Align Nucleoside permease; Flags: Precursor (characterized, see rationale)
to candidate 6936789 Sama_0971 nucleoside transporter (RefSeq)
Query= uniprot:A0KU05 (419 letters) >FitnessBrowser__SB2B:6936789 Length = 419 Score = 756 bits (1953), Expect = 0.0 Identities = 389/419 (92%), Positives = 406/419 (96%) Query: 1 MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVS 60 M+ILMSLVGV VLL IGFLLSNNKKAI++R VGGALAIQAAFGGFVLYVP GKDILK+VS Sbjct: 1 MSILMSLVGVAVLLGIGFLLSNNKKAISVRAVGGALAIQAAFGGFVLYVPWGKDILKTVS 60 Query: 61 DAVSSVIGYAQNGIGFLFGDLANFKLGFIFAVNVLPVIVFFSSLIAVLYYLGIMQWIIRI 120 D VS+VIGY QNGI FLFGDLA FK+GFIFA+NVLPVI+FFSSLIAVLYYLGIMQW+IRI Sbjct: 61 DGVSAVIGYGQNGINFLFGDLAQFKVGFIFAINVLPVIIFFSSLIAVLYYLGIMQWVIRI 120 Query: 121 IGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGGLASIAGS 180 IGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGGLASIAGS Sbjct: 121 IGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGGLASIAGS 180 Query: 181 VLAGYAQMGVPIEYLVAASFMAAPGGLLMAKLMHPETEVAKNDMDELPEDPDKPANVLDA 240 VLAGYA MGV IEYLVAASFMAAPGGLLMAKLMHPETE KN+MDELPEDPDKPANVLDA Sbjct: 181 VLAGYASMGVKIEYLVAASFMAAPGGLLMAKLMHPETENTKNEMDELPEDPDKPANVLDA 240 Query: 241 AAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEGLTLELILGYIFMPLAF 300 AAAGASSGMHLALNVGAML+AFVGLIAMINGIIGGVGGWFGVEGLTLELILGYIFMPLAF Sbjct: 241 AAAGASSGMHLALNVGAMLIAFVGLIAMINGIIGGVGGWFGVEGLTLELILGYIFMPLAF 300 Query: 301 LIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADGGMIVADTGLAMTDRTKAII 360 LIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADGG++VA+TG AM+DRTKAI+ Sbjct: 301 LIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADGGIVVAETGAAMSDRTKAIV 360 Query: 361 SFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLANLMSATIAGLFLAI 419 SFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLANLMSAT+AGLFLAI Sbjct: 361 SFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLANLMSATLAGLFLAI 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: 816 Number of extensions: 33 Number of successful extensions: 1 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: 419 Length adjustment: 32 Effective length of query: 387 Effective length of database: 387 Effective search space: 149769 Effective search space used: 149769 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