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 BPHYT_RS21960 BPHYT_RS21960 nucleoside transporter
Query= TCDB::Q9KPL5 (418 letters) >FitnessBrowser__BFirm:BPHYT_RS21960 Length = 425 Score = 498 bits (1282), Expect = e-145 Identities = 246/419 (58%), Positives = 328/419 (78%), Gaps = 9/419 (2%) Query: 6 SLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFSDAVSN 65 +++G+AVLL IA + S+NR+AI LRTV A +Q +GAFIL+VP+G+ +L G + AV++ Sbjct: 7 NILGIAVLLLIAFIFSTNRRAIRLRTVISALLVQIGIGAFILFVPFGKSILSGAASAVNH 66 Query: 66 VINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGVMQWVI 125 V+ YGN G FLFGGLV KMF+VFG GGF+FA RVLP +IF +ALISVLYYLGVM+W++ Sbjct: 67 VLGYGNAGIEFLFGGLVQAKMFQVFGDGGFVFAVRVLPAIIFVTALISVLYYLGVMRWIV 126 Query: 126 RILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGGLASIA 185 +LG QK LG S+ ES SA IF+GQ+E P VV+PF +MT +ELFAVM G+A++A Sbjct: 127 IVLGTVFQKLLGVSKIESFSAVTTIFLGQSEMPAVVKPFTAEMTGAELFAVMSSGMAAVA 186 Query: 186 GGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDN-EDITLDGGDDKPAN 244 G VLAGYA +GV+IEYL+AASFMA PGGLLFAK++ P TE + + E++ D + +PAN Sbjct: 187 GSVLAGYAGLGVRIEYLLAASFMAVPGGLLFAKIIHPSTEPSRVHLENLNFD--EKRPAN 244 Query: 245 VIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLLGWLFA 304 +I+AA+ GA+ GL++A+ VGAMLIAF+GLIAL+NG++GG+GGWFG P+L ++ +LG +FA Sbjct: 245 IIEAASSGATVGLKIAVMVGAMLIAFVGLIALLNGIVGGVGGWFGHPQLSMQSVLGVIFA 304 Query: 305 PLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAPV------VLSEKTKAI 358 PLA+LIGVPWNEAT+AG F+G K + NEFVAY+ +PYL +AA V L +T AI Sbjct: 305 PLAYLIGVPWNEATIAGNFLGQKVILNEFVAYASLSPYLKDAASVSAAGLAALDPRTIAI 364 Query: 359 ISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIAGFFLS 417 +SFALCGFAN SSIA+L GG ++AP RR ++AR G++ V+A TLSNLM+ATIAG F++ Sbjct: 365 LSFALCGFANFSSIAVLTGGFSAVAPARRAEVARYGLRVVLAATLSNLMSATIAGMFIT 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: 574 Number of extensions: 28 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