RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1131
(353 letters)
>1twf_A B220, DNA-directed RNA polymerase II largest subunit;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB:
1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A
1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A*
1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 255 bits (653), Expect = 1e-76
Identities = 105/174 (60%), Positives = 136/174 (78%), Gaps = 5/174 (2%)
Query: 86 RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR 145
R+ +LVR G +++PGAKY++RD+G+RIDLR+ + D+ LQ G+KVERHI D D V+FNR
Sbjct: 387 RLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNR 446
Query: 146 QPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHV 205
QP+LHKMSMM HRV+V+P+STFR+NLS TSPYNADFDGDEMNLHVPQS ETRAE+ +
Sbjct: 447 QPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCA 506
Query: 206 TPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVE-----RHIRDGDLVI 254
P QI++PQ+N+P MGIVQDTL +RK+T RD F++ + + D D VI
Sbjct: 507 VPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVI 560
Score = 189 bits (482), Expect = 9e-54
Identities = 79/113 (69%), Positives = 95/113 (84%)
Query: 241 DKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNL 300
KVERHI D D V+FNRQP+LHKMSMM HRV+V+P+STFR+NLS TSPYNADFDGDEMNL
Sbjct: 430 WKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNL 489
Query: 301 HVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353
HVPQS ETRAE+ + P QI++PQ+N+P MGIVQDTL +RK+T RD F++
Sbjct: 490 HVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIE 542
Score = 144 bits (364), Expect = 4e-38
Identities = 53/85 (62%), Positives = 72/85 (84%)
Query: 1 MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQ 60
+ +LVR G +++PGAKY++RD+G+RIDLR+ + D+ LQ G+KVERHI D D V+FNRQ
Sbjct: 388 LTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQ 447
Query: 61 PTLHKMSMMGHRVRVLPWSTFRMNL 85
P+LHKMSMM HRV+V+P+STFR+NL
Sbjct: 448 PSLHKMSMMAHRVKVIPYSTFRLNL 472
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 253 bits (646), Expect = 1e-75
Identities = 110/174 (63%), Positives = 141/174 (81%), Gaps = 5/174 (2%)
Query: 86 RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR 145
++ ELVR G ++PGAKYI+RD GERIDLR+H + D+ L+ G++VERHIRDGD+VIFNR
Sbjct: 393 QLQELVRNGPDEHPGAKYIIRDTGERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNR 452
Query: 146 QPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHV 205
QP+LHKMSMMGHR+RV+P+STFR+NLS TSPYNADFDGDEMN+HVPQS ETRAE++ I +
Sbjct: 453 QPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSEETRAEIQEITM 512
Query: 206 TPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVE-----RHIRDGDLVI 254
P+QI++PQ+N+PVMGIVQDTL VRK + RD FL + + D D ++
Sbjct: 513 VPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLWVPDWDGIL 566
Score = 189 bits (482), Expect = 9e-54
Identities = 84/113 (74%), Positives = 101/113 (89%)
Query: 241 DKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNL 300
+VERHIRDGD+VIFNRQP+LHKMSMMGHR+RV+P+STFR+NLS TSPYNADFDGDEMN+
Sbjct: 436 WRVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNM 495
Query: 301 HVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353
HVPQS ETRAE++ I + P+QI++PQ+N+PVMGIVQDTL VRK + RD FL
Sbjct: 496 HVPQSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLT 548
Score = 141 bits (357), Expect = 3e-37
Identities = 59/85 (69%), Positives = 75/85 (88%)
Query: 1 MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQ 60
+ ELVR G ++PGAKYI+RD GERIDLR+H + D+ L+ G++VERHIRDGD+VIFNRQ
Sbjct: 394 LQELVRNGPDEHPGAKYIIRDTGERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQ 453
Query: 61 PTLHKMSMMGHRVRVLPWSTFRMNL 85
P+LHKMSMMGHR+RV+P+STFR+NL
Sbjct: 454 PSLHKMSMMGHRIRVMPYSTFRLNL 478
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A
2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Length = 880
Score = 223 bits (571), Expect = 2e-66
Identities = 80/161 (49%), Positives = 107/161 (66%), Gaps = 2/161 (1%)
Query: 86 RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDL--HLQCGYKVERHIRDGDLVIF 143
++ + V G ++PGA Y++R +G RIDLR+ +L L GY VERH+ DGD+V+F
