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hupfam [2010/02/10 12:02]
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 +====== HUP residue analysis - supplementary material ======
  
 +The data on this page are organised in three major sections: (1) analysis of residue conservation across the entire superfamily, (2) analysis of
 +residue conservation in functional sub-groups (FSGs) that group together protein domains with similar functional mechanisms but not necessarily identical specificities (3) analysis of residue conservation within families of protein domains sharing identical functional specificities 
 +
 +Each structural alignment presented on this page is in FASTA format, with the amino acid sequence of each protein structure displayed one at a time with the sequence reading from left to right across the page. Conservation scores on this page were generated using Scorecons. The conservation scores files show the same structural alignment as the FASTA files, but the protein sequences are displayed in columns, each column corresponding to one protein sequence, with the sequence going from top to bottom. The first column shows the conservation score. This ranges from 0 for unconserved residues to 1 for the most highly conserved. In all alignment files, sequences are identified by a CATH domain ID if they represent domains classified in CATH, or by a unique MD5 string that is used as identifier in the Gene3D database otherwise.
 +
 +
 +===== Conservation across superfamily =====
 +
 +  * Structural alignment ([[http://release.cathdb.info/v3.3.0/supplementary/fasta_across_sf.txt|Click here]])
 +
 +  * Conservation scores (calculated using scorecons) with catalytic residues shown in lower case ([[http://release.cathdb.info/v3.3.0/supplementary/hup_across_superfams_csa.txt|Click here]])
 +
 +  * Conservation scores (calculated using scorecons) with ligand binding residues shown in lower case ([[http://release.cathdb.info/v3.3.0/supplementary/hup_across_superfams_lig.txt|Click here]])
 +
 +
 +
 +
 +
 +
 +===== Conservation within functional subgroups (FSGs) =====
 +
 +The first link for each FSG presented here is of an image file of this
 +alignment with catalytic residues shaded brown and ligand binding residues
 +shaded light blue. Conservation scores for each position in the alignment
 +is calculated using the algorithm scorecons and are shown as a histogram
 +underneath the alignment. The consensus secondary structure as predicted
 +by jpred is also displayed underneath the alignment. Some of the
 +structural alignments contain a large number of sequences, in which case
 +you may find you have to use the zoom function to view the image in your
 +browser. The raw FASTA file containing the alignment can be downloaded by
 +following the second link. The last two link display the raw data from the
 +scorecons algorithm, with annotated catalytic residues and ligand-binding
 +residues in the first and second links, respectively. See general page description above for more details on file formats.
 + Functional residues (for example a catalytic
 +residue or a ligand binding residue) are shown in lower case.
 +
 +  * FSG1 - Electron transfer flavoproteins:
 +      - [[http://release.cathdb.info/v3.3.0/supplementary/fsg1_gemma.png|Click here]] to display the annotated alignment  
 +      - [[http://release.cathdb.info/v3.3.0/supplementary/fsg1_gemma_nr40_tcoffee.fasta_aln|Click here]] to download the alignment
 +      - [[http://release.cathdb.info/v3.3.0/supplementary/fsg1_gemma_csa.txt|Click here]]  to download the conservation scores with catalytic residues in lower case.
 +      - [[http://release.cathdb.info/v3.3.0/supplementary/fsg1_gemma_lig.txt|Click here]]  to download conservation scores with ligand binding residues in lower case.
 +
 +
 +  * FSG2 - Aminoacyl-tRNA synthetases:
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg2_gemma.png|Click here]] to display the annotated alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg2_gemma_nr40_tcoffee.fasta_aln|Click here]] to download the alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg2_gemma_csa.txt|Click here]] to download the conservation scores with catalytic residues in lower case.
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg2_gemma_lig.txt|Click here]] to download the conservation scores with ligand binding residues in lower case.
 +     
 + 
 +   * FSG3 - ATP-pyrophosphatases:
 +      - [[http://release.cathdb.info/v3.3.0/supplementary/fsg3_gemma.png|Click here]] to display the annotated alignment
 +      - [[http://release.cathdb.info/v3.3.0/supplementary/fsg3_gemma_nr40_tcoffee.fasta_aln|Click here]] to download the  alignment
 +      - [[http://release.cathdb.info/v3.3.0/supplementary/fsg3_gemma_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +      - [[http://release.cathdb.info/v3.3.0/supplementary/fsg3_gemma_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      
 +
 +
 +
 +  * FSG4 - Cryptochromes/DNA-phosphatases:
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg4_gemma.png|Click here]] to display the annotated alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg4_gemma_nr40_tcoffee.fasta_aln|Click here]] to download the alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg4_gemma_csa.txt|Click here]] to download the conservation scores with catalytic residues in lower case.
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg4_gemma_lig.txt|Click here]] to download the conservation scores with ligand binding residues in lower case.
 +    
 +
 +
 +
 +
 +  * FSG5 - Nucleotidyltransferases:
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg5_gemma.png|Click here]] to display the annotated alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg5_gemma_nr40_tcoffee.fasta_aln|Click here]] to download the alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg5_gemma_csa.txt|Click here]] to download the conservation scores with catalytic residues in lower case.
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg5_gemma_lig.txt|Click here]] to download the conservation scores with ligand binding residues in lower case.
 +  
 +
 +
 +  * FSG6 - Pantothenate synthetases:
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg6_gemma.png|Click here]] to display the annotated alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg6_gemma_nr40_tcoffee.fasta_aln|Click here]] to download the alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg6_gemma_csa.txt|Click here]]  to download the conservation scores with catalytic residues in lower case.
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg6_gemma_lig.txt|Click here]]  to download the conservation scores with ligand binding residues in lower case.
 +    
 +
 +  * FSG7 - tRNA 2-thiouridylases:
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg7_gemma.png|Click here]] to display the annotated alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg7_gemma_nr40_tcoffee.fasta_aln|Click here]] to download the alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg7_gemma_csa.txt|Click here]]  to download the conservation scores with catalytic residues in lower case.
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg7_gemma_lig.txt|Click here]]  to download the conservation scores with ligand binding residues in lower case.
 +    
 +
 +  * FSG8 - Phosphoadenylyl-sulphate reductases:
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg8_gemma.png|Click here]] to display the annotated alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg8_gemma_nr40_tcoffee.fasta_aln|Click here]] to download the  alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg8_gemma_csa.txt|Click here]]  to download the conservation scores with catalytic residues in lower case.
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg8_gemma_lig.txt|Click here]]  to download the conservation scores with ligand binding residues in lower case.
 +    
 +
 +
 +
 +  * FSG9 - Universal stress proteins A:
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg9_gemma.png|Click here]] to display the annotated  alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg9_gemma_nr40_tcoffee.fasta_aln|Click here]] to download the  alignment
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg9_gemma_csa.txt|Click here]]  to download the conservation scores with catalytic residues in lower case.
 +     - [[http://release.cathdb.info/v3.3.0/supplementary/fsg9_gemma_lig.txt|Click here]]  to download the conservation scores with ligand binding residues in lower case.
 +   
 +
 +
 +
 +===== Conservation within specificity groups =====
 +
 +Here, we provide raw text FASTA files as well as scorecons output files for each specificity group. Specificity groups are grouped together according to the FSGs to which they belong. N/A indicates that no specificity groups alignments with known functional residues could be found for the given FSG. See general page description above for more details on file formats.
 +
 +
