ProtoNet: Site Map.

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ProtoNet: Site Map.

Version 6.1


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Type: Individual protein

Query: Get Protein Card Each cluster in the system has an associated ProtoNet ID. The smaller IDs are reserved for the leaf clusters and the larger IDs are associated with clusters of 2 or more proteins.

To view the protein card of a protein, click "Navigation Tools" and then "Get Protein Card". Proteins may be accessed using either their SWISS-PROT ID or accession number, their name (full or partial), or according to variety of keywords (such as InterPro, NCBI ID or taxonomy name, SWISS-PROT, SCOP, GO).

In this example, we have chosen to search by SWISSPROT ID or SWISSPROT accession number, and entered "AACT_HUMAN" or "P01011" as the search string. After hitting the "Search" button, the following page opens:

The protein card shows various data about the protein. Some of the data fields are hyper-linked to the corresponding databases to which they refer. A natural choice would be to view the cluster corresponding to this protein. To do this, click on the "go to cluster" button.

The protein's sequence is color-coded as follows to illustrate the distribution of amino acids functional groups in the protein:

1 61 121 181 241 301 361 421
MERMLPLLALGLLAAGFCPAVLCHPNSPLD EENLTQENQDRGTHVDLGLASANVDFAFSL YKQLVLKAPDKNVIFSPLSISTALAFLSLG AHNTTLTEILKGLKFNLTETSEAEIHQSFQ HLLRTLNQSSDELQLSMGNAMFVKEQLSLL DRFTEDAKRLYGSEAFATDFQDSAAAKKLI NDYVKNGTRGKITDLIKDLDSQTMMVLVNY IFFKAKWEMPFDPQDTHQSRFYLSKKKWVM VPMMSLHHLTIPYFRDEELSCTVVELKYTG NASALFILPDQDKMEEVEAMLLPETLKRWR DSLEFREIGELYLPKFSISRDYNLNDILLQ LGIEEAFTSKADLSGITGARNLAVSQVVHK AVLDVFEEGTEASAATAVKITLLSALVETR TIVRFNRPFLMIIVPTDTQNIFFMSKVTNP KQA
30 90 150 210 270 330 390

Red - Lys(K), Arg(R), His(H)
Blue - Asp(D), Glu(E)
Black - Ser(S), Ala(A), Thr(T), Pro(P), Gly(G)
Purple - Leu(L), Met(M), Val(V), Ile(I)
Green - Asn(N), Gln(Q)
Orange - Cys(C)
Brown - Phe(F), Trp(W), Tyr(Y)

The sequence (or a part of it) can be easily copied using the browser's cut-and-paste capabilities.

Beneath the sequence, you may click "Get Motifs and Domains", to see a window similar to this:

(We show here only the leftmost part of the window). The available motifs, as defined by PFAM, Prints, ProDom, PROSITE and SMART are indicated and color-coded. The total number of domains appears in parentheses. Each motif is clickable, and directs the user to its location in the sequence. The motif can be easily copied using the browser's cut-and-paste capabilities. When the mouse pointer hovers above a motif, a tooltip appears: tooltip

Next appears a table listing the various keywords associated with the protein, providing a general description of the protein features.

The last part of this table depicts the protein's taxonomy. The branches in the taxonomy tree are linked to the NEWT database to provide easy access to the taxonomical description of the organism.

Taxonomy of protein 888:


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