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RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 4NT DNA-RNA HYBRID AND SOAKED WITH AMPCPP
Sequence Clustering and Redundancy Reduction Results
4A3M
Sequence Clusters for the Sequence Entities in PDB 4A3M
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% 36 96 203
95% 36 96 287
90% 36 96 300
70% 36 96 316
50% 36 97 338
40% 36 97 361
30% 36 97 374
Entity #10: Chains: J - DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 protein, length: 70 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 38 102 181
95% 38 102 259
90% 38 102 270
70% 38 103 280
50% 38 103 311
40% 38 111 294
30% 38 111 311
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% 36 98 200
95% 36 98 282
90% 36 98 295
70% 36 98 311
50% 36 98 347
40% 36 99 356
30% 36 99 367
Entity #12: Chains: L - DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 protein, length: 70 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 38 101 186
95% 38 101 267
90% 38 101 278
70% 38 101 295
50% 38 101 327
40% 38 101 351
30% 38 101 362
Entity #13: Chains: N - 5'-D(*AP*AP*GP*TP*AP*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(*AP*GP*GP*A)-3' rna, length: 4 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
Entity #15: Chains: T - 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*TP* TP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-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% 35 97 201
95% 36 98 279
90% 36 98 292
70% 36 98 309
50% 36 99 331
40% 36 107 301
30% 36 107 319
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% 36 96 205
95% 36 96 288
90% 36 96 301
70% 36 96 318
50% 36 97 341
40% 36 97 363
30% 36 97 376
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% 18 49 444
95% 18 49 642
90% 18 49 675
70% 18 50 698
50% 18 50 757
40% 18 50 769
30% 18 50 776
Entity #5: Chains: E - DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 protein, length: 215 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 39 103 176
95% 39 103 250
90% 39 103 261
70% 39 103 287
50% 39 104 301
40% 39 104 328
30% 39 104 339
Entity #6: Chains: F - DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 protein, length: 155 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 38 100 188
95% 38 100 271
90% 38 100 282
70% 38 100 301
50% 38 102 316
40% 38 102 339
30% 38 102 350
Entity #7: Chains: G - DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 protein, length: 171 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 19 51 413
95% 19 51 605
90% 19 51 636
70% 19 51 667
50% 20 53 638
40% 20 53 664
30% 20 53 664
Entity #8: Chains: H - DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 protein, length: 146 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 37 102 180
95% 38 103 251
90% 38 103 263
70% 38 103 288
50% 38 103 317
40% 38 103 340
30% 38 105 336
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% 36 97 202
95% 36 97 286
90% 36 97 299
70% 36 97 315
50% 36 98 335
40% 36 98 358
30% 36 98 371
 

Documentation

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