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 16270 b2161 predicted nucleoside transporter (NCBI)
Query= TCDB::Q9UA35 (683 letters) >FitnessBrowser__Keio:16270 Length = 416 Score = 265 bits (676), Expect = 4e-75 Identities = 145/415 (34%), Positives = 238/415 (57%), Gaps = 23/415 (5%) Query: 201 GLILYILLVFIFSKHPTKVRWRIVIWGLLLQFIFGLIILRTKPGLDAFNWLGIQVQTFLK 260 G+++ + + F+ S + K+ R V L+LQ + G I+L PG + V + Sbjct: 9 GMVVLLTIAFLLSVNKKKISLRTVGAALVLQVVIGGIMLWLPPGRWVAEKVAFGVHKVMA 68 Query: 261 YTDAGSRFLFGD----------DFQDHFFAFAVLPIVIFFSTVMSMMYYLGLMQWLILKV 310 Y+DAGS F+FG D F F VLP +IF + ++S++YY+G+M LI + Sbjct: 69 YSDAGSAFIFGSLVGPKMDTLFDGAGFIFGFRVLPAIIFVTALVSILYYIGVMGILIRIL 128 Query: 311 GWLMQITMGTSPMESMVSAGNIFVGQTESPLLIRPYLADLTISEMHSVMSSGFATIAGSV 370 G + Q + S +ES V+ IF+GQ E P +++P++ L +E+ + + SG A+IAGS Sbjct: 129 GGIFQKALNISKIESFVAVTTIFLGQNEIPAIVKPFIDRLNRNELFTAICSGMASIAGST 188 Query: 371 LGAYISLGIPAAHLLTASVMSAPAALAISKTFWPETKKSKNSTQTSIKLEKGQENNLVEA 430 + Y +LG+P +LL AS+M+ P + ++ P T+ S+ S ++ + +++EA Sbjct: 189 MIGYAALGVPVEYLLAASLMAIPGGILFARLLSPATESSQVSF-NNLSFTETPPKSIIEA 247 Query: 431 ASQGASAAVPLVANIAANLIAFLAVLAFINATLSWLGSMFNYPQFSFEIICSYVLMPFAF 490 A+ GA + + A +A ++AF+A++A IN + +G F + S E I Y+L P A+ Sbjct: 248 AATGAMTGLKIAAGVATVVMAFVAIIALINGIIGGVGGWFGFEHASLESILGYLLAPLAW 307 Query: 491 MMGVNYDDSFLVAELLGMKTFFNEFVAYQRLSEYIHNRESGGPLFVDGVRQYMSVRSEAI 550 +MGV++ D+ L L+G K NEFVAY S Y+ ++ G L ++ AI Sbjct: 308 VMGVDWSDANLAGSLIGQKLAINEFVAYLNFSPYL---QTAGTL---------DAKTVAI 355 Query: 551 ATYALCGFANFGSLGIMIGGLSSLAPHRKSDIASCGIRALIAGTIACFSTACIAG 605 ++ALCGFANFGS+G+++G S++APHR +IA G+RAL A T++ +A IAG Sbjct: 356 ISFALCGFANFGSIGVVVGAFSAVAPHRAPEIAQLGLRALAAATLSNLMSATIAG 410 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: 579 Number of extensions: 31 Number of successful extensions: 4 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: 416 Length adjustment: 35 Effective length of query: 648 Effective length of database: 381 Effective search space: 246888 Effective search space used: 246888 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