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 BPHYT_RS21960 BPHYT_RS21960 nucleoside transporter
Query= TCDB::Q9UA35 (683 letters) >FitnessBrowser__BFirm:BPHYT_RS21960 Length = 425 Score = 273 bits (697), Expect = 2e-77 Identities = 147/416 (35%), Positives = 243/416 (58%), Gaps = 15/416 (3%) Query: 201 GLILYILLVFIFSKHPTKVRWRIVIWGLLLQFIFGLIILRTKPGLDAFNWLGIQVQTFLK 260 G+ + +L+ FIFS + +R R VI LL+Q G IL G + V L Sbjct: 10 GIAVLLLIAFIFSTNRRAIRLRTVISALLVQIGIGAFILFVPFGKSILSGAASAVNHVLG 69 Query: 261 YTDAGSRFLFG--------DDFQDHFFAFAV--LPIVIFFSTVMSMMYYLGLMQWLILKV 310 Y +AG FLFG F D F FAV LP +IF + ++S++YYLG+M+W+++ + Sbjct: 70 YGNAGIEFLFGGLVQAKMFQVFGDGGFVFAVRVLPAIIFVTALISVLYYLGVMRWIVIVL 129 Query: 311 GWLMQITMGTSPMESMVSAGNIFVGQTESPLLIRPYLADLTISEMHSVMSSGFATIAGSV 370 G + Q +G S +ES + IF+GQ+E P +++P+ A++T +E+ +VMSSG A +AGSV Sbjct: 130 GTVFQKLLGVSKIESFSAVTTIFLGQSEMPAVVKPFTAEMTGAELFAVMSSGMAAVAGSV 189 Query: 371 LGAYISLGIPAAHLLTASVMSAPAALAISKTFWPETKKSKNSTQTSIKLEKGQENNLVEA 430 L Y LG+ +LL AS M+ P L +K P T+ S+ + ++ ++ + N++EA Sbjct: 190 LAGYAGLGVRIEYLLAASFMAVPGGLLFAKIIHPSTEPSRVHLE-NLNFDEKRPANIIEA 248 Query: 431 ASQGASAAVPLVANIAANLIAFLAVLAFINATLSWLGSMFNYPQFSFEIICSYVLMPFAF 490 AS GA+ + + + A LIAF+ ++A +N + +G F +PQ S + + + P A+ Sbjct: 249 ASSGATVGLKIAVMVGAMLIAFVGLIALLNGIVGGVGGWFGHPQLSMQSVLGVIFAPLAY 308 Query: 491 MMGVNYDDSFLVAELLGMKTFFNEFVAYQRLSEYIHNRESGGPLFVDGVRQYMSVRSEAI 550 ++GV ++++ + LG K NEFVAY LS Y+ + S + + R+ AI Sbjct: 309 LIGVPWNEATIAGNFLGQKVILNEFVAYASLSPYLKDAASVSAAGLAA----LDPRTIAI 364 Query: 551 ATYALCGFANFGSLGIMIGGLSSLAPHRKSDIASCGIRALIAGTIACFSTACIAGV 606 ++ALCGFANF S+ ++ GG S++AP R++++A G+R ++A T++ +A IAG+ Sbjct: 365 LSFALCGFANFSSIAVLTGGFSAVAPARRAEVARYGLRVVLAATLSNLMSATIAGM 420 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: 592 Number of extensions: 27 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: 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