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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% 31 103 205
95% 31 103 288
90% 31 103 301
70% 31 103 323
50% 31 104 347
40% 31 104 378
30% 31 104 381
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% 33 109 189
95% 33 109 263
90% 33 109 276
70% 33 110 290
50% 33 118 274
40% 33 118 310
30% 33 118 320
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% 31 105 201
95% 31 105 286
90% 31 105 296
70% 31 105 319
50% 31 105 350
40% 31 106 368
30% 31 106 374
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% 33 108 191
95% 33 108 266
90% 33 108 280
70% 33 108 300
50% 33 108 328
40% 33 108 362
30% 33 108 365
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% 31 104 202
95% 31 105 284
90% 31 105 295
70% 31 105 318
50% 31 106 334
40% 31 114 320
30% 31 114 329
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% 31 103 206
95% 31 103 289
90% 31 103 302
70% 31 103 324
50% 31 104 349
40% 31 104 380
30% 31 104 384
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 51 464
95% 15 51 673
90% 15 51 708
70% 15 52 753
50% 15 52 843
40% 15 52 864
30% 15 52 864
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% 34 110 184
95% 34 110 256
90% 34 110 268
70% 34 110 292
50% 34 111 310
40% 34 111 344
30% 34 111 353
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% 33 107 192
95% 33 107 272
90% 33 107 285
70% 33 107 305
50% 33 109 317
40% 33 109 349
30% 33 109 358
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 53 437
95% 16 53 638
90% 16 53 670
70% 16 53 721
50% 17 55 712
40% 17 55 740
30% 17 55 741
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% 32 109 188
95% 33 110 257
90% 33 110 269
70% 33 110 293
50% 33 110 318
40% 33 110 350
30% 33 112 350
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% 31 104 204
95% 31 104 287
90% 31 104 300
70% 31 104 322
50% 31 105 343
40% 31 105 375
30% 31 105 379
 

Documentation

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