Align Nucleoside permease; Flags: Precursor (characterized, see rationale)
to candidate WP_057507837.1 ABB28_RS06365 Na+ dependent nucleoside transporter domain-containing protein
Query= uniprot:A0KU05 (419 letters) >NCBI__GCF_001431535.1:WP_057507837.1 Length = 432 Score = 349 bits (895), Expect = e-100 Identities = 191/424 (45%), Positives = 270/424 (63%), Gaps = 23/424 (5%) Query: 7 LVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVSDAVSSV 66 L G+ VL+ I +L SNNK+A++ + V L +Q AF VL VP G+D+ ++ V Sbjct: 12 LFGLAVLIGITWLFSNNKRAVDWKLVATGLLLQIAFAAVVLLVPGGRDVFDALGHGFVKV 71 Query: 67 IGYAQNGIGFLFGDLANFK-LGFIFAVNVLPVIVFFSSLIAVLYYLGIMQWIIRIIGGGL 125 + + G GF+FG L N + GFIFA VLP I+FFS+L+ VLY+L +MQ I+R++ + Sbjct: 72 LSFVNEGSGFIFGSLMNVESYGFIFAFQVLPTIIFFSALMGVLYHLNVMQAIVRVMALAI 131 Query: 126 QKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGGLASIAGSVLAGY 185 K + S E+ S A++F+GQTEAPL VRP+I MT+SEL +M+GG+A IAG VLA Y Sbjct: 132 TKVMRVSGAETTSVCASVFIGQTEAPLTVRPYISRMTESELLTMMIGGMAHIAGGVLAAY 191 Query: 186 AQM---GVP------IEYLVAASFMAAPGGLLMAKLMHPETEVAKNDMDELPEDPDKPAN 236 M G P ++L+AAS MAAP L++AKL+ PET E +N Sbjct: 192 VGMLGGGDPESQAFYAKHLLAASIMAAPATLVVAKLLIPETGTPLTRGTVKMEVEKTSSN 251 Query: 237 VLDAAAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEG-----LTLELIL 291 ++DAAA GA+ G+ LALN+GAMLLAF+ LIA++N + +G G+ L I Sbjct: 252 IIDAAAGGAADGLRLALNIGAMLLAFIALIALLNAPLTWIGDVTGLAAAIGRPTNLSTIF 311 Query: 292 GYIFMPLAFLIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADGGMIVADTGLA 351 GY+ P+A++IG PW +A GS IGQK+V+NEFVAY L I +G + G+ Sbjct: 312 GYLLAPIAWVIGTPWADASTVGSLIGQKVVINEFVAYSE----LSRIINGQV----PGVT 363 Query: 352 MTDRTKAIISFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLANLMSAT 411 +++ + I ++ALCGFAN SSIAI +GG+G +AP RR DLA+ G+RAV+ G++A M+AT Sbjct: 364 LSEEGRLIATYALCGFANFSSIAIQIGGIGGLAPERRQDLARFGLRAVLGGTIATFMTAT 423 Query: 412 IAGL 415 IAG+ Sbjct: 424 IAGV 427 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: 558 Number of extensions: 27 Number of successful extensions: 6 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: 432 Length adjustment: 32 Effective length of query: 387 Effective length of database: 400 Effective search space: 154800 Effective search space used: 154800 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