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 6936789 Sama_0971 nucleoside transporter (RefSeq)
Query= TCDB::Q9KPL5 (418 letters) >FitnessBrowser__SB2B:6936789 Length = 419 Score = 575 bits (1482), Expect = e-169 Identities = 296/426 (69%), Positives = 350/426 (82%), Gaps = 17/426 (3%) Query: 1 MSLFMSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFS 60 MS+ MSL+G+AVLLGI LLS+N+KAI++R VGGA AIQ + G F+LYVPWG+++L+ S Sbjct: 1 MSILMSLVGVAVLLGIGFLLSNNKKAISVRAVGGALAIQAAFGGFVLYVPWGKDILKTVS 60 Query: 61 DAVSNVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGV 120 D VS VI YG +G +FLFG L K+ GFIFA VLP +IFFS+LI+VLYYLG+ Sbjct: 61 DGVSAVIGYGQNGINFLFGDLAQFKV-------GFIFAINVLPVIIFFSSLIAVLYYLGI 113 Query: 121 MQWVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGG 180 MQWVIRI+GGGLQKALGTSR ESMSA ANIFVGQTEAPLVVRPF+P MTQSELFA+M GG Sbjct: 114 MQWVIRIIGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGG 173 Query: 181 LASIAGGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGGDD 240 LASIAG VLAGYASMGVKIEYLVAASFMAAPGGLL AKLM PETE + NE L D Sbjct: 174 LASIAGSVLAGYASMGVKIEYLVAASFMAAPGGLLMAKLMHPETENTK-NEMDELPEDPD 232 Query: 241 KPANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLLG 300 KPANV+DAAA GAS+G+ LALNVGAMLIAF+GLIA+ING++GG+GGWFG+ L LE++LG Sbjct: 233 KPANVLDAAAAGASSGMHLALNVGAMLIAFVGLIAMINGIIGGVGGWFGVEGLTLELILG 292 Query: 301 WLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAP---------VVL 351 ++F PLAFLIGVPWNEA VAG FIG K V NEFVAY FAPYL + A + Sbjct: 293 YIFMPLAFLIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADGGIVVAETGAAM 352 Query: 352 SEKTKAIISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATI 411 S++TKAI+SFALCGFANLSSIAILLGGLG++AP RR D+A++G++AVIAG+L+NLM+AT+ Sbjct: 353 SDRTKAIVSFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLANLMSATL 412 Query: 412 AGFFLS 417 AG FL+ Sbjct: 413 AGLFLA 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: 684 Number of extensions: 38 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: 419 Length adjustment: 32 Effective length of query: 386 Effective length of database: 387 Effective search space: 149382 Effective search space used: 149382 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 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