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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 96 288
90% 36 96 303
70% 36 96 321
50% 36 97 345
40% 36 97 366
30% 36 97 381
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% 38 102 186
95% 38 102 265
90% 38 102 277
70% 38 103 286
50% 38 112 272
40% 38 112 301
30% 38 112 317
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% 36 98 200
95% 36 98 284
90% 36 98 299
70% 36 98 315
50% 36 98 354
40% 36 99 362
30% 36 99 374
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% 38 101 188
95% 38 101 270
90% 38 101 282
70% 38 101 300
50% 38 101 335
40% 38 101 357
30% 38 101 370
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 98 281
90% 36 98 296
70% 36 98 313
50% 36 99 339
40% 36 108 308
30% 36 108 326
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 96 289
90% 36 96 304
70% 36 96 322
50% 36 97 348
40% 36 97 368
30% 36 97 383
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 49 447
95% 18 49 646
90% 18 49 679
70% 18 50 712
50% 18 50 789
40% 18 50 807
30% 18 50 809
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% 39 103 180
95% 39 103 254
90% 39 103 266
70% 39 103 291
50% 39 104 309
40% 39 104 336
30% 39 104 348
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% 38 100 190
95% 38 100 274
90% 38 100 286
70% 38 100 306
50% 38 102 325
40% 38 102 347
30% 38 102 360
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 51 417
95% 19 51 608
90% 19 51 639
70% 19 51 678
50% 20 53 648
40% 20 53 678
30% 20 53 679
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% 37 102 185
95% 38 103 255
90% 38 103 268
70% 38 103 292
50% 38 103 326
40% 38 103 348
30% 38 105 344
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 97 287
90% 36 97 302
70% 36 97 319
50% 36 98 343
40% 36 98 364
30% 36 98 378
 

Documentation

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