Protein sequences accession numbers

Filippov V. A., Filippova M. A. and Sehnal F. (1995) Lipocahn-like brain-specific protein. Unpublished sequence, Accession Number L41640. 

Guirong W. and Yuyuan G. (2000) Cloning and expression of general odorant-binding protein gene from Spodoptera exigua. Unpublished sequence, Accession Number A J294808. 

Jacquin-Joly E., Francois M. C. and Nagnan-Le Meillour P. (1999) cDNA cloning of Rhynchophoruspalmarum odorant-binding protein. Unpublished sequences, Accession Number AF139912. 

In addition to bcl-2, another hitherto completely unexpected target for the actions of chronic lithium and VPA has been identified from the mRNA RT-PCR DD study described above. Another clone, also derived from a transcript whose levels were increased by both lithium and VPA, shows very strong homology to a human mRNA-binding protein, the AUH protein ([54, 55] Genbank accession number X79888). BESTFIT analysis revealed 83.2% sequence homology between this rodent clone and the human AUH protein [54—56]. 

The SWISS-PROT and TrEMBL ID lines differ in the first two parts of the ID line. The first part is the entry name "ANP NOTCO" in the case of the SWISS-PROT example and "Q12757" in the TrEMBL example. The entry name used in all SP-TrEMBL entries is always the same as the accession number of the entry. The entry name used in REM-TrEMBL is the Protein ID tagged to the corresponding CDS in the EMBL Nucleotide Sequence Database. To the right of the entry name you will find either "preliminary" (in the TrEMBL entry) or STANDARD (in the SWISS-PROT entry). The data class used in TrEMBL is always PRELIMINARY. That means that the data are thoroughly checked by a computer,... 

Accession number ] protein sequence Gene sequence ] literature... 

There are increasing numbers of protein sequences available as a result of the increasing numbers of genome sequences that are now accessible in public databanks. It is estimated that there were experimentally determined structures for 1% of the protein sequences known in 1999, meaning that inferences about structure had to rely on information from models for the remaining 99%. 

Only a few proteins from antennal extracts are were able to bind the four compounds tested (Figure 17.3). Fraction 29 included proteins with sequences DAPAA and SEEDK no proteins in this fraction bound compounds. A protein with sequence AKLTT from fractions 30, 31 and 32 bound compounds. The full sequence of the AKLTT protein has been obtained by molecular cloning and identified as a CSP (Jacquin-Joly et al., unpublished, accession number AY026760 see section 17.7). The sequence AKLTT is also found in band 1 of fraction 33 (Figure 17.2), but here this protein fails to bind any compound (Figure 17.3). 

Figure 18.3 Alignment of moth ABPX and DmeIPBPRP proteins. Sources of the sequences and accession numbers are reported in Table 18.1. The amino acids conserved in ABPXs and DmelPBPRP-1 are represented in bold. Those amino acids found in DmelPBPRP-1 and ABPX or AipsABPX-1 and DmelPBPRP-1 are represented in italics. Conserved cysteines are underlined. These specific amino acids support the classification of these sequences as OBP1 type of proteins.

Databases are electronic filing cabinets that serve as a convenient and efficient means of storing vast amounts of information. An important distinction exists between primary (archival) and secondary (curated) databases. The primary databases represent experimental results with some interpretation. Their record is the sequence as it was experimentally derived. The DNA, RNA, or protein sequences are the items to be computed on and worked with as the valuable components of the primary databases. The secondary databases contain the fruits of analyses of the sequences in the primary sources such as patterns, motifs, functional sites, and so on. Most biochemical and/or molecular biology databases in the public domains are flat-file databases. Each entry of a database is given a unique identifier (i.e., an entry name and/or accession number) so that it can be retrieved uniformly by the combination of the database name and the identifier. 

The Sequence Retrieval System (Etzold et ah, 1996) is a network browser for databases at EBI. The system allows users to retrieve, link, and access entries from all the interconnected resources such as nucleic acid, EST, protein sequence, protein pattern, protein structure, specialist/boutique, and/or bibliographic databases. The SRS is also a database browser of DDBJ, ExPASy, and a number of servers as the query system. The SRS can be accessed from EBI Tools server at http // www2.ebi.ac.uk/Tools/index.html or directly at http //srs6.ebi.ac.uk/. The SRS permits users to formulate queries across a range of different database types via a single interface in three different methods (Figure 3.4) ... 

Each PIR entry consists of Entry (entry ID), Title, Alternate names, Organism, Date, Accession (accession number), Reference, Function (description of protein function), Comment (e.g., enzyme specificity and reaction, etc.), Classification (superfamily), Keywords (e.g., dimer, alcohol metabolism, metalloprotein, etc.), Feature (lists of sequence positions for disulfide bonds, active site and binding site amino acid residues, etc.), Summary (number of amino acids and the molecular weight), and Sequence (in PIR format, Chapter 4). In addition, links to PDB, KEGG, BRENDA, WIT, alignments, and iProClass are provided. 

Each SWISS-PROT entry consists of general information about the entry (e.g., entry name and date, accession number), Name and origin of the protein (e.g., protein name, EC number and biological origin), References, Comments (e.g., catalytic activity, cofactor, subuit structure, subcellular location and family class, etc.), Cross-reference (EMBL, PIR, PDB, Pfam, ProSite, ProDom, ProtoMap, etc.), Keywords, Features (e.g., active site, binding site, modification, secondary structures, etc.), and Sequence information (amino acid sequence in Swiss-Prot format, Chapter 4). 

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