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 200392 SO1214 NupC family protein (NCBI ptt file)
Query= TCDB::Q9KPL5 (418 letters) >FitnessBrowser__MR1:200392 Length = 432 Score = 563 bits (1450), Expect = e-165 Identities = 291/439 (66%), Positives = 351/439 (79%), Gaps = 30/439 (6%) Query: 1 MSLFMSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFS 60 M++ MSL+G+ VLL I LLS+N+KAINLRTVGGA AIQ + G F+LYVP G+++L+G S Sbjct: 1 MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKGMS 60 Query: 61 DAVSNVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGV 120 DAVS+VI + +G FLFG L + K+ GFIFA VLP ++FFS+LI+VLYYLGV Sbjct: 61 DAVSSVIGFAQNGIGFLFGDLANFKL-------GFIFAVNVLPVIVFFSSLIAVLYYLGV 113 Query: 121 MQWVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGG 180 MQW+IRI+GGGLQKALGTSR ESMSA ANIFVGQTEAPLVVRPF+P MTQSELFAVM GG Sbjct: 114 MQWIIRIIGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAVMVGG 173 Query: 181 LASIAGGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGGDD 240 LASIAG VLAGYA MGV IE+LVAASFMAAPGGLL AKLM PETE +++ D L D Sbjct: 174 LASIAGSVLAGYAQMGVPIEFLVAASFMAAPGGLLMAKLMHPETEVAKNDMD-ELPEDPD 232 Query: 241 KPANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLLG 300 KPANV+DAAA GAS+G+ LALNVGAML+AF+GLIA+ING++GG+GGWFG+ L LE++LG Sbjct: 233 KPANVLDAAAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEGLTLELILG 292 Query: 301 WLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAA------------- 347 ++F PLAFLIGVPWNEA VAG FIG K + NEFVAY FAPY++EAA Sbjct: 293 YVFMPLAFLIGVPWNEALVAGSFIGQKIIVNEFVAYLNFAPYISEAATACTSVAAEVVKG 352 Query: 348 ---------PVVLSEKTKAIISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAV 398 V++ +T+AI+SFALCGFANLSSIAILLGGLG++AP RR D+A+MG++AV Sbjct: 353 SLPLCVAETQAVMTSRTQAIVSFALCGFANLSSIAILLGGLGAMAPNRRHDLAKMGIRAV 412 Query: 399 IAGTLSNLMAATIAGFFLS 417 IAG+L+NLM+ATIAG FL+ Sbjct: 413 IAGSLANLMSATIAGLFLA 431 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: 661 Number of extensions: 35 Number of successful extensions: 5 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: 432 Length adjustment: 32 Effective length of query: 386 Effective length of database: 400 Effective search space: 154400 Effective search space used: 154400 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: 51 (24.3 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