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RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 7NT DNA-RNA HYBRID AND SOAKED WITH AMPCPP
Sequence Clustering and Redundancy Reduction Results
4A3L
Sequence Clusters for the Sequence Entities in PDB 4A3L
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% 21 96 204
95% 21 96 289
90% 21 96 304
70% 21 96 322
50% 21 97 346
40% 21 97 367
30% 21 97 383
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% 23 102 188
95% 23 102 266
90% 23 102 278
70% 23 103 287
50% 23 112 272
40% 23 112 301
30% 23 112 317
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% 21 98 201
95% 21 98 285
90% 21 98 300
70% 21 98 316
50% 21 98 355
40% 21 99 363
30% 21 99 376
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% 23 101 190
95% 23 101 271
90% 23 101 283
70% 23 101 301
50% 23 101 336
40% 23 101 358
30% 23 101 372
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*CP*CP*AP*GP*GP*AP)-3' rna, length: 7 [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*BRU*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% 21 97 202
95% 21 98 282
90% 21 98 297
70% 21 98 314
50% 21 99 340
40% 21 108 309
30% 21 108 327
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% 21 96 206
95% 21 96 290
90% 21 96 305
70% 21 96 323
50% 21 97 349
40% 21 97 369
30% 21 97 385
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% 10 49 455
95% 10 49 656
90% 10 49 690
70% 10 50 729
50% 10 50 816
40% 10 50 831
30% 10 50 832
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% 24 103 183
95% 24 103 258
90% 24 103 270
70% 24 103 293
50% 24 104 311
40% 24 104 337
30% 24 104 350
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% 23 100 192
95% 23 100 275
90% 23 100 287
70% 23 100 307
50% 23 102 327
40% 23 102 349
30% 23 102 362
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% 11 51 418
95% 11 51 611
90% 11 51 643
70% 11 51 693
50% 12 53 679
40% 12 53 709
30% 12 53 709
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% 22 102 186
95% 23 103 259
90% 23 103 272
70% 23 103 294
50% 23 103 328
40% 23 103 350
30% 23 105 345
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% 21 97 203
95% 21 97 288
90% 21 97 303
70% 21 97 320
50% 21 98 344
40% 21 98 365
30% 21 98 380
 

Documentation

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