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= 047634
(82 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 = 72.0 bits (175), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 38/99 (38%), Positives = 57/99 (57%), Gaps = 18/99 (18%)
Query: 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNKL---- 56
G++GFV+A+ +++IG G+I+ G GFV +PV+ + IVFRPF+GE++ A VT VNK+
Sbjct: 40 GKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFT 99
Query: 57 -------------IPDDMELQ-TGDLPNYTTSDGSVCIS 81
IP +ME + P Y T D + I
Sbjct: 100 EIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQ 138
>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 = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 50/95 (52%), Gaps = 20/95 (21%)
Query: 1 GRHGFVVAIMGVESIG--TGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK--- 55
G++G+++ ++ +I G + G GF F V+ + +++RPFRGE++ A VT VNK
Sbjct: 41 GQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLWRPFRGEVVDAIVTTVNKMGF 100
Query: 56 --------------LIPDDMELQ-TGDLPNYTTSD 75
L+P DM+ T + PNY+ D
Sbjct: 101 FANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGED 135
>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii
Length = 215
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/101 (22%), Positives = 46/101 (45%), Gaps = 20/101 (19%)
Query: 1 GRHGFVVAIMGVESIG--TGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVT------- 51
G+ G+++ ++ ++I G I G F V+ + +VF+PF+GE++ V
Sbjct: 40 GKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGF 99
Query: 52 ----------MVNKLIPDDMELQTG-DLPNYTTSDGSVCIS 81
+ L+P D+ G + P+Y +S+ + I
Sbjct: 100 EVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIK 140
>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 = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/101 (22%), Positives = 46/101 (45%), Gaps = 20/101 (19%)
Query: 1 GRHGFVVAIMGVESIG--TGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVT------- 51
G+ G+++ ++ ++I G I G F V+ + +VF+PF+GE++ V
Sbjct: 40 GKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGF 99
Query: 52 ----------MVNKLIPDDMELQTG-DLPNYTTSDGSVCIS 81
+ L+P D+ G + P+Y +S+ + I
Sbjct: 100 EVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIK 140
>pdb|3AYH|B Chain B, Crystal Structure Of The C1725 SUBCOMPLEX FROM S. POMBE
RNA Polymerase Iii
Length = 203
Score = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 24/43 (55%)
Query: 4 GFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEIL 46
G + + IG G+I+ G G V + I+FRPFRGE++
Sbjct: 43 GLAICVYDFLKIGEGIIKYGDGSSYMNVVFRLIIFRPFRGEVM 85
>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 = 29.6 bits (65), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 27/50 (54%)
Query: 4 GFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMV 53
GFV++I+ V+ IG G + G G PV + +V+ P E++ V V
Sbjct: 43 GFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVVDV 92
>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 = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 25/48 (52%)
Query: 4 GFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVT 51
G + I + ++ G ++ G G V + +VF+PF GEI+ ++
Sbjct: 43 GLCITIYDLLTVEEGQLKPGDGSSYINVTFRAVVFKPFLGEIVTGWIS 90
>pdb|4AGF|A Chain A, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
pdb|4AGF|B Chain B, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
pdb|4AGF|C Chain C, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
pdb|4AGF|D Chain D, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
pdb|4AGF|E Chain E, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
pdb|4AGF|F Chain F, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
pdb|4AGF|G Chain G, Mtssl Spin Labeled L124c Mutant Of Mscs In The Open Form
Length = 286
Score = 26.9 bits (58), Expect = 2.7, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 6 VVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRG 43
V+A++G + GL G C++FRPFR
Sbjct: 96 VIAVLGAAGLAVGLALQG-SLSNLAAGVLCVMFRPFRA 132
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
0.328 0.147 0.455
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,515,114
Number of Sequences: 62578
Number of extensions: 83481
Number of successful extensions: 144
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 137
Number of HSP's gapped (non-prelim): 8
length of query: 82
length of database: 14,973,337
effective HSP length: 51
effective length of query: 31
effective length of database: 11,781,859
effective search space: 365237629
effective search space used: 365237629
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)