Align Nucleoside permease; Flags: Precursor (characterized, see rationale)
to candidate 16273 b2164 predicted nucleoside transporter (NCBI)
Query= uniprot:A0KU05 (419 letters) >FitnessBrowser__Keio:16273 Length = 416 Score = 414 bits (1065), Expect = e-120 Identities = 212/426 (49%), Positives = 297/426 (69%), Gaps = 18/426 (4%) Query: 1 MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVS 60 M+I+ S+VG+VVLLAI FLLS NKK+I+LRTVG AL +Q A GG +LY P GK ++ + Sbjct: 1 MDIMRSVVGMVVLLAIAFLLSVNKKSISLRTVGAALLLQIAIGGIMLYFPPGKWAVEQAA 60 Query: 61 DAVSSVIGYAQNGIGFLFGDLANFKL-------GFIFAVNVLPVIVFFSSLIAVLYYLGI 113 V V+ Y+ G F+FG L K+ GFIFA VLP I+F ++LI++LYY+G+ Sbjct: 61 LGVHKVMSYSDAGSAFIFGSLVGPKMDVLFDGAGFIFAFRVLPAIIFVTALISLLYYIGV 120 Query: 114 MQWIIRIIGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGG 173 M +IRI+G QKAL S+ ES A IF+GQ E P +V+PFI M ++ELF + G Sbjct: 121 MGLLIRILGSIFQKALNISKIESFVAVTTIFLGQNEIPAIVKPFIDRMNRNELFTAICSG 180 Query: 174 LASIAGSVLAGYAQMGVPIEYLVAASFMAAPGGLLMAKLMHPETEVAKNDMDELPEDPDK 233 +ASIAGS++ GYA MGVPI+YL+AAS MA PGG+L A+++ P TE ++ + L Sbjct: 181 MASIAGSMMIGYAGMGVPIDYLLAASLMAIPGGILFARILSPATEPSQVTFENLSFSETP 240 Query: 234 PANVLDAAAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEGLTLELILGY 293 P + ++AAA+GA +G+ +A V +++AFV +IA+INGIIGG+GGWFG +LE I GY Sbjct: 241 PKSFIEAAASGAMTGLKIAAGVATVVMAFVAIIALINGIIGGIGGWFGFANASLESIFGY 300 Query: 294 IFMPLAFLIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADGGMIVADTGLAMT 353 + PLA+++GV W++A +AGS IGQK+ +NEFVAYL+F+PYL+ TG + Sbjct: 301 VLAPLAWIMGVDWSDANLAGSLIGQKLAINEFVAYLSFSPYLQ-----------TGGTLE 349 Query: 354 DRTKAIISFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLANLMSATIA 413 +T AIISFALCGFAN SI +++G A++P R ++A+LG+RA+ A +L+NLMSATIA Sbjct: 350 VKTIAIISFALCGFANFGSIGVVVGAFSAISPKRAPEIAQLGLRALAAATLSNLMSATIA 409 Query: 414 GLFLAI 419 G F+ + Sbjct: 410 GFFIGL 415 Lambda K H 0.325 0.142 0.407 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: 594 Number of extensions: 34 Number of successful extensions: 3 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: 419 Length of database: 416 Length adjustment: 32 Effective length of query: 387 Effective length of database: 384 Effective search space: 148608 Effective search space used: 148608 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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