Align Broadly selective nucleoside:Na+ cotransporter, hfCNT (transports uridine, thymidine, inosine, 3'-azido-3'deoxythymidine, 2'3'dideoxycytidine, and 2'3'dideoxyinosine) (Na+/uridine = 2) (characterized)
to candidate BWI76_RS04125 BWI76_RS04125 NupC/NupG family nucleoside CNT transporter
Query= TCDB::Q9UA35 (683 letters) >FitnessBrowser__Koxy:BWI76_RS04125 Length = 425 Score = 285 bits (728), Expect = 4e-81 Identities = 149/422 (35%), Positives = 252/422 (59%), Gaps = 15/422 (3%) Query: 196 VIPFFGLILYILLVFIFSKHPTKVRWRIVIWGLLLQFIFGLIILRTKPGLDAFNWLGIQV 255 ++ G+++ + + + S + + R V+ ++Q G +IL G A + V Sbjct: 4 IMGLIGMVVLLAIAVLLSSNRKAINLRTVLGAWIIQVGIGALILYVPAGRTALLAMSNGV 63 Query: 256 QTFLKYTDAGSRFLFGDDFQDHFF----------AFAVLPIVIFFSTVMSMMYYLGLMQW 305 + Y + G F+FG D F A VLP+++FFS++++++YYLG+MQ+ Sbjct: 64 ANVIAYGNEGIGFIFGGLVSDKMFEVFGGGGFVFALRVLPVIVFFSSLIAVLYYLGIMQF 123 Query: 306 LILKVGWLMQITMGTSPMESMVSAGNIFVGQTESPLLIRPYLADLTISEMHSVMSSGFAT 365 +I +G ++ + TS ES+ + NIFVGQTE+PL++RPY+A +T SE+ +VM G A+ Sbjct: 124 VIRILGGALRAVLKTSRTESLSATANIFVGQTEAPLVVRPYIATMTRSELFAVMCGGLAS 183 Query: 366 IAGSVLGAYISLGIPAAHLLTASVMSAPAALAISKTFWPETKKSK-NSTQTSIKLEKGQE 424 +AGSVL Y +G+P +L+ AS M+AP L +K PET++ + N + Sbjct: 184 VAGSVLAGYAQMGVPLEYLIAASFMAAPGGLLFAKIIVPETEQPRDNPAMEKNDADPQAP 243 Query: 425 NNLVEAASQGASAAVPLVANIAANLIAFLAVLAFINATLSWLGSMFNYPQFSFEIICSYV 484 N+++AA+ GA++ + L N+ A L+AF+A++A +N LS +G FN+P S ++I +V Sbjct: 244 ANVLDAAASGAASGMQLALNVGAMLLAFIALIALVNGILSGVGGWFNHPDLSLQMILGWV 303 Query: 485 LMPFAFMMGVNYDDSFLVAELLGMKTFFNEFVAYQRLSEYIHNRESGGPLFVDGVRQYMS 544 P A+++GV ++++ + +G K NEFVAY EY+ ++ + G+ Q +S Sbjct: 304 FSPLAWVIGVPWNEATVAGSFIGQKLIINEFVAYMNFGEYL---KADTEVAAAGL-QVIS 359 Query: 545 VRSEAIATYALCGFANFGSLGIMIGGLSSLAPHRKSDIASCGIRALIAGTIACFSTACIA 604 ++AI ++ALCGFAN S+ I+IGGL +AP+R+ +IA G+RA+ AGT++ +A IA Sbjct: 360 THTKAIISFALCGFANLSSIAILIGGLGGMAPNRRQEIAQLGMRAVAAGTLSNLMSATIA 419 Query: 605 GV 606 GV Sbjct: 420 GV 421 Lambda K H 0.325 0.139 0.424 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: 584 Number of extensions: 20 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: 683 Length of database: 425 Length adjustment: 35 Effective length of query: 648 Effective length of database: 390 Effective search space: 252720 Effective search space used: 252720 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: 52 (24.6 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