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 WP_011386447.1 AMB_RS20720 nucleoside:proton symporter
Query= TCDB::Q9UA35 (683 letters) >NCBI__GCF_000009985.1:WP_011386447.1 Length = 413 Score = 195 bits (496), Expect = 3e-54 Identities = 132/425 (31%), Positives = 215/425 (50%), Gaps = 38/425 (8%) Query: 201 GLILYILLVFIFSKHPTKVRWRIVIWGLLLQFIFGLIILRTKPGLDAFNWLGIQVQTFLK 260 G+I I + F+ S+ V WR+V+ GL +Q + L++L+ F L V Sbjct: 8 GIIALIGVAFLLSEDRRAVSWRVVVAGLAVQGLLALLLLKVPAAKLLFLGLDRAVAALQT 67 Query: 261 YTDAGSRFLFG------------DDFQDHFFAFAVLPIVIFFSTVMSMMYYLGLMQWLIL 308 T AG+ F+FG + AF LP+V+ S + +++Y+ ++ ++ Sbjct: 68 ATRAGTSFVFGYVGGAPAPWTAANPASGFILAFQALPLVLLMSALSALLYHWRILPVVVR 127 Query: 309 KVGWLMQITMGTSPMESMVSAGNIFVGQTESPLLIRPYLADLTISEMHSVMSSGFATIAG 368 L++ +MG + ++ F+G E+PLLIRPY+ L+ E+ VM++G +TIAG Sbjct: 128 AASRLLEKSMGVGGAVGVSASATAFLGMIEAPLLIRPYVGKLSRGELFLVMTAGMSTIAG 187 Query: 369 SVLGAYISLG---IPAA--HLLTASVMSAPAALAISKTFWPETKKSKNSTQTSIKLEKGQ 423 +V+ Y + IP A HLLTAS++S PA L I K P+ + KL G Sbjct: 188 TVMVLYATFLDGIIPDAIGHLLTASLISVPAGLMIGKIMVPDCALTGAG-----KLGDGH 242 Query: 424 EN-NLVEAASQGASAAVPLVANIAANLIAFLAVLAFINATLSWLGSMFNYPQFSFEIICS 482 + ++A +G V L+ I A L+ +A+++ NA L+ L + P + + + Sbjct: 243 DYAGSMDAVVKGTMDGVRLLVGIVAMLVVLVALVSLANAGLALLPEVAGAP-LTLQRVLG 301 Query: 483 YVLMPFAFMMGVNYDDSFLVAELLGMKTFFNEFVAYQRLSEYIHNRESGGPLFVDGVRQY 542 + + P + MG+ + L+G KT NE +AY L+ + Sbjct: 302 WAMAPVVWAMGIPAGEMVTAGALMGTKTVLNELLAYLDLAHL--------------PPEA 347 Query: 543 MSVRSEAIATYALCGFANFGSLGIMIGGLSSLAPHRKSDIASCGIRALIAGTIACFSTAC 602 +S RS I TY LCGFAN GSLGI+I GLS +AP R+++I + G R++I+GT+A T Sbjct: 348 LSARSRLIMTYGLCGFANLGSLGILIAGLSVMAPERRAEIVALGGRSIISGTMASCLTGS 407 Query: 603 IAGVL 607 + G+L Sbjct: 408 MVGLL 412 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: 532 Number of extensions: 21 Number of successful extensions: 6 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: 413 Length adjustment: 35 Effective length of query: 648 Effective length of database: 378 Effective search space: 244944 Effective search space used: 244944 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