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= 030170
(182 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2C35|B Chain B, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|D Chain D, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|F Chain F, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|H Chain H, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
Length = 172
Score = 72.4 bits (176), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 52/178 (29%), Positives = 91/178 (51%), Gaps = 8/178 (4%)
Query: 1 MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGE 60
MF + L +++ GP L ++ +L + T G+ +AVTT++NIG
Sbjct: 1 MFYHISLEHEILLHPRYF---GPNLLNTVKQKLFTE-VEGTCTGKYGFVIAVTTIDNIGA 56
Query: 61 GRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPD 120
G ++ G VL+PV + I F+ F+GEV+D V +V K G+F + GP+ S +
Sbjct: 57 GVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSE 116
Query: 121 YRYVQAENPVFLS--EKNPKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPVS 176
+ NP +++ I++D +R+ ++GT+ + + A+ SL D+LG VS
Sbjct: 117 MEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV--DKNDIFAIGSLMDDYLGLVS 172
>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii
Length = 215
Score = 65.9 bits (159), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 47/160 (29%), Positives = 77/160 (48%), Gaps = 7/160 (4%)
Query: 22 GPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIG--EGRVRENTGEVLFPVVFSGI 79
GP +++ + +LL++ T GY L V +NI GR+ G F V + +
Sbjct: 19 GPRMKQYLKTKLLEE-VEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAV 77
Query: 80 TFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMP-DYRYVQAENPVFLSEKNPK 138
FK F+GEV+DGTV +HG ++ GP++ +++T MP D + NP
Sbjct: 78 VFKPFKGEVVDGTVVSCSQHGFEVQVGPMK-VFVTKHLMPQDLTFNAGSNPPSYQSSEDV 136
Query: 139 IEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPVSCE 178
I +RV + G + A+ S++ D+LG +S E
Sbjct: 137 ITIKSRIRVKIEGC--ISQVSSIHAIGSIKEDYLGAISHE 174
>pdb|3H0G|G Chain G, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|S Chain S, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 172
Score = 64.3 bits (155), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 47/155 (30%), Positives = 79/155 (50%), Gaps = 7/155 (4%)
Query: 22 GPMLQRSIVVRLLDDFARRKATKDLGYFLAV--TTLENIGEGRVRENTGEVLFPVVFSGI 79
GP +Q + +LL D + GY + V + +I +GRV G F V + +
Sbjct: 20 GPRMQDYLKAKLLAD-VEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAV 78
Query: 80 TFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKM-PDYRYVQAENPVFLSEKNPK 138
++ FRGEV+D V V K G F GP+ N++++ + PD ++ NP S ++
Sbjct: 79 LWRPFRGEVVDAIVTTVNKMGFFANIGPL-NVFVSSHLVPPDMKFDPTANPPNYSGEDQV 137
Query: 139 IEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLG 173
IEK VR+ ++GT+ E A+ +++ D+LG
Sbjct: 138 IEKGSNVRLKIVGTR--TDATEIFAIATMKEDYLG 170
>pdb|1NT9|G Chain G, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|G Chain G, Rna Polymerase Ii-Tfiis Complex
pdb|1WCM|G Chain G, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|G Chain G, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|G Chain G, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|G Chain G, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|G Chain G, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|1Y14|B Chain B, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
pdb|1Y14|D Chain D, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
pdb|2B63|G Chain G, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2JA5|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|S Chain S, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2R7Z|G Chain G, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|G Chain G, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|G Chain G, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|G Chain G, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3FKI|G Chain G, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3H3V|H Chain H, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|G Chain G, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|S Chain S, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|G Chain G, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|G Chain G, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|G Chain G, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|G Chain G, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|G Chain G, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|G Chain G, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|G Chain G, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|G Chain G, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3PO2|G Chain G, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|G Chain G, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|G Chain G, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3J0K|G Chain G, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|G Chain G, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|G Chain G, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|G Chain G, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|G Chain G, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 171
Score = 62.8 bits (151), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 49/178 (27%), Positives = 81/178 (45%), Gaps = 10/178 (5%)
Query: 1 MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIG- 59
MF L N+ + GP +++ + +LL++ T GY L V +NI
Sbjct: 1 MFFIKDLSLNITLHPSFF---GPRMKQYLKTKLLEE-VEGSCTGKFGYILCVLDYDNIDI 56
Query: 60 -EGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKM 118
GR+ G F V + + FK F+GEV+DGTV +HG ++ GP++ +++T M
Sbjct: 57 QRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMK-VFVTKHLM 115
Query: 119 P-DYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPV 175
P D + NP I +RV + G + A+ S++ D+LG +
Sbjct: 116 PQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEG--CISQVSSIHAIGSIKEDYLGAI 171
>pdb|1GO3|E Chain E, Structure Of An Archeal Homolog Of The Eukaryotic Rna
Polymerase Ii Rpb4RPB7 COMPLEX
pdb|1GO3|M Chain M, Structure Of An Archeal Homolog Of The Eukaryotic Rna
Polymerase Ii Rpb4RPB7 COMPLEX
Length = 187
Score = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 44/170 (25%), Positives = 85/170 (50%), Gaps = 10/170 (5%)
Query: 1 MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGE 60
M+ +++ V VP E G L+ ++ L++ + R KD+G+ L++ +++IGE
Sbjct: 1 MYKILEIADVVKVPPEEF---GKDLKETVKKILMEKYEGR-LDKDVGFVLSIVDVKDIGE 56
Query: 61 GRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPD 120
G+V G PVVF + + E+++G V V++ G F++ GP++ + M D
Sbjct: 57 GKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDD 116
Query: 121 YRYVQAENPVFLSEKNPK---IEKDVVVRVIVIGTKWLEAEREFQALVSL 167
Y + + ++ K I V R++ I L+AER+ + ++L
Sbjct: 117 YVSYDPKREAIIGKETGKVLEIGDYVRARIVAIS---LKAERKRGSKIAL 163
>pdb|3AYH|B Chain B, Crystal Structure Of The C1725 SUBCOMPLEX FROM S. POMBE
RNA Polymerase Iii
Length = 203
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 7/89 (7%)
Query: 41 KATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHG 100
K +++G + V IGEG ++ G VVF I F+ FRGEV+ G + + G
Sbjct: 37 KVIQNIGLAICVYDFLKIGEGIIKYGDGSSYMNVVFRLIIFRPFRGEVMLGKIKSCSEEG 96
Query: 101 VFLKCGPVENIYL-------TCSKMPDYR 122
+ + ++I++ C PD R
Sbjct: 97 IRVTISFFDDIFIPKDMLFDPCVFRPDER 125
>pdb|2CKZ|B Chain B, X-Ray Structure Of Rna Polymerase Iii Subcomplex C17-C25.
