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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 97 340
40% 31 97 363
30% 31 97 377
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% 33 102 182
95% 33 102 261
90% 33 102 272
70% 33 103 280
50% 33 103 311
40% 33 111 295
30% 33 111 312
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 98 283
90% 31 98 296
70% 31 98 312
50% 31 98 349
40% 31 99 358
30% 31 99 369
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% 33 101 268
90% 33 101 279
70% 33 101 296
50% 33 101 328
40% 33 101 352
30% 33 101 363
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 98 280
90% 31 98 293
70% 31 98 310
50% 31 99 333
40% 31 107 302
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 97 343
40% 31 97 365
30% 31 97 379
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 49 445
95% 15 49 643
90% 15 49 676
70% 15 50 701
50% 15 50 760
40% 15 50 771
30% 15 50 779
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% 34 103 177
95% 34 103 251
90% 34 103 262
70% 34 103 287
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% 33 100 272
90% 33 100 283
70% 33 100 302
50% 33 102 316
40% 33 102 339
30% 33 102 351
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 51 414
95% 16 51 606
90% 16 51 637
70% 16 51 669
50% 17 53 639
40% 17 53 666
30% 17 53 671
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% 32 102 181
95% 33 103 252
90% 33 103 264
70% 33 103 288
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 98 337
40% 31 98 360
30% 31 98 373
 

Documentation

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