CREATE TABLE `VERSION` (
  `pfam_release` tinytext,
  `swiss_prot_version` tinytext,
  `trembl_version` tinytext,
  `hmmer_versiion` tinytext
);
 
CREATE TABLE `architecture` (
  `auto_architecture` int(10) unsigned NOT NULL auto_increment,
  `architecture` text,
  PRIMARY KEY  (`auto_architecture`),
  KEY `architecture` (`architecture`(255))
);
 
CREATE TABLE `clan_database_links` (
  `auto_clan` int(10) unsigned NOT NULL default '0',
  `db_id` tinytext NOT NULL,
  `comment` tinytext,
  `db_link` tinytext NOT NULL,
  `other_params` tinytext,
  KEY `auto_clan` (`auto_clan`)
);
 
CREATE TABLE `clan_lit_refs` (
  `auto_clan` int(10) unsigned NOT NULL default '0',
  `auto_lit` int(10) unsigned NOT NULL default '0',
  `order_added` tinyint(4) default NULL,
  `comment` tinytext,
  KEY `auto_clan` (`auto_clan`)
);
 
CREATE TABLE `clan_locks` (
  `auto_clan` int(10) unsigned NOT NULL default '0',
  `locked` tinyint(4) default NULL,
  `user` tinytext,
  `updated` timestamp(14) NOT NULL,
  UNIQUE KEY `auto_clan` (`auto_clan`)
);
 
CREATE TABLE `clan_membership` (
  `auto_clan` int(10) unsigned NOT NULL default '0',
  `auto_pfamA` int(10) unsigned NOT NULL default '0'
);
 
CREATE TABLE `clan_versions` (
  `auto_clan` int(10) unsigned NOT NULL default '0',
  `current` tinyint(4) default NULL,
  `version` tinyint(4) default NULL,
  `rcs_trace` longtext NOT NULL,
  `message` longtext,
  `user` tinytext NOT NULL,
  `updated` timestamp(14) NOT NULL,
  KEY `auto_clan` (`auto_clan`)
);
 
CREATE TABLE `clans` (
  `auto_clan` int(10) unsigned NOT NULL auto_increment,
  `clan_acc` varchar(6) NOT NULL default '',
  `clan_description` varchar(100) default NULL,
  `clan_author` tinytext,
  `clan_comment` longtext,
  `updated` timestamp(14) NOT NULL,
  `created` datetime default NULL,
  PRIMARY KEY  (`auto_clan`),
  UNIQUE KEY `clan_acc` (`clan_acc`)
);
 
CREATE TABLE `context_pfam_regions` (
  `auto_pfamseq` int(10) unsigned NOT NULL default '0',
  `auto_pfamA` int(10) unsigned NOT NULL default '0',
  `seq_start` mediumint(8) unsigned NOT NULL default '0',
  `seq_end` mediumint(8) unsigned NOT NULL default '0',
  `domain_score` double(16,2) default NULL,
  PRIMARY KEY  (`auto_pfamseq`,`auto_pfamA`,`seq_start`)
);
 
CREATE TABLE `dead_clans` (
  `clan_acc` varchar(7) NOT NULL default '',
  `clan_description` varchar(100) default NULL,
  `clan_membership` longtext NOT NULL,
  `comment` mediumtext,
  `forward_to` varchar(6) default NULL,
  `user` tinytext,
  `killed` timestamp(14) NOT NULL,
  UNIQUE KEY `clan_acc` (`clan_acc`)
);
 
CREATE TABLE `dead_families` (
  `pfamA_acc` varchar(7) NOT NULL default '',
  `pfamA_id` varchar(40) NOT NULL default '',
  `comment` mediumtext,
  `forward_to` varchar(7) default NULL,
  UNIQUE KEY `pfamA_acc` (`pfamA_acc`)
);
 
CREATE TABLE `genome_pfamseq` (
  `ncbi_code` int(10) unsigned NOT NULL default '0',
  `auto_pfamseq` int(10) unsigned NOT NULL default '0',
  KEY `ncbi_code` (`ncbi_code`),
  KEY `auto_pfamseq` (`auto_pfamseq`)
);
 
CREATE TABLE `genome_seqs` (
  `ncbi_code` int(10) unsigned NOT NULL default '0',
  `auto_pfamseq` int(10) unsigned NOT NULL default '0',
  `auto_pfamA` int(10) unsigned NOT NULL default '0',
  `count` int(10) unsigned default NULL,
  KEY `ncbi_code` (`ncbi_code`),
  KEY `auto_pfamseq` (`auto_pfamseq`),
  KEY `auto_pfamA` (`auto_pfamA`)
);
 
