Align Nucleoside permease; Flags: Precursor (characterized, see rationale)
to candidate CCNA_02171 CCNA_02171 nucleoside permease nupC
Query= uniprot:A0KU05 (419 letters) >FitnessBrowser__Caulo:CCNA_02171 Length = 426 Score = 237 bits (604), Expect = 6e-67 Identities = 139/430 (32%), Positives = 242/430 (56%), Gaps = 36/430 (8%) Query: 4 LMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVSDAV 63 + +L G+ + L + +L+S N+K GA+ IQ + +P + +L+ V+ AV Sbjct: 7 VQALAGLALTLGLCWLVSENRKRFPWGLAIGAVVIQVLLVLVLFGLPQAQQMLRGVNGAV 66 Query: 64 SSVIGYAQNGIGFLFGDLA---------NFKLGFIFAVNVLPVIVFFSSLIAVLYYLGIM 114 + Q G F+FG LA N GFIFA VLPVI+ +L A+L++ I+ Sbjct: 67 EGLAASTQAGTAFVFGFLAGGDQPYPVSNPGAGFIFAFRVLPVILVVCALSALLWHWKIL 126 Query: 115 QWIIRIIGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGGL 174 +W+ + G QK LG +++ A IF+GQ E P+ +R ++ +++SELF ++ G+ Sbjct: 127 KWLAQGFGFVFQKTLGLRGPPALATAATIFMGQVEGPIFIRAYLDKLSRSELFMLIAVGM 186 Query: 175 ASIAGSVLAGYAQMGVPI-----EYLVAASFMAAPGGLLMAKLMHPETEVAKN-DMDELP 228 A ++GS + YA + + +++ AS ++AP G+L+A+++ P + K+ D+D Sbjct: 187 ACVSGSTMVAYATILADVLPNAAAHVLTASIISAPAGVLLARIIVPSDPMEKSADLDLST 246 Query: 229 EDPDKPANVLDAAAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGG---VGGWFGVEGL 285 ED +++ DA G + G+ +ALNVGA L+ FV L M++ ++G VGG E L Sbjct: 247 EDKTYGSSI-DAVMKGTTDGLQIALNVGATLIVFVALATMVDKVLGAFPPVGG----EPL 301 Query: 286 TLELILGYIFMPLAFLIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADGGMIV 345 ++ LG +F PLA+ +G+PW EA AG +G K+++ EF A++ + + + D Sbjct: 302 SIARGLGVVFAPLAWSMGIPWKEAGTAGGLLGVKLILTEFTAFIQLSKVGEALLD----- 356 Query: 346 ADTGLAMTDRTKAIISFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLA 405 +RT+ I+++ALCGFAN+ S+ + + G + P RR ++ L +A++AG LA Sbjct: 357 --------ERTRMIMTYALCGFANIGSVGMNVAGFSVLVPQRRQEVLGLVWKAMMAGFLA 408 Query: 406 NLMSATIAGL 415 ++A++ GL Sbjct: 409 TCLTASLVGL 418 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: 468 Number of extensions: 23 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: 426 Length adjustment: 32 Effective length of query: 387 Effective length of database: 394 Effective search space: 152478 Effective search space used: 152478 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