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RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 6NT DNA-RNA HYBRID
Sequence Clustering and Redundancy Reduction Results
4A3D
Sequence Clusters for the Sequence Entities in PDB 4A3D
Entity #1: Chains: A - DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 protein, length: 1732 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 10 108 198
95% 10 108 274
90% 10 108 288
70% 10 108 310
50% 10 109 330
40% 10 109 360
30% 10 109 366
Entity #10: Chains: J - DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 protein, length: 70 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 12 114 184
95% 12 114 252
90% 12 114 262
70% 12 115 273
50% 12 123 270
40% 12 123 296
30% 12 123 311
Entity #11: Chains: K - DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 protein, length: 120 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 10 110 194
95% 10 110 271
90% 10 110 284
70% 10 110 305
50% 10 110 334
40% 10 111 354
30% 10 111 363
Entity #12: Chains: L - DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 protein, length: 70 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 12 113 187
95% 12 113 254
90% 12 113 265
70% 12 113 291
50% 12 113 318
40% 12 113 350
30% 12 113 357
Entity #13: Chains: N - NON TEMPLATE DNA 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP *GP*AP*GP*CP*TP)-3' dna, length: 14 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
Entity #14: Chains: P - TRANSCRIPT RNA 5'-R(*CP*CP*AP*GP*GP*AP)-3' rna, length: 6 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
Entity #15: Chains: T - TEMPLATE DNA 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP *TP*TP*TP*TP*TP*CP*CP*TP*BRUP*GP*GP*TP*CP*AP*TP*TP)-3' dna, length: 26 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
Entity #2: Chains: B - DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 protein, length: 1224 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 10 109 195
95% 10 110 267
90% 10 110 280
70% 10 110 302
50% 10 111 321
40% 10 119 308
30% 10 119 319
Entity #3: Chains: C - DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 protein, length: 318 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 10 108 200
95% 10 108 277
90% 10 108 291
70% 10 108 311
50% 10 109 331
40% 10 109 364
30% 10 109 368
Entity #4: Chains: D - DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 protein, length: 221 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 4 55 428
95% 4 55 617
90% 4 55 648
70% 4 56 689
50% 4 56 778
40% 4 56 805
30% 4 56 804
Entity #5: Chains: E - DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 protein, length: 215 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 13 115 171
95% 13 115 240
90% 13 115 250
70% 13 115 279
50% 13 116 305
40% 13 116 335
30% 13 116 342
Entity #6: Chains: F - DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 protein, length: 155 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 12 112 188
95% 12 112 256
90% 12 112 268
70% 12 112 294
50% 12 114 313
40% 12 114 341
30% 12 114 351
Entity #7: Chains: G - RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 protein, length: 171 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 5 57 400
95% 5 57 589
90% 5 57 617
70% 5 57 668
50% 6 59 672
40% 6 59 703
30% 6 59 704
Entity #8: Chains: H - DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 protein, length: 146 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 12 114 180
95% 12 115 242
90% 12 115 252
70% 12 115 282
50% 12 115 314
40% 12 115 342
30% 12 117 336
Entity #9: Chains: I - DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 protein, length: 122 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 10 109 196
95% 10 109 273
90% 10 109 287
70% 10 109 309
50% 10 110 329
40% 10 110 359
30% 10 110 365
 

Documentation

Click here for more detailed documentation on the redundancy reduction and sequence clustering procedure used by RCSB.