GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_02171
          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 (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:

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. 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