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= 029485
(192 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 109 bits (272), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 74/216 (34%), Positives = 107/216 (49%), Gaps = 29/216 (13%)
Query: 1 MFYLSKIEHTXXXXXXXXXXXXNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVY 60
MF LSKI AI +L N F +K+I N+GLCI+IYD+ +E G +
Sbjct: 1 MFILSKIADLVRIPPDQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLK 60
Query: 61 PGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLS-LGFFEDIYVPSHLLPSPSR 119
PG+G+S V FR VVF+PF+GEI+ + + A G+++S LG F+DI++P ++L
Sbjct: 61 PGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCY 120
Query: 120 SEPDPYGRYEVKWIWEFG-DTKYVIDGLDEIKFRVLSVNY----PSIPIEQA-------- 166
P+ E WIW +TK D ++I+FR+ + P P E+
Sbjct: 121 YTPE-----ESAWIWPMDEETKLYFDVNEKIRFRIEREVFVDVKPKSPKERELEERAQLE 175
Query: 167 ---EGSKPFAPM-------VINGSIDYDGLGPVSWW 192
EG P + GS DG+G VSWW
Sbjct: 176 NEIEGKNEETPQNEKPPAYALLGSCQTDGMGLVSWW 211
>pdb|3AYH|B Chain B, Crystal Structure Of The C1725 SUBCOMPLEX FROM S. POMBE
RNA Polymerase Iii
Length = 203
Score = 107 bits (268), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 64/207 (30%), Positives = 101/207 (48%), Gaps = 20/207 (9%)
Query: 1 MFYLSKIEHTXXXXXXXXXXXXNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVY 60
MF LS+ EA+ E+ + +KVI N+GL I +YD +I G +
Sbjct: 1 MFLLSRFSDIISIHPSNFWKPTKEALAEEIHKKYANKVIQNIGLAICVYDFLKIGEGIIK 60
Query: 61 PGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRS 120
G+G+S V FRL++FRPF GE++ K+K G+R+++ FF+DI++P +L P
Sbjct: 61 YGDGSSYMNVVFRLIIFRPFRGEVMLGKIKSCSEEGIRVTISFFDDIFIPKDMLFDPCVF 120
Query: 121 EPDPYGRYEVKWIWEF------GDTKYVIDGLDEIKFRVLSVNYPSI---------PIEQ 165
PD E W+W+ T+ D +EI+F++ S ++ I I
Sbjct: 121 RPD-----ERAWVWKIEGEDGSEGTELYFDIDEEIRFQIESEDFVDISPKRNKNATAITG 175
Query: 166 AEGSKPFAPMVINGSIDYDGLGPVSWW 192
E + +P + S DGLG +WW
Sbjct: 176 TEALESVSPYTLIASCSRDGLGIPAWW 202
>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii
Length = 215
Score = 53.5 bits (127), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 44 LCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGF 103
LC+ YD +I+ G + P +G++ VK+R VVF+PF GE++ + +G + +G
Sbjct: 46 LCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGP 105
Query: 104 FEDIYVPSHLLPS 116
+ ++V HL+P
Sbjct: 106 MK-VFVTKHLMPQ 117
>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 = 53.5 bits (127), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 38/154 (24%), Positives = 65/154 (42%), Gaps = 6/154 (3%)
Query: 1 MFYLSKIEHTXXXXXXXXXXXXNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVY 60
MFY +EH +K +L G I++ I I G +
Sbjct: 1 MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ 60
Query: 61 PGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRS 120
PG G + VK++ +VFRPF GE++ A + + + GL +G ++ H +PS
Sbjct: 61 PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMS-CFISRHSIPSEMEF 119
Query: 121 EPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVL 154
+P+ ++ D VI DEI+ +++
Sbjct: 120 DPNSN-----PPCYKTMDEDIVIQQDDEIRLKIV 148
>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 = 53.1 bits (126), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 44 LCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGF 103
LC+ YD +I+ G + P +G++ VK+R VVF+PF GE++ + +G + +G
Sbjct: 46 LCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGP 105
Query: 104 FEDIYVPSHLLPS 116
+ ++V HL+P
Sbjct: 106 MK-VFVTKHLMPQ 117
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 47/79 (59%), Gaps = 1/79 (1%)
Query: 44 LCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGF 103
+C+ + +I+ G V PG+G + VK+R V++RPF GE++ A + + G ++G
Sbjct: 47 ICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLWRPFRGEVVDAIVTTVNKMGFFANIGP 106
