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= 038078
(165 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3EBY|A Chain A, Crystal Structure Of The Beta Subunit Of A Putative
Aromatic-Ring- Hydroxylating Dioxygenase
(Yp_001165631.1) From Novosphingobium Aromaticivorans
Dsm 12444 At 1.75 A Resolution
Length = 163
Score = 30.8 bits (68), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 5/37 (13%)
Query: 3 DMVLTIPKGTLFPMCGMNLAFDRHLIGPAMYFGLMGD 39
D V+ + K +FP F+RHLIG A+ G+ GD
Sbjct: 72 DRVVALRKANVFPE-----HFNRHLIGRAVITGVEGD 103
>pdb|2I7T|A Chain A, Structure Of Human Cpsf-73
pdb|2I7V|A Chain A, Structure Of Human Cpsf-73
Length = 459
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/124 (19%), Positives = 60/124 (48%), Gaps = 12/124 (9%)
Query: 45 RYDDMWAGWCTKVICDHLNLGVKTGLPYIFHSKASNPFVNLKKEYKGIFWQED----IIP 100
+ ++ A +C V D +N G + +P +A + L + +WQ IP
Sbjct: 214 KREEREARFCNTV-HDIVNRGGRGLIPVFALGRAQELLLILDE-----YWQNHPELHDIP 267
Query: 101 FFQAVTLPKECTTVQECYIE-LSKQVKEKLSKVDPYFDKLADAMVTWIEAWDELNPAGAA 159
+ A +L K+C V + Y+ ++ +++++++ +P+ K + + ++ +D++ P+
Sbjct: 268 IYYASSLAKKCMAVYQTYVNAMNDKIRKQININNPFVFKHISNLKS-MDHFDDIGPSVVM 326
Query: 160 VANG 163
+ G
Sbjct: 327 ASPG 330
>pdb|1DZF|A Chain A, Rpb5 From S.Cerevisiae
pdb|1I3Q|E Chain E, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|E Chain E, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|E Chain E, Rna Polymerase Ii Elongation Complex
pdb|1K83|E Chain E, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|E Chain E, Wild Type Rna Polymerase Ii
pdb|1NT9|E Chain E, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|E Chain E, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|E Chain E, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|E Chain E, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|E Chain E, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|E Chain E, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|E Chain E, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|E Chain E, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|E Chain E, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|E Chain E, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|E Chain E, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|E Chain E, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|E Chain E, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|E Chain E, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|E Chain E, 12-Subunit Rna Polymerase Ii
pdb|2E2H|E Chain E, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|E Chain E, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|E Chain E, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|Q Chain Q, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|E Chain E, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|E Chain E, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|E Chain E, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|E Chain E, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|E Chain E, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|E Chain E, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|E Chain E, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|E Chain E, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|E Chain E, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|E Chain E, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|E Chain E, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|E Chain E, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|E Chain E, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|E Chain E, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|F Chain F, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|E Chain E, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|Q Chain Q, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|E Chain E, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|E Chain E, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|E Chain E, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|E Chain E, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|E Chain E, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|E Chain E, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|E