PASS2
  • About the database
  • About Domains
  • Features

About the database

PASS2 is an automatic version of the original superfamily alignment database, CAMPASS (CAMbridge database of Protein Alignments organised as Structural Superfamilies, Sowdhamini et al., 1998). PASS2 contains alignments of protein structures at the superfamily level and is in direct correspondence with SCOP 1.75 release (Structural Classification Of Proteins, Murzin et al.,1995).

The superfamilies are named after their codes in SCOP database: for example, 46548 refers to 'alpha-helical ferredoxin' superfamily.The superfamilies are chosen from SCOP and all the representative members are extracted by using cut-off of 40% sequence identity and good resolution. For all Multi Member Superfamilies the alignment of family members is based on the conservation of structural features like solvent accessibility, hydrogen bonding and the presence of secondary structures. We have employed COMPARER (Sali et al., 1990; Sali et al.,1992) to obtain the multiple sequence alignment of distantly related proteins. The final alignment of multi Member Superfamilies and Single Member Superfamilies are presented in JOY format (Mizuguchi et al., 1998) to display three-dimensional (3D) structural information in a sequence alignment, which helps to understand the conservation of amino acids in their specific local environment.

Cite us

Gandhimathi, A., Nair, A. and Sowdhamini, R. PASS2.4: An update of database of structure-based sequence alignments of structural domain superfamilies. Nucleic Acids Research,2012,40(D1): D531-D534.

Methodology Flowchart

PASS2 Methodology

Protein (Domain)s in the database

SCOP superfamilies have been considered for the curation of the database. Members of the database share no more than 40% sequence identity among themselves. Alignments for the multi-member superfamilies are based on conservation of structural features like solvent accessibility, hydrogen bonding and the presence of secondary structures. A preliminary superposition has been done using MINRMS (Jewett et al., 2003) and STAMP (Russell et al., 1992) for two member and multi member superfamilies respectively. Deriving initial equivalences from the alignment, a refined structural alignment is done using COMPARER (Sali et al., 1990; Sali et al.,1992). The final alignment is presented in JOY format (Mizuguchi et al., 1998) to display three-dimensional (3D) structural features.

We have classified our superfamilies into single member, two member and multi member superfamilies. The current version contains 731 multi member superfamilies, 366 two member superfamilies and 864 structure based sequence annotated single member superfamilies. Sequence members for the superfamilies in different genomes have been listed and aligned.

S. No Class Number of SMS Number of TMS Number of MMS  Total 
1 All alpha proteins 263 98 146 507
2 All beta proteins 150 60 144 354
3 Alpha and beta proteins (a+b) 229 106 216 551
4 Alpha and beta proteins (a/b) 59 41 144 244
5 Membrane and cell surface proteins and peptides 71 20 19 110
6 Multi-domain proteins (alpha and beta) 35 15 16 66
7 Small proteins 57 26 46 129
Total 864 366 731 1961

Features

The updated version of PASS2 has been designed in a very user-friendly manner. Superfamilies can be accessed in a very easy way and information about the list of domains, structural alignment, phylogenetic tree and HMM can be accessed and downloaded through links. Sequence alignment with PASS2 members are possible using MALIGN. Sequence searches against the PASS2 database using PSI-BLAST and PHI-BLAST can also be pursued. Prediction of a superfamily based on structural compatibility can also be performed. Each entry of PASS2 has been linked to other databases and tools for easy access of information.

We have additionally providing information about each superfamily in a form of features such as HMM, Structural Motif, structural phylogeny, PCA analysis, CUSP are discussed extensively in the previous versions of PASS2.Other utilities which were available for the previous PASS2 database such as, PSI-BLAST, PHI-BLAST, constructed hmm profiles based on PASS2 alignments, and 3D-structural annotation of query alignment/sequence, were modified and updated corresponding to the latest PASS2 database. Some general utilizes such as Alistat, different formats of the alignment and a README file which will be helpful for the user to know more details about the each superfamily.