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ProtoNet: Site Map.

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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).

get protein card

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:

protein card

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:

Motifs and Domains of protein
(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.

keywords

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:

SUPERKINGDOM - eukaryota |_ KINGDOM - metazoa |_ PHYLUM - chordata |_ SUBPHYLUM - craniata |_ SUPERCLASS - gnathostomata |_ CLASS - mammalia |_ ORDER - primates |_ SUBORDER - catarrhini |_ FAMILY - hominidae |_ GENUS - homo |_ SPECIES - homo sapiens

 


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