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 H281DRAFT_03110 H281DRAFT_03110 concentrative nucleoside transporter, CNT family
Query= TCDB::Q9KPL5 (418 letters) >FitnessBrowser__Burk376:H281DRAFT_03110 Length = 425 Score = 488 bits (1257), Expect = e-142 Identities = 244/418 (58%), Positives = 321/418 (76%), Gaps = 7/418 (1%) Query: 6 SLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFSDAVSN 65 +++G+AVLL IA + S+NR+AI LRTV A Q +GAFIL+VP G+ +L + V+N Sbjct: 7 NVLGIAVLLFIAFIFSTNRRAIRLRTVSSALLAQVCIGAFILFVPLGKTILAAAAAGVNN 66 Query: 66 VINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGVMQWVI 125 V+ YGN G FLFGGLV +MFEVFG GGF+FA RVLP +IF +ALISVLYYLGVM+W++ Sbjct: 67 VLGYGNAGIEFLFGGLVQSRMFEVFGNGGFVFAVRVLPAIIFVTALISVLYYLGVMRWIV 126 Query: 126 RILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGGLASIA 185 +LG QK LG S+ ES SA IF+GQ+E P VV+PF MT +ELFAVM G+A++A Sbjct: 127 IVLGTVFQKLLGVSKLESFSAVTTIFLGQSEMPAVVKPFTRDMTGAELFAVMSSGMAAVA 186 Query: 186 GGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGGDDKPANV 245 G VLAGYA +GV+IEYL+AASFMA PGGLLFAK++ P TE + + D L+ + +PANV Sbjct: 187 GSVLAGYAGLGVRIEYLLAASFMAVPGGLLFAKIIHPSTEPSRVHLD-NLNFDEKRPANV 245 Query: 246 IDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLLGWLFAP 305 I+AA+ GA+ GL++A+ VGAMLIAF+GLIAL+NG++GGIG WFG P+L ++ +LG +FAP Sbjct: 246 IEAASSGATVGLRIAVMVGAMLIAFVGLIALLNGLVGGIGAWFGHPQLSMQSVLGVVFAP 305 Query: 306 LAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAPV------VLSEKTKAII 359 LA+LIGVPWNEA +AG F+G K + NEFVAY+ +PYL +AA V L +T AI+ Sbjct: 306 LAWLIGVPWNEAVIAGNFLGQKIILNEFVAYASLSPYLKDAASVTAAGLHALDPRTIAIL 365 Query: 360 SFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIAGFFLS 417 SFALCGFAN +SIA+L GG ++AP+RR ++AR G++ V+A TLSNLM+ATIAG F++ Sbjct: 366 SFALCGFANFASIAVLTGGFSAVAPERRAEVARYGLRVVLAATLSNLMSATIAGMFIT 423 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: 569 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: 418 Length of database: 425 Length adjustment: 32 Effective length of query: 386 Effective length of database: 393 Effective search space: 151698 Effective search space used: 151698 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