Align Nucleoside permease; Flags: Precursor (characterized, see rationale)
to candidate Echvi_2954 Echvi_2954 Nucleoside permease
Query= uniprot:A0KU05 (419 letters) >FitnessBrowser__Cola:Echvi_2954 Length = 428 Score = 324 bits (831), Expect = 3e-93 Identities = 187/441 (42%), Positives = 277/441 (62%), Gaps = 36/441 (8%) Query: 1 MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVS 60 M+ L ++G+V LL + FL S ++K+++ + VG + +Q FG + V + + S+S Sbjct: 1 MDYLRGMIGIVALLGVAFLFSASRKSVDWKLVGIGVILQIVFGFLITKVAFVESVFASIS 60 Query: 61 DAVSSVIGYAQNGIGFLFGDLANFKLGFIFAVNVLPVIVFFSSLIAVLYYLGIMQWIIRI 120 A ++ +AQ G FLFGDLA G IFA VLP I+FFS++ A LYYLG++Q I+ Sbjct: 61 GAFVKLLSFAQAGAIFLFGDLATDSFGTIFAFQVLPTIIFFSTVSAGLYYLGVLQKIVFG 120 Query: 121 IGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGGLASIAGS 180 I + + + S ES+SA NIF+GQTEAPL+VRPFIPTMT+SEL +M GG+A+IAG Sbjct: 121 IAWVMARTMKLSGAESLSAAGNIFLGQTEAPLLVRPFIPTMTRSELMCLMTGGMATIAGG 180 Query: 181 VLAGY---------AQMGVPIEYLVAASFMAAPGGLLMAKLMHPET-EVAKNDMDELPED 230 VLA Y A+ YL+ AS M AP ++M+KL+ PET + ND E+ + Sbjct: 181 VLAAYVAFLGGDDPAEQSKFASYLLGASIMNAPAAIVMSKLIIPETNKEGLNDKLEVSSE 240 Query: 231 PDKPANVLDAAAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGV-GGWFGV------- 282 N++DA + GA+ G+ LALNVG MLLAF+ +IAM+N ++ GV G G+ Sbjct: 241 -GMGVNLIDAMSIGAADGLKLALNVGGMLLAFIAVIAMLNYLLSGVLGDVTGLNQFVVDT 299 Query: 283 -----EGLTLELILGYIFMPLAFLIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKD 337 +G +LE ILG +F A+L+GV W + L GS +GQK V+NEFVAY + + +K Sbjct: 300 TNGRFDGFSLEYILGQVFRIFAWLMGVEWQDTLQVGSLLGQKTVINEFVAYSDLSS-MKA 358 Query: 338 IADGGMIVADTGLAMTDRTKAIISFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIR 397 D ++ ++ I ++ALCGF+N SSIAI +GG+G++AP ++ +L+KLG+ Sbjct: 359 EGD-----------LSPKSIIIATYALCGFSNFSSIAIQVGGIGSIAPGQQGNLSKLGMH 407 Query: 398 AVIAGSLANLMSATIAGLFLA 418 A++A +LA +M+ATIAG+ + Sbjct: 408 ALLAATLACMMTATIAGMLFS 428 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: 525 Number of extensions: 24 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: 428 Length adjustment: 32 Effective length of query: 387 Effective length of database: 396 Effective search space: 153252 Effective search space used: 153252 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 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