Sbjct: 360 KLRQFVINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYVVERHLTDGDVVLF 419
Query: 144 NRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENI 203
NRQP+LH++SMM HRVRVL TFR+NL PYNADFDGDEMNLHVPQS E AE + I
Sbjct: 420 NRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEEAIAEAKEI 479
Query: 204 HVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVE 244
+ + IITP+ P++G QD ++ +T + L K E
Sbjct: 480 MLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEE 520
Score = 180 bits (457), Expect = 1e-50
Identities = 61/113 (53%), Positives = 78/113 (69%)
Query: 241 DKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNL 300
VERH+ DGD+V+FNRQP+LH++SMM HRVRVL TFR+NL PYNADFDGDEMNL
Sbjct: 405 YVVERHLTDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNL 464
Query: 301 HVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353
HVPQS E AE + I + + IITP+ P++G QD ++ +T + L
Sbjct: 465 HVPQSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLT 517
Score = 114 bits (288), Expect = 3e-28
Identities = 46/87 (52%), Positives = 62/87 (71%), Gaps = 2/87 (2%)
Query: 1 MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDL--HLQCGYKVERHIRDGDLVIFN 58
+ + V G ++PGA Y++R +G RIDLR+ +L L GY VERH+ DGD+V+FN
Sbjct: 361 LRQFVINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYVVERHLTDGDVVLFN 420
Query: 59 RQPTLHKMSMMGHRVRVLPWSTFRMNL 85
RQP+LH++SMM HRVRVL TFR+NL
Sbjct: 421 RQPSLHRISMMAHRVRVLKGLTFRLNL 447
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D-
structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB:
1i6v_D* 2gho_D
Length = 1265
Score = 63.5 bits (155), Expect = 4e-11
Identities = 40/194 (20%), Positives = 75/194 (38%), Gaps = 23/194 (11%)
Query: 141 VIFNRQPTLHKMSMM--------GHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQ 192
V+ NR PTLH++ + G +++ P L C +NADFDGD+M +HVP
Sbjct: 440 VLLNRAPTLHRLGIQAFQPVLVEGQSIQLHP-------LVCE-AFNADFDGDQMAVHVPL 491
Query: 193 SMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDL 252
S +AE ++ +++P + P+ +D + + +T+ +
Sbjct: 492 SSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEE 551
Query: 253 VIF---NRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETR 309
+ + L+ V S R+ +P A L + ++ TR
Sbjct: 552 ALAAYERGEVALNAPI----VVAGRETSVGRLKFVFANPDEALLAVAHGLLDLQDTVTTR 607
Query: 310 AEVENIHVTPRQII 323
+ P +I+
Sbjct: 608 YLGRRLETNPGRIL 621
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2
PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D*
2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D*
3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Length = 1524
Score = 62.9 bits (153), Expect = 7e-11
Identities = 42/147 (28%), Positives = 68/147 (46%), Gaps = 29/147 (19%)
Query: 220 MGIVQDTLTAVRKMTKRDVFL-----DKVERHIRDGDLVIFNRQPTLHKMSMM------- 267
GI + A R+M +R + D +E I +V+ NR PTLH++ +
Sbjct: 664 KGIAP-NVKAARRMLERQRDIKDEVWDALEEVIHG-KVVLLNRAPTLHRLGIQAFQPVLV 721
Query: 268 -GHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQ 326
G +++ P L C +NADFDGD+M +HVP S +AE ++ +++P
Sbjct: 722 EGQSIQLHP-------LVCE-AFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPA 773
Query: 327 NNRPVMGIVQDT------LTAVRKMTK 347
+ P+ +D +T VRK K
Sbjct: 774 SGEPLAKPSRDIILGLYYITQVRKEKK 800
Score = 62.5 bits (152), Expect = 9e-11
Identities = 33/109 (30%), Positives = 53/109 (48%), Gaps = 22/109 (20%)
Query: 141 VIFNRQPTLHKMSMM--------GHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQ 192
V+ NR PTLH++ + G +++ P L C +NADFDGD+M +HVP
Sbjct: 700 VLLNRAPTLHRLGIQAFQPVLVEGQSIQLHP-------LVCE-AFNADFDGDQMAVHVPL 751
Query: 193 SMETRAEVENIHVTPRQIITPQNNRPVMGIVQDT------LTAVRKMTK 235
S +AE ++ +++P + P+ +D +T VRK K
Sbjct: 752 SSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKK 800
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_D*
Length = 1407
Score = 55.4 bits (134), Expect = 2e-08
Identities = 45/133 (33%), Positives = 70/133 (52%), Gaps = 32/133 (24%)
Query: 221 GIVQDTLTAVRKMTKR------DVFLDKVERHIRDGDLVIFNRQPTLHKMSMM------- 267
G+ T+ A +KM +R D+ LD+V IR+ V+ NR PTLH++ +
Sbjct: 389 GLAT-TIKAAKKMVEREEAVVWDI-LDEV---IRE-HPVLLNRAPTLHRLGIQAFEPVLI 442
Query: 268 -GHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQ 326
