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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 96 203
95% 31 96 287
90% 31 96 300
70% 31 96 316
50% 31 97 338
40% 31 97 361
30% 31 97 374
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% 33 102 181
95% 33 102 259
90% 33 102 269
70% 33 103 279
50% 33 103 311
40% 33 111 294
30% 33 111 311
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% 31 98 200
95% 31 98 282
90% 31 98 295
70% 31 98 311
50% 31 98 347
40% 31 99 356
30% 31 99 367
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% 33 101 186
95% 33 101 267
90% 33 101 278
70% 33 101 295
50% 33 101 327
40% 33 101 351
30% 33 101 362
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 97 201
95% 31 98 279
90% 31 98 292
70% 31 98 309
50% 31 99 331
40% 31 107 301
30% 31 107 319
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% 31 96 205
95% 31 96 288
90% 31 96 301
70% 31 96 318
50% 31 97 341
40% 31 97 363
30% 31 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% 15 49 444
95% 15 49 642
90% 15 49 675
70% 15 50 698
50% 15 50 756
40% 15 50 768
30% 15 50 776
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% 34 103 175
95% 34 103 249
90% 34 103 260
70% 34 103 286
50% 34 104 301
40% 34 104 328
30% 34 104 339
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% 33 100 188
95% 33 100 271
90% 33 100 282
70% 33 100 301
50% 33 102 316
40% 33 102 339
30% 33 102 350
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 51 413
95% 16 51 604
90% 16 51 635
70% 16 51 667
50% 17 53 636
40% 17 53 662
30% 17 53 663
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% 32 102 179
95% 33 103 250
90% 33 103 262
70% 33 103 287
50% 33 103 317
40% 33 103 340
30% 33 105 336
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% 31 97 202
95% 31 97 286
90% 31 97 299
70% 31 97 315
50% 31 98 335
40% 31 98 358
30% 31 98 371
 

Documentation

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