Information about each superfamily:

Protein code :

    Each superfamily member has a 6 letter unique identifier starts with number.
One can get the details of this protein in various databases by using the link
provided in 6 letter code.

First 4 letter :pdb code(start with number)
Fifth digit    :Chain identifier.(- indicates that no chains in that protein)
Sixth dogit    :Domain number (as given in SCOP.(- indicates that the whole 
                protein is considered as single domain)
For example

1. 1fpoa1

   1fpo       -----> pdbcode
   a          -----> Chain A
   1          -----> DOmain 1 of 1fpo


2. 1gh6a-

   1gh6       -----> pdbcode
   a          -----> Chain A
   -          -----> Single domain

Start residue    : Number assigned (in PDB file) to the first residue of the domain region

Start chain      : Chain identifier(as mentioned in PDB file) of  the domain region

End residue      : Number assigned (in PDB file) to the last residue of the domain region

End chain        : Chain identifier(as mentioned in PDB file) of  the domain region

Protein size     : Size of the domain

Protein name     : The common name of the protein and/or its short description(as given PDB file).

Source           : The organism producing the protein

Superfamily code : This is a unique identifier(5 digit code) for each protein described within 
                   the SCOP database

Superfamily name : Name of the superfamily as in SCOP

Fold name        : Name of the fold as in SCOP

Class name       : Name of the class as given SCOP

Number of members: Total Number of domains having less than 40% sequence identity among themselves

Average size : Average size of domains in a particular superfamily

Resolution       :

R-factor         :

Predict closest superfamily of your query:

Association of structure to respective superfamily could be performed using
this tool. Superfamily assignment is initially done using the HMMPFAM with 
liberal E-value. 
To test structural compatibility,representive member of the superfamily are 
then aligned and superposed using the uploaded structure to test structural 
compatibility.

To find the closest superfamily,

1. Upload the pdbfile

2. Press submit button

Output:

   The output contains the following information

 1.Protein code of the representative member,Protein name,Source,Resolution,superfamily 
   code(One can reach the details about the superfamily by using the link provided in 
   superfamily code) and Superfamily name.

 2.Structural superposition of Query with representative member using LSQMAN

 3.User can download the superposed coordinates  using the "Download superposed coordinates" 
   option
Predict closest superfamily of your query sequence based on HMMs:

Association of query sequence to respective superfamily could be performed using
this tool. Superfamily assignment is done using the HMMPFAM with the E-value of 
0.1. The query is matched to the PASS2 HMMs using the above mentioned program.

Align your  query:

Sequence Alignment using MALIGN

One can align their sequence with the members of a given
superfamily using MALIGN.
To align sequence,

1.Enter superfamily code

2.Paste sequence in PIR format

3.Click "Submit Query" button

Structure Based Alignment using JOY

One can align their sequence with the members of a given
superfamily using JOY.The user's sequences are aligned 
with the members of the superfamily using MALIGN.
Then JOY4.0 is used to create the final alignment in
JOY format.
To align using JOY,

1.Enter superfamily code

2.Paste sequence in PIR format

3.Click "Submit Query" button


Structural Alignment using LSQMAN

One can align and superpose their structure with the representative member 
of a given superfamily using LSQMAN.

1.Enter superfamily code 

2.Upload pdb file

3.Click the "Submit form" button



Phylogeny of  the members:

Structure and sequence based phylogenetic trees are provided for superfamilies 
having more than two superfamily members. 

Sequence based tree has been built using the sequence dissimilarity matrix while
the structure based phylogenetic tree is based on the RMSD matrix derived
from MNYFIT.


Hidden Markov Models based on the Structural Alignments:

Structural alignments of evolutionary related proteins have been used for 
build sensitive HMMs for the different superfamilies. HMM build have been 
used to build global and local models.
The basic strengths of profile HMMs are:


  1. the model can be used to search a database and/or parse sequences for
     the presence of similar domains

  2. profile HMMs can be used to maintain alignments of huge numbers of
     sequences, starting from carefully constructed "seed" alignments of a 
     representative set of sequences. 

  Usr can download the profiles by using the links provided in pass_fs and pass_ls

Interacting Motifs for PASS2 Members:

Interacting Motifs represents equivalent conserved interacting regions of the
superfamily members.Conserved regions of proteins have been determined comparing
the proteins to there homologues. Interactions is between conserved stretches
have been estimated studying the electrostatic potential, dipole interactions
Vander Waal interactions and hydrophobic interactions. The conserved interacting
region is plotted back onto the structural alignments of the superfamily.Regions
sharing similar conserved interacting form the interacting motifs for a superfamily.
Both conserved motifs in the protein and superfamily level have been tablulated and
reported. The motifs represent structural and functionally important regions for a
superfamily.

