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= psy8360
(152 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QKL|A Chain A, Hrpabc14.4, Essential Subunit Of Human Rna Polymerases I,
Ii And Iii
Length = 127
Score = 130 bits (326), Expect = 4e-31, Method: Compositional matrix adjust.
Identities = 63/69 (91%), Positives = 65/69 (94%)
Query: 83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
+YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct: 59 KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118
Query: 143 GIDELKIID 151
G+DEL I D
Sbjct: 119 GVDELIITD 127
>pdb|3H0G|F Chain F, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|R Chain R, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 142
Score = 112 bits (279), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 49/65 (75%), Positives = 59/65 (90%)
Query: 83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
+YERAR+LGTRALQI+M APV+V+LEGETDPLQIAMKEL +KIP+++RRYLPD SYEDW
Sbjct: 77 KYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDW 136
Query: 143 GIDEL 147
+ EL
Sbjct: 137 SVAEL 141
>pdb|1I3Q|F Chain F, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|F Chain F, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|F Chain F, Rna Polymerase Ii Elongation Complex
pdb|1K83|F Chain F, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|F Chain F, Wild Type Rna Polymerase Ii
pdb|1NT9|F Chain F, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|F Chain F, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|F Chain F, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|F Chain F, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|F Chain F, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|F Chain F, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|F Chain F, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|F Chain F, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|F Chain F, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|F Chain F, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|F Chain F, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|F Chain F, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|F Chain F, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|F Chain F, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|F Chain F, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|F Chain F, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|F Chain F, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|F Chain F, 12-Subunit Rna Polymerase Ii
pdb|2E2H|F Chain F, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|F Chain F, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|F Chain F, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|F Chain F, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|F Chain F, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|F Chain F, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|F Chain F, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|F Chain F, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|F Chain F, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|F Chain F, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|F Chain F, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|R Chain R, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|F Chain F, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|F Chain F, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|F Chain F, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|F Chain F, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|F Chain F, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|F Chain F, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|F Chain F, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|F Chain F, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|F Chain F, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|F Chain F, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|F Chain F, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|F Chain F, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|F Chain F, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|F Chain F, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|F Chain F, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|F Chain F, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|G Chain G, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|F Chain F, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|R Chain R, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|F Chain F, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|F Chain F, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|F Chain F, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|F Chain F, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|F Chain F, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|F Chain F, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|F Chain F, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|F Chain F, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|F Chain F, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|F Chain F, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|F Chain F, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|F Chain F, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|F Chain F, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|F Chain F, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|F Chain F, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|F Chain F, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|F Chain F, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|F Chain F, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|F Chain F, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|F Chain F, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|F Chain F, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|F Chain F, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|F Chain F, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|F Chain F, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|F Chain F, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|F Chain F, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4A3C|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|F Chain F, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|F Chain F, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|F Chain F, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|F Chain F, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 155
Score = 110 bits (275), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 50/69 (72%), Positives = 62/69 (89%), Gaps = 1/69 (1%)
Query: 83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
+YERAR+LGTRALQI+M APV V+LEGETDPL+IAMKEL +KIP++IRRYLPD S+EDW
Sbjct: 87 KYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDW 146
Query: 143 GIDELKIID 151
++EL I+D
Sbjct: 147 SVEEL-IVD 154
>pdb|3J0K|F Chain F, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 84
Score = 108 bits (271), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 50/69 (72%), Positives = 62/69 (89%), Gaps = 1/69 (1%)
Query: 83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
+YERAR+LGTRALQI+M APV V+LEGETDPL+IAMKEL +KIP++IRRYLPD S+EDW
Sbjct: 16 KYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDW 75
Query: 143 GIDELKIID 151
++EL I+D
Sbjct: 76 SVEEL-IVD 83
>pdb|2Y0S|I Chain I, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|K Chain K, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|K Chain K, Rnap At 3.2ang
pdb|4B1O|K Chain K, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|I Chain I, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 95
Score = 52.8 bits (125), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 37/56 (66%), Gaps = 2/56 (3%)
Query: 83 RYERARVLGTRALQIAMCAPVMVELE--GETDPLQIAMKELKARKIPIIIRRYLPD 136
RYE ARV+ RALQ+AM AP ++++ TD + IA +E K +PI IRR LP+
Sbjct: 29 RYEIARVISARALQLAMGAPALIDINNISSTDVISIAEEEFKRGVLPITIRRRLPN 84
>pdb|2WAQ|K Chain K, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|I Chain I, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|K Chain K, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 95
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 37/56 (66%), Gaps = 2/56 (3%)
Query: 83 RYERARVLGTRALQIAMCAPVMVELE--GETDPLQIAMKELKARKIPIIIRRYLPD 136
RYE ARV+ RALQ+AM AP ++++ TD + IA +E + +PI IRR LP+
Sbjct: 29 RYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPITIRRRLPN 84
>pdb|2PMZ|K Chain K, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|W Chain W, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|K Chain K, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|U Chain U, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 95
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 37/56 (66%), Gaps = 2/56 (3%)
Query: 83 RYERARVLGTRALQIAMCAPVMVELE--GETDPLQIAMKELKARKIPIIIRRYLPD 136
RYE ARV+ RALQ+AM AP ++++ TD + IA +E + +PI IRR LP+
Sbjct: 29 RYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPITIRRRLPN 84
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 0.139 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,035,811
Number of Sequences: 62578
Number of extensions: 129198
Number of successful extensions: 299
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 289
Number of HSP's gapped (non-prelim): 7
length of query: 152
length of database: 14,973,337
effective HSP length: 90
effective length of query: 62
effective length of database: 9,341,317
effective search space: 579161654
effective search space used: 579161654
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)