Query: 104 FEDIYVPSHLLPSPSRSEP 122
+++V SHL+P + +P
Sbjct: 107 L-NVFVSSHLVPPDMKFDP 124
>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 = 46.6 bits (109), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 39/134 (29%), Positives = 70/134 (52%), Gaps = 7/134 (5%)
Query: 23 NEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVG 82
NE EL + +K++ +LGL ++I ++K E G + G+GA+ H V+F ++ + P V
Sbjct: 23 NEIALNELRQQYQEKILKDLGLVLAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPVVQ 82
Query: 83 EIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYV 142
E++ ++ + D G+ ++LG P L S+ D V+ I +K V
Sbjct: 83 EVVEGEVLQVDNYGVFVNLG-------PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKV 135
Query: 143 IDGLDEIKFRVLSV 156
I D+++ RV+SV
Sbjct: 136 IQKGDKVRARVISV 149
>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 = 46.6 bits (109), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 39/134 (29%), Positives = 70/134 (52%), Gaps = 7/134 (5%)
Query: 23 NEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVG 82
NE EL + +K++ +LGL ++I ++K E G + G+GA+ H V+F ++ + P V
Sbjct: 23 NEIALNELRQQYQEKILKDLGLVLAILNVKTSEEGILVFGDGATYHEVEFDMITYVPVVQ 82
Query: 83 EIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYV 142
E++ ++ + D G+ ++LG P L S+ D V+ I +K V
Sbjct: 83 EVVEGEVLQVDNYGIFVNLG-------PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKV 135
Query: 143 IDGLDEIKFRVLSV 156
I D+++ RV+SV
Sbjct: 136 IQKGDKVRARVISV 149
>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 = 46.6 bits (109), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 39/134 (29%), Positives = 70/134 (52%), Gaps = 7/134 (5%)
Query: 23 NEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVG 82
NE EL + +K++ +LGL ++I ++K E G + G+GA+ H V+F ++ + P V
Sbjct: 23 NEIALNELRQQYQEKILKDLGLVLAILNVKTSEEGILVFGDGATYHEVEFDMITYVPVVQ 82
Query: 83 EIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYV 142
E++ ++ + D G+ ++LG P L S+ D V+ I +K V
Sbjct: 83 EVVEGEVLQVDNYGIFVNLG-------PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKV 135
Query: 143 IDGLDEIKFRVLSV 156
I D+++ RV+SV
Sbjct: 136 IQKGDKVRARVISV 149
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 39/154 (25%), Positives = 75/154 (48%), Gaps = 12/154 (7%)
Query: 23 NEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVG 82
E +K L + ++ ++G +SI D+K+I G V G+G++ H V F +V+ P +
Sbjct: 23 KETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMY 82
Query: 83 EIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFG-DTKY 141
E+I ++ + G + LG + + S ++ D Y Y+ K G +T
Sbjct: 83 ELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIM--------DDYVSYDPKREAIIGKETGK 134
Query: 142 VIDGLDEIKFRVLSVNYPSIPIEQAEGSKPFAPM 175
V++ D ++ R++++ S+ E+ GSK M
Sbjct: 135 VLEIGDYVRARIVAI---SLKAERKRGSKIALTM 165
>pdb|3TMA|A Chain A, Crystal Structure Of Trmn From Thermus Thermophilus
Length = 354
Score = 26.9 bits (58), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 9/42 (21%)
Query: 59 VYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLS 100
+YPGEGA K R+ + R +VGE +A GLRL+
Sbjct: 41 LYPGEGAEVDARKGRVRIPRAWVGE---------EALGLRLA 73
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
0.320 0.142 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,020,756
Number of Sequences: 62578
Number of extensions: 261752
Number of successful extensions: 591
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 578
Number of HSP's gapped (non-prelim): 12
length of query: 192
length of database: 14,973,337
effective HSP length: 93
effective length of query: 99
effective length of database: 9,153,583
effective search space: 906204717
effective search space used: 906204717
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)