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_073037325.1 BUB04_RS04420 nucleoside:proton symporter
Query= TCDB::Q9KPL5 (418 letters) >NCBI__GCF_900129305.1:WP_073037325.1 Length = 414 Score = 282 bits (722), Expect = 1e-80 Identities = 163/424 (38%), Positives = 259/424 (61%), Gaps = 18/424 (4%) Query: 1 MSLFMSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFS 60 M S +G+ +L+ +A S NR+ + R V G +Q +L +L +P + + + Sbjct: 1 MLQLQSALGLVMLVFLAWGFSENRRRLAWREVAGGIVLQVALAFILLKMPGARLVFAWLN 60 Query: 61 DAVSNVINYGNDGTSFLFGGLVSGKM-FEVFGGGG-FIFAFRVLPTLIFFSALISVLYYL 118 AV + GT F+FG L G F+V G +I AFR LP ++ SAL ++LY+ Sbjct: 61 QAVQALSAATEAGTGFVFGYLGGGDPPFQVRPGASTYILAFRGLPLVLVMSALSALLYHW 120 Query: 119 GVMQWVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMC 178 G++ V+R L L++A G S E++ AANIFVG EAP++VRP++ ++++SELF +M Sbjct: 121 GIIPRVVRALAWMLKRATGISGVEALGTAANIFVGMVEAPVLVRPYLERVSRSELFTIMA 180 Query: 179 GGLASIAGGVLAGYASM------GVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNED 232 G+A+IAG V+ YAS+ GV + +L+ AS ++AP + +KLM+P E+ + Sbjct: 181 AGMATIAGTVMVLYASILEPVIPGV-MGHLLVASIISAPAAVTVSKLMVPPVEEGVEG-S 238 Query: 233 ITLDGGDDKPANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPE 292 + L + + + +DA G AGL L LN+ AMLI F+ L+ L N +LG + W G P Sbjct: 239 LAL---EREARSAMDAVTQGTLAGLSLLLNIIAMLIVFVALVHLANMILGWVPSWGGEP- 294 Query: 293 LKLEMLLGWLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAPVVLS 352 ++ LLG + AP+ +L+GVPW+EA AG +G+KT+ NEF+AY Q A +A LS Sbjct: 295 WTVQRLLGLIMAPVTWLMGVPWSEAHTAGSLMGVKTILNEFLAYLQMAALPADA----LS 350 Query: 353 EKTKAIISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIA 412 +++ I+++ALCGFAN+ S+ I++GGLG++AP RR +I +GV++++AGTL+ M + Sbjct: 351 PRSRLILTYALCGFANMGSLGIMIGGLGAMAPARRPEIVELGVRSIVAGTLATCMTGAVI 410 Query: 413 GFFL 416 G + Sbjct: 411 GLLV 414 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: 487 Number of extensions: 20 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: 414 Length adjustment: 31 Effective length of query: 387 Effective length of database: 383 Effective search space: 148221 Effective search space used: 148221 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 24 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