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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% 10 101 208
95% 10 101 292
90% 10 101 310
70% 10 101 329
50% 10 102 352
40% 10 102 381
30% 10 102 387
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% 12 107 189
95% 12 107 269
90% 12 107 282
70% 12 108 293
50% 12 116 277
40% 12 116 310
30% 12 116 322
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% 10 103 202
95% 10 103 287
90% 10 103 303
70% 10 103 321
50% 10 103 356
40% 10 104 376
30% 10 104 382
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% 12 106 192
95% 12 106 271
90% 12 106 285
70% 12 106 303
50% 12 106 332
40% 12 106 365
30% 12 106 371
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% 10 102 205
95% 10 103 284
90% 10 103 298
70% 10 103 318
50% 10 104 345
40% 10 112 324
30% 10 112 332
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% 10 101 209
95% 10 101 293
90% 10 101 311
70% 10 101 330
50% 10 102 354
40% 10 102 384
30% 10 102 390
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 51 457
95% 4 51 664
90% 4 51 696
70% 4 52 744
50% 4 52 834
40% 4 52 856
30% 4 52 859
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% 13 108 187
95% 13 108 262
90% 13 108 276
70% 13 108 296
50% 13 109 314
40% 13 109 344
30% 13 109 353
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% 12 105 196
95% 12 105 279
90% 12 105 291
70% 12 105 310
50% 12 107 324
40% 12 107 357
30% 12 107 360
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 53 432
95% 5 53 630
90% 5 53 660
70% 5 53 711
50% 6 55 708
40% 6 55 738
30% 6 55 739
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% 12 107 188
95% 12 108 263
90% 12 108 277
70% 12 108 297
50% 12 108 325
40% 12 108 358
30% 12 110 350
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% 10 102 207
95% 10 102 291
90% 10 102 309
70% 10 102 327
50% 10 103 350
40% 10 103 379
30% 10 103 385
 

Documentation

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