Align Concentrative nucleoside transporter, CNT, of 418 aas and 12 TMSs. A repeat-swapped model of VcCNT predicts that nucleoside transport occurs via a mechanism involving an elevator-like substrate binding domain movement across the membrane (characterized)
to candidate CCNA_02171 CCNA_02171 nucleoside permease nupC
Query= TCDB::Q9KPL5 (418 letters) >FitnessBrowser__Caulo:CCNA_02171 Length = 426 Score = 260 bits (664), Expect = 6e-74 Identities = 147/415 (35%), Positives = 246/415 (59%), Gaps = 13/415 (3%) Query: 6 SLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFSDAVSN 65 +L G+A+ LG+ L+S NRK GA IQ L + +P Q++LRG + AV Sbjct: 9 ALAGLALTLGLCWLVSENRKRFPWGLAIGAVVIQVLLVLVLFGLPQAQQMLRGVNGAVEG 68 Query: 66 VINYGNDGTSFLFGGLVSGKM-FEVFG-GGGFIFAFRVLPTLIFFSALISVLYYLGVMQW 123 + GT+F+FG L G + V G GFIFAFRVLP ++ AL ++L++ +++W Sbjct: 69 LAASTQAGTAFVFGFLAGGDQPYPVSNPGAGFIFAFRVLPVILVVCALSALLWHWKILKW 128 Query: 124 VIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGGLAS 183 + + G QK LG +++ AA IF+GQ E P+ +R ++ K+++SELF ++ G+A Sbjct: 129 LAQGFGFVFQKTLGLRGPPALATAATIFMGQVEGPIFIRAYLDKLSRSELFMLIAVGMAC 188 Query: 184 IAGGVLAGYASMGVKI-----EYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGG 238 ++G + YA++ + +++ AS ++AP G+L A++++P ++ + + D+ L Sbjct: 189 VSGSTMVAYATILADVLPNAAAHVLTASIISAPAGVLLARIIVP-SDPMEKSADLDLSTE 247 Query: 239 DDKPANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEML 298 D + IDA G + GLQ+ALNVGA LI F+ L +++ +LG G P L + Sbjct: 248 DKTYGSSIDAVMKGTTDGLQIALNVGATLIVFVALATMVDKVLGAFPPVGGEP-LSIARG 306 Query: 299 LGWLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAPVVLSEKTKAI 358 LG +FAPLA+ +G+PW EA AG +G+K + EF A+ Q L++ +L E+T+ I Sbjct: 307 LGVVFAPLAWSMGIPWKEAGTAGGLLGVKLILTEFTAFIQ----LSKVGEALLDERTRMI 362 Query: 359 ISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIAG 413 +++ALCGFAN+ S+ + + G L P+RR ++ + KA++AG L+ + A++ G Sbjct: 363 MTYALCGFANIGSVGMNVAGFSVLVPQRRQEVLGLVWKAMMAGFLATCLTASLVG 417 Lambda K H 0.325 0.141 0.414 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: 487 Number of extensions: 21 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: 418 Length of database: 426 Length adjustment: 32 Effective length of query: 386 Effective length of database: 394 Effective search space: 152084 Effective search space used: 152084 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