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) >lcl|FitnessBrowser__Koxy:BWI76_RS19710 BWI76_RS19710 NupC/NupG family nucleoside CNT transporter 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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