pdb|2CKZ|D Chain D, X-Ray Structure Of Rna Polymerase Iii Subcomplex C17-C25
Length = 218
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 34/74 (45%)
Query: 28 SIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITFKIFRGE 87
S + L++ K ++G + + L + EG+++ G V F + FK F GE
Sbjct: 24 SAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLKPGDGSSYINVTFRAVVFKPFLGE 83
Query: 88 VLDGTVHKVLKHGV 101
++ G + K G+
Sbjct: 84 IVTGWISKCTAEGI 97
>pdb|2Y0S|E Chain E, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|T Chain T, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|E Chain E, Rnap At 3.2ang
pdb|4B1O|E Chain E, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|T Chain T, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 180
Score = 34.3 bits (77), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 37/137 (27%), Positives = 63/137 (45%), Gaps = 3/137 (2%)
Query: 39 RRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLK 98
+ K KDLG LA+ ++ EG + G V F IT+ EV++G V +V
Sbjct: 35 QEKILKDLGLVLAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPVVQEVVEGEVLQVDN 94
Query: 99 HGVFLKCGPVENIYLTCSKMPD--YRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156
+GVF+ GP++ + + S++ D +Y +F + I+K VR VI
Sbjct: 95 YGVFVNLGPMDGL-VHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTV 153
Query: 157 AEREFQALVSLEGDFLG 173
R + +++ +LG
Sbjct: 154 TGRLPRIALTMRQPYLG 170
>pdb|2WAQ|E Chain E, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|E Chain E, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|T Chain T, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 180
Score = 33.1 bits (74), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 36/137 (26%), Positives = 63/137 (45%), Gaps = 3/137 (2%)
Query: 39 RRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLK 98
+ K KDLG LA+ ++ EG + G V F IT+ EV++G V +V
Sbjct: 35 QEKILKDLGLVLAILNVKTSEEGILVFGDGATYHEVEFDMITYVPVVQEVVEGEVLQVDN 94
Query: 99 HGVFLKCGPVENIYLTCSKMPD--YRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156
+G+F+ GP++ + + S++ D +Y +F + I+K VR VI
Sbjct: 95 YGIFVNLGPMDGL-VHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTV 153
Query: 157 AEREFQALVSLEGDFLG 173
R + +++ +LG
Sbjct: 154 TGRLPRIALTMRQPYLG 170
>pdb|2PMZ|E Chain E, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|T Chain T, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|E Chain E, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|Q Chain Q, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 180
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 36/137 (26%), Positives = 63/137 (45%), Gaps = 3/137 (2%)
Query: 39 RRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLK 98
+ K KDLG LA+ ++ EG + G V F IT+ EV++G V +V
Sbjct: 35 QEKILKDLGLVLAILNVKTSEEGILVFGDGATYHEVEFDMITYVPVVQEVVEGEVLQVDN 94
Query: 99 HGVFLKCGPVENIYLTCSKMPD--YRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156
+G+F+ GP++ + + S++ D +Y +F + I+K VR VI
Sbjct: 95 YGIFVNLGPMDGL-VHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTV 153
Query: 157 AEREFQALVSLEGDFLG 173
R + +++ +LG
Sbjct: 154 TGRLPRIALTMRQPYLG 170
>pdb|1SZH|A Chain A, Crystal Structure Of C. Elegans Her-1
pdb|1SZH|B Chain B, Crystal Structure Of C. Elegans Her-1
Length = 161
Score = 26.2 bits (56), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 95 KVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKW 154
+++K G ++CG Y K+P Y Y +N +F E KI D V V G
Sbjct: 29 EIMKFGTPIRCG-----YDRDPKLPGYVYKCLQNVLFAKEPKKKINLDDSVCCSVFGNDQ 83
Query: 155 LEAEREFQ 162
++ R +
Sbjct: 84 EDSGRRCE 91
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
0.322 0.142 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,495,059
Number of Sequences: 62578
Number of extensions: 214802
Number of successful extensions: 425
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 413
Number of HSP's gapped (non-prelim): 16
length of query: 182
length of database: 14,973,337
effective HSP length: 93
effective length of query: 89
effective length of database: 9,153,583
effective search space: 814668887
effective search space used: 814668887
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)