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_011386447.1 AMB_RS20720 nucleoside:proton symporter
Query= TCDB::Q9KPL5 (418 letters) >NCBI__GCF_000009985.1:WP_011386447.1 Length = 413 Score = 253 bits (646), Expect = 7e-72 Identities = 150/417 (35%), Positives = 239/417 (57%), Gaps = 16/417 (3%) Query: 7 LIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFSDAVSNV 66 LIG+ L+G+A LLS +R+A++ R V A+Q L +L VP + L G AV+ + Sbjct: 6 LIGIIALIGVAFLLSEDRRAVSWRVVVAGLAVQGLLALLLLKVPAAKLLFLGLDRAVAAL 65 Query: 67 INYGNDGTSFLFG--GLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGVMQWV 124 GTSF+FG G GFI AF+ LP ++ SAL ++LY+ ++ V Sbjct: 66 QTATRAGTSFVFGYVGGAPAPWTAANPASGFILAFQALPLVLLMSALSALLYHWRILPVV 125 Query: 125 IRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGGLASI 184 +R L+K++G A +SA+A F+G EAPL++RP+V K+++ ELF VM G+++I Sbjct: 126 VRAASRLLEKSMGVGGAVGVSASATAFLGMIEAPLLIRPYVGKLSRGELFLVMTAGMSTI 185 Query: 185 AGGVLAGYASM--GV---KIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGGD 239 AG V+ YA+ G+ I +L+ AS ++ P GL+ K+M+P+ + L G Sbjct: 186 AGTVMVLYATFLDGIIPDAIGHLLTASLISVPAGLMIGKIMVPDCALTGAGK---LGDGH 242 Query: 240 DKPANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLL 299 D A +DA G G++L + + AML+ + L++L N L + G P L L+ +L Sbjct: 243 DY-AGSMDAVVKGTMDGVRLLVGIVAMLVVLVALVSLANAGLALLPEVAGAP-LTLQRVL 300 Query: 300 GWLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAPVVLSEKTKAII 359 GW AP+ + +G+P E AG +G KTV NE +AY L P LS +++ I+ Sbjct: 301 GWAMAPVVWAMGIPAGEMVTAGALMGTKTVLNELLAYLD----LAHLPPEALSARSRLIM 356 Query: 360 SFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIAGFFL 416 ++ LCGFANL S+ IL+ GL +AP+RR +I +G +++I+GT+++ + ++ G L Sbjct: 357 TYGLCGFANLGSLGILIAGLSVMAPERRAEIVALGGRSIISGTMASCLTGSMVGLLL 413 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: 485 Number of extensions: 28 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: 413 Length adjustment: 31 Effective length of query: 387 Effective length of database: 382 Effective search space: 147834 Effective search space used: 147834 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