Output
        
 Protein:1vii--
  0  SXEDF    start:  2    end:  7
  1  FGMTR    start: 10    end: 15
  2  PXWKQ    start: 21    end: 26
  3  KKEKG    start: 29    end: 34

where

1vii--          ---------> Protein code
0   1   2   3   ---------> Motif number
SXEDF           ---------> Interacting Motif
start           ---------> Starting position of the motif in the COMPARER alignment
end             ---------> End position of the motif in the COMPARER alignment
Improved search facility:

The database can be browsed efficiently using several search facility. The 
database may be queried using the superfamily code, superfamily name, Fold name,
PDB code and keywords.


1.The search pattern should contain atleast four character.

2.Protein code should contain atleast four character.

3.Select the  search option.

Search by superfamily code : 

To search by superfamily  code, enter a valid superfamily  code ( 5 digit code 
as mentioned in SCOP), select the "Superfamily code" option from radio button 
given),then submit the form.The result page contains superfamily code (with link) 
and Superfamily name . User can reach the choosen entry by using link provided 
in superfamily code.


Search by superfamily name : 

To search by superfamily  name, enter a valid superfamily  name (as mentioned in SCOP), 
select the "Superfamily name" option from radio button given),then submit
 the form.The result page contains superfamily code (with link) and Superfamily 
name . User can reach the choosen entry by using link provided in superfamily 
code.


Search by fold  name : 

To search by fold  name, enter a valid Fold  name (as mentioned in SCOP), 
select the "Fold name" option from radio button given),then submit the form.The 
result page contains superfamily code (with link) and Superfamily name . User 
can reach the choosen entry by using link provided in superfamily code.


Search by Class  name : 

To search by class  name, enter a valid Class name (as mentioned in SCOP), 
select the "Class name" option from radio button given),then submit the form.The 
result page contains superfamily code (with link) and Superfamily name . User can 
reach the choosen entry by using link provided in superfamily code.

PASS2 contains the superfamily from the following 7 major classes

1.All alpha proteins
 
2.All beta proteins
 
3.Alpha and beta proteins (a/b)
 
4.Alpha and beta proteins (a+b)
 
5.Multi-domain proteins (alpha and beta)
 
6.Membrane and cell surface proteins and peptides

7.Small proteins
  


Search by PDB code : 

To search by PDB code, enter a  valid PDB code ( starts with number), select the 
"PDB Code" option from radio button given), then submit the form.The result page 
contains superfamily code (with link) and Superfamily name . User can reach the 
choosen entry by using link provided in superfamily code.
     

Search by Keyword  : 

To search by keyword, enter keyword and select the "Key word" option from radio 
button given ,then submit the form. The result page contains superfamily code 
(with link) and Superfamily name. User can reach the choosen entry by using link 
provided in superfamily code.

Search facility in all pages :   

 In each page in the database, there is a search box. You can search any word  
that appears in a PASS2 (titles, comments, pdb entries,Superfamily code ,
Superfamily name,fold name and class name). 
 
Genome Distribution:

A search for homologues have been performed using PSI-BLAST and Hmmsearch.
Both methods are sensitive in identify distant homologues. Domains assigned
have been aligned using clustalW . The first 10 hits have been aligned with 
the structural members of PASS2 and have been displayed in the JOY format 
as shown below.One may download the hits obtained from different genomes.

1grj-1  (   2 )    qaipmtlrgAeklreeldflksvrrpeIiaaIaeArehgdlkenaeyhaa    Structural member
NP-212  (   2 )             LNKKQKELKYLKEVEIPENSKEIGKARELGDLKENAEYHSA    Genome hit1
NP-218  (   2 )    RGLVVTAKMLNAKKKELQDLLDVRIPENSREIGRALELGDLRENAEYKAA    Genome hit2
NP-224  (   2 )         TSESFSRMKAKLQSLVGKEMVDNAKEIEDARSLGDLRENSEYKFA    Genome hit3
NP-296  (   2 )         TSESFTRMKAKLQSLIGKEMVDNAKEIEDARALGDLRENSEYKFA    Genome hit4
NP-220  (   2 )         TSDSFTRMKNKLQSLVGKEMVENAKEIEDARALGDLRENSEYKIA    Genome hit5
AAL576  (   2 )    REVKLTKAGYERLMKQLEQ-ERERLQEATKILQELMESSDDYDDSGLEAA    Genome hit6
AAL576  (   2 )    REVKLTKAGYERLMQQLER-ERERLQEATKILQELMESSDDYDDSGLEAA    Genome hit7
NP-295  (   2 )    KQVRLTREGFERLEKALEQ-EQNRLNEATRILQEQMETSADNEDTGLEDA    Genome hit8
NP-296  (   2 )    QPLPLTPEGLSRLQAALER-EQARREEARRVVQEQME-ANENESLDLAAA    Genome hit9
AAL576  (   2 )    KPVYLTPEGFRRLQEELNHLKTTKRQEISADFEQALEEGDLRENAGYDEA    Genome hit10
                     bbbbaaaaaaaaaaaaaaaa aaaaaaaaaaaaa    333 aaaaaa

Your suggestions and further clarifications are most welcome.

please send a mail to mini@ncbs.res.in

PASS2 group : Dr.R.Sowdhamini
            Anirban Bhaduri
            Pugalenthi G