BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy14375
(206 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2C35|A Chain A, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|C Chain C, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|E Chain E, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|G Chain G, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
Length = 152
Score = 191 bits (485), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 101/151 (66%), Positives = 110/151 (72%), Gaps = 3/151 (1%)
Query: 59 SDRVSIGYIIMTHVLD---QVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTXXXXX 115
S R S+G + D VEEDA L FPKEFE AETLL SEVHMLL+HRK
Sbjct: 2 SRRASVGSQMAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESA 61
Query: 116 XXXXXFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEA 175
SEVF KTL YT RF +FKNRETI SVR+LL QKKLHKFELA +ANLCPET EE+
Sbjct: 62 EDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEES 121
Query: 176 KALIPSLECRFEEEELRQILDDIQTKRSLQY 206
KALIPSLE RFE+EEL+QILDDIQTKRS QY
Sbjct: 122 KALIPSLEGRFEDEELQQILDDIQTKRSFQY 152
>pdb|3H0G|D Chain D, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|P Chain P, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 135
Score = 76.6 bits (187), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 45/131 (34%), Positives = 69/131 (52%), Gaps = 2/131 (1%)
Query: 76 VVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTXXXXXXXXXX-FSEVFQKTLTYTER 134
+ EEDA L+ EFEN + L +SE +L++ ++V +KT+ Y
Sbjct: 5 IFEEDAAQLKLGPEFENEDMLTVSEAKILIETVLAQRARETNGEIPMTDVMKKTVAYFNV 64
Query: 135 FRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQI 194
F +FK E + +L + HKFE A + LC E EEA+ LIPSL + +++ L+ I
Sbjct: 65 FARFKTAEATYACERILGNR-FHKFERAQLGTLCCEDAEEARTLIPSLANKIDDQNLQGI 123
Query: 195 LDDIQTKRSLQ 205
LD++ T R Q
Sbjct: 124 LDELSTLRKFQ 134
>pdb|1Y14|A Chain A, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
pdb|1Y14|C Chain C, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
Length = 187
Score = 59.7 bits (143), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 49/80 (61%)
Query: 125 FQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLEC 184
+ T+ Y F +F+++ET+ +V LL LH FE+A + +L +T +EAK LIPSL
Sbjct: 107 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN 166
Query: 185 RFEEEELRQILDDIQTKRSL 204
+ ++EL +IL ++ +L
Sbjct: 167 KISDDELERILKELSNLETL 186
>pdb|1NT9|D Chain D, Complete 12-Subunit Rna Polymerase Ii
pdb|1Y1W|D Chain D, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|D Chain D, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|D Chain D, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|D Chain D, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|D Chain D, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|D Chain D, 12-Subunit Rna Polymerase Ii
pdb|2JA5|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|P Chain P, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2R7Z|D Chain D, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|D Chain D, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|D Chain D, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|D Chain D, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3FKI|D Chain D, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3H3V|E Chain E, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|D Chain D, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|P Chain P, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|D Chain D, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|D Chain D, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|D Chain D, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|D Chain D, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|D Chain D, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|D Chain D, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|D Chain D, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|D Chain D, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3PO2|D Chain D, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|D Chain D, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3J0K|D Chain D, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|D Chain D, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|D Chain D, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|D Chain D, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|D Chain D, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 221
Score = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 49/80 (61%)
Query: 125 FQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLEC 184
+ T+ Y F +F+++ET+ +V LL LH FE+A + +L +T +EAK LIPSL
Sbjct: 141 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN 200
Query: 185 RFEEEELRQILDDIQTKRSL 204
+ ++EL +IL ++ +L
Sbjct: 201 KISDDELERILKELSNLETL 220
>pdb|3QT1|D Chain D, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
Length = 219
Score = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 47/74 (63%)
Query: 125 FQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLEC 184
+ T+ Y F +F+++ET+ +V LL LH FE+A + +L +T +EAK LIPSL
Sbjct: 139 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN 198
Query: 185 RFEEEELRQILDDI 198
+ ++EL +IL ++
Sbjct: 199 KISDDELERILKEL 212
>pdb|1PQV|D Chain D, Rna Polymerase Ii-Tfiis Complex
Length = 221
Score = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 47/74 (63%)
Query: 125 FQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLEC 184
+ T+ Y F +F+++ET+ +V LL LH FE+A + +L +T +EAK LIPSL
Sbjct: 141 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN 200
Query: 185 RFEEEELRQILDDI 198
+ ++EL +IL ++
Sbjct: 201 KISDDELERILKEL 214
>pdb|1WCM|D Chain D, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
Length = 177
Score = 58.5 bits (140), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 47/74 (63%)
Query: 125 FQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLEC 184
+ T+ Y F +F+++ET+ +V LL LH FE+A + +L +T +EAK LIPSL
Sbjct: 97 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN 156
Query: 185 RFEEEELRQILDDI 198
+ ++EL +IL ++
Sbjct: 157 KISDDELERILKEL 170
>pdb|2WAQ|F Chain F, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|F Chain F, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|U Chain U, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|F Chain F, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|U Chain U, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|F Chain F, Rnap At 3.2ang
pdb|4B1O|F Chain F, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|U Chain U, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 113
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 27/39 (69%), Gaps = 1/39 (2%)
Query: 162 AAIANLCPETPEEAKALIPSLECR-FEEEELRQILDDIQ 199
A +A++CP TP+E ++++ R + E++++I+D I+
Sbjct: 70 AVLASICPITPDEVRSILIMDSNRTYTSEDIQKIIDIIR 108
>pdb|2PMZ|F Chain F, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|U Chain U, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|F Chain F, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|R Chain R, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 113
Score = 27.3 bits (59), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 44/82 (53%), Gaps = 8/82 (9%)
Query: 122 SEVFQKTLTY---TERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKA- 177
S + Q+T Y E+ ++ I + N+++++ + A +A++CP T +E ++
Sbjct: 31 SNLLQRTYDYLNSVEKCDAESAQKVIEELSNIVSREDVR----AILASICPTTSDEVRSI 86
Query: 178 LIPSLECRFEEEELRQILDDIQ 199
L+ + E++++I+D I+
Sbjct: 87 LVMDTNKTYTSEDIQKIIDIIR 108
>pdb|3AYH|A Chain A, Crystal Structure Of The C1725 SUBCOMPLEX FROM S. POMBE
RNA Polymerase Iii
Length = 136
Score = 26.6 bits (57), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 150 LLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQT 200
+ + +L K E+ I N P + E A I +E RF+EE++ ++++ I T
Sbjct: 83 IFNEFELTKAEILVILNNKPSSVPELYACIEGIEERFKEEDIFKLVEKINT 133
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.133 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,044,408
Number of Sequences: 62578
Number of extensions: 164776
Number of successful extensions: 423
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 410
Number of HSP's gapped (non-prelim): 14
length of query: 206
length of database: 14,973,337
effective HSP length: 94
effective length of query: 112
effective length of database: 9,091,005
effective search space: 1018192560
effective search space used: 1018192560
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)