CREATE TABLE `genome_species` (
  `ncbi_code` int(10) unsigned NOT NULL default '0',
  `species` varchar(100) default NULL,
  `grouping` varchar(20) default NULL,
  `num_distinct_regions` int(10) unsigned default NULL,
  `num_total_regions` int(10) unsigned default NULL,
  `num_proteins` int(10) unsigned default NULL,
  `sequence_coverage` int(3) unsigned default NULL,
  `residue_coverage` int(3) unsigned default NULL,
  `total_genome_proteins` int(10) unsigned default NULL,
  `total_aa_length` bigint(20) default NULL,
  PRIMARY KEY  (`ncbi_code`),
  KEY `grouping` (`grouping`)
);
 
CREATE TABLE `int_atom` (
  `auto_atom_int` int(15) unsigned NOT NULL auto_increment,
  `pdb_atom` varchar(5) default NULL,
  `partner_pdb_atom` varchar(5) default NULL,
  `auto_bonds` int(10) unsigned default NULL,
  PRIMARY KEY  (`auto_atom_int`),
  UNIQUE KEY `auto_atom_int` (`auto_atom_int`)
);
 
CREATE TABLE `int_bond` (
  `auto_bonds` int(10) unsigned NOT NULL auto_increment,
  `bond_name` varchar(20) NOT NULL default '',
  PRIMARY KEY  (`auto_bonds`),
  UNIQUE KEY `bond_name` (`bond_name`)
);
 
CREATE TABLE `int_pfamAs` (
  `auto_pfamA` int(10) unsigned NOT NULL default '0',
  `auto_partner_pfamA` int(10) unsigned NOT NULL default '0',
  `auto_dom_int` int(10) unsigned NOT NULL auto_increment,
  PRIMARY KEY  (`auto_dom_int`)
);
 
CREATE TABLE `interaction` (
  `auto_int` int(15) unsigned NOT NULL auto_increment,
  `auto_dom_int` int(10) unsigned default NULL,
  `auto_atom_int` int(15) unsigned default NULL,
  `auto_pdb` int(10) unsigned default NULL,
  `chain_A` char(3) default NULL,
  `pdb_seq_number_A` int(10) unsigned default NULL,
  `auto_pfamseq_A` int(10) unsigned default NULL,
  `pfamseq_acc_A` varchar(6) NOT NULL default '',
  `auto_pfamA_A` int(10) unsigned NOT NULL default '0',
  `pfamA_acc_A` varchar(7) NOT NULL default '',
  `pfamA_id_A` varchar(40) NOT NULL default '',
  `pfamseq_seq_number_A` int(10) unsigned default NULL,
  `chain_B` char(3) default NULL,
  `pdb_seq_number_B` int(10) unsigned default NULL,
  `auto_pfamseq_B` int(10) unsigned default NULL,
  `pfamseq_acc_B` varchar(6) NOT NULL default '',
  `auto_pfamA_B` int(10) unsigned NOT NULL default '0',
  `pfamA_acc_B` varchar(7) NOT NULL default '',
  `pfamA_id_B` varchar(40) NOT NULL default '',
  `pfamseq_seq_number_B` int(10) unsigned default NULL,
  PRIMARY KEY  (`auto_int`),
  KEY `auto_dom_int` (`auto_dom_int`),
  KEY `auto_atom_int` (`auto_atom_int`),
  KEY `auto_pdb` (`auto_pdb`),
  KEY `auto_pfamseq_A` (`auto_pfamseq_A`),
  KEY `auto_pfamA_A` (`auto_pfamA_A`),
  KEY `auto_pfamseq_B` (`auto_pfamseq_B`),
  KEY `auto_pfamA_B` (`auto_pfamA_B`)
);
 
CREATE TABLE `interpro_and_go` (
  `auto_interpro` int(10) unsigned NOT NULL auto_increment,
  `interpro_id` tinytext,
  `interpro_abstract` longtext,
  `go_function` tinytext,
  `go_component` tinytext,
  `go_process` tinytext,
  PRIMARY KEY  (`auto_interpro`)
);
 
CREATE TABLE `literature_references` (
  `auto_lit` int(10) unsigned NOT NULL auto_increment,
  `medline` int(10) unsigned NOT NULL default '0',
  `title` tinytext,
  `author` tinytext,
  `journal` tinytext,
  PRIMARY KEY  (`auto_lit`),
  UNIQUE KEY `medline` (`medline`)
);
 