Chain E, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|E Chain E, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|E Chain E, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|E Chain E, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|E Chain E, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|E Chain E, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|E Chain E, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|E Chain E, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|E Chain E, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|E Chain E, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|E Chain E, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|E Chain E, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|E Chain E, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|E Chain E, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|E Chain E, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|E Chain E, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|E Chain E, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|E Chain E, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|E Chain E, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 215
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 10/70 (14%)
Query: 32 MYFGLMGDGQPIGRYDDMWAGWCTKVICDHLNLGVKTGLPYIFHSKASNPFVNLKKEYKG 91
M F + I ++ DM + W CD ++GVKT ++ H + K G
Sbjct: 58 MSFQANPTEESISKFPDMGSLWVE--FCDEPSVGVKTMKTFVIH-------IQEKNFQTG 108
Query: 92 IF-WQEDIIP 100
IF +Q +I P
Sbjct: 109 IFVYQNNITP 118
>pdb|1ULZ|A Chain A, Crystal Structure Of The Biotin Carboxylase Subunit Of
Pyruvate Carboxylase
Length = 451
Score = 28.5 bits (62), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 131 KVDPYFDKLADAMVTWIEAWDE 152
+V PY+D + ++TW WDE
Sbjct: 376 EVTPYYDSMIAKLITWAPTWDE 397
>pdb|3SXN|A Chain A, Mycobacterium Tuberculosis Eis Protein Initiates
Modulation Of Host Immune Responses By Acetylation Of
Dusp16MKP-7
pdb|3SXN|B Chain B, Mycobacterium Tuberculosis Eis Protein Initiates
Modulation Of Host Immune Responses By Acetylation Of
Dusp16MKP-7
pdb|3SXN|C Chain C, Mycobacterium Tuberculosis Eis Protein Initiates
Modulation Of Host Immune Responses By Acetylation Of
Dusp16MKP-7
pdb|3SXN|D Chain D, Mycobacterium Tuberculosis Eis Protein Initiates
Modulation Of Host Immune Responses By Acetylation Of
Dusp16MKP-7
pdb|3SXN|E Chain E, Mycobacterium Tuberculosis Eis Protein Initiates
Modulation Of Host Immune Responses By Acetylation Of
Dusp16MKP-7
pdb|3SXN|F Chain F, Mycobacterium Tuberculosis Eis Protein Initiates
Modulation Of Host Immune Responses By Acetylation Of
Dusp16MKP-7
Length = 422
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 1 YVDMVLTIPKGTLFPMCGMNL 21
Y+DM LT+P G + P+ G++
Sbjct: 84 YLDMQLTVPGGEVLPVAGISF 104
>pdb|2J66|A Chain A, Structural Characterisation Of Btrk Decarboxylase From
Butirosin Biosynthesis
Length = 428
Score = 27.3 bits (59), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 57 VICDHLNLGVKTGLPYIFHSKA 78
++C+ +NLG G+PY H KA
Sbjct: 218 IVCECINLGGGFGVPYFSHEKA 239
>pdb|4I9Y|A Chain A, Structure Of The C-terminal Domain Of Nup358
pdb|4I9Y|B Chain B, Structure Of The C-terminal Domain Of Nup358
pdb|4I9Y|C Chain C, Structure Of The C-terminal Domain Of Nup358
pdb|4I9Y|D Chain D, Structure Of The C-terminal Domain Of Nup358
pdb|4I9Y|E Chain E, Structure Of The C-terminal Domain Of Nup358
pdb|4I9Y|F Chain F, Structure Of The C-terminal Domain Of Nup358
Length = 167
Score = 26.9 bits (58), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 26 HLIGPAMYFGLMGDGQPIGR 45
H+ P ++F + DG+P+GR
Sbjct: 3 HMTNPVVFFDVCADGEPLGR 22
>pdb|4A8F|A Chain A, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8F|B Chain B, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8F|C Chain C, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8K|A Chain A, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8K|B Chain B, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8K|C Chain C, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8M|P Chain P, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8M|Q Chain Q, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8M|R Chain R, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
