Align Nucleoside permease; Flags: Precursor (characterized, see rationale)
to candidate WP_066605839.1 V473_RS13315 nucleoside transporter
Query= uniprot:A0KU05 (419 letters) >NCBI__GCF_001046645.1:WP_066605839.1 Length = 440 Score = 409 bits (1052), Expect = e-119 Identities = 214/454 (47%), Positives = 306/454 (67%), Gaps = 49/454 (10%) Query: 1 MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVS 60 M++L+ L G++++LAI F LS++++AI R VG A +QA VLYVP G+ I+ +S Sbjct: 1 MHLLIGLAGILLILAIAFALSSDRRAIRPRVVGAAFLLQAGIAILVLYVPAGRAIIGGMS 60 Query: 61 DAVSSVIGYAQNGIGFLFGDLANFKLGFI-FAVNVLPVIVFFSSLIAVLYYLGIMQWIIR 119 V++++ YAQ G F+FG LA ++G FA+ LPVI+FF+SL+++LYYLGIMQ+I+R Sbjct: 61 RGVANLLSYAQAGTDFIFGPLAKPEIGGASFAIAALPVIIFFASLVSILYYLGIMQFIVR 120 Query: 120 IIGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGGLASIAG 179 +GG ++ G S+ ES+ A ANIFVGQ+E+PLV+RP++ +T +LFA+M G+A +AG Sbjct: 121 WVGGAIEWVTGVSKVESLCAAANIFVGQSESPLVIRPYLAGLTPPQLFAVMTSGMAGVAG 180 Query: 180 SVLAGYAQMGVPIEYLVAASFMAAPGGLLMAKLMH---------------------PETE 218 ++LA YA MG+ I+YL+AASFMAAPGGLLMAK+M PET Sbjct: 181 TILAAYASMGIKIDYLLAASFMAAPGGLLMAKIMMPDPRAPVQGELPLGDHPDLLLPETR 240 Query: 219 VA-------------KNDMDELPEDPDKPANVLDAAAAGASSGMHLALNVGAMLLAFVGL 265 ++ M + D +KPAN++ AAA GA +G+ LA+ VGAM+LAFV L Sbjct: 241 ISGAGPAALLPEGTPGEPMPQASHDEEKPANLIMAAAQGAQTGVKLAVAVGAMVLAFVAL 300 Query: 266 IAMINGIIGGVGGWFGVEGLTLELILGYIFMPLAFLIGVPWNEALVAGSFIGQKIVVNEF 325 +A+ NGI+GG+G WFG L+ +++LGY+F P+ +L+ +PW EA VAG G K+V+NEF Sbjct: 301 VALANGILGGIGAWFGYPTLSFQMLLGYVFQPVMYLLNIPWAEAQVAGGLFGTKVVLNEF 360 Query: 326 VAYLNFAPYLKDIADGGMIVADTGLAMTDRTKAIISFALCGFANLSSIAILLGGLGAMAP 385 VAY+N G + A++ T AII+FALCGFAN SSIAI + G +AP Sbjct: 361 VAYINL----------GQVQG----ALSPATIAIITFALCGFANFSSIAIQMAVTGNLAP 406 Query: 386 NRRHDLAKLGIRAVIAGSLANLMSATIAGLFLAI 419 N+R +AKLG++A++AGSLANLMSA +AGL L++ Sbjct: 407 NQRPMIAKLGLKALVAGSLANLMSAALAGLMLSL 440 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: 634 Number of extensions: 34 Number of successful extensions: 4 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: 440 Length adjustment: 32 Effective length of query: 387 Effective length of database: 408 Effective search space: 157896 Effective search space used: 157896 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: 51 (24.3 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