CREATE TABLE `msd_data` (
  `auto_pdb` int(10) unsigned NOT NULL default '0',
  `msd_chain` char(3) default NULL,
  `chain` char(3) default NULL,
  `serial` int(10) unsigned default NULL,
  `pdb_res` char(3) default NULL,
  `pdb_seq_number` int(10) unsigned default NULL,
  `auto_pfamseq` int(10) unsigned default NULL,
  `pfamseq_res` char(3) default NULL,
  `pfamseq_seq_number` int(10) unsigned default NULL,
  KEY `auto_pdb` (`auto_pdb`),
  KEY `auto_pfamseq` (`auto_pfamseq`)
);
 
CREATE TABLE `ncbi_taxonomy` (
  `ncbi_code` int(10) unsigned NOT NULL default '0',
  `species` varchar(100) default NULL,
  `taxonomy` mediumtext,
  PRIMARY KEY  (`ncbi_code`),
  KEY `ncbi_code` (`ncbi_code`)
);
 
CREATE TABLE `nested_domains` (
  `auto_pfamA` int(10) unsigned NOT NULL default '0',
  `nests_auto_pfamA` int(10) unsigned NOT NULL default '0',
  KEY `auto_pfamA` (`auto_pfamA`),
  KEY `nests_auto_pfamA` (`nests_auto_pfamA`)
);
 
CREATE TABLE `old_pfamseq` (
  `auto_pfamseq` int(10) unsigned NOT NULL default '0',
  `pfamseq_acc` varchar(6) NOT NULL default '',
  `data_deleted` timestamp(14) NOT NULL,
  `created` datetime default NULL,
  PRIMARY KEY  (`auto_pfamseq`),
  UNIQUE KEY `pfamseq_acc` (`pfamseq_acc`)
);
 
CREATE TABLE `other_reg` (
  `region_id` int(10) unsigned NOT NULL auto_increment,
  `auto_pfamseq` int(10) unsigned NOT NULL default '0',
  `seq_start` mediumint(8) unsigned NOT NULL default '0',
  `seq_end` mediumint(6) unsigned NOT NULL default '0',
  `type_id` varchar(20) NOT NULL default '',
  `source_id` varchar(20) NOT NULL default '',
  `score` double(16,4) default NULL,
  `orientation` varchar(4) default NULL,
  PRIMARY KEY  (`region_id`),
  KEY `auto_pfamseq` (`auto_pfamseq`),
  KEY `type_id` (`type_id`)
);
 
CREATE TABLE `pdb` (
  `auto_pdb` int(10) unsigned NOT NULL auto_increment,
  `pdb_id` varchar(5) NOT NULL default '',
  `header` tinytext,
  `title` mediumtext,
  PRIMARY KEY  (`auto_pdb`),
  UNIQUE KEY `pdb_id` (`pdb_id`)
);
 
CREATE TABLE `pdbmap` (
  `auto_pdb` int(10) unsigned NOT NULL default '0',
  `chain` char(2) default NULL,
  `pdb_start_res` varchar(10) default NULL,
  `pdb_end_res` varchar(10) default NULL,
  `auto_pfam` int(10) unsigned NOT NULL default '0',
  `pfam_region` tinyint(4) default NULL,
  `auto_pfamseq` int(10) unsigned NOT NULL default '0',
  `pfam_start_res` varchar(10) default NULL,
  `pfam_end_res` varchar(10) default NULL,
  `complex` tinyint(4) default NULL,
  `hex_colour` varchar(6) default NULL,
  KEY `auto_pdb` (`auto_pdb`),
  KEY `auto_pfam` (`auto_pfam`)
);
 