Length = 665
Score = 26.9 bits (58), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 43 IGRYDDMWAGWCTKVICDH-LNLG 65
+ +D W GW +ICD LN+G
Sbjct: 326 VSDHDTFWPGWLRDLICDELLNMG 349
>pdb|1WAC|A Chain A, Back-Priming Mode Of Phi6 Rna-Dependent Rna Polymerase
pdb|1WAC|B Chain B, Back-Priming Mode Of Phi6 Rna-Dependent Rna Polymerase
pdb|1WAC|C Chain C, Back-Priming Mode Of Phi6 Rna-Dependent Rna Polymerase
Length = 662
Score = 26.9 bits (58), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 43 IGRYDDMWAGWCTKVICDH-LNLG 65
+ +D W GW +ICD LN+G
Sbjct: 325 VSDHDTFWPGWLRDLICDELLNMG 348
>pdb|4A8O|A Chain A, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8O|B Chain B, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8O|C Chain C, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8Q|A Chain A, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8Q|B Chain B, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8Q|C Chain C, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8S|A Chain A, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8S|B Chain B, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8S|C Chain C, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8W|A Chain A, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8W|B Chain B, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8W|C Chain C, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8Y|A Chain A, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8Y|B Chain B, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
pdb|4A8Y|C Chain C, Non-Catalytic Ions Direct The Rna-Dependent Rna Polymerase
Of Bacterial Dsrna Virus Phi6 From De Novo Initiation To
Elongation
Length = 665
Score = 26.9 bits (58), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 43 IGRYDDMWAGWCTKVICDH-LNLG 65
+ +D W GW +ICD LN+G
Sbjct: 326 VSDHDTFWPGWLRDLICDELLNMG 349
>pdb|2JL9|A Chain A, Structural Explanation For The Role Of Mn In The Activity
Of Phi6 Rna-Dependent Rna Polymerase
pdb|2JL9|B Chain B, Structural Explanation For The Role Of Mn In The Activity
Of Phi6 Rna-Dependent Rna Polymerase
pdb|2JL9|C Chain C, Structural Explanation For The Role Of Mn In The Activity
Of Phi6 Rna-Dependent Rna Polymerase
Length = 665
Score = 26.9 bits (58), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 43 IGRYDDMWAGWCTKVICDH-LNLG 65
+ +D W GW +ICD LN+G
Sbjct: 326 VSDHDTFWPGWLRDLICDELLNMG 349
>pdb|1HHS|A Chain A, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
pdb|1HHS|B Chain B, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
pdb|1HHS|C Chain C, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
pdb|1HHT|P Chain P, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
Plus Template
pdb|1HHT|Q Chain Q, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
Plus Template
pdb|1HHT|R Chain R, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
Plus Template
pdb|1HI0|P Chain P, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
Plus Initiation Complex
pdb|1HI0|Q Chain Q, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
Plus Initiation Complex
pdb|1HI0|R Chain R, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
Plus Initiation Complex
pdb|1HI1|A Chain A, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
Plus Bound Ntp
pdb|1HI1|B Chain B, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
Plus Bound Ntp
pdb|1HI1|C Chain C, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
Plus Bound Ntp
pdb|1UVI|A Chain A, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
With 6nt Rna
pdb|1UVI|B Chain B, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
With 6nt Rna
pdb|1UVI|C Chain C, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
With 6nt Rna
pdb|1UVJ|A Chain A, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
With 7nt Rna
pdb|1UVJ|B Chain B, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
With 7nt Rna
pdb|1UVJ|C Chain C, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
With 7nt Rna
pdb|1UVK|A Chain A, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
Dead-End Complex
pdb|1UVK|C Chain C, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
Dead-End Complex
pdb|1UVK|E Chain E, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
