GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nupC in Caulobacter crescentus NA1000

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 CCNA_02171 CCNA_02171 nucleoside permease nupC

Query= TCDB::Q9KPL5
         (418 letters)



>lcl|FitnessBrowser__Caulo:CCNA_02171 CCNA_02171 nucleoside permease
           nupC
          Length = 426

 Score =  260 bits (664), Expect = 6e-74
 Identities = 147/415 (35%), Positives = 246/415 (59%), Gaps = 13/415 (3%)

Query: 6   SLIGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFSDAVSN 65
           +L G+A+ LG+  L+S NRK        GA  IQ  L   +  +P  Q++LRG + AV  
Sbjct: 9   ALAGLALTLGLCWLVSENRKRFPWGLAIGAVVIQVLLVLVLFGLPQAQQMLRGVNGAVEG 68

Query: 66  VINYGNDGTSFLFGGLVSGKM-FEVFG-GGGFIFAFRVLPTLIFFSALISVLYYLGVMQW 123
           +      GT+F+FG L  G   + V   G GFIFAFRVLP ++   AL ++L++  +++W
Sbjct: 69  LAASTQAGTAFVFGFLAGGDQPYPVSNPGAGFIFAFRVLPVILVVCALSALLWHWKILKW 128

Query: 124 VIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGGLAS 183
           + +  G   QK LG     +++ AA IF+GQ E P+ +R ++ K+++SELF ++  G+A 
Sbjct: 129 LAQGFGFVFQKTLGLRGPPALATAATIFMGQVEGPIFIRAYLDKLSRSELFMLIAVGMAC 188

Query: 184 IAGGVLAGYASMGVKI-----EYLVAASFMAAPGGLLFAKLMMPETEKPQDNEDITLDGG 238
           ++G  +  YA++   +      +++ AS ++AP G+L A++++P ++  + + D+ L   
Sbjct: 189 VSGSTMVAYATILADVLPNAAAHVLTASIISAPAGVLLARIIVP-SDPMEKSADLDLSTE 247

Query: 239 DDKPANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEML 298
           D    + IDA   G + GLQ+ALNVGA LI F+ L  +++ +LG      G P L +   
Sbjct: 248 DKTYGSSIDAVMKGTTDGLQIALNVGATLIVFVALATMVDKVLGAFPPVGGEP-LSIARG 306

Query: 299 LGWLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAPVVLSEKTKAI 358
           LG +FAPLA+ +G+PW EA  AG  +G+K +  EF A+ Q    L++    +L E+T+ I
Sbjct: 307 LGVVFAPLAWSMGIPWKEAGTAGGLLGVKLILTEFTAFIQ----LSKVGEALLDERTRMI 362

Query: 359 ISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIAG 413
           +++ALCGFAN+ S+ + + G   L P+RR ++  +  KA++AG L+  + A++ G
Sbjct: 363 MTYALCGFANIGSVGMNVAGFSVLVPQRRQEVLGLVWKAMMAGFLATCLTASLVG 417


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: 21
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: 426
Length adjustment: 32
Effective length of query: 386
Effective length of database: 394
Effective search space:   152084
Effective search space used:   152084
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.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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