYGMAFDFFNISGSLFVEGQADPSIRASAQGLFMLMTNGIGAV 359 Query: 360 VGSILSGMAVDYF--SVDGVKDWQTIWLVFAGYALFLAVIFFFGFKYNHDPE 409 +GS +SG +D F DG K+W IW+ F+ Y+L +AV+F F FK+ HDP+ Sbjct: 360 LGSSVSGWMIDAFFTQADGSKNWHGIWITFSLYSLIVAVLFVFLFKHKHDPK 411 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: 567 Number of extensions: 33 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: 420 Length adjustment: 32 Effective length of query: 386 Effective length of database: 388 Effective search space: 149768 Effective search space used: 149768 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