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_RS04125 BWI76_RS04125 NupC/NupG family nucleoside CNT transporter
Query= TCDB::Q9KPL5 (418 letters) >FitnessBrowser__Koxy:BWI76_RS04125 Length = 425 Score = 577 bits (1487), Expect = e-169 Identities = 295/424 (69%), Positives = 352/424 (83%), Gaps = 7/424 (1%) Query: 1 MSLFMSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFS 60 M + M LIGM VLL IAVLLSSNRKAINLRTV GA+ IQ +GA ILYVP G+ L S Sbjct: 1 MQIIMGLIGMVVLLAIAVLLSSNRKAINLRTVLGAWIIQVGIGALILYVPAGRTALLAMS 60 Query: 61 DAVSNVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGV 120 + V+NVI YGN+G F+FGGLVS KMFEVFGGGGF+FA RVLP ++FFS+LI+VLYYLG+ Sbjct: 61 NGVANVIAYGNEGIGFIFGGLVSDKMFEVFGGGGFVFALRVLPVIVFFSSLIAVLYYLGI 120 Query: 121 MQWVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGG 180 MQ+VIRILGG L+ L TSR ES+SA ANIFVGQTEAPLVVRP++ MT+SELFAVMCGG Sbjct: 121 MQFVIRILGGALRAVLKTSRTESLSATANIFVGQTEAPLVVRPYIATMTRSELFAVMCGG 180 Query: 181 LASIAGGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGGDD 240 LAS+AG VLAGYA MGV +EYL+AASFMAAPGGLLFAK+++PETE+P+DN + + D Sbjct: 181 LASVAGSVLAGYAQMGVPLEYLIAASFMAAPGGLLFAKIIVPETEQPRDNPAMEKNDADP 240 Query: 241 K-PANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLL 299 + PANV+DAAA GA++G+QLALNVGAML+AFI LIAL+NG+L G+GGWF P+L L+M+L Sbjct: 241 QAPANVLDAAASGAASGMQLALNVGAMLLAFIALIALVNGILSGVGGWFNHPDLSLQMIL 300 Query: 300 GWLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYL---TEAAPV---VLSE 353 GW+F+PLA++IGVPWNEATVAG FIG K + NEFVAY F YL TE A V+S Sbjct: 301 GWVFSPLAWVIGVPWNEATVAGSFIGQKLIINEFVAYMNFGEYLKADTEVAAAGLQVIST 360 Query: 354 KTKAIISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIAG 413 TKAIISFALCGFANLSSIAIL+GGLG +AP RR +IA++G++AV AGTLSNLM+ATIAG Sbjct: 361 HTKAIISFALCGFANLSSIAILIGGLGGMAPNRRQEIAQLGMRAVAAGTLSNLMSATIAG 420 Query: 414 FFLS 417 FL+ Sbjct: 421 VFLA 424 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: 642 Number of extensions: 28 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: 425 Length adjustment: 32 Effective length of query: 386 Effective length of database: 393 Effective search space: 151698 Effective search space used: 151698 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