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 200392 SO1214 NupC family protein (NCBI ptt file)
Query= TCDB::Q9UA35 (683 letters) >FitnessBrowser__MR1:200392 Length = 432 Score = 298 bits (762), Expect = 5e-85 Identities = 160/428 (37%), Positives = 257/428 (60%), Gaps = 16/428 (3%) Query: 194 NQVIPFFGLILYILLVFIFSKHPTKVRWRIVIWGLLLQFIFGLIILRTKPGLDAFNWLGI 253 N ++ G+++ + + F+ S + + R V L +Q FG +L G D + Sbjct: 2 NILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKGMSD 61 Query: 254 QVQTFLKYTDAGSRFLFGD--DFQDHF-FAFAVLPIVIFFSTVMSMMYYLGLMQWLILKV 310 V + + + G FLFGD +F+ F FA VLP+++FFS++++++YYLG+MQW+I + Sbjct: 62 AVSSVIGFAQNGIGFLFGDLANFKLGFIFAVNVLPVIVFFSSLIAVLYYLGVMQWIIRII 121 Query: 311 GWLMQITMGTSPMESMVSAGNIFVGQTESPLLIRPYLADLTISEMHSVMSSGFATIAGSV 370 G +Q +GTS ESM + NIFVGQTE+PL++RP++ +T SE+ +VM G A+IAGSV Sbjct: 122 GGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAVMVGGLASIAGSV 181 Query: 371 LGAYISLGIPAAHLLTASVMSAPAALAISKTFWPETKKSKNSTQTSIKLEKGQENNLVEA 430 L Y +G+P L+ AS M+AP L ++K PET+ +KN + + + N+++A Sbjct: 182 LAGYAQMGVPIEFLVAASFMAAPGGLLMAKLMHPETEVAKND-MDELPEDPDKPANVLDA 240 Query: 431 ASQGASAAVPLVANIAANLIAFLAVLAFINATLSWLGSMFNYPQFSFEIICSYVLMPFAF 490 A+ GAS+ + L N+ A L+AF+ ++A IN + +G F + E+I YV MP AF Sbjct: 241 AAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEGLTLELILGYVFMPLAF 300 Query: 491 MMGVNYDDSFLVAELLGMKTFFNEFVAYQRLSEYIHNR------------ESGGPLFVDG 538 ++GV ++++ + +G K NEFVAY + YI + PL V Sbjct: 301 LIGVPWNEALVAGSFIGQKIIVNEFVAYLNFAPYISEAATACTSVAAEVVKGSLPLCVAE 360 Query: 539 VRQYMSVRSEAIATYALCGFANFGSLGIMIGGLSSLAPHRKSDIASCGIRALIAGTIACF 598 + M+ R++AI ++ALCGFAN S+ I++GGL ++AP+R+ D+A GIRA+IAG++A Sbjct: 361 TQAVMTSRTQAIVSFALCGFANLSSIAILLGGLGAMAPNRRHDLAKMGIRAVIAGSLANL 420 Query: 599 STACIAGV 606 +A IAG+ Sbjct: 421 MSATIAGL 428 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: 599 Number of extensions: 24 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: 432 Length adjustment: 35 Effective length of query: 648 Effective length of database: 397 Effective search space: 257256 Effective search space used: 257256 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