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 Echvi_2954 Echvi_2954 Nucleoside permease
Query= TCDB::Q9KPL5 (418 letters) >FitnessBrowser__Cola:Echvi_2954 Length = 428 Score = 314 bits (804), Expect = 4e-90 Identities = 182/439 (41%), Positives = 267/439 (60%), Gaps = 33/439 (7%) Query: 1 MSLFMSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFS 60 M +IG+ LLG+A L S++RK+++ + VG +Q G I V + + + S Sbjct: 1 MDYLRGMIGIVALLGVAFLFSASRKSVDWKLVGIGVILQIVFGFLITKVAFVESVFASIS 60 Query: 61 DAVSNVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGV 120 A ++++ G FLFG L + G IFAF+VLPT+IFFS + + LYYLGV Sbjct: 61 GAFVKLLSFAQAGAIFLFGDLATDSF-------GTIFAFQVLPTIIFFSTVSAGLYYLGV 113 Query: 121 MQWVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGG 180 +Q ++ + + + + S AES+SAA NIF+GQTEAPL+VRPF+P MT+SEL +M GG Sbjct: 114 LQKIVFGIAWVMARTMKLSGAESLSAAGNIFLGQTEAPLLVRPFIPTMTRSELMCLMTGG 173 Query: 181 LASIAGGVLAGY---------ASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNE 231 +A+IAGGVLA Y A YL+ AS M AP ++ +KL++PET K N+ Sbjct: 174 MATIAGGVLAAYVAFLGGDDPAEQSKFASYLLGASIMNAPAAIVMSKLIIPETNKEGLND 233 Query: 232 DITLDGGDDKPANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGI-GGWFGM 290 + + + N+IDA + GA+ GL+LALNVG ML+AFI +IA++N +L G+ G G+ Sbjct: 234 KLEV-SSEGMGVNLIDAMSIGAADGLKLALNVGGMLLAFIAVIAMLNYLLSGVLGDVTGL 292 Query: 291 PE------------LKLEMLLGWLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQ 338 + LE +LG +F A+L+GV W + G +G KTV NEFVAYS Sbjct: 293 NQFVVDTTNGRFDGFSLEYILGQVFRIFAWLMGVEWQDTLQVGSLLGQKTVINEFVAYSD 352 Query: 339 FAPYLTEAAPVVLSEKTKAIISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAV 398 + E LS K+ I ++ALCGF+N SSIAI +GG+GS+AP ++G+++++G+ A+ Sbjct: 353 LSSMKAEGD---LSPKSIIIATYALCGFSNFSSIAIQVGGIGSIAPGQQGNLSKLGMHAL 409 Query: 399 IAGTLSNLMAATIAGFFLS 417 +A TL+ +M ATIAG S Sbjct: 410 LAATLACMMTATIAGMLFS 428 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: 532 Number of extensions: 28 Number of successful extensions: 7 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: 428 Length adjustment: 32 Effective length of query: 386 Effective length of database: 396 Effective search space: 152856 Effective search space used: 152856 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