Align Nucleoside permease; Flags: Precursor (characterized, see rationale)
to candidate WP_086510575.1 BZY95_RS14240 NupC/NupG family nucleoside CNT transporter
Query= uniprot:A0KU05 (419 letters) >NCBI__GCF_002151265.1:WP_086510575.1 Length = 423 Score = 573 bits (1477), Expect = e-168 Identities = 293/423 (69%), Positives = 354/423 (83%), Gaps = 8/423 (1%) Query: 1 MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVS 60 M +MSLVG+ L+ I + S N+ AI LRTVGGA AIQA G FVLYVP G+ +L+++S Sbjct: 1 MTAIMSLVGMATLIVIALIFSTNRGAIRLRTVGGAFAIQAGIGAFVLYVPFGQTVLQTIS 60 Query: 61 DAVSSVIGYAQNGIGFLFGDLANF-KLGFIFAVNVLPVIVFFSSLIAVLYYLGIMQWIIR 119 VS V+ YA +GI FLFG LA+ +GF+FA+ VLPVI+FFSSLIAVLYY+GIMQW+IR Sbjct: 61 AGVSQVVLYANDGIDFLFGGLADTGNIGFVFAIKVLPVIIFFSSLIAVLYYIGIMQWVIR 120 Query: 120 IIGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGGLASIAG 179 I+GG LQKALGTSRTES+SATANIFVGQTEAPLVVRPFI MT S+LFA+M GGLAS+AG Sbjct: 121 ILGGALQKALGTSRTESLSATANIFVGQTEAPLVVRPFIARMTPSQLFAVMCGGLASVAG 180 Query: 180 SVLAGYAQMGVPIEYLVAASFMAAPGGLLMAKLMHPETEVAKNDMD---ELPEDPDKPAN 236 SVLAGYA +G+P+EYLVAASFMAAPGGLL AKL+ PETE +D++ E+ E D+P N Sbjct: 181 SVLAGYAALGIPMEYLVAASFMAAPGGLLFAKLIMPETEKPVDDVEEASEVIEAEDRPVN 240 Query: 237 VLDAAAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEGLTLELILGYIFM 296 VLDAAAAGASSG+ LA NVGAMLLAF+GLIA+ING++GGVGGW G E L+LELILG++F Sbjct: 241 VLDAAAAGASSGLRLAANVGAMLLAFIGLIALINGMLGGVGGWVGFEQLSLELILGWLFA 300 Query: 297 PLAFLIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADGGMIVADTGLAMTDRT 356 PLAF++GVPW EA +AGSFIGQK+VVNEFVAY+N APY+ DG IV +TG AM+ T Sbjct: 301 PLAFVLGVPWAEATLAGSFIGQKLVVNEFVAYINLAPYI----DGDAIVTNTGQAMSGHT 356 Query: 357 KAIISFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLANLMSATIAGLF 416 AI+SFALCGFANLSSIAILLGGLG++AP+RRHD+A+ G++AV+AG+L+NLMSA IAG F Sbjct: 357 IAILSFALCGFANLSSIAILLGGLGSIAPSRRHDIARFGVKAVLAGTLSNLMSAAIAGFF 416 Query: 417 LAI 419 L+I Sbjct: 417 LSI 419 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: 668 Number of extensions: 28 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: 419 Length of database: 423 Length adjustment: 32 Effective length of query: 387 Effective length of database: 391 Effective search space: 151317 Effective search space used: 151317 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 24 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