CREATE TABLE `pfamA` (
  `auto_pfamA` int(10) unsigned NOT NULL auto_increment,
  `pfamA_acc` varchar(7) NOT NULL default '',
  `pfamA_id` varchar(40) NOT NULL default '',
  `description` varchar(100) default NULL,
  `model_length` mediumint(8) unsigned default NULL,
  `author` tinytext,
  `seed_source` tinytext,
  `alignment_method` tinytext,
  `type` tinytext,
  `ls_sequence_GA` double(16,4) default NULL,
  `ls_domain_GA` double(16,4) default NULL,
  `fs_sequence_GA` double(16,4) default NULL,
  `fs_domain_GA` double(16,4) default NULL,
  `ls_sequence_TC` double(16,4) default NULL,
  `ls_domain_TC` double(16,4) default NULL,
  `fs_sequence_TC` double(16,4) default NULL,
  `fs_domain_TC` double(16,4) default NULL,
  `ls_sequence_NC` double(16,4) default NULL,
  `ls_domain_NC` double(16,4) default NULL,
  `fs_sequence_NC` double(16,4) default NULL,
  `fs_domain_NC` double(16,4) default NULL,
  `ls_mu` double(16,4) default NULL,
  `ls_kappa` double(16,4) default NULL,
  `fs_mu` double(16,4) default NULL,
  `fs_kappa` double(16,4) default NULL,
  `comment` longtext,
  `previous_id` tinytext,
  `hmmbuild_ls` tinytext,
  `hmmcalibrate_ls` tinytext,
  `hmmbuild_fs` tinytext,
  `hmmcalibrate_fs` tinytext,
  `num_seed` int(10) unsigned default NULL,
  `num_full` int(10) unsigned default NULL,
  `updated` timestamp(14) NOT NULL,
  `created` datetime default NULL,
  PRIMARY KEY  (`auto_pfamA`),
  UNIQUE KEY `pfamA_acc` (`pfamA_acc`),
  UNIQUE KEY `pfamA_id` (`pfamA_id`)
);
 
CREATE TABLE `pfamA_architecture` (
  `auto_pfamA` int(10) unsigned NOT NULL default '0',
  `auto_architecture` int(10) unsigned NOT NULL default '0',
  KEY `auto_pfamA` (`auto_pfamA`),
  KEY `auto_architecture` (`auto_architecture`)
);
 
CREATE TABLE `pfamA_database_links` (
  `auto_pfamA` int(10) unsigned NOT NULL default '0',
  `db_id` tinytext NOT NULL,
  `comment` tinytext,
  `db_link` tinytext NOT NULL,
  `other_params` tinytext,
  KEY `auto_pfamA` (`auto_pfamA`)
);
 
CREATE TABLE `pfamA_literature_references` (
  `auto_pfamA` int(10) unsigned NOT NULL default '0',
  `auto_lit` int(10) unsigned NOT NULL default '0',
  `comment` tinytext,
  `order_added` tinyint(4) default NULL
);
 
CREATE TABLE `pfamA_reg_full` (
  `auto_pfamA` int(10) unsigned NOT NULL default '0',
  `auto_pfamseq` int(10) unsigned NOT NULL default '0',
  `seq_start` mediumint(8) unsigned NOT NULL default '0',
  `seq_end` mediumint(8) unsigned NOT NULL default '0',
  `model_start` mediumint(8) unsigned NOT NULL default '0',
  `model_end` mediumint(8) unsigned NOT NULL default '0',
  `domain_bits_score` double(16,4) NOT NULL default '0.0000',
  `domain_evalue_score` varchar(15) NOT NULL default '0',
  `sequence_bits_score` double(16,4) NOT NULL default '0.0000',
  `sequence_evalue_score` varchar(15) NOT NULL default '0',
  `mode` char(2) NOT NULL default '0',
  `significant` tinyint(4) NOT NULL default '0',
  `in_full` tinyint(4) default NULL,
  `tree_order` mediumint(9) default NULL,
  KEY `auto_pfamA` (`auto_pfamA`),
  KEY `auto_pfamseq` (`auto_pfamseq`)
);
 
CREATE TABLE `pfamA_reg_seed` (
  `auto_pfamA` int(10) unsigned NOT NULL default '0',
  `auto_pfamseq` int(10) unsigned NOT NULL default '0',
  `seq_start` mediumint(8) unsigned NOT NULL default '0',
  `seq_end` mediumint(8) unsigned default NULL,
  KEY `auto_pfamA` (`auto_pfamA`),
  KEY `auto_pfamseq` (`auto_pfamseq`)
);
 
CREATE TABLE `pfamA_web` (
  `auto_pfamA` int(10) unsigned NOT NULL default '0',
  `average_length` double(16,1) default NULL,
  `percentage_id` int(3) default NULL,
  `status` tinytext
);
 
CREATE TABLE `pfamB` (
  `auto_pfamB` int(10) unsigned NOT NULL auto_increment,
  `pfamB_acc` char(8) NOT NULL default '',
  `pfamB_id` char(12) NOT NULL default '',
  PRIMARY KEY  (`auto_pfamB`),
  KEY `pfamB_acc` (`pfamB_acc`)
);
 
