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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% 31 108 198
95% 31 108 273
90% 31 108 287
70% 31 108 308
50% 31 109 329
40% 31 109 359
30% 31 109 365
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% 33 114 183
95% 33 114 251
90% 33 114 261
70% 33 115 272
50% 33 123 270
40% 33 123 296
30% 33 123 311
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% 31 110 194
95% 31 110 270
90% 31 110 283
70% 31 110 304
50% 31 110 333
40% 31 111 353
30% 31 111 362
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% 33 113 187
95% 33 113 253
90% 33 113 264
70% 33 113 290
50% 33 113 317
40% 33 113 349
30% 33 113 356
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% 31 109 195
95% 31 110 265
90% 31 110 278
70% 31 110 301
50% 31 111 320
40% 31 119 308
30% 31 119 319
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% 31 108 200
95% 31 108 277
90% 31 108 291
70% 31 108 310
50% 31 109 330
40% 31 109 363
30% 31 109 367
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 55 430
95% 15 55 619
90% 15 55 651
70% 15 56 689
50% 15 56 776
40% 15 56 803
30% 15 56 804
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% 34 115 170
95% 34 115 239
90% 34 115 249
70% 34 115 277
50% 34 116 305
40% 34 116 335
30% 34 116 342
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% 33 112 188
95% 33 112 255
90% 33 112 267
70% 33 112 293
50% 33 114 312
40% 33 114 340
30% 33 114 350
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 57 402
95% 16 57 589
90% 16 57 619
70% 16 57 670
50% 17 59 672
40% 17 59 703
30% 17 59 703
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% 32 114 179
95% 33 115 241
90% 33 115 251
70% 33 115 280
50% 33 115 313
40% 33 115 341
30% 33 117 336
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% 31 109 196
95% 31 109 272
90% 31 109 286
70% 31 109 307
50% 31 110 328
40% 31 110 358
30% 31 110 364
 

Documentation

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