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 BWI76_RS19710 BWI76_RS19710 NupC/NupG family nucleoside CNT transporter
Query= TCDB::Q9KPL5 (418 letters) >FitnessBrowser__Koxy:BWI76_RS19710 Length = 416 Score = 422 bits (1085), Expect = e-123 Identities = 216/416 (51%), Positives = 293/416 (70%), Gaps = 3/416 (0%) Query: 1 MSLFMSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFS 60 M + SL+GM VLL IA LS N+K I++RTVG A +Q +G +LY P G+ L+ + Sbjct: 1 MDIMRSLLGMVVLLAIAFALSVNKKRISIRTVGAALLLQIVIGGVMLYFPPGKWLVEQAA 60 Query: 61 DAVSNVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGV 120 V V++Y + G++F+FG LV KM +F G GFIFAFRVLP +IF +ALIS+LYYLGV Sbjct: 61 LGVHKVMSYSDAGSAFIFGSLVGPKMDVLFDGAGFIFAFRVLPAIIFVTALISLLYYLGV 120 Query: 121 MQWVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGG 180 M +IRILGG QKAL S+ ES A IF+GQ E P +V+PF+ K+ ++ELF +C G Sbjct: 121 MGLLIRILGGIFQKALNISKIESFVAVTTIFLGQNEIPAIVKPFINKLNRNELFTAICSG 180 Query: 181 LASIAGGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGGDD 240 +ASIAG ++ GYA MGV I+YL+AAS MA PGG+LFA+++ P TE Q D L + Sbjct: 181 MASIAGSMMIGYAGMGVPIDYLLAASLMAIPGGILFARMLSPATEASQVTFD-NLSFSET 239 Query: 241 KPANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLLG 300 P +VI+AAA GA GL++A V +++AF+ +IAL+NG++GGIGGWFG LE + G Sbjct: 240 PPKSVIEAAASGAMTGLKIAAGVATVVMAFVAIIALLNGIIGGIGGWFGFGHATLEGIFG 299 Query: 301 WLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAPVVLSEKTKAIIS 360 +L APLA+++GV W++AT+AG IG K NEFVAY F+PYL L KT AIIS Sbjct: 300 FLLAPLAWIMGVDWSDATLAGSLIGQKLAINEFVAYLNFSPYLQSGGN--LDVKTVAIIS 357 Query: 361 FALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIAGFFL 416 FALCGFAN SI +++G +++P+R +IA++G++A+ A TLSNLM+ATIAGFF+ Sbjct: 358 FALCGFANFGSIGVVVGAFSAISPQRAPEIAQLGLRALAAATLSNLMSATIAGFFI 413 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: 552 Number of extensions: 38 Number of successful extensions: 3 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: 416 Length adjustment: 31 Effective length of query: 387 Effective length of database: 385 Effective search space: 148995 Effective search space used: 148995 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