CREATE TABLE `pfamB_reg` (
  `auto_pfamB` int(10) unsigned NOT NULL default '0',
  `auto_pfamseq` int(10) unsigned NOT NULL default '0',
  `seq_start` mediumint(8) unsigned NOT NULL default '0',
  `seq_end` mediumint(8) unsigned NOT NULL default '0',
  KEY `auto_pfamseq` (`auto_pfamseq`),
  KEY `auto_pfamB` (`auto_pfamB`)
);
 
CREATE TABLE `pfam_to_interpro` (
  `auto_pfamA` int(10) unsigned NOT NULL default '0',
  `auto_interpro` int(10) unsigned NOT NULL default '0',
  KEY `auto_pfamA` (`auto_pfamA`),
  KEY `auto_interpro` (`auto_interpro`)
);
 
CREATE TABLE `pfamseq` (
  `auto_pfamseq` int(10) unsigned NOT NULL auto_increment,
  `pfamseq_id` varchar(12) NOT NULL default '',
  `pfamseq_acc` varchar(6) NOT NULL default '',
  `crc64` varchar(16) NOT NULL default '',
  `description` text NOT NULL,
  `length` mediumint(8) unsigned NOT NULL default '0',
  `species` varchar(100) NOT NULL default '',
  `taxonomy` mediumtext,
  `is_fragment` tinyint(4) default NULL,
  `version` varchar(6) default NULL,
  `current` tinyint(4) default NULL,
  `non_cons` tinyint(4) default NULL,
  `sequence` blob NOT NULL,
  `updated` timestamp(14) NOT NULL,
  `created` datetime default NULL,
  PRIMARY KEY  (`auto_pfamseq`),
  UNIQUE KEY `pfamseq_acc` (`pfamseq_acc`),
  KEY `crc64` (`crc64`),
  KEY `pfamseq_id` (`pfamseq_id`)
);
 
CREATE TABLE `pfamseq_architecture` (
  `auto_pfamseq` int(10) unsigned NOT NULL default '0',
  `auto_architecture` int(10) unsigned NOT NULL default '0',
  `frag` tinyint(4) default NULL,
  KEY `auto_pfamseq` (`auto_pfamseq`),
  KEY `auto_architecture` (`auto_architecture`)
);
 
CREATE TABLE `pfamseq_ncbi` (
  `auto_pfamseq` int(10) unsigned NOT NULL default '0',
  `ncbi_code` int(10) unsigned NOT NULL default '0',
  KEY `auto_pfamseq` (`auto_pfamseq`),
  KEY `ncbi_code` (`ncbi_code`)
);
 
CREATE TABLE `rosetta_pfam_structures` (
  `auto_pfamA` int(10) unsigned NOT NULL default '0',
  `structure` varchar(15) default NULL,
  `model_num` tinyint(4) default NULL,
  `auto_pdb` int(10) unsigned default NULL,
  `chain` varchar(4) default NULL,
  `mammoth_Z_score` double(10,8) default NULL,
  `length_ratio` double(6,4) default NULL
);
 
CREATE TABLE `rosetta_pfam_values` (
  `auto_pfamA` int(10) unsigned NOT NULL default '0',
  `group_confidence` double(6,4) default NULL,
  `scop_confidence` double(6,4) default NULL,
  PRIMARY KEY  (`auto_pfamA`)
);
 
CREATE TABLE `secondary_pfamseq_acc` (
  `auto_pfamseq` int(10) unsigned NOT NULL default '0',
  `secondary_acc` varchar(6) default NULL,
  KEY `secondary_acc` (`secondary_acc`)
);
 
CREATE TABLE `smart` (
  `auto_smart` int(10) unsigned NOT NULL auto_increment,
  `smart_acc` varchar(7) NOT NULL default '',
  `smart_id` varchar(40) default NULL,
  PRIMARY KEY  (`auto_smart`)
);
 
CREATE TABLE `smart_regions` (
  `auto_smart` int(10) unsigned NOT NULL default '0',
  `auto_pfamseq` int(10) unsigned NOT NULL default '0',
  `seq_start` mediumint(8) unsigned default NULL,
  `seq_end` mediumint(8) unsigned default NULL,
  `domain_bits_score` double(16,4) default NULL,
  `domain_evalue_score` varchar(15) default NULL,
  KEY `auto_smart` (`auto_smart`),
  KEY `auto_pfamseq` (`auto_pfamseq`)
);
 
