Align Concentrative nucleoside transporter, CNT, of 418 aas and 12 TMSs. A repeat-swapped model of VcCNT predicts that nucleoside transport occurs via a mechanism involving an elevator-like substrate binding domain movement across the membrane (characterized)
to candidate WP_086510575.1 BZY95_RS14240 NupC/NupG family nucleoside CNT transporter
Query= TCDB::Q9KPL5 (418 letters) >NCBI__GCF_002151265.1:WP_086510575.1 Length = 423 Score = 566 bits (1459), Expect = e-166 Identities = 294/424 (69%), Positives = 344/424 (81%), Gaps = 13/424 (3%) Query: 1 MSLFMSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFS 60 M+ MSL+GMA L+ IA++ S+NR AI LRTVGGAFAIQ +GAF+LYVP+GQ +L+ S Sbjct: 1 MTAIMSLVGMATLIVIALIFSTNRGAIRLRTVGGAFAIQAGIGAFVLYVPFGQTVLQTIS 60 Query: 61 DAVSNVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGV 120 VS V+ Y NDG FLFGGL G GF+FA +VLP +IFFS+LI+VLYY+G+ Sbjct: 61 AGVSQVVLYANDGIDFLFGGLADT------GNIGFVFAIKVLPVIIFFSSLIAVLYYIGI 114 Query: 121 MQWVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGG 180 MQWVIRILGG LQKALGTSR ES+SA ANIFVGQTEAPLVVRPF+ +MT S+LFAVMCGG Sbjct: 115 MQWVIRILGGALQKALGTSRTESLSATANIFVGQTEAPLVVRPFIARMTPSQLFAVMCGG 174 Query: 181 LASIAGGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDN--EDITLDGG 238 LAS+AG VLAGYA++G+ +EYLVAASFMAAPGGLLFAKL+MPETEKP D+ E + Sbjct: 175 LASVAGSVLAGYAALGIPMEYLVAASFMAAPGGLLFAKLIMPETEKPVDDVEEASEVIEA 234 Query: 239 DDKPANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEML 298 +D+P NV+DAAA GAS+GL+LA NVGAML+AFIGLIALINGMLGG+GGW G +L LE++ Sbjct: 235 EDRPVNVLDAAAAGASSGLRLAANVGAMLLAFIGLIALINGMLGGVGGWVGFEQLSLELI 294 Query: 299 LGWLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAPV-----VLSE 353 LGWLFAPLAF++GVPW EAT+AG FIG K V NEFVAY APY+ A V +S Sbjct: 295 LGWLFAPLAFVLGVPWAEATLAGSFIGQKLVVNEFVAYINLAPYIDGDAIVTNTGQAMSG 354 Query: 354 KTKAIISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIAG 413 T AI+SFALCGFANLSSIAILLGGLGS+AP RR DIAR GVKAV+AGTLSNLM+A IAG Sbjct: 355 HTIAILSFALCGFANLSSIAILLGGLGSIAPSRRHDIARFGVKAVLAGTLSNLMSAAIAG 414 Query: 414 FFLS 417 FFLS Sbjct: 415 FFLS 418 Lambda K H 0.325 0.141 0.414 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: 653 Number of extensions: 30 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: 418 Length of database: 423 Length adjustment: 32 Effective length of query: 386 Effective length of database: 391 Effective search space: 150926 Effective search space used: 150926 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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