Dead-End Complex
pdb|1UVL|A Chain A, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
With 5nt Rna Conformation B
pdb|1UVL|C Chain C, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
With 5nt Rna Conformation B
pdb|1UVL|E Chain E, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
With 5nt Rna Conformation B
pdb|1UVM|A Chain A, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
With 5nt Rna Conformation A
pdb|1UVM|B Chain B, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
With 5nt Rna Conformation A
pdb|1UVM|C Chain C, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
With 5nt Rna Conformation A
pdb|1UVN|A Chain A, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
Ca2+ Inhibition Complex
pdb|1UVN|C Chain C, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
Ca2+ Inhibition Complex
pdb|1UVN|E Chain E, The Structural Basis For Rna Specificity And Ca2
Inhibition Of An Rna-Dependent Rna Polymerase Phi6p2
Ca2+ Inhibition Complex
pdb|4B02|A Chain A, The C-Terminal Priming Domain Is Strongly Associated With
The Main Body Of Bacteriophage Phi6 Rna-Dependent Rna
Polymerase
pdb|4B02|B Chain B, The C-Terminal Priming Domain Is Strongly Associated With
The Main Body Of Bacteriophage Phi6 Rna-Dependent Rna
Polymerase
pdb|4B02|C Chain C, The C-Terminal Priming Domain Is Strongly Associated With
The Main Body Of Bacteriophage Phi6 Rna-Dependent Rna
Polymerase
Length = 664
Score = 26.9 bits (58), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 43 IGRYDDMWAGWCTKVICDH-LNLG 65
+ +D W GW +ICD LN+G
Sbjct: 325 VSDHDTFWPGWLRDLICDELLNMG 348
>pdb|2JLF|A Chain A, Structural Explanation For The Role Of Mn In The Activity
Of Phi6 Rna-dependent Rna Polymerase
pdb|2JLF|B Chain B, Structural Explanation For The Role Of Mn In The Activity
Of Phi6 Rna-dependent Rna Polymerase
pdb|2JLF|C Chain C, Structural Explanation For The Role Of Mn In The Activity
Of Phi6 Rna-dependent Rna Polymerase
pdb|2JLG|A Chain A, Structural Explanation For The Role Of Mn In The Activity
Of Phi6 Rna-Dependent Rna Polymerase
pdb|2JLG|B Chain B, Structural Explanation For The Role Of Mn In The Activity
Of Phi6 Rna-Dependent Rna Polymerase
pdb|2JLG|C Chain C, Structural Explanation For The Role Of Mn In The Activity
Of Phi6 Rna-Dependent Rna Polymerase
Length = 664
Score = 26.9 bits (58), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 43 IGRYDDMWAGWCTKVICDH-LNLG 65
+ +D W GW +ICD LN+G
Sbjct: 325 VSDHDTFWPGWLRDLICDELLNMG 348
>pdb|1HI8|A Chain A, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
pdb|1HI8|B Chain B, Rna Dependent Rna Polymerase From Dsrna Bacteriophage Phi6
Length = 664
Score = 26.6 bits (57), Expect = 7.0, Method: Composition-based stats.
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 43 IGRYDDMWAGWCTKVICDHL 62
+ +D W GW +ICD L
Sbjct: 325 VSDHDTFWPGWLRDLICDEL 344
>pdb|1ORR|A Chain A, Crystal Structure Of Cdp-tyvelose 2-epimerase Complexed
With Nad And Cdp
pdb|1ORR|B Chain B, Crystal Structure Of Cdp-tyvelose 2-epimerase Complexed
With Nad And Cdp
pdb|1ORR|C Chain C, Crystal Structure Of Cdp-tyvelose 2-epimerase Complexed
With Nad And Cdp
pdb|1ORR|D Chain D, Crystal Structure Of Cdp-tyvelose 2-epimerase Complexed
With Nad And Cdp
Length = 347
Score = 26.2 bits (56), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 36/91 (39%), Gaps = 22/91 (24%)
Query: 22 AFDRHLIGPAMYFGL---------MGDGQPIGRYDDMWAGW-CTKVICDHLNLGVKTGLP 71
A D++++ A FGL M G+ YD W GW C K + +K G+
Sbjct: 171 AADQYMLDYARIFGLNTVVFRHSSMYGGRQFATYDQGWVGWFCQKAV------EIKNGIN 224
Query: 72 YIFHSKASNPFVNLKKEYKGIFWQEDIIPFF 102
F + K+ + + ED+I +
Sbjct: 225 KPFTISGNG------KQVRDVLHAEDMISLY 249
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
0.323 0.140 0.461
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,479,084
Number of Sequences: 62578
Number of extensions: 224244
Number of successful extensions: 456
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 441
Number of HSP's gapped (non-prelim): 19
length of query: 165
length of database: 14,973,337
effective HSP length: 91
effective length of query: 74
effective length of database: 9,278,739
effective search space: 686626686
effective search space used: 686626686
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)