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RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 2NT DNA-RNA HYBRID AND SOAKED WITH GMPCPP
Sequence Clustering and Redundancy Reduction Results
4A3J
Sequence Clusters for the Sequence Entities in PDB 4A3J
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% 31 96 208
95% 31 96 292
90% 31 96 309
70% 31 96 326
50% 31 97 351
40% 31 97 376
30% 31 97 387
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% 33 102 190
95% 33 102 269
90% 33 102 281
70% 33 103 295
50% 33 111 276
40% 33 111 305
30% 33 111 318
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% 31 98 204
95% 31 98 287
90% 31 98 304
70% 31 98 319
50% 31 98 360
40% 31 99 372
30% 31 99 381
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% 33 101 192
95% 33 101 274
90% 33 101 287
70% 33 101 304
50% 33 101 341
40% 33 101 366
30% 33 101 376
Entity #13: Chains: N - 5'-D(*GP*TP*AP*GP*AP*AP*AP*GP*CP*TP*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 - 5'-R(*CP*AP)-3' rna, length: 2 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
Entity #15: Chains: T - 5'-D(*AP*GP*CP*TP*AP*GP*CP*TP*TP*TP*CP*BRUP*AP*CP*CP *TP*GP*AP*AP*CP*AP*AP*CP*TP*AP*AP*CP)-3' dna, length: 27 [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% 31 97 205
95% 31 98 284
90% 31 98 300
70% 31 98 317
50% 31 99 344
40% 31 107 316
30% 31 107 328
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% 31 96 210
95% 31 96 294
90% 31 96 311
70% 31 96 327
50% 31 97 354
40% 31 97 379
30% 31 97 389
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% 15 49 464
95% 15 49 660
90% 15 49 695
70% 15 50 736
50% 15 50 821
40% 15 50 840
30% 15 50 842
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% 34 103 184
95% 34 103 263
90% 34 103 275
70% 34 103 298
50% 34 104 322
40% 34 104 346
30% 34 104 355
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% 33 100 194
95% 33 100 278
90% 33 100 291
70% 33 100 310
50% 33 102 332
40% 33 102 356
30% 33 102 368
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% 16 51 422
95% 16 51 615
90% 16 51 648
70% 16 51 698
50% 17 53 683
40% 17 53 715
30% 17 53 714
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% 32 102 187
95% 33 103 265
90% 33 103 277
70% 33 103 299
50% 33 103 333
40% 33 103 357
30% 33 105 350
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% 31 97 206
95% 31 97 290
90% 31 97 307
70% 31 97 323
50% 31 98 350
40% 31 98 375
30% 31 98 386
 

Documentation

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