G +++ P L C YNADFDGD+M +HVP ++E + E + ++ I++P
Sbjct: 443 EGKAIQLHP-------LVCA-AYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPA 494
Query: 327 NNRPVMGIV--QD 337
N P+ IV QD
Sbjct: 495 NGEPI--IVPSQD 505
Score = 55.4 bits (134), Expect = 2e-08
Identities = 33/95 (34%), Positives = 51/95 (53%), Gaps = 20/95 (21%)
Query: 141 VIFNRQPTLHKMSMM--------GHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQ 192
V+ NR PTLH++ + G +++ P L C YNADFDGD+M +HVP
Sbjct: 421 VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHP-------LVCA-AYNADFDGDQMAVHVPL 472
Query: 193 SMETRAEVENIHVTPRQIITPQNNRPVMGIV--QD 225
++E + E + ++ I++P N P+ IV QD
Sbjct: 473 TLEAQLEARALMMSTNNILSPANGEPI--IVPSQD 505
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 34.3 bits (78), Expect = 0.063
Identities = 45/304 (14%), Positives = 81/304 (26%), Gaps = 154/304 (50%)
Query: 78 WSTFRMNLR-----MFELVRRGNSQYPGAKY---IVRD---NGERIDLRFHPKP----SD 122
W +F +++R +F + R YP I+ D N E + P P S+
Sbjct: 289 WESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGV-----PSPMLSISN 343
Query: 123 LHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFD 182
L + +V+ ++
Sbjct: 344 LTQE---QVQDYV----------------------------------------------- 353
Query: 183 GDEMNLHVPQSMETRAEVENIHV----TPRQIITPQNNRPVMGIVQDTL----TAVRKMT 234
++ N H+P + + + + ++ V G Q L +RK
Sbjct: 354 -NKTNSHLPAG-------KQVEISLVNGAKNLV-------VSGPPQS-LYGLNLTLRKA- 396
Query: 235 KRDVFLD--KVERHIRDGDLVIFN-RQPTLHKMSMMGHRVRVLPWST-FRMNLSCTSPY- 289
K LD ++ F+ R+ R LP ++ F S
Sbjct: 397 KAPSGLDQSRIP----------FSERKLKFS--------NRFLPVASPFH------SHLL 432
Query: 290 --------------NADFDGDEMNLHVPQ-SMET----RAEVENIHVTPR---QIITPQN 327
N F+ + + +P R +I + R II
Sbjct: 433 VPASDLINKDLVKNNVSFNAKD--IQIPVYDTFDGSDLRVLSGSI--SERIVDCIIR--- 485
Query: 328 NRPV 331
PV
Sbjct: 486 -LPV 488
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 32.9 bits (74), Expect = 0.18
Identities = 13/114 (11%), Positives = 44/114 (38%), Gaps = 26/114 (22%)
Query: 176 PYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQ---------IITPQNNRPVMGIVQDT 226
+ +FD ++ +P+S+ ++ E+++I ++ + + V V++
Sbjct: 28 AFVDNFDCKDV-QDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEV 86
Query: 227 L--------TAVRKMTK-----RDVFLDKVERHIRDGDLVI---FNRQPTLHKM 264
L + ++ + +++++ +R D + +R K+
Sbjct: 87 LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKL 140
>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca
cleavage, DNA damage, DNA repair, DNA replication,
DNA-BIND hydrolase; 1.37A {Thermotoga maritima}
Length = 196
Score = 27.5 bits (62), Expect = 5.4
Identities = 19/69 (27%), Positives = 27/69 (39%), Gaps = 20/69 (28%)
Query: 212 TPQNNRPVMGIV------------QDTLTAVRKMTKR--DVFLDKV------ERHIRDGD 251
+ +N P++G + +D + D FL KV E HI DGD
Sbjct: 69 SIRNKIPLIGEIRAGEKREAIEYLEDYIEIPESFLSSGYDHFLLKVKGESMIEEHICDGD 128
Query: 252 LVIFNRQPT 260
LV+ RQ
Sbjct: 129 LVLVRRQDW 137
>1k0e_A P-aminobenzoate synthase component I; aminodeoxychorismate
synthase, chorismate, glutamine, tryptophan, PABA
synthase, lyase; HET: TRP; 2.00A {Escherichia coli}
SCOP: d.161.1.1 PDB: 1k0g_A*
Length = 453
Score = 27.5 bits (62), Expect = 8.2
Identities = 15/94 (15%), Positives = 33/94 (35%), Gaps = 12/94 (12%)
Query: 233 MTKRDVFLDKVER---HIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRM-NLSCTSP 288
MT+ + +K + ++ GD + + W F N + +P
Sbjct: 188 MTREQ-YGEKFRQVQEYLHSGD--CYQVNLA-QRFHA---TYSGDEWQAFLQLNQANRAP 240
Query: 289 YNADFDGDEMNLHVPQSMETRAEVENIHVTPRQI 322
++A ++ + + S E +N + R I
Sbjct: 241 FSAFLRLEQGAI-LSLSPERFILCDNSEIQTRPI 273
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.324 0.138 0.426
Gapped
Lambda K H
0.267 0.0623 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,644,828
Number of extensions: 349093
Number of successful extensions: 1105
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1093
Number of HSP's successfully gapped: 30
Length of query: 353
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 258
Effective length of database: 4,049,298
Effective search space: 1044718884
Effective search space used: 1044718884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.3 bits)