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 202800 SO3706 NupC family protein (NCBI ptt file)
Query= TCDB::Q9KPL5 (418 letters) >FitnessBrowser__MR1:202800 Length = 422 Score = 509 bits (1312), Expect = e-149 Identities = 254/422 (60%), Positives = 331/422 (78%), Gaps = 7/422 (1%) Query: 1 MSLFMSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFS 60 M + +SL+G+ LL +A L S NR+AIN RTVG AF +Q +LGAF++Y GQ ++ + Sbjct: 1 MQILVSLLGIITLLAVAYLASENRRAINYRTVGLAFLLQLALGAFVMYSALGQSMIFSMA 60 Query: 61 DAVSNVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGV 120 AVSNVI+Y NDG SF+FGGLVS KM+E+FG GGF+ AF+VLP ++FFSAL +VLYYLG+ Sbjct: 61 AAVSNVISYSNDGMSFMFGGLVSDKMYELFGAGGFVIAFKVLPIIVFFSALSAVLYYLGI 120 Query: 121 MQWVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGG 180 MQ V++ +GG LQK L TS+AESMSA+ANIF+G TEAPL+++P++P+MT+SELFAVMCGG Sbjct: 121 MQLVVKAVGGALQKLLNTSKAESMSASANIFLGVTEAPLLIKPYMPRMTRSELFAVMCGG 180 Query: 181 LASIAGGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGGDD 240 LASIAG +LAGYA +G+K+EYL+AASFMAAPGGLLFAKL++P+TE D + ++ Sbjct: 181 LASIAGTMLAGYAQLGIKMEYLLAASFMAAPGGLLFAKLLIPQTETINDAHLQLTE--EN 238 Query: 241 KPANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLLG 300 +P N++DAA G +GL LAL VGAML +FI L+AL NGMLGGIG WFG+ L L+ +LG Sbjct: 239 QPRNLLDAATTGTMSGLSLALAVGAMLFSFISLVALFNGMLGGIGAWFGLEGLTLQQILG 298 Query: 301 WLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAPVV-----LSEKT 355 +LFAPLA+L+G+ WNEA +AG FIG K V NEF AY APYL+ A V +SE+T Sbjct: 299 YLFAPLAWLMGISWNEAMLAGSFIGQKIVINEFFAYINLAPYLSGDALVATTGQPMSERT 358 Query: 356 KAIISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIAGFF 415 + I+SFALCGFAN+ ++AI + G+G L P+RR +IA +G+KA+ AG LSNLMAATIAG F Sbjct: 359 QVILSFALCGFANIGTVAIAIAGIGGLVPERRAEIASLGLKALAAGILSNLMAATIAGLF 418 Query: 416 LS 417 +S Sbjct: 419 MS 420 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: 632 Number of extensions: 30 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: 422 Length adjustment: 32 Effective length of query: 386 Effective length of database: 390 Effective search space: 150540 Effective search space used: 150540 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