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 203375 SO4296 NupC family protein (NCBI ptt file)
Query= TCDB::Q9KPL5 (418 letters) >FitnessBrowser__MR1:203375 Length = 401 Score = 394 bits (1013), Expect = e-114 Identities = 211/414 (50%), Positives = 289/414 (69%), Gaps = 13/414 (3%) Query: 3 LFMSLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFSDA 62 + S++G+ VLLG+ +L S NR I+ R V GAF I +L F+L G ++L S+ Sbjct: 1 MIQSILGIFVLLGVGLLFSDNRSLISWRAVIGAFGIIIALAFFVLATEIGADVLLAVSNT 60 Query: 63 VSNVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGVMQ 122 V V YG +G F FG LV+ F V G GF++A +VLP +IF +AL S+LYYLG+MQ Sbjct: 61 VGKVFGYGTEGIKFAFGSLVN---FSV-EGIGFVWALQVLPQIIFTAALTSLLYYLGIMQ 116 Query: 123 WVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGGLA 182 W + I+GG LQK LGTSRAESM+AA NI +GQTEAPL+++P+ +T++++FAVM GGL+ Sbjct: 117 WFVLIIGGSLQKVLGTSRAESMNAAGNIILGQTEAPLLIKPYHRVLTRAQIFAVMVGGLS 176 Query: 183 SIAGGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGGDDKP 242 SIAG +LAG A MGV + YL+ A FM+AP GL+FAKL++PETE P NE L D+KP Sbjct: 177 SIAGSILAGLAGMGVALNYLIMACFMSAPAGLMFAKLLIPETE-PTVNEVPELP-DDEKP 234 Query: 243 ANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLLGWL 302 ++ IDA A GA AG+ +A VGA++IA IGL+AL+NG LG IG FGMP L ++M+LG L Sbjct: 235 SSFIDAIAKGAIAGMGIAAIVGAVIIACIGLMALLNGGLGAIGELFGMPTLTVDMILGTL 294 Query: 303 FAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAPVVLSEKTKAIISFA 362 FAP+A+LIG+PW EA+ AG F+G K NEFVA++ V LS ++ AI++ A Sbjct: 295 FAPVAWLIGIPWVEASTAGAFLGQKIAMNEFVAFANM-------GNVELSARSNAIMTIA 347 Query: 363 LCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIAGFFL 416 LCGFAN+ S+A++ G L + P+R G I ++G+K ++A TL+NLM A I F+ Sbjct: 348 LCGFANIGSVAMVCGALSKMIPQRAGLIGQLGMKVLLAATLANLMNAAIVSLFI 401 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: 528 Number of extensions: 24 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: 401 Length adjustment: 31 Effective length of query: 387 Effective length of database: 370 Effective search space: 143190 Effective search space used: 143190 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