 +  * **FSG1: (Electron-Transfer Flavoproteins)**
 +       * Electron-Transfer Flavoprotein B
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/7499.png|Click here]] to display the annotated alignment  
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/7499.aln|Click here]] to download the alignment
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/7499_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/7499_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +
 +  * **FSG2: (Aminoacyl-tRNA synthetases)**
 +       * Trp-tRNA Synthetase
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/6411.png|Click here]] to display the annotated alignment
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/6411.aln|Click here]] to download the alignment
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/6411_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/6411_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      * Met-tRNA Synthetase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6466.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6466_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6466_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      * Leu/Val/Ile-rRNA Synthetase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6490.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6490_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6490_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      * Tyr-tRNA Synthetase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7419.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7419.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7419_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7419_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case. 
 +      * Arg-tRNA Synthetase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7507.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7507_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7507_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      * Tyr-tRNA Synthetase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7593.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7593.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7593_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7593_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +
 +  * **FSG3: (ATP-pyrophosphatases)**
 +       * Beta-lactam-synthase
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/3622.png|Click here]] to display the annotated alignment
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/3622.aln|Click here]] to download the alignment
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/3622_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/3622_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +       * CarA
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/5063.png|Click here]] to display the annotated alignment
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/5063.aln|Click here]] to download the alignment
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/5063_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/5063_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      * GMP synthase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6896.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6896.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6896_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6896_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      * Argininosuccinate synthase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7186.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7186.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7186_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7186_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      * NAD synthetase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7401.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7401.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7401_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7401_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      * Asparagine synthetase B
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7541.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7541.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7541_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7541_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      * Argininosuccinate synthase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7586.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7586.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7586_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7586_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +  * **FSG4: (Cryptochromes/DNA-phosphatases)**
 +      *  N/A
 +  * **FSG5: (Nucleotidyltransferases)**
 +      * Riboflavin kinase/FMN adenylyltransferase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6740.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6740.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6740_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6740_log.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      * Sulfate adenylyltransferase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6765.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6765.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6765_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/6765_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      * Glycerol-3-phosphate cytidylytransferase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7432.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7432.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7432_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7432_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      * Nicotinamide-nucleotide adenylyltransferase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7718.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7718.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7718_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7718_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +      * Nicotinamide-nucleotide adenylyltransferase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7791.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7791.aln/|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7791_csa.txt/|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7791_lig.txt/|Click here]] to download conservation scores with ligand binding residues in lower case.
 +       * Phosphopantetheine adenylyltransferase
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/7908.png|Click here]] to display the annotated alignment
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/7908.aln|Click here]] to download the alignment
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/7908_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/7908_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +       * Nicotinate-nucleotide adenylyltransferase
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/8001.png|Click here]] to display the annotated alignment
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/8001.aln|Click here]] to download the alignment
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/8001_csa.txt |Click here]] to download conservation scores with catalytic residues in lower case.
 +         - [[http://release.cathdb.info/v3.3.0/supplementary/8001_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +  * **FSG6: (Pantothenate synthetase)**
 +      * Pantothenate synthetases
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7529.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7529.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7529_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7529_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +  * **FSG7: (tRNA 2-thiouridylases)**
 +      * tRNA-specific 2-thiouridylase
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7793.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7793.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7793_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/7793_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.
 +
 +  * **FSG8: (Phosphoadenylyl-sulphate reductases)**
 +     * N/A
 +  * **FSG9: (Universal stress proteins A)**
 +      * Universal stress protein A
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/1639.png|Click here]] to display the annotated alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/1639.aln|Click here]] to download the alignment
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/1639_csa.txt|Click here]] to download conservation scores with catalytic residues in lower case.
 +        - [[http://release.cathdb.info/v3.3.0/supplementary/1639_lig.txt|Click here]] to download conservation scores with ligand binding residues in